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1
Institute of Laboratory Medicine, Clinical Chemistry, and Molecular Diagnostics, University Hospital Leipzig, Liebigstrasse 27, 04103 Leipzig, Germany.
2
Institute of Clinical Chemistry, Grosshadern, University
Hospital Munich, Marchioninistrasse 15, 81377 Munich, Germany.
aAuthor for correspondence. Fax 49-341-9722209; e-mail daniel{at}teupser.de.
| Abstract |
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Methods: CAD patients (n = 150) with known TaqIB genotype, as determined by restriction fragment length polymorphism (RFLP) analysis, were selected, including three groups of 50 patients, carrying the B1/1, B1/2, and B2/2 genotypes, respectively. The genotypes were also analyzed by fluorescence-based allele-specific TaqMan PCR and melting curve analysis (LightCycler). In addition, DNA sequencing was applied.
Results: The TaqIB genotypes obtained by fluorescence analysis corresponded to those determined by RFLP analysis with the exception of three heterozygous patients (B1/2), who were misclassified as homozygous B2 carriers with the TaqMan system. Melting curve analysis of these samples demonstrated an additional melting point at 59.1 °C, which was also found in four patients homozygous for the B1 allele. DNA sequencing revealed a previously unknown C270T nucleotide exchange in intron 1 of the CETP gene, only nine base pairs from the TaqIB site.
Conclusions: Determination of the TaqIB polymorphism with the TaqMan system led to misclassifications because of a previously unknown C270T polymorphism of the CETP gene. The base substitution was detected with the LightCycler because of the occurrence of an additional melting point. Our data indicate the importance of thorough evaluation of new gene analysis systems before using them on a routine basis.
| Introduction |
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The TaqIB polymorphism is one of the polymorphisms of the CETP gene that has been studied in detail. It is located in intron 1 of the CETP gene (5). The presence of the TaqI restriction site was designated B1 and its absence as B2 (6). Individuals carrying the B2 allele showed lower CETP activity (7) and CETP mass concentrations (8) and higher HDL-cholesterol (5)(6)(8)(9)(10) and apolipoprotein AI plasma concentrations (6)(8)(10).
The role of the TaqIB polymorphism in the progression of coronary atherosclerosis has recently been studied in a subgroup of the Regression Growth Evaluation Statin Study (REGRESS) collective. It was confirmed that the B1 variant of the CETP gene was associated with both higher CETP and lower HDL-cholesterol concentrations. In addition, the B1 allele was dose-dependently associated with a faster progression of coronary atherosclerosis, as indicated by a decrease in mean luminal diameter, in the placebo group. This association was abolished by pravastatin. Pravastatin therapy slowed the progression of coronary atherosclerosis in patients homozygous for the B1 allele but not in those homozygous for the B2 allele (4).
The results of the studies mentioned above make the CETP TaqIB polymorphism an interesting genetic variation to study in large atherosclerosis trials. In previous studies, the TaqIB polymorphism was analyzed by digestion of DNA with the restriction enzyme TaqI and subsequent detection of the fragments either by agarose gel electrophoresis or by hybridization. However, restriction fragment length polymorphism (RFLP) analysis is time- consuming and difficult to automate because it requires postamplification procedures, such as restriction enzyme digestion and electrophoresis. Currently, two fluorescence-based PCR detection systems, the LightCycler (Roche Diagnostics) and the TaqMan SDS 7700 (Applied Biosystems), have become available that can be applied to screen large study cohorts for polymorphisms within a short period of time. The short analysis time is mainly achieved by performing PCR and the subsequent fluorescence analysis of the PCR products in the same run.
Thus, the aim of our study was to compare the performance of the new detection systems (the TaqMan SDS 7700 and LightCycler) to determine the CETP TaqIB polymorphism in 150 patients with known TaqIB genotypes previously characterized by RFLP analysis.
| Materials and Methods |
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genotyping by rflp
Genotyping of the TaqIB polymorphism by RFLP was
essentially performed as described previously (5). Briefly,
a 991-bp fragment of intron 1 of the CETP gene was amplified
using the following primer pair: 5'-CAG GGG TCT TTT CAT GGA CAC-3'
(forward) and 5'-CAC TTG TGC AAC CCA TAC TTG ACT-3' (reverse). The PCR
product was subsequently digested at 65 °C with the restriction
enzyme
-TaqI (New England BioLabs) and analyzed on a 2%
agarose gel. The presence of the TaqI restriction site led
to the generation of two fragments (249 and 742 bp) and was designated
B1, the absence of the TaqI restriction site was designated
B2 (5).
genotyping by allele-specific taqman pcr
This PCR method is based on the accumulation of fluorescence
during the nucleolytic degradation of an internally quenched
allele-specific probe. However, probes that differ from the template
sequence by as little as a single nucleotide exhibit a lower melting
point temperature and remain intact during PCR. They will be displaced
from the template strand but not degraded by the exonuclease activity
of Taq polymerase. The correct extension temperature is
crucial for the performance of the assay.
Allelic discrimination is achieved by the use of two oligonucleotide
probes, each complementary to one of the two alleles and labeled with a
different fluorescent reporter dye. The design of suitable probes is
dependent on the sequence of the two alleles. To our knowledge, the
sequence of the B2 allele has not been published; therefore, we
sequenced DNA from three patients carrying the B2/2 isoform as
determined by RFLP analysis. In the B2 allele, we found a single G
A
base exchange at nucleotide position 279 of intron 1 in all three
patients (start of intron 1 according to GenBank Accession Nos. M32992
or J02898, corresponding to nucleotide position 784 of that sequence).
With this information, we designed primers and probes for the allelic
discrimination assay. The TaqMan probe for detection of the B1 allele
(5'-TGA ACC CTA ACT CGA ACC CCA GTG AT-3') was 5'-labeled
with the reporter dye 6-carboxyfluorescein (FAM), the TaqMan probe for
the B2 allele (5'-TCT GAA CCC TAA CTT GAA CCC CAG TGA T-3')
was 5'-labeled with VIC® (Fig. 1A
). The underlined nucleotides indicate the position of the base
exchange of the TaqMan polymorphism. The primers 5'-TGT CTG CGA CCC AGA
ATC ACT-3' (forward) and 5'-ACC CCC TAA CCT GGC TCA GA-3' (reverse)
were used for amplification. The primers and TaqMan probes were
synthesized by Applied Biosystems.
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The PCR reaction was performed in a volume of 25 µL containing 12.5 µL of TaqMan 2x Universal PCR Master Mix, with ROX as passive reference (PE Applied Biosystems) and 4 µL of genomic DNA (80240 ng). The final concentration of the oligonucleotides was 400 nM for each primer and 600 nM and 175 nM for the labeled B1 and B2 probes, respectively. The PCR program included one hold at 50 °C for 2 min, followed by one hold at 95 °C for 10 min, and 43 cycles at 95 °C for 15 s for denaturing and 62 °C for annealing/extension. PCR, endpoint reading of fluorescence, and analysis of the data were performed with the 7700 Sequence Detection System (Applied Biosystems).
genotyping by melting curve analysis (lightcycler)
In contrast to the TaqMan system, allelic discrimination with the
LightCycler is based on the generation of a melting profile after PCR
amplification of the target sequence. The polymorphic site of the
sequence is spanned by a fluorescein-labeled "detection probe",
complementary to the sequence of one of the alleles (the B1 allele in
this case). Next to it, a second probe, designated the "anchor
probe", is designed to bind more stably to the target DNA. It is
labeled with LightCycler Red 640 at its 5' end, emitting fluorescence
through fluorescence resonance energy transfer when the adjacent
fluorescein of the detection probe is excited. A melting curve can be
generated by continuous monitoring of fluorescence while increasing the
temperature from annealing to denaturing conditions. The melting point
of the probe can be detected by a rapid decrease of fluorescence,
allowing the discrimination of different alleles by their specific
melting points.
The primers 5'-TCT TTT CAT GGA CAC CCA CTA TG-3' (forward) and 5'-CCC CAA CAC CAA ATA TAC ACC A-3' (reverse) were used to amplify a 328-bp fragment of intron 1 of the CETP gene. The sequence of the detection probe 5'-AAC CCT AAC TCG AAC CCT AGT GAT TCT-3' was complementary to the CETP B1 allele with the exception of an additional mismatch at nucleotide 272 to increase the discrimination of the alleles (11). The detection probe was labeled with fluorescein at the 3' end. The anchor probe 5'-TCG CAG ACA AAC ACA AAT CCC TAT ACC TGG-3' was labeled with LightCycler Red 640 at its 5' end and 3'-phosphorylated to prevent extension. The anchor probe of the LightCycler assay was constructed on the basis of the information obtained from GenBank. The sequencing of intron 1 of the CETP gene later showed an adenine at position 257 instead of a cytosine (GenBank Accession Nos. M32992 or J02898) in all patients. The mismatch did not interfere with the LightCycler assay.
PCR was performed in a reaction volume of 10 µL containing 500 nM of each primer, 188 nM of the detection probe, and 113 nM of the anchor probe. DNA (1 µL), 0.9 µL of 25 mM MgCl2, and 1 µL of a LightCycler-DNA Master Hybridization Probes reaction mixture (containing Taq DNA Polymerase, reaction buffer, dNTP mixture with dUTP instead of dTTP, and 10 mM MgCl2; Roche Diagnostics) were added. The cycling conditions included one initial denaturation step (2 min at 95 °C) and 43 cycles of 95 °C for 0 s, 59 °C for 5 s, and 72 °C for 18 s with a temperature transition rate of 20 °C/s. After amplification was complete, melting curves were generated by denaturing the reaction at 95 °C for 0 s, followed by 10 s at 45 °C, and then by slowly heating the samples to 85 °C at 0.1 °C/s with continuous monitoring of fluorescence (F2/F1).
genotyping by sequencing
To determine the DNA sequence in the vicinity of the
TaqIB site, we first amplified DNA samples by PCR with the
primers and conditions as described above (genotyping by RFLP). The PCR
products (40 µL) were subsequently purified using the QIAquick PCR
purification method (QIAGEN), and the DNA concentration was determined.
DNA (400 ng) was sequenced in each direction by dye-terminator
chemistry using a 377 DNA sequencer (Applied Biosystems).
pcr mutagenesis
A fragment of the CETP gene with the C
T base
exchange at position 270 on the B2 allele was generated by PCR
mutagenesis using two complementary mismatch primers (5'-AGA ATC ATT
GGG GTT CAA GTT AGG-3' and 5'-CCT AAC TTG AAC CCC AAT GAT TCT-3') and
the forward and reverse primers used for LightCycler PCR. The presence
of the nucleotide exchanges at positions 270 (C
T) and 279 (G
A) of
the resulting fragment was confirmed by DNA sequencing.
| Results |
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The samples were analyzed by allele-specific TaqMan PCR. Eight samples
from a patient with the B1/1 genotype and eight samples from a patient
carrying the B2/2 genotype, previously determined by DNA sequencing,
were included in each assay for calibration. After PCR amplification,
the fluorescence was read and the genotypes of the samples were
automatically assigned with an algorithm according to the fluorescence
signal of the calibrators (Fig. 1B
). All patients homozygous for the B1
or B2 alleles were correctly genotyped, in agreement with the results
of the RFLP analysis. However, unexpectedly, 3 of 50 patients carrying
the B1/2 genotype were misclassified as homozygous for the B2 allele by
this method.
Samples from all patients were also analyzed by melting curve
analysis in the LightCycler. With the increase of temperature, samples
from patients carrying the B2 isoform showed a rapid drop of
fluorescence at 55.4 °C corresponding to the dissociation of the
fluorescence-labeled probe from the template. In most samples from
patients carrying the B1 isoform, the decrease occurred at 63.3 °C
because of the higher homology of sample and probe. In the first
negative derivative (-dF/dT), the melting
temperatures appeared as maxima, as shown in Fig. 2A
. Heterozygotes (B1/2) showed composite melting peaks,
representing the signals obtained from the B1 and B2 alleles.
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The melting patterns in samples from four patients with the B1/1
genotype and from three patients with the B1/2 genotype were clearly
divergent from the characteristic melting curves of the corresponding
genotypes. The four B1/1 patients showed a melting point at 59.1 °C
in addition to that at 63.3 °C. Samples from the three B1/2 patients
also showed a shift in melting temperatures with one melting point at
59.1 °C and one at 55.4 °C (Fig. 2B
). Careful analysis of the
melting curves of the samples from patients homozygous for the B2
genotype revealed no shift in the melting points. Interestingly, the
three B1/2 patients showing the shift of the melting point from
63.3 °C to 59.1 °C were the same who had been previously
misclassified as B2/2 by TaqMan allelic discrimination.
This observation prompted us to analyze the DNA sequences of all
samples showing a melting point at 59.1 °C. We could confirm that
the four B1/1 patients were homozygous for the B1 genotype (G at
nucleotide position 279). In addition, we found that these B1/1
patients were heterozygous for a previously unknown C
T base exchange
at position 270. The same single nucleotide polymorphism was also found
in the samples from the three B1/2 patients with a melting point at
59.1 °C.
A comparison of the specificities of the three methods to analyze
the TaqIB genotype in the study population is given in Table 1
. The melting-point data indicated that the C
T polymorphism
occurred only on the B1 allele and led to a reduction of the melting
temperature of the detection probe. To investigate the effect of the
polymorphism on the reduction of the melting temperature if it occurred
on the B2 allele, we generated a fragment of the B2 allele bearing the
270T variant. As expected, melting curve analysis of this fragment in
the LightCycler led to a further destabilization of the detection probe
with a melting point at 50.2 °C. We have not observed the occurrence
of this melting point in any of our patient samples.
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To study the underlying causes of the limitations of the TaqMan assay to classify B1 270T/B2 samples correctly, we analyzed endpoint fluorescence measurements and continual monitoring of fluorescence in the quantification mode of the SDS 7700. Because VIC fluorescence is derived from nucleolytic degradation of a VIC-labeled probe complementary to the B2 allele, one could assume that in a heterozygous B1/2 situation, the increase of VIC fluorescence would be one-half that of a homozygous B2 sample. However, VIC fluorescence exceeded this value in our experimental situation, and there was overlap with B2 homozygotes depending on PCR efficiency. Thus, the assignment of the genotype had to be made taking the FAM data also into account. With this information, B2 homozygotes and B1/2 heterozygotes (without 270T variation) could be clearly discriminated because the FAM signal showed no overlap between both genotypes. In contrast, FAM fluorescence in B1 270T/B2 heterozygotes was within the range of B2 homozygotes and among those B2/2 samples with highest FAM signal. This was true for endpoint reading, as well as continual monitoring of fluorescence during PCR. Thus, based on the signals of FAM and VIC fluorescence, B1 270T/B2 samples resembled B2 homozygotes.
| Discussion |
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In our study, the determination of the TaqIB polymorphism by allelic discrimination using TaqMan PCR led to misclassifications because of a previously unknown C270T variation in intron 1 of the CETP gene located only 9 base pairs upstream of the TaqIB site. The misclassification only appeared in B1/2 heterozygotes with the 270T variant on the B1 allele, which were classified as B2 homozygous. B1 homozygotes with the 270T variant were correctly classified. It appears that the vicinity of this single nucleotide polymorphism led to a destabilization and decreased melting temperature of the FAM-labeled TaqMan probe, which was unable to bind firmly to the variant B1 strand. The probe was thus only displaced from the strand and not cleaved by the exonuclease activity of the Taq polymerase, leading to a low FAM fluorescence signal. B1 homozygous samples were correctly assigned in the presence of the 270T variant because the FAM fluorescence was high (presence of one B1 270C allele) and VIC fluorescence was low (absence of a B2 allele), resembling the fluorescence pattern of a B1 homozygous sample. However, in case of B1 270T/B2 heterozygosity, the FAM signal was in the range of B2 homozygous samples because of the low binding affinity of the FAM-labeled B1 probe to the variant B1 strand. Because there was overlap of the VIC signal between B1/2 heterozygotes and B2 homozygotes, this situation was misclassified as B2 homozygous by the allele discrimination software.
Our data show that a TaqMan assay, which has 100% specificity and sensitivity for detecting the B1 or B2 alleles of the TaqIB polymorphism in the "wild-type" situation, failed when a previously unknown sequence variation occurred at the probe binding site that was not taken into account when the assay was designed. Theoretically, this situation can happen in any gene sequence at any position, and our data suggest that because of its biochemical principle, the TaqMan system is less flexible to circumvent this problem.
In contrast to the TaqMan data, the previously unknown C270T polymorphism did not interfere with the LightCycler assay and could be detected by the occurrence of an additional melting point at 59.1 °C. These results show that the determination of single nucleotide polymorphisms by the melting pattern of fluorescently labeled hybridization probes added safety to the analysis that was not provided by the TaqMan procedure. Different mismatches destabilize oligonucleotides to different extents and can be often distinguished (12)(13)(14). However, it must be pointed out that melting curve analysis can also lead to misclassifications when unexpected additional nucleotide exchanges in one allele led to a melting point comparable to that of the other allele (12). The LightCycler detection probe used in this assay had a mismatch at position 272 that was initially added to increase discrimination. We must point out that probes with artificial mismatches theoretically do not detect wild type with 100% specificity. Misclassifications may be encountered in the unlikely event that a WatsonCrick base pair forms at the mismatch site. However, the results of our study show that the LightCycler assay presented here had a specificity of 100% in the collective of patients tested.
Our results and findings from previous studies (12)(13)(14)(15) indicate that melting profiles generated by hybridization procedures should be interpreted with great care and sequencing should be applied when unusual patterns occur. With knowledge of the newly discovered polymorphism, an appropriate assay to determine the TaqIB polymorphism for the TaqMan system could be developed (e.g., by constructing a probe that does not overlap the polymorphic site at nucleotide 270). However, this was not the aim of the present study.
The interference of a previously unknown nucleotide exchange has been
reported for the PCR-based restriction endonuclease assay of the factor
V Leiden mutation (16). In one patient, a silent A
C
transition at nucleotide 1692 (no amino acid exchange) led to the loss
of the MnlI restriction site. Although the correlation of
functional and restriction digestion assays suggests a low frequency of
the nucleotide exchange (17)(18), it may
nevertheless lead to an overestimation of the factor V Leiden mutation.
This problem has been discussed by others describing fluorescence-based
assays for factor V Leiden genotyping (14)(19).
The effect of gene variants in the vicinity of mutations of interest on
the melting pattern of hybridization probes has been shown for factor
V, apolipoprotein B, cystic fibrosis, and hemochromatosis
mutations (12)(13)(14)(15)(20). Recently, the
discovery of previously unknown mutations with a probe-based design has
been described (15)(21).
In the collective of coronary heart disease patients analyzed in our
study, the newly discovered C270T polymorphism in intron 1 of the
CETP gene was found only on the B1 allele with a frequency
of
5%. To confirm that we did not miss the polymorphism on the B2
allele, we generated a fragment with both polymorphisms (T at position
270 and A at position 279). As expected, the fragment could be
distinguished clearly by its low melting point at 50.2 °C. These
data indicate that, in our study population, the polymorphism was
associated only with the B1 allele. We also did not observe patients
homozygous for T at position 270 of intron 1, possibly because of the
low frequency of the polymorphism. Determination of plasma
HDL-cholesterol concentrations did not show an association with the
C270T genotype, but the number of carriers of the T allele (n = 7)
may have been too small (data not shown). We are currently studying the
effect of the C270T variation on plasma lipids and lipoprotein
concentrations and progression of coronary artery disease in a larger
population.
In conclusion, we have shown that determination of the TaqIB polymorphism of the CETP gene with fluorescence-based PCR techniques is possible. However, thorough evaluation of the test systems is important to avoid unexpected misclassifications because of previously unknown sequence variations.
| Acknowledgments |
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| Footnotes |
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| References |
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