Professional Documents
Culture Documents
cystic fibrosis testing, DNA obtained by a rapid involved. The amount of sample loaded could
extraction method, involving the use of a lysis be changed by injecting electrokinetically for
buffer and heating to 55°C for one hour, was periods of one to five seconds at 10 kV or
adequate. For DNA amplification by polymer- 15 kV. Electrophoresis in EDTA containing lx
ase chain reaction (PCR), one of the two prim- GeneScan Analyzer buffer remained constant
ers was labelled at its 5' end with the at 15 kV and 60°C, but the run varied from
fluorochrome 6-FAM. The following muta- 12-30 minutes depending on the amplicon
tions were sought on the basis of fragment size size. Data were collected and analysed using
differences between mutant and wild-type alle- the ABI PRISMTm Data Collection software
les: 3 base pairs AF508 deletion in cystic fibro- and GENESCANTm Analysis software, respec-
sis, the (CAG)n triplet repeat in Huntington tively.
disease, and the 20 kb deletion in the South
-
Table 1 Comparison of HD (CAG). triplet repeats determined by slab gel electrophoresis has meant that (CAG)n results are often
and capillary electrophoresis qualified-for example, 37 +/- 2 repeats.
Results for two alleles
However, this is different from that experi-
enced with capillary electrophoresis because in
Example Slab gel electrophoresis Capillary electrophoresis Comments all 79 cases assayed, capillary electrophoresis
1 17/21 15/19 Normal range generated results with a consistently lower n
2 17/17 15/15 Homozygous pattern value than that obtained from slab gel electro-
3 17/35-36 15/35 Intermediate range
4 18/37-38 16/36 Equivocal result phoresis (table 1).
5 23/39 21/38 Affected range
6 17/42-43 15/42 Affected range
7 15/54 13/52 High affected range aI THALASSAEMIA
8 29/52 26/26 False negative
9 17.69 (3.66)/ 16.05 (3.68)/ 29.24 (11.01) Composite of 78 results A five second injection time at 10 kV, followed
31.00 (11.03) (excluding #8) by a 30 minute capillary electrophoresis run,
Except for example 8, all 78 results obtained by capillary electrophoresis had an n value that was
enabled the mutant (- 697 base pairs) and
1-2 repeats smaller than slab gel electrophoresis. Examples read differently by two scientists are wild-type alleles (- 1006 base pairs) to be
reported as such. Corresponding capillary electrophoresis results were not subject to this variation. separated adequately in a prenatal test for a
Example 9 represents the mean (1 SD) of 78 results and confirms the consistent 1-2 repeat dif- thalassaemia resulting from a deletion of the
ference between the two methods.
South East Asian type (fig 1). Again, the sizing
been missed by capillary electrophoresis be- of the two alleles on capillary electrophoresis
cause the mutant allele was not seen and the did not correspond to that expected from
report, if issued, would have indicated a sequence data (660 and 980 base pairs) but, on
homozgyous normal pattern of n = 26 for the this occasion, the difference was in the higher
(CAG)n. range. The discrepancy was attributed to the
A discrepancy with capillary electrophoresis, GS2500 TAMRA marker that was required
similar to that described for cystic fibrosis, was because of the larger fragments present. This
also found when testing for the (CAG)n repeat marker proved to be unsatisfactory, frequently
in Huntington disease. The current experience giving split peaks, and making sizing particu-
with quantitation of triplet repeats in a number larly difficult because it was not clear which of
of neurological disorders is based on slab gel the two peaks should be taken as the reference
electrophoresis. For example, a cut off used for one. This artefact was not found with the
the mutant allele in Huntington disease is an n smaller GS500 TAMRA molecular weight
value > 37. However, this has to be redefined marker. In the above prenatal diagnosis exam-
when the capillary electrophoresis results show ple, the anomalous result depicted in fig 1 led
consistently lower repeat numbers ofbetween 1 to further testing using a chromosome 15 mic-
and 2 fewer repeats (table 1). Like the cystic rosatellite (AFM320). This confirmed non-
fibrosis results described earlier, the triplet paternity (fig 1).
repeat quantitation on capillary electrophoresis
was highly reproducible. The different meth- DNA SEQUENCING
ods in use and the inherent problems of slab Three missense mutations (A149P, A174D,
gels, when used to quantitate triplet repeats, and N334K) in the aldolase B gene account for
- 70-90% of cases with hereditary fructose
300 450 600 750 900 1050 1200 1350 1500 intolerance in the USA and UK.4 Two of these
A mutations (A149P, which is a G to C transver-
01 sion, and A174D, which is a C to A
EU 5B: T992-5 / EU 5R: T992-5 / transversion) are found in exon 5 of the gene.
B
0~~~~~~~
tIUi lR:
EU 1B: T991-1 T991 -1/
In a family with this disorder, the proband was
known to be heterozygous for the A149P
mutation, which can be detected easily because
C
0 =-
EU 6B: T993-6 I 6R: T993-6 /
it creates a new site for the restriction enzyme
AcyL. However, the second mutation was
unknown. To detect the latter, the relatively
small exon 5 of the gene was sequenced rapidly
by capillary electrophoresis. This showed the
D
0, proband to be a compound heterozygote for
DE 8Y: T991-AFM320-8 / EU 8R: T991-AFM320-8 I the A149P and A174D defects.
E Comparative studies of the ABI PRISMTM
310 Genetic Analyzer with the ABI PRISMTM
F
377 model, which uses fluorescent based tech-
0 nology with slab gel electrophoresis, gave the
DE 9Y: T992-AFM320-9 / 9U9R: T992-AFM320-9 1 following results for DNA sequencing (table
2). These showed that for a relatively small
Figure 1 a Thalassaemia testing showing that the mother (B) is heterozygous for the sized amplicon, such as the aldolase B gene, the
common SEA deletion and the fetus (C) is homozygous for this defect because there is only ABI PRISMTM 310 Genetic Analyzer was very
the smaller (mutant) allele present. The father (A) appears to be normal, which suggests sensitive and gave both satisfactory and rapid
non-paternity. Another explanation would be a second, more extensive deletion in the father results. However, for sequencing of a larger
and fetus which has not been detected by PCR. (D-F) Microsatellite analysis (AFM320)
shows that the fetus (E) shares a common band with the mother (D) and father (F), but amplicon, such as would be required with the
has a second band that is not found in his father; this result confirms non-paternity. UBE3A gene (mutations in which give rise to
Another feature of the traces illustrated is the co-migrating DNA size markers (small peaks the Angelman syndrome)5 the ABI PRISMTM
at the bottom of each trace). This is possible because the size markers are labelled with a
different fluorochrome to the PCR primers. 377 would be a more efficient option.
264 Le, Fung, Trent
Table 2 Comparison of direct sequencing of PCR derived products from the UBE3A and mated DNA analysis, the comparable model to
aldolase B genes the ABI PRISMTm 310 (that is, one that offers
ABI PRISMTm 310 multicolour fluorescence and both fragment
Feature ABI PRISMTrm 377 Genetic Analyzer analysis and sequencing capabilities) is the ABI
Average length of sequence read 600 bases 350 bases
PRISMTm 377. However, the latter is consider-
Number of samples processed in 8 hours Up to 64 Up to 15 ably more expensive to purchase. The impres-
Running time per sample -7 hours (irrespective of -30 minutes (for sive reproducibility demonstrated by the ABI
template length) template of 250 bp) PRISMTm 310 Genetic Analyzer has improved
Sensitivity*
Injection volume -2 il -0.1 p1 the quality of the results coming from this
fmol of dye terminator/peak 2x fmol 0.01 6x fmol laboratory because it takes away observer error
*Assume that at the completion of the reaction there are x pmol of sequencing product. For the in gel reading and the intrinsic deficiencies
ABI PRISMTm 377 analysis, the product was dissolved in 4 pl of buffer and for the ABI PRISMTm associated with slab gel electrophoresis. In
310 it was dissolved in 24 p1 of buffer. A 2 pl aliquot was used to load the ABI PRISMTM 377 association with this, the availability of hard
(0.5x pmol) and an estimated 0.1 p1 aliquot was used for the ABI PRISMTm 310 (0.004x pmol). data for comparative purposes, rather than
For a reading of 250 bases in the aldolase B gene sequence, each peak, on average, would repre-
sent 0.5x/250 pmol (ABI PRISMTm 377) or 0.004x/250 pmol (ABI PRISMTm 310) of dye termi- estimations of DNA fragment sizes from slab
nator. Thus, the ABI PRISMTm 310 is _102 times more sensitive than the ABI PRISMTm 377. The gels, will facilitate quality assurance.
above calculation uses a conservative loading volume of 0.1 1 for the capillary3 and is based on One false negative result in the present study
sequencing runs (ABI PRISMTm 377 and 310) that demonstrated comparable signal intensities.
was obtained when testing for the Huntington
COSTS disease mutation. However, it is more likely
Over a period of approximately six months it that this represented a PCR error, rather than a
was estimated that each sample electro- capillary electrophoresis problem, since the
phoresed with the ABI PRISMTm 310 Genetic latter technique is more sensitive than slab gel
Analyzer cost, in terms of consumables, an electrophoresis and two different PCRs were
additional AUD$ 10 to process. Although there involved. In cases in which a homozygous
are other automated means to undertake DNA result is obtained, reports are not issued until a
analysis including sequencing (for example, the second PCR using a different set of primers is
ABI PRISMTm 377), the ABI PRISMTm 310 undertaken. The additional work required to
was competitively priced with a platform cost do this has been eased by developing a capillary
of around AUD$80 000 compared with about electrophoresis based assay.
AUD$200 000 for the 377 model. There are A problem with capillary electrophoresis is
cheaper instruments that allow capillary elec- fragment sizing, which can differ from that
trophoresis to be undertaken, but these do not obtained with conventional slab gel electro-
have the multicolour capability. phoresis. In some circumstances, such as
forensic testing, these may not be significant
Discussion because comparisons are being made. How-
The numbers of forensic, industrial, and clini- ever, the detection of genetic disorders requires
cal applications that utilise capillary electro- both comparisons and, in the case of triplet
phoresis are growing. Analytes that can be repeat quantitation, the calculation of an abso-
separated by this technique are also extensive lute number. For Huntington disease, the
and include amino acids, proteins, drugs, (CAG)n result will place an individual into one
chemicals, oligonucleotides, and DNA.2 In the of three groups: normal, n < 31; intermediate,
area of DNA genetic diagnosis, capillary n = 31-37; and affected, n > 37. Interpreting
electrophoresis has been successful in detecting results in this disorder becomes difficult when
the G1 69 1A mutation in the factor V gene,6 in triplet repeats fall at the normal/intermediate
mutation analysis for familial defective apolipo- or intermediate/mutant cut off values. This
protein B-100,7 and in screening of the p53 could be resolved by: testing two populations
gene.8 and determining the normal and affected
The present study describes the experience triplet repeat ranges based on capillary electro-
of a molecular genetics laboratory that provides phoresis, or providing DNA reports that place
a DNA diagnostic service for a range of genetic patients into the three groups by running the
disorders. In this laboratory, the availability of appropriate known controls with each assay.
capillary electrophoresis and, thus, the option Either would be reasonable. The first option
to automate, has increased productivity by has the potential to cause confusion, since units
allowing staff additional time to use their skills would not be directly comparable unless it was
in more relevant activities. Thus, it will become clear which method (capillary electrophoresis
possible to increase the range of tests available, or slab gel) was followed. The second approach
a move that would not have been considered may also require identification of individuals
when the manual methods were in use. Assays who have an upper intermediate value for the
are now electrophoresed overnight and the (CAG)n and, therefore, are at risk of transmit-
results are scanned on the following day (each ting a premutation or even Huntington disease
sample takes - 30 minutes to run). While a run to their offspring.9
is in progress, the ABI PRISMTm 310 can be The discrepancies in band sizing between
programmed to retest unsatisfactory samples slab gel electrophoresis and capillary electro-
or change the order of samples to be assayed. phoresis can be explained partly by the
The ability to use primers labelled with different sieving effect of cross linked polyacry-
different coloured fluorochromes has ex- lamide compared to the linear polymer used in
panded the potential for multiplexing, which is capillary electrophoresis.'0 An electro-osmotic
essential when dealing with genetic disorders effect, which would alter the migration of DNA
produced by multiple mutations. Although fragments, could be another factor. It is
there are other machines available for auto- difficult to assess the latter variable, because
DNA capillary electrophoresis 265
the specific composition of the polymers is not The additional running costs associated with
obtainable from the manufacturers. However, capillary electrophoresis need to be balanced
the use of coated capillaries would exclude an by its usefulness. For a laboratory with a high
electro-osmotic effect.' We have discussed the throughput of DNA samples, the costs are rea-
sizing problem with the manufacturers on a sonable because they are offset by the produc-
number of occasions but, to date, no definitive tivity gained. Each laboratory will need to
explanations have been forthcoming. assess its needs and resources in this respect. In
As polymer technology is evolving rapidly, view of the potential for this technology, labo-
the range and types of separation matrices are ratories that are involved in the provision of a
considerable.' The changing of commercial DNA diagnostic service should consider utilis-
polymers by the manufacturer (as happened to ing techniques that are more compatible with
us) or the use of alternative polymers including capillary electrophoresis. Thus, the value of
"home made" ones will mean that mobility hybridisation based strategies should be re-
and, therefore, band sizes could change. The viewed and more effort placed in those that rely
concentration of the amplicon used for capil- on fragment size analysis.
lary electrophoresis analysis can also be crucial
because overloading has the potential to This work was supported by the NHMRC and grants from the
complicate data interpretation. If necessary, RebeccaAlfredL Cooper Medical Research Foundation and the Royal
this can be avoided by checking the PCR prod- Prince Hospital Research Foundation. We thank Dr A
Fimmel and Mr B Watson for their help with DNA analyses.
ucts on minigels before capillary electrophore-
sis. 1 Cotton RGH. Slowly but surely towards better scanning for
The routine diagnostic laboratory may be 2 Altria mutations. Trends Genet 1997;13:43-6.
KD, ed. Capillary electrophoresis guidebook. Princi-
faced with mutation detection for a genetic ples, operation and applications. In: Methods in molecular
disorder in which it would be easier to 3 biology. Vol 52. New Jersey: Humana, 1996:1-122.
Barron AE, Blanch HW. DNA separations by slab gel and
sequence a segment of DNA than test for indi- capillary electrophoresis: theory and practice. Sep Purif
vidual mutations. This approach is illustrated 4 TolanMethod 1995;24:1-118.
DR, Brooks CC. Molecular analysis of common aldo-
by the hereditary fructose intolerance example lase B alleles for hereditary fructose intolerance in North
in which two common mutations (A149P and Americans. Biochem Med Metab Biol 1992;48:19-25.
T, Sutcliffe JS, Fang P, Galjaard R-J, Jiang Y-H,
A174D) are present in a small exon. As shown 5 Matsuura
Benton CS, et al. De novo truncating mutations in E6-AP
in this particular case, DNA sequencing ubiquitin-protein ligase gene (UBE3A) in Angelman
allowed both to be detected or screened for in 6 Van syndrome. Nat Genet 1997;15:74-7.
de Locht LTR, Kuypers AWHM, Verbruggen BW, Lin-
the one capillary electrophoresis run. On the ssen PCM, Novakova IRO, Mensink EJBM. Semi-
automated detection of the factor V mutation by allele spe-
other hand, capillary electrophoresis in its cific amplification and capillary electrophoresis. Thromb
present form (a single capillary with samples Haemostas 1995;74:1276-9.
7 Lehmann R, Koch M, Pfohl M, Voelter W, Haring H-U,
loaded sequentially) is less suitable for se- Iiebich HM. Screening and identification of familial defec-
quencing large DNA fragments or for laborato- tive apolipoprotein B-100 in clinical samples by capillary
gel electrophoresis. J Chromatogr 1996;744: 187-94.
ries in which DNA sequencing is a major work 8 Katsuragi K, Kitagishi K, Chiba W, Ikeda S, Kinoshita M.
component. This may change as the polymers Fluorescence-based polymerase chain reaction-single-
for capillary electrophoresis are developed strand conformation analysis of p53 gene by capillary elec-
trophoresis.J Chromatogr 1996;744:311-20.
further-for example, a claim for the latest ABI 9 Kremer B, Goldberg P, Andrew SE, Theilmann J, Telenius
polymer (Performance Optimized Polymer 6) H, Zeisler J, et al. A worldwide study of the Huntington's
disease mutation. The sensitivity and specificity of measur-
is that it can resolve 600 bases in a shorter run ing CAG repeats. N Engl Jf Med 1994;330:1401-6.
time than would be possible with the 377 10 Quesada MA. Replaceable polymers in DNA sequencing by
capillary electrophoresis. Curr Opin Biotechnol 1997;8:82-
model. 93.