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Research Report

Quantitative Real-Time PCR Assay for


Determining Transgene Copy Number in
Transformed Plants
BioTechniques 31:132-140 (July 2001)

David J. Ingham, Sandra INTRODUCTION ues are determined during the logarith-
Beer, Stephanie Money, and mic phase of amplification, PCR
Geneviève Hansen Efficient transformation procedures reagents are nonlimiting, and reactions
for plants necessitate the development will be most efficient (2). Therefore,
Syngenta, Research Triangle of rapid assays for the analysis of the use of real-time (kinetic) detection
Park, NC, USA putative transformants. To determine techniques both simplifies and increas-
whether the insertion of the transgene is es the accuracy of quantitative PCR as-
simple (one copy) or complex (multiple says (reviewed in Reference 2).
and truncated copies), scientists have In the assay described here, we use
traditionally relied on labor-intensive duplexed TaqMan reactions to accu-
nucleic acid blotting techniques (South- rately quantitate the level of a transgene
ern blots) (16). To overcome this limita- relative to an endogenous calibrator
tion, we have developed an assay for gene. This relative quantitation ap-
transgene insertion characterization that proach provides a simplified, accurate
utilizes the speed, throughput, and alternative to using standard curves and
quantitative accuracy of the fluorogenic absolute quantitation. Because the en-
5′-nuclease assay known as TaqMan dogenous calibrator sequence remains
(Applied Biosystems, Foster City, CA, constant relative to total genomic DNA,
USA) (4,7,8,10,12). any variation in the relative level of the
The TaqMan assay is a real-time transgene to the endogenous gene is in-
ABSTRACT PCR detection technique in which the dicative of a difference in copy number.
accumulation of PCR product is moni- As shown in Figure 1, 2-fold differ-
The development of transgenic events tored directly during the progress of the ences in copy number are easily distin-
can be limited by many factors. These in- reaction. The details of the TaqMan as- guished using TaqMan technology. The
clude expression levels, insert stability and say have been described previously TaqMan copy number assay allows the
inheritance, and the identification of simple (4,8,10,12). Degradation of target-spe- screening of hundreds of plants with
insertion events. All of the factors can be re- cific probe molecules by the 5′ to 3′ ex- greater accuracy within hours as com-
lated to the copy number of the transgene. onuclease activity of Taq DNA poly- pared to weeks using conventional
Traditionally, copy number has been deter- merase during each cycle of methods. This allows greater numbers
mined by laborious blotting techniques. We amplification produces an accumula- of independent transformation events to
have developed an alternative approach tion of fluorescence. Increased levels of be screened for desired traits in shorter
that utilizes the fluorogenic 5′ nuclease fluorescence are directly related to the time and at significant cost savings.
(TaqMan) assay to quantitatively deter- accumulation of PCR product and are Advantages and limitations of the Taq-
mine transgene copy level in plants. Using detected during each cycle of amplifi- Man assay over conventional proce-
this assay, hundreds of samples can be ana- cation through the use of specialized in- dures are also discussed.
lyzed per day in contrast to the low through- strumentation (ABI PRISM 7700; Ap-
put encountered with traditional methods. plied Biosystems, Foster City, CA,
To develop the TaqMan copy number assay, USA). Cycle thresholds (Ct) are as- MATERIALS AND METHODS
we chose to utilize our highly efficient signed automatically to each sample
Agrobacterium-mediated transformation according to the cycle at which the flu- Plant Material
system of maize. This transformation proce- orescence exceeds a specific level
dure generates predominantly low copy above background (Figure 1). Samples Transgenic maize plants from the in-
number insertion events, which simplified with higher levels of template at the be- bred line A188 were obtained via
assay development. We have also successful ginning of the reaction will amplify to Agrobacterium-mediated transforma-
applied this assay to other crops and trans- detectable levels more quickly and tion. The selectable marker phospho-
formation systems. yield a lower Ct. Because threshold val- mannose isomerase (pmi) under the

132 BioTechniques Vol. 31, No. 1 (2001)


Research Report
Table 1. Description of Primers and Probes USA) basically according to manufac-
PCR turer’s instruction, except all steps were
Target Product Forward Primer Reverse Primer conducted in 1.2-mL 96-well plates.
Gene Size (bp) (5′′→3′′) (5′′→3′′) Probe (5′′→3′′)
The dried DNA pellet was resuspended
in 500 µL TE (10 mM Tris-HCl, pH
8.0, 1 mM EDTA).
adh 71 GAACGTGTGT TCCAGCAATCC TGCAGCCTAACC
TGGGTTTGCAT TTGCACCTT ATGCGCAGGGTA
Primers and Probes
pmi 60 CCGGGTGAA GCCGTGGCCTT TGCCGCCAACGA
TCAGCGTTT TGACAGT ATCACCGG PCR primers and probes were de-
signed using Primer Express software
(Applied Biosystems). Primers and
control of the Zea mays ubiquitin pro- maize leaves of transgenic and non- probes were purchased from Integrated
moter was used to recover transgenic transgenic plants. After collecting leaf DNA Technologies (Coraville, IA,
plants as described by Negrotto et al. samples of approximately 7 × 25 mm USA). For the endogenous control,
(13). Regenerated plants were trans- in wells of a 96-well plate (Corning, primers and probes were designed spe-
ferred to soil and hardened off in a phy- Corning, NY, USA) containing ap- cific to the Zea mays alcohol dehydro-
totron (16/8-h light). After 2–3 weeks, proximately 100 mg l-mm glass beads genase (adh) gene (GenBank acces-
plants were transferred to the green- (BioSpec Products, Bartlesville, OK, sion no. AF044295). For the transgene,
house and grown in commercial, soil- USA), the plates were placed into a mi- primers and probes were designed spe-
less potting mixture. Greenhouse condi- nus 80°C freezer for greater than 30 cific to the selectable marker gene pmi
tions for plant growth were 28°C days, min and lyophilized overnight. (GenBank accession no. M15380) (13).
23°C nights, and a 16-h day length. Tissues were ground by an adapted Probes were labeled at their 5′ end with
reciprocating saw for 30 s, rotated a reporter fluorophore [tetrachloro-6-
180°, and ground for 30 s. Genomic carboxyfluorescein (TET) for adh and
DNA Preparation from Plant Samples fluorescein (FAM) for pmi] and at the
DNA was extracted using the
Puregene Genomic DNA Extraction 3′ end with the quencher fluorophore
Genomic DNA for TaqMan copy
kit (Gentra Systems, Minneapolis, MN, tetramethylrhodamine (TAMRA). Se-
number assays was isolated from
quences of primers and probes used in
this work are shown in Table 1.

TaqMan Reactions

PCRs were carried out in 96-well re-


action plates (Marsh Bio Products,
Rochester, NY, USA). Reactions were
multiplexed to simultaneously amplify
pmi and adh. For each sample, a master
mixture was generated by combining
20 µL extracted genomic DNA with 35
µL 2× TaqMan Universal PCR Master
Mix (Applied Biosystems) supplement-
ed with primers to a final concentration
of 900 nM each, probes to a final con-
centration of 100 nM each, and water to
a 70 µL final total volume. This mixture
was distributed into three replicates of
20 µL each in 96-well amplification
plates and sealed with optically clear
heat seal film (Marsh Bio Products).
PCR was run in the ABI PRISM 7700 in-
strument using the following amplifica-
tion parameters: 2 min at 50°C and 10
min at 95°C, followed by 35 cycles of
Figure 1. Example of TaqMan results representing amplification plots from serial dilutions of tem- 15 s at 95°C and 1 min at 60°C. Post-
plate DNA. Template DNA was serially diluted 2-fold and run in triplicate in standard TaqMan copy run manipulations of data were per-
number assays. Data for the endogenous control (TET layer) extension phase were extracted and plotted.
Each 2-fold dilution should be separated by 1 Ct. The cycle threshold (red horizontal line) provides an formed according to the manufacturer’s
arbitrary cutoff at which a Ct value for each sample is assigned (see text). instructions and as described below.

134 BioTechniques Vol. 31, No. 1 (2001)


Research Report
Calculation of Gene Copy Number copy) of the gene of interest. By com- number of insertion loci (Figure 3, A
paring the ∆Ct value of the unknown and B). Following digestion, DNA frag-
During the TaqMan reaction, the samples to the ∆Ct of a known control, ments were separated on a 0.8%
software accompanying the ABI PRISM ∆∆Ct is obtained [∆∆Ct = ∆Ct(Un- agarose gel and blotted to positively
7700 instrument detects the accumula- known) - ∆Ct(Known)]. Copy number charged nylon membrane following
tion of PCR product by the accumula- can then be calculated using the ∆∆Ct standard procedures (15). A pmi-specif-
tion of fluorescence. Normalized fluo- value using the equation: Copy Number ic restriction fragment was labeled with
rescence relative to established baseline = 2(∆∆Ct). For example, when normal- [32P]-dCTP by random priming using
levels (∆Rn) is plotted versus cycle ized to a known one-copy control, a one the ReadyPrime II DNA Labeling Kit
number. A Ct value is obtained by copy insert should have a ∆∆Ct value of (Amersham Pharmacia Biotech, Upp-
drawing an arbitrary cutoff through the zero (2(∆∆Ct = 0) = 1 copy), a two copy sala, Sweden). Hybridization was car-
reactions so that the line passes through insert ∆∆Ct will be one (2(∆∆Ct = 1) = 2 ried out overnight at 65°C in hybridiza-
the log phase of each reaction (Figure copies), a four copy insert will display tion buffer (500 mM sodium phosphate,
1). The sequence detection system soft- a ∆∆Ct value of 2 (2(∆∆Ct = 2) = 4 pH 7.0, 1 mM EDTA, 7% SDS, 1%
ware with the ABI PRISM 7700 instru- copies), etc. Through the inclusion of a BSA) containing approximately
ment provides the cycle number at known copy control sample in each as- 100 000 cpm of labeled probe. The first
which the accumulation of fluores- say, accurate relative copy number is wash was carried out at 65°C with (40
cence (PCR product) of a particular re- calculated for each unknown sample. mM sodium phosphate, pH 7.0, 1 mM
action crosses the threshold (Ct). The EDTA, 5% SDS, 0.5% BSA) for 15
FAM Ct (pmi) value is compared to the Southern Blot Hybridization min. The final wash was carried out at
TET Ct (adh) value to normalize the 65°C with (40 mm sodium phosphate,
FAM Ct value of each reaction to the For Southern blot analysis, total pH 7.0, 1 mM EDTA, 1% SDS) for 15
level of total nucleic acids present to DNA was isolated from approximately min. The membrane was exposed to X-
yield ∆Ct [∆Ct = Ct(FAM) - Ct(TET)]. 1 g leaf tissues from nontransformed ray film at -80°C for two days.
This calculation removes any variation control plants and putative transfor-
contributed by unequal template input mants as described previously (3).
in reactions and therefore allows the as- DNA (5–10 µg) was digested with RESULTS AND DISCUSSION
say to be conducted without prior de- EcoRV. Digestion with this enzyme and
termination and normalization of DNA subsequent hybridization with a pmi- Development of the TaqMan Copy
concentrations. Because the number of specific probe allows the identification Number Assay
copies of endogenous gene per genome of the border fragment between the in-
remains constant, a change in ∆Ct cor- sert and the plant DNA and provides an To estimate the copy number of pmi
responds to a change in quantity (or estimate of transgene copy number and gene in transgenic plants, we have cho-
sen the ∆∆Ct method for duplexed Taq-
Man reactions. In this approach, the
transgene level is determined relative to
an endogenous control gene to normal-
ize all reaction variations that are due to
initial template DNA concentration dif-
ferences. For an endogenous control,
one should select a sequence with few
copies per genome, and the gene should
be well conserved through different
ecotypes or lines of the crop being used
to allow the assay to be broadly applic-
able. This approach will simplify the
assay development process (see below).
To analyze the efficiency of du-
plexed TaqMan assays, we conducted
experiments similar to that in Figure 2.
In these experiments, a dilution series
of a transformed DNA sample is gener-
ated, and duplexed assays are run in
triplicate for each dilution. By plotting
Figure 2. TaqMan assay efficiencies for pmi and adh primer and probe sets. DNA from a single-copy the average Ct and ∆Ct values for each
pmi transgenic Zea mays plant sample was serially diluted 2-fold and used in duplexed TaqMan copy num- dilution and fitting a logarithmic curve
ber assays as discussed in Materials and Methods. Averaged Ct values of three replicates of each sample to each set of data, one can determine
for the FAM (pmi) or TET (adh) layers were plotted versus dilution factor. In addition, the ∆Ct values ob-
tained by subtracting average Ct values of adh from pmi were plotted on the secondary axis. A logarithmic the relative efficiencies of the reactions.
curve was fitted to each data set, and the corresponding R2 value was displayed on the plot. A reaction having an efficiency of

136 BioTechniques Vol. 31, No. 1 (2001)


100% would yield a Ct R2 value of 1.0. variation over the dilution series. This
Therefore, the closer a R2 value is to result is also an indication of the ro-
1.0, the more efficient the reaction bustness of the assay. Because little or
(Figure 2). The R2 values for pmi and no variation is observed in ∆Ct over the
adh TaqMan sets are 0.9908 and dilution range, calculated copy number
0.9942, respectively; therefore, each re- will also change little over that range.
action is highly efficient, and there is Therefore, the assay can accurately pre-
no evidence of competition for dict copy number among samples of
reagents. In addition, if both assays varying DNA concentrations. This al-
have approximately equal efficiency, lows us to perform assays on samples
then one would expect ∆Ct values to without prior DNA quantitation and
change little over the dilution range. normalization. This reduces the turn-
Therefore, the expected ∆Ct R2 value around time and cost of the assay.
for reactions of equal efficiency would The instructions that accompany the
be zero. As shown in Figure 2, the R2 TaqMan instrumentation detail the re-
value for the plotted ∆Ct values of this quirement for determining appropriate
experiment was 0.0001, indicating little limiting primer concentrations for mul-

Figure 3. Southern blot showing the correlation of TaqMan copy number assay data with Southern
analysis. (A) Graphic representation of the putative insertion event (not to scale). Open box indicates the
Agrobacterium insertion cassette with left (LB) and right (RB) borders represented by hatched boxes.
The position of the pmi gene is indicated by the filled arrow. Flanking plant genomic sequences are indi-
cated by the solid lines. Positions of EcoRV restriction sites are indicated above the T-DNA insert and at
an unknown position in the genomic DNA flanking the insert. The fragment used to generate pmi-spe-
cific probes is indicated by the speckle-filled box below the pmi gene. (B) As described in Materials and
Methods, DNA samples from 16 single-copy events as determined by TaqMan copy number assay were
digested with EcoRV, fractionated by agarose gel electrophoresis, blotted to nylon, and probed with a
pmi-specific probe. Results confirm all 16 events as single copy for the pmi transgene. Position of mole-
cular weight size markers is indicated to the left of the figure.

Vol. 31, No. 1 (2001) BioTechniques 137


Research Report
tiplexed reactions. Because we are pri- Table 2. Correlation of TaqMan to Southern Blot Assay for Transgene Copy Determination
marily interested in simple insertion TaqMan Copy Assaya Correlation with Southernb
events and Agrobacterium-mediated (% of Total) (No. Analyzed)
transformation produces predominantly
simple insertion events (6), the du-
plexed targets (pmi and adh) would be 1 Copy 201 (70%) 100% (27)
at approximately the same starting con- 2 Copies 62 (21%) 75% (8)c
centration. Therefore, we reasoned
>2 Copies 24 (8%) 100% (2)
there would be little need to use limit-
ing primer concentrations for our as- Total No. Assayed 289 95% (37)
says because there would be little (if aNumber of samples determined to have the indicated copy number by TaqMan
any) competition for reagents during
assay.
the log phase of each reaction. This is
bPercentage of samples in which Southern data confirmed TaqMan results (only
in contrast to duplexed reactions in
which one target is in large excess of a subset of samples were analyzed by Southern).
the other (as in expression studies using cTwo samples called 2 copy by TaqMan assay displayed a single band on a
18S ribosomal RNA as a normalizing Southern blot.
control), which may deplete reagents
before the less abundant target reaction
accumulates to detectable levels. This assay was then run using samples in These results are consistent with previ-
type of a result is detrimental to the ef- which the copy number of the gene of ous observations for Agrobacterium-
ficiency (and therefore the accuracy) of interest was already determined by transformed dicotyledonous and mono-
the low-abundance target reaction (2). Southern analysis. A high degree of cotyledonous plants (6).
To test our reasoning, we performed re- correlation was observed between the Although developed in Zea mays, the
action efficiency experiments similar to TaqMan data and data from Southern TaqMan copy number assay discussed
Figure 2 comparing limiting and non- analysis (Table 2 and Figure 3). This re- here is also applicable to other crops
limiting primer concentrations for each sult indicated that the developed Taq- (both monocotyledonous and dicotyle-
target. We found that for all TaqMan Man copy assay was highly accurate; donous plants) and diverse organisms.
assays tested, primer limitation in- therefore, we implemented the assay on We have successfully adapted this assay
creased the variability and decreased large numbers of samples with un- for copy number determination in a va-
the dynamic range of the assays. For known copy number (see below). riety of transgenic plants, including
example, when we examined the Taq- wheat, barley, rice, watermelon, tomato,
Man sets used in this report, we found Copy Number of pmi in cotton, and sugarbeet. In addition, simi-
the standard deviations for ∆Ct calcu- Transgenic Plants lar assays have also been reported for
lated over a dilution series to drop to the quantitative analysis of protoonco-
0.11 for nonlimited primer conditions, Copy number was assessed for trans- gene amplification in cancer studies
from 0.22 under limiting primer condi- genic maize containing the pmi-selec- (1,5,7,9,11,14). Thus, it is not surprising
tions. In addition, we found the ∆Ct R2 table marker. To calculate the number of for the TaqMan copy number assay to
values were reduced from a range of copies of pmi for each plant, DNA ex- be widely applicable to any organism.
0.1–0.2 under limiting conditions to tracted from each plant was run, in trip- Taking advantage of the optimized Taq-
less than 0.07 under nonlimiting condi- licate, in a duplex TaqMan assay com- Man copy number assay developed
tions, indicating greater accuracy of paring pmi level to the endogenous here, we are evaluating extensive num-
copy number calculation when using control gene (adh). Copy number was bers of transformation events for a vari-
nonlimiting primer concentrations calculated for each sample as described ety of crops to better characterize the
(Figure 2). Therefore, we decided to above by comparison of each unknown transformation process and to more pre-
use the maximal recommended primer to a one-copy control sample included cisely identify desirable events.
concentration (900 nM) for each primer in each assay. In general, there was very
in the reaction. The elimination of the little variation (<0.2 ∆Ct) between the Accuracy of TaqMan
requirement to find limiting primer triplicate reactions. Copy Number Assay
concentrations for each duplex reaction We evaluated 289 putative transfor-
has significantly reduced our assay de- mants and found that the Agrobacteri- The accuracy of the assay developed
velopment time. um-mediated transformation system here can be assessed in two ways. First,
In addition to testing the TaqMan developed for Zea mays (13) produced by comparing results obtained from
sets on transformed samples, the set for a majority of simple transformants TaqMan assays to those from Southern
pmi was tested for background signal in (Table 2). Transformants (70%) were blot analysis, we can determine the rate
samples from nontransgenic plants. For found to contain only one copy of the of correlation. We compared TaqMan
pmi, no detectable background signal insert, and only 21% had two copies. and Southern results for a total of 37
was obtained (data not shown). Once The remaining 8% of plants contained samples for this report. These results
all criteria were satisfactorily met, the greater than two copies of the insert. are summarized in Table 2 and exem-

138 BioTechniques Vol. 31, No. 1 (2001)


Table 3. TaqMan Assay Copy Discrimination Southern blot analysis. Because Taq-
Capability Man assays are specific to a small se-
Copy quence of the gene, it is not possible to
No.a nb SDc cvd
rule out the presence of truncated or
mutated copies of the transgene that
may not be detected by the assay.
1 47 0.10 10% Therefore, both TaqMan and Southern
2 41 0.24 12% blot analyses are important assays for
comprehensive analysis of transforma-
3 10 0.43 14% tion events. Currently, every sample
4 8 0.32 8% that passes the copy number criteria by
the TaqMan assay is independently
5 18 0.53 11%
confirmed by additional assays includ-
6 ing nucleic acid blotting before exten-
7
sive field testing.
A second approach to determining
8 11 1.22 15% the level of accuracy of the TaqMan as-
9 13 1.39 15% say involves the comparison of results
of replicate samples. The Ct difference
10 between consecutive copy numbers di-
11 minishes as the copy number increases.
Therefore, the most accurate differenti-
12 13 1.82 15% ation is obtained between one and two
aTransgene copy number as copy events with discrimination capa-
determined by TaqMan and/or bility diminishing as copy number in-
creases. To test these predicted limita-
Southern assay
tions, we conducted replicate assays on
bTotal number of samples analyzed. samples of various copy number (Table
cStandarddeviation of calculated 3). The standard deviation for the calcu-
copy numbers. lated copy numbers of replicate sam-
ples increases from 0.1 copy variation
dCoefficientof variation (standard for one-copy samples to greater than
deviation/copy number). 1.0 copy deviations for samples greater
than or equal to eight copies. These re-
sults are consistent with our observation
plified in Figure 3. We found a 95% of ∆Ct standard deviations in the range
overall correlation rate between South- of 0.1–0.2 for most assays (unpublished
ern blot and TaqMan assay data for observations). If we also look at the cal-
these transgenic plants. The two non- culated coefficient of variation (CV) for
correlative samples were identified as each copy number in this assay, they
two copy insertion events by TaqMan fall in the range of 8%–15% (average
copy number assay but displayed a sin- 12%), illustrating the high level of con-
gle band when analyzed by Southern sistency of the assay over a broad range
blot. We have not determined which as- of target copy number. If we use an av-
say result is correct. It is possible that erage CV of 12% to predict the ability of
the single hybridizing band observed in the assay to differentiate sequential
the Southern blot could be generated by copy numbers, we find the discrimina-
the insertion of two T-DNA copies in a tion ability of the assay will stop around
tandem inverted orientation. Such a four copies of a target (12% of 4 copies
two-copy insertion event would yield a = about 0.5 copy variation). The ob-
single hybridizing band that would vary served standard deviation shown for a
in size depending on the amount of in- four-copy sample in Table 3 illustrates
tervening sequence. This scenario, al- the assay’s discrimination ability to be
though speculative, illustrates the po- slightly better than this prediction. For
tential pitfalls of well-established these reasons, we limit assigning exact
procedures such as Southern analysis. copy values to results of four copies and
These results illustrate both the high below. This limitation was not problem-
levels of accuracy of the TaqMan assay atic for our studies because simple in-
and the limitations of both TaqMan and sertion events were the desired product.

Vol. 31, No. 1 (2001) BioTechniques 139


Research Report
Similar limitations for high copy num- copy number assay also has an advan- tion-based homogeneous assay with fluoro-
ber samples can also be observed for tage over Southern blot analysis in the genic probes to measure c-erbB-2 oncogene
amplification. Clin. Chem. 43:752-758.
copy number analysis by Southern blot size of sample required for each assay. 6.Hansen, G. and M.D. Chilton. 1999. Lessons
(unpublished observation). Complex Because TaqMan is a PCR-based assay, in gene transfer to plants by a gifted microbe.
banding patterns create added subjec- much less sample is required. Current- Curr. Top. Microbiol. Immunol. 240:21-57.
tivity and therefore reduce the confi- ly, we use about 1/20th the amount of 7.Heid, C.A., J. Stevens, K.J. Livak, and P.M.
dence level for copy determination. sample required for Southern analysis. Williams. 1996. Real time quantitative PCR.
Genome Res. 6:986-994.
Although the TaqMan copy assay Theoretically, this could be reduced 8.Holland, P.M., R.D. Abramson, R. Watson,
does have some limitations, the high much further because each sample and D.H. Gelfand. 1991. Detection of specif-
degree of accuracy and robustness preparation for TaqMan analysis yields ic polymerase chain reaction product by utiliz-
combined with throughput and assay enough DNA for about 25 assays. In ing the 5′→3′ exonuclease activity of Thermus
aquaticus DNA polymerase. Proc. Natl. Acad.
cost provides numerous advantages addition, because of the small sample Sci. USA 88:7276-7280.
over traditional Southern blot tech- size required, the TaqMan assay can be 9.Laurendeau, I., M. Bahuau, N. Vodovar, C.
niques. These benefits should establish conducted much earlier in the produc- Larramendy, M. Olivi, I. Bieche, M. Vi-
TaqMan copy assay as standard assay tion of transgenic events. This allows daud, and D. Vidaud. 1999. TaqMan PCR-
for high-throughput plant biotechnolo- undesirable events (those with greater based gene dosage assay for predictive testing
in individuals from a cancer family with INK4
gy research and development. Each than one copy) to be eliminated before locus haploinsufficiency. Clin. Chem. 45:982-
TaqMan copy number assay plate can lengthy and expensive greenhouse cul- 986.
analyze, in triplicate, 30 unknown and tivation procedures. 10.Lee, L.G., C.R. Connell, and W. Bloch.
two control samples in less than 2 h. 1993. Allelic discrimination by nick-transla-
tion PCR with fluorogenic probes. Nucleic
Currently, the only other limitations to Acids Res. 21:3761-3766.
the number of samples that can be run ACKNOWLEDGMENTS 11.Lehmann, U., S. Glockner, W. Kleeberger,
in the assay are determined by the num- H.F. von Wasielewski, and H. Kreipe. 2000.
ber of ABI PRISM 7700 instruments Detection of gene amplification in archival
The authors would like to thank breast cancer specimens by laser-assisted mi-
available and the rate/throughput of John Arbuckle for technical advice on crodissection and quantitative real-time poly-
sample preparation. In addition to DNA preparation procedure and the merase chain reaction. Am. J. Pathol.
speed and throughput, the TaqMan Greenhouse and Transformation groups 156:1855-1864.
12.Livak, K.J., S.J. Flood, J. Marmaro, W.
for generating and maintaining the Giusti, and K. Deetz. 1995. Oligonucleotides
plants used in this study. In addition, with fluorescent dyes at opposite ends provide
we would like to acknowledge Tina a quenched probe system useful for detecting
Hammer and Nadine Carozzi for help- PCR product and nucleic acid hybridization.
ful discussions. We would also like to PCR Methods Appl. 4:357-362.
13.Negrotto, D.M., M. Jolley, S. Beer, A.R.
thank Carla Thomas, Mary Fielder, Jim Wenck, and G. Hansen. 2000. The use of
Beck, and Henry-York Steiner for care- phosphomannose-isomerase as a selectable
ful review of the manuscript. marker to recover transgenic maize plants
(Zea mays L.) via Agrobacterium transforma-
tion. Plant Cell Rep. 19:2798-2803.
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Vol. 31, No. 1 (2001)

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