Toolgen Inc V Fisher (No 2) (2023) FCA 794

FEDERAL COURT OF AUSTRALIA
ToolGen Incorporated v Fisher (No 2) [2023] FCA 794
File number: NSD 1909 of 2018
Judgment of: NICHOLAS J
Date of judgment: 14 July 2023
Catchwords: PATENTS – appeal against decision of delegate of

Commissioner of Patents upholding opposition to patent
application (“PA”) for compositions and methods using
the CRISPR/Cas9 system for genome editing in
eukaryotic cells – identity of person skilled in the art
(“PSA”) – whether PSA comprises a team including a
microbiologist with expertise in CRISPR/Cas system in
prokaryotes – meaning of phrase “nucleic acid encoding
a guide RNA” in the claims – interrelationship between
independent claim and dependant claim – whether
dependent claim lacks clarity due to inconsistency
between it and independent claim – whether priority
document (“P1”) provides an enabling disclosure of the
invention as required by s 43(2A) of the Patents Act
1990 (Cth) (“the Act”) – whether invention disclosed by
P1 when read in light of the common general knowledge
at date of filing of P1 – whether certain publications
were common general knowledge at date of filing of P1
– whether disclosure clear enough and complete enough
for invention to be performed by a person skilled in the
art – whether work required of PSA would be an undue
burden – consideration of priority date – whether claims
lack novelty or do not involve an inventive step at the
deferred priority date – whether PA provides an
enabling disclosure of invention of the claims as
required by s 40(2)(a) of the Act – whether work
required of PSA would be an undue burden – whether
claims supported by matter disclosed in specification as
required by s40(3) of the Act – consideration of who
should determine the appellant’s foreshadowed
application to amend the specification
Held: dependent claim lacks clarity – invention of

claims not disclosed by P1 – no enabling disclosure by
P1 of invention of claims – work required of PSA would
be an undue burden – claims not entitled to priority
based on P1 claims – claims lack novelty and/or do not
involve an inventive step – no enabling disclosure by
PA of invention of claims – claims not supported by
matter disclosed in the specification – any application to
amend the specification should be heard and determined
by the Court
Legislation: Intellectual Property Laws Amendment (Raising the

Bar) Act 2012 (Cth)
Patents Act 1990 (Cth) ss 7(1), 7(2), 7(3), 18(1)(b)(i),
40, 40(2)(a), 40(3), 43(1), 43(2), 43(2A), 43(2A)(b),
43(3), 49, 60(3A), 60(4), 105(1A), 112A
Patents Regulations 1992 (Cth) reg 3.12(4), 3.13A
Patents Act 1977 (UK) ss 14(3), 14(5), 14(5)(c),
72(1)(c)
Explanatory Memorandum to the Intellectual Property
Laws Amendment (Raising the Bar) Act 2012 (Cth)
Cases cited: Aktiebolaget Hässle v Alphapharm Pty Ltd (2002) 212

CLR 411
Allsop Inc v Bintang Ltd (1989) 15 IPR 686
Apotex Pty Ltd v Warner-Lambert Company LLC (No 2)
(2016) 122 IPR 17
British Acoustic Films Ltd v Nettlefold Productions
(1936) 53 RPC 221
Catnic Components Ltd v Hill & Smith Ltd [1982] RPC
183
Commissioner of Patents v Sherman (2008) 172 FCR
394
Eli Lilly & Co Ltd v Apotex Pty Ltd (2013) 100 IPR 451
Eli Lilly & Co v Pfizer Overseas Pharmaceuticals
(2005) 64 IPR 506
Eli Lilly & Co v Human Genome Sciences Inc [2008]
RPC 29
Encompass Corporation Pty Ltd v InfoTrack Pty Ltd
(2018) 130 IPR 387
EXXON/Fuel Oils (T-409/91) [1994] OJ EPO 653
Fisher v ToolGen Inc (2018) 144 IPR 315
Freeman v TJ and FL Pohlner Pty Ltd (1994) 30 IPR
377
General Tire & Rubber Company v Firestone Tyre &
Rubber Company Limited [1972] RPC 457
Genentech I/Polypeptide expression (T292/85) 27
January 1988
Gilead Sciences Pty Ltd v Idenix Pharmaceuticals LLC
(2016) 117 IPR 252
GlaxoSmithKline Consumer Healthcare Investments
(Ireland) (No 2) Limited v Generic Partners Pty Limited

(2018) 264 FCR 474
Halliburton Energy Services Inc v Smith International
(North Sea) Ltd [2006] EWCA Civ 1715
HTC Corp v Gemalto SA [2014] EWCA Civ 1335
Icescape Ltd v Ice-World International BV [2019] FSR
5
Idenix Pharmaceuticals LLC v Gilead Sciences Pty Ltd
(2017) 134 IPR 1
Jupiters Ltd v Neurizon Pty Ltd (2005) 222 ALR 155
Kimberly-Clark Australia Pty Limited v Multigate
Medical Products Pty Limited (2011) 92 IPR 21
Kimberly-Clark Australia Pty Ltd v Arico Trading
International Pty Ltd (2001) 207 CLR 1
Kirin-Amgen Inc v Hoechst Marion Roussel Ltd (2004)
64 IPR 444
Lockwood Security Products Pty Ltd v Doric Products
Pty Ltd (2004) 217 CLR 274
Lockwood Security Products Pty Ltd v Doric Products
Pty Ltd (No 2) (2007) 235 CLR 173
Meat and Livestock Australia Limited v Branhaven LLC
(2020) 281 FCR 640
MedImmune Ltd v Novartis Pharmaceuticals UK Ltd
[2013] RPC 27
Mentor Corp v Hollister Inc [1993] RPC 7
Merck & Co Inc v Arrow Pharmaceuticals Ltd (2006)
154 FCR 31
Merck Sharp & Dohme Corporation v Wyeth LLC (No
3) (2020) 155 IPR 1
Minnesota Mining and Manufacturing Company v
Beiersdorf (Australia) Limited (1980) 144 CLR 253
Nicaro Holdings Pty Ltd v Martin Engineering Co
(1990) 16 IPR 545
Novartis AG v Johnson & Johnson Medical Ltd [2009]
EWHC 1671
Novozymes A/S v Danisco A/S (2013) 99 IPR 417
Patent Gesellschaft AG v Saudi Livestock Transport and
Trading Company (1997) 37 IPR 523
Pfizer Overseas Pharmaceuticals v Eli Lilly & Co
(2005) 225 ALR 416
Ranbaxy Laboratories Ltd v AstraZeneca AB (2013) 101
IPR 11
RD Werner & Co Inc v Bailey Aluminium Products Pty
Ltd (1989) 25 FCR 565
Regeneron Pharmaceuticals Inc v Kymab Ltd [2020]
UKSC 27

Schering Biotech Corp’s Application [1993] RPC 249
Schlumberger Holdings Ltd v Electromagnetic
Geoservices AS [2010] RPC 33
Valensi v British Radio Corporation [1973] RPC 337
Wake Forest University Health Sciences v Smith &
Nephew Pty Ltd (No 2) (2011) 92 IPR 496
Warner-Lambert Co LLC v Apotex Pty Ltd (2018) 129
IPR 205
Warner-Lambert LLC v Generics (UK) Ltd t/a Mylan
[2018] UKSC 56
Welch Perrin & Co Pty Ltd v Worrell (1961) 106 CLR
588
Winner v Ammar Holdings Pty Ltd (1993) 41 FCR 205
Division: General Division
Registry: New South Wales
National Practice Area: Intellectual Property
Sub-area: Patents and associated Statutes
Number of paragraphs: 436
Date of hearing: 21-25, 28-30 September 2020
Counsel for the Appellant/Cross- Mr T Cordiner QC with Mr P Flynn SC

Respondent:
Solicitor for the Jones Day

Appellant/Cross-Respondent:
Counsel for the Respondents/ Mr C Dimitriadis SC with Ms C Cunliffe

Cross-Appellants:
Solicitor for the Respondents/ Ashurst Australia

Cross-Appellants:

Table of Corrections
19 July 2023 [95] and [96] delete the word “Type II” where appearing in
those paragraphs
[196] replace reference to (f)-(g) with (a)-(b)
[260] and [261] corrections to formatting
[334] replace reference to (d)-(j) with (a)-(g)
[408] insert the words “in relation to P1” in penultimate

sentence and the words “they say” in the last sentence

ORDERS
NSD 1909 of 2018
BETWEEN: TOOLGEN INCORPORATED

Appellant
AND: GRANT FISHER

First Respondent
ACN 004 552 363 PTY LTD

Second Respondent
AND BETWEEN: GRANT FISHER

First Cross-Appellant
ACN 004 552 363 PTY LTD

Second Cross-Appellant
AND: TOOLGEN INCORPORATED

Cross-Respondent
ORDER MADE BY: NICHOLAS J

DATE OF ORDER: 14 JULY 2023
THE COURT ORDERS THAT:
1. The appellant file and serve any interlocutory application seeking an order directing
that the complete specification be amended pursuant to s 105(1A) of the Patents Act 1990
(Cth) together with any affidavit in support of such application by 4.00pm, 11 August 2023.
2. The proceeding be stood over to 9.30am on 17 August 2023 for the making of:
(a) final orders in the event no application is filed pursuant to order 1;
(b) for the making of further orders in relation to any application filed pursuant to order
1; and
(c) other orders (including in relation to costs) as may be considered appropriate.
Note: Entry of orders is dealt with in Rule 39.32 of the Federal Court Rules 2011.
ToolGen Incorporated v Fisher (No 2) [2023] FCA 794 vi

REASONS FOR JUDGMENT
INTRODUCTION [1]
PRINCIPAL ISSUES [10]
ONUS OF PROOF [14]
BACKGROUND TO TECHNOLOGY [20]
Eukaryotic and prokaryotic cells [20]
DNA and RNA [21]
Protein expression [25]
Cellular expression of proteins [30]
Nuclear localisation sequence [33]
RNA interference, Zinc finger nucleases and TALEN nucleases [35]
CRISPR/Cas system [36]
WITNESSES [46]
ToolGen’s Witnesses [47]
Respondents’ Witnesses [49]
Joint Expert Reports [51]
THE EARLIEST PRIORITY DOCUMENT (P1) [52]
THE PATENT APPLICATION [56]
Body of the Specification [56]
The Claims [73]
THE NOTIONAL SKILLED ADDRESSEE [76]
Background [76]
P1 [82]
THE PATENT APPLICATION [91]
COMMON GENERAL KNOWLEDGE [97]
PRINCIPLES OF CONSTRUCTION [101]
CONSTRUCTION ISSUES [113]
“a nucleic acid encoding” [113]
ToolGen Incorporated v Fisher (No 2) [2023] FCA 794 vii

“paired Cas9 nickases” [146]
RELEVANT LEGISLATIVE PROVISIONS [160]
THE DISCLOSURE REQUIREMENT [167]
P1 – DISCLOSURE AND ENABLEMENT [194]
A nucleic acid encoding a guide RNA [199]
A Type II CRSIPR/Cas system from a bacterial species other than S.
pyogenes [213]
Chimeric guide RNA other than sgRNA (+48) [366]
Nuclear localisation sequences (NLSs) and their location [371]
Single guide RNA fusion other than with a GAAA linker [377]
Use of “paired Cas9 nickases” and Cas9 endonucleases that create
staggered-ended double-stranded DNA breaks [379]
PATENT APPLICATION – DISCLOSURE AND ENABLEMENT [383]
PATENT APPLICATION – SUPPORT [391]
THE PRIORITY DATE [412]
NOVELTY [415]
INVENTIVE STEP [423]
AMENDMENT [432]
DISPOSITION [434]
ToolGen Incorporated v Fisher (No 2) [2023] FCA 794 viii

NICHOLAS J
INTRODUCTION
1 This proceeding concerns an opposed patent application for what is now a well-
known gene editing system known as the CRISPR/Cas9 system. The CRISPR/Cas9 system
described in the application can be used to edit target DNA sequences in eukaryotic cells so
as to disable or modify gene expression through (inter alia) the deletion or insertion of such
sequences using an RNA-guided endonuclease.
2 The appellant (“ToolGen”) is the applicant in Australian Patent Application

2013335451 (“the patent application”). The patent application relates to compositions and
methods involving a system for introducing a site-specific double-stranded break (or
cleavage) at a target nucleic acid sequence in a eukaryotic cell comprising a nucleic acid
encoding a Cas9 polypeptide and a nucleic acid encoding a guide RNA specific for the target
DNA. The system disclosed in the patent application is referred to as a “Type II Clustered
Regularly Interspaced Short Palindromic Repeats/Cas system” or “CRISPR/Cas system”.
The patent application has 21 claims including independent claim 1 for a composition and
independent claim 10 for a method.
3 The patent application was filed on 23 October 2013 and relies on an earliest priority
date of 23 October 2012 based on US Provisional Patent Application 61/717,324 (“P1”).
There are two other priority documents referred to in the patent application being US
Provisional Patent Application 61/803/599 (“P2”) with a filing date of 20 March 2013 and
US Provisional Patent Application 61/837,481 (“P3”) with a filing date of 20 June 2013. No
submissions were made by either party in relation to P2 or P3 and none of the experts were
questioned about them. I will say a little more about them later in these reasons. It is
sufficient to say at this point that P2 is incapable of conferring priority on any claim in the
patent application and P3 was filed after the publication date of various journal articles that
deprive the claims of novelty or any inventive step.
4 The first respondent opposed the patent application before the Commissioner of
Patents. That opposition was successful in relation to claims 1-8 and 10-18 of the patent
application, which the Delegate of the Commissioner of Patents (“Delegate”) found were not
novel and did not involve an inventive step in circumstances where none of those claims was
entitled to priority from P1. Claim 19 was found to lack clarity. Claim 21 was also found to
ToolGen Incorporated v Fisher (No 2) [2023] FCA 794 9

not involve an inventive step. The Delegate indicated that she would allow ToolGen two
months to propose appropriate amendments. (See Fisher v ToolGen Inc (2018) 144 IPR 315,
[2018] APO 65).
5 ToolGen appealed the Delegate’s decision pursuant to s 60(4) of the Patents Act 1990
(Cth) (“the Act”). The second respondent was named as an additional respondent. The
respondents filed a cross-appeal in relation to claims 9 and 20. They have also raised
additional grounds of invalidity which were rejected by the Delegate.
6 Even though this proceeding is referred to as an appeal, it is well-established that it is

not an appeal in the strict sense but is conducted as a hearing de novo in the original
jurisdiction of the Court: Commissioner of Patents v Sherman (2008) 172 FCR 394 at [18].
7 It is common ground that if claims 1-8 and 10-18 are not entitled to priority from P1,
they are not novel and lack an inventive step. As to claims 9 and 19-21, the respondents
contend that they also lack novelty and do not involve an inventive step if they are not
entitled to priority from P1.
8 In these reasons I refer to various publications in the scientific literature. Sometimes I

refer to these publications by their full citation but more often than not it is sufficient to
identify them by the lead authors name and the year of publication (eg. Wang (2013)). Full
details of these publications are set out in the Bibliography in Annexure A to these reasons.
9 The Primer (Exhibit A) which was agreed between the parties was of considerable
assistance to me. It covers a range of topics including the basics of cell biology, the genetic
code, molecular biology, and gene editing. The matters described in paras 14-101 of the
Primer (which I need not reproduce) are elementary and were very well known to molecular
biologists before the priority date.
PRINCIPAL ISSUES
10 The parties agreed on a lengthy and detailed statement of issues which I found helpful
and have had regard to, even though I have chosen not to frame my reasons for judgment
around it.
11 Broadly stated, the principal issues addressed in these reasons are as follows:
(a) who is the skilled addressee of P1 and the patent application and what was the common
general knowledge of the skilled addressee (or skilled team) as at 23 October 2012?

(b) what construction should be given to claims 1 and 10 (and their dependent claims) of
the patent application, including to the phrase “nucleic acid encoding a guide RNA”?
(c) do claims 1 and 10 (and their dependent claims) extend to “paired Cas nickases”?
(d) does claim 19 of the patent application lack clarity?
(e) does P1 provide an enabling disclosure of the invention claimed in each of the claims of
the patent application?
(f) if the priority date is deferred, does the invention claimed in each of claims 9, 19 and 20
of the patent application lack novelty in light of Wang (2013)?
(g) if the priority date is deferred, does the invention claimed in each of claims 9, 19, 20
and 21 of the patent application not involve an inventive step in light of the common
general knowledge at the relevant date considered together with each of Cong (2013),
Mali (2013) and Wang (2013) (taken separately)?
(h) does the complete specification of the patent application comply with s 40(2)(a) of the
Act in respect of the invention claimed in each claim?
(i) is each claim of the patent application supported in accordance with s 40(3) of the Act
by matter disclosed in the complete specification?
ToolGen accepts that if the priority date is deferred, then claims 1-8 and 10-18 will lack
novelty and an inventive step. ToolGen makes no such concession in relation to claims 9, 19,
20 or 21.
12 With regard to issues (e), (h) and (i), the respondents contend that these questions
should be answered in the negative because neither P1 nor the patent application discloses the
invention as claimed or, alternatively, does not enable its use across the full scope of each
claim. These issues raise questions as to the proper construction and application of
s 40(2)(a), s 40(3) and s 43(2A) in the form they have taken since the Act was amended by
the RTB Act.
13 For the reasons that follow I have concluded:
(a) None of the claims are entitled to priority based on P1 (s 43(2A)).

(b) All of the claims lack novelty or do not involve an inventive step (s 18(1)(b)).
(c) The complete specification does not provide an enabling disclosure of the invention
(s 40(2)(a)).
(d) The claims are not supported by matter disclosed in the specification (s 40(3)).

(e) Claim 19 lacks clarity (s 40(3)).
ONUS OF PROOF
14 Each party made submissions concerning the onus of proof. ToolGen emphasised
that the legal burden on all issues is on the opponent. The respondents did not dispute that
they carry the legal burden in this proceeding. However, they drew attention to the following
observations in the Explanatory Memorandum to the Intellectual Property Laws Amendment
(Raising the Bar) Act 2012 (Cth) (“RTB Act”) concerning the amendment to s 40(2)(a) of the
Act and the requirement that there be an enabling disclosure:
A specification that provides a single example of the invention may satisfy the
requirements, but only where the skilled person can extend the teaching of the
specification to produce the invention across the full width of the claims, without
undue burden, or the need for further invention.
However, it is expected to be more likely that, where the claims are broad, the
specification will need to give a number of examples or describe alternative
embodiments or variations extending over the full scope of the claims. This ensures
that the monopoly extends only to that which could reasonably be said to be
disclosed and no further.
If, on its face, the specification would appear to the skilled person to lack sufficient
disclosure, the onus of establishing that the invention is described in enough detail
lies with the applicant (see item 14).
15 The statement concerning onus in the Explanatory Memorandum appears to be

directed to the onus at the examination stage. I note that the reference to item 14 is to a
proposed amendment to s 49 of the Act. That section is concerned with acceptance of a
patent request rather than the hearing and determination of any opposition to the grant of a
patent following acceptance. With regard to the opposition, s 60(3A) of the Act provides:
(3A) If the Commissioner is satisfied, on the balance of probabilities, that a ground

of opposition to the grant of the standard patent exists, the Commissioner
may refuse the application.
16 In their submissions the respondents referred to the shifting of the evidentiary onus to
ToolGen in circumstances where, in their submission, P1 does not on its face, purport to
provide an enabling disclosure extending to, for example, use of a Type II CRISPR/Cas9
system derived from bacterial species other than S. pyogenes. They submitted, in effect, that
in these circumstances the evidentiary onus shifted to ToolGen to establish that there was an
enabling disclosure.

17 I do not consider it helpful to speak of a shifting evidential onus in this case.
Ultimately, it is for the respondents to persuade the Court that P1 does not provide an
enabling disclosure. To the extent it is necessary to resolve a disputed issue of fact in
determining whether that objection is established, the issue is to be determined on the balance
of probabilities.
18 In deciding whether there is an enabling disclosure, the Court will necessarily have
regard to the content of P1 when read in light of the common general knowledge, the cogency
of the evidence relied on by each side as to adequacy of the information made available, the
difficulties that would be faced by the skilled addressee in seeking to perform the invention,
and whether the work involved amounts to an undue burden. The determination of that
question involves an evaluative judgment based on a consideration of both the nature of the
technology and the work required of the skilled addressee to perform the invention across the
scope of the claims.
19 Even though the burden of proof is on the respondents, circumstances may still arise
in which ToolGen’s failure to adduce any evidence or any sufficient evidence on some
particular matter (eg. a fact which it asserts was common general knowledge) may ultimately
lead the Court to conclude, on the totality of the relevant evidence, that the invention cannot
be performed across the full scope of the claims without undue burden. This may be
particularly true in relation to matters in respect of which P1 is wholly silent.
BACKGROUND TO TECHNOLOGY
Eukaryotic and prokaryotic cells

20 Eukaryotes are organisms comprised of one or more eukaryotic cells. A eukaryotic
cell has a defined nucleus which is an organelle that contains DNA enclosed within a nuclear
envelope (double membrane). Mammals (including humans) are classified as eukaryotes as
they are comprised of eukaryotic cells. Prokaryotes are unicellular organisms comprised of a
prokaryotic cell. A prokaryotic cell has no nucleus or membrane bound organelles, and DNA
in prokaryotic cells is found in the form of supercoiled circular DNA that is not enclosed by a
nuclear membrane. Bacteria are an example of a prokaryote.
DNA and RNA

21 DNA (deoxyribonucleic acid) and RNA (ribonucleic acid) are both nucleic acids
consisting of a series (or string) of nucleotides. The nucleotides in DNA and RNA each

contain a sugar, a nitrogenous base and a phosphate group. In DNA, the sugar is deoxyribose
whereas in RNA the sugar is ribose. The nitrogenous base in each nucleotide in a DNA
molecule is either a purine (being adenine (A) or guanine (G)) or a pyrimidine (being
cytosine (C) or thymine (T)). The nitrogenous bases in RNA are the same as those in DNA
except that uracil (U) is substituted for thymine (T). Nucleotides are joined together to form a
long chain of DNA or RNA. This long chain is termed a polynucleotide.
22 In DNA, the sequence in which the four bases (A, C, G, T) are arranged in the
polynucleotide chain comprises the DNA code. The bases in one polynucleotide chain of
DNA pair with complementary bases in the other polynucleotide chain of DNA (so called
“base pairing”) to form a double-stranded helical structure. In the double-stranded DNA
structure, the nitrogenous base guanine (G) base pairs with cytosine (C), while the
nitrogenous base adenosine (A) base pairs with thymine (T).
23 In biological cells, molecules of RNA predominantly consist of a single

polynucleotide chain or strand. However, the sugar-phosphate backbone of the chain is
flexible and can fold so that self-complementary sequences within the RNA pair with each
other (to form a duplex, or double-stranded structure).
24 The nucleotide sequence of both DNA and RNA can be identified by a technique
known as sequencing.
Protein expression
25 Proteins are produced (or “expressed”) in a cell by the processes of transcription
(DNA to RNA) and translation (RNA to protein). In a eukaryotic cell, transcription occurs in
the nucleus (where DNA is located) and translation occurs in the cytoplasm (where
ribosomes are located). In a prokaryotic cell, transcription and translation occurs in the
cytoplasm (where DNA and ribosomes are located). The cytoplasm is the gelatinous liquid
that fills the inside of a cell that is comprised of water, salts and other organic molecules, and
a ribosome is an organelle within the cytoplasm that is the site of protein synthesis.
26 During transcription, the DNA double-stranded helix unwinds and one of the two
strands (the template or non-coding strand) acts as a template for the synthesis of a single-
stranded RNA molecule. Transcription generates a synthesised RNA (pre-mRNA) molecule
with bases complementary to the template DNA strand and with bases identical (with the

exception that “U” is substituted for “T”) to the coding DNA strand. Pre-mRNA is then
processed to form mature messenger RNA (mRNA).
27 During translation, mRNA acts as a template for the synthesis of a polypeptide chain
(a sequence of amino acids joined together by peptide bonds) which make up a protein. The
mRNA sequence is read consecutively in groups of three nucleotides, known as codons. Each
codon specifies either one amino acid or comprises a start or stop codon that starts and ends
the translation process.
28 There are only 20 amino acids that are commonly found in proteins, however, there
are 64 possible combinations of nucleotide triplets to make up a codon (given that there are
four different nucleotides which could be in each position in the triplet). This is because the
same amino acid can be coded for by more than one codon. This is referred to as the
degeneracy or redundancy of the genetic code.
29 The codons in a molecule of mRNA are recognised by small RNA molecules known
as transfer RNA (tRNA) that are located in ribosomes. One region of the tRNA (the
anticodon) binds complementarily to an mRNA codon while another region of the tRNA
binds to the amino acid that matches the mRNA codon attached to the tRNA. As the mRNA
sequence is read from start codon to stop codon, the amino acids coded for by the intervening
codons are brought together to form a polypeptide chain (protein).
Cellular expression of proteins

30 Proteins can be expressed in eukaryotic cells (including mammalian cells) via
recombinant DNA technology using vectors. Vectors can be plasmids (small circular pieces
of DNA from bacteria) or phages (viruses) that transfer foreign DNA into a cell. The
insertion of a foreign DNA sequence into the vector enables the DNA sequence to be
propagated (cloning vectors) or used to express a protein or RNA (expression vectors).
31 The foreign DNA inserted into a vector can comprise a DNA fragment of a particular
size, including DNA synthesised outside the cell (in vitro), a section of DNA from another
clone to be subcloned (that is, taking a smaller part of the larger fragment), a section of DNA
produced using restriction enzymes (enzymes that cut DNA) or a PCR fragment.
32 In a plasmid vector, the plasmid and foreign DNA insert are both cut with restriction
enzymes which generate compatible 5’ and 3’ ends. The plasmid and insert are then
combined and ligated (stitched together). The newly formed plasmid (with DNA insert) is

transformed (delivered) into bacteria and selected for using antibiotic-containing growth
medium.
Nuclear localisation sequence

33 As set out above, proteins are produced by the process of translation which occurs in
the ribosome in the cytoplasm of cells. In eukaryotic cells, the protein must pass into the
nucleus through the nuclear membrane in order for a protein to access and interact with
chromosomal DNA. Nuclear proteins (ie. proteins that function in the nucleus) commonly
enter the nucleus by passing through a nuclear pore channel. This can be contrasted to
prokaryotic cells, where chromosomal DNA is found in the cytoplasm.
34 As of October 2012, scientists were using a number of different nuclear localisation

sequences (“NLS”) as modular tags to deliver proteins or protein fragments from the
cytoplasm to the nucleus. A NLS is a short peptide derived from proteins which enter the
nucleus of a cell (nuclear proteins). For example, the sequence PKKKRKV is an NLS which
was widely used and studied prior to October 2012.
RNA interference, Zinc finger nucleases and TALEN nucleases

35 The patent application is set against the backdrop of tools and methodologies used
prior to October 2012 for introducing mutations into DNA sequences. The patent application
describes how the CRISPR/Cas system is used to recognise and silence exogenous genetic
elements in a manner analogous to the process of RNA interference (RNAi) in eukaryotic
organisms. RNAi is a biological system in which RNA molecules inhibit gene expression by
neutralising targeted mRNA molecules. RNAi was known to those in the field of genetic
engineering well before October 2012. The patent application and P1 also refer in particular
to the use of other gene-editing tools known as Zinc finger nucleases (ZFNs) and TALEN
nucleases (TALENs) that are derived from eukaryotic transcription factors.
CRISPR/Cas system
36 CRISPR is an acronym for “Clustered Regularly Interspaced Short Palindromic
Repeats”. Cas9 is the CRISPR associated protein 9, which is a prokaryotic dual RNA-guided
DNA endonuclease (an enzyme that cuts DNA within the internal part of the DNA sequence).
These components are associated with the CRISPR/Cas adaptive immune system found in
bacteria, an example of which is the Type II CRISPR/Cas system which is characterised by
(inter alia) its use of Cas9 protein (or polypeptide). In essence, these systems are a defence

mechanism which protects the bacteria from invading viruses by cleaving the DNA of the
virus and thereby disabling it.
37 Type II CRISPR/Cas systems were known to exist in certain prokaryotic cells and
function in the genomes of bacteria as part of their acquired bacterial immune system.
Specifically, Type II CRISPR/Cas systems were understood to confer bacterial resistance to
exogenous (external) genetic elements such as plasmids (small circular DNA found in
bacteria that replicate in bacterial cells) and phages (viruses that infect and replicate in cells).
38 This bacterial resistance is achieved by way of short segments of plasmid/phage

DNA, called spacers, which are incorporated into the bacterial genome between (and
separate) CRISPR repeats (short palindromic sequences). Together, these spacers and repeats
make up what is known as the CRISPR array. The CRISPR spacers serve as a memory of
past exposure to plasmids and phages and are used to recognise and silence foreign DNA
from invading bacteria and phages.
39 Figure 2(A) in Horvath (2010) (reproduced below) shows the process of spacer
incorporation which is taking DNA from an invading virus or plasmid and incorporating this
into the CRISPR array as spacer units. Figure 2(B) illustrates the function of CRISPR-Cas in
targeting and cleaving invading DNA that is cognate to a spacer. This is done by transcribing
the CRISPR repeat-spacer array into “pre-crRNA” which is then processed through RNA
cleavage into individual “crRNA” (CRISPR RNA) units incorporating the spacer and
sequence derived from the repeat. The spacer sequence in the crRNA unit guides the crRNA-
Cas complex to the invading nucleic acid. The crRNA unit complexed with Cas protein(s) is
the active form of the CRISPR defence system which performs the cleavage of the invading
DNA.

40 The patent application describes how the Cas9 component of the Type II CRISPR/Cas
system forms an active endonuclease when complexed with two RNA molecules designated
CRISPR RNA (crRNA) and trans-activating crRNA (tracrRNA) that are fused together to
form a chimeric (single) guide RNA that guide the CRISPR/Cas 9 complex to its target DNA
sequence. The RNA guided endonuclease is then able to break foreign genetic elements in
invading phages or plasmids and protect the host cell (bacteria) from infection.
41 The composition and role of the crRNA and tracrRNA that make up the single guide
RNA (“sgRNA”) are of some importance to understanding the background to the
CRISPR/Cas9 system. The crRNA is transcribed from the spacer sequence of the CRISPR
array into pre-crRNA which is further processed into mature crRNA that is complementary to

the target DNA sequence. This complementarity is used to guide the Cas9 to the target DNA
sequence of interest where it will cleave. The tracrRNA is transcribed from a gene outside of
the CRISPR array but it is complementary to the repeat sequences of the CRISPR array. This
complementarity is used to process pre-crRNA into mature crRNA so that it can perform its
guiding function.
42 The invention described in the specification involves the use of individual

components of the CRISPR/Cas9 system as a programmable system for introducing a site-
specific double-stranded break in a target nucleic acid of a eukaryotic cell (i.e. outside of a
prokaryotic system). The system can be used in vitro (outside the cell) or in vivo (in the cell)
to introduce mutations into DNA sequences including in so-called “gene-editing”
experiments or research.
43 The reference to a site-specific double-stranded break is a reference to the ability of

the system to target and cleave a precise site which is within a DNA target sequence that is
complementary to the variable part of the guide RNA, and which contains a PAM recognised
by Cas9. PAM refers to “protospacer adjacent motif” which is a nucleotide sequence
adjacent to the target DNA sequence (known as the protospacer) to be cleaved by Cas9. The
PAM sequence is the means by which a Cas9 recognises where to cleave DNA. Each Cas9
derived from a bacterial species recognises a specific PAM sequence. For example, the patent
application discloses that Cas9 derived from Streptococcus pyogenes recognises a “NGG” or
“NAG” PAM sequence where “N” stands for any nucleotide and “GG” stands for two
guanine nucleotides. S. pyogenes Cas9 will therefore cleave DNA adjacent to the nucleotide
sequence “NGG” where the Cas9 is complexed with a guide RNA that has a variable region
of the crRNA that is complementary to the target DNA sequence.
44 The sgRNA depicted in Figure 1a of the patent application and Figure 1A of P1 are
identical and reproduced below. The target DNA sequence is shown in green. The PAM
sequence “CGG” recognised by Cas9 is shown in orange and the triangles indicate cleavage
sites. Cas9 is shown in yellow and the sequences of the guide RNA derived from crRNA and
tracrRNA are shown in red and blue, respectively. Vertical bars between the target DNA and
crRNA sequence and between the crRNA and tracrRNA denote complementarity. The
coloured boxes do not appear in Figure 1a of the patent application or Figure 1A of P1 and
have been added to assist explanation of the figure.

Figure 1A/ Figure 1a
45 In summary, the particular CRISPR/Cas9 system the subject of the patent application
(and P1) is said to be comprised of a Cas9 polypeptide, that when complexed with a chimeric
(single) guide RNA, has endonuclease activity in eukaryotic cells.
WITNESSES
46 There were four principal witnesses each of whom provided written and oral
evidence.
ToolGen’s Witnesses
Associate Professor Ron Firestein

47 Associate Professor Firestein made two affidavits dated 13 September 2019
(“Firestein 1”) and 25 March 2020 (“Firestein 2”). He also annexed to Firestein 1 his
Declaration in the Patent Office opposition proceedings. He is the Head of the Centre for
Cancer Research at the Hudson Institute of Medical Research, and a consulting pathologist in
molecular genetic pathology at Monash Health. By his expertise and training he can be
described as a molecular biologist. At October 2012, Associate Professor Firestein was
generally aware of the existence of bacterial innate immunity but did not have knowledge of
the mechanistic details of the system, nor was this work of interest to him because the
potential impact of the CRISPR/Cas9 system for molecular biology and gene editing had not
been identified. He has used the CRISPR/Cas9 system since mid-2013.

Professor Philip Giffard
48 Professor Giffard made two affidavits dated 13 September 2019 (“Giffard 1”) and 16
March 2020 (“Giffard 2”). He is the Head of Laboratory Science at the Menzies School of
Health Research and Professor and Associate Dean for Research and Innovation in the
College of Health and Human Sciences at Charles Darwin University. He has specialised
knowledge in the field of bacterial genetics and physiology, molecular bacteriology,
bioinformatics and molecular microbiology. By his expertise and training he can be
described as a microbiologist. Before October 2012, he co-authored two papers reporting
research into the CRISPR loci of the bacterial species C. jejuni and the Staphylococcus
bacterial strain MSHR1132.
Respondents’ Witnesses
Professor Paul Thomas

49 Professor Thomas made two affidavits dated 8 April 2019 (“Thomas 1”) and 20
August 2020 (“Thomas 2”). He is a Professor of Biochemistry at the University of Adelaide
and is the Head of the Genome Editing Laboratory at the South Australian Health and
Medical Research Institute. Since 1995, he has engaged in genetic research in eukaryotes,
including gene targeting to inactivate genes of interest using homologous recombination, the
development of mouse models with genetic changes, and using molecular biology technology
to screen for genetic mutations. By his expertise and training he can be described as a
molecular biologist. At October 2012, Professor Thomas was generally aware of the
CRISPR/Cas9 system in bacteria, but not to a high level of detail. He did not actively follow
literature developments relating to bacterial systems. He became interested in using
CRISPR/Cas9 systems in mid-2013 after reading Mali (2013) and Wang (2013). Since then,
he has produced more than 60 novel mouse models using CRISPR/Cas9 systems, as well as
cell lines with modified genomes.
Associate Professor Marco Herold

50 Associate Professor Herold made two affidavits dated 4 April 2019 (“Herold 1”) and
20 December 2019 (“Herold 2”). He is a molecular biologist and the Laboratory Head at the
Walter and Eliza Hall Institute of Medical Research. From 2001, he focused on the
molecular regulation of cell death, including by introducing foreign genomic material into the
genome of host cells using retroviruses. From 2005, he worked on genetic manipulation
using RNA interference (RNAi) technology to silence or “knock down” particular genes in

eukaryotes, using both mouse models and in vitro systems. At October 2012, Associate
Professor Herold was generally aware of CRISPR/Cas9 systems in bacteria after reading
Jinek, but was not aware of the specific details of the system. He started working with
CRISPR/Cas9 systems in eukaryotic cells and organisms in May 2013, after reading Cong
(2013), Mali (2013) and Wang (2013). Since then, he has made around 220 mouse models
using CRISPR/Cas9 systems.
Joint Expert Reports

51 There were two expert conclaves held prior to the hearing and two concurrent
sessions of expert evidence at the hearing. The first expert conclave included the molecular
biologists Associate Professor Firestein, Associate Professor Herold and Professor Thomas
who prepared a Joint Expert Report dated 1 September 2020 (“JER 1”). These experts also
gave evidence in a concurrent session. The second expert conclave included the
microbiologist Professor Giffard, Professor Thomas and Associate Professor Herold. They
prepared a Joint Expert Report dated 2 September 2020 (“JER 2”) and also gave evidence in
another concurrent session.
THE EARLIEST PRIORITY DOCUMENT (P1)

52 It is common ground that P1 was filed on 23 October 2012. P1 is a relatively short
document which resembles an unpublished journal article to which has been added an
additional paragraph headed “Summary of the Invention”. Nothing turns on the purpose for
which P1 was prepared. P1 states at pages 1-6:
[Page 1]
Abstract:
We present a novel genome editing technology based on RNA-guided Cas9
endonucleases (RGENs). Cas9 is a sequence-specific endonuclease in type II
CRISPR/Cas systems, which confer prokaryotes with adaptive immunity against
invading phages and plasmids. Cas9 recognizes and cleaves target DNA sequences
complementary to small synthetic guide RNAs embedded in this protein, generating
site-specific DNA double-strand breaks in vitro and in human cells, whose
spontaneous repair induces targeted genome modifications at high frequencies.
Unlike ZFNs and TALENs, which are used widely in research and biotechnology,
RGENs are customized without any cloning step, making them a broadly useful,
scalable and expeditious platform for genome engineering in cells and organisms.
Summary of the Invention
In some embodiments, the present invention provides compositions and methods for
research, clinical and screening applications for genome editing. In some
embodiments, the present invention provides nucleic acids encoding RNA-guided

Cas9 endonucleases, vectors comprising Cas-9 endonucleases, Cas-9 polypeptides,
and uses of such compositions.
Additional embodiments are described herein.
[Page 2]
Main Text:
We exploited the clustered regularly interspaced short palindromic repeats
(CRISPR)/CRISPR- associated protein (Cas) system (1), an adaptive immune
response in bacteria and archaea, to develop a novel genome editing technology
based on RNA-guided endonucleases (RGENs). Cas9, an essential protein
component in the Type II CRISPR/Cas system, forms an active endonuclease when
complexed with two RNAs termed CRISPR RNA (crRNA) and trans-activating
crRNA (tracrRNA), thereby slicing foreign genetic elements in invading phages or
plasmids to protect the host cells. crRNA is transcribed from the CRISPR element in
the host genome, which was previously captured from such foreign invaders.
Recently, Jinek et al. (2) elegantly demonstrated that a single-chain chimeric RNA
produced by fusing an essential portion of crRNA and tracrRNA could replace the
two RNAs in the Cas9/RNA complex to form a functional endonuclease, raising the
possibility of using this system for genome editing in cells and organisms. Here, we
present the first evidence that RGENs can indeed induce site-specific genome
modifications in mammalian cells at high frequencies.
We first tested the DNA cleavage activity of Cas9 derived from Streptococcus
pyogenes in the presence or absence of a chimeric guide RNA in vitro. To this end,
we used recombinant Cas9 protein that was expressed in and purified from E. coli to
cleave a predigested or circular plasmid DNA that contained the 23-base pair (bp)
human CCR5 target sequence. A Cas9 target sequence consists of a 20-bp DNA
sequence complementary to crRNA or a chimeric guide RNA and the trinucleotide
(5'-NGG-3') protospacer adjacent motif (PAM) recognized by Cas9 itself (Fig. 1A);
Cas9 cleaved the plasmid DNA efficiently at the expected position only in the
presence of the synthetic RNA and did not cleave a control plasmid that lacked the
target sequence (Fig. 1B).
Next, we used a RFP-GFP reporter to investigate whether the Cas9/guide RNA
complex can cleave the target sequence incorporated between the RFP and GFP
sequences in mammalian [Page 3] cells. In this reporter, the GFP sequence is fused
to the RFP sequence out-of-frame (3). The active GFP is expressed only when the
target sequence is cleaved by site-specific nucleases, which causes frameshifting
small insertions or deletions (indels) around the target sequence via error-prone non-
homologous end-joining (NHEJ) repair of the double-strand break (DSB). We co-
transfected the Cas9-encoding plasmid, the guide RNA, and the RFP-GFP reporter
plasmid into human embryonic kidney (HEK) 293T cells, and found that GFP-
expressing cells were obtained only when the cells were co-transfected with the Cas9
plasmid and the guide RNA (Fig. 2), demonstrating that RGENs could recognize and
cleave the target DNA sequence in cultured human cells.
To test whether RGENs could be used for targeted disruption of endogenous genes in
mammalian cells, we analyzed genomic DNA isolated from transfected cells using
T7 endonuclease I (T7E1), a mismatch-sensitive endonuclease that specifically
recognizes and cleaves heteroduplexes formed by the hybridization of wild-type and
mutant DNA sequences (4). We found that mutations were induced only when the
cells were co-transfected with both Cas9 and guide RNA (Fig. 3). Mutation
frequencies (Indels (%) in Fig. 3A) estimated from the relative DNA band intensities
were RNA-dosage dependent, ranging from 1.3% to 5.1%. DNA sequencing analysis

of the PCR amplicons corroborated the induction of RGEN-mediated mutations at
the endogenous sites. Indels and microhomologies, characteristic of error-prone
NHEJ, were observed at the target site. The mutation frequency measured by direct
sequencing was 7.3% (= 7 mutant clones/96 clones), on par with those obtained with
zinc finger nucleases (ZFNs) or transcription-activator-like effector nucleases
(TALENs).
Both ZFNs and TALENs have been successfully developed to disrupt the human
CCR5 gene (4-7), which encodes a G-protein-coupled chemokine receptor, an
essential co-receptor of HIV infection. A CCR5-specific ZFN is now under clinical
investigation in the US for the treatment of AIDS (8). These ZFNs and TALENs,
however, have off-target effects, inducing both local [Page 4] mutations at sites
whose sequences are homologous to the on-target sequence (7, 9-11) and genome
rearrangements that arise from the repair of two concurrent DSBs induced at on-
target and off-target sites (12-13). The most striking off-target sites associated with
these CCR5-specific engineered nucleases reside in the CCR2 locus, a close homolog
of CCR5, located 15-kbp upstream of CCR5. To avoid off-target mutations in the
CCR2 gene and unwanted deletions, inversions, and duplications of the 15-kbp
chromosomal segment between the CCR5 on-target and CCR2 off-target sites, we
intentionally chose the target site of our CCR5-specific RGEN to recognize a region
within the CCR5 sequence that has no apparent homology with the CCR2 sequence.
We investigated whether the CCR5-specific RGEN had off-target effects. To this
end, we searched for potential off-target sites in the human genome by identifying
sites that are most homologous to the intended 23-bp target sequence. As expected,
no such sites were found in the CCR2 gene. Instead, we found four sites, each of
which carries 3-base mismatches with the on-target site (Fig. 4A). The T7E1 assays
showed that mutations were not detected at these sites (assay sensitivity, ⁓0.5%),
demonstrating exquisite specificities of RGENs (Fig. 4B). Furthermore, we used
PCR to detect the induction of chromosomal deletions in cells separately transfected
with plasmids encoding the ZFN and RGEN specific to CCR5. Whereas the ZFN
induced deletions, the RGEN did not (Fig. 4C). Although we did not detect any off-
target effects with RGENs in this study, deep sequencing of candidate sites and
whole genome or exome sequencing may reveal off-target mutations induced by
RGENs.
Next, we reprogrammed RGENs by replacing the CCR5-specific guide RNA with a
newly-synthesized RNA designed to target the human C4BPB gene, which encodes
the beta chain of C4b-binding protein, a transcription factor. This RGEN induced
mutations at the chromosomal target site in K562 cells at high frequencies (Fig. 38):
Mutation frequencies measured by the T7E1 assay and by direct sequencing were
14% and 8.3% (= 4 mutant clones/48 clones), [Page 5] respectively. Out of four
mutant sequences, two clones contained a single-base or two-base insertion precisely
at the cleavage site, a pattern that was also observed at the CCR5 target site. These
results indicate that RGENs cleave chromosomal target DNA at expected positions in
cells.
ZFNs and TALENs enable targeted mutagenesis in mammalian cells (14-16), model
organisms (17-20), plants (21-23), and livestock (24-25), but the mutation
frequencies obtained with individual nucleases are widely different from each other.
Furthermore, some ZFNs and TALENs fail to show any genome editing activities
(26-29). DNA methylation may limit the binding of these engineered nucleases to
target sites (30). In addition, it is technically challenging and time-consuming to
make custom nucleases. In this regard, RGENs based on Cas9 could provide useful
options for genome editing. Compared to ZFNs and TALENs, RGENs can be more
readily customized because only the synthetic RNA component is replaced to make a

new genome-editing nuclease: No sub-cloning steps are involved to make customized
RGENs. Furthermore, the relatively small size of the Cas9 gene (4.2 kbp) as
compared to a pair of TALEN genes (⁓6 kbp) provides an advantage for this system
in some applications such as virus-mediated gene delivery. These features will make
RGENs scalable, versatile, and convenient tools for genome engineering in cells and
organisms.
The specificity of DNA recognition by RGENs is somewhat limited by the
requirement for a 5'-GG-3' dinucleotide in the PAM sequence. This motif is
recognized by the Cas9 protein but not by the guide RNA. Thus, RGENs can be
designed to cleave DNA once per 8 bp (= 4x4/2) on average. This limitation might be
relieved by engineering Cas9 or employing Cas9 derived from other species.
Unlike Fokl-based ZFNs and TALENs, which produce 4- to 6-base 5' overhangs at
cleavage sites, RGENs yield blunt ends rather than cohesive ends (2). Our results
show that DSBs with blunt ends can also be readily repaired in mammalian cells. It
would be interesting to investigate [Page 6] how and whether blunt DSB ends would
be differentially repaired by endogenous end-joining processes.
Taken together, these findings indicate that RGENs are a new member in the family
of genome editing tools that have revolutionized basic and biomedical research but
with their own unique features that make them an ideal platform in many
applications. We propose that RGENs should find broad utility in research,
biotechnology, and medicine in the post-genomic era.
53 These three sections of P1 are followed by 30 references to various journal articles,

the second of which is the article first published in Science online on 28 June 2012 and
published in print on 17 August 2012 by Jinek et al that is of some importance to the issue of
enablement. The article is by Martin Jinek, Krzysztof Chylinski, Ines Fonfara, Michael
Hauer, Jennifer A. Doudna, and Emmanuelle Charpentier, and is entitled “A Programmable
Dual-RNA-Guided DNA Endonuclease in Adaptive Bacterial Immunity” Science 337, 816
(2012) (“Jinek”). The question whether the invention involves an inventive step in light of
Jinek does not arise in this proceeding.
54 The 30 references are then followed by a description of various figures reproduced in

P1 including Figure 1A which includes a schematic representation of a guide RNA and a
Cas9 protein used to cleave plasma DNA in vitro. The PAM sequence recognised by the
Cas9 protein is identified in Figure 1A as CGG which is a PAM sequence recognised by Cas9
derived from S. pyogenes (ie. a 5’-NGG-3’ PAM where N stands for any nucleotide A, T, C
or G). Triangles in Figure 1A depict the site of the intended break which is in a
complimentary position on each DNA strand. Figure 3 provides mutation frequencies for
RGEN-driven mutations at sites on the CCR5 gene and the C4BPB gene. The authors state
that they reprogrammed the guide RNA used with the Cas9 protein to target the CCR5 gene
with a different guide RNA to target the C4BPB gene. Accordingly, there is a specific

disclosure of the use of two different guide RNAs targeting these two different genes in
mammalian cells.
55 The description of the figures is followed by a section of P1 headed “Materials and

Methods” which describes (inter alia) the construction of Cas9 encoding plasmids derived
from S. pyogenes strain M1 GAS and the preparation of RNA in vitro using a
MEGAshortscript T7 kit (Ambion). This is followed by a description of the genome-editing
assay whereby mammalian cells (K562 cells) were transfected with 20µg of Cas9-encoding
plasmid followed (after 24 hours) by the introduction of 10-40µg of in vitro transcribed
chimeric RNA.
THE PATENT APPLICATION
Body of the Specification

56 The complete specification (“the Specification”) is entitled “COMPOSITION FOR
CLEAVING A TARGET DNA COMPRISING A GUIDE RNA SPECIFIC FOR THE
TARGET DNA AND CAS PROTEIN-ENCODING NUCLEIC ACID OR CAS PROTEIN,
AND USE THEREOF”. The Specification is divided into a number of different sections.
The first section contains a brief description of the “Technical Field” of the invention. The
Specification states at [1]:
The present invention relates to targeted genome editing in eukaryotic cells or

organisms. More particularly, the present invention relates to a composition for
cleaving a target DNA in eukaryotic cells or organisms comprising a guide RNA
specific for the target DNA and Cas protein-encoding nucleic acid or Cas protein,
and use thereof.
57 The second section is headed “Background Art” and includes a brief discussion at [3]-
[9] of the relevant technology including some prior art. The prior art referred to includes
Jinek.
58 The Specification states at [3]-[4]:
[3] CRISPRs (Clustered Regularly Interspaced Short Palindromic Repeats) are

loci containing multiple short direct repeats that are found in the genomes of
approximately 40% of sequenced bacteria and 90% of sequenced archaea.
CRISPR functions as a prokaryotic immune system, in that it confers
resistance to exogenous genetic elements such as plasmids and phages. The
CRISPR system provides a form of acquired immunity. Short segments of
foreign DNA, called spacers, are incorporated into the genome between
CRISPR repeats, and serve as a memory of past exposures. CRISPR spacers
are then used to recognize and silence exogenous genetic elements in a
manner analogous to RNAi in eukaryotic organisms.

[4] Cas9, an essential protein component in the Type II CRISPR/Cas system,
forms an active endonuclease when complexed with two RNAs termed
CRISPR RNA (crRNA) and trans-activating crRNA (tracrRNA), thereby
slicing foreign genetic elements in invading phages or plasmids to protect the
host cells. crRNA is transcribed from the CRISPR element in the host
genome, which was previously captured from such foreign invaders.
Recently, Jinek et al. (1) demonstrated that a single-chain chimeric RNA
produced by fusing an essential portion of crRNA and tracrRNA could
replace the two RNAs in the Cas9/RNA complex to form a functional
endonuclease.
59 The Cas9 protein is an essential part of the genome editing technology described. It is
an enzyme which, when complexed with a suitable guide RNA, provides a functional
endonuclease that cuts each strand of DNA within the internal part of its sequence (rather
than at its end) so as to generate a double-stranded break. A nuclease is an enzyme that
cleaves DNA. An endonuclease is an enzyme that cuts DNA within the internal part of its
sequence (in comparison to an exonuclease which trims the DNA at its ends). Endonucleases
can generate two types of “ends”. One type of endonuclease cuts the DNA at the same
position on the sense and antisense strands of the DNA to generate what is known as a
“blunt” end. Another type of endonuclease cuts DNA at different positions on the sense and
antisense strands to generate a “staggered” (or “sticky”) end. This second type of double-
stranded break, sometimes referred to as “composite” double-stranded break, will have single
stranded overhangs on either the 5’ or 3’ side of the DNA formation.
60 Two well-known gene editing tools discussed in the Specification are Zinc finger
nucleases (ZFNs) and TALEN nucleases (TALENs). Zinc finger technology uses artificial
restriction enzymes which can be used to cleave (cut) DNA strands generated by fusing a
zinc finger DNA-binding domain to a DNA-cleavage domain. Zinc finger nucleases can be
engineered to target specific desired DNA sequences and this enables them to target unique
sequences within complex genomes. TALEN is an acronym for “Transcription Activator-like
Effector Nuclease”, which are DNA-binding proteins that can be engineered to cut specific
sequences of DNA. “RFLP” is an acronym for “Restriction Fragment Length
Polymorphism”. This refers to the presence of a difference in the nucleotide sequence
between two homologous DNA sequences that can be detected by use of a restriction enzyme
that will preferentially recognise (and cut) only one variant of those two sequences. RFLP
analysis allows polymorphisms to be identified based on the differences in the cutting activity
of the restriction enzyme.
61 The Specification states at [5]-[9]:

[5] CRISPR/Cas systems offer an advantage to zinc finger and transcription
activator-like effector DNA-binding proteins, as the site specificity in
nucleotide binding CRISPR-Cas proteins is governed by a RNA molecule
instead of the DNA-binding protein, which can be more challenging to
design and synthesize.
[6] However, until now, a genome editing method using the RNA-guided
endonuclease (RGEN) based on CRISPR/Cas system has not been
developed.
[7] [BLANK]
[8] Meanwhile, Restriction fragment length polymorphism (RFLP) is one of the
oldest, most convenient, and least expensive methods of genotyping that is
still used widely in molecular biology and genetics but is often limited by the
lack of appropriate sites recognized by restriction endonucleases.
[9] Engineered nuclease-induced mutations are detected by various methods,
which include mismatch-sensitive T7 endonuclease I (T7El) or Surveyor
nuclease assays, RFLP, capillary electrophoresis of fluorescent PCR
products, Dideoxy sequencing, and deep sequencing. The T7El and Surveyor
assays are widely used but are cumbersome. Furthermore, theses enzymes
tend to underestimate mutation frequencies because mutant sequences can
form homoduplexes with each other and cannot distinguish homozygous bi-
allelic mutant clones from wildtype cells. RFLP is free of these limitations
and therefore is a method of choice. Indeed, RFLP was one of the first
methods to detect engineered nuclease-mediated mutations in cells and
animals. Unfortunately, however, RFLP is limited by the availability of
appropriate restriction sites. It is possible that no restriction sites are available
at the target site of interest.
62 The “Technical Problem” to which the invention is directed is described as follows at

[11]-[13]:
Disclosure of Invention
Technical Problem
[11] Until now, a genome editing and genotyping method using the RNA-guided
endonuclease (RGEN) based on CRISPR/Cas system has not been
developed.
[12] Under these circumstances, the present inventors have made many efforts to
develop a genome editing method based on CRISPR/Cas system and finally
established a programmable RNA-guided endonuclease that cleave DNA in a
targeted manner in eukaryotic cells and organisms.
[13] In addition, the present inventors have made many efforts to develop a novel
method of using RNA-guided endonucleases (RGENs) in RFLP analysis.
They have used RGENs to genotype recurrent mutations found in cancer and
those induced in cells and organisms by engineered nucleases including
RGENs themselves, thereby completing the present invention.
63 The section of the Specification headed “Solution to the Problem” includes at [15] a
lengthy statement of what are said to be objects of the invention. At least some of these are

in a form that reflects the language of the claims including claims 1 and 10. For convenience,
the ten paragraphs that make up [15] have been numbered as [15.1]-[15.10]. All of these
paragraphs but for the first appear to have been introduced by amendments made in 2016.
The first ten objects are said to be:
[15.1] It is an object of the present invention to provide a composition for cleaving

target DNA in eukaryotic cells or organisms comprising a guide RNA
specific for target DNA or DNA that encodes the guide RNA, and Cas
protein-encoding nucleic acid or Cas protein.
[15.2] It is another object of the present invention to provide a composition for
inducing targeted mutagenesis in eukaryotic cells or organisms, comprising a
guide RNA specific for target DNA or DNA that encodes the guide RNA,
and Cas protein-encoding nucleic acid or Cas protein.
[15.3] It [sic] an object of the present invention to provide a composition
comprising a Type II Clustered Regularly Interspaced Short Palindromic
Repeats (CRISPR)/Cas system for use in introducing a site-specific, double
stranded break at a target nucleic acid sequence in a eukaryotic cell, said
CRISPR/Cas system comprising (i) a nucleic acid encoding a Cas9
polypeptide comprising a nuclear localization sequence, and (ii) a nucleic
acid encoding a guide RNA that hybridizes to a target nucleic acid, wherein
the guide RNA is a chimeric guide RNA comprising a CRISPR RNA
(crRNA) portion fused to a trans activating crRNA (tracrRNA) portion.
[15.4] It is still another object of the present invention to provide a kit for cleaving a
target DNA in eukaryotic cells or organisms comprising a guide RNA
specific for target DNA or DNA that encodes the guide RNA, and Cas
[15.5] It is still another object of the present invention to provide a kit for inducing
targeted mutagenesis in eukaryotic cells or organisms comprising a guide
RNA specific for target DNA or DNA that encodes the guide RNA, and Cas
[15.6] It is still another object of the present invention to provide a method for
preparing a eukaryotic cell or organism comprising Cas protein and a guide
RNA comprising a step of co-transfecting or serial-transfecting the
eukaryotic cell or organism with a Cas protein-encoding nucleic acid or Cas
protein, and a guide RNA or DNA that encodes the guide RNA.
[15.7] It is an objection [sic] of the present invention to provide a method of
introducing a site-specific, double-stranded break at a target nucleic acid
sequence in a eukaryotic cell, the method comprising introducing into the
eukaryotic cell a Type II Clustered Regularly Interspaced Short Palindromic
Repeats (CRISPR)/Cas system, wherein the CRISPR/Cas system comprises:
a) a nucleic acid encoding a Cas9 polypeptide comprising a nuclear
localization signal, wherein the nucleic acid is codon-optimized for
expression in eukaryotic cells, and
b) a nucleic acid encoding a guide RNA that hybridizes to the target
nucleic acid, wherein the guide RNA is a chimeric guide RNA
comprising a CRISPR RNA (crRNA) portion fused to a trans
activating crRNA (tracrRNA) portion, wherein the target nucleic acid

sequence comprises a first strand that binds to the crRNA portion and
a second strand having a trinucleotide protospacer adjacent motif
(PAM),
and wherein the Cas9 polypeptide and the guide RNA form a Cas9/RNA
complex in the eukaryotic cell, whereby a site-specific, double stranded
break at the target nucleic acid sequence is introduced.
[15.8] It is still another object of the present invention to provide a eukaryotic cell
or organism comprising a guide RNA specific for target DNA or DNA that
encodes the guide RNA, and Cas protein-encoding nucleic acid or Cas
protein.
cleaving a target DNA in eukaryotic cells or organisms comprising a step of
transfecting the eukaryotic cells or organisms comprising a target DNA with
a composition comprising a guide RNA specific for target DNA or DNA that
protein.
inducing targeted mutagenesis in a eukaryotic cell or organism comprising a
step of treating a eukaryotic cell or organism with a composition comprising
a guide RNA specific for target DNA or DNA that encodes the guide RNA,
and Cas protein-encoding nucleic acid or Cas protein.
(sub-paragraph numbering added)
Mutagenesis refers to changes in DNA (either naturally occurring or artificially engineered)

that result in gene mutation.
64 It is apparent that sub-paragraph [15.1] distinguishes between a composition

comprising (inter alia) “a guide RNA” that targets a particular DNA sequence and “DNA that
encodes the guide RNA”. Sub-paragraph [15.3], which mirrors the language of claim 1, also
refers to nucleic acid “encoding” a Cas9 polypeptide and nucleic acid “encoding” a guide
RNA. The Specification makes similar use of the word “encoding” at [156] where there is
reference to “a component in the form of a protein or in the form of a nucleic acid encoding
Cas protein.”
65 Further objects are set out at [31], [33], [35], [37]-[38], [40], [42], [44], [46], [48],
[50], [52], [54], [56], [58], [60], [62], [64], [66] and [68]. The advantageous effects of the
invention are described as follows at [69]:
The present composition for cleaving a target DNA or inducing a targeted

mutagenesis in eukaryotic cells or organisms, comprising a guide RNA specific for
the target DNA and Cas protein-encoding nucleic acid or Cas protein, the kit
comprising the composition, and the method for inducing targeted mutagenesis
provide a new convenient genome editing tools. In addition, because custom RGENs
can be designed to target any DNA sequence, almost any single nucleotide

polymorphism or small insertion/deletion (indel) can be analyzed via RGEN-
mediated RFLP, therefore, the compostion [sic] and method of the present invention
may be used in detection and cleaving naturally-occurring variations and mutations.
66 In the section entitled “Best Mode for Carrying out the Invention” the Specification
states at [137] – [145]:
[137] In accordance with one aspect of the invention, the present invention
provides a composition for cleaving target DNA in eukaryotic cells or
organisms comprising a guide RNA specific for target DNA or DNA that
protein. In addition, the present invention provides a use of the composition
for cleaving target DNA in eukaryotic cells or organisms comprising a guide
RNA specific for target DNA or DNA that encodes the guide RNA, and Cas
[138] [BLANK]
[139] In the present invention, the composition is also referred to as a RNA-guided
endonuclease (RGEN) composition.
[140] [BLANK]
[141] ZFNs and TALENs enable targeted mutagenesis in mammalian cells, model
organisms, plants, and livestock, but the mutation frequencies obtained with
individual nucleases are widely different from each other. Furthermore, some
ZFNs and TALENs fail to show any genome editing activities. DNA
methylation may limit the binding of these engineered nucleases to target
sites. In addition, it is technically challenging and time-consuming to make
customized nucleases.
[142] [BLANK]
[143] The present inventors have developed a new RNA-guided endonuclease
composition based on Cas protein to overcome the disadvantages of ZFN s
and TALENs.
[144] [BLANK]
[145] Prior to the present invention, an endonuclease activity of Cas proteins has
been known. However, it has not been known whether the endonuclease
activity of Cas protein would function in an eukaryotic cell because of the
complexity of the eukaryotic genome. Further, until now, a composition
comprising Cas protein or Cas protein-encoding nucleic acid and a guide
RNA specific for the target DNA to cleave a target DNA in eukaryotic cells
or organisms has not been developed.
67 The Specification refers at [153] to the three types of CRISPR-Cas system found in
bacteria including the Type II system involving the Cas9 protein. However, as will been
seen, the claims all involve compositions or methods that make use of the Type II system and
the Cas9 protein which is integral to that system.

68 According to the Specification at [158]-[159], in the present invention, the Cas protein
may be any Cas protein provided that it has an endonuclease or nickase activity when
complexed with a guide RNA, but preferably, it is Cas9 protein or variants thereof. The
Specification states at [161]-[162]:
[161] Further, Cas protein may be the one isolated from an organism such as
Streptococcus sp., preferably Streptococcus pyogens or a recombinant
protein, but it is not limited thereto.
[162] The Cas protein derived from Streptococcus pyogens may recognizes NGG
trinucleotide. The Cas protein may comprise an amino acid sequence of SEQ
ID NO: 109, but it is not limited thereto.
(Errors in original).
69 Streptococcus pyogenes (“S. pyogenes”) is a particular species of bacteria which

recognises the PAM sequence “NGG” (5’-NGG-3’ PAM) where N designates any nucleotide
and “GG” represents two guanine nucleotides running in the 5’ to 3’ direction.
70 The Specification also states at [176]-[179]:
[176] The guide RNA may be transferred into a cell or an organism in the form of
RNA or DNA that encodes the guide RNA. The guide RNA may be in the
form of an isolated RNA, RNA incorporated into a viral vector, or is encoded
in a vector. Preferably, the vector may be a viral vector, plasmid vector, or
agrobacterium vector, but it is not limited thereto.
[177] A DNA that encodes the guide RNA may be a vector comprising a sequence
coding for the guide RNA. For example, the guide RNA may be transferred
into a cell or organism by transfecting the cell or organism with the isolated
guide RNA or plasmid DNA comprising a sequence coding for the guide
RNA and a promoter.
[178] Alternatively, the guide RNA may be transferred into a cell or organism
using virus-mediated gene delivery.
[179] When the guide RNA is transfected in the form of an isolated RNA into a cell
or organism, the guide RNA may be prepared by in vitro transcription using
any in vitro transcription system known in the art. The guide RNA is
preferably transferred to a cell in the form of isolated RNA rather than in the
form of plasmid comprising encoding sequence for a guide RNA. As used
herein, the term “isolated RNA” may be interchangeable to “naked RNA”.
This is cost- and time-saving because it does not require a step of cloning.
However, the use of plasmid DNA or virus-mediated gene delivery for
transfection of the guide RNA is not excluded.
71 Transfection refers to the introduction of foreign DNA into a cell. The first sentence
of [176] indicates that the guide RNA may take the form of isolated (or naked) RNA
introduced into the cell or, alternatively, guide RNA encoded by DNA in the cell. The DNA

may be transfected (introduced) into the cell using a vector (i.e. a plasmid). Once inside the
cell, the transcription process will be initiated by a promoter included in the plasmid and the
DNA will then transcribe the guide RNA. Thus, as [179] indicates, the guide RNA can be
prepared in vitro before it is introduced into the cell in the form of “isolated” or “naked”
RNA, or the guide RNA can be prepared in vivo after a plasmid containing the RNA-
encoding DNA is transfected into the cell. The use of isolated RNA prepared in vitro is said
to be preferable to the use of RNA-encoding plasmid DNA prepared in vivo because the
former is the cheaper and less time consuming alternative and it does not involve a cloning
step of inserting a target DNA fragment into a plasmid.
72 A nickase is an enzyme that cuts only one of the two strands of DNA to create a
single strand break in the DNA. A Cas9 nickase is a mutant version of the wild-type Cas9
protein. A “paired Cas nickase” as defined in the Specification “may refer to the guide RNA
and the Cas protein functioning as a pair” which may be used to make two breaks at the same
or different locations on each of the complementary DNA strands. The Specification
suggests that there may be advantages in using paired Cas9 nickases. The discussion in the
Specification concerning Example 7 suggests that paired Cas9 nickases may produce
composite double-stranded breaks which trigger DNA repair leading to efficient mutagenesis
(ie. the generation of mutations) and a doubling in the specificity of Cas9-based genome
editing. Various other possible advantages are also discussed.
The Claims
73 Claims 1 to 21 are as follows:
1 A composition comprising a Type II Clustered Regularly Interspaced Short

Palindromic Repeats (CRISPR)/Cas system for use in introducing a site-
specific, double stranded break at a target nucleic acid sequence in a
eukaryotic cell, said CRISPR/Cas system comprising (i) a nucleic acid
encoding a Cas9 polypeptide comprising a nuclear localization sequence, and
(ii) a nucleic acid encoding a guide RNA that hybridizes to a target nucleic
acid, wherein the guide RNA is a chimeric guide RNA comprising a CRISPR
RNA (crRNA) portion fused to a trans activating crRNA (tracrRNA) portion.
2. The composition of claim 1, wherein said Cas9 polypeptide is a
Streptococcus Cas9 polypeptide.
3. The composition of claim 2, wherein said Cas9 polypeptide is a
Streptococcus pyogenes Cas9 polypeptide.
4. The composition of any one of claims 1-3, wherein said nucleic acid
encoding a Cas9 polypeptide is codon-optimized for expression in eukaryotic
cells.

5. The composition of claim 4, wherein said nucleic acid encoding a Cas9
polypeptide is codon-optimized for expression in mammalian cells.
6. The composition of any one of claims 1-5, wherein said nuclear localization
sequence is located at the C terminus of the Cas9 polypeptide.
7. The composition of any one of claims 1-5, wherein the target nucleic acid is
an endogenous target nucleic acid.
8. The composition of any one of claims 1-5, wherein the guide RNA is in the
form of a vector.
9. The composition of any one of claims 1-5, wherein said guide RNA
comprises 2 additional guanine nucleotides at the 5' end.
10. A method of introducing a site-specific, double-stranded break at a target
nucleic acid sequence in a eukaryotic cell, the method comprising
introducing into the eukaryotic cell a Type II Clustered Regularly Interspaced
Short Palindromic Repeats (CRISPR)/Cas system, wherein the CRISPR/Cas
system comprises:
(a) a nucleic acid encoding a Cas9 polypeptide comprising a nuclear
localization signal, wherein the nucleic acid is codon-optimized for
expression in eukaryotic cells, and
(b) a nucleic acid encoding a guide RNA that hybridizes to the target
nucleic acid, wherein the guide RNA is a chimeric guide RNA
comprising a CRISPR RNA (crRNA) portion fused to a trans
activating crRNA (tracrRNA) portion, wherein the target nucleic acid
sequence comprises a first strand that binds to the crRNA portion and
a second strand having a trinucleotide protospacer adjacent motif
(PAM),
and wherein the Cas9 polypeptide and the guide RNA form a Cas9/RNA
complex in the eukaryotic cell, whereby a site-specific, double stranded
break at the target nucleic acid sequence is introduced.
11. The method of claim 10, wherein the Cas9 polypeptide is a Streptococcus
Cas9 polypeptide.
12. The method of claim 11, wherein the Cas9 polypeptide is a Streptococcus
pyogenes Cas9 polypeptide.
13. The method of any one of claims 10-12, wherein the nucleic acid encoding
the Cas 9 polypeptide is codon-optimized for expression in mammalian cells.
14. The method of any one of claims 10-13, wherein the nuclear localization
signal is located at the C terminus of the Cas9 polypeptide.
15. The method of any one of claims 10-14, wherein the eukaryotic cell is a
mammalian cell.
16. The method of claim 15, wherein the mammalian cell is a human cell.
17. The method of any one of claims 10-16, wherein the target nucleic acid
sequence is a genomic sequence located at its endogenous site in the genome
of the eukaryotic cell.

the guide RNA is a vector.
the guide RNA is in vitro transcribed RNA.
20. The method of any one of claims 10-16, wherein said guide RNA comprises
2 additional guanine nucleotides at the 5' end.
the Cas9 polypeptide is introduced into the eukaryotic cell before introducing
the nucleic acid encoding the guide RNA into the eukaryotic cell.
74 The claims refer to a “Cas9 polypeptide” rather than a “Cas9 protein” but, as used in
both the description of the invention and the claims, these terms have the same meaning and
are used interchangeably.
75 The following points should also be noted:
(1) Each of the independent claims 1 and 10 also refer to “nucleic acid encoding” a
chimeric guide RNA. There is a question as to whether these words encompass a guide RNA
that is prepared in vitro (outside the cell) and introduced into the cell in naked (or isolated)
form or whether the claim limits what is described to guide RNA encoded by DNA in vivo (in
the cell).
(2) Each of the independent claims 1 and 10 also refer to a composition or method for
introducing “a site-specific, double-stranded break”. There is a question as to whether these
words are apt to describe not only a blunt end break made by a single active endonuclease,
but also a break having staggered ends of the kind made using “paired Cas nickase” in which
there will be two Cas9 polypeptides each with its own guide RNA and each producing its
own single strand break.
(3) Neither of the independent claims is limited to a Cas9 polypeptide derived from
S. pyogenes (although some dependent claims are) that recognises the 5’-NGG-3’ PAM.
(4) Claim 8 refers to the relevant composition wherein the guide RNA “is in the form of a
vector”. It is common ground, and I accept, that this should be understood as guide RNA
encoded by DNA in a vector.
THE NOTIONAL SKILLED ADDRESSEE
Background
76 The question of who is the notional skilled addressee (or person skilled in the art)
arises both in relation to P1 and the patent application.

77 There was a dispute between the parties as to the identity of the notional skilled
addressee both in relation to the patent application and P1. ToolGen contends that the
notional skilled addressee comprises a team that includes a molecular biologist such as
Associate Professors Firestein and Herold and Professor Thomas and a microbiologist such as
Professor Giffard. The respondents says that the skilled team does not include a
microbiologist. On that basis they contend that Professor Giffard’s evidence is not relevant.
78 The notional skilled addressee is a legal construct and a tool of analysis framed by
reference to the available evidence. This will include the patent specification and, typically,
evidence of persons with knowledge and experience in the field of the invention.
79 The notional skilled addressee is a person who is likely to have a practical interest in
the subject matter of the invention: Catnic Components Ltd v Hill & Smith Ltd [1982] RPC
183 at 242 per Lord Diplock. A person may have a practical interest in an invention at a
number of levels. He or she may have an interest in using the products or methods of the
invention, making the products of the invention, or making products used to carry out the
methods of the invention either alone or in collaboration with others having such an interest:
Apotex Pty Ltd v Warner-Lambert Company LLC (No 2) (2016) 122 IPR 17 (“Warner-
Lambert”) at [27]. Broadly speaking, the skilled addressee will be a person who also has
knowledge and experience in the field of the invention and who will bring to the reading of
the relevant document the background knowledge and experience available to those working
in that field.
80 In General Tire & Rubber Company v Firestone Tyre & Rubber Company Limited
[1972] RPC 457 (“General Tire”) the English Court of Appeal referring to both the
construction of the patent in suit and relevant prior art said at 485:
… If the art is one having a highly developed technology, the notional skilled reader
to whom the document is addressed may not be a single person but a team, whose
combined skills would normally be employed in that art in interpreting and carrying
into effect instructions such as those which are contained in the document to be
construed. We have already described the composite entity deemed to constitute the
notional skilled addressee.
81 In some cases involving complex technology in which the notional skilled addressee
is a team, the composition of the team may vary depending on the issue under consideration.
As observed by Jacob LJ in Schlumberger Holdings Ltd v Electromagnetic Geoservices AS
[2010] RPC 33 at [44] “… the notional team for considering obviousness may have wider

skills than the team required for sufficiency” (original emphasis). Referring to Genentech
Inc’s Patent [1989] RPC 147, his Lordship observed at [45]:
On the facts the patent was held obvious. The important point to note for present
purposes is that the team for obviousness included a protein chemist whereas the
team for implementation (sufficiency) did not need him. Different teams for different
purposes.
P1
82 The invention described in P1 is said to be a novel genome editing technology. The
system described is said to be based on RNA-guided endonucleases (RGENs). The RGENs
described in P1 use a Type II CRISPR/Cas system in which the Cas9 protein, when
complexed with a guide RNA (crRNA) and trans-activating RNA (tracrRNA), forms an
active endonuclease. It is apparent from the opening paragraphs of P1 that it follows on from
Jinek which P1 describes as raising the possibility of using the system disclosed in that
publication for genome editing in cells and organisms. It is clear from P1 that the focus of
the inventors was on the use of their invention in genome editing in eukaryotic cells and in
human cells in particular.
83 In support of its submission that the notional skilled addressee would comprise a team
including a microbiologist, ToolGen relied on the reference to Jinek in P1 and evidence given
by Associate Professor Firestein that the reference to Jinek was directing him to an important
paper regarding the development and repurposing of CRISPR/Cas9 technology.
84 I do not consider that P1 directs the notional skilled addressee to Jinek at least not as a
source of anything more than general background that gives context to the invention
described in P1.
85 It was submitted by ToolGen that the reference to Jinek in P1 must be regarded as part
of the disclosure of P1, because the “draftsman had adopted the cross-referencing system
solely as a shorthand means of incorporating a writing disclosing the invention”. The
authority relied upon by ToolGen in support of that proposition is a passage in the judgment
of Lockhart J in Nicaro Holdings Pty Ltd v Martin Engineering Co (1990) 16 IPR 545. In the
context of considering whether a prior publication disclosed all the features of the invention
of the patent in suit, his Honour said at 549:
The invention must appear in a single disclosure, so it is not permissible to make a

pattern or mosaic of or to read together various pieces of prior art in different patents.
It is however, permissible, to refer not only to the patent relied on as the source of

disclosure but to another patent or other patents incorporated by reference provided
that it is plain that the incorporation by reference unequivocally and plainly
demonstrates that the draftsman has adopted the cross-referencing system solely as a
shorthand means of incorporating a writing disclosing the invention: George C
Warner Laboratories Pty Ltd v Chemspray Pty Ltd (1967) 37 AOJP 2513 at 2516;
Blanco White, 5th ed, at para 4.107 and Gratwick, “Having Regard to What was
Known and Used” (1972) 88 LQR 341 at 343.
86 In my view, the reference to Jinek in P1 falls well short of meeting that test.
87 The evidence of the molecular biologists made clear that the invention disclosed in P1
could be performed without recourse to Jinek. However, ToolGen contended that the
notional skilled team (which on its case includes a microbiologist) would refer to Jinek for
the purpose of producing a RGEN derived from a bacterial species other than S. pyogenes.
The difficulty with this argument is that the reference in P1 to “Cas9 derived from other
species” is a mere conjecture that does not form part of the invention described in P1.
Importantly, the inventors do not state that other species can be used to perform the
invention. The suggestion is much more tentative and does no more than refer to the
possibility that other species might prove useful in overcoming the need for a 5’-GG-3’
dinucleotide in the PAM sequence. The fact that a microbiologist with expertise in bacterial
CRISPR/Cas systems might be engaged by a molecular biologist who was interested in
exploring that possibility is in my opinion not of itself sufficient to justify a finding that such
a person would be part of the skilled team. In any event, all of the molecular biologists said
that they would not have sought to establish if Cas9 from bacteria other than S. pyogenes
recognises a non-NGG PAM on reading P1.
88 In my opinion, the notional skilled addressee to whom P1 is addressed is a molecular

biologist with expertise in the field of gene editing in eukaryotic cells. The reference to Jinek
in P1 does not justify a finding that a microbiologist would be part of the skilled team.
89 The molecular biologist (working alone or with other molecular biologists and
laboratory assistants) will be a highly qualified scientist with a PhD in the field of molecular
biology with expertise in gene screening, targeting and manipulation in eukaryotes including
in mouse models and in vitro systems. They will be engaged in high level research in a well-
resourced laboratory in a medical research institute.
90 If, contrary to my finding, there was a microbiologist on the team, they would have a
PhD in the field of microbiology or bacteriology with expertise in the CRISPR/Cas systems

found in bacteria and archaea. This member of the team would most likely be engaged in
academic research within the biology faculty or department of a University.
The Patent Application

91 In the present case, ToolGen submitted that the patent application is directed to the
repurposing of bacterial Type II CRISPR/Cas systems for cleaving target DNA in eukaryotic
cells or organisms and that the skilled addressee will comprise a team that includes a person
with knowledge of these systems. Hence, ToolGen says that the notional team will have
expertise in the field of gene editing in eukaryotic cells, and the expertise of a microbiologist
with expertise in bacterial CRISPR/Cas systems. It is on this basis that ToolGen contends
that the team will include persons with the knowledge and experience of Associate Professors
Herold and Firestein and Professor Thomas (as experts in gene editing in eukaryotic cells)
and also a person like Professor Giffard (an expert in bacterial CRISPR/Cas systems). In
support of its submissions, ToolGen refers to the description in the patent application of Type
II CRISPR/Cas systems involving Cas9 and crRNA and tracrRNA and, in particular, the
statements to the effect that the invention is not limited to such systems from S. pyogenes.
92 The respondents submitted that the person who has a practical interest in the subject
matter of the invention is a molecular biologist with an interest in genome editing in
eukaryotic cells. They submitted that this reflects the “field of the invention” specified in the
patent application as well as the express purpose of the invention as described and claimed.
On that basis they submitted that a microbiologist such as Professor Giffard, with expertise in
relation to bacteria and prokaryotes (not eukaryotic cells) would not form part of the team.
They submitted that a microbiologist would have no interest in the subject matter of the
invention as described and claimed and that such a person would not be interested in making
or using the compositions or methods of the claims for genome editing in eukaryotic cells.
93 The invention disclosed in the patent application is not limited to a system which uses
a Cas9 protein derived from S. pyogenes. The Specification makes clear at [161]-[162] that
the Cas9 protein which is integral to the Type II CRISPR/Cas system may be derived from S.
pyogenes but is not limited to that bacteria and that it may be derived from a different
organism. The claims also make clear that claims 1 and 10 are not limited to Cas9 derived
from S. pyogenes and that they may be derived from other species. I think it must follow that
the invention, as described and claimed, is directed to a notional team including a person with
expertise in identifying Cas9 derived from other bacterial species.

94 The respondents submitted that the notional skilled addressee should not be defined in
order to fill a gap in the disclosure of the patent application. It submitted that it was not
legitimate to attempt to make up for an absence of disclosure by artificially adding to the
skilled team a person whose skills might be thought to assist with the development of
products or methods that are not disclosed.
95 As I have explained, the patent application makes clear that the invention can be
performed using different species of bacteria. Unlike P1, the statements to that effect are
clear and unequivocal and indicate that the invention extends to systems that use Cas9
derived from other bacterial species. Molecular biologists reading the patent application
would necessarily understand that the invention is not confined to a system that uses Cas9
derived from one species only. If they wished to perform the invention using Cas9 derived
from a different bacterial species they would turn to a microbiologist with expertise in
CRISPR/Cas systems who could assist in identifying a suitable substitute for S. pyogenes.
For that reason I think such a person should be taken to form part of the notional skilled team.
96 In my opinion, the notional skilled addressee to whom the patent application is

addressed is a team comprising a molecular biologist with expertise in the field of gene
editing in eukaryotic cells and a microbiologist with expertise in CRISPR/Cas systems.
COMMON GENERAL KNOWLEDGE

97 The common general knowledge is a general body of knowledge attributed to the
hypothetical non-inventive skilled person or team. In Minnesota Mining and Manufacturing
Company v Beiersdorf (Australia) Limited (1980) 144 CLR 253, Aickin J at 292 referred to
common general knowledge as “… the background knowledge and experience which is
available to all in the trade in considering the making of new products, or the making of
improvements in old, and it must be treated as being used by an individual as a general body
of knowledge”. It is knowledge actually known and used by skilled persons in the relevant
field generally or accepted by the bulk of those who are engaged in the particular art:
Ranbaxy Laboratories Ltd v AstraZeneca AB (2013) 101 IPR 11, Middleton J at [215]
(“Ranbaxy Laboratories”) citing British Acoustic Films Ltd v Nettlefold Productions (1936)
53 RPC 221 at 250 (“British Acoustic Films”). Knowledge is not common general knowledge
unless it is sufficiently widely known or used to become generally accepted and assimilated
into the minds of people skilled in the relevant art and therefore part of the common general
knowledge: see Gilead Sciences Pty Ltd v Idenix Pharmaceuticals LLC (2016) 117 IPR 252

at [210]-[214] (“Gilead”) where Jagot J referred to some of the leading authorities including,
Aktiebolaget Hässle v Alphapharm Pty Ltd (2002) 212 CLR 411 at [31]. It will include
publications to which the skilled addressee would refer as a matter of course: ICI Chemicals
and Polymers Ltd v Lubrizol Corporation Inc (1999) 45 IPR 577 at [112] per Emmett J.
98 However, information does not become common general knowledge merely because
it might appear in a journal even if it is one read by persons in the art: Ranbaxy Laboratories
at [217] per Middleton J citing (inter alia) Eli Lilly & Co Ltd v Apotex Pty Ltd (2013) 100
IPR 451 at [468]; Wake Forest University Health Sciences v Smith & Nephew Pty Ltd (No 2)
(2011) 92 IPR 496 at [96], General Tire at 482-3. In the latter case, the English Court of
Appeal referred with approval to the following passage in the judgment of Luxmoore J in
British Acoustic Films at 250:
In my judgment it is not sufficient to prove common general knowledge that a

particular disclosure is made in an article, or series of articles, in a scientific journal,
no matter how wide the circulation of that journal may be, in the absence of any
evidence that the disclosure is accepted generally by those who are engaged in the art
to which the disclosure relates. A piece of particular knowledge as disclosed in a
scientific paper does not become common general knowledge merely because it is
widely read, and still less because it is widely circulated. Such a piece of knowledge
only becomes general knowledge when it is generally known and accepted without
question by the bulk of those who are engaged in the particular art; in other words,
when it becomes part of their common stock of knowledge relating to the art.
99 I have applied these principles in this case in determining the common general
knowledge at the priority date. In that regard, I accept that certain publications relied on by
the appellants (Horvath (2010), Bhaya (2011), Deltcheva (2011) and Makarova (2011)) were
common general knowledge to a microbiologist specialising in the CRISPR/Cas systems of
prokaryotes at the priority date and therefore common general knowledge of the skilled team
if it included a microbiologist working in that field. Further, the matters referred to in [20]-
[35] above were common general knowledge of a molecular biologist with expertise in the
field of gene editing in eukaryotic cells at the priority date. The matters referred to in [36]-
[39] above were common general knowledge of a microbiologist with expertise in
CRISPR/Cas systems of prokaryotes at the priority date.
100 Jinek was first published online in Science on 28 June 2012, and in print on 17 August
2012, and is referred to in the patent application and P1. I am not persuaded that Jinek was
common general knowledge at the priority date. Associate Professor Herold gave evidence
that he had read Jinek before the priority date. Associate Professor Firestein gave evidence

that it was very likely he may have read the title and abstract of Jinek but that he had not read
the paper in full before the priority date. Professor Thomas gave evidence that he had not
read Jinek as at the priority date. There was no evidence led from Professor Giffard,
(assuming he is to be treated as a member of the skilled team) that he had read or had even
heard of Jinek before the priority date. The evidence does not show that Jinek was widely
known and accepted as at the priority date.
PRINCIPLES OF CONSTRUCTION
101 There was no dispute between the parties as to the principles governing the
construction of a patent specification or, in this case, a patent application. The relevant
principals were conveniently summarised by the Full Court in Jupiters Ltd v Neurizon Pty Ltd
(2005) 222 ALR 155 (Hill, Finn and Gyles JJ) as follows at [67]:
…
(i) the proper construction of a specification is a matter of law: Décor
Corporation Pty Ltd v Dart Industries Inc (1988) 13 IPR 385 at 400;
(ii) a patent specification should be given a purposive, not a purely literal,
construction: Flexible Steel Lacing Co v Beltreco Ltd (2000) 49 IPR 331;
[2000] FCA 890 at [81] (Flexible Steel Lacing); and it is not to be read in the
abstract but is to be construed in the light of the common general knowledge
and the art before the priority date: Kimberley-Clark Australia Pty Ltd v
Arico Trading International Pty Ltd (2001) 207 CLR 1; 177 ALR 460; 50
IPR 513; [2001] HCA 8 at [24];
(iii) the words used in a specification are to be given the meaning which the
normal person skilled in the art would attach to them, having regard to his or
her own general knowledge and to what is disclosed in the body of the
specification: Décor Corporation Pty Ltd at 391;
(iv) while the claims are to be construed in the context of the specification as a
whole, it is not legitimate to narrow or expand the boundaries of monopoly as
fixed by the words of a claim by adding to those words glosses drawn from
other parts of the specification, although terms in the claim which are unclear
may be defined by reference to the body of the specification: Kimberley-
Clark v Arico at [15]; Welch Perrin & Co Pty Ltd v Worrel (1961) 106 CLR
588 at 610; Interlego AG v Toltoys Pty Ltd (1973) 130 CLR 461 at 478; the
body of a specification cannot be used to change a clear claim for one subject
matter into a claim for another and different subject matter: Electric &
Musical Industries Ltd v Lissen Ltd [1938] 4 All ER 221 at 224–5; (1938) 56
RPC 23 at 39;
(v) experts can give evidence on the meaning which those skilled in the art
would give to technical or scientific terms and phrases and on unusual or
special meanings to be given by skilled addressees to words which might
otherwise bear their ordinary meaning: Sartas No 1 Pty Ltd v Koukourou &
Partners Pty Ltd (1994) 30 IPR 479 at 485–6 (Sartas No 1 Pty Ltd); the court
is to place itself in the position of some person acquainted with the

surrounding circumstances as to the state of the art and manufacture at the
time (Kimberley-Clark v Arico at [24]); and
(vi) it is for the court, not for any witness however expert, to construe the
specification; Sartas No 1 Pty Ltd at 485–6.
102 The notion of purposive construction, as explained by the Full Court in

GlaxoSmithKline Consumer Healthcare Investments (Ireland) (No 2) Limited v Generic
Partners Pty Limited (2018) 264 FCR 474 (“GlaxoSmithKline”), requires that the
specification be read as a whole and in light of the common general knowledge, and that a
practical and common sense approach be adopted to construction. The Full Court said at
[106]-[110]:
[106] More recent cases have continued to emphasise the need to read a patent
specification as a whole and in light of the common general knowledge. They
also confirm that a patent specification should be read in a practical and
common sense way and given a “purposive” construction. This approach to
construction requires the court to read the specification through the eyes of
the skilled addressee with practical knowledge and experience in the field of
work in which the invention was intended to be used and a proper
understanding of the purpose of the invention.
[107] A well-known case in which these principles were applied was the earlier
decision of the House of Lords in Catnic Components Ltd v Hill & Smith Ltd
[1982] RPC 183 (HL). The question in that case was whether the defendant
had infringed the plaintiffs’ patent for a galvanized steel lintel that the claim
required should have a rear support member “extending vertically” from the
base plate. The defendant’s lintel was not precisely vertical, but instead
extended upwardly at an angle of 84°. The House of Lords held that the
defendant’s lintel was nevertheless within the claim. This was because the
person skilled in the art would recognise that in order to perform the same
function as the rear support member described in the claim, it was not
essential that the rear support member in the defendant’s lintel be precisely
vertical.
[108] One criticism made of the decision of the House of Lords in Catnic was that
it permitted the court to adopt an interpretation of a claim that travelled
beyond what was conveyed by the language used so that the forbidden
territory extended to devices with rear support members that were not truly
vertical. However, as Lord Hoffmann later explained in Kirin-Amgen Inc v
Hoechst Marion Roussel Ltd (2004) 64 IPR 444 at [34]:
“Purposive construction” does not mean that one is extending or
going beyond the definition of the technical matter for which the
patentee seeks protection in the claims. The question is always what
the person skilled in the art would have understood the patentee to be
using the language of the claim to mean. And for this purpose, the
language he has chosen is usually of critical importance. The
conventions of word meaning and syntax enable us to express our
meanings with great accuracy and subtlety and the skilled man will
ordinarily assume that the patentee has chosen his language
accordingly. As a number of judges have pointed out, the

specification is a unilateral document in words of the patentee’s own
choosing. Furthermore, the words will usually have been chosen
upon skilled advice. The specification is not a document inter
rusticos for which broad allowances must be made. On the other
hand, it must be recognised that the patentee is trying to describe
something which, at any rate in his opinion, is new; which has not
existed before and of which there may be no generally accepted
definition. There will be occasions upon which it will be obvious to
the skilled man that the patentee must in some respect have departed
from conventional use of language or included in his description of
the invention some element which he did not mean to be essential.
But one would not expect that to happen very often.
[109] It is important to note that Lord Hoffmann was referring here to the meaning
conveyed to the skilled addressee by the language used and was not directing
himself to a situation in which the skilled addressee deduced that the
language of the claim, although conveying to him or her a particular
meaning, could never have been intended to mean what it conveyed.
[110] Thus, a skilled addressee may understand a claim that required that
something be “vertical” to mean “substantially vertical” or that a claim that
includes a requirement that a device “prevents air from coming into contact
with the surface of the ink” did not require that it prevent all the air from
doing so: Henrikson v Tallon [1965] RPC 434 (HL). These are situations in
which the court endeavours to give effect to the skilled addressee’s
understanding of the claim language in preference to a purely literal or
grammatical construction, not because the skilled addressee understands that
the claim contains a mistake that requires correction, but because, when read
in the context of the document as a whole and the common general
knowledge, the words used would convey that meaning to the skilled
addressee.
103 The speech of Lord Hoffman in Kirin-Amgen Inc v Hoechst Marion Roussel Ltd
(2004) 64 IPR 444 (“Kirin-Amgen”) has been referred to with approval in many decisions
Full Court decisions. In Kimberly-Clark Australia Pty Limited v Multigate Medical Products
Pty Limited (2011) 92 IPR 21 (“Multigate”), which was concerned with s 40 of the Act prior
to its amendment by the RTB Act, the plurality (Greenwood and Nicholas JJ) said at [44]-
[45]:
[44] Since a patent specification must include a detailed description of the

invention, and the best method known to the inventor of performing the
invention, a patent specification will usually contain a detailed description of
at least one embodiment of the invention. But provided a claim is fairly based
upon matter disclosed in the specification, a claim may define the invention
as having fewer integers than are present in an embodiment so described.
Equally, the claim may define an invention as having more features than are
present in any such embodiment. It is always open to the patentee to
introduce such a limitation if he or she so chooses provided that the claim is
fairly based on the matter disclosed in the specification. But if such a
limitation has been introduced, it cannot be disregarded simply because the
patentee could have framed a valid claim without it.

[45] A patentee may have good reason for introducing a limitation into a claim.
As Lord Hoffman explained in Kirin-Amgen Inc v Hoechst Marion Roussel
Ltd (2004) 64 IPR 444; [2005] 1 All ER 667; [2004] UKHL 46 at [35]
(Kirin-Amgen), a seemingly inexplicable limitation may have been
introduced to avoid arguments in relation to prior art. Lord Upjohn made the
same point in Rodi & Wienenberger AG v Henry Showell Ltd [1969] RPC
367 at 392 (Rodi): “… some claims may on a superficial reading appear to be
unnecessarily circumscribed, but those who have drafted them may have
done so in the light of the prior art …”. See also the judgment of Dixon J in
Walker v Alemite Corporation (1933) 49 CLR 643 at 656; [1933] ALR 437
(Walker) where his Honour quoted the following well known statement of
Lord Parker in Fellows v Thomas William Lench Ltd (1917) 34 RPC 45 at 55
who said “[a] claiming clause operates as a disclaimer of what is not
specifically claimed and for such disclaimer there may be reasons known to
the inventor but not to the court”.
104 Their Honours also said at [41]:
[41] There are two aspects to the principle which requires that a patent
specification be given a purposive rather than a purely literal construction.
The first concerns the well recognised need to read words in their proper
context. The second is directly related to the nature and function of a patent
specification. It is a document that is taken as intended to be read through the
eyes of the skilled addressee who is equipped with the common general
knowledge in the relevant art. The question is what, in an objective sense,
such a person would understand the relevant words of the claim to mean.
Ultimately, however, it is the claim that must be construed, and it is not
permissible to vary or qualify the plain and unambiguous meaning of the
claim by reference to the body of the specification: Interlego AG v Toltoys
Pty Ltd (1973) 130 CLR 461 at 478.
105 GlaxoSmithKline was a case in which the patentee contended that the skilled
addressee would recognise that certain words that appeared in the relevant claim were
included by mistake and that those words could be disregarded. As the Full Court observed
at [111]-[112]:
[111] In the present case the primary judge found that the skilled addressee would
understand that the reference to a reciprocating basket in claim 1 was an error
and that he or she would have simply disregarded those words.
[112] GSK relies on the skilled addressee’s understanding of the claim to establish
not what the language of the claim actually conveys to the skilled addressee,
but for the purpose of ignoring some of the language used on the basis that it
must have been included by mistake. The question is whether, if the court
were to also interpret the claim so as to correct the mistake, it would be re-
writing the claim or merely interpreting it through the eyes of the skilled
addressee in accordance with the principles to which we have referred.
106 The Full Court upheld the primary judge’s decision which gave effect to the words
which the patentee contended should be disregarded. I should make clear that ToolGen did

not contend that the approach rejected by the primary judge and the Full Court in
GlaxoSmithKline should be adopted in this case. I will return to consider the details of the
construction issues shortly but it is important to observe that ToolGen’s case on the first issue
of construction that arises for decision was that the language of claim 1 was capable of
supporting the broad meaning which ToolGen sought to attribute to it. I have referred to
GlaxoSmithKline not because the present case is said to involve any mistake in the drafting of
claim 1, but merely to draw attention to the Full Court’s observations concerning the role,
and limits, of purposive construction.
107 It is convenient to refer at this point to the Full Court decision in Novozymes A/S v
Danisco A/S (2013) 99 IPR 417 (Greenwood, Jessup and Yates JJ) (“Novozymes”) which was
relied on by ToolGen in its submissions as raising an issue of construction similar to one that
arises here. The patent in suit in that case included 17 claims. Claims 1, 7 and 9 were for:
1. A process for preparing a foodstuff suitable for consumption comprising an

emulsifier, the process comprising the steps of
(i) providing a food material containing a fatty acid ester and a second
constituent;
(ii) contacting the food material with an enzyme such that an emulsifier
is generated by the enzyme from the fatty acid ester and a second
functional ingredient is generated from the second constituent;
(iii) inactivating or denaturing the enzyme to provide the foodstuff
comprising the emulsifier, the fatty acid ester and the enzyme in an
inactive form or a denatured form.
…
7. A process according to any one of the preceding claims wherein the foodstuff
comprises at least the emulsifier and the second functional ingredient, and
wherein the emulsifier and the second functional ingredient have been
generated from the fatty acid ester and the second constituent of the food
material by the enzyme.
…
9. A process according to any one of the preceding claims wherein the second
constituent is selected from a constituent comprising a hydroxy group (-OH),
polyvalent alcohols, including glycerol; water, ethanol, sugars including
sucrose, fructose, glucose (dextrose), lactose, and galactose; dextrins
including maltodextrin, sorbitol, mannitol, fruit acids and hydroxy acids
including citric acid, tartaric acid, lactic acid and ascorbic acid; mixtures and
derivatives thereof.

108 The primary judge in that case found that water could act as the “second constituent”
in claim 1 but not claim 7. However, as Jessup J (with whom Yates J relevantly agreed) said
at [70]:
[70] That conclusion turned upon the terms of claim 9, which is dependent on
claim 1. Absent claim 9, the primary judge considered that water could not be
the second constituent under claim 1. However, claim 9 specified water as
within the range of permissible second constituents, and was consistent with
the specification in doing so. It followed, according to her Honour, that the
skilled addressee would understand that at least a permissible second
constituent under claim 1 would be water. Her Honour gave instances, within
the compass of the claim, in which water would be the second constituent…
109 It is not necessary to explore the intricacies of the claims and, in particular, the
relationship between claims 1, 7 and 9. Importantly, however, Jessup J rejected the primary
judge’s conclusion that the skilled addressee would read claim 7 as excluding a process in
which there was one reaction only and water was the second constituent. His Honour
continued at [87]-[88]:
[87] That brings me back to claim 9, the passage in the specification

corresponding to which is set out in the third extract in [42] above. Under
claim 9, what is claimed, among other things, is a process according to claim
7 in which water is permitted as a second constituent. If we are to read the
claims sensibly, it would seem to follow that any ambiguity in claim 7 must
be resolved by allowing water to be the second constituent. The primary
judge deflected that conclusion by reasoning that, in the eye of the skilled
reader, “the specificity of claim 7 would be understood to exclude water,
even though it was one of the broad class of second constituents of claim 9”.
The point was, it seems, that, although the wording of other claims might aid
in the construction of the claim of interest, that was only an aid to
construction, and had to yield to specific indications as to the meaning of the
latter. In the context of the present debate, according to her Honour, it was
clear from the words of claim 7 itself that water could not be the second
constituent, and that conclusion was not to be displaced by the more indirect
constructional indications that might be derived from another claim. A
submission along these lines was also made by the respondents before the
Full Court.
[88] It should be clear that I do not share her Honour’s perception as to the clarity
of the specific meaning of claim 7 itself. But there is, in my respectful view,
a more direct, and less tractable, impact which the terms of claim 9 have
upon the construction of claim 7. Claim 9 bears upon the issue not merely
because it provides a point of reference for the achievement of consistency of
meaning within the patent as a printed document. More importantly, there is
a structural relationship between claim 7 and claim 9: that the patent claims a
process according to claim 7 in which water is the second constituent is the
inevitable result of the way claim 9 is expressed. Claim 9 could not be clearer
in relevant respects. It tells the reader, both scientific and lay, that water must
be within the class of second constituents permissible under each of the
preceding claims, including claim 7.

110 It is important to note that Jessup J did not consider that there was anything in claim 7
that expressly, or by necessary implication, excluded a process in which water was the second
constituent. However, even if claim 9 was ambiguous as to whether or not it excluded water
as the second constituent, the position was made clear by the presence of claim 9 which
expressly contemplated that water could act as the second constituent.
111 His Honour went on to consider, against the background of those conclusions, the
issue of clarity and, in particular, whether claims 1 and 7 were invalid because they were not
“clear and succinct” as required by s 40(3) of the Act as it then stood. Neither the primary
judge nor the Full Court considered claim 7 to be invalid for lack of clarity, although they
disagreed as to how claim 7 was to be interpreted. On the issue of lack of clarity his
Honour’s observations included the following at [93]:
[93] The problem of locating the dividing line which separates a claim which is
bad for want of clarity from a claim which, though troublesome in its
construction, is sufficiently clear to be valid, is scarcely less difficult than the
problem of construction itself. In the present case, both sides have been able
to draw upon general statements in the cases which provide some support for
the opposite positions which they take. For my own part, I would find it
sufficient for present purposes to refer to Welch Perrin & Co Pty Ltd v
Worrel (1961) 106 CLR 588, in which the High Court said (at 610):
If it is impossible to ascertain what the invention is from a fair
reading of the specification as a whole, that, of course, is an end of
the matter. But this objection is not established by reading the
specification in the abstract. It must be construed in the light of the
common knowledge in the art before the priority date. The general
principles governing the construction of specifications are well
known, and no lengthy reference to them is necessary. It is, however,
fitting that we remind ourselves of the criterion to be applied when it
is said that a specification is ambiguous. For, as the Chief Justice
pointed out in Martin v Scribal (1954) 92 CLR 17 at 59, referring to
Lord Parker’s remarks in National Colour Kinematograph Co Ltd v
Bioschemes Ltd (1915) 32 RPC 256, we are not construing a written
instrument operating inter partes, but a public instrument which
must, if it is to be valid, define a monopoly in such a way that it is
not reasonably capable of being misunderstood. Nevertheless, it is to
be remembered that any purely verbal or grammatical question that
can be resolved according to ordinary rules for the construction of
written documents, does not, once it has been resolved, leave
uncertain the ambit of the monopoly claimed (see Kauzal v Lee
(1936) 58 CLR 670 at 685).
112 I should note in relation to his Honour’s reference to Welch Perrin & Co Pty Ltd v
Worrell (1961) 106 CLR 588 that the High Court is not to be understood as suggesting (as his
Honour no doubt appreciated) that uncertainty of meaning can always be resolved by

application of the rules for the construction: see Freeman v TJ and FL Pohlner Pty Ltd (1994)
30 IPR 377 at 381-382.
CONSTRUCTION ISSUES
“a nucleic acid encoding”

113 The first construction issue concerns the references to “nucleic acid encoding” in
claims 1 and 10 and their dependent claims. Claims 1 and 10 both use the phrase “a nucleic
acid encoding” when referring to “a nucleic acid encoding a Cas9 polypeptide” (component
1) and again when referring to “a nucleic acid encoding a guide RNA” (component 2). The
debate between the parties was primarily concerned with the meaning of the phrase as used in
component 2.
114 The respondents submitted that ToolGen’s construction of the word “encoding” when
referring to a nucleic acid encoding a guide RNA in claims 1 and 10 involves giving the word
“encoding” a meaning which is different from its ordinary use in the field of molecular
biology. But ToolGen argues (correctly) that this does not in itself exclude the possibility
that the word is used in claim 1 and 10 in a different sense. ToolGen says that the word
encoding is also apt to mean, in the context in which it is used here, “providing the sequence
for” a guide RNA. It says that the word has a broader meaning which includes not only a
string of nucleotides that are transcribed into a guide RNA, but also a string of nucleotides
that enables the guide RNA to perform its function (i.e. to guide a Cas9 protein). As such,
ToolGen says no act of transcription within the cell to produce the guide RNA is required by
the use of the word “encoding” and, further, if there must be an act of transcription, then it is
not one that must occur inside the eukaryotic cell in which the target nucleic acid sequence
resides. According to ToolGen, “nucleic acid encoding a guide RNA” in claims 1 and 10
includes both DNA which is transcribed to RNA in vivo in a eukaryotic cell and RNA which
is transcribed in vitro prior to it being introduced into the eukaryotic cell and which provides
the information for the guide RNA to perform its function of guiding the cas9 to the target
DNA once inside a eukaryotic cell.
115 ToolGen placed considerable reliance on claim 19 which, when read with claim 10,
requires that the nucleic acid encoding the guide RNA is in vitro transcribed RNA.
According to ToolGen, claim 19 makes no sense if “encoding” refers to the process of
transcription because a nucleic acid “encoding” (in the conventional sense of the word) the
guide RNA could only be DNA whereas claim 19 requires that the nucleic acid encoding the

guide RNA is in vitro transcribed RNA. On that view, claim 19 refers to a situation in which
in vitro transcribed RNA transcribes the guide RNA. The experts agreed that does not make
sense.
116 ToolGen says if the words “a nucleic acid encoding a guide RNA” are understood as a
nucleic acid “providing the sequence for” a guide RNA, then claim 10 and claim 19 can be
read together. On that approach, claim 19 requires that in vitro transcribed RNA provide the
sequence for the guide RNA.
117 ToolGen also placed considerable reliance on the fact that nucleic acid may be either
DNA or RNA. It submitted that the wider term used in the claims should be presumed to
have been deliberately chosen. As I understand the argument, use of the term nucleic acid
rather than DNA is consistent with the language of claim 19 which requires that the nucleic
acid encoding the guide RNA is in vitro transcribed RNA. ToolGen says that since RNA
cannot be transcribed into guide RNA, the word “encoding” as used in claims 1, 10 and 19,
should not be given its conventional meaning.
118 As previously mentioned, the respondents submitted, and the Delegate found, that
claim 19 lacks clarity. The respondents say that the phrase “a nucleic acid encoding” as used
in claim 10 is conventional language that would be used by a molecular biologist to describe
the processes of transcription in which the guide RNA is encoded by DNA. The respondents
say that ToolGen’s argument based on claim 19 is one in which “the tail wags the dog”.
119 In support of its submissions, ToolGen relied on the Full Court’s decision is
Novozymes to which I have previously referred. In my opinion, that case merely reflects the
application of the ordinary principles of construction and, in particular, the need to read the
complete specification, including the claims, as a whole. In the present case, the question is
what claims 1, 10 and 19 mean in light of the complete specification when read as a whole
through the eyes of the skilled addressee. The process of construction necessarily includes a
consideration of claim 19 and the implications that its presence may have for claims 1 and 10.
120 There are two points to make about the relationship between claims 1, 10 and 19.
First, claim 1 is for a composition and claim 10 is for a method. I consider the skilled
addressee would understand that claim 1 defines a composition suitable for use in carrying
out the method of claim 1. They are two aspects of the same invention. The second point is

that claim 19 is dependent on claim 10, but not claim 1. It is the relationship between claim
10 and claim 19 that is at the core of ToolGen’s argument.
121 Claim 10 makes clear that the method of the claim requires that the nucleic acid
encoding a polypeptide and the nucleic acid encoding a guide RNA do the encoding in the
eukaryotic cell in which the target nucleic acid sequence is located. The word encoding is
used as a transitive verb to describe the relationship between the relevant action (encoding),
the subject (the nucleic acid) and the object (a polypeptide or a guide RNA). That the
relevant action occurs inside the cell is made clear by the introductory words of claim 10
which refer to a method in which the CRISPR/Cas system is introduced into the eukaryotic
cell. That system comprises the nucleic acid encoding a Cas9 polypeptide (component 1) and
the nucleic acid encoding a guide RNA (component 2). In my opinion, claim 10 requires that
nucleic acid be introduced into the eukaryotic cell where it will then encode a polypeptide
and a guide RNA.
122 ToolGen’s construction of claim 10 requires only that the nucleic acid “provide the
sequence for a guide RNA”. On ToolGen’s construction of claim 10 when read with claim
19, the transcription of the guide RNA can also occur in vitro (outside the eukaryotic cell in
which the target sequence resides). ToolGen’s argument is that the verb “encoding” can
mean both providing the sequence for producing the guide RNA (through the process of
transcription from DNA to RNA) as well as providing the sequence that enables the guide
RNA to perform its function. I do not accept that the later interpretation involves any action
at all as the guide RNA once produced from DNA in vitro does not provide the information
for its guiding function in any meaningful sense, and merely exists as an RNA capable of
guiding Cas9 to the target sequence. The action that the word “encoding” describes is that of
producing the RNA which, according to the express language of claim 10, must occur within
the eukaryotic cell. Accordingly, it cannot be said that in vitro transcribed RNA which is
produced outside of the cell and introduced into the cell in a “naked” or “isolated” form is
consistent with what is described in claim 10.
123 Furthermore, if the nucleic acid referred to in claim 10 is isolated RNA transcribed in
vitro (ie. before introduction to the cell) then what is described, on ToolGen’s construction, is
isolated RNA providing the sequence for the guide RNA or, more specifically, a guide RNA
(transcribed in vitro) providing the sequence for a guide RNA. That leads to the rather odd
result in which the isolated RNA and the guide RNA are one and the same thing.

124 ToolGen also submitted that the term “nucleic acid encoding” used in claims 1 and 10
is never used in the body of the specification to refer only to DNA encoding a guide RNA.
Further, ToolGen submitted that the words “nucleic acid encoding” are deliberately broader
and different from the words that are used in the body of the specification, which refers to
“DNA that encodes the guide RNA”. ToolGen submitted that the different language used
shows that there is an important difference between “nucleic acid encoding the guide RNA”
and “DNA that encodes the guide RNA” beyond the fact that the latter language refers only
to DNA and not to all forms of nucleic acid. ToolGen also referred to [176]-[179] of the
Specification which I have previously set out including, in particular, the statement in [176]
that “[t]he guide RNA may be transferred into a cell or an organism in the form of RNA or
DNA that encodes the guide RNA”. However, this statement is clearly distinguishing
between two different approaches, the first in which the guide RNA is transferred into the cell
“in the form of RNA” and the second in which DNA that encodes the guide RNA is
transferred into the cell.
125 As to the use of the word “encodes” in [176] and [177] rather than “encoding” as used
in the claims, there is in my view no material difference between the two. Both refer to
nucleic acid that encodes a guide RNA. If anything, the language of the claims confirms that
the relevant action (encoding of the guide RNA) is occurring inside the cell.
126 ToolGen also drew attention to the final sentence in [179] which states, in effect, that
the introduction of DNA encoding a guide RNA is not excluded. That statement when read
in the context of the balance of [179] indicates that this approach is less preferred to the
introduction of an isolated (or naked) guide RNA. According to [179], the preferable
approach is that in which “[t]he guide RNA is preferably transferred to a cell in the form of
isolated RNA rather than in the form of plasmid comprising encoding sequence for a guide
RNA”. Those words are referring to the use of a plasmid to introduce into the cell DNA
encoding the guide RNA. The Specification refers at [328] to some of the potential problems
associated with the use of plasmid DNA including unwanted immune responses in plants and
animals.
127 The word “encoding” is used in the Specification to distinguish nucleic acid encoding
a Cas protein from a Cas9 protein. For example, [156] distinguishes between a Cas
component “in the form of a protein or in the form of a nucleic acid encoding Cas protein”. It
is apparent that in the latter case the DNA will be transcribed to mRNA which in turn will be

translated to a Cas protein. The Specification elsewhere refers to “Cas protein-encoding
nucleic acid” which may be in the form of a vector such as a plasmid: see, for example,
[166], [207], [217], [222] and [224]. The Specification states at [199]:
Using Cas protein rather than a nucleic acid encoding Cas protein to induce a
targeted mutagenesis is advantageous because exogeneous DNA is not introduced
into an organism. Thus, the composition comprising Cas protein and a guide RNA
may be used to develop therapeutics or value-added crops, livestock, poultry, fish,
pets, etc.
128 However, while the first of these methods is said to have advantages, the
Specification distinguishes repeatedly between use of a Cas protein and use of nucleic acid
encoding a Cas protein: see, for example, [203], [207] and [215]. The Specification states at
[217]:
In the present invention, a Cas protein-encoding nucleic acid or Cas protein and a
guide RNA or DNA that encodes the guide RNA may be transferred into a cell by
various methods known in the art …
Here again the Specification is distinguishing between a Cas protein and nucleic acid
encoding for a Cas protein either of which may be transferred into the cell. The same
distinction is drawn with respect to the guide RNA, which may be introduced into the cell in
its naked or isolated form, or in the form of DNA that encodes the guide RNA. The
Specification also refers to “guide RNA encoding plasmid”: see, for example, [319] and
[440]. The latter paragraph distinguishes between the use of (inter alia) “synthetic guide
RNA” (ie. naked or isolated RNA) and “guide RNA encoding plasmids”.
129 ToolGen submitted that it would be surprising if the patent applicant sought to protect
the less preferred method while not seeking protection for the preferred method which uses
isolated RNA transcribed in vitro.
130 In my opinion, ToolGen’s submission is answered by Lord Hoffmann’s speech in

Kirin-Amgen and the other authorities referred to in Multigate which emphasise that a
patentee may have a good reason for introducing a seemingly inexplicable limitation. Here,
the language of claim 10 when read in the context of the Specification as a whole indicates
that (for whatever reason) the claim has been limited to a method in which the nucleic acid
encodes the guide RNA in the eukaryotic cell. In my opinion, this requires that the guide
RNA be transcribed from nucleic acid in the eukaryotic cell.

131 At a more general level, and focusing on the relationship between claim 10 and 19,
ToolGen submitted that the respondents’ interpretation of claim 19 does not make any
sufficient attempt to read the two claims together so as to give them a clear and consistent
meaning which also avoids the conclusion that claim 19 lacks clarity. ToolGen submitted, in
effect, that claim 10 must be interpreted so as to accommodate the language of claim 19 in
order to ensure that claim 19 is given meaning and work to do.
132 As to ToolGen’s reliance on the use of the term “nucleic acid” rather than DNA in
claim 10, there are two matters which would explain why the broader term is used. The first
concerns the transcription and translation of the Cas9 polypeptide which will involve both
DNA and RNA (in particular mRNA) in the transcription and translation process. The
second relates to the use of viral RNA. The experts agreed that the use of the term “nucleic
acid” will cover a situation in which viral RNA is introduced into the cell which then encodes
DNA which in turn encodes the guide RNA. Although the use of viral RNA is not discussed
in the Specification, this method of producing RNA in the cell was common general
knowledge at the priority date. For that reason I do not think the use of the term “nucleic
acid” (rather than DNA) in claim 10 assists ToolGen’s argument.
133 The question is whether the presence of claim 19 justifies the conclusion that the
words “a nucleic acid encoding a guide RNA”, when read in the context of the Specification
as a whole, are reasonably capable of meaning simply “providing the sequence for” a guide
RNA. ToolGen relied on the evidence of Associate Professors Firestein and Herold in
support of this construction of the word “encoding” in claims 1 and 10.
134 In JER 1 Associate Professor Firestein said that he understood the relevant phrase to:
… encompass also the guide RNA itself, agnostic to the method by which the guide
RNA was generated (eg. including when generated in the in vitro transcribed form).
135 In support of this understanding he referred to claim 18 in which the nucleic acid
encoding the guide RNA is a vector and claim 19 in which the nucleic acid encoding the
guide RNA is in vitro transcribed RNA.
136 In Firestein 1, Associate Professor Firestein said that he understood the relevant
phrase to refer to the nucleic acid sequence or code that comprises the DNA itself or the
DNA from which it can be expressed. He went on to say that the phrase is referring to the

information (ie. code) provided by the nucleic acid sequence that defines the composition of
the guide RNA.
137 Associate Professor Firestein was cross-examined at some length on this topic. His
answers were quite often not directly responsive to the question asked. He referred to an
interpretation of claims 1 and 10 in which nucleic acid encoding a guide RNA might be
understood as encompassing RNA providing the sequence for the guide RNA. Of the phrase
“nucleic acid encoding a guide RNA” Associate Professor Firestein said:
… the phrase doesn’t say nucleic acid transcribing a guide RNA, it says encoding a
guide RNA, so I view the word encoding simply as providing the sequence for
providing the code. And that may come through transcription, or it may come from
the sequence itself.
138 Associate Professor Firestein agreed that this would not be typical usage in the field
of molecular biology. But it is clear that he was conscious of the difficulty with this
construction because, as a molecular biologist, he understands that synthetic RNA (ie.
isolated or naked RNA) introduced into the cell does not encode the guide RNA. Moreover,
on his interpretation of the relevant claims, the nucleic acid encoding the guide RNA and the
guide RNA are precisely the same thing: ie. a sequence of non-coding RNA. In cross-
examination Associate Professor Firestein eventually accepted that the use of the word
encoding as meaning no more than providing a sequence or code was different from its
ordinary meaning in molecular biology. But he went on to add that “encoding” can have a
broader meaning outside the field of molecular biology.
139 At least in his oral evidence Associate Professor Firestein referred to this
interpretation as a possible interpretation of the claims. In this regard, he gave the following
evidence:
MR DIMITRIADIS: You referred to the use of encoding in a molecular biology

context and in other contexts. May we take it from what you’ve said, Professor
Firestein, that your broader interpretation of this claim involves giving a meaning to
encoding which differs from its meaning in the context of molecular biology.
ASSOC PROF FIRESTEIN: Yes, I – well, as I’ve said before, it’s not the typical
language that I would use, but at the same time, I wouldn’t want to speculate exactly
what the authors meant when they used this phrase, because I do understand that
there’s other ways to interpret it.
140 Moving to Associate Professor Herold’s evidence on this topic, he stated in Herold 1:
150. Upon reading the phrase “nucleic acid encoding a guide RNA” in claim 1, my

immediate understanding is that the “nucleic acid” referred to is DNA, in the
form of a vector or plasmid. DNA “encodes” the guide RNA because it is
transcribed by the cell's machinery into the guide RNA.
151. I would not typically consider the “nucleic acid encoding a guide RNA” to
refer to the guide RNA itself. This is because it would not be my usual use of
“encoding” to speak of “RNA encoding a guide RNA”.
152. However, I note that claim 19 of the Patent Application is directed to the
“method of any one of claims 10-16, wherein the nucleic acid encoding the
guide RNA is in vitro transcribed RNA”. If claim 19 is within the scope of
claim 10, then this indicates that the phrase “nucleic acid encoding a guide
RNA”, at least in claim 10, is intended to include RNA itself. I expect the
words to have the same meaning in claim 1. Claims 9, 20 and 21, which I
discuss below, also appear to be consistent with the phrase “nucleic acid
encoding a guide RNA” in claims 1 and 10 including in vitro transcribed
RNA.
153. As stated above, nearly all of the examples are directed to in vitro transcribed
guide RNA, and the experimental detail in relation to DNA encoding the
guide RNA is very limited. Although DNA (plasmids) encoding chimeric
sgRNA are referred to in Examples 1-3 and 6, there are no details about how
the plasmids are made.
141 He restated this view in JER 1 by referring to those same paragraphs of Herold 1. In
his oral evidence he agreed that claim 19 makes sense if the broader construction of the word
“encoding” is adopted. But he was clear that this involves giving the word a different
meaning to that which it is given in the field of molecular biology. In particular, he agreed
with the following evidence given by Professor Thomas in concurrent evidence:
MR DIMITRIADIS: … Professor Thomas, you understand that Professor Firestein’s

broader interpretation of the claim is that it – in the phrase “nucleic acid encoding a
guide RNA encompasses the guide RNA itself, such as a in vitro transcribed guide
RNA”. Is it your view not that that interpretation of the claim involves giving the
word “encoding” its ordinary meaning in molecular biology as at October 2012, or
some other meaning?
PROF THOMAS: I think Professor Firestein’s view involved attaching a meaning to
“encoded” [sic] that is not one that is used in molecular biology. And further, I would
say that given that the phrase starts “nucleic acid”, we are definitely in the realms of
molecular biology when looking at this particular phrase.
MR DIMITRIADIS: Professor Herold, can I ask you do you agree or not with
Professor Thomas’ evidence on that point?
PROF HEROLD: Yes. I do agree.
142 My view of Associate Professor Herold’s evidence is that he has approached the
interpretation of claim 10 on the basis that claims 10 and 19 must be read consistently and
that this is only possible if the words “nucleic acid encoding a guide RNA” encompass the
introduction of isolated or naked RNA into the cell. In my opinion his approach overlooks

the possibility that claim 19 cannot be sensibly read with claim 10 and that the meaning of
claim 19 when read with claim 10 is unclear. Of the molecular biologists who gave evidence
on this topic, I prefer the evidence of Professor Thomas. In my opinion, his evidence is likely
to be representative of the notional skilled addressee who, when reading the Specification as
a whole in light of the common general knowledge, would have a very clear understanding of
the system described in claim 10 as one in which nucleic acid encoding the guide RNA is
introduced into the cell where the guide RNA is transcribed. As Professor Thomas said in his
oral evidence in relation to the words nucleic acid encoding a guide RNA:
PROF THOMAS: … for me, the statement “nucleic acid encoding a guide RNA”
does not encompass the guide RNA itself. To me, that’s a very clear molecular
biology statement in which we have a DNA or RNA sequence that provides the
information for the guide RNA. So I would be stronger in my statement.
What I understood Professor Thomas to be saying is that the nucleic acid provides the
information from which the guide RNA is transcribed. Claim 19 does not make sense to
Professor Thomas because he does not consider that in vitro transcribed guide RNA is a
nucleic acid that encodes anything. I regard his evidence on this topic as highly persuasive.
143 The relevant paragraphs of the body of the Specification, including the description of
a system in which nucleic acid (DNA) encodes the guide RNA in the eukaryotic cell, and the
language used to describe that system, weigh heavily against ToolGen’s construction. In my
opinion, the word “encoding” is used in claim 10 in its conventional sense (ie. as it would be
understood by a molecular biologist) to refer to the production of a Cas9 polypeptide by
transcription and translation and the production of a guide RNA by transcription in the cell.
The nucleic acid referred to in the claim provides the information which is used in the cell to
produce the guide RNA. Claim 10 does not encompass a system in which an existing guide
RNA is introduced into the cell.
144 As Jessup J observed in Novozymes at [95]:
[A] conclusion that a claim lacks clarity is proper to be made only if the court, using
all the properly available aids and looking at the matter through the eyes of the
skilled addressee, is unable to give a clear meaning to the claim.
145 Claim 10 requires that the guide RNA be transcribed in the cell but claim 19
contemplates that the guide RNA will have been transcribed outside the cell. Claim 19
cannot be read sensibly with claim 10 on which it is dependent. In my opinion claim 19 lacks
clarity.

“paired Cas9 nickases”
146 I have previously referred to the definition of “paired Cas9 nickase” in the
Specification which refers to the guide RNA and Cas9 protein functioning as a pair. The
Specification states at [187]:
The guide RNA and the Cas protein may function as a pair. As used herein, the term
“paired Cas nickase” may refer to the guide RNA and the Cas protein functioning as
a pair. The pair comprises two guide RNAs. The guide RNA and Cas protein may
function as a pair, and induce two nicks on different DNA strand. The two nicks may
be separated by at least 100 bps, but are not limited thereto.
147 The definition is somewhat awkward but the experts were in agreement as to what a
paired Cas9 nickase is in terms broadly consistent with the definition. A composition that
uses paired Cas9 nickases is one in which there are two different guide RNAs each guiding a
Cas9 nickase. Each nickase produces a single break in a strand of DNA. A pair of nickases
produces two such breaks.
148 The question is whether either claim 1 or claim 10 encompasses paired Cas9 nickases.
Although the Specification refers to paired Cas9 nickases, including in the definition to which
I have referred and in Examples 7 and 8, none of the claims made any explicit reference to
them. There are two main points of contention in relation to this construction issue. The first
is whether a composition that includes paired Cas9 nickases that produce staggered ended
breaks at two different positions on two DNA strands is capable of being said to produce a
“site-specific double-stranded break” as required by claims 1 and 10. The second is whether a
composition that includes paired Cas9 nickases which uses two different RNAs paired with
two Cas9 nickases can be correctly characterised as “a Cas9/RNA complex” as required by
claim 10.
149 To give some context to this discussion, I should note that the respondents contend
that claim 1 extends to such a composition, but that the disclosure of P1 does not. It follows
according to the respondents’ argument that claim 1 is not entitled to priority based on P1.
The same argument is relied on by the respondents in relation to the method defined by claim
10.
150 Professor Thomas considered that both claim 1 and claim 10 use language that
extends to the use of paired Cas9 nickases. He did not draw any relevant distinction between
claim 1 and claim 10 in this respect. While Professor Thomas accepted that the language
used to denote both the guide RNA and the Cas9 polypeptide are expressed in the singular, he

understood both claim 1 and claim 10 to not exclude the use of two different complexes
consisting of two different guide RNAs and two Cas9 nickases to generate a double-stranded
break.
151 Senior Counsel for ToolGen put to Professor Thomas that the claims referred to the
introduction of a site-specific double-stranded break, and that this was inconsistent with the
use of paired Cas9 nickases that would produce breaks at different nucleotides on each
strand. He did not accept this. In his view, the nickase system produces a site-specific
double-stranded break at different positions on the two DNA strands. Associate Professor
Herold agreed that a site-specific double-stranded break could be either blunt (meaning that
the breaks were at the same location on each DNA strand) or staggered (meaning that the
breaks could occur at different locations).
152 ToolGen submitted that the concept of “site-specific” in relation to a DNA strand
means a particular nucleotide position on that strand. ToolGen submitted that if the breaks
occur at two different nucleotide positions on the two strands, then the break in the DNA is
not “a site-specific double-stranded break” but “a two site-specific double-stranded break”
outside the scope of the claims. I do not accept that submission which, in my opinion, relies
on an overly literal analysis of the claim language that is inconsistent with what I consider
would be the notional skilled addressee’s understanding of this requirement.
153 Professor Thomas said that the nickase system would produce a site-specific double-
stranded break where the breaks on each strand are in close proximity. He said that if the
breaks are not in close proximity there will be large overhangs which will prevent the two
strands from separating (hence the name “sticky ends”). He gave the following evidence:
PROF THOMAS: Yes, I believe, based on my knowledge of the way that the nickase
system works, that the nicks must be in relatively close proximity to generate a
double stranded break, and that they’re separated by a distance, in this case the
reference to 100 based pairs or more, then that will not constitute a double – an
effective – double stranded break, because the strands don’t separate.
…
MR CORDINER: … Would you agree with me … a more natural understanding of a
paired cas9 nickases, is that it doesn’t produce a site specific double stranded break.
It produces a double stranded break, but not a site-specific one.
PROF THOMAS: I can’t agree with you there, actually. I wouldn’t say – so in terms
of a site-specific double stranded break, each of the nicks that occur is occurring at a
site-specific location, and if they’re in close proximity, they would generate a double
stranded break. So to me, the nickase system does include a site-specific double
stranded break.

MR CORDINER: Yes. But I put it to you that another way of interpreting that, given
what the specification has said, it’s not unreasonable to hold the view that the
reference to … a site-specific is really referring to the fact that this is happening at a
single nucleotide.
PROF THOMAS: No, again, I can’t agree with you there, in the sense that it is a
single – it is a very specific location that is targeted by each of the nickases, so it’s a
– it’s – the term site-specific totally encompasses, in this – in this context, to me, a
double stranded break generated by two nickases on each strand of the DNA in close
proximity.
Associate Professor Herold was also of the view that a site-specific double-stranded break
could be one with staggered end breaks.
154 In his evidence, Professor Thomas made clear that the breaks would need to be
closely proximate to each other. ToolGen says that the difficulty with this approach is that
there is no requirement in the claims that the two breaks be any particular distance from each
other. However, Professor Thomas’ evidence was that if the breaks are too far apart, there
will be no effective double-stranded break because the two strands will not separate.
155 Associate Professor Firestein, who did not consider either claims 1 or 10 to extend to
paired Cas9 nickases, saw some difficulty with the language of “site-specific double-stranded
break” but he agreed that this was not the reason behind his view. He explained the difficulty
with that phrase and the reason he considered paired Cas9 nickases were outside the claims in
the following evidence:
MR DIMITRIADIS: Professor Firestein, just to back up that point, the use of the
phrase “site-specific” in claims 1 and 10 is not the reason why you regard the use of
paired Cas9 nickases as being outside the claim, it’s for a different reason that you
regard them as being outside the claim. Correct?
ASSOC PROF FIRESTEIN: That’s correct.
MR DIMITRIADIS: And you would agree, would you not, that the action of a paired
Cas9 nickase is site-specific in the sense that that system will lead to the introduction
of a double-stranded break at a particular location in the DNA sequence. Correct?
ASSOC PROF FIRESTEIN: I would not necessarily agree with that because – you
know, I think the definition of what is site-specific is – can be a bit nebulous and
confounding. As the patent application itself shows and discusses, the distance
between the two components on the paired nickase system can be quite close. They
could be 100 base pairs, they could be 1000 base pairs, they can be 10,000 base pairs
apart. So at what point does it become site-specific? If you have two guide RNA
Cas9 complexes that are potentially 10,000 base pairs apart, is that site-specific, or
are we talking about two sites? So, to me, the definition of site-specific would be a
bit confusing, so I interpret more strongly the use of the words around the complex,
being a complex and a guide RNA rather than the interpretation around the term
“site-specific.”

MR DIMITRIADIS: Yes. It’s the latter point that is your reason for excluding the
Cas9 nickases from the claims. Correct?
ASSOC PROF FIRESTEIN: Yes. It’s really about the fact that you have two
different heterologous complexes that are working in the paired system.
156 Associate Professor Herold considered that claim 1 encompassed a paired Cas9
nickase but that claim 10 did not. With regard to claim 10, he appears to have given
particular weight to the last integer of that claim and the requirement that “the Cas9
polypeptide and guide RNA [which] form a Cas9/complex in the eukaryotic cell, whereby a
site-specific double-stranded break at the target nucleic acid sequence is introduced”. This
language is different from the language of claim 1.
157 I do not think the term “site-specific” requires that the double-stranded break occur at
a singular nucleotide position on both strands. All experts accepted that the term extended to
staggered ended breaks occurring at different nucleotide positions on the two DNA strands.
Both Professor Thomas and Associate Professor Herold were of this view. Associate
Professor Firestein had some difficulty with the meaning of site-specific, but he did not
suggest that a site-specific (see his oral evidence quoted above) double-stranded break must
occur at the same nucleotide position on each strand. Accordingly, I find that the language of
claims 1 and 10 does extend to staggered ended breaks that are in close proximity.
158 However, I do not think that either claim 1 or claim 10 encompass paired Cas9
nickases for the reasons identified by Associate Professor Firestein. This is another situation
in which the patent applicant has claimed less than what it disclosed in the body of the
Specification. The use of the singular to define the Cas9 polypeptide and the guide RNA
coupled with a proper understanding of the role each of the guide RNA and the polypeptide
play is consistent with a description of a complete system in which a single guide RNA and a
single Cas9 polypeptide combine to introduce a site-specific double-stranded break in DNA.
Claim 1 does not extend to what I consider is a different system utilising a pair of Cas9
nickases each with its own guide RNA. The language of claim 10 makes very clear that what
is being described in claim 10 is a complex consisting of a guide RNA and a Cas9
polypeptide which create a double-stranded break. In this respect, claim 1 and claim 10 are
describing the same invention but in slightly different language that, apart from the fact that
one is for a composition and the other a method, are not relevantly different.
159 The respondents placed some reliance in their written submissions on the definition of
the words “comprising” and “comprises” which appear at page 61 of the Specification. It

stated that, unless the context requires otherwise, those words do not imply the exclusion of
any other integer or group of integers. That definition does not assist the respondents for two
reasons. First, as the respondents would have me read them, the claims include a system for
introducing a site-specific double-stranded break that is different from the system that is
described, and not merely by reason of the addition of further integers. On the respondents’
construction of the claims, each pair of guide RNAs and nickases produces a single rather
than a double break. The function performed by each nickase is in that respect materially
different from the function performed by a single guide RNA and endonuclease. Giving
effect to the definition in those circumstances would have implications for the validity of the
claim. Secondly, and relatedly, in my view “the context requires otherwise” and, therefore,
the definition does not apply.
RELEVANT LEGISLATIVE PROVISIONS

160 Section 40(2) and (3) of the Act relevantly provide:
Requirements relating to complete specifications

(2) A complete specification must:
(a) disclose the invention in a manner which is clear enough and
complete enough for the invention to be performed by a person
skilled in the relevant art; and
…
(3) The claim or claims must be clear and succinct and supported by matter
disclosed in the specification.
161 Section 43(2) and (2A) of the Act provide:
(2) The priority date of a claim is:

(a) if subsection (2A) applies to the claim—the date determined under
the regulations; or
(b) otherwise—the date of the filing of the specification.
(2A) This subsection applies to a claim if:
(a) prescribed circumstances apply in relation to the invention defined in
the claim; and
(b) a prescribed document discloses, or a prescribed set of prescribed
documents considered together disclose, the invention in the claim in
a manner that is clear enough and complete enough for the invention
to be performed by a person skilled in the relevant art.

162 Regulation 3.13A(2) of the Patents Regulations 1992 (Cth) relevantly provides that
the “prescribed circumstances” are where a PCT application claims priority of an earlier basic
application made no more than 12 months before the filing date of the PCT application. It is
common ground that P1 is such an application. Given the patent application is a PCT
application, reg 3.13A applies. Regulation 3.13A(1)(b)(i) requires that the earlier basic
application (“the prescribed document”) be a document that “clearly discloses the invention
in the claim”.
163 Regulation 3.12(4) provides that in “this Division [which includes reg 3.13A], a
document … clearly discloses an invention if the document, or set of documents, discloses
the invention in a manner that is clear enough, and complete enough, for the invention to be
performed by a person skilled in the relevant art”.
164 Accordingly, reg 3.12(4) deems that reg 3.13A(1)(b)(i) will be satisfied where the
earlier basic application “discloses the invention in a manner that is clear enough, and
complete enough, for the invention to be performed by a person skilled in the relevant art”
(“the priority date test”).
165 There is no additional requirement imposed by the words “clearly discloses” in

reg 3.13A(1)(b)(i). Notably, the priority date test is the same as that set out not only in
s 43(2A)(b) of the Act but also s 40(2)(a) (“the sufficiency test”). There is no longer a
requirement for the claimed invention to be fairly based on matter disclosed in the priority
document.
166 Section (40)(2)(a) requires that the complete specification make the necessary
disclosure. Since the claims form part of the complete specification they may contribute to
the disclosure. However, for the purposes of s 43(2A), the claims in the complete
specification, although defining the invention, do not contribute to the disclosure. They serve
only to define the invention which must be disclosed in the priority document “… in a
manner that is clear enough and complete for the invention to be performed by a person
skilled in the relevant are”. That said, the language used in s 40(2)(a) and s 43(2A)(b) is
essentially the same: in both cases the invention must be disclosed in a manner that is clear
enough and complete enough for the invention to be performed by a person skilled in the
relevant art. Section 43(2A)(b) expresses the disclosure obligation by reference to the
invention “in the claim”. In my view, nothing turns on the absence of the words “in the

claims” in s 40(2)(a). The disclosure obligation imposed by s 40(2)(a) of the Act relates to
the invention as claimed.
THE DISCLOSURE REQUIREMENT

167 The Explanatory Memorandum to the RTB Act made it clear that the new s 40(2)(a)
of the Act:
… is intended to align the disclosure requirement with that applying in other

jurisdictions with the effect that sufficient information must be provided to enable
the whole width of the claimed invention to be performed by the skilled person
without undue burden, or the need for further invention …
An alternative to the existing Australian description requirement is the more stringent
requirement that the skilled person reading the specification must be able to
perform the invention across the whole width of the claims, not merely in
relation to one among other embodiments within their scope. This requirement is
consistent with the principle that the description accords with the scope of the
monopoly granted.
The item is intended to modify the wording of paragraph 40(2)(a) of the Act so as to
require enablement across the full width of the claims, while adopting language
that is consistent with that used in other jurisdictions. The wording in the
amendment is similar to s 14(3) of the UK patents legislation … The wording is also
similar to art 83 of the European Patent Convention which has been interpreted with
similar effect. The intention is that paragraph 40(2)(a) be given, as close as is
practicable, the same effect as the corresponding provisions of UK legislation and
the European Patent Convention.
(Emphasis added. Footnotes omitted.)
168 It is apparent that the amendments to s 40(2)(a) of the Act were made with the
intention of aligning the Australian law of sufficiency with UK and European law. In
particular, the old law, which had generally been held to require the enablement of only a
single embodiment of the invention within each claim, was done away with.
169 Article 83 of the European Patent Convention (“EPC”) provides:
The European patent application shall disclose the invention in a manner sufficiently
clear and complete for it to be carried out by a person skilled in the art.
170 Article 100(b) of the EPC provides that it is a ground of opposition that:
the European patent does not disclose the invention in a manner sufficiently clear and
complete for it to be carried out by a person skilled in the art;
171 Sections 14(3) and 72(1)(c) of the Patents Act 1977 (UK) (“the UK Act”) correspond
to Articles 83 and 100(b) of the EPC respectively.

172 In Eli Lilly & Co v Human Genome Sciences Inc [2008] RPC 29 (“Eli Lilly”) Kitchin
J (as his Lordship then was) referred to the key elements of the sufficiency requirement at
[239]-[243]:
[239] The specification must disclose the invention clearly and completely enough
for it to be performed by a person skilled in the art. The key elements of this
requirement which bear on the present case are these:
(i) the first step is to identify the invention and that is to be done by
reading and construing the claims;
(ii) in the case of a product claim that means making or otherwise
obtaining the product;
(iii) in the case of a process claim, it means working the process;
(iv) sufficiency of the disclosure must be assessed on the basis of the
specification as a whole including the description and the claims;
(v) the disclosure is aimed at the skilled person who may use his
common general knowledge to supplement the information contained
in the specification;
(vi) the specification must be sufficient to allow the invention to be
performed over the whole scope of the claim;
(vii) the specification must be sufficient to allow the invention to be so
performed without undue burden.
[240] Elements (vi) and (vii) merit a little elaboration. It has long been a principle
of patent law that the specification must enable the invention to be performed
to the full extent of the monopoly claimed. If the invention discloses a
principle of general application, the claims may be in correspondingly
general terms. But if the claims include a number of discrete methods or
products, the patentee must enable the invention to be performed in respect of
each of them: Genentech I/Polypeptide expression T 292/85 [1989] OJEPO
275; Biogen Inc v Medeva plc [1997] R.P.C. 1 at [48].
[241] The question whether a burden is undue must be sensitive to the nature of the
invention, the abilities of the skilled person and the art in which the invention
has been made. The court must consider whether the effort required of the
skilled person is undue having regard to the fact that the specification should
explain to him how the invention can be performed. Each case must be
decided on its own facts. Nevertheless, helpful guidance is to be found in the
decision of the Court of Appeal in Mentor Corp. v Hollister Inc [1993]
R.P.C. 7. Lloyd L.J. explained at 13–14:
“ …. if a working definition is required then one cannot do better

than that proposed by Buckley L.J. in giving the judgment of the
Court of Appeal in Valensi v British Radio Corporation [1973]
R.P.C. 337. After referring to a number of earlier authorities,
including Edison & Swan v Holland, he said:
‘We think that the effect of these cases as a whole is to show
that the hypothetical addressee is not a person of exceptional
skill and knowledge, that he is not to be expected to exercise

any invention nor any prolonged research, inquiry or
experiment. He must, however, be prepared to display a
reasonable degree of skill and common knowledge of the art
in making trials and to correct obvious errors in the
specification if a means of correcting them can readily be
found.’
Then a little later:
‘Further, we are of the opinion that it is not only inventive
steps that cannot be required of the addressee. While the
addressee must be taken as a person with a will to make the
instructions work, he is not to be called upon to make a
prolonged study of matters which present some initial
difficulty: and, in particular, if there are actual errors in the
specification—if the apparatus really will not work without
departing from what is described—then, unless both the
existence of the error and the way to correct it can quickly be
discovered by an addressee of the degree of skill and
knowledge which we envisage, the description is
insufficient.’
In that case there was a mistake in the specification. But Buckley
L.J.’s language is equally apt to cover an omission.
….
Before leaving the authorities, I should mention No-Fume Ltd v
Frank Pitchford & Co Ltd (1935) 52 R.P.C. 231. Quoting from the
judgment of Romer L.J. in that case, Buckley L.J. in Valensi is
reported as saying:
‘The test to be applied for the purpose of ascertaining
whether a man skilled in the art can readily correct the
mistakes or readily supply the omissions, has been stated to
be this: Can he rectify the mistakes and supply the omissions
with the exercise of any inventive faculty? If he can, then the
description of the specification is sufficient. If he cannot, the
patent will be void for insufficiency.’
‘With’ in that quotation must be a misprint for ‘without’.
I turn to the judge’s conclusion on the law. What he said was this:
‘The section requires the skilled man to be able to perform
the invention, but does not lay down the limits as to the time
and energy that the skilled man must spend seeking to
perform the invention before it is insufficient. Clearly there
must be a limit. The sub-section, by using the words, clearly
enough and completely enough, contemplates that patent
specifications need not set out every detail necessary for
performance, but can leave the skilled man to use his skill to
perform the invention. In so doing he must seek success. He
should not be required to carry out any prolonged research,
enquiry or experiment. He may need to carry out the
ordinary methods of trial and error, which involve no
inventive step and generally are necessary in applying the

particular discovery to produce a practical result. In each
case, it is a question of fact, depending on the nature of the
invention, as to whether the steps needed to perform the
invention are ordinary steps of trial and error which a skilled
man would realise would be necessary and normal to
produce a practical result.’
I have already quoted the remainder of that paragraph.
I can find no vestige of error in that statement of the law. It was at
first argued that the skilled man should not have to carry out any
research, enquiry or experiment at all, whether prolonged or
otherwise. But Mr. Thorley subsequently retreated from that extreme
position. There is no support for setting so high a standard of
disclosure, whether in Valensi itself or in any of the previous
authorities, save possibly the judgment of Lindley L.J. in Edison &
Swan v Holland. When, a little later, Aldous J. came to apply the law
to the facts of this case, he refers to ‘routine trials’ and ‘normal
routine matters that the skilled man would seek to do and would be
able to do’. Mr. Thorley criticises the use of the word ‘routine’. To
require the performance of routine trials is, he said, to ask too much
of the addressee. I do not agree. ‘Routine’ is just the word I would
have chosen myself to describe the sort of trial and error which has
always been regarded as acceptable; and ‘routine trials’ has the
further advantage that it is a positive concept, which is easily
understood and applied. In practice, therefore, it may provide a surer
test of what is meant by ‘clearly enough and completely enough’ in
s.72(1) of the Act than the negative test proposed in Valensi, namely
the absence of prolonged research, enquiry and experiment. If the
trials are unusually arduous or prolonged, they would hardly be
described as routine.”
[242] A little later (at page 17, lines 4–14) the court accepted the requirement was
not to produce a successful commercial product but rather a workable
prototype. This is an important point and one which must be kept well in
mind in assessing inventions in the pharmaceutical field as much as any
other.
[243] The case law of the EPO is, I believe, entirely consistent. Even though a
reasonable amount of trial and error is permissible, when it comes to
sufficiency of disclosure, for example in an unexplored field or where there
are many technical difficulties, the skilled person has to have at his disposal,
either in the specification or on the basis of his common general knowledge,
adequate information leading necessarily and directly towards success
through the evaluation of initial failures: see eg Unilever (1987) T 226/85.
173 Article 83 of the EPC was considered by the United Kingdom Supreme Court in
Regeneron Pharmaceuticals Inc v Kymab Ltd [2020] UKSC 27 (“Regeneron”). Lord Briggs
(with whom Lord Reed, Lord Hodge and Lord Sales agreed) said at [56]:
[56] Reflection upon those European and UK authorities yields the following
principles:
(i) The requirement of sufficiency imposed by article 83 of the EPC

exists to ensure that the extent of the monopoly conferred by the
patent corresponds with the extent of the contribution which it makes
to the art.
(ii) In the case of a product claim, the contribution to the art is the ability
of the skilled person to make the product itself, rather than (if
different) the invention.
(iii) Patentees are free to choose how widely to frame the range of
products for which they claim protection. But they need to ensure
that they make no broader claim than is enabled by their disclosure.
(iv) The disclosure required of the patentee is such as will, coupled with
the common general knowledge existing as at the priority date, be
sufficient to enable the skilled person to make substantially all the
types or embodiments of products within the scope of the claim. That
is what, in the context of a product claim, enablement means.
(v) A claim which seeks to protect products which cannot be made by
the skilled person using the disclosure in the patent will, subject to de
minimis or wholly irrelevant exceptions, be bound to exceed the
contribution to the art made by the patent, measured as it must be at
the priority date.
(vi) This does not mean that the patentee has to demonstrate in the
disclosure that every embodiment within the scope of the claim has
been tried, tested and proved to have been enabled to be made.
Patentees may rely, if they can, upon a principle of general
application if it would appear reasonably likely to enable the whole
range of products within the scope of the claim to be made. But they
take the risk, if challenged, that the supposed general principle will
be proved at trial not in fact to enable a significant, relevant, part of
the claimed range to be made, as at the priority date.
(vii) Nor will a claim which in substance passes the sufficiency test be
defeated by dividing the product claim into a range denominated by
some wholly irrelevant factor … The requirement to show
enablement across the whole scope of the claim applies only across a
relevant range. Put broadly, the range will be relevant if it is
denominated by reference to a variable which significantly affects
the value or utility of the product in achieving the purpose for which
it is to be made.
(viii) Enablement across the scope of a product claim is not established
merely by showing that all products within the relevant range will, if
and when they can be made, deliver the same general benefit
intended to be generated by the invention, regardless how valuable
and ground-breaking that invention may prove to be.
174 Both Eli Lilly and Regeneron were revocation actions. The question was therefore
whether the specification as a whole made a disclosure sufficient to enable the notional
skilled addressee to perform the invention (leaving aside de minimis or irrelevant exceptions)
across the scope of the relevant claims. What the invention is depends on the proper

construction of the claim. Once the claim is construed it is then necessary to determine
whether performance of the invention as claimed is enabled.
175 In the case of the patent application the same question must be addressed. The claims
must be construed for the purpose of identifying the invention. It is then necessary to
consider whether performance of the invention by the person skilled in the relevant art is
sufficiently enabled by the complete specification. Although s 40(2)(a) of the Act does not
expressly refer to the invention as the invention defined by the claim, or the invention in the
claim (cf. s 43(2A)(b) of the Act), there is no reason to doubt that the sufficiency of the
disclosure is to be assessed against the invention as claimed. This is confirmed by those parts
of the Explanatory Memorandum to which I have referred which describe the requirement
that the skilled person reading the specification be able to perform the invention across the
whole width of the claims.
176 On the topic of priority dates and the requirements of s 43(2A) of the Act, the
Explanatory Memorandum to the RTB Act stated:
Applicants should not be able to secure a priority date on the basis of a disclosure in
a provisional or other relevant application that is less complete than required in a
complete specification. Otherwise the applicant is in a position to deter competitors
before they have fully realised the invention. Since an enabling disclosure will be
required, the amendment will also align the requirements for securing a priority date
with most other major patent jurisdictions.
177 Article 87 of the EPC is concerned with priority right. It provides:
Any person who has duly filed, in or for

(a) any State party to the Paris Convention for the Protection of Industrial
Property or
(b) any Member of the World Trade Organization,
an application for a patent, a utility model or a utility certificate, or his successor in
title, shall enjoy, for the purpose of filing a European patent application in respect of
the same invention, a right of priority during a period of twelve months from the date
of filing of the first application.
178 The right of priority referred to is available only where the first application (ie. the
priority document) is “in respect of the same invention” as the European patent application.
That requirement was considered by the English Court of Appeal in MedImmune Ltd v
Novartis Pharmaceuticals UK Ltd [2013] RPC 27 (“MedImmune”). Kitchin LJ (with whom

Moore-Bick and Lewison LJJ agreed) referred to the relevant principles as follows at [152]-
[154]:
[152] The requirement that the earlier application must be in respect of the same
invention was explained by the enlarged Board of Appeal of the EPO in
G02/98, X/Same Invention, [2001] OJ EPO 413, [2002] E.P.O.R. 17:
‘The requirement for claiming priority of ‘the same invention’,
referred to in Article 87(1) EPC, means that priority of a previous
application in respect of a claim in a European patent application in
accordance with Article 88 EPC is to be acknowledged only if the
skilled person can derive the subject-matter of the claim directly and
unambiguously, using common general knowledge, from the
previous application as a whole.’
[153] The approach to be adopted was elaborated by this court in Unilin Beheer BV
v Berry Floor NV [2004] EWCA (Civ) 1021, [2005] F.S.R. 6 at [48]:
“48 ... The approach is not formulaic: priority is a question about
technical disclosure, explicit or implicit. Is there enough in the
priority document to give the skilled man essentially the same
information as forms the subject of the claim and enables him to
work the invention in accordance with that claim.”
[154] In Abbott Laboratories Ltd v Evysio Medical Devices ULC [2008] EWHC
800 (Pat), [2008] R.P.C. 23, I added this:
“228. So the important thing is not the consistory clause or the claims
of the priority document but whether the disclosure as a whole is
enabling and effectively gives the skilled person what is in the claim
whose priority is in question. I would add that it must “give” it
directly and unambiguously. It is not sufficient that it may be an
obvious development of what is disclosed.”
179 Having referred to those paragraphs of Kitchin LJ’s judgment in MedImmune, Floyd
LJ (with whom Vos and Laws LJJ agreed) said in HTC Corp v Gemalto SA [2014] EWCA
Civ 1335 at [65]:
[65] The skilled person must be able to derive the subject matter of the claim
directly and unambiguously from the disclosure of the priority document.
Mr Tappin stressed that the question was one of what was disclosed to the
skilled person, not what was made obvious to him by the priority document,
for example in the light of his common general knowledge. I agree that, as
the above passage shows, that is the correct approach. That does not mean,
however, that the priority document should be read in a vacuum. The
question of what a document discloses to a skilled person takes account of
the knowledge and background of that person. A document may mean one
thing to an equity lawyer and another to a computer engineer, because each
has a different background. The document still only has one meaning because
it is only the relevant skilled person’s understanding which is relevant. What
is not permissible is to go further than eliciting the explicit or implicit
disclosure and take account of what a document might lead a skilled person
to do or try, or what it might prompt him to think of.

180 Kitchin LJ (with whom Floyd and Longmore LJJ agreed) referred to that passage with
approval in Icescape Ltd v Ice-World International BV [2019] FSR 5 at [42]. His Lordship
then said at [43]:
[43] In my judgment the application of these principles provides a clear answer to

the question before us. I accept that the key novel and inventive feature of the
claimed invention is the use of joint elements (70) which enable the folding
of the unit to take place. I am also prepared to accept that the skilled person
would readily appreciate that one element of the kind depicted in figure 6 of
the priority document could be joined to another to increase the width of the
ice rink. But that does not alter the fact that there is no express or implicit
disclosure in the priority document of two such elements joined together or
of features A, D or E of claim 1 of the patent. Nor is it possible to derive
these features directly and unambiguously, using common general
knowledge, from the priority document as a whole. The skilled person
seeking to implement the teaching of the priority document might join two
elements together, but equally he might not, for he might have no need to do
so. In these circumstances I have no doubt that Mr Alexander is inviting us to
take a course which has been closed to us by the decision of the Enlarged
Board in decision G2/98. It is not enough to say that features A, D and E do
not relate to the function and effect, and hence to the character and nature, of
the invention. The claim to priority depends upon the express or implicit
disclosure of those features in the priority document and, since there is no
such disclosure, the claim to priority must fail.
181 For the purposes of s 40(2)(a) it is necessary to identify the invention in the relevant
claim of the complete specification and then ask whether there is a disclosure that is clear
enough and complete enough for the invention to be performed by a person skilled in the art.
Where the requirement of s 40(2)(a) is in issue, the claim and any related disclosure will be
found within the one document (ie. the complete specification). However, where the
requirement of s 43(2A)(b) is in issue, the sufficiency of the disclosure of the priority
document will be assessed against the invention of the claim in the complete specification.
Since that claim may not be reproduced in the priority document (which, as in the case of P1,
might not include any claims at all) it is necessary to determine whether there is any
disclosure of the invention in the claim in the priority document and, if so, whether it is clear
enough and complete enough for it to be performed by the person skilled in the art.
182 ToolGen drew attention to the phrase “in respect of the same invention” in Art 87(1)
of the EPC and the absence of those words in s 43(2A)(b) of the Act and submitted that
s 43(2A)(b) imposed no requirement that the priority document and the patent application be
in respect of the same invention.

183 The implication of ToolGen’s submission is that, under the Act, unlike the position
under Art 87(1) of the EPC, a claim may be entitled to a priority date earlier in time than
would otherwise be the case based on a prior application that is directed to an invention that
is different from that in the claim. I do not think that is correct. In my opinion, the invention
of the claim must be disclosed in the prior application and must be also disclosed in a manner
that is clear enough and complete enough for the invention in the claim to be performed by
the person skilled in the art.
184 ToolGen placed considerable reliance on the decision of Perram J in Encompass

Corporation Pty Ltd v InfoTrack Pty Ltd (2018) 130 IPR 387 (“Encompass”). It submitted
that Perram J’s decision was authority for the proposition that s 40(2)(a) does not require that
the complete specification disclose the invention.
185 Encompass was concerned with s 40(2)(a) of the Act and the question whether the
complete specification in suit (there was a number of them) complied with that provision.
The question to which his Honour’s observations in that case were directed concerned a
situation in which the description of the invention in a complete specification did not provide
any explanation for the inclusion of a limitation in the relevant claim. The invention, as
claimed, included a limitation which required a search “from at least one of a number of
remote data sources”. As his Honour said at [152]:
[152] Section 40(2)(a) of the Act requires the specification to ‘disclose the
invention in a manner which is clear enough and complete enough for the
invention to be performed by a person skilled in the art’. The Respondent
submitted that the defining characteristics of the invention as claimed was the
requirement that the data sources to be accessed or queried should be ‘remote
data sources’. Yet nothing in the specification of either Patent gave any hint
as to why that limitation should exist. It was said that the invention variously
described in the specifications was ‘database agnostic’.
His Honour continued at [155]:
[155] The specifications are, therefore, indifferent as to whether the data sources
need to be remote or local. The invention described in them is unconcerned
with issue of whether the data sources need to be remote. Yet the invention as
claimed involves only a method which involves querying remote data
sources. In that sense, the invention claimed is narrower than the invention
disclosed. The narrowing is perhaps not very substantial given the very broad
reading I would give the expression ‘remote data sources’. Nevertheless, I
accept that what is claimed is not the same as what is described in the
specification. As disclosed, the querying of ‘remote data sources’ is not an
essential part of the invention yet the invention as claimed has this
moderately limiting feature.

186 His Honour went on to note that, although the respondents agreed that the
specifications were sufficient to enable a person skilled in the art to perform the invention, it
submitted that s 40(2)(a) also required that the disclosure of the invention in the specification
should be clear and that, in particular, s 40(2)(a) picked up the old “fair basis” requirement of
a real and reasonably clear disclosure.
187 His Honour continued at [160]-[161]:
[160] The earlier form of s 40(2)(a) had, therefore, required that the invention be
described fully. The concept of the ‘invention’ had been interpreted to mean
‘the embodiment which is described, and around which the claims are
drawn’: Kimberly-Clark Australia Pty Ltd v Arico Trading International Pty
Ltd (2001) 207 CLR 1; 177 ALR 460; 50 IPR 513; [2001] HCA 8 at [21].
The former requirement of s 40(2)(a) that the invention, in that sense, be fully
described was interpreted as having two requirements:
(a) the specification had to make the nature of the invention plain to
persons having reasonably competent knowledge of the subject; and
(b) it also had to make plain, to persons having reasonable skill, how to
perform the invention.
(see Patent Gesellschaft AG v Saudi Livestock Transport and Trading
Company (1997) 37 IPR 523 at 530 per Carr J, Jenkinson and Sackville JJ
agreeing)
[161] The immediate question is whether that previous interpretation of the
expression ‘describe the invention fully’ as including a requirement of
making plain the nature of the invention to persons of reasonably competent
knowledge of the subject has survived into the amended form of s 40(2)(a)
which no longer includes that expression.
188 The question considered by his Honour was framed by him by reference to a
judgment of the Full Court in Patent Gesellschaft AG v Saudi Livestock Transport and
Trading Company (1997) 37 IPR 523 (“Patent Gesellschaft”) in which Carr J (with whom
Jenkinson and Sackville JJ agreed) said when referring to s 40(2)(a) of the Act before
amendment by the RTB Act at 530-531:
The specification contains a full description if it makes the nature of the invention
plain to persons having reasonably competent knowledge of the subject and also
makes it plain, to persons having reasonable skill, how to perform the invention:
Edison & Swan United Electric Light Co v Holland (1889) 6 RPC 243 at 279;
Samuel Taylor Pty Ltd v SA Brush Co Ltd (1950) 83 CLR 617 at 624-5. See also
AMP Inc v Utilux Pty Ltd (1971) 45 ALJR 123 at 128 and Valensi v British Radio
Corp Ltd [1973] RPC 337 at 377.
189 The respondents in Encompass contended that s 40(2)(a) of the Act required that the
complete specification “make the nature of the invention plain” to persons skilled in the art.

It is by no means clear what Carr J was referring to when using that phrase in Patent
Gesellschaft. Certainly, s 40(2)(a) of the Act does not require that the specification identify
the inventive step: see, for example, Winner v Ammar Holdings Pty Ltd (1993) 41 FCR 205 at
217 per Davis J (with whom Morling J agreed). I would also add that Patent Gesellschaft
was decided before the High Court decided Lockwood Security Products Pty Ltd v Doric
Products Pty Ltd (2004) 217 CLR 274 (“Lockwood”) and Kimberly-Clark Australia Pty Ltd v
Arico Trading International Pty Ltd (2001) 207 CLR 1 (“Kimberly-Clark”). Lockwood does
not make reference to the Full Court’s decision, and Kimberly-Clark only does so in support
of the statement that s 40(2)(a) of the Act has never been construed to require that the body of
the specification say what was essential to the invention. In my opinion, those decisions are
inconsistent with there ever having been a requirement under s 40(2)(a) of the Act that the
specification make “the nature of the invention plain” to persons skilled in the art.
190 In Encompass, Perram J rejected the argument that s 40(2)(a) of the Act as amended
by the RTB Act required that the specification must make the nature of the invention plain.
His Honour said at [163]:
… [T]he new form of s 40(2)(a) contains a requirement as to a clear disclosure but it

is expressed to be ‘clear enough and complete enough’ for a particular purpose viz
‘for the invention to be performed by a person skilled in the relevant art’. I cannot see
that any part of the wording of the new s 40(2)(a) which lends itself to being
interpreted as containing a further requirement that the nature of the invention be
made plain. Even if, which I do not accept, there was some peg in the language of s
40(2)(a) upon which such an interpretation might be hung, I do not see how it could
be rescued from the purposive effect of the phrase ‘for the invention to be performed
by a person skilled in the relevant art’. In short, s 40(2)(a) does not say as a matter of
ordinary language that the specification must make the nature of the invention plain.
191 After referring to the Explanatory Memorandum to the RTB Act, Perram J observed
at [165]-[167]:
[165] The Respondent submitted that removing the requirement of making the
nature of the invention plain would hardly be raising the bar. There may be
some rhetorical force in that flourish. Nevertheless, it seems to me that whilst
the Explanatory Memorandum clearly demonstrates that its authors were
aware of the former requirement of making the nature of the invention plain,
it is silent on what they intended for the former requirement to continue. The
entire discussion of the authors is given over to the second requirement of
enablement. I think the better view is that the Exploratory Memorandum is
silent on the topic of whether it was intended to remove the requirement to
make the nature of the invention plain.
[166] … [T]here is accordingly no reason to depart from the language of s 40(2)(a)
as it now stands.

[167] It follows that the only requirement now in s 40(2)(a) relates to enablement.
Since the Respondent no longer advances a case that the specifications do not
enable a person skilled in the relevant art to perform the invention, its case
under s 40(2)(a) must fail.
192 His Honour’s decision is authority for the proposition that s 40(2)(a) does not require
that the complete specification make the nature of the invention plain. In my opinion, his
Honour is not to be taken as suggesting that there is no requirement under s 40(2)(a) that the
invention be disclosed. Section 40(2)(a) expressly requires that the invention be disclosed in
a manner which is clear enough and complete enough for the invention to be performed by
the person skilled in the art.
193 Although neither s 43(2A) nor reg 3.13A(2) requires that the invention as claimed be
“in respect of the same invention”, it does not follow that the priority document need not
disclose the invention claimed. The invention claimed must be disclosed in the priority
document if priority is to be obtained. It is not sufficient for the priority document to provide
a starting point from which the person skilled in the art may transition from one invention to
another by the use of the common general knowledge. The mere fact that it would be
obvious to the person skilled in the art to use the disclosure in the priority document to
produce what is claimed is not enough to obtain priority if, properly characterised, the
priority document and the claim are for different inventions. In this respect, and
notwithstanding differences between statutory language in the relevant UK and EPC
provisions and s 40(2)(a) of the Act, I consider the position under Australian law is not
materially different from the UK law as explained in the English authorities to which I have
referred. The question is not what is made obvious to the person skilled in the art from the
disclosure of the priority document but what it explicitly or implicitly discloses to that
person. The distinction is important even though it is often not easily drawn.
P1 – DISCLOSURE AND ENABLEMENT

194 Section s 43(1) of the Act provides that each claim must have a priority date and
different claims may have different priority dates. Section 43(3) of the Act provides that
where a claim defines more than one invention, then, for the purpose of determining the
priority date of the claim, it must be treated as if it were a separate claim for each form of the
invention that is defined. Section 43(2A)(b) of the Act requires that there be a disclosure of
“the invention in the claim” if a claim is to obtain priority in accordance with s 43(2A) of the
Act.

195 For reasons previously stated, I do not accept ToolGen’s submission that s 43(2A)(b)
does not require that there be a disclosure of the invention in the claim in the priority
document. It follows from what I said that the invention claimed in claims 1 and 10 will only
be entitled to priority if it is disclosed in P1. For this purpose, neither party drew a distinction
between claim 1 and claim 10 and the submissions proceeded on the assumption that the
priority date for claim 1 and claim 10 would be the same.
196 ToolGen submitted that the invention disclosed in P1 is an invention involving the use
of:
(a) a Cas9 endonuclease (derived from a Type II CRISPR/Cas system) comprising a

nuclear localisation sequence (NLS), which guides the Cas9 to the nucleus of a eukaryotic
cell; and
(b) a single guide RNA comprising portions of CRISPR RNA (crRNA) and
transactivating crRNA (tracrRNA) (also derived from the Type II CRISPR/Cas system),
to generate a site-specific double stranded break in the DNA of a eukaryotic cell at a target
sequence adjacent to a protospacer adjacent motif (PAM).
197 I should say at once that there is a difficulty with ToolGen’s formulation of the
invention in these terms. While it may be accepted that the invention disclosed in P1
involves the use of a Cas9 endonuclease and a single guide RNA of the kind described by
ToolGen, it does not follow that it is the invention disclosed.
198 The same comment may be made in relation to the Abstract in P1 which refers to “a
novel genome editing technology based on RNA-guided Cas9 endonucleases” which
language is repeated in the first paragraph of the section of P1 headed Main Text. That does
not constitute a disclosure of any genome editing technology based on RNA-guided Cas9
endonucleases. The Abstract is no more than a general introduction to what is disclosed in
P1 and does not disclose the invention of the claims. It is an introductory statement that
provides context for what follows.
A nucleic acid encoding a guide RNA

199 The respondents’ case on this issue is focused on the method of introducing the
nucleic acid encoding the guide RNA into the eukaryotic cell as required in claim 10, given
that there is no express requirement in claim 1. On the use of plasmid DNA encoding the
guide RNA as a means of introducing the guide RNA into the cell, Associate Professor

Firestein accepted that P1 does not disclose the use of plasmid DNA encoding either of the
single guide RNAs that it discloses. Professor Thomas and Associate Professor Herold
agreed. Associate Professor Firestein also accepted that the particular CRISPR/Cas9 system
disclosed in P1 involves the use of in vitro transcribed guide RNA and does not disclose the
use of plasmid DNA encoding the guide RNA as a means of introducing into the cell the
guide RNA. Associate Professor Firestein said:
It does not disclose that, but to me this would be a obvious thing that could be done
based on my experience with expressing similarly sized RNAs via plasmid encoded
DNA.
200 Under the heading the “Summary of the Invention” appears a reference to “nucleic
acid encoding RNA-guided Cas9 endonucleases”. Associate Professor Firestein considered
that the phrase “RNA-guided Cas9 endonucleases” referred to both the guide RNA and the
endonuclease or, in other words, the complex which is formed in the cell. ToolGen
contended that the reference to RNA-guided Cas9 endonucleases is a broad disclosure that is
ambiguously agnostic as to how the guide RNA is made and therefore extends to plasmid
DNA that is transcribed into guide RNA in the eukaryotic cell. ToolGen submitted, in effect,
that the language used in the Summary of Invention was, deliberately broad, and should not
be read down by reference to what is more specifically described elsewhere in P1, including
by reference to the experiments conducted which did not use plasmid encoded guide RNA.
201 Associate Professor Herold considered that the reference in the Summary of the
Invention to “nucleic acids encoding RNA-guided Cas9 endonucleases” is referring only to
the Cas9 endonuclease which is encoded by plasmid DNA introduced into the cell. On this
interpretation of the relevant phrase, the word “RNA-guided” is an adjective that describes
the Cas9 endonuclease that is encoded rather than the guide RNA and Cas9 endonuclease
individually. This is not the interpretation that was adopted by Professor Thomas, but it is
fair to say that he agreed that Associate Professor Herold’s view was a reasonable one.
Professor Thomas gave the following evidence:
MR CORDINER: Yes. Now, I put it to you, if the word or term “RNA guided Cas9
nucleases” is being used as it’s used almost – well, used everywhere else in P1, it
means the guide RNA and the endonuclease; do you agree with that?
PROF THOMAS: As I said before, I have interpreted it in that fashion, in terms of it
being the complex, that’s true, but you could also construe it as being an RNA guided
endonuclease, in other words, referring to Cas9.
MR CORDINER: And if we’re talking about the complex, if you’re describing, here,

an embodiment of the invention – sorry, some embodiment of the present invention
to providing nucleic acids encoding the complex, if I put it that way, a reasonable
position to take would be it’s describing, there, using nucleic acids to encode the
guide RNA and to encode the Cas9; could you agree with that?
PROF THOMAS: Well, that’s a difficult one for me to answer in the sense that I was
asked to interpret P1 in the context of the entire document.
MR CORDINER: Yes.
PROF THOMAS: And I cannot see any evidence in this document for, for example, a
DNA encoding an – the RNA component of the complex. So to me, the most correct
interpretation of this – this phrase, within the summary of the Summary of the
Invention, is that it refers to a nucleic acid, let’s say DNA, encoding the RNA guided
Cas9 endonuclease. To me, that’s the most straightforward interpretation when I look
at the document as a whole.
MR CORDINER: And when you’re looking at the document as a whole, the
document itself doesn’t, at any point, say you can’t use plasmid encoded guide RNA,
does it.
PROF THOMAS: It makes no reference to plasmid encoded guide RNA.
MR CORDINER: So it doesn’t say you can’t use plasmid encoded guide RNA, does
it.
PROF THOMAS: It doesn’t say that it can’t be used.
202 Associate Professor Herold’s interpretation is consistent with what is disclosed in P1.
The Cas9 protein is produced using “Cas9-encoding plasmids” whereby DNA encoding the
relevant protein is introduced into the cell using a plasmid. However, in each of the two
working examples described in P1, the guide RNA is in vitro transcribed RNA and is
introduced into the cell in naked or isolated form (and without the use of a plasmid). There
are various other statements in P1 which tend to support Associate Professor Herold’s
interpretation of the Summary of the Invention.
203 First, the Abstract makes reference to “synthetic guide RNAs”. As Professor Thomas
explained, this is a reference to the preparation of the guide RNA by a synthetic means using
ribonucleotides (a nucleotide containing ribose) or in vitro transcription in which the RNA
polymerase enzyme opens a double-stranded DNA and one strand of the exposed nucleotides
is used as a template for the synthesis of RNA. The phrase “synthetic guide RNA” does not
describe RNA transcribed from DNA in vivo. Associate Professor Firestein agreed that a
guide RNA which is produced in a cell by transcription using plasmid DNA which encodes
the guide RNA it is not accurately described as a synthetic guide RNA.

204 Secondly, the Abstract makes clear that RGENS are customised without any cloning
step (ie. without inserting a DNA fragment into a vector). In Thomas 1, Professor Thomas
referred to some of the difficulties associated with the use of ZFNs and TALENs in genome
editing which, because they are proteins, are difficult to introduce into the cell. To overcome
this difficulty, molecular cloning techniques were developed to make circular DNA
constructs that encode ZFNs and TALENs that were then introduced into the cell. In relation
to the guide RNA, Professor Thomas explained that the advantage of having a system that
could be customised without any cloning step means that the target location for DNA
cleavage provided by the guide RNA in the Cas9 system can be changed by synthesising a
new guide RNA without the need to clone nucleotide sequences into vectors such as
plasmids. This means that different DNA sequences can be targeted by changing the guide
RNA. From Professor Thomas’ evidence on this topic, which I accept, it is apparent that, at
least as presented in the Abstract, a significant advantage of the genome editing technology
described in P1 is that it uses synthetic guide RNAs that may be customised without any
cloning step and, in the words of the authors, providing a “… broadly useful, scalable and
expeditious platform for genome engineering in cells and organisms”.
205 It was suggested by Associate Professor Firestein in his evidence that the in vitro
transcription templates appearing at page 11 of P1 were templates from which DNA encoding
the guide RNA could be constructed for in vivo use. He gave evidence that the DNA
templates could be cloned into a plasmid in vitro and then introduced into the cell to
transcribe RNA in vivo. He estimated that this would take approximately one week to do as
his laboratory would have had the plasmids available. He also gave evidence of an alternative
method whereby the DNA templates could be introduced into the cell to transcribe RNA in
vivo. He did not give evidence of how long this would take. He acknowledged that both
approaches would only work if the promoters were changed from a T7 promoter to a U6 or
H1 promoter (which are eukaryotic promoters).
206 Associate Professor Herold gave evidence that cloning the DNA template into a
plasmid would definitely take longer than a week but could be done. Professor Thomas gave
evidence that using a linear DNA strand in vivo was, in his opinion, not an approach that
anyone would routinely use because of concerns that it might degrade in the cell and that it is
much easier to generate a circular plasmid which is more stable in the cell. He also agreed
that the promoters would need to be changed for both approaches and said that this would
take several weeks to validate. I think the significance of this evidence is that P1 does not

disclose a DNA template for a guide RNA suitable for in vivo use. Rather, what is disclosed
are two DNA templates suitable for in vitro preparation of a guide RNA.
207 I accept that it would not be a difficult exercise for a molecular biologist in possession
of the information in P1 coupled with the common general knowledge to use a plasmid DNA
encoding the guide RNA to produce the guide RNA in vivo using standard techniques that
were well known at the priority date. I also accept that it would be obvious to the skilled
addressee that he or she could use plasmid DNA encoding a guide RNA as a means of
generating the guide RNA in the cell. On this particular point, I accept Associate Professor
Firestein’s evidence.
208 I also accept, as did all three expert witnesses who gave evidence on this topic, that P1
does not exclude the use of plasmid DNA encoding the guide RNA in place of naked RNA
created in vitro. However, to say that this is not excluded does not mean that it is disclosed.
P1 makes no reference to plasmid DNA encoding a guide RNA.
209 Further, P1 does not disclose the use of plasmid DNA encoding a guide RNA as a
means of introducing a guide RNA into the cell. P1 is directed to the use of a guide RNA
produced in vitro (ie. naked or isolated RNA) which is then introduced into the cell. There is
no disclosure of any system in which DNA (or viral RNA) is introduced into the cell in order
to transcribe the guide RNA in vivo.
210 With regard to the term RNA-guided endonucleases in the Summary of the Invention,
the language used is in my opinion ambiguous. But if the Summary of the Invention is read
in the context of P1 as a whole, I think the notional skilled addressee would, like Associate
Professor Herold, understand the term as referring to the Cas9 endonucleases which are
elsewhere described as having been introduced into the cell by means of a Cas9 encoding
plasmid. In this regard, I prefer the evidence of Associate Professor Herold to that of
Associate Professor Firestein and, to the extent that it was inconsistent with Associate
Professor Herold’s evidence on this point, the evidence of Professor Thomas.
211 Even if I am wrong about this, there is another way of understanding the Summary of
the Invention that avoids any redundancy in the use of the words “vectors comprising Cas9
endonucleases” which immediately follow the words “RNA-guided Cas9 endonucleases” and
which is consistent with what is more specifically described in P1. As I have explained, P1
does describe nucleic acid encoding guide RNA in the transcription templates. However,

these are DNA templates for encoding guide RNAs in vitro. In those circumstances, it makes
sense to interpret the phrase “nucleic acids encoding RNA-guided Cas9 endonucleases” as
referring to nucleic acids encoding the guide RNAs in vitro (as shown in P1) and nucleic
acids encoding the Cas9 endonuclease in vivo using a vector (as shown in P1). This
construction of the Summary of the Invention avoids any redundancy arising from the
presence of the words “vectors comprising Cas9 endonucleases” which, as ToolGen
submitted, arises on Associate Professor Herold’s interpretation. In any event, whether or not
the relevant phrase is construed as referring to nucleic acids encoding an endonuclease or
nucleic acids encoding both the guide RNA and the endonuclease, the Summary of the
Invention does not encompass the use of nucleic acids encoding a guide RNA in the cell,
such as through the use of plasmid DNA introduced into the cell.
212 Claims 1 and 10 (and, with the exception of claim 19, the dependent claims) are
directed to an invention in which the guide RNA of the claims is introduced into the cell in
the form of nucleic acid (DNA or viral RNA) which then encodes the guide RNA in the
eukaryotic cell. P1 does not disclose any such system either explicitly or implicitly. It
follows that those claims are not entitled to priority based on P1.
A Type II CRSIPR/Cas system from a bacterial species other than S. pyogenes

213 The next question is whether P1 discloses a system for cleaving DNA using a Cas9
polypeptide derived from a bacterial species other than S. pyogenes in a manner which is
clear enough and complete enough for the invention of the claims to be performed by a
person skilled in the art. Although some of the dependent claims are limited to a Cas9
polypeptide derived from S. pyogenes, none of claims 1, 2, 10 or 11 are so limited.
214 It is common ground that P1 discloses a CRISPR/Cas9 system derived from S.

pyogenes. However, ToolGen submitted that the disclosure of the bacterial species from
which the Cas9 endonuclease is derived is not limited to S. pyogenes, and that the only
relevant limitation is that the Cas9 comes from a Type II CRISPR system capable of forming
an active endonuclease when complexed with a guide RNA. In this regard, ToolGen placed
emphasis upon the following express disclosure in P1:
“Cas9, an essential protein component in the Type II CRISPR/Cas system, forms an

active endonuclease when complexed with two RNAs termed CRISPR RNA
(crRNA) and transactivating crRNA (tracrRNA), thereby slicing foreign genetic
elements in invading phages or plasmids to protect the host cells.”

However, that passage is describing Cas9 in the Type II CRISPR/Cas system in bacteria
where it provides immunity against invading phages and plasmids. It is background
information which assists the reader’s understanding of the mechanism of action of the
invention disclosed in P1. It is not a disclosure of the invention.
215 ToolGen also drew attention to the use of the word “systems” as appearing in the
Abstract. It submitted that word indicates that the authors are not merely referring to the S.
pyogenes system, but to all Type II CRISPR/Cas systems. Reliance also was placed on the
statements in P1 (at page 5) concerning the limitations of the requirement for a 5’-GG-3’
dinucleotide in the PAM sequence and the suggestion that “[t]his limitation might be relieved
by engineering Cas9 or employing Cas9 derived from another species”. Here again, the use
of the word “systems” occurs in the context of a description of the background to the
technology including the role such systems play in protecting prokaryotes against invading
phages and plasmids.
216 ToolGen also submitted that the disclosure in P1 of PAMs which Type II Cas9
endonucleases recognise is not limited to those derived from S. pyogenes, but also encompass
any PAM that is recognised by a Type II Cas9 protein, and that this set of PAMs, as it
described them, is implicitly disclosed by P1 because it discloses that “Cas9 is a sequence-
specific endonuclease in Type II CRISPR systems”. ToolGen submitted that the disclosure
of P1 extends to Cas9 from all bacterial species which have a Type II CRISPR system,
provided that the Cas9 is used in combination with a PAM that it recognises. It further
submitted that there is no requirement for P1 to disclose the nucleotide sequences for all such
PAMs or all such Cas9s polypeptides.
217 In essence, ToolGen’s argument is that P1 discloses a system in which any Type II
Cas9 polypeptide that recognises any known PAM (including but not limited to 5’-NGG-3’)
may be used. I do not accept that any of the claims of the patent application are limited in
their scope to the use of a Type II Cas9 polypeptide that recognises any known PAM. Even
if they were to be construed as limited to the use of a Type II Cas9 polypeptide that
recognises a known PAM sequence, that would not mean that the use of any Type II Cas9
was sufficiently enabled. This is because P1 does not identify any principle of general
application which would permit the skilled addressee to determine whether any particular
Type II Cas9 might reasonably be expected to work.

218 A similar argument to that relied on by ToolGen was considered by Kitchin J (as his
Lordship then was) in Novartis AG v Johnson & Johnson Medical Ltd [2009] EWHC 1671.
His Lordship said at [244]:
It follows, in my judgment, that a claim to a class of products said to possess a useful

activity must be based upon the identification of a common principle which permits a
reasonable prediction to be made that substantially all the claimed products do indeed
share that activity. Further, it is not permissible to by-pass that requirement simply by
adding a functional limitation which restricts the scope of the claim to all the
products which do have the relevant activity, that is to say all those which “work”. In
the case of a claim limited by function, it must still be possible to perform the
invention across the scope of the scope of the claim without undue effort. That will
involve a question of degree and depend upon all the circumstances including the
nature of the invention and the art in which it is made. Such circumstances may
include a consideration of whether the claims embrace products other than those
specifically described for achieving the claimed purpose and, if they do, what those
other products may be and how easily they may be found or made; whether it is
possible to make a reasonable prediction as to whether any particular product
satisfies the requirements of the claims; and the nature and extent of any testing
which must be carried out to confirm any such prediction.
219 I respectfully agree with his Lordship that if a claim is limited by a functional
requirement it may still be necessary to consider whether there is an undue burden involved
in identifying whether embodiments not specifically described in the specification or, in this
case, the priority document, meet the functional requirement. It is not necessary to consider
the matter further because, in my view, none of the claims include any such functional
requirement.
220 Senior Counsel for the respondents put to Associate Professor Firestein by that P1
does not disclose a system from any other bacterial species (apart from S. pyogenes) that can
mediate DNA cleavage in the eukaryotic cell. He said that it did not show that directly, but
that it does not exclude the possibility of that occurring. When pressed on this topic, he said:
I will just be very exact and say that P1 does not show any experiments or provides
[sic] any direct information on another CRISPR-Cas9 system, but it does disclose the
existence of other CRISPR-Cas9 systems, and raises the potential for employing
these other Cas9 systems for similar purposes.
In Firestein 1 (which he cross-referenced in JER 1) Associate Professor Firestein referred to

the statement in P1 (at page 5) that engineering Cas9 or employing Cas9 derived from other
species might relieve the limitation arising out of the requirement for a 5’-GG-3’ dinucleotide
when using a Cas9 protein derived from S. pyogenes. He said that this contemplates the use
of other Cas9 proteins.

221 I accept that P1 discloses, in a general sense, the existence of Cas9 proteins derived
from other bacterial species and the possibility that they may be used to mediate DNA
cleavage in eukaryotic cells. But what is clear from P1 is that this is raised by the authors as
a mere possibility. P1 does not include any further discussion of this possibility nor does it
present any evidence or commentary from which it may be inferred that all, or even some,
Type II Cas9 proteins derived from other bacterial species could reasonably be expected to
work with either the 5’-GG-3’ PAM or other PAMs to mediate DNA cleavage in eukaryotic
cells.
222 Associate Professor Firestein went on to say that P1 was a “starting point” or a
“springboard for potentially exploring their use in a similar assay”. He agreed that P1 does
not disclose which species of bacteria (apart from S. pyogenes) have a Type II system or
which of the different Type II systems may work in eukaryotes. He also agreed that it does
not disclose what Type II systems may recognise a non-NGG PAM. Professor Thomas and
Associate Professor Herold agreed that P1 does not show CRISPR/Cas9 components from
any bacterial species other than S. pyogenes. This includes not only the polypeptide, but also
the guide RNA and its components. They also agreed that P1 does not disclose which other
species of bacteria or archaea have a Type II system or whether any would work in
eukaryotes.
223 In Firestein 1, Associate Professor Firestein said that, in his opinion, P1 does not
exclude the possibility that S.pyogenes CRISPR/Cas9 system may utilise non-NGG PAMs.
Although Associate Professor Firestein suggested in his oral evidence that Cas9 derived from
S. pyogenes might recognise other PAM sequences apart from 5’-NGG-3’ and that this is
something he would investigate, he did not suggest this was disclosed in P1. Professor
Thomas and Associate Professor Herold were clear that P1 does not disclose the use of a
Cas9 polypeptide which recognises PAM sequences other than those recognised by S.
pyogenes derived Cas9.
224 I do not accept ToolGen’s argument that P1 provides a broad disclosure of any Type
II Cas9 polypeptide that recognises any PAM sequence or any known PAM sequence.
Rather, P1 suggests that the use of Cas9 derived from other species might enable other PAM
sequences to be used. This accords with Associate Professor Firestein’s evidence that P1
provides a starting point from which to explore such possibilities.

225 I previously found that P1 does not incorporate Jinek by reference. However, even if
P1 is considered together with Jinek there is still no disclosure of a system using a Cas9
polypeptide derived from a bacterial species other than S. pyogenes. Although Jinek provides
sequences for other Cas9 orthologs (sometimes spelt orthologues) (including S. thermophilus
and L. innocua), they are only shown to work with a 5’-NGG-3’ PAM in vitro in prokaryotes.
Jinek did not test their ability to recognise a non-NGG PAM and did not identify a non-NGG
PAM recognised by Cas9 from any other bacterial species.
226 Moreover, the chimeric sgRNA disclosed in Jinek is a S. pyogenes derived chimeric
sgRNA (ie. the same as disclosed in P1). Associate Professor Firestein gave evidence that he
would use the information in Jinek to test the Cas9 orthologs identified in the paper (L.
innocua and S. thermophilus Cas9) in combination with the chimeric guide RNA from S.
pyogenes for their ability to mediate CRISPR/Cas9 DNA at non-NGG PAM sites. Even if
that were considered an obvious thing to do, that does not broaden the disclosure of P1 to
encompass a system for cleaving DNA using a Cas9 polypeptide derived from other bacterial
species.
227 I find that P1 does not disclose an invention in which the Cas9 protein is derived from
any species of bacteria other than S. pyogenes. Nor does it disclose an invention which
encompasses the use of any Cas9 which is shown to recognise a non 5’-NGG-3’ PAM.
However, if I am wrong about that and it does make such a disclosure, the next question is
whether that disclosure is clear enough, and complete enough, for the invention to be
performed by the person skilled in the relevant art.
228 The respondents submitted that even if P1 does disclose an invention the components
of which are derived from bacterial species that are not limited to S. pyogenes, the skilled
addressee is not enabled by P1 to work the invention across the breadth of the claims. They
submitted that P1 does not provide any meaningful guidance as to how the work required to
perform the invention across the breadth of the claims could be done. They further submitted
that any such work would not be routine, and would impose an undue burden on the person
skilled in the art by requiring them to undertake a considerable amount of work in
circumstances where it would not have been clear that such a research project would
ultimately succeed.
229 The respondents submitted that the work involved in developing another Type II
CRISPR/Cas system would include at least:

(a) identifying a Cas9 nuclease from another bacterial species and how to localise it to the
nucleus of a eukaryotic cell;
(b) identifying the endogenous crRNA direct repeat and spacer sequences associated with
it;
(c) identifying what portion of a direct repeat sequence is required for a mature crRNA
molecule;
(d) identifying the endogenous tracrRNA sequence associated with the Cas9 nuclease;
(e) identifying and validating the PAM site recognised by the Cas9 nuclease in eukaryotic
cells;
(f) identifying and validating the length of the target nucleic acid sequence that can be
cleaved by the Cas9 nuclease;
(g) identifying which portions of the mature crRNA molecule and tracrRNA sequence are
required for the crRNA and tracrRNA portions of a sgRNA;
(h) designing a sgRNA that successfully guides the Cas9 to effect DNA cleavage in
eukaryotic cells; and
(i) investigating whether system can effect cleavage in a eukaryotic cell.
230 ToolGen contended that the respondents’ summary of the tasks that would need to be
performed by the skilled addressed involved “… atomising the task which must be performed
to as final level of granularity as possible, so as to multiple them …”. However, ToolGen
acknowledged that, in substance, the main tasks involved in performing the invention of the
claims using Cas9 derived from species other than S. pyogenes involved the following main
tasks:
(a) identifying another bacterial species with a Type II CRISPR system;

(b) determining the endogenous crRNA and tracrRNA sequences;
(c) characterising the mature crRNA and tracrRNA molecules endpoints and lengths;
(d) ascertaining the PAM sequence which the Cas9 of that bacterial species recognises;
and
(e) combining the crRNA and a portion of the tracrRNA into a single chimeric guide
RNA using the methods disclosed in Jinek.
231 ToolGen also submitted that it is not necessary for P1 to disclose all of the bacterial
species that could be used to perform the invention. It submitted that the sequences of the

Cas9 polypeptide, mature crRNA and mature tracrRNA (including knowledge as to the PAM
recognised by the Cas9) are all “input elements” which are not required to be available at the
priority date for enablement across the whole scope of the claims. It further submitted that all
that P1 and the patent application must enable is how those input elements are combined and
that such combinations become available to be used in the claims as and when they become
known. ToolGen relied on a decision of the Technical Board of Appeal in, Genentech
I/Polypeptide expression (T292/85) 27 January 1988 (“Polypeptide”) where the Board stated
at [3.1.3]:
What is also important in the present case is the irrelevancy of the particular choice
of a variant within the functional terms ‘bacteria’, ‘regulon’ or ‘plasmid’. It is not just
that some result within the range of polypeptides is obtained in each case but it is the
same polypeptide which is expressed, independent of the choice of these means. A
term of this kind must, of course, be clear and enable the skilled person to find
suitable specimens without undue difficulty. In the present application enough choice
is available, although some vehicles and hosts are preferred for practical reasons.
232 The reasoning in the Polypeptide case does not apply here. There is no evidence
presented in P1 to suggest that all Type II CRISPR/Cas9 systems can cleave DNA in
eukaryotic cells. Nor is there evidence presented in P1 to suggest that the Cas9 polypeptide
in S. pyogenes is the same as that found in other bacteria with a Type II CRISPR/Cas system.
That the Cas9 polypeptides will vary between species is apparent from P1 itself which
recognises that different species may recognise different PAMs. P1 does not disclose any
principle of general application from which it would appear reasonably likely that use of all
species within the scope of the claims (whether known or yet to be discovered) are enabled:
Regeneron at [56] (vi)-(viii).
233 The question whether P1 enables the invention of claim 1 and 10 to be performed
across their breadth depends at least to some extent, on whether, as I have found, the skilled
addressee is a molecular biologist or, as ToolGen submitted, a skilled team comprising a
molecular biologist and a microbiologist. In ToolGen’s submissions Professor Giffard was
identified as a microbiologist with expertise in bacterial CRISPR/Cas systems and that a
person such as him would form part of the skilled team. For reasons previously explained, I
do not accept that submission.
234 ToolGen’s analysis of how the skilled team would proceed to develop a system using
another bacterial species drew heavily on the evidence of Professor Giffard and certain
papers which he identified (Bhaya (2011), Makarova (2011) and Deltcheva (2011)) which

ToolGen submitted were common general knowledge of microbiologists as at the priority
date. It also made submissions which assumed that one or more of those papers would have
been ascertained by a molecular biologist working in the field of gene editing in eukaryotic
cells by means of a literature search. In this way the papers identified by Professor Giffard
were said by ToolGen to be relevant to sufficiency even if the microbiologist was not a
member of the skilled team.
235 The evidence of the molecular biologists, in particular, Associate Professor Herold,
establishes that Bhaya (2011), Makarova (2011) and Deltcheva (2011) were not common
general knowledge of molecular biologists working in the field of gene editing in eukaryotic
cells at the priority date. I make the same finding in relation to the CRISPRFinder tool
referred to in Professor Giffard’s evidence based on Associate Professor Herold’s evidence
that this was not something he was familiar with in October 2012.
236 As to Professor Giffard, he was cross-examined extensively on his knowledge of

Makarova (2011) and Deltcheva (2011) as at the priority date. Although he was unable to be
certain whether or not he had read Makarova (2011) and Deltcheva (2011) prior to October
2012, I accept his evidence that it is likely that he did so. I also accept his evidence that, as at
March 2012 when he referred to Bhaya (2011) in a document he prepared in connection with
a funding submission, it was a key publication in the field. Bhaya (2011) was a review article
which discussed the question of the proper classification of CRISPR systems and, in this
context, referred to the paper by Makarova et al published in Nature Reviews Microbiology in
June 2011 and the paper by Deltcheva et al published in Nature in March 2011. In my view,
it is likely these were significant publications in the field as at October 2012. Professor
Giffard considered the journals in which they were published to be prominent and prestigious
and he regarded each of the three papers as important in either summarising or advancing
research into CRISPR/Cas systems in bacteria and archaea at the time of publication. He
considered them essential reading for a microbiologist wishing to have an understanding of
such systems. I accept that evidence. I note that both Makarova (2011) and Deltcheva
(2011) were cited in Bhaya (2011) and that both Bhaya (2011) and Deltcheva (2011) are cited
in Jinek. I accept that Bhaya (2011), Makarova (2011) and Deltcheva (2011) were common
general knowledge of a microbiologist working in the CRISPR/Cas field in October 2012. I
should note that Professor Giffard did not give any evidence to suggest that he was familiar
with Jinek as at the priority date.

237 ToolGen submitted that Makarova (2011) and Deltcheva (2011) were relevant not
only as common general knowledge of a microbiologist, but also as information likely to
have been ascertained by a molecular biologist working in the field of gene editing in
eukaryotic cells who was seeking to carry out what ToolGen says is the invention disclosed
by P1 using Cas9 derived from bacterial species other than S. pyogenes. ToolGen submitted
that there was nothing wrong in principle in having regard to information obtained by means
of a literature search provided that it could not be said that the exercise imposed an undue
burden.
238 The authorities are clear that the question of sufficiency is to be ascertained by
reference to the scope of the relevant disclosure to a person skilled in the art armed with the
relevant common general knowledge. Unless the skilled addressee is directed to another
document that discloses additional information or which forms part of the skilled addressee’s
common general knowledge, it is outside the scope of information that may be taken into
account when considering whether or not there is an enabling disclosure. The test is whether
the invention can be performed using information disclosed by the relevant publication
coupled with the common general knowledge without imposing an undue burden. Moreover,
the fact that it is necessary for a worker in the field to utilise scientific literature that is not
common general knowledge (especially if it is from a different field) in order to perform the
invention would suggest that there is no enabling disclosure: Gilead at [221].
Identifying another bacterial species with a Type II CRISPR/Cas System

239 There are a number of approaches which ToolGen submitted the skilled addressee
could have taken, as at the priority date, in order to identify other bacterial species with
endogenous Type II CRISPR/Cas9 systems that could be used to perform the invention of the
claims without undue burden. One such approach was laid out in the evidence of Professor
Giffard, assuming he is a reasonable proxy for a microbiologist with expertise in the field of
bacterial CRISPR/Cas9 systems in October 2012 and who would form part of a skilled team.
It involved using Makarova (2011) (and particularly the information in the supplementary
table S1) to identify a bacterial species with a Type II CRISPR system. This would have
provided the microbiologist with a non-exhaustive list of approximately 120 bacterial species
(including S. pyogenes and S. thermophilus) with Type II CRISPR systems.
240 Professor Giffard also adopted an alternative approach to identifying other bacterial
species with an endogenous Type II CRISPR/Cas system. It involved conducting a search of

the NCBI genome sequence database known as Genebank maintained by the National
Institutes of Health. This database was a standard research tool used by scientific researchers
in October 2012. Associate Professor Herold agreed that different specialities within the
molecular biology field used different tools and that NCBI was a standard tool used by all
molecular biologists. Professor Giffard used it at the time of preparing his evidence to search
for nucleotide sequences that were annotated as coding for the Cas9 or Csn1 protein (the
latter being an earlier name used to describe Cas9). He refined his search to results limited to
bacteria and those that were released between 1 January 1900 and 30 September 2012.
According to his evidence, 1,513 results were generated, the second of which was identified
as “streptococcus thermophilus MS-ZLW-002”.
241 Upon inspecting the NCBI search result, Professor Giffard observed that it included
an annotation indicating that the sequence included a gene encoding for Csn1/Cas 9 and he
was able to locate the position of this gene. He was also able to identify the genes encoding
for Cas 1 and Cas 2 through annotations but he was not able to identify the CRISPR array as
there was no annotation identifying it.
242 Using the genomic sequence obtained for S. thermophilus MS-ZLW-002, Professor
Giffard then used the CRISPRFinder tool to identify the DNA sequences for the CRISPR
array and its location in the bacterial genome. He conducted his search by copying and
pasting the genome sequence of S. thermophilus MS-ZLW-002 from the NCBI database into
CRISPRFinder and searching for a CRISPR array within the sequence. The results of the
search showed two CRISPR arrays in different positions. The second CRISPR array was
2000 base pairs from the gene for Csn1/Cas9 which he considered to be “extremely close”.
He therefore concluded that this was a component of the same Type II CRISPR/Cas locus as
the genes for Csn1/Cas9, Cas1 and Cas2. By this means he was able to identify the CRISPR
array comprising the repeat sequences (shown in yellow to the left in the figure below) and
the spacer sequences (shown in various colours to the right in the figure below).

243 According to Professor Giffard, if he was able to identify Cas1, Cas2, Cas9/Csn1 and
the CRISPR array within reasonably close proximity of each other within the bacterial
genome, he would have a high degree of confidence that he had identified the Type II
CRISPR/Cas system of the bacterial genome in question. He considered it would not be
necessary to also identify the other Cas associated proteins, Cas4 or Csn2, since, in his
experience, the identification of the other components provides an extremely reliable
identification of a functional CRISPR system. I accept that evidence which in my opinion is
likely to reflect the use by Professor Giffard of the common general knowledge and the
ordinary skill of a microbiologist working in the field of CRISP/Cas systems at the priority
date.
244 It may be observed that Professor Giffard’s exercise identified one bacterial species
with a Type II CRISPR system, ie. S. thermophilus. The evidence shows that the Type II
CRISPR system of S. thermophilus recognises a 5’-NGG-3’ PAM when used in vitro. A post
priority date paper by Fonfara et al (“Fonfara (2013)”) published in late 2013 indicates that

S. thermophilus recognises an NGGNG PAM sequence (which encompasses NGG) in vivo.
Accordingly, S. thermophilus does not overcome the limitation of S. pyogenes referred to at
page 5 of P1.
245 Associate Professor Firestein also proposed an alternative approach to identify and
investigate Cas9 orthologs which involved conducting a homology search using the S.
pyogenes Cas9 sequence as the reference sequence to identify genes in bacteria that show a
high degree of homology. He said that he would undertake a homology analysis because
prior to October 2012 he understood that enzymes that are highly homologous are likely to
work by the same or a similar mechanism of action. Given this, he reasoned that it was
logical that two Cas9 orthologs, when highly homologous to each other, may exhibit similar
activity.
246 Associate Professor Firestein gave evidence that he would undertake the homology
search either at the level of DNA using NCBI BLAST or at the level of amino acids using
UniProt, which were both databases routinely used by him before October 2012. He said he
would use the search results to assess the degree of sequence homology across the Cas9 gene
and would select Cas9 orthologs that have conservation in specific effector domains (eg.
endonuclease domains) and homology (of at least 50-60%) across the entire sequence.
Determining the endogenous crRNA and tracrRNA sequences

247 The next step identified by ToolGen that the skilled addressee would need to take to
perform the invention of the claims in other Type II CRISPR-Cas bacterial species was to
identify the endogenous crRNA and tracrRNA sequences.
248 In Giffard 1, Professor Giffard stated that he understood from his own work prior to
October 2012 that crRNA arises from the transcription of the CRISPR array into a single pre-
crRNA molecule, which is then processed into individual crRNA molecules by RNA
cleavage events. He also understood that each crRNA molecule contained a transcribed
spacer sequence. He therefore understood that the nucleotide sequence comprising the
CRISPR array is the DNA coding for crRNA. Given that he had already identified the
nucleotide sequence and location of the CRISPR array through his search on the
CRISPRFinder, he was able to determine the DNA sequence coding for crRNA in S.
thermophilus MS-ZLW-002.

249 When it came to determining the DNA sequence coding for tracrRNA, Professor
Giffard relied on the Bhaya (2011) which stated that:
It was also recently established that a trans-encoded small CRISPR RNA (tracrRNA)
is involved in the processing of pre-crRNA into crRNA in Type II systems through
the formation of a duplex with the CRISPR repeat sequence.
He stated that he understood the expression “formation of a duplex” to mean that tracrRNA
can associate with the repeat-derived RNA by base pairing. This means that the tracrRNA
can bind with the parts of the single stranded pre-crRNA that are transcribed from the repeat
sequences of the CRISPR array (recalling that pre-crRNA is comprised of both transcribed
repeat and spacer sequences). This understanding is confirmed by another passage in Jinek
which ToolGen relied on and which states:
[T]ype II systems process pre-crRNAs by different mechanisms in which a trans-

activating crRNA (tracrRNA) complementary to the repeat sequences in the pre-
crRNA triggers processing.
250 ToolGen submitted that the implication of this statement is that the DNA sequence
comprising the repeat sequence in the CRISPR array is complementary to the nucleotides
comprising tracrRNA and must therefore be identical to the DNA sequence that codes for
tracrRNA. Therefore, using the repeat sequence obtained from the CRISPRFinder search,
Professor Giffard could identify the DNA sequence that would be the same nucleotide
sequence as the DNA sequence coding for tracrRNA.
251 In oral evidence, Professor Thomas gave evidence that appeared to confirm Professor
Giffard’s understanding:
MR FLYNN: Yes. Now, if you take that as your identification of the DNA sequence
that corresponds to the type 2 Crispr/Cas system, could you explain your comment in
the joint report that the DNA sequence encompassing the sequence specifies Crispr
RNA and tracrRNA would be available?
PROF THOMAS: Yes. Although I wasn’t referring specifically to that sequence.
You would understand of course. But as a general point, what I was trying to
communicate there was that the equivalent system for the hypothetical type 2
Crispr/Cas system, for that particular bacteria, would have the arrangement of
spacers and then repeat sequences in a similar manner to what’s shown in that figure
[referring to the CRISPRFinder figure].
MR FLYNN: Yes. And then, if you had the spacer and the repeat sequences [from
the CRISPRFinder figure], then how do you get from that to the DNA sequence
encompassing the sequence specifying firstly, the Crispr RNA?
PROF THOMAS: Well, I know from my knowledge of the system that there are two
parts to the Crispr RNA. There’s the part that binds to the pathogen and there’s a

repeat spacer sequence as well, which binds to the tracrRNA. So, the unique part of
each of those would correspond to the Crispr RNA specific sequence, if you like, the
rainbow colours that you referred to previously [from the CRISPRFinder figure],
whereas the spacer region I would predict would be the path that binds to the
tracrRNA.
MR FLYNN: Yes, so could you turn a couple of pages through in Professor Giffard’s
first affidavit, to paragraph 77. That’s where he says, if you look at the second
sentence, he says: “I understood there were critical property of individual Crispr
RNA molecules”. So, he’s talking about the molecule, but he says: “Is that they each
contain a transcribed spacer sequence”. Do you see that?
PROF THOMAS: Yes.
MR FLYNN: And what you understand him to be saying there is that an individual
Crispr RNA molecule contains the RNA form of the spacer sequence in DNA. Do
you agree with that?
PROF THOMAS: Well, it includes it. It includes it, but you can’t directly take the
DNA sequence and just predict with certainty what the Crispr RNA is based on that
sequence. There’s some processing involved.
MR FLYNN: Yes, but it will include what some or all of a transcribed spacer
sequence. Correct?
PROF THOMAS: Yes, that’s correct.
MR FLYNN: And that’s why in the joint report you used the word, “encompass”,
correct?
PROF THOMAS: Yes, I was trying to communicate that concept.
252 Professor Giffard’s next step was to find where the DNA sequence coding for
tracrRNA is located in the bacterial genome. He said that he was aware from his own work
prior to October 2012 that the stretches of DNA specifying the Cas proteins and the CRISPR
array are in very close proximity. In support of this opinion he referred to Deltcheva (2011)
which showed that in six out of seven species, DNA encoding the tracrRNA is located either
immediately adjacent to or within the Type II CRISPR/Cas loci as defined by the presence of
the Cas/Csn genes and the CRIPSR array.
253 Using that information, Professor Giffard searched for a DNA sequence that was
either within or immediately adjacent to the S. thermophilus strain CRISPR/Cas locus that,
once transcribed, produce an RNA molecule that is complementary to the repeat sequence of
the CRISPR array. Put another way, he searched for a DNA sequence that was identical to
the repeat sequence of the CRISPR array. He did this using a pairwise BLAST analysis
where one of the pair is the entire S. thermophilus strain MN-ZLW-002 genome sequence
(from NCBI) and the other is a single copy of the CRISPR repeat from that strain (from

CRISRFinder). In this way, Professor Giffard was able to ascertain the location and sequence
of the DNA coding for tracrRNA.
254 In the result, Professor Giffard was able to identify the DNA coding for both crRNA
and tracrRNA and determine the endogenous crRNA and tracrRNA sequences for the Type II
CRISPR/Cas system of the S. thermophilus strain MN-ZLW-002.
255 The respondents submitted that Professor Giffard’s identification of the DNA coding
for the tracrRNA sequence was infected by an impermissible reliance on Deltcheva (2011)
which provided him with the knowledge that tracrRNA is encoded by a gene separate from the
CRISPR array but very close to or within the CRISPR-Cas locus. I agree with ToolGen’s
submission that the respondents’ criticisms based on Professor Giffard’s reliance on
Deltcheva (2011) ultimately falls away given my finding that it was likely that he had read
Deltcheva (2011) and that it was common general knowledge of a microbiologist at the
priority date.
256 The respondents also submitted that the CRISPRFinder was not common general
knowledge of molecular biologists or microbiologists at the priority date. I accept, based on
the evidence of Associate Professor Herold, that it was not common general knowledge of
molecular biologists working in the field of gene editing in eukaryotic cells. However, I
consider it was a tool that is likely to have been commonly used by microbiologists
specialising in the study of CRISPR systems. In Giffard 1, Professor Giffard referred to
CRISPRFinder as a publically available resource which he typically referred to in the course
of his work. In his oral evidence, he acknowledged that it was likely he had not used the
CRISPRFinder prior to, or in, October 2012 for the purpose of seeking to identify a CRISPR
array. However, Professor Giffard’s evidence shows that CRISPRFinder was one of a
number of tools available for that purpose and that it was the subject of a paper by Grissa et
al (“Grissa 2007”) published in Nucleic Acid Research in 2007.
257 The fact that Professor Giffard may not have used the CRISPRFinder himself before
October 2012 is not determinative of whether it was at that date common general knowledge
in his field. In light of his evidence considered as a whole, including the description of the
tool published by Grissa (2007), I find that CRISPRFinder was a well-known tool available
for use by microbiologists engaged in CRISPR research in October 2012. On this issue, I
consider it significant that the respondents did not directly challenge Professor Giffard’s
evidence to that effect nor call evidence from any other microbiologist refuting it.

Identifying and characterising the mature crRNA and tracrRNA
identify and characterise the mature (fully processed) crRNA and tracrRNA.
259 ToolGen submitted that once the putative crRNA and putative tracrRNA sequences
are ascertained in the manner previously outlined, the length and endpoints of the mature
crRNA and tracrRNA could be ascertained by obtaining the bacterial isolate and using
techniques which were standard as at October 2012.
260 In JER 2, Professor Thomas identified several techniques to identify the crRNA and
tracrRNA molecules. In relation to identifying the crRNA molecule he stated:
To identify the crRNA molecule in its fully processed form, I would seek bacterial
RNA expression data (RNAseq) from [sic] bacterial isolate in question. I would
search that data for sequences corresponding to the putative crRNA sequence. This
might provide me with the sequence of the processed/ functional form. If RNAseq
data were unavailable, then I would seek to obtain the bacterial isolate for
experimentation. If the bacterial isolate was available for experimentation, I would
perform experiments such as northern blot/ RNAse protection and RNAseq to
identify the length/ content of the crRNA.
261 Associate Professor Herold and Professor Giffard both broadly agreed with Professor
Thomas’ approach, and Professor Giffard added that this approach was similar to the RNA
sequencing (“RNA-Seq”) based approach taken by Deltcheva and her co-workers in
Deltcheva (2011). RNA-Seq data provides what for present purposes may be described as a
snapshot of the RNA in a cell at a given time.
262 In relation to identifying the tracrRNA molecule, Professor Thomas stated that he
would follow the same approach as he took to identify the crRNA molecule. Associate
Professor Herold and Professor Giffard both broadly agreed with Professor Thomas’
approach and Professor Giffard added that this approach was consistent with what he
described in Giffard 2 with reference to Deltcheva (2011).
263 The authors of Deltcheva (2011) used RNA-Seq to characterise and quantify RNA
derived from S. pyogenes strain SF-370. Professor Giffard stated that this involved: (1)
extracting RNA from cells; (2) converting RNA to complementary DNA (cDNA); (3)
sequencing the cDNA using high-throughput next generation sequencing technology and (4)
using bioinfomatic techniques to map the sequencing data on the genome sequences of the
organisms from which the RNA originated. Professor Giffard went on to state that during the

preparation of purified RNA, half of the sample was treated with a compound (TEX) which
depletes the RNA of processed transcripts, thereby enriching for primary transcripts. This
enabled the authors to distinguish between RNA that had been produced in the cell by
cleavage events (i.e processed RNA) and those that were the primary products of
transcription (i.e. unprocessed RNA). This process yielded the nucleotide sequence including
the beginning and end positions of any RNA identified and provided information on the
relative abundance of particular RNA molecules, and whether the RNA was a product of a
processing event within the cell. The authors identified both crRNA and tracrRNA.
264 In oral evidence, Professor Thomas ultimately agreed that if he was provided with the
CRISPRFinder result for a particular bacterial species of interest coupled with the knowledge
from a microbiologist that individual crRNA molecules each contain a transcribed spacer
sequence, he could find sequences that correspond with the spacer sequences, and if he were
confident that he could see a match to those sequences within the RNA-Seq Library, then he
would have confidence that he had identified an endogenous RNA molecule that could be the
crRNA.
265 Professor Thomas was questioned about whether high-throughput RNA sequencing
technology was well-known before October 2012, and he gave the following evidence:
PROF THOMAS: It’s known, but reasonably specialised. It’s not the kind of thing,
certainly, that [sic] – molecular biology labs generally would outsource that type of
technology, because relatively complex machinery is required to perform the
analysis. We – we were not doing RNA-Seq studies of that nature at the time. Some
specialised labs were. You also need a bioinformatician to interpret the data, because
you [sic] imagine you’re getting back an awful lot of information, so you need
someone who’s experienced in the area to process that information and interpret it for
you.
MR FLYNN: Yes. Now, if we read on in the joint report, you say if RNA-Seq data
were unavailable, then you would seek to obtain the bacterial isolate for
experimentation. Do you see that?
PROF THOMAS: Yes, I do, and the reason I – I’ve said that was that I think it’s
actually probably pretty unlikely that RNA-Seq data would be available, because
that’s an experiment that someone has to perform, so you would need to really have
characterised that strain or that isolate in a lot of detail to inspire you to do an RNA
Seq experiment. So actually, I suspect, given the nature of the searches we’ve been
talking about, they could identify anything on the database that fits the criteria. The
chances of that having an RNA-Seq data library available for that particular strain, I
think, is probably pretty unlikely. But that’s – so that’s why I said it.
MR FLYNN: But you don’t know, as at October 2012, what was or wasn’t available
in the library; is that right?
PROF THOMAS: No. No, I do not, but I just make the point that I think it’s unlikely.

266 The respondents submitted that Professor Thomas’ evidence establishes that it was
unlikely that, for any particular strain of bacteria (leaving aside S. pyogenes) RNA-Seq data
would have been available in October 2012. Professor Giffard agreed that in October 2012,
he would have expected there to be no more than a small number of Type II repeat spacer
expression data made available, and that, in 2013, there were only around six species other
than S. pyogenes for which Type II CRISPR array expression data had been made available.
267 Associate Professor Herold gave evidence that the use of RNA-Seq data to identify
the mature crRNA and tracrRNA components of a bacterial species other than S. pyogenes
would require a tremendous amount of work including bioinformational analysis and
experimental validation. Associate Professor Herold said:
… [T]he tracrRNA is required for specificity and also CRISPR RNA for the
individual Cas proteins to work. So that would be the first step to identifying. The
identification of the CRISPR is the first thing which would be difficult. You could do
this bioinformatically but then you had to confirm experimentally, that would be the
first step. And then identifying the tracrRNA, in October 2012 – at the time when the
P1 came out and Jinek came out – the only tracr which has been described in the
literature was S. pyogenes in the Deltcheva paper in 2011. And this was a Nature
paper, again, showing this tremendous amount of work they required to get this up
and running...So I would assume that it’s not as easy just taking a tracr and a
CRISPR because we don’t even know where to find and where to look for and what
size to be used. So it’s very, very difficult to get this working and would require very,
very significant amount of work from a specialised lab.
(Errors in original).
Professor Thomas agreed.
268 One difficulty I have with this evidence is the use that Associate Professor Herold
seeks to make of Deltcheva (2011). It may be accepted that Deltcheva (2011) was ground
breaking even though, on the respondents’ case, Associate Professor Herold knew nothing of
Deltcheva (2011), the focus of which was outside his field of expertise. Deltcheva (2011)
was important, not so much because it provided the RNA-Seq for S. pyogenes, but because of
its contribution to the understanding of the role of tracrRNA in directing the maturation of
crRNAs. I give little weight to Associate Professor Herold’s evidence based on Deltcheva
(2011).
269 The respondents also sought to support Associate Professor Herold’s views as to the
difficulty involved in identifying mature tracrRNA in a bacterial species other than
S. pyogenes by reference to Jinek. They submitted that Associate Professor Herold’s

perception of the difficulties involved was confirmed by the fact that the authors of Jinek
(who included the eminent microbiologists, Charpentier and Doudna) did not use
experimentally validated tracrRNA from L. innocua and N. meningitidis. The supplementary
figures of Jinek show that in evaluating the DNA cleavage of Cas9 orthologs related to
S. pyogenes, the authors used predicted tracrRNA sequences based on the northern blot data
published in Deltcheva (2011) for S. pyogenes.
270 The fact that the authors of Jinek relied on predicted tracrRNA sequences for L.
innocua and N. meningitidis, was the basis for a suggestion in Associate Professor Herold’s
evidence that, if the authors could have used the actual tracrRNA sequences derived from the
bacteria using their own experimentally derived data, then they would have done so; the
implication of them not doing so was, according to Associate Professor Herold, that it was
too difficult even for them. However, as Associate Professor Herold acknowledged in his
evidence, the authors do not suggest that identifying the tracrRNA for those bacteria would
have been difficult.
271 In JER 2, Professor Thomas also identified northern hybridisation (or northern blot)
and RNase protection as means to identify the mature crRNA and tracrRNA molecules.
Professor Thomas accepted that these techniques were well-known in October 2012 and that
both could be used to determine the length of RNA molecules. Professor Giffard also gave
evidence that these techniques were well known at the priority date.
272 I find that both northern hybridisation (northern blot) and RNase protection were
standard techniques used by the notional skilled addressee at the priority date, and that both
techniques could be used to identify mature crRNA and tracRNA molecules.
273 In cross-examination, Senior Counsel for the respondents questioned Professor

Giffard regarding potential difficulties involved in using these techniques each of which
requires access to the bacterial isolate of interest. He gave the following evidence:
MR DIMITRIADIS: You would need to conduct some other sort of experimentation

of the kind that you referred to, in order to – if you weren't using the RNA-Seq, is
that right?
PROF GIFFARD: As I got fairly specific in my second affidavit, a combination of
northern blots and primer extension, despite being old technology, is very effective
and very robust and would be effective at identifying the ends of the molecules, you
know, the exact natures of these molecules, and as a backup technique, the additional
technique that was described by Deltcheva was the circularised RNA combined with
PCR, which is essentially just a belt and braces thing; it’s just another armoury to
make sure that you can really nail down exactly these molecules.

MR DIMITRIADIS: And each of those techniques that you’ve just referred to,
require having a bacterial isolate in question, available, before experimentation,
correct?
PROF GIFFARD: That is correct. Or I guess, in theory, someone else could have it
and could send you the – send you a physical RNA preparation. That would not be a
common thing but…in theory, if someone else extracted the RNA, then sent it to you,
then you could experiment on that. But yes, you need to have an actual preparation of
the RNA from the bacterial cell.
274 The evidence was quite vague as to how difficult it would be to obtain samples for use
in a northern hybridisation or RNase protection experiment. Professor Thomas gave evidence
that the difficulty with requiring a biological sample for experimentation was that it may not
be possible to obtain if the DNA sequence of interest was not cultured in a laboratory.
275 Professor Giffard gave evidence that if the bacterial isolate was obtained, the
experimentation process for northern hybridisation (northern blot) or RNase protection could
then be conducted. He gave this evidence, which I accept, as to the difficultly involved in
conducting such experiments:
MR DIMITRIADIS: Now, would you agree with this: if RNA sequence data or data
that you are seeking to obtain from the experiments of the kind that you referred was
available, that those – that work would be extensive and would require a significant
amount of experimentation in order to obtain the data. Is that fair?
PROF GIFFARD: No. I don’t think it is because, as I mentioned, the dRNA-Seq in
not essential to analyse the RNA molecules. And techniques such as northern
hybridisation and primer extension are old, relatively low tech and even quite cheap
experiments that can be carried out in a matter of days. And so, in theory, assuming
everything goes right and with those – those methods, if you have got some
reasonable skills in the lab, there’s no reason to think they wouldn’t go right. And it
would be a – quite small project to use northern hybridisation and primer extension
or RNase protection, or even the circularisation of the PCR. None of those are
particularly challenging or particularly time consuming. I mean, I – as I have said, I
had – I have published northern hybridisation, RNase protection and primer
extension in 1993 and 1995, and I – part of that I did myself, and part of it my
research assistants at the time did. And the northern hybridisation took a bit of time
because we had a bit of trouble figuring out how to purify the RNA from oral
bacteria, which are very robust cells that are hard to bust open, without breaking the
RNA as well, but once we had the RNA it’s so similar to southern hybridisation,
which I’ve been doing a lot. And it’s really within the remit of anyone with
confidence in recombinant DNA technology and DNA detection technology to do
these relatively straightforward experiments. In fact, they’re within the range of what
could be done in undergraduate classes.
276 Professor Giffard’s evidence makes clear that northern hybridisation (northern blot)
and RNAse protection do not require RNA-Seq to identify the mature crRNA and tracrRNA.
Accordingly, the difficulties identified by Associate Professor Herold regarding the need for

a bioinformatician to process and interpret the RNA-Seq data and experimental validation
which requires next generation sequencing is not relevant to a consideration of these two
alternate techniques. In my opinion, the evidence of Professor Thomas and Professor Giffard
in relation to northern hybridisation (northern blot) and RNase protection techniques renders
Associate Professor Herold’s evidence concerning the difficulties involved in using RNA-Seq
largely irrelevant.
277 However, Professor Thomas identified two further difficulties regarding these
techniques. First, the DNA sequence for the bacterial strain of interest must being publicly
available. Second, for northern hybridisation (northern blot), the relevant RNA molecules
(i.e. the putative crRNA and tracrRNA) must be identified before northern blot experiments
can be carried out.
278 As to Professor Thomas’ first point on the public availability of the DNA sequence of
interest, this would have been identified in the two preceding steps of, first, identifying a cas9
from another Type-II CRISPR-Cas9 system using the NCBI and, second, identifying the
DNA coding for the tracrRNA using a pairwise BLAST analysis to compare a whole genome
sequence (from NCBI) with a single copy of the CRISPR repeat from that strain obtained
from CRISRFinder. As such, it can be assumed that by the stage that the skilled addressee
attempts this step, they will have access to a publicly available copy of the DNA sequence of
interest.
279 As to the identity of the crRNA molecule, Professor Thomas accepted in his oral
evidence that this would be the spacer sequence of the CRISPR array or some portion of it.
However, in earlier oral evidence and in Thomas 2, he explained that even with the DNA
from the CRISPR array, it is difficult to identify the crRNA molecules because it is not
possible to predict with certainty that the crRNA molecule is based on that sequence because
of processing involved (from pre-crRNA to crRNA). However, he accepted that the crRNA
would include some or all of a transcribed spacer sequence.
280 As to the identity of the tracrRNA molecule, Professor Thomas gave evidence that it
could also be difficult to identify the tracrRNA because it would not be clear what part of the
repeat sequence would be complementary to the tracrRNA and there is the potential for
mismatches between the tracrRNA and the repeat sequence. In other words, even if the
repeat sequence is known, it is not possible to know how much of it is going to be present in
the tracrRNA and where any potential mismatches will be. Professor Giffard did not agree

with Professor Thomas. He said that Professor Thomas’ argument about complementarity
was not correct and disregarded the involvement of the tracrRNA in the pre-crRNA
processing where the pre-crRNA itself is cleaved, which process is made possible by
complementarity. On this issue, I prefer the evidence of Professor Thomas to that of
Professor Giffard. I think Professor Giffard was most likely understanding the potential
difficulties that may arise due to mismatches between the tracrRNA and the repeat sequence.
Identifying and validating the PAM sequence which the Cas9 of a non-S. pyogenes
bacterial species recognises
identify and validate the PAM sequence which the Cas9 of that species recognises in
eukaryotic cells. ToolGen relied on two approaches discussed in Associate Professor
Firestein’s evidence: the first involved using a PAM variant library in vitro or in vivo and the
second involved using an in silico approach (experimentation done by computer).
PAM variant library in an in vitro and/or in vivo system

282 In Firestein 1, Associate Professor Firestein set out three methodologies to use a PAM
variant library and test cleavage in an in vitro and/or in vivo system.
283 Associate Professor Firestein set out his first methodology for identifying PAM
variants for Cas9 orthologs homologous to S. pyogenes which included:
(a) Using high scale cloning methods to generate a PAM variant library which represents
all possible PAM variants for S. pyogenes up to eight nucleotides in length.
(b) Constructing a sgRNA with the same sequence as the composition taken from S.
pyogenes as shown in Figure 1A of P1 (“S. pyogenes sgRNA”) which would be customised
by replacing the 20 base pair portion of the crRNA with a different sequence of interest.
(c) Performing a DNA cleavage assay such as that described in experiment 1 of P1,
where the Cas9 is co-expressed with the sgRNA and is incubated with the PAM variant
library.
(d) Isolating, purifying and deep sequencing (using next generation sequencing) the cut
plasmid DNA generated from the cleavage assay to identify the different putative PAM
sequences. A bioinformatician would be required to analyse the sequencing data.

284 Associate Professor Firestein stated that the second methodology involved the same
steps as the first methodology, except he would specifically test the four cas9 orthologs
identified in Jinek, namely, L. innocua, S. thermophilus, C. jejuni and N. meningitides. He
said that he would test these homologous orthologs with the S. pyogenes sgRNA as he would
expect that Cas9 orthologs, when highly homologous to each other, may exhibit similar
activity even when interchanging certain system components (i.e. the sgRNA).
285 Associate Professor Firestein said that his third methodology involved the same steps
as the first methodology, except instead of using the S. pyogenes sgRNA, he would construct
either a sgRNA or a crRNA:tracrRNA duplex based on the endogenous crRNA and
tracrRNA sequences for a particular bacterial species. I have previously discussed the
process of identifying the endogenous crRNA and tracrRNA as explained in Professor
Giffard’s evidence. Associate Professor Firestein said that he would prefer the approach of
using a crRNA:tracrRNA duplex (by which I understood him to mean a crRNA and
tracrRNA not fused into a single guide RNA), but that if he were to design and construct a
sgRNA, he would use the approach taken in Jinek.
286 Use of a crRNA:tracrRNA duplex involves introducing the Cas9 and the mature
crRNA:tracrRNA duplex to the pool of candidate plasmids and performing an in vitro
cleavage assay as set out in P1. The cut plasmids are then isolated, purified and deep
sequenced.
287 The in vivo PAM approach involves inserting the PAM variant library into a
eukaryotic system so that every cell only has one PAM variant sequence. The cells express a
RFP-GFP (red and green fluorescent protein) reporter system that allows for screening to
identify GFP (green fluorescent protein) positive cells that have undergone CRISPR-Cas9
cleavage using a barcode approach. The GFP positive cells would then be isolated by flow
cytometry and specific DNA fragments from the GFP positive cells as well as GFP negative
cells would undergo next-generation sequencing to identify the PAM variants that are
enriched in the GFP-positive cells and depleted in the GFP negative cells. Associate
Professor Firestein gave evidence that since this is occurring in eukaryotic cells, a “barcode”
would be externally placed as part of this reporter which would enable the skilled person to
map back what the sequence of that PAM variant is in cases where cellular repair
mechanisms may cause insertion or deletion across the PAM site itself.

288 The respondents submitted that because Associate Professor Firestein had never used
a PAM variant library before or undertaken the computational analysis required as part of the
analysis (which would require the expertise of a bioinformatician) it could not be said that
this was routine work. Additionally, Associate Professor Herold gave evidence that at the
priority date, although he had some familiarity with the approach taken by Associate
Professor Firestein, it was not routine. In relation to the creation of a PAM variation library.
Associate Professor Herold said:
…I would not say that is something in particular for me or a general normal

molecular biological lab to do that as a routine work and could cause significant
amount of work, and the chances of success would, in my opinion, be relatively low.
289 He identified several other issues with the use of a PAM variant library in an in vitro
or in vivo system.
290 In Herold 2, Associate Professor said that he did not think the in vitro PAM variant
library approach would be successful unless a large amount of time and effort was invested.
He said:
[37] I do not consider that A/P Firestein's in vitro PAM approach would be
successful in identifying other PAM sites recognised by a Cas9 in eukaryotic
cells, unless a very large amount of time and energy was invested in the
process. The approach involves the generation of 65,536 unique plasmids,
representing all possible candidate PAM sites in an eight base pair sequence
(4*4*4*4*4*4*4*4), of which only a very low number of plasmids would be
cleaved…
[38] For example, if A/P Firestein's in vitro PAM approach was used for
S pyogenes, a maximum of eight out of 65,536 plasmids (i.e. 0.01 % of all
candidates generated) would be cleaved (the eight plasmids represent all four
possible "NGG" variations, and all four possible "NAG" variations, in the
PAM). Each cleaved plasmid would represent only one out of 65,536
plasmids (i.e. 0.0015% of all plasmids generated).
291 In oral evidence, Associate Professor Herold corrected his calculations by a factor of
1,000 and said that 8,192 out of 65,536 plasmids (12.5%) would be cleaved. Ultimately, he
also accepted that the detection was no longer “almost impossible” but a “possibility” with no
guarantee that any plasmid would be cleaved. When asked by me whether the probabilities
of success were remote or something more, he suggested they would be something more.
292 Associate Professor Firestein gave evidence that even at low percentages, deep
sequencing technology is sensitive enough to detect cut plasmids at low levels and Associate

Professor Herold ultimately agreed with this evidence. The respondents had several issues
with Associate Professor Firestein’s reliance on deep sequencing technology which, he
accepted, would require the use of a next generation sequencer. Associate Professor Herold
gave evidence that although next generation sequencers were available at the priority date,
they were not standard equipment. Associate Professor Firestein accepted this and said that
next generation sequencers would have only been available at a commercial laboratory for a
fee or at core facilities in academic laboratories. Associate Professor Herold agreed with this.
293 Associate Professor Herold also gave evidence that commercially-sourced assays
containing unique plasmids are generated in a Guassian distribution with concentrations of
some candidate plasmids being very low, resulting in an uneven distribution of variants in the
PAM library. Thus, if the correct PAM sequences are in low concentrations, it would be
even more difficult to identify these PAMs using Associate Professor Firestein’s
methodology.
294 Associate Professor Firestein accepted the premise of Associate Professor Herold’s
evidence, but made clear that he did not accept the cut plasmid would not be detected and that
the concerns raised by Associate Professor Herold would not arise in practice unless all of the
8,000 PAM variants respond to an active PAM that is present at low frequencies.
Additionally, he suggested that this issue could be overcome by either conducting the assay
so that each variant is represented in hundreds or thousands of plasmid copies or through
quality control checks, whereby libraries that do not have appropriate representations of
different variants that are sought would be discarded. Associate Professor Herold agreed that
you could increase the number of molecules but that one may still struggle to find cut
plasmids using next generation sequencing. According to Associate Professor Herold, use of
next generation sequencing would significantly increase costs and take three to six months.
Associate Professor Firestein disagreed and stated that because each molecule with a specific
PAM would be represented 1000-fold times, it could easily be identified by next generation
sequencing.
295 Associate Professor Herold identified one further issue pertaining to Associate
Professor Firestein’s first and second methodologies which use the S. pyogenes sgRNA. His
evidence was that Associate Professor Firestein’s first and second methodologies, which used
a 20 nucleotide target sequence and an eight nucleotide candidate PAM site, would limit the
detection of PAMs for a particular species where the target sequence and PAM site have

nucleotides different to 20 and eight respectively. In their closing submissions, the
respondents rely on two examples which became known after the priority date. These are a
C. jejuni Cas9 which recognises a 22 base pair target site and a seven nucleotide PAM
(NNNNACA), and N. meningitidis Cas9 which recognises a 24 nucleotide target sequence
and an eight nucleotide PAM (NNNNGATT).
296 Whilst I accept that using a S. pyogenes sgRNA which is limited to 20 variable
nucleotides for the target sequence and an eight nucleotide PAM may result in some PAM
sequences not being identified, in circumstances where Associate Professor Firestein has
proposed as an alternate approach the use of a duplex, which avoids this complication, and
where he has specifically stated that he prefers this approach to using a sgRNA, I find that the
issues identified in relation to the use of a sgRNA could not constitute a significant problem
for him. But it does not seem to me to be likely that the notional skilled addressee working
with P1 would adopt that approach given that it teaches the use of a sgRNA rather than a
crRNA:tracrRNA duplex.
297 Associate Professor Herold identified two further issues that relate only to Associate
Professor Firestein’s in vivo approach. As mentioned above, the in vivo approach relies on
using eukaryotic cells that express a RFP-GFP reporter system that allows for screening to
identify GFP positive cells that have undergone CRISPR-Cas9 cleavage using a barcode
approach.
298 Associate Professor Herold referred to the cellular repair mechanism (“NHEJ”) in
eukaryotic cells that repairs breaks in DNA. He said that a cut made at the PAM site may
have been repaired and mutated by NHEJ which may make it impossible to determine
whether the plasmid DNA was cut. In response, Associate Professor Firestein stated that he
would address this issue by generating an alternative pooled PAM variant library that
incorporates a barcode DNA sequence upstream of the target PAM site, which would enable
the identification of a PAM variant even where the PAM sequence may have been lost due to
insertions or deletions caused by NHEJ. Associate Professor Herold said that this approach
would require much more additional work and there would be no guarantee that the barcodes
were not destroyed by the Cas9 or cellular machinery. Associate Professor Firestein
explained that he did not see the possibility that the barcodes may be destroyed as an issue as
there were usually only really small deletions of a few nucleotides and if they were to occur

this would only be in some proportion of the approximately 1,000 copies of the particular
variant available for analysis.
299 Associate Professor Herold said that to use barcodes and the RFP/GFP reporter in the
cloning step of the in vivo approach would require that the task be outsourced to a
commercial laboratory which would cost a considerable amount of money. I accept that
evidence.
300 Professor Thomas also said that Associate Professor Firestein’s in vitro or in vivo
approaches of finding the PAM for a particular Cas9 created a so called “catch 22” issue, in
that it is necessary to have a functional guide RNA in order to cleave the plasmid library and
the investigator cannot know whether they do without first knowing the PAM for the Cas9.
Associate Professor Firestein said that this is only an issue where the in vitro or in vivo DNA
cleavage assay produces a negative result. Professor Thomas agreed and stated that the issue
was that if there was a negative result, you could not know whether that was because there
was no PAM or because the guide RNA and Cas9 was not complexing properly to cut if a
PAM was present.
301 The respondents submitted that the catch 22 arises regardless of whether duplex guide
RNA or a sgRNA is used. Senior Counsel for ToolGen asked Professor Thomas and
Associate Professor Herold whether this issue could be overcome by adopting Associate
Professor Firestein’s third approach of using the mature crRNA and tracrRNA for a specific
species to prepare a crRNA:tracrRNA duplex to identify species-specific CRISPR Cas9 PAM
sites. He suggested that this would overcome one unknown variable in the “catch 22” issue
which is whether or not the sgRNA complexed with the Cas9 is able to cut as no sgRNA is
used. Associate Professor Herold responded that this removes the issue of something going
wrong in the fusing process to create a sgRNA but the issue is still whether the right mature
crRNA and tracrRNA are identified. I accept that evidence. However, I also note that the
identification of the mature crRNA and tracrRNA molecules could be identified using either
the RNase protection or northern hybridisation (northern blot) approaches proposed by
Professor Thomas.
In silico PAM identification

302 In Firestein 1, Associate Professor Firestein explained his alternate approach of in
silico identification, which uses in silico analysis of the CRISPR/Cas9 gene locus for each

bacterial species to identify the putative PAMs for Cas9 orthologs. He set out the following
methodology:
(a) Search each particular bacterial species genome for the presence of a CRISPR array,
which, based on Figure S1 of Jinek, he would expect would be in the vicinity of the Cas9
gene. Identify within the CRIPSR array the repeat and spacer sequences and extract the
spacer sequences.
(b) Identify the bacterial phage DNA target site (protospacer) from which the spacer
originated by performing an NCBI BLAST search using the DNA of the spacers identified in
subparagraph (a) above. The identified bacterial phage sequences that are identical or highly
homologous (greater than 90%) to the sequences of the spacers would be designated as
putative target DNA sites.
(c) Undertake computational analysis of the target DNA sites identified in subparagraph
(b) above to identify a consensus sequence that defines the PAM site.
(d) Verify experimentally the putative PAMs identified by performing an in vitro
cleavage assay as set out in experiment 1 of P1.
303 In Firestein 1, Associate Professor Firestein gave this evidence concerning the in
silico approach:
[261] This in silica approach could be undertaken using simple computational tools
(or undertaken manually). Where the genomic sequence data from the
invading bacterial phage is available, this analysis can be done in a very short
period of time (hours). The statistical power of this analysis is proportional to
the number of spacers and protospacers that can be analysed and used to
build a consensus plot for each Cas9 ortholog.
304 Associate Professor Herold agreed that if it is a “consistent PAM site” the in silico
approach would identify the PAM. There was no evidence of any “inconsistent PAM site”
identified by the respondents. Additionally, both Associate Professor Herold and Professor
Thomas agreed that the in silico approach eliminates many of the issues raised in relation to
the pooled variant library approach. However, they both raised several issues in relation to
this approach.
305 Professor Thomas and Associate Professor Herold gave evidence that the phage
sequence containing the PAM will not necessarily have been available on the NCBI database
at the priority date. However, both accepted that as at the priority date, this was knowledge
that would have been relevantly held by a microbiologist and not a molecular biologist.

Professor Giffard did not give any evidence concerning the availability of phage sequences at
the priority date. In those circumstances, the evidence does not establish that the in silico
approach is feasible at least to the extent that it depended on the availability of phage
sequences that were identical or highly homologous to the relevant spacer sequences.
306 Associate Professor Herold also made the point that it cannot be assumed that the
phage sequences in the NCBI database are complete, correctly entered and correctly
annotated. However, he accepted that he had no personal knowledge as to how extensive the
phage, plasmid or genomic data was on the NCBI database at the priority date, and did not
provide any specific examples where an incorrect, incomplete or untagged phage sequence
would have prevented PAM identification.
307 In oral evidence, Professor Giffard stated that errors, truncated sequences and
incomplete sequences in the NCBI database are rare. He viewed the likelihood that any
sequence would be completely incorrect to be “probably zero” and stated that where there is a
truncated or incomplete sequence, these still could include the information sought.
308 ToolGen rely on two ways to overcome the difficulties identified by Professor
Thomas and Associate Professor Herold. First, ToolGen submitted that neither Professor
Thomas nor Associate Professor Herold were able to provide any specific examples where an
unavailable phage sequence would have prevented PAM identification. Second, ToolGen
submitted that Professor Thomas readily accepted, to the extent that some genomic data was
not present in the database, its absence was readily addressed by authors of Fonfara (2013) by
searching for other isolates of the same species. Fonfara (2013) was published online in
November 2013 and is a post priority date paper. I accept that this could be done. But this
still assumes that the relevant phage sequence would be available to the investigator.
309 Associate Professor Herold also raised several other issues, including:
(a) The information in Jinek identifying the position and arrangement of individual
components of the CRISPR/Cas9 locus is not generally applicable to all CRISPR/Cas 9 loci
and varies between different bacterial species and strains.
(b) There is also a possibility that multiple CRISPR arrays exist in a single bacteria which
would create difficultly.
(c) There is the further possibility that the fragments of DNA that make up the spacer
may no longer be identical to the target site because of mutations.

310 I accept what appears in subparagraph (a) which is confirmed by the evidence more
generally. I also accept that the other difficulties identified by him may arise.
Designing and constructing the sgRNA

311 ToolGen submitted that once it is appreciated that the disclosure of the sgRNA in P1
is not limited to the specific form of sgRNA used in the experiments of P1, the skilled
addressee or team would use Jinek to design and construct the sgRNA. Accordingly,
ToolGen’s submission on constructing a sgRNA from a bacterial species other than S.
pyogenes relies on Jinek either being part of the disclosure of P1 by incorporation, or part of
the common general knowledge of a microbiologist and molecular biologist. As I have
previously found that Jinek does not form part of the disclosure of P1, and was not common
general knowledge of a microbiologist or molecular biologist at the priority date, the
following considerations are only relevant in circumstances where either of those conclusions
is wrong.
312 In JER 1, Associate Professors Firestein and Herold and Professor Thomas agreed
that the reference to Jinek in P1 “is a reference to the data in Jinek describing a technical
advance regarding the fusion of tracrRNA and CRISPR RNA to generate a single guide
(single chain chimeric) RNA.” Further, all three experts agreed that the tracrRNA and
crRNA could be fused together and tested in a CRISPR/Cas9 cleavage assay in vitro using
the principles detailed in Figure 5 of Jinek, which states that the chimeric RNA is generated
by fusing the 3’ end of the crRNA to the 5’ end of the tracrRNA.
313 In Jinek, the authors identified the essential portions of tracrRNA and crRNA of an S.
pyogenes sgRNA capable of guiding Cas9 mediated DNA cleavage. In oral evidence,
Professor Thomas agreed that while one would not simply supplant the minimal portions of
crRNA and tracrRNA for the S. pyogenes sgRNA shown in Jinek and apply this to a non-S.
pyogenes Cas9 system, the minimal portions of crRNA and tracrRNA for a non-S. pyogenes
sgRNA could be determined using a “classic experimental approach”. The “classic
experimental approach” was described as starting with the full length of the mature crRNA
and tracrRNA molecules and deleting regions of the molecules until one can determine what
is the minimal amount required for Cas9 mediated cleavage.
314 Professor Thomas also gave evidence that the experiments undertaken to identify the
minimal portions of crRNA and tracrRNA in Jinek adopt this same classic experimental
approach. Associate Professors Firestein and Herold agreed that this approach could be

employed to determine the minimal amount of crRNA and tracrRNA for any other Cas9
species.
315 Jinek also makes use of a radiolabeled assay and radioactive gel to test whether or not
certain truncated forms of both crRNA and tracrRNA and the Cas 9 will cleave double-
stranded DNA in vitro. The experts agreed that a cleavage test would be required to confirm
that the truncated portions were indeed the essential portions of crRNA and tracrRNA
required for Cas9 cleavage. When asked by Senior Counsel for ToolGen how difficult it
would be to perform this radiolabeled assay, Professor Thomas said that it would involve a
significant amount of work because of the nature of the assay and that it uses radioactively
labelled oligonucleotides as the type of DNA sequence. Associate Professor Herold stated
that it was not something standard that he would have done at the priority date and agreed
with Professor Thomas that it would require a significant amount of work which could take
up to three months or more. Associate Professor Firestein said that he did not have experience
with radiolabeled assays and so would use the standard cutting assay shown in Figure 1B of
P1. Associate Professor Herold agreed this approach could be taken but that he would be
cautious about adopting it because it is much less sensitive than the radiolabeled assay.
316 Associate Professor Herold gave evidence that to construct a sgRNA from the
endogenous crRNA and tracrRNA components of other Cas9 species of interest that had not
yet been described would be very difficult and would require a significant amount of work
from a specialised laboratory. The difficulties with identifying and characterising the mature
crRNA and tracrRNA molecules have already been discussed above in a preceding step.
317 Associate Professor Herold raised two further issues with starting with the full length
of the mature crRNA and tracrRNA molecules. First, he stated he would not have done this
because at the priority date a sgRNA using a full length tracrRNA had not been shown to
work. Second, he stated that he would have concerns about using a full length tracrRNA due
to the possibility of a more complex RNA structure causing an interferon response which
cause cell death in a eukaryotic cells. However, ToolGen do not simply propose using the
full length tracrRNA and crRNA molecules and stopping there. What it proposed is to
replicate the approach taken by the authors of Jinek and use the mature crRNA and tracrRNA
molecules as a starting point from which to cut down portions to identify the essential
portions of crRNA and tracrRNA needed for Cas9 mediated cleavage.

Analysis
318 Against that complex background it is now necessary to ask whether the invention of
claims 1 and 10 of the patent application are sufficiently enabled by the disclosure of P1. In
particular, did P1, as at the priority date, provide sufficient information to the notional skilled
addressee armed with the common general knowledge to perform the invention of the claim
without undue burden over the whole scope of each claim? In deciding this question it is of
course necessary to take account of my previous findings as to who is the notional skilled
person or skilled team. It is also necessary to have regard to the nature of the invention of the
claims, the field of technology, and the breadth of the relevant claims.
319 As to the nature of the invention, I do not think P1 discloses any principle of general
application. It does not represent that all, or substantially all, system components (including
a particular Cas9) derived from other bacterial species that have a Type II CRISPR/Cas
system can be used to cleave DNA in eukaryotic cells, and does not state or imply that there
is any reasonable scientific basis for concluding that most, or a substantial number of the
many different bacterial species with a Type II CRISPR/Cas system, would be suitable for
use in the compositions or the methods of the claims.
320 P1 shows that the inventors tested components derived from S. pyogenes only. There
is nothing said in P1 which would indicate that S. pyogenes was likely to be representative of
other bacterial species with a Type II CRISPR/Cas system or that the results of the
experimentation with S. pyogenes derived components provided any reasonable scientific
basis for inferring that Cas9 polypeptides derived from other bacterial species could also be
expected to cleave DNA in eukaryotic cells.
321 Those observations are relevant to enablement because, as will be apparent from what
I have previously said, P1 does not provide the skilled addressee with any encouragement,
whether by the elucidation of a general principle or a series of working examples, that a
system using Cas9 components derived from other bacterial species can reasonably be
expected to cleave DNA in eukaryotic cells.
322 If, as I have found, P1 is not directed to a skilled team including a microbiologist, it
follows that the claims are not sufficiently enabled. The molecular biologist is not told by P1
what other bacterial species have Type II CRISPR/Cas systems or how to determine the
endogenous crRNA and tracrRNA sequences for such a species. The papers relied on by
Professor Giffard when seeking to ascertain those sequences for S. thermophilus were not the

common general knowledge of the molecular biologist and the CRISPRFinder, although a
standard tool used by microbiologists, was not a standard tool used by molecular biologists.
Nor was Professor Giffard’s knowledge as to the proximity of the Cas1, Cas2, Cas9 and the
CRISPR array to each other in the bacterial genome as a means of identifying bacteria with a
Type II CRISPR/Cas system common general knowledge of molecular biologists. Further,
for the reasons previously stated, I do not accept that deficiencies in the common general
knowledge of molecular biologists could be filled by the use of literature searches that might
generate results that included Bhaya (2011), Makarova (2011) or Deltcheva (2011).
Accordingly, the following considerations are only relevant in circumstances where I am
wrong about whether a microbiologist is a skilled addressee for P1 and the skilled team has
the benefit of the skills and common general knowledge of a microbiologist such as Professor
Giffard.
323 In his written evidence, Associate Professor Firestein appears to have accepted that
not all CRISPR/Cas9 systems that work in vitro or in prokaryotic cells are necessarily able to
cleave target DNA in eukaryotic cells. In Firestein 2, Associate Professor Firestein stated at
para 129:
Furthermore, although AP Herold states that he is now aware that not all
CRISPR/Cas9 systems that work in vitro or in prokaryotic cells are “necessarily able
to target and cleave DNA in eukaryotic cells”, in my opinion, this statement
acknowledges that some systems that work in vitro also work in vivo. In this regard,
my approach does not assume that in vitro activity correlates with in vivo activity, but
rather tests and identifies systems that show activity in both contexts. Indeed, there
are a number of reports in the literature that demonstrate multiple CRISPR/Cas9
systems, derived from different bacterial species, which are able to target and cleave
genomic DNA in eukaryotic cells (as I discuss below in relation to Hou et al (N.
meningitidis), Ran 2015 (S. aureus), Muller et al (S. thermophilus), Kim 2017 (C.
jejuni) and Chatterjee et al (S. canis)).
324 It is clear from the context in which these observations were made that Associate
Professor Firestein was referring to Type II CRISPR/Cas9 systems. I note that each of the
articles to which he refers is concerned with a Type II CRISPR/Cas9 system derived from
different bacterial species.
325 In my opinion, it would have been apparent to the skilled team as at the priority date
that there was considerable uncertainty as to whether or not a CRISPR/Cas9 system derived
from any particular bacterial species other than S. pyogenes would work in eukaryotic cells.
The experts agreed that the ability of a CRISPR/Cas9 system to work in eukaryotic cells
cannot be assumed by activity shown in an in vitro DNA cleavage assay and that additional

work is required to test the CRISPR/Cas9 system in eukaryotic cells. They also agreed that
the in vitro DNA cleavage assay is a relatively straightforward first approach that they would
have undertaken to test a CRISPR/Cas9 system and, if it showed cleavage activity, would
lead them to test the system in a eukaryotic cell.
326 Both Professor Thomas and Associate Professor Herold said that they would cease
work on the candidate if it failed to show activity in vitro, although Associate Professor
Firestein said that he would not assume that a candidate that did not work in vitro would not
work in vivo. However, he did not refer to any examples in which a system that worked in
vivo would not work in vitro. I regard Associate Professor Herold’s and Professor Thomas’
approach as more representative of the thinking of the notional skilled team on this topic.
327 Associate Professor Herold and Professor Thomas were also of the view that
significant experimental work would need to be done to validate the use of the system in
eukaryotic cells. Professor Thomas gave evidence that this would require conducting in vivo
experiments at a wide range of different target sites and in a wide range of different cell lines.
Associate Professor Firestein said in JER 1 that those steps would be straightforward and that
the time taken to perform the work could depend on how much optimisation would be
required for any particular system. The evidence of all three witnesses was somewhat vague
as to how long such work would take but I am persuaded that it would involve a multi-step
process requiring a significant amount of work with each step in the process dependant on the
success of the previous step.
328 The skilled team would not know whether its work was likely to yield a product
capable of achieving double stranded breaks at target locations in eukaryotic cells until the
relevant candidate had been trialled and validated by in vitro and then in vivo experiments.
329 In relation to Associate Professor Firestein’s statements in JER 1 and his affidavit
evidence suggesting that experimental validation of a Type II CRISPR/Cas9 system derived
from other species would be straightforward, I refer to the following exchanges in the
concurrent evidence:
MR DIMITRIADIS: Would you agree, Professor Firestein, that your approaches that
you’ve discussed in your affidavit would involve a very significant amount of work –
a research project – firstly?
ASSOC PROF FIRESTEIN: It’s difficult for me to – to speculate on that. It may
involve a lot of work or it may be done quite quickly because, you know, if I bring up
the case of streptococcal canis again, this is a system that’s nearly 90 per cent

homologous to strep pyogenes. It works with the same – well, not the same but let’s
say the tracrRNA is exactly the same, the crRNA differs by only one nucleotide.
Using that type of system, it could be repurposed quite quickly. If I had to go through
hundreds of different CRISPR Cas9 systems, then, obviously that would be a
significant amount of work. But it may also be that I – I hit upon a system much
more quickly than that. And I think the important thing is that this is – that’s why his
approach and the same approach applies for every CRISPR Cas9 system that I’m
utilising.
MR DIMITRIADIS: Professor Firestein, you used the language “I can’t speculate”. I
suggest to you that that is because you have never engaged a process of this kind
seeking to identify a component of a CRISPR Cas9 system from another bacterial
species, correct?
ASSOC PROF FIRESTEIN: It is true that I have never sought to identify a CRISPR
Cas9 from another species. And I refer back to my comments on that, that I’ve not
found the NGG to be a practical limitation. The reason that I cannot speculate is,
based on my broader experience in research, that sometimes we set out a logical
approach to [sic] certain problem, we conduct experiments, sometimes those
experiments work quite quickly, sometimes they take longer. And I also would, in
that respect, disagree with Professor Herold’s assertion that a Nature paper
necessarily implies that there has been a lot of work involved.
330 Associate Professor Firestein therefore accepted that at least in some cases the amount
of work involved in using a system derived from another bacterial species would be
significant, but that in other cases the work could be done quite quickly. He cites as an
example a system derived from S. canis that he suggested could be developed quite quickly,
because it is nearly 90% homologous to S. pyogenes. His evidence was, in effect, that if he
“hit upon” a system like that, it could be developed very quickly. There are several points to
make about this evidence.
331 The evidence suggests that the system derived from S. canis was first characterised in
a paper authored by Chatterjee et al published in 2018 (“Chatterjee 2018”) which described a
Cas9 protein derived from S. canis and the PAM sequences it recognised. I will say more
about this paper shortly, but it constitutes post priority date information that would not have
been available to the skilled team. In particular, Associate Professor Firestein’s reference to
the S. canis system being nearly 90% homologous to the S. pyogenes system seems to be
derived from Chatterjee (2018) which reported S. canis Cas9 as having 89.2% sequence
similarity to S. pyogenes Cas9. The sequence appears not to have been characterised or
functionally validated until Chatterjee et al undertook that work.
332 However, I accept that some support for Associate Professor Firestein’s reasoning is
found in Jinek. This paper showed that of four S. pyogenes orthologs investigated in vitro,

two Cas9 derived from L. innocua and S. thermophilus which are bacterial species that are
homologous to S. pyogenes (54% and 58% homology respectively) could be complexed with
the same S. pyogenes sgRNA to cleave DNA in prokaryotic cells. This was not so in the case
of two Cas9 derived from C. jejuni and N. meningitidis which are bacterial species that have
lower homology to S. pyogenes Cas 9 (16% homology for both). I also note that Associate
Professor Herold and Professor Thomas agreed that homology between S. canis and
S. pyogenes Cas9 and their crRNA and tracrRNA are nearly identical and that it is therefore
very likely that the Cas9 and sgRNA components of these systems could be interchanged to
mediate CRISPR/Cas9 cutting. Therefore, whilst I do accept the proposition that it may be
easier to develop a functional system in bacterial species that are highly homologous to S.
pyogenes, including because the same S. pyogenes sgRNA or a very similar sgRNA can be
used, I think it must also follow that there is likely to be a very substantial proportion of Cas9
derived from other bacterial species that are not sufficiently homologous to S. pyogenes Cas9
to enable use of the same sgRNA or a very similar sgRNA to cleave DNA in eukaryotic cells.
333 Importantly, claims 1 and 10 are not confined to Streptococcus Cas9 polypeptides and
extend to any bacterial species with a Type II CRISPR/Cas system whether or not within the
Streptococcus genus and whether or not the Cas9 protein for that species is highly
homologous to Cas9 derived from S. pyogenes. The disclosure required of P1 is that it be
such as would enable the skilled team armed with the common general knowledge to make
all, or substantially, all, embodiments within the scope of the claims without undue burden.
Associate Professor Firestein’s evidence concerning the ease with which the sgRNA used in
Jinek could be re-purposed to Cas9 from other species would not hold true across the scope
of the claims.
334 The respondents relied on the paper by Ran et al published in Nature in 2015 by a
group of researchers associated with the Broad Institute which appears to be a collaboration
involving MIT and Harvard. In their closing submission, ToolGen objected to the
respondent’s reliance on Ran (2015) and submitted that it and other post priority date papers
should be given no weight on the issue of undue burden for the following reasons:
(a) no persons who did that work were called to give evidence;
(b) the articles are notable for their lack of reporting any difficulty at all, or any difficulty
which was not easily overcome;

(c) the reviewers of the article were not called to give evidence to say precisely what
aspect of the work they regarded as qualifying it for publication;
(d) the articles often involved many different tasks and experiments, and it is impossible
to ascertain how much work was involved in any individual task relevant to the specific
questions of enablement in this case;
(e) it is impossible to separate the work which may have gone into writing up and
reporting upon the experiment in a form suitable for publication in a journal from the actual
scientific work involved;
(f) the articles were not contemporaneous records of the amount of work done, but rather
were highly polished accounts of work done, specifically drafted for the purpose of
impressing reviewers and achieving publication; and
(g) the respondents have adduced no evidence that any of the work the subject of those
papers was inventive or non-routine, and mere publication does not prove it to be so.
335 Each of the articles to which ToolGen’s submission was directed was admitted into
evidence without objection or limitation as to the use which might be made of it. That said,
in deciding what weight to give Ran (2015) and other post priority date papers I have had
regard to ToolGen’s submission. However, I have also had regard to the fact that at least
some of these papers were relied on by Associate Professor Firestein as demonstrating that
multiple CRISPR/Cas9 systems derived from different bacterial species are able to target and
cleave genomic DNA in eukaryotic cells. He accepted, speaking in the context of Ran
(2015), that a paper published in Nature would be one that the publisher and reviewers
considered to be a fairly substantial piece of original research or, in his words, “substantial in
its concept and advancement of the field”. He did not accept that you could draw any
inference as to the amount of time the research work took. I agree with that, but I also accept
Professor Thomas’ evidence who, also speaking of Ran (2015), said that it must have
reflected a very large amount of work.
336 Both Associate Professor Herold and Associate Professor Firestein referred to
Chatterjee (2018) which was submitted in May 2018 and published in October 2018 in
Science Advances as a research article. Chatterjee (2018) states that while numerous Cas9
homologs have been sequenced, only a handful of Streptococcus orthologs have been
characterised or functionally validated. The authors describe how they characterised an
orthologous Cas9 protein from S. canis which, as mentioned earlier, had a sequence

homology of 89.2% similarity to that of S. pyogenes Cas9. They explain in some detail how
they determined the PAM sequences recognised by S. canis Cas9 first in vitro and then in
vivo in human cells.
337 Another paper by Kim (2017) submitted in October 2016 and published in February
2017 in Nature Communications (whose authors included Jin-Soo Kim and other researchers
that are named inventors of P1 and the patent application) noted that several CRISPR/Cas9
orthologs had been used for genome editing. Kim (2017) describes a new Cas9 ortholog
derived from C. jejuni an advantage of which is said to be its smaller size. The paper
describes the steps taken by the authors to determine the PAM sequence for this Cas9
ortholog and to optimise the length of the sgRNA before delivering the system via an adeno-
associated virus (AAV) to mammalian cells for in vivo genome editing.
338 With reference to Ran (2015), the respondents submitted:
179. The nature and standard of work required to develop another Type II
CRISPR/Cas9 system for use in gene editing in eukaryotic cells are well
illustrated by reference to the Ran paper. This was a publication in Nature, a
prestigious journal, where the authors studied six CRISPR/Cas9 systems
which showed cleavage in vitro but only identified two species which
showed cleavage in vivo (including S. Aureus).
…
180. Ran was by members of the Broad Institute, which was not a typical
academic laboratory, because of its breadth of expertise. The paper represents
an enormous body of work, and is a combination of many peoples’ efforts. Its
publication in Nature reflects the cutting edge nature of the research
involved. It was an original piece of research that is substantial in its concept
and advancement of the field.
339 The research work the subject of Ran (2015) involved more than finding and
validating another bacterial species that could be used in place of S. pyogenes. It appears that
the researchers specifically focused on Cas9 derived from other bacterial species with a lower
molecular weight than S. pyogenes Cas9 because these were thought to be better suited for
delivery using AAV vectors. However, in my opinion, Ran (2015) does provide some insight
into the work involved in identifying S. aureus derived Cas9, the crRNA and tracrRNA
associated with it and, in particular, whether the work involved would constitute an undue
burden.
340 Ran (2015) describes the steps taken by the researchers to determine the endogenous
crRNA and tracrRNA sequences for Cas9 derived from the six species that were investigated,

the PAM sequences for each of them (using a plasmid library) and the ability of each Cas9
paired with a single guide RNA to cleave target sites first, in vitro, and then in vivo in
mammalian cells. This ultimately led the researchers to identify S. aureus Cas9 as one which
produced “indels” (ie. insertions or deletions) with efficiencies comparable to S. pyogenes
Cas9.
341 The authors of Ran (2015) state at page 186:
In search of smaller Cas9 enzymes for efficient in vivo delivery by AAV, we have
previously described a short Cas9 from the CRISPRI locus of Streptococcus
thermophiles LMD-9 (St1 Cas9, ~3.3 kb) as well as a rationally-designed truncated
form of SpCas9 (ref. 18) for genome editing in human cells. However, both systems
have important practical drawbacks: the former requires a complex protospacer-
associated motif (PAM) sequence (NNAGAAW), which restricts the range of
accessible targets, whereas the latter exhibits reduced activity. Given the substantial
diversity of CRISPR-Cas systems present in sequenced microbial genomes, we
therefore sought to interrogate and discover additional Cas9 enzymes that are small,
efficient and broadly targeting.
(footnotes omitted)
In support of that statement the authors referenced Chylinski (2014) (co-authors including
Makarova and Charpentier) published in 2014 and by Chylinski (2013) (co-authors including
Charpentier) published in 2013 (both post priority date).
342 The authors of Ran (2015) then referred to their analysis of over 600 Cas9 orthologs
with protein sizes approximately 1,350 and 1,000 amino acid residues in length. From the
600 Cas9 orthologs, the authors selected six candidates for profiling which involved
ascertaining the crRNA and the tracrRNA for each Cas9, and designing a single guide RNA
(sgRNA) for each of the six orthologs. The authors then identified the PAM sequence for
each Cas9 by constructing a library of plasma DNA and performing an in vitro cleavage
assay. The authors reported that the Cas9 orthologs, in combination with the sgRNA,
successfully cleaved their targets in vitro. They then proceeded to investigate whether they
would do the same in mammalian cells, after noting that “DNA cleavage activity in cell-free
assays does not necessarily predict activity in mammalian cells”. Of the six orthologs tested,
only S. aureus produced indels with efficiencies comparable to those of S. pyogenes. The
authors’ investigation thereafter focused on S. aureus. It is apparent that by that stage of their
work, they had successfully cleaved DNA in mammalian cells using components derived
from S. aureus which they then sought to optimise in various ways.

343 I think Ran (2015) is useful in so far as it describes the work that its authors
undertook in order to identify other Cas9 orthologs which could be used to cleave DNA in in
vitro assays, and the work its authors took to confirm that S. aureus Cas9 could be used to
cleave DNA in vivo in human cells. Ran (2015) and the various other post priority date
papers also tend to show that for some years after the priority date there were various
research groups attempting to identify, characterise and validate Cas9 orthologs derived from
bacterial species other than S. pyogenes with the aim of identifying CRISPR/Cas9 systems
that were better suited for use in AAV vectors, that were able to target a wider variety of
PAM sites, and that also had reduced “off-target” effects (ie. the introduction of unintended
breaks).
344 In another paper Wang (2013) received by the publisher in March 2013 and published
in Cell in May 2013, the authors state:
There are several potential limitations of the CRISPR/Cas technology. First, the
requirement for a NGG PAM sequence of S. pyogenes Cas9 limits the target space in
the mouse genome. It has been shown that the Streptococcus thermophilus LMD-9
Cas9 using different PAM sequence can also induce targeted DNA cleavage in
mammalian cells (Cong et al., 2013). Therefore, exploiting different Cas9 proteins
may enable [sic] to target most of the mouse genome. Second, although the sgRNAs
used here showed high targeting efficiency, much work is needed to elucidate the
rules for designing sgRNAs with consistent high targeting efficiency, which is
essential for multiplexed genome engineering. Third, although our off-target analysis
for the seven most likely off targets of Tet1 and Tet2 sgRNAs failed to detect
mutations in these loci, it is possible that other mutations were induced following as
yet unidentified rules. A more thorough sequencing analysis for a large number of
sgRNAs will provide more information about the potential off-target cleavage of the
CRISPR/Cas system and lead to a better prediction of potential off-target sites.
345 The paper which was published not long after the priority date was by a research
group associated with the Broad Institute. Associate Professor Firestein described the Broad
Institute as “a very well-oiled machine … not like a typical academic lab”. He was referring
to the breadth of its expertise and the speed with which its research groups could generate
data. The paper is consistent with what is in my view the effect of the evidence more
generally that the development of new CRISPR/Cas9 systems for use in genome editing
using bacterial species that recognised PAM sequences different from those recognised by S.
pyogenes and S. thermophilus, would require considerable work in relation to the design of
the sgRNA with high targeting efficiency and investigation of the different systems’ off-
target effects. I do not consider that the work involved in identifying and characterising
systems derived from different bacterial species was likely to have been straightforward or

routine. It appears to have been innovative and advanced research work undertaken by
highly specialised groups of researchers which included leaders in the field. None of the
experts who gave evidence had any experience either individually or as part of a team as at
the priority date investigating the use of different CRISPR/Cas9 systems in genome editing
or, in particular, the selection or characterisation of bacterial species that might be suitable for
that purpose. Of course, that is hardly surprising given the state of the art as at the priority
date.
346 On the question of undue burden, ToolGen placed considerable reliance on the Full
Court’s decision in Warner-Lambert Co LLC v Apotex Pty Ltd (No. 2) (2018) 129 IPR 205
(“Warner-Lambert FC”), the decision at first instance in the same case in Warner-Lambert,
and also the decision of Heerey J in Eli Lilly & Co v Pfizer Overseas Pharmaceuticals (2005)
64 IPR 506 (“Eli Lilly”). Both cases were concerned with methods of treatment using known
pharmaceutical compounds, and both were concerned with the application of s 40 of the Act
prior to the its amendment by the RTB Act. It was also common ground in both cases that
the patent specification in suit contained the information necessary to enable the skilled
addressee to prepare some compositions within the claims. In Eli Lilly Heerey J said at
[193]:
It would be necessary to test for oral bioavailabilty, toxicity and effectiveness, but the
evidence shows that while these steps call for skill, they are essentially routine for
those skilled in this area. The term routine here (and in other contexts in this case) is
not used as a synonym for simple and easy. In the present case the hypothetical
skilled workers at the hypothetical workbench are persons holding academic
qualifications at the Ph D [sic] level together with practical experience. It would not
be necessary to employ such persons unless the task they had to perform was a
difficult one. Yet this does not of itself mean that the patent could not be worked
without further invention.
His Honour’s decision on this issue was upheld on appeal: Pfizer Overseas Pharmaceuticals
v Eli Lilly & Co (2005) 225 ALR 416 (“Pfizer”) at [342] per French and Lindgren JJ.
347 Pfizer was applied at first instance in Warner-Lambert FC at [262]-[263] which

concerned a patent involving a method of treating pain using pregabalin. Dismissing the
appeal, the Full Court in Warner-Lambert FC said at [129]:
In this connection, we accept that the appellants raise a valid point of distinction
which is relevant to the respondent’s criticism that the specification does not contain,
for example, specific dosages or a safety and toxicity profile in respect of the use of
the compounds for the treatment of pain in human subjects, and that a clinician
would not use the compounds for this purpose without this information. Whilst the

primary judge appears to have accepted that, from the clinician’s perspective, this
information would be necessary — with the consequence that further work would
need to be carried out in this regard before the compound would be put to use in
clinical practice — his Honour was not satisfied that this meant that the requirements
of s 40(2)(a) of the Act had not been met. This was because, in the circumstances of
the present case, the work required to put the invention into practice was of a routine
(that is, non-inventive) nature for the person skilled in the art (now accepted on
appeal), even though the work to be undertaken would require considerable skill,
effort and resources or be complex, time-consuming and expensive.
348 However, it is clear that even if the work required of the skilled addressee is non-
inventive and routine, it may still amount to undue burden. The skilled addressee is not
expected to engage in an unreasonable amount of experimentation, research or study. If the
work required involves “… prolonged study of matters presenting initial difficulty” the claim
will not be properly enabled: see Gilead at [438] per Jagot J, upheld on appeal Idenix
Pharmaceuticals LLC v Gilead Sciences Pty Ltd (2017) 134 IPR 1 at [144] (considering
s 40(2)(a) of the Act before amendment by the RTB Act); see also Mentor Corp. v Hollister
Inc [1993] RPC 7 at 13 per Lloyd LJ citing with approval the judgment of Buckley LJ in
Valensi v British Radio Corporation [1973] RPC 337 at 377.
349 The routine work referred to in both Eli Lilly and Warner-Lambert FC included work
necessary to support an application for regulatory approval. In Merck & Co Inc v Arrow
Pharmaceuticals Ltd (2006) 154 FCR 31 at [108] the Full Court observed (although not in
the context of sufficiency) that “… it is a matter of notoriety that prolonged testing for the
purpose of regulatory approval must occur between the stage of patent application and
commercial marketing”. The same point was made by Jacob LJ who, when considering the
concept of enabling disclosure, said of genetic engineering and pharmaceutical inventions,
“[t]he work that goes into bringing them to market relates to testing efficacy and safety – not
in actually making the invented product”: Halliburton Energy Services Inc v Smith
International (North Sea) Ltd [2006] EWCA Civ 1715 at [18]. His Lordship also observed
that the test of “undue effort” and the words of the relevant statutory provision (“clearly
enough and completely enough”) emphasise that the question is one of degree. As to how
one is to say when the work involved is too much, his Lordship said at [21]:
The answer is that the line is one to be drawn by an exercise of judgment, taking into
account all of the relevant factors, one of which is of course the nature of the
invention itself and its field of technology. But there are other factors too – for
instance, the width of the patent claim or whether it has functional limitations which
require too much work to explore.

350 Besides the width of the claim and any relevant functional limitations, it is also
necessary to consider what information has been provided by P1. It is all very well for
ToolGen to say that the necessary information forms part of the common general knowledge,
but that does not mean that the deployment of the common general knowledge to solve a
problem raised in P1 (how to avoid the 5’-NGG-3’ PAM limitation) is routine work that does
not amount to an undue burden. P1 provides no direction at all as to what options for
approaching and solving the problem exist, how they should be prioritised or whether any of
them can be expected to work.
351 The work that the notional skilled team would need to undertake at the priority date to
perform the invention of claims 1 and 10 using a bacterial species other than S. pyogenes
would in my opinion involve a significant research project that would not be straightforward
or routine. My reasons are as follows.
352 First, to the extent that P1 might be understood as inviting the skilled addressee to
attempt to perform the invention using Cas9 derived from another species, it offers no
relevant encouragement or direction. Nor, as I have previously explained, does P1 disclose
any principle of general application.
353 Second, the microbiologist would need to identify one or more suitable candidates.
P1 provides no guidance on that topic. If the microbiologist were to rely on the Makarova
(2011), the list of potential candidates would number around 120. If the microbiologist used
Genebank for this purpose, the list of potential candidates would exceed 1,500. The fact that
Professor Giffard chose S. thermophilus (which had been singled out for use in genome
editing by Cong et al in early 2013) out of the 1,513 search results generated, seems to have
involved a remarkable stroke of luck assuming his selection was not influenced by post
priority date developments. Moreover, as previously noted, the S. thermophilus system did
not relieve the 3’-NGG-5’ PAM sequence limitation.
354 Third, assuming the microbiologist identified another candidate (eg. Professor
Giffard’s S. thermophilus) and determined its endogenous crRNA and tracrRNA sequences, it
would be necessary to identify and characterise the mature crRNA and tracrRNA. P1 does
not provide any guidance on to how that is to be done. I accept that this task may be within
the skill of the microbiologist with expertise in CRISPR/Cas systems, but I do not consider
that this would be routine work. There was no evidence to suggest that Professor Giffard had
himself performed this task before the priority date.

355 Fourth, the RNA-seq data for most bacterial strains of interest was unlikely to be
publicly available at the priority date. At that time, there were only around seven species of
bacteria for which Type II repeat spacer expression data had been made available.
356 Fifth, while there were alternative methods of identifying and characterising the
relevant sequences (eg. RNA-seq experiment, northern hybridisation/northern blot or RNase
protection experiments) that could have been adopted by the skilled team, these depended on
obtaining a bacterial isolate for the bacterial species of interest. None of the experts
suggested that bacterial isolates for every known species of interest, or even a substantial
proportion of them, were publically available at the priority date.
357 Sixth, the use of next generation sequencing needed to perform a RNA-seq
experiment and to analyse the cut plasmids generated from the cleavage assays for PAM
identification was not something that was routine at the priority date. This was a task that
would need to be outsourced to a specialist laboratory.
358 Seventh, the requirement to identify the crRNA and tracrRNA molecules as the first
step of a northern hybridisation (northern blot) experiment could be difficult for the reasons
explained by Professor Thomas. In particular, it may be difficult to predict with certainty the
mature crRNA from the spacer sequences of the CRISPR array because of the processing of
pre-crRNA into mature crRNA. It may also be difficult to identify the tracrRNA because it
would not be clear what part of the repeat sequence of the CRISPR array would be
complementary to the tracrRNA.
359 Eighth, the compilation of a PAM variant library to identify and validate the PAM site
was not routine work as at the priority date. None of the molecular biologists had used a
PAM variant library at the priority date. Further, if using the in vivo approach proposed by
Associate Professor Firestein, cellular repair mechanisms in eukaryotic cells may mutate the
cut which would inhibit detection of the PAM. I accept Associate Professor Herold’s
evidence that using a barcode approach to overcome this issue would create considerable
additional work which would need to be outsourced to a specialist laboratory.
360 Ninth, the alternative method of using an in silico approach for PAM site
identification relied on identifying the protospacer of the phage where a particular spacer
originated. This method depends on the DNA sequence for the phage being publicly
available. Professor Thomas and Associate Professor Herold questioned whether that DNA

sequences for all potential phages of interest were publically available at the priority date.
Both accepted that, as at the priority date, this would be a matter for the microbiologist to
investigate. Professor Giffard did not give evidence on the availability of phage sequences at
the priority date. In the absence of evidence to the contrary, it cannot be assumed that the
DNA sequence for any particular candidate would have been available. Nor would this
method of identifying the PAM site be regarded as routine or straightforward.
361 Tenth, for any Cas9 derived from bacterial species that are not highly homologous to
S. pyogenes, the S. pyogenes sgRNA could not be used, in which case Associate Professor
Firestein’s third approach of using the endogenous tracrRNA and crRNA to create a sgRNA
would need to be adopted. Even if it was possible to use the S. pyogenes sgRNA in another
system using Cas9 derived from a different bacterial species, this would not be possible for
any Cas9 that was not highly homologous.
362 In my opinion the skilled team would be required to carry out prolonged research and
experimentation and would most likely encounter significant difficulties along the way.
Much of the work would be non-routine and would be carried out in circumstances where P1
provided no meaningful guidance or direction and no assurance of success.
363 I am persuaded that as at the priority date, P1 did not enable a skilled team including a
molecular biologist specialising in genome editing in eukaryotic cells and a microbiologist
with expertise in CRISPR/Cas systems in prokaryotes, to make the compositions of claim 1,
or perform the methods of claim 10, using a bacterial species other than S. pyogenes, without
undue burden.
Engineering S. pyogenes Cas9 to recognise a non-NGG PAM sequence

364 The respondents contended that it would not have been possible for the skilled
addressee to engineer Cas9 derived from S. pyogenes, so that it recognised a non-5’-NGG-3’
PAM based on the information in P1 and the common general knowledge at the priority date.
Professor Thomas gave evidence, which was not challenged by ToolGen, that the crystal
structure of the S. pyogenes Cas9-sgRNA complex with a target DNA and the amino acid
residues of S. pyogenes Cas9 involved in PAM recognition were not known in October 2012.
He said that, without that structure and the knowledge of what amino acid residues are
involved in PAM recognition, it would not be possible for him to engineer those parts of the
complex involved in PAM recognition. Associate Professor Herold’s evidence was to a

similar effect. He gave evidence, which I accept, that P1 (whether read with or without
Jinek) does not provide any guidance as to how to engineer S. pyogenes Cas 9.
365 According to Professor Thomas’ evidence in Thomas 2:
[I]n October 2012 I did not know the crystal structure of the S. pyogenes Cas9-
sgRNA complex with a target DNA, and I now know that the crystal structure was
not solved and published until 2014. For this reason, I consider that engineering S.
pyogenes Cas9 in a manner suggested by P1 in October 2012 would require a
considerable amount of complex work by a team of biologists (including a structural
biologist). Because the structure of the S. pyogenes Cas9-sgRNA complex with a
target DNA was not available in October 2012, the amino acid residues of S.
pyogenes Cas9 involved in PAM recognition were not known. Without the structure
of the S. pyogenes Cas9-sgRNA complex with a target DNA, it would not be possible
to rationally engineer the domain(s) of the Cas9 complex involved in PAM
recognition. This would mean that engineering Cas9 by making changes to the S.
pyogenes Cas9 amino acid sequence, and then testing the resulting mutants for
activity, would involve an immense amount of work, and some luck, including
because any changes made could impact the interactions between the Cas9 and the
sgRNA (which were also not understood until the structure of the Cas9-sgRNA
complex was solved). Alternatively this work would involve first solving the
structure of the complex, which requires specialised expertise that is not in the
domain of standard molecular biology laboratories.
In light of Professor Thomas’ evidence, which I accept, I find that engineering a S. pyogenes
Cas9 to recognise a non-NGG PAM sequence in October 2012 would have involved a
significant research effort outside the skill set of the notional skilled addressee. The
possibility that there may have been specialist laboratories that may have been engaged to
resolve the problem identified by Professor Thomas merely reinforces that conclusion.
Chimeric guide RNA other than sgRNA (+48)

366 Figure 1A in P1 discloses a chimeric guide RNA comprising a crRNA portion fused
to a tracrRNA portion which was referred to in the evidence as the “sgRNA (+48)”. This is
due to the fact that the sgRNA is truncated at the +48 position of the native S. pyogenes
tracrRNA. This truncated form of the tracrRNA, retaining only nucleotides 23 to 48 of the
native sequence, is disclosed in Jinek. In JER 1, the experts agreed that P1 does not expressly
disclose any chimeric guide RNA other than that depicted in Figure 1A with the truncated
tracrRNA.
367 While P1 refers to Jinek, it does so, as I have previously mentioned, by providing
background to the genome editing system disclosed in P1 and, in particular, the single-chain
chimeric guide RNA. P1 does not provide any information as to how the inventors went
about designing the sgRNA (+48) and, in particular, does not provide any guidance or

directions enabling the skilled addressee to alter the length of the sgRNA depicted in
Figure 1A.
368 In its written submissions, ToolGen relied on oral evidence of Associate Professor
Herold and Professor Thomas which was said to support the proposition that the statement in
P1 regarding Jinek should not be understood as limiting itself to any particular length of
crRNA or tracrRNA that might be used in the single guide as long as the length included the
essential portions. The essential portions will comprise the least number of nucleotides of the
native tracrRNA sequence necessary for Cas9 mediated cleavage in a eukaryotic cell. P1 does
not include any statement to that effect and none can be implied. There is no disclosure in P1
of tracrRNAs of variable length.
369 Further, I did not understand ToolGen to contend that the use of a different sgRNA
having a tracrRNA of some different length to that shown in P1 would not involve undue
burden if, as I have found, Jinek is neither incorporated by reference, nor common general
knowledge. I am satisfied that it would be an undue burden for the skilled addressee (or
skilled team if one includes the microbiologist) to redesign the sgRNA without the benefit of
the information in Jinek.
370 If I am wrong about my findings in relation to Jinek as not being incorporated into P1
and not being common general knowledge of the skilled addressee (or skilled team if one
includes the microbiologist), then I find based on the evidence of Professor Thomas and
Associate Professor Herold, which I accept, that developing a longer guide RNA than sgRNA
(+48) would involve a significant amount of non-standard work and would involve undue
burden even with the assistance of Jinek. The evidence relating to this issue was previously
considered in the context of the design and construction of a sgRNA using a bacterial species
other than S. pyogenes. Professor Thomas and Associate Professor Herold both agreed that
the experimental approach taken by the authors of Jinek, which made use of radiolabeled
assays and radioactive gels to test whether or not certain truncated forms of both crRNA and
tracrRNA and the Cas 9 cleave double-stranded DNA in vitro, would not have been standard
techniques at the priority date and would involve a significant amount of work which could
take months. Associate Professor Firestein accepted that he did not have experience with
radiolabeled assays at the priority date.

Nuclear localisation sequences (NLSs) and their location
371 A nuclear localisation sequence, or nuclear localisation signal, is a protein (amino-
acid sequence) tag that, when added to a protein, “tags” the protein for import into the
eukaryotic cell nucleus, across the nuclear membrane, by the cell’s endogenous nuclear
transport system. In this case, the NLS will facilitate the entry of the Cas9 protein from the
cytoplasm where it is translated into the nucleus of the cell where DNA cleavage occurs.
372 The experts agreed that P1 expressly discloses a particular NLS with the nuclear
localisation sequence “PKKKRKV” located at the C-terminus of the Cas9 protein. They also
agreed that no other NLS is expressly disclosed. It is common ground that the PKKKRKV
NLS was widely used and studied before the priority date, but that there were other NLSs
known and used in the art as well. Associate Professor Firestein’s evidence was that he
views the sequence and location of the NLS used in P1 as a design choice, and that P1 more
broadly discloses the use of any suitable NLS to drive nuclear localisation of the Cas9
protein.
373 ToolGen submitted that P1 implicitly discloses the use of any NLS capable of
mediating the entry of the Cas9 protein into the nucleus and is not limited to the PKKKRKV
NLS expressly disclosed. The respondents submitted that the choice and position of an NLS
can adversely affect the location and function of the protein and is therefore an important
matter. They submitted that P1 makes no disclosure of any NLS apart from the PKKKRKV
NLS located at the C-terminus.
374 Associate Professor Firestein gave evidence that there are really only 2 positions (the
N-terminus and the C-terminus) where the NLS could be located and the testing of those
possibilities would be quite straightforward. Associate Professor Herold agreed. Associate
Professor Firestein accepted that the position of the NLS could adversely affect localisation
and functioning of the protein. In cross-examination he was taken to a post priority date
paper concerning the use of Cas9 derived from N. meningitis in genome engineering by Hou
et al (2013). He accepted that in the case of N. meningitis Cas9, the paper showed that the
protein would not localise in the nucleus with the NLS at either the N-terminus or the C-
terminus and that it was necessary for an NLS to be attached to both the C-terminus and the
N-terminus if it was to do so. He said that there were other publications that showed that this
particular protein can work with a single NLS, but he did not identify the publications or the
particular NLS used.

375 I accept Associate Professor Firestein’s characterisation of this aspect of the
disclosure. In my view, his interpretation of P1 is analogous to the description of an
embodiment of a mechanical device in which a screw is used to fasten two components. To
the person skilled in the art this could be fairly understood as a disclosure not only of a screw,
but of other forms of suitable fasteners such as a bolt or rivet. I do not think the disclosure of
P1 is limited to the PKKKRKV NLS (whether by sequence or location) to what is shown in
Figure 1A of P1.
376 I am not persuaded that the skilled addressee would not be able to use another NLS
with a different sequence at the same or a different location without undue burden. The
evidentiary references provided by the respondents in support of the contrary proposition do
not advance its case except perhaps for Associate Professor Herold’s evidence that it could
take a month or two to get a different NLS to work. However, Associate Professor Herold
and Professor Thomas agreed that this is the type of problem that arises in the work of a
molecular biologist and it is dealt with using known techniques. In my opinion, the work
associated with the use of a different NLS, positioned at either the C-terminus or N-terminus
or at both, would be routine and straightforward and not such as would create undue burden.
Single guide RNA fusion other than with a GAAA linker

377 The crRNA and tracrRNA in the chimeric guide RNA in P1 are fused together with a
GAAA linker that forms a hairpin loop as shown in Figure 1A of P1. The experts agreed that
P1 does not expressly disclose any linker besides the GAAA linker. However, they also
agreed that the GAAA linker is a tool used to connect two RNA molecules and that there is
nothing in P1 that excludes the possibility of using another linker. Associate Professor
Firestein and Professor Thomas both gave evidence that the nucleotide sequence could be
changed but that the length of the nucleotides (i.e. four nucleotides) would need to remain the
same. Associate Professor Firestein was of the opinion that P1 more broadly discloses the use
of a linker to fuse the crRNA and the tracrRNA sequence in a hairpin loop configuration. I
accept Associate Professor Firestein’s characterisation of the relevant disclosure. I think the
analogy I previously drew in relation to the disclosure of the NLSis equally applicable here.
378 In my opinion, P1 impliedly discloses to the skilled addressee the use of a suitable
linker. The respondents accepted, and I find, that as at the priority date, the skilled addressee
would be able to employ a different linker without undue burden.

Use of “paired Cas9 nickases” and Cas9 endonucleases that create staggered-ended
double-stranded DNA breaks
379 Given my earlier finding that claims 1 and 10 and their dependent claims do not
extend to the use of paired Cas9 nickases, I do not need to consider whether P1 discloses or
enables their use. But I should note that ToolGen accepted that P1 does not disclose a system
that utilises paired Cas9 nickases.
380 I did find that claims 1 and 10 and their dependent claims include Cas9 endonucleases
that create staggered-end double-stranded DNA breaks. The evidence shows that Cas9
derived from Francisella novicida (“FnCas9”), which is used in a CRISPR/Cas9 system
described by Chen (2017), creates staggered-end double-stranded DNA breaks. In that
system, FnCas9 is complexed with a sgRNA to mediate DNA cutting in eukaryotic cells.
Chen (2017) reported that FnCas9 cleaves the target DNA to create four nucleotide long
overhands at the 5’ end of each strand. Claims 1 and 10 would cover such a system where it
was deployed in vivo using DNA molecules encoding the FnCas9 and the sgRNA.
381 The respondents submitted that P1 does not disclose the use of the FnCas9 system (or
any system like it) which produces staggered (or sticky) ended breaks. The three experts
accepted that the statement at page 5 of P1 that “RGENs yield blunt ends rather than cohesive
ends” meant that the CRISPR/Cas9 system disclosed in P1 produces blunt-ended double-
stranded DNA breaks and not staggered-ended double-stranded breaks such as those
produced by the FnCas9 based system. I accept that P1 does not disclose a system that
produces staggered-ended breaks. The respondents submit that a FnCas9 based system,
although within the claims, is not disclosed or enabled by P1.
382 The difficulty I have in relation to the respondents’ submission based on FnCas9 is
that the point now taken was not identified in the agreed statement of issues. Although there
is discussion in JER 1 concerning Chen (2017), it is directed to a different point (see
Question 25). Moreover, the system identified by Chen (2017) is not from the Streptococcus
genus and does not provide a basis for finding that a claim based on a Streptococcus Cas9
polypeptide or a S. pyogenes Cas9 polypeptide, would not be enabled or supported by P1.
For those reasons I think the respondents should be held to the agreed issues which precludes
their reliance on their submissions based on FnCas9 and Chen (2017).

PATENT APPLICATION – DISCLOSURE AND ENABLEMENT
383 The internal disclosure requirement is found in s 40(2)(a) of the Act which states that
“a complete specification must disclose the invention in a manner which is clear enough and
complete enough for the invention to be performed by a person skilled in the relevant art”. I
have previously referred to the Explanatory Memorandum to the RTB Act which states that
the new s 40(2)(a) is intended to align the disclosure requirement with that applicable in other
jurisdictions which require that the patent application enable the invention to be performed
across the scope of the claim: cf. Kimberly-Clark at [25]. I refer to my earlier consideration
of the post RTB Act disclosure requirement.
384 There are six points to note in relation to internal disclosure.
385 First, although ToolGen contended that Jinek was incorporated by reference into the
patent application, I am satisfied that it is not. As with P1, there is no indication that the
authors of the patent application intended that any additional information contained in Jinek
beyond what is expressly disclosed should be treated by the reader as incorporated in the
patent application whether by reference or otherwise. The information from Jinek referred to
in the patent application is no greater (and in fact slightly less) than in P1.
386 Second, the respondents accepted that the patent application, unlike P1, discloses an
invention that comprises “a nucleic acid encoding a guide RNA”. They do not contend that
the invention of the claims is, in this particular respect, not sufficiently enabled.
387 Third, the patent application differs from P1 in that it discloses the existence of a
nucleic acid encoding a Cas9 polypeptide derived from S. pyogenes which in Example 9 is
shown to recognise and bind to a 5’-NAG-3’ PAM sequence. It is important to note,
however, that Example 9 used Cas9 derived from S. pyogenes. There is no Example in which
CRISPR/Cas9 components from other bacterial species are used. The respondents submitted
that the patent application does not disclose the invention in each claim in a manner that is
clear enough and complete enough for it to be performed by a person skilled in the relevant
art because the patent application does not enable an invention comprising a system (or
components of a system) derived from a bacterial species other than S. pyogenes without
undue burden. I accept that submission essentially for the reasons given in relation to P1. I
also accept that the patent application does not enable the use of engineered S. pyogenes
derived Cas9 in the compositions or methods of the claims, essentially for the same reasons
given in relation to P1.

388 Fourth, ToolGen relied on similar arguments to those which I have previously
considered in support of its contention that the length of the sgRNAs disclosed in the patent
application are not confined by the single example shown in Figure 1a of the patent
application, being a sgRNA (+48). Figure 1a of the patent application reproduces Figure 1A
of P1. There is no material difference between the disclosures of P1 and the patent
application regarding the design of the sgRNA including its tracrRNA component. In my
opinion, the patent application does not provide an enabling disclosure of a sgRNA having a
length different from that shown in Figure 1a of the patent application.
389 Fifth, ToolGen relied on similar arguments to those which I have previously
considered in support of its submission that the NLSs disclosed in the patent application are
not limited to the PKKKRKV NLS and that all other suitable NLSs are implicitly disclosed.
I accept that submission. In my opinion, the patent application implicitly discloses an
invention that uses any suitable NLS apart from the PKKKRKV NLS both in terms of its
sequence and location. I consider that their use would be routine and straightforward, and not
such as to create undue burden for the skilled addressee.
390 Sixth, the respondents did not press their ground of opposition based on the disclosure
of the GAAA linker in the context of the patent application which makes the same disclosure
in Figure 1a of the patent application as is made by Figure 1A in P1.
PATENT APPLICATION – SUPPORT

391 The support requirement is found in s 40(3) of the Act which relevantly provides that
the “claims must be supported by the matter disclosed in the specification”. The support
requirement in s 40(3) was discussed in the Explanatory Memorandum to the RTB Act. The
Explanatory Memorandum states:
Overseas law generally requires there to be a relationship between the claims and the
description, and between the claims and any document from which priority is being
claimed. This is expressed by the requirement that a claim be ‘supported by’ or ‘fully
supported by’ the description. Broadly speaking, the terms ‘support’ and ‘full
support’ pick up two concepts:
 there must be a basis in the description for each claim; and
 the scope of the claims must not be broader than is justified by the extent of the
description, drawings and contribution to the art.
Despite the underlying concept and policy between fair basis and support being
similar, the different terminology has produced different substantive law in different
countries.

The difference in substantive law in different countries causes unnecessary
complexity and uncertainty for applicants seeking protection in Australia and other
jurisdictions. As discussed above (see item 7), having different standards in different
countries imposes costs on global innovators, who must familiarise themselves with
the varying requirements.
This item is intended to align the Australian requirement with overseas jurisdictions’
requirements (such as the UK). Overseas case law and administrative decisions in
respect of the ‘support’ requirement will be available to Australian courts and
administrative decision-makers to assist in interpreting the new provision.
392 In Merck Sharp & Dohme Corporation v Wyeth LLC (No 3) (2020) 155 IPR 1
(“Merck”) Burley J, after referring to the relevant extrinsic material (including the
Explanatory Memorandum referred to above), observed at [514]:
Having regard to the content of the secondary materials, there can be little doubt that
Parliament considers that it is appropriate for the Court to have regard to the law in
the European Union and the United Kingdom in considering the scope of the
requirement for “support”: Acts Interpretation Act 1901 (Cth) s 15AB.
393 His Honour went on to consider the law in Europe and the United Kingdom
concerning Art 84 of the EPC and s 14(5) of the UK Act. Article 84 of the EPC, which is
enshrined in s 14(5), provides:
The claims shall define the matter for which protection is sought. They shall be clear
and concise and be supported by the description.
Subparagraph (c) of s 14(5) of the UK Act requires that the claims “be supported by the
description”.
394 The effect of Burley J’s analysis of the European and UK law is that the “support”
requirement or what he called the “claim support obligation” requires that the technical
contribution to the art disclosed by the specification justify the breadth of the claim. His
Honour referred at [546] to the judgment of Aldous J in Schering Biotech Corp’s Application
[1993] RPC 249 (“Schering Biotech”) where his Lordship said at 252-3:
In my view the correct approach under the 1977 Act is to consider the description
and claims in the specification through the eyes of the skilled man in the art. Under
section 125(1) the invention is that specified in the claims. Thus to decide whether
the claims are supported by the description it is necessary to ascertain what is the
invention which is specified in the claims and then compare that with the invention
which has been described in the specification. Thereafter the court's task is to decide
whether the invention in the claims is supported by the description. I do not believe
that the mere mention in the specification of features appearing in the claim will
necessarily be a sufficient support. The word "support" means more than that and
requires the description to be the base which can fairly entitle the patentee to a
monopoly of the width claimed. This approach is I believe consistent with the

decision of the European Patent Office's Technical Board of Appeals in the Riogen
case T301l87 of 16 February 1989 [Biogen NV v Hoffmann-La Roche & Co. AG
(Decision T30l/87), [19901 Official Journal E.P.O. 335.]. They said: “The scope of
protection in the claims must be fair having regard to the way in which the invention
is described and having regard to the information which the skilled person has been
given in the description as to how the invention can be carried out”.
Burley J said at [547]:
That approach encapsulates broadly the claim support obligation under s 40(3). To it
may be added the requirement that the technical contribution to the art must be
ascertained. Where it is a product, it is that which must be supported in the sense that
the technical contribution to the art disclosed by the specification must justify the
breath [sic] of the monopoly claimed.
395 I agree with Burley J that the approach by Aldous J in Schering Biotech at 252-3
broadly encapsulates the support obligation under s 40(3) of the Act.
396 The question whether a disclosure in a patent application fairly entitles the patentee to
a monopoly of the width claimed calls for an assessment of the patentee’s contribution to the
art, which must be weighed against the scope of the patentee’s monopoly as defined by the
claims. The monopoly, according to UK and European authorities, must be justified by the
technical contribution to the art that arises from the disclosure of the specification.
397 At least two difficulties can arise in applying the test. First, as the UK authorities
show, determining the patentee’s technical contribution to the art is often not easy. While it
has been suggested that the technical contribution may correspond with the inventive step,
there will be situations in which this is not so including where, for example, the invention of
the claim involves a very significant inventive step and yet, by reason of some deficiency in
the disclosure of the specification, the public is deprived of its side of the patent bargain.
Leaving aside what the UK authorities sometimes refer to as “classical insufficiency”
(broadly corresponding to the requirements of s 40(2)(a) of the Act), this may arise when the
specification discloses how to perform the invention across the scope of the claims (eg. by
using a known pharmaceutical compound in a new method of treatment) but not the basis
upon which the invention of the claim might reasonably be expected to work (ie. by
delivering the relevant therapeutic effect). The practice of claiming inventions that are not
shown to have a sufficiently plausible or credible justification or support is sometimes
referred to as speculative claiming.

398 An important decision in the UK that was directly concerned with the support
requirement enshrined in Art 84 of the EPC and s 14(5)(c) of the UK Act is the UK Supreme
Court’s decision in Warner-Lambert LLC v Generics (UK) Ltd t/a Mylan [2018] UKSC 56
(“Warner-Lambert UK”) . The leading judgment was given by Lord Sumption (with whom
Lord Reed agreed). Much of the discussion in Warner-Lambert UK focused on “second use”
claims to new methods of treatment using known pharmaceutical compounds and related
Swiss-style claims. But it also includes more general discussion regarding the support
requirement albeit in the context of the somewhat different statutory scheme which Burley J
elucidated in Merck at [527].
399 Lord Sumption referred at [17] to the “patent bargain” which he described as the
foundation of modern patent law both in the UK and the EPO. In this regard, his Lordship
referred to the following statement from the decision in EXXON/Fuel Oils (T-409/91) [1994]
OJ EPO 653 at paras 3.3 and 3.4 in which the EPO Technical Board observed that it was:
… the general legal principle that the extent of the patent monopoly, as defined by
the claims should correspond to the technical contribution to the article in order for it
to be supported, or justified. … This means that the definitions in the claims should
essentially correspond to the scope of the invention as disclosed in the description. …
Although the requirements of articles 83 and 84 are directed to different parts of the
patent application, since article 83 relates to the disclosure of the invention, whilst
article 84 deals with the definition of the invention by the claims, the underlying
purpose of the requirement of support by the description, insofar as its substantive
aspect is concerned, and of the requirement of sufficient disclosure is the same,
namely to ensure that the patent monopoly should be justified by the actual technical
contribution to the art.
400 His Lordship went on to discuss the problem of speculative claiming and the patentee
who attempts to claim a monopoly more extensive than could be justified by his or her
contribution to the art. This may arise in different contexts including in cases involving
claims to wide classes of chemical compounds or cases involving second use patents where
known compounds are the subject of claims for methods of treatment or Swiss-style claims
directed to new indications. Warner-Lambert UK, which concerned the UK patent for a
method of treating pain using pregabalin, was such a case. Lord Sumption, having referred to
the discussion in the Court of Appeal’s judgment regarding speculative claiming, said at [22]-
[23]:
[22] The Court of Appeal’s reference to “armchair inventors” suggests that what
they meant by speculative claiming was claiming by persons who had done
nothing new or inventive at all but had simply sought to patent abstract
possibilities. That may well be a particular risk in the case of patents for new

uses of known compounds, especially when they are commercially successful
in their existing use. In reality, however, speculative claiming of this kind is
simply one of a number of ways in which a patentee may attempt to claim a
monopoly more extensive than anything which is justified by his contribution
to the art. Other ways in which this can happen include claiming a monopoly
wider than the disclosure in the patent can support. An over-broad claim will
not necessarily be speculative. The inventor may really have invented
something corresponding to the full breadth of the claim. Research may
subsequently demonstrate this. But the claim will still exceed his contribution
to the art if that contribution is not sufficiently disclosed in the patent.
[23] The concept of plausibility originates in the case law of the EPO as a
response to over-broad claims, in particular claims to whole classes of
chemical compounds supported by a description which fails to show which
compounds can be expected to work. The Technical Board of Appeal treats
the condition of sufficiency under EPC article 83 as satisfied if it is possible
to work the invention across the scope of the claim from the information in
the specification, interpreted in the light of common general knowledge at the
priority date. It addresses the broader question whether the disclosed
contribution to the art is commensurate with the monopoly claimed under
EPC article 56, in the context of inventive step. In that context, its case law
requires the formulation of a problem which the claims of the patent could be
said to solve: see T 939/92 AGREVO/Triazole sulphonamides [1996] EPOR
171. It imports a requirement that the patent should disclose not just what the
invention is and how to replicate it, but some reason for expecting that it will
work. Plausibility was the standard to which the patentee was expected to
demonstrate this.
It can be seen that the concept of plausibility has been developed in the UK authorities as a
check on speculative claiming and to ensure that the patentee’s monopoly is no more
extensive than the contribution to the art made by the relevant disclosure.
401 Lord Sumption referred in some detail to the distinction drawn in the UK cases
between so-called “classical insufficiency” (where the skilled person is unable to perform the
invention from the information disclosed in the specification) and so-called Biogen
insufficiency (where the claim is said to be too broad, because it exceeds the disclosed
contribution to the art). The expression Biogen insufficiency is derived from the decision of
the House of Lords in Biogen Inc v Medeva Plc [1997] RPC 1. His Lordship said of Biogen
insufficiency at [25]:
… The House of Lords imported into section 14(3) of the Act a concept similar to the
former requirement of fair basis in section 32(1)(i) of the Patents Act 1949 (“that any
claim of the complete specification is not fairly based on the matter disclosed in the
specification”). It held that if the claim extended beyond the technical contribution to
the art disclosed in the patent, it failed for insufficiency independently of any
objection based on want of an inventive step and notwithstanding that the skilled
person could perform the invention across the whole scope of the claim. Lord
Hoffmann, delivering the leading speech, said at p 50:

But the fact that the skilled man following the teaching of Biogen 1 would
have been able to make HBcAg and HBsAg in bacterial cells, or indeed in
any cells, does not conclude the matter. I think that in concentrating upon the
question of whether Professor Murray’s invention could, so to speak, deliver
the goods across the full width of the patent or priority document, the courts
and the EPO allowed their attention to be diverted from what seems to me in
this particular case the critical issue. It is not whether the claimed invention
could deliver the goods, but whether the claims cover other ways in which
they might be delivered: ways which owe nothing to the teaching of the
patent or any principle which it disclosed.
He went on to make the same point in the context of the objection of insufficiency.
Adopting the statement of principle cited above from EXXON/Fuel oils, he pointed
out, at p 54, that the purpose of requiring sufficiency of disclosure could not be
limited to enabling the public to work the invention after the patent had expired:
Section 72(1)(c) of the 1977 is not only intended to ensure that the public can
work the invention after expiration of the monopoly. It is also intended to
give the court in revocation proceedings a jurisdiction which mirrors that of
the Patent Office under section 14(3) or the EPO under article 83 of the EPC,
namely, to hold a patent invalid on the substantive ground that, as the EPO
said in Exxon/Fuel Oils (T 409/91) [1994] OJ EPO 653, para 3.3, the extent
of the monopoly claimed exceeds the technical contribution to the art made
by the invention as described in the specification.
Lord Hoffmann was not, in these observations, addressing the question of second use
patents. But such patents raise a similar problem. If it is enough to disclose how to
make a known compound and for what conditions, the patentee has acquired a
monopoly without adding anything to the sum of knowledge. He will have satisfied
the condition of sufficiency but without satisfying its purpose.
402 Lord Sumption set out at [37] a number of propositions relevant to the concept of
plausibility. Some of these were expressed in terms most relevant to claims for methods of
treatment, Swiss-style claims and suggested therapeutic effects, but they are also relevant to
the concept of support more generally. His Lordship observed that the proposition that a
product is efficacious for the treatment of a particular condition is not made plausible by a
bare assertion to that effect. He went on to consider what information may render an
assertion that a product is efficacious plausible. His Lordship observed:
… the claimed therapeutic effect may well be rendered plausible by a specification

showing that something was worth trying for a reason, ie not just because there was
an abstract possibility that it would work but because reasonable scientific grounds
were disclosed for expecting that it might well work. The disclosure of those grounds
marks the difference between a speculation and a contribution to the art. This is in
substance what the Technical Board of Appeal has held in the context of article 56,
when addressing the sufficiency of disclosure made in support of claims extending
beyond the teaching of the patent …
403 ToolGen submitted that while claim 1 is ostensibly to a product, namely a Type II
CRISPR/Cas system, it is limited by the requirement that it be suitable to make a double-

stranded break in a target DNA sequence in a eukaryotic cell. I have already addressed this
argument. I do not accept it. The claim is not limited to those compositions capable of
making a double-stranded break. Whether or not the composition would make such a break
in use would depend on a variety of factors including whether the sgRNA and Cas9 complex
was successful in locating and interacting with the target DNA.
404 ToolGen also submitted that the inventors’ technical contribution to the art is, in
substance, use of a bacterial Type II CRISPR/Cas system to achieve a double-stranded cut in
DNA in a eukaryotic cell using a Cas9 polypeptide from that Type II system with the other
components referred to in the claim. It submitted that no one had previously described the
use of a CRISPR/Cas system in eukaryotic cells with that ability, and the disclosure of that
system represented a substantial contribution to the art. It further submitted that the technical
contribution was one of general application and that the width of claims 1 and 10 could be
supported on that basis.
405 The respondents submitted that the technical contribution to the art made by the
patent application is at best a disclosure of a particular Type II CRISPR/Cas systems derived
from S. pyogenes having the following features and characteristics:
(i) a requirement for a 5’-NGG-3’ or 5’-NAG-3’ PAM sequence;

(ii) a chimeric guide RNA having the crRNA and tracrRNA portions identified in
Figure 1a a of the patent application and the examples;
(iii) a GAAA linker fusing the crRNA and tracrRNA components in the guide RNA; and
(iv) a particular NLS (PKKKRKV) located at the C-terminus of the Cas9 polypeptide.
They submitted that the scope of the monopoly claimed far exceeds the extent of the
contribution to the art given that no Type II CRISPR/Cas9 system is illustrated in the patent
application except for the particular system based on S. pyogenes. The last two of these
features and characteristics identified by the respondents (i.e. (iii) and (iv)) can be
disregarded in light of my previous findings.
406 It is useful to refer back to the patent application and the sections of the specification
entitled “Technical Problem” and “Solution of the Problem”. The technical problem
disclosed was that a genome editing method for using RNA guided endonuclease based on
the CRISPR/Cas system had not been developed. It is then stated that the inventors made
many efforts to develop such a system “… and finally established a programmable RNA-

guided endonuclease that cleave DNA in a targeted manner in eukaryotic cells and
organisms”.
407 The patent application includes statements in [161] that the Cas protein may be
isolated from a Streptococcus species, preferably, S. pyogenes, or a recombinant protein, but
is not limited to Cas protein so derived. There are also statements in [158] that any Cas
protein may be used provided that it has endonuclease or nickase activity when complexed
with a guide RNA. The statements that any such Cas protein can be used can be put aside
because claim 1 is limited to a composition that uses a Cas9 polypeptide. As I have
mentioned, there are no examples given in the patent application of the invention using
components derived from any species other than S. pyogenes.
408 In closing submissions ToolGen relied on the decision in Warner-Lambert UK

including, in particular, Lord Sumption’s observation at [36] that the test of plausibility is
“relatively undemanding” while at the same time expressing a preference for the dissenting
judgment of Lady Black. However, ToolGen also stated that it understood the respondents
did not rely on any lack of plausibility on the face of the patent application. Having reviewed
the respondents’ submissions on this point closely, I think ToolGen’s understanding is
correct. This is because the respondents say (as I have already found in relation to P1) that
the patent application does not disclose any principle of general application. Accordingly,
they say the issue of plausibility does not arise.
409 The respondents submitted that the support requirement in s 40(3) in combination
with the requirement of disclosure in s 40(2)(a), operates to ensure that there is an enabling
disclosure, and if the disclosure does not enable the invention to be performed to the full
extent of the claim, the claim will lack the support required by s 40(3).
410 The facts in Warner-Lambert UK show how a claim might meet the requirement of
s 40(2)(a) by providing an enabling disclosure, but not meet the support requirement of
s 40(3). However, it is difficult to see how a claim to an invention for which there was no
enabling disclosure could meet the support requirement. In such circumstances, the scope of
the monopoly defined by the claim could not be justified by the technical contribution to the
art. The two requirements are closely interrelated and not wholly distinct in their fields of
operation.

411 In the present case, the broadest claims (ie. claims 1, 2, 10 and 11) fail to meet the
requirements of both s 40(2)(a) and s 40(3) of the Act due to the fact that they are not
confined to the use of Cas9 derived from S. pyogenes. Further, all of the claims, insofar as
they encompass other sgRNAs of different lengths to that shown in Figure 1a of the patent
application (i.e. sgRNA (+48)), also fail to meet the requirements of both s 40(2)(a) and
s 40(3) of the Act.
THE PRIORITY DATE

412 The hearing of the appeal was conducted on the premise that if the claims were not
entitled to priority based on P1, then a deferred date of 20 June 2013 would apply
(“the deferred priority date”). Although the evidence included two US provisional patent
applications filed on 20 March 2013 (P2) and 20 June 2013 (P3), none of the evidence or
submissions of the parties made reference to them. P2 is a provisional application entitled
“Genotyping with CRISPR/Cas-derived RNA-guided endonucleases” which appears to be
solely concerned with a method of using RNA-guided endonucleases in restriction fragment
length polymorphism analysis. It does not disclose the invention of any of the claims in the
patent application. P3 is a provisional application entitled “Composition for cleaving a target
DNA comprising a guide RNA specific for the target DNA and Cas protein-encoding nucleic
acid or Cas protein”. The parties did not make any submissions in relation to P3 presumably
because it is common ground that even if there are claims entitled to priority based on P3, it
was filed too late in time to save the claims of the patent application in light of various
journal articles published between the filing of P1 (23 October 2012) and the filing of P3 (20
June 2013).
413 The following publications are relevant to the issues of novelty and inventive step:
 Cong et al, “Multiplex Genome Engineering Using CRISPR/Cas Systems” (2013)

Science 339, 819-823 and Supplementary Materials;
 Mali et al, “RNA-Guided Human Genome Engineering via Cas9” (2013) Science 339,
823-826 and Supplementary Materials; and
 Wang et al, “One-Step Generation of Mice Carrying Mutations in Multiple Genes by

CRISPR/Cas-Mediated Genome Engineering” (2013) Cell 153, 910-918 and Supplementary
Information.

414 ToolGen has admitted that Cong (2013) was published on 15 February 2013 and that
the Supplementary Materials for Cong (2013) were published on 13 June 2014. However,
there is other evidence which shows, and I find, that the Supplementary Materials for Cong
(2013) were published on 3 January 2013. ToolGen has admitted that Mali (2013) and its
Supplementary Materials were published on 15 February 2013. ToolGen has also admitted
that Wang (2013) was published on 9 May 2013 and that its Supplementary Information was
published on 2 May 2013.
NOVELTY
415 Section 18(1)(b)(i) of the Act provides that an invention is a patentable invention, for
the purposes of a standard patent, if the invention, so far as claimed in any claim, when
compared with the prior art base as it existed before the priority date, is novel. Section 7(1)
of the Act provides that an invention is taken to be novel when compared with the prior art
base unless it is not novel in light of relevant prior art information (as defined in the Act).
416 The test for whether a patent claim lacks novelty by reason of a prior publication (or
is “anticipated” by a prior publication) has been described as follows in General Tire at 486:
To anticipate the patentee’s claim the prior publication must contain clear and
unmistakable directions to do what the patentee claims to have invented … A
signpost, however clear, upon the road to the patentee's invention will not suffice.
The prior inventor must be clearly shown to have planted his flag at the precise
destination before the patentee.
(Citations omitted.)
417 As previously mentioned, ToolGen accepts that if claims 1-8 and 10-18 are not
entitled to priority from P1 then the Delegate’s findings that those claims lacked novelty will
stand.
418 With regard to claims 9, 19 and 20, the respondents contend that if, contrary to my
findings, those claims include the use of in vitro transcribed sgRNA, then they are anticipated
by Wang 2013 which discloses systems and methods within those claims.
419 With regard to claims 9 and 20, Associate Professor Herold and Professor Thomas
gave unchallenged evidence that T7 promoters were well-known and widely used to drive
RNA transcription in vitro and that these produced an RNA molecule with two guanine (G)
nucleotides at the 5’ end.

420 There was unchallenged evidence given by Associate Professor Herold in relation to
Wang (2013) and its disclosure including the use of a guide RNA with two additional
guanine nucleotides at the 5’ end. He said in Herold 1:
The experiments reported in Table 2 that targeted Tet3 were conducted using sgRNA
with two extra guanine molecules at the 5' end. I understand this from the bottom of
Table S3, which includes the oligonucleotides used to add the T7 promoter to the
sgRNA template for in vitro transcription of the sgRNA (see Experimental Section:
“Production of Cas9 mRNA and sgRNA” on page 916 and Table S3).
421 ToolGen did not adduce any evidence in answer or make any submission in relation to
this evidence. If, as I found, the patent application is not entitled to priority based on P1, and
if, contrary to my findings, claims 9 and 20 include the use of in vitro transcribed guide RNA,
then those claims, so construed, would lack novelty based on the publication of Wang 2013.
422 Further, if claim 19 (when read with claim 10) does not lack clarity and includes the
use of in vitro transcribed guide RNA then that claim would also lack novelty based on the
publication of Wang 2013.
INVENTIVE STEP
423 An invention is a patentable invention if the invention, when compared with the prior
art base, involves an inventive step: see s 18(1)(b)(ii) of the Act. Sections 7(2) and (3) of the
Act identify the nature of the enquiry. They provide:
(2) For the purposes of this Act, an invention is to be taken to involve an

inventive step when compared with the prior art base unless the invention
would have been obvious to a person skilled in the relevant art in the light of
the common general knowledge as it existed (whether in or out of the patent
area) before the priority date of the relevant claim, whether that knowledge is
considered separately or together with the information mentioned in
subsection (3).
(3) The information for the purposes of subsection (2) is:
(a) any single piece of prior art information; or
(b) a combination of any 2 or more pieces of prior art information that
the skilled person mentioned in subsection (2) could, before the
priority date of the relevant claim, be reasonably expected to have
combined.
424 A “scintilla of invention” can sustain a valid patent, but there must be “some
difficulty overcome, some barrier crossed” or something “beyond the skill of the calling”:
Lockwood Security Products Pty Ltd v Doric Products Pty Ltd (No 2) (2007) 235 CLR 173 at

[52]; RD Werner & Co Inc v Bailey Aluminium Products Pty Ltd (1989) 25 FCR 565 at 574;
Allsop Inc v Bintang Ltd (1989) 15 IPR 686 at 701.
425 ToolGen accepts that if claims 1-8 and 10-18 are not entitled to priority from P1 then
the Delegate’s finding that those claims lack an inventive step will stand.
426 With regard to claims 9 and 20, I accept it would have been a simple and routine
matter for the skilled addressee to use T7 promoters and, by so doing, produce two additional
guanine nucleotides at the 5’ end of the guide RNA. Use of T7 promoters would not require
any inventive capacity or imagination.
427 Having regard to the unchallenged evidence on this topic, I accept that if, contrary to
my findings, the Court was to construe claims 9, 19 and 20 as including the use of in vitro
transcribed guide RNA then the evidence shows that these claims would have been obvious
in light of each of Wang (2013), Cong (2013) and Mali (2013) taken together with the
common general knowledge as at the deferred priority date.
428 On the construction of claims 9 and 20 which limits them to the use of a nucleic acid
(such as plasmid DNA) encoding a guide RNA, then the evidence also establishes that each
of those claims is obvious in light of each of Cong (2013) and Mali (2013) taken together
with the common general knowledge as at the deferred priority date. Cong (2013) and Mali
(2013) each describe experiments in which the guide RNA is encoded by a plasmid DNA.
429 Claim 21 introduces the additional step to the method described in any of claims 10-
16 wherein the nucleic acid encoding the Cas9 polypeptide is introduced into the eukaryotic
cell before introducing the nucleic acid encoding the guide RNA. ToolGen made some very
brief oral submissions in relation to claim 21 in which it drew attention to what was said by
Associate Professor Herold in Herold 1 concerning claim 21. ToolGen submitted the
evidence filed by the respondents does not reach the level required to demonstrate a lack of
inventive step for claim 21.
430 The respondents submitted that to introduce the components of the system described
in claim 10 in a stepwise fashion would be a simple and routine matter. In their oral evidence
each of Professor Thomas, Associate Professor Firestein and Associate Professor Herold
agreed that it would be possible to employ the method of the claims using a stepwise
approach with a DNA plasmid that encoded for the guide RNA being introduced as a second

step. None of the witnesses was asked whether it would be desirable or routine to adopt that
approach nor was any of them asked whether it would have been an obvious thing to do.
431 The patent application does not provide any indication that there is anything added by
claim 21 to what is claimed in claims 10-20 which could renders claim 21 inventive if (as is
the case) none of those claims involves an inventive step. I find that it would be obvious to
the skilled addressee that the method of claim 10 (which was itself obvious in light of each of
Wang (2013), Cong (2013) and Mali (2013)) could be performed in a stepwise fashion in the
manner described in claim 21. Adoption of that method would not require any inventive
capacity or imagination or the exercise of skill beyond that of the calling. I therefore find that
claim 21 does not involve an inventive step.
AMENDMENT
432 For the reasons explained each of the claims would, if granted, be invalid. In its
closing submissions, ToolGen indicated that it may wish to amend the patent application in
the event that I was to find that any one or more of the claims was invalid. Presumably, this
would involve amendments aimed at narrowing the scope of the claims and aligning them
with the disclosure of P1.
433 The Court has power to hear and determine an application to amend in this case: see
s 105(1A) and s 112A of the Act and Meat and Livestock Australia Limited v Branhaven LLC
(2020) 281 FCR 640 at [17]-[20], [91]-[93]. ToolGen submitted that it may be appropriate to
remit the matter to the Patents Office so that the Delegate could consider the amendment
application. I do not think that would be desirable. Given the complexity of this matter, I
think ToolGen should make any application to amend the patent application to this Court so
that that application may be determined before any final order is made or any application for
leave to appeal any such final order is filed. It is plainly desirable that any application to
amend the claims be heard and determined in advance of any appeal so that the Full Court
may give consideration not only to the issues addressed in these reasons, but any further
issues arising out of the foreshadowed amendment application. In this regard, I note that the
respondents have already foreshadowed that they will oppose any application that may be
made by ToolGen to amend the claims.

DISPOSITION
434 The only orders I propose to make at this time are procedural orders relating to any
application to amend the patent application. In the event that no application to amend is filed
within 28 days, I propose to make orders dismissing the appeal and allowing the cross-appeal
together with an order directing the Commissioner to refuse the patent application.
435 There does not appear to be any reason why the appellant should not pay the
respondents’ costs of the appeal and cross-appeal. I will hear from the parties in relation to
costs when the proceeding is next before the Court.
436 Orders accordingly.
I certify that the preceding four

hundred and thirty-six (436)
numbered paragraphs are a true copy
of the Reasons for Judgment of the
Honourable Justice Nicholas.
Associate:
Dated: 14 July 2023

Annexure A
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Toolgen Inc V Fisher (No 2) (2023) FCA 794

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Toolgen Inc V Fisher (No 2) (2023) FCA 794

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FEDERAL COURT OF AUSTRALIA

ToolGen Incorporated v Fisher (No 2) [2023] FCA 794

File number: NSD 1909 of 2018

Judgment of: NICHOLAS J

Date of judgment: 14 July 2023

Catchwords: PATENTS – appeal against decision of delegate of

Held: dependent claim lacks clarity – invention of

Legislation: Intellectual Property Laws Amendment (Raising the

Cases cited: Aktiebolaget Hässle v Alphapharm Pty Ltd (2002) 212

ToolGen Incorporated v Fisher (No 2) [2023] FCA 794

ToolGen Incorporated v Fisher (No 2) [2023] FCA 794

Division: General Division

Registry: New South Wales

National Practice Area: Intellectual Property

Sub-area: Patents and associated Statutes

Number of paragraphs: 436

Date of hearing: 21-25, 28-30 September 2020

Counsel for the Appellant/Cross- Mr T Cordiner QC with Mr P Flynn SC

Solicitor for the Jones Day

Counsel for the Respondents/ Mr C Dimitriadis SC with Ms C Cunliffe

Solicitor for the Respondents/ Ashurst Australia

ToolGen Incorporated v Fisher (No 2) [2023] FCA 794

[196] replace reference to (f)-(g) with (a)-(b)

[260] and [261] corrections to formatting

[334] replace reference to (d)-(j) with (a)-(g)

[408] insert the words “in relation to P1” in penultimate

ToolGen Incorporated v Fisher (No 2) [2023] FCA 794

NSD 1909 of 2018

BETWEEN: TOOLGEN INCORPORATED

AND: GRANT FISHER

ACN 004 552 363 PTY LTD

AND BETWEEN: GRANT FISHER

ACN 004 552 363 PTY LTD

AND: TOOLGEN INCORPORATED

ORDER MADE BY: NICHOLAS J

THE COURT ORDERS THAT:

ToolGen Incorporated v Fisher (No 2) [2023] FCA 794 vi

ToolGen Incorporated v Fisher (No 2) [2023] FCA 794 vii

ToolGen Incorporated v Fisher (No 2) [2023] FCA 794 viii

2 The appellant (“ToolGen”) is the applicant in Australian Patent Application

ToolGen Incorporated v Fisher (No 2) [2023] FCA 794 9

6 Even though this proceeding is referred to as an appeal, it is well-established that it is

8 In these reasons I refer to various publications in the scientific literature. Sometimes I

ToolGen Incorporated v Fisher (No 2) [2023] FCA 794 10

13 For the reasons that follow I have concluded:

(a) None of the claims are entitled to priority based on P1 (s 43(2A)).

ToolGen Incorporated v Fisher (No 2) [2023] FCA 794 11

15 The statement concerning onus in the Explanatory Memorandum appears to be

(3A) If the Commissioner is satisfied, on the balance of probabilities, that a ground

ToolGen Incorporated v Fisher (No 2) [2023] FCA 794 12

Eukaryotic and prokaryotic cells

DNA and RNA

ToolGen Incorporated v Fisher (No 2) [2023] FCA 794 13

23 In biological cells, molecules of RNA predominantly consist of a single

ToolGen Incorporated v Fisher (No 2) [2023] FCA 794 14

Cellular expression of proteins

ToolGen Incorporated v Fisher (No 2) [2023] FCA 794 15

Nuclear localisation sequence

34 As of October 2012, scientists were using a number of different nuclear localisation

RNA interference, Zinc finger nucleases and TALEN nucleases

ToolGen Incorporated v Fisher (No 2) [2023] FCA 794 16

38 This bacterial resistance is achieved by way of short segments of plasmid/phage

ToolGen Incorporated v Fisher (No 2) [2023] FCA 794 17