Next-Generation Sequencing (NGS)

Sample Preparation and Informatics

Survey
Discussion Guide

Questionnaire
NGS Market Overview

Filter: All respondents

RANK RESPONSE
Q1. What are the key drivers for adoption of NGS testing? Please specify if the following
attributes are of HIGH, MEDIUM or LOW importance. Also, comment on the short (2
years) and long term (3+years) impact of these drivers in terms of HIGH, MEDIUM or
LOW importance.
Please share details using the following table:
Short Term Long term
Drivers
(2 years) (3+ years)
Decrease in cost of sequencing
Sample volumes increase
Large-scale population sequencing projects
Shift towards personalized medicine / therapy approaches
Integration of AI into data analytics
Increasing uptake of NGS technology
Need for better interpretation and simplification of data
Trend towards whole genome vs. whole exome sequencing
Growth in clinical applications as clinical informatics
offerings increase
Reimbursement in certain application areas (such as
Oncology, NIPT)
Increased off-the shelf options available to select from
Other (please specify)

Filter: All respondents

RANK RESPONSE
Q2. What are the key restraints for adoption of NGS testing? Please specify if the
following attributes are of HIGH, MEDIUM or LOW importance. Also, comment on the
short (2 years) and long term (3+years) impact of these restraints in terms of HIGH,
MEDIUM or LOW importance.
Please share details using the following table:
Short
Long term (3+
Restraints Term (2
years)
years)
In-house developed and open source tools usage
Desire to have customized NGS tools
Standardization and accuracy issues plague commercial
solutions
Cost-based competition due to extensive competitor base
(prices based on competition rather than consumer-
oriented pricing)
Complexity of vendor selection due to large selection of
brands/tools
Reimbursement policies and approval of NGS tests
Shortage of skilled informatics workforce in some regions
Storage of NGS data
Bioinformatics expertise (interpretation of NGS data)
Challenges in reporting out results from sequencing
Other (please specify)

Filter: All respondents, show the range provided in S8

OPEN TEXT, NUMERIC
Q3. Do you expect the number of NGS samples sequenced using NGS technology by
your lab to increase, decrease, or stay the same over the next 5 years? If increase or
decrease, by what percentage? What are some of the reasons for this expectation? Can
you please comment on the percentage change in NGS sample volume in last two years
(2017-2018 and 2018- 2019)?
% %
change change
Annual Increase, Expected
in NGS in NGS
NGS Decrease or Growth
Segment sample sample Reasons
volume Stay the 2019-2024
volume volume
(2019) Same (%)
(2017 – (2018 –
2018) 2019)
Samples
sequenced

Filter: All respondents, show the range provided in S9=a.

NUMERIC
Q4. Your lab processed “X” NGS samples in-house per week, what % of these total NGS
samples per week were for clinical v. translational research purposes? Could you
provide a % split across routine clinical v. translational research work?

Research type % of total samples [X samples processed in – house per

week]
Clinical research*
Translational research*

*Clinical testing - Labs conducting testing for Routine diagnostic testing on patient samples
used directly for making or supporting patient management decisions (e.g. at screening,
diagnosis, treatment or monitoring) (i.e. not for research or developmental purposes)
Translational research testing - Translational and/or Clinical research (e.g., using patient
derived samples for activities NOT related to patient management)

Other - Clinical trials enrolment and / or clinical trials associated testing (which is also
research aimed at enhancing the adoption of best practices in the community.

Filter: Filter for the applications mentioned in S12, show the applications and % of NGS
samples run in-house per week per application
NUMERIC
Q5. Now we want to understand a little more about the NGS applications and methods
your lab performs, some of which you mentioned in the screener. Please can you tell the
percentage breakdown of your samples run per week by these applications and methods
respectively?

Please share details using the following table:

Application Percentage of Methods (for each application) Percentage

NGS Samples of NGS
run per week Samples run
per per week per
application method
Somatic Oncology – a)Targeted sequencing (amplicon
solid tumors ONLY only)
b) Targeted sequencing (Capture
based)
c) Whole exome sequencing
d) Whole genome sequencing
e) RNA-Sequencing for gene
expression analysis / pathway
analysis
f) RNA-Sequencing for isoform and
structural variant identification
including whole transcriptome
g) Single cell sequencing (DNA
based)
h) Single cell sequencing (RNA
based)
i) Methylation sequencing, ATAC-
seq
j) Other, please specify______
TOTAL 100%
Somatic Oncology –
heme malignancies
ONLY
Hereditary Oncology
((e.g. BRCA testing,
BRCA 1&2 gene)
Human genetics
(e.g. carrier
screening, newborn
screening,
cardiology,
neurology,etc.) –
excluding hereditary
oncology
Non-invasive
prenatal testing
(NIPT)
Infectious diseases
(e.g. pathogen ID,
subtyping, Host
response, resistance
monitoring, etc.)
Pharmacogenomics
Epigenetics
Other (please
specify)

Filter: Filter by all the applications mentioned for Whole exome sequencing method in Q5
NUMERIC
Q6. If performing Whole Exome Sequencing, can you tell how many genes are you
targeting through this workflow for each application? Please place an [X] in the
appropriate boxes and (___enter no of genes)

Please share details using the following table:

Method Application All exonic Medically Other

genes relevant (please
exome specify)
[X] (____enter [X] (____enter
no. of genes) no. of genes)
Whole Somatic Oncology – solid
exome tumors ONLY
sequencing Somatic Oncology – heme
malignancies ONLY
Hereditary Oncology (e.g.
BRCA testing, BRCA 1&2
gene)
Human genetics (e.g. carrier
screening, newborn
screening, cardiology,
neurology,etc.) – excluding
hereditary oncology
Non-invasive prenatal
testing (NIPT)
Infectious diseases (e.g.
pathogen ID, subtyping,
Host response, resistance
monitoring, etc.)
Pharmacogenomics
Epigenetics
Other (please specify)
Filter: Filter for all the applications mentioned in S12
NUMERIC VALUE
Q7. What is your local currency? Please answer the following question in your local
currency. What is the cost per test* (in local currency) for each of the NGS application
your lab performs?
[*Definition of cost / test (local currency) (This includes ALL-IN costs post extraction from
library preparation/target enrichment to report out to patient; does NOT include labour
costs or tech time)]
Please share details using the following table:

Application Cost/ test* (local currency)

Somatic Oncology – solid tumors ONLY
Somatic Oncology – heme malignancies ONLY
Hereditary Oncology (e.g. BRCA testing, BRCA
1&2 gene)
Human genetics (e.g. carrier screening, newborn
screening, cardiology, neurology,etc.) –
excluding hereditary oncology
Non-invasive prenatal testing (NIPT)
Infectious diseases (e.g. pathogen ID, subtyping,
Host response, resistance monitoring, etc.)
Pharmacogenomics
Epigenetics
Other (please specify)

NGS Sample Preparation (library preparation and target enrichment reagents

AND sample preparation automation)

Library preparation – NGS library preparation involves generating a collection of DNA

fragments for sequencing, with optional library amplification. NGS libraries are typically
prepared by fragmenting a genomic DNA or cDNA sample and ligating specialized
“adapters” to both fragment ends.

Target enrichment - In Targeted sequencing applications, a desired subset of genes or

regions of the genome are captured from an existing library. This may be performed by the
two methods below–

 Amplicon-based target enrichment methods for next-generation sequencing

(NGS) rely on PCR-amplification of target regions of interest using sequence-
specific primers and probes

 Hybridization based target enrichment - Target enrichment works by capturing

genomic regions of interest by hybridization to target-specific biotinylated probes,
which are then isolated using magnetic pulldown.

For purposes of this discussion, Automation of NGS sample preparation process includes
steps from post extraction to sequencing preparation.
Examples include, sample quantification/QC, library preparation, target enrichment, pooling,
library quantification & QC

Filter: All respondents

RANK RESPONSE
Q8. What are the key drivers for the NGS sample preparation market? Please specify if
the following attributes are of HIGH, MEDIUM or LOW importance. Also, comment on the
short (2 years) and long term (3+years) impact of these drivers in terms of HIGH,
MEDIUM or LOW importance.
Please share details using the following table:
Short Term Long term
Drivers
(2 years) (3+ years)
Decrease in cost of sequencing
Large-scale population sequencing projects
Increasing installed base of NGS instruments will increase
uptake of library prep instruments, particularly in the high
throughput segment
Increasing uptake of NGS technology
Demand for clinical diagnostics – early disease detection to
avoid long term healthcare treatment costs and improve patient
care
Improvement of liquid handling instrument robotics to reduce
hands on time and risk or error during sample preparation
Government initiatives towards realizing NGS potential is
leading to greater awareness and better genomic infrastructure
development (e.g. 100,000 Genomes Project)
Customer push to reduce reagent volume usage /reagent costs
and overall NGS system cost
Device/Instrument miniaturization
Other (please specify)

Filter: All respondents

RANK RESPONSE
Q9. What are the key restraints for the NGS sample preparation market? Please specify if
the following attributes are of HIGH, MEDIUM or LOW importance. Also, comment on the
short (2 years) and long term (3+years) impact of these restraints in terms of HIGH,
MEDIUM or LOW importance.
Please share details using the following table:
Short Term Long term
Restraints
(2 years) (3+ years)
High cost of most liquid handling systems, making it unlikely
that labs will purchase sample prep automation for
specifically in front of these systems
Reimbursement policies
Complexity of liquid handling systems, including
implementation, programming, usage, and maintenance
requires expertise in the lab
Ability for low-to-mid throughput NGS labs to conduct manual
library prep
Availability of skilled workforce not matching the rapid growth
in the industry
High competition leading to downward pricing pressure
Legacy laboratory mind-set to shift towards automation
Other (please specify)

Filter: Filter for all the applications mentioned in S12

OPEN TEXT
Q10. Of the NGS methods and applications you said your lab performs, can you tell what
reagents you use for library preparation and for target enrichment (including the brand
and name of product for both library preparation and target enrichment)? Also mention
what proportion of NGS volume you run using that brand / vendor for both library
preparation and target enrichment.
[POPULATE LIST OF the applications selected in S12]
Please share details using the following table:

What vendor Which % NGS What Which % NGS

do you use product volum vendor do product volume
for library do you e by you use for do you by
Application preparation use from Vendo Target use vendor
reagents? the r/ enrichment from the /
selected produ reagents? selected produc
vendor? ct vendor? t
Somatic
Oncology – solid
tumors ONLY
Somatic
Oncology – heme
malignancies
ONLY
Hereditary
Oncology (e.g.
BRCA testing,
BRCA 1&2 gene)
Human genetics
(e.g. carrier
screening,
newborn
screening,
cardiology,
neurology,etc.) –
excluding
hereditary
oncology
Non-invasive
prenatal testing
(NIPT)
Infectious
diseases (e.g.
pathogen ID,
subtyping, Host
response,
resistance
monitoring, etc.)
Pharmacogenomi
cs
Epigenetics
Other (please
specify)
Filter: Filter for all answers for Q10
NUMERIC
Q11. Can you provide % usage across the different target enrichment brands you
mentioned in Q10?
Please share details using the following table:

TE Panel type % usage by volume of samples processed

with TE step
*Fixed off the shelf panels
*Customized panels
*Fixed made to order panels
TOTAL 100%

*Fixed off the shelf panels: These panels are readily available for use and have pre-defined
set of genes (the kits which are customized and are available off-the-shelf will also be
considered under off-the-shelf category. E.g. = AmpliSeq community panels)

Customized panels: When a customer designs a panel and then orders them OR these
panels are designed based on requirements of research (with genes of interest). E.g.
SureSelect Custom panels

Fixed made to order panels – These panels are initially designed based on requirements of
research for a particular customer and now available to other customers on request.

NGS Sample preparation (opportunities and challenges)

Filter: All respondents

OPEN TEXT
Q12. What are the major challenges while using a library preparation kit within your NGS
workflow?

Filter: All respondents

OPEN TEXT
Q13. What are the major challenges while using a target enrichment kit within your NGS
workflow? What improvements would you like to see in the target enrichment kits in the
future based on your current and future workflow requirements?

Filter: All respondents

OPEN TEXT
Q14. How do you see the market evolving for library preparation and target enrichment
reagents over the next 3-5 years? Please comment. (e.g. automation, miniaturization of
sample volume, workflow standardization)
 NGS SAMPLE PREPARATION (LP/TE) – AUTOMATION INSTRUMENTS

IMPORTANT: For the next set of questions, please consider all workflow steps after nucleic
acid extraction and before sequencing. We are specifically evaluating the use of instruments
used to automate NGS library preparation, target enrichment and sample quantification /
QC, pooling prior to sequencing set up.

Filter – Filter for all answers S13 = automated (from Library preparation to pooling step in the
NGS workflow)
OPEN TEXT
Q15. What liquid handling system [vendor and product name] do you use to automate
steps from post extraction to pre-sequencing in the NGS workflow? Please note that we
are only asking about instruments used for automating steps after nucleic acid extraction
and before sequence run. Please place an X in the appropriate boxes and mention the
number of instruments against each X. Also, please the % split of NGS volume by
product. Also, please tell us whether the vendor customizes automated system for you?
If yes, please explain what is the customization?
[MODERATOR INSTRUCTION]: Please ask to explain the reason for choosing the
product.
Please share details using the following table:
Automated Vendor Product [X] Vendor Mention % NGS
task (From (numb Customizatio the volume
sample er of n available for customi by
preparation instru automated zation product
step in the ments) systems [Yes/
NGS No]
workflow)
Library Agilent Magnis
Construction Bravo NGS
(Library Workstation
preparation) Thermo Ion Chef
Fisher
Qiagen QIAcube
Connect
Hamilto STAR
n
VANTAGE
Perkin SciClone
Elmer G3 NGSx
Tecan Freedom
EVO NGS
Workstation
Dream Prep
Beckma Biomek
n 4000
Coulter Biomek i7
Biomek i5
Biomek NX
Others
(please
specify)
Filter: Filter for all the brands and products selected in Q15
OPEN TEXT
Q16. For all the vendors and products mentioned in the Q15, please mention why did your
lab choose this brand and particular instrument? What are some of the pros and cons of
this instrument? Also, mention the CapEX cost for each instrument and the annual cost
($) for consumables/ accessorises associated with automated systems.
Please share details using the following table:

Vendor Product Reason Pros and CapEx What is the annual

cons of cost for costs of consumables
each each and accessorises
product instrum associated with the
ent automated systems ($)
Agilent Magnis
Bravo NGS
Workstation
Thermo Ion Chef
Fisher
Qiagen QIAcube Connect
Hamilton STAR
VANTAGE
Perkin Elmer SciClone G3
NGSx
Tecan Freedom EVO
NGS Workstation
Dream Prep
Beckman Biomek 4000
Coulter Biomek i7
Biomek i5
Biomek NX
Others
(please
specify)

Filter: All respondents who have indicated they have automation platforms for sample
preparation in the screener S13
SELECT ALL THAT APPLY
Q17. For which NGS applications does your lab utilize automation systems for sample
preparation? Please check mark the appropriate box.
Application Utilize automation systems
for sample preparation
Somatic Oncology – solid tumors ONLY 
Somatic Oncology – heme malignancies ONLY 
Hereditary Oncology 
Human genetics (e.g. carrier screening, newborn screening, 
cardiology, neurology,etc.) – excluding hereditary oncology
Non-invasive prenatal testing (NIPT) 
Infectious diseases (e.g. pathogen ID, subtyping, Host 
response, resistance monitoring, etc.)
Pharmacogenomics 
Epigenetics 
Other (please specify) 
Filter: All respondents
RANK RESPONSE
Q18. When evaluating sample preparation automation products, what attributes you value
the most? Please specify if the following attributes are of HIGH, MEDIUM, LOW or NO
importance.
Feature High (H), Medium (M), Low (L), No (N)
Importance
Cost per sample
Upfront instrument cost
Ease-of-use
Reliability (performs as it should always)
Ease of programming – scripts for LDT workflows
Hands-on-time
Walk-away time
Size of the instrument (footprint)
Quality of sample output
Ability to rapidly design and automate new
workflows with custom gene panels of your
choosing
Ability to use reagents from any vendor
Brand name
Software interface (having icon of the software)
Others (please specify)

Filter: Filter for all the NGS sequencers mentioned in S7

OPEN TEXT
Q19. How often do you upgrade your NGS sequencers? In future are you planning to
upgrade the brand or will you switch brand of the sequencer from the existing brand?
Please mention the timeframe for switching/ upgrading the sequencer.

Please share the details using following table:

Instrument In the future In the future will Timeframe

would you you switch for
upgrade brand of switching /
brand of sequencer from upgrading
sequencer your existing
brand
Illumina – NovaSeq 6000
Illumina - HiSeq X Five/X Ten
Illumina - HiSeq 3000/4000
Illumina - HiSeq 2000/2500
Illumina - NextSeq500/550
Illumina- NextSeq 550Dx
Illumina – GENOME ANALYZER /
GENOME ANALYZER II series
Illumina - MiSeq
Illumina - MiSeq Dx
Illumina - MiniSeq
Illumina – iSeq100
Thermo Fisher - Ion PGM
Thermo Fisher - Ion PGM Dx
Thermo Fisher - Ion Proton
Thermo Fisher - Ion GeneStudio S5
Series (previously called as S5/S5XL)
(includes S5, S5 prime, S5 Plus)
Thermo Fisher – GENEXUS
Thermo Fisher - SOLiD
Pacific Biosciences - RS / RSII
Pacific Biosciences – Sequel/ Sequel II
Oxford Nanopore Tech.- MinION
Oxford Nanopore Tech.- Flongle +
MinION
Oxford Nanopore Tech.- GridIon X5
Oxford Nanopore Tech. – PromethION
Qiagen – GeneReader NGS
BGI - BGISEQ-50
BGI - BGISEQ-100
BGI - BGISEQ-500
BGI - BGISEQ-1000
MGI -MGISEQ – 200
MGI -MGISEQ – 2000
MGI -MGISEQ – T7

NGS Informatics
In this section, the questions will be on the dry lab workflow within your facility. We would like
to understand your bioinformatics / data analysis capabilities for NGS workflows (specifically
the secondary, tertiary data analysis and reporting)

Secondary Analysis Tools

(Secondary analysis includes QA filtering of raw reads, alignment/assembly of reads, QA
and variant calling of aligned reads)

Filter: All respondents

OPEN TEXT

Q20. After samples are sequenced and primary analysis is performed by the sequencer,
does your laboratory conduct secondary analysis in-house or outsource to a commercial
NGS informatics service provider? Please indicate in % how much of secondary analysis
is done in-house vs. outsourced to outside service. Please mention the reason for out-
sourcing the analysis? [Ask open ended question. Please place an X in the appropriate
boxes and mention the percentage of secondary analysis work done in-house or
outsourced in the appropriate box, should add up to 100%] [MODERATOR
INSTRUCTION]: Please ask to explain the reason.
 Secondary [X] % of NGS volume by secondary Reason
analysis analysis done in-house vs.
outsourced
In-house
Outsource

Analysis conducted In-house

Filter: Q20=In-house
OPEN TEXT
Q21. If the secondary analysis is conducted in-house, please mention the type of solution
used (vendor/ commercial solution/ in-house developed or open-source), please place
an X in the appropriate boxes. Also, mention the name of the brand/ product/ software
for each of the solution. Please comment pros of using that product and please comment
on the features that are not present in currently used software solutions but are
considered essential or needed for more accurate analysis. Also, comment on the
algorithms used for conducting secondary analysis and number of samples run per week
through secondary analysis. Please share details using the following table:

Solution Used [X] Brand name/ Pros Features not Algorithm Number of
product/ of present in s for samples run
software each software conductin per week
(mention all produ solutions g through
the products ct but secondar secondary
used in the essential or y analysis analysis
lab) needed for
analysis
Vendor/
commercial
Solution
In-house
developed
pipeline
Open-source
Majorly open-
source
combined with
in-house
developed
pipeline

Filter for Q20= In-house and Q21= Vendor/ commercial Solution

OPEN TEXT
Q22. If commercial/ vendor solutions are used, please mention the pricing model for this
solution. Please place an X in the appropriate boxes. Also, can you tell us how much you
pay for these secondary solutions? Please share details using the following table:

Pricing Model [X] Cost of the secondary analysis solution

One-off license
Per report fee / per sample
Per user (users of the
bioinformatics solution within
the facility)
Annual subscription
Bundled solution – provided
with reagents
Other
Filter for Q20= In-house and Q21= Vendor/ commercial Solution
OPEN TEXT

Q23. Can you comment on the implementation fee of the commercial software used in
your facility?

Filter for Q20= In-house

OPEN TEXT

Q24. In near future, are you planning to replace the existing product/ software solutions in
your lab? Please mention the reason for the replacement.
[1] Yes (Why_________?)
[2] No

Filter for Q20= In-house

OPEN TEXT

Q25. Also, please comment on whether you are planning to add/ buy new software/
analysis solutions for your lab? If yes, can you tell us what all products are you planning
to buy and the reason for that particular product?
[1] Yes (Why_________?)
[2] No

Outsource secondary analysis to commercial service provider

Filter for Q20= Outsource

OPEN TEXT
Q26. If the secondary analysis is outsourced, please mention the name of the vendor,
brand/ product/ software. Please comment on the reason for using each vendor, pros of
that vendor and please comment on the features that are not present in currently used
software solutions but are considered essential or needed for more accurate analysis.
Also, comment on the pricing model for the service and the cost of each service.
MODERATOR INSTRUCTION]: Please ask to explain the reason.
Please share details using the following table:

Vendor Reason Pricing Cost of Pros Features not

/Brand/Software model for this present in
Name this service service SERVICE
solutions but
essential or
needed for
analysis
Filter for Q20= Outsource
OPEN TEXT
Q27. If secondary analysis is outsourced, are you planning on performing secondary
analysis in-house in the near future? If yes, can you comment on the reason for moving
to in-house analysis?
[1] Yes (Why_________?)
[2] No

Filter for Q20= Outsource, Q27=No

OPEN TEXT
Q28. Also, please comment on whether you are planning to change to a new provider in
the near future and if yes, can you tell us what vendors you consider and why?
[1] Yes (Vendor name_______; Why_________?)
[2] No

Tertiary Analysis Tools

(Tertiary analysis and interpretation includes variant annotation and filtering, data
aggregation, population structure analysis, diagnostic interpretation, clinical report
generation, etc.)

Filter: All respondents

OPEN TEXT
Q29. After secondary analysis is performed, does your laboratory conduct tertiary analysis
and interpretation in-house or outsource to a commercial NGS informatics service
provider? Please indicate in % how much of tertiary analysis is done in-house vs
outsourced. Please mention the reason for out-sourcing the analysis? [Ask open ended
question. Please place an X in the appropriate boxes and mention the percentage of
tertiary analysis work done in-house vs outsourced in the appropriate box, should add up
to 100%] and provide the reasoning. [MODERATOR INSTRUCTION]: Please ask to
explain the reason.

Tertiary analysis [X] % of work done in- Reason

house/ outsourced
In-house
Outsource

Analysis conducted In-house

Filter: Q29=In-house
OPEN TEXT
Q30. If the tertiary analysis is conducted in-house, please mention the type of solution
used (vendor/ commercial solution/ in-house developed or open-source), please place
an X in the appropriate boxes. Also, mention the name of the brand/ product/ software
for each of the solution. Please comment on the reason for using each product, pros of
using that product and please comment on the features that are not present in currently
used software solutions but are considered essential or needed for more accurate
 analysis. Also, please mention which NGS applications are you running through this
tertiary analysis SW? MODERATOR INSTRUCTION]: Please ask to explain the reason.
Please share details using the following table:

Solution [X] Brand name/ Reason Pros Features not Which NGS
Used product/ for present in application
software using software are you
(mention all each solutions but running
the products brand/ essential or through this
used in the product/ needed for tertiary
lab) software analysis analysis SW?
Vendor/
commercial
Solution
In-house
developed
Manual
interpretation
(e.g.
spreadsheet,
web and
literature
search )
Open-source
Other___

Filter: Q29=In-house, Q30= Vendor/ commercial Solution

OPEN TEXT
Q31. If commercial/ vendor solutions are used, please mention the pricing model for this
solution. Please place an X in the appropriate boxes. Also, can you tell us how much you
pay for these tertiary analysis solutions.
Please share details using the following table:

Pricing Model [X] Cost of the tertiary analysis

solution
One-off license
Per report fee / per sample fee
Per user (number of users limit)
Annual subscription
Bundled solution – provided with
reagents
Other
Filter: Q29=In-house, Q30= Vendor/ commercial Solution
OPEN TEXT

Q32. Can you comment on the implementation fee of the commercial software used in
your facility?

Filter: Q29=In-house
OPEN TEXT
Q33. In near future, are you planning to replace the existing product/ software solutions in
your lab? Please mention the reason for the replacement.
[1] Yes (Why_________?)
[2] No

Filter: Q29=In-house
OPEN TEXT
Q34. Also, please comment on whether you are planning to add/ buy new software/
analysis solutions for your lab? If yes, can you tell us what all products are you planning
to buy and the reason for that particular product?
[1] Yes (Why_________?)
[2] No

Outsource tertiary analysis to commercial service provider

Filter for Q29= Outsource

OPEN TEXT
Q35. If the tertiary analysis is outsourced, please mention the name of the vendor, brand/
product/ software. Please comment on the reason for using each vendor, pros of that
vendor and please comment on the features that are not present in currently used
software solutions but are considered essential or needed for more accurate analysis.
Also, comment on the pricing model for the service, the cost of each service and
turnaround time for receiving the report. And what all NGS applications are outsourced?
MODERATOR INSTRUCTION]: Please ask to explain the reason.

Please share details using following table:

Vendor / Reason Pricing Cost Report Pros Features What all NGS
Brand/So model for of this turnaroun not present applications
ftware this servic d time in SERVICE are
Name service e solutions outsourced?
but
essential or
needed for
analysis

Filter for Q29= Outsource

OPEN TEXT
Q36. If tertiary analysis is outsourced, are you planning to stop outsourcing the analysis in
near future? If yes, can you comment on the reason for moving to in-house analysis?
Also, what type of solutions would you prefer?
[1] Yes (Why_________?)
[2] No

Filter for Q29= Outsource, Q36=No

OPEN TEXT
Q37. Also, please comment on whether you are planning to change to a new provider in
the near future and if yes, can you tell us what vendors you consider and why?
[1] Yes (Vendor name_______; Why_________?)
[2] No

Vendor Selection Criteria

Filter: All respondents

SINGLE RESPONSE
Q38. If you are using vendor solutions or are planning to would you prefer a solution that
supports both secondary and tertiary analysis and interpretation? Can you please
explain the reason for your answer?
[1] Yes (Why_________?)
[2] No (Why_________?)

Filter: All respondents

RANK RESPONSE
Q39. What are the factors considered for evaluating vendors when procuring secondary
and tertiary analysis tools and elaborate why do you think so? Please rank each factor
from 1-5 with 5 as the highest priority and 1 being the lowest. [MODERATOR
INSTRUCTION]: Please ask to explain the reason for ranking.Please share details using
the following table:
Factors Rank Reason for a rank

Latest technology
Easy-to-use/ Good user interface
Product compatibility
Training and education programs
Product customization / flexibility
Accuracy
Knowledge base (content)
Cost
Contract structure and flexibility
Service and maintenance, software upgrades
Established relationship with the vendor
Brand reputation
Others (please specify)

Filter: All respondents

SINGLE RESPONSE
Q40. Does your lab use cloud solution for NGS data analysis/sharing? Please elaborate on
the reason for using or not using cloud.
[1] Yes (Why_________?)
[2] No (Why_________?)

Filter: Q40=No
SELECT ALL THAT APPLY
Q41. What are the hurdles to embracing cloud services? Please place an X in the
appropriate boxes.
 Hurdles [X]
Cost
Availability
Institutional policies
Knowledge
Not advanced enough
Data transfer issues
Security
Internal resources
Other (please specify)

Filter: All respondents

RANK RESPOSE
Q42. Overall, what are some of the challenges and bottlenecks that still remain in
analysing NGS data and elaborate on why you think so? Please rank each factor from 1-
5 with 5 as the most challenging and 1 being the least challenging. [MODERATOR
INSTRUCTION]: Please ask to explain the reason for ranking.

Please share details using the following table:

Challenges Rank Reason for a rank

Commercial Software availability

User intuitive software
Not turnkey solution (process NOT
completely automated)
Predictive algorithm improvement
Better data quality output
Reduce data processing burden
Long read data sequence improvement
Ability to detect ALL variant types (SNVs,
CNVs, fusions, INDELs)
Ineffective long read analysis
Affordable one-stop platform for NGS
data from analysis to visualization
Other (please specify)

NGS Market Opportunities

Filter: All Respondents
OPEN TEXT
Q43. How do you see the market evolving for informatics over the next 3-5 years? Please
comment.

Filter: All respondents

OPEN TEXT
Q44. Who are the key customer segments in addition to the current that you would want to
target in the next 2-3 years?

Filter: All respondents

OPEN TEXT
Q45. What are the steps in terms of service offerings, partnerships, areas of work that you
would want to improve in the next 2-3 years?

---Thank You---