Detection of APC Gene Deletions Using Quantitative Multiplex PCR of Short Fluorescent Fragments

patients

Between 1999 and 2007, 121 FAP families (75 classic and 46 AFAP) were referred to our Genetic Counseling Unit. Semiautomated sequencing of the entire coding region of APC and analysis of the 2 most prevalent MUTYH gene mutations (G382D and Y165C) revealed pathogenic mutations in the APC or MUTYH genes in 76 families (62 classic and 14 AFAP). We selected 45 (13 classic and 32 AFAP) unrelated affected members of APC/MUTYH mutation-negative families for a study of possible gross APC gene rearrangements. We used DNA samples obtained from peripheral blood lymphocytes of 23 hereditary nonpolyposis colorectal cancer (HNPCC) patients as negative controls, since a pathogenic mutation in MSH2 or MLH1 had already been found. As a positive control, we used a FAP case with a cytogenetic deletion in the 5q region associated with mental retardation. All control DNA samples were obtained using the same DNA extraction protocol (FlexiGene DNA kit; Qiagen). Written informed consent was obtained from all patients participating in the study, and the study protocol was approved by the Ethics Committee.

apc qmpsf

Between 8 and 10 exons can be amplified together in quantitative multiplex PCR assays (14)(16). The APC gene (≈100 kb) is composed of 14 small exons and exon 15, which covers more than three quarters of the coding sequence. Thus, 18 amplicons of between 130 and 330 bp were designed to cover the entire 8.5-kb coding region and distributed across 3 multiplex reactions (Table 1⇓ ). As a negative control, we included in each reaction a fragment of a different gene in which deletion was not expected (HMBS, hydroxymethylbilane synthase at 11q23.3). Primers, designed using Primer Premier 5 (Premier Biosoft International), shared common melting temperatures of between 58 and 60 °C. At least 1 of the primers was located in the exonic region, and no primer covered polymorphic regions. All primers were chimeric and carried 10-nt extensions on their 5′ ends to homogenize annealing temperatures and relative primer concentrations (available on request). One primer from each pair was 5′-labeled with 6-FAM fluorochrome (Table 1⇓ ). We set the distribution of the primers across the 3 multiplex reactions using WinMultiPLX v1.00 (BioData Ltd.). We amplified 100 ng genomic DNA in a final volume of 25 μL including 0.4–1 μmol/L primers, 200 μmol/L dNTPs, 1.5 mmol/L MgCl₂, 1 U Taq polymerase (Thermoprime Plus DNA Polymerase; ABgene), 1 μL DMSO, and 1.25 μL triethylammonium acetate. After an initial denaturing step, samples underwent 23 cycles (10 s at 94 °C, 15 s at 50 °C, 20 s at 72 °C), which ensured that the amplification ended during the exponential phase. After the multiplex reactions, the DNA fragments were separated on an ABI Prism 3130 DNA sequencer and analyzed using GeneScan Analysis Software v3.1.2 (Applied Biosystems).

Three different methods were used to calculate allele dosage in this study: visual sample-to-control comparison, numerical sample-to-control comparison, and numerical cumulative comparison. For the visual sample-to-control comparison, we estimated allele dosage by superimposing the electropherogram of the tested sample onto the corresponding image for a control DNA sample after adjusting the vertical scale of the different amplicons. Allelic losses of one or more amplicons are represented by a 2-fold reduction in the intensity (peak heights) of an amplicon of the sample analyzed. In the numerical sample-to-control comparison, we calculated numerical normalized ratios (R) using the formula: R = (peak intensity_{amplicon x sample}/peak intensity_{amplicon x control})/(peak intensity_{amplicon ref sample}/peak intensity_{amplicon ref control}). An R value close to 0.5 (0.4–0.6) represented a 2-fold reduction. For numerical cumulative comparison, we adapted the analytical method used in MLPA (www.mrc-holland.com) to QMPSF. After normalization of all peak intensities to the intensity of the reference (HMBS) peak, we obtained the numerical normalized ratio (R′) of a given exon and sample using the formula R′ = normalized peak intensity of analyzed sample/mean of normalized peak intensities of all samples. As above, R′ values close to 1 and 0.5 indicate whole and half allele dosage, respectively.

mlpa analysis

MLPA analysis, carried out using an APC-specific MLPA test (Salsa MLPA Kit P043 APC, MRC-Holland) according to the manufacturer’s instructions, used 300 ng genomic DNA. After hybridization, ligation, and amplification, we calculated the PCR product ratios by dividing each measured peak area by the sum of all peak areas for the sample. The ratio of each peak’s individual relative probe area was normalized to the mean obtained with 2 control samples. We analyzed the products using the ABI 3700 DNA sequencer and Peak Scanner Software v1.0 (Applied Biosystems).

molecular characterization of deletions

We performed PCR to characterize the deletion of exons 9 and 10 (forward flanking primer 5′-ACCTATAGTCTAAATTATACCATC-3′; reverse 5′-CTGAGCTATCTTAAGAAATACATG-3′) in a final volume of 50 μL containing 0.2 μmol/L each primer, 1 U Taq polymerase (Thermoprime Plus DNA Polymerase; ABgene), 200 μmol/L dNTPs, and 1.5 mmol/L MgCl₂. After denaturation at 94 °C for 10 min, 30 cycles of PCR were performed (94 °C for 30 s; 55 °C for 30 s; 72 °C for 5 min). After using the PCR Product Purification Spin Kit/250 (Genomed), 1 μL of the amplified product was sequenced using the BigDye® Terminator v3.1 Cycle Sequencing Kit (Applied Biosystems) according to the manufacturer’s instructions. The primers used for sequencing the breakpoint were 5′-TTTCCGGTTTCTAATCTGCTTCT-3′ as the forward primer and 5′-CCTTTTTATGCCAGTTTCTCCAC-3′ as the reverse primer.

We performed QRT-PCR with the Roche LightCycler® 2.0 System according to the SYBR Green Detection methodology. We used 8 sets of primer pairs, including a pair that amplified a fragment used as a reference for the presence of the 2 alleles (APC_e5) and a pair that amplified a deleted fragment (APC_e15) (see Supplemental Table 1 in the Data Supplement that accompanies the online version of this article at http://www.clinchem.org/content/vol54/issue7 ). Reactions were performed in a volume of 10 μL containing 1 μL LightCycler Fast Start DNA Master SYBR Green I (Roche), 1.5 mmol/L MgCl₂, 0.5 μmol/L of each primer, and 50 ng genomic DNA for 40 cycles (95 °C for 6 s; melting temperature for 16 s; 72 °C for 20 s). The samples were then subjected to melting curve analysis from 60 to 95 °C. Crossing points (the cycle number when the amplification becomes exponential) were determined using LightCycler software. We calculated the gene copy number using the relative standard curve method (17).

We performed FISH on chromosome spreads obtained from peripheral blood of the relevant patients. Cultures were set up a few hours after blood collection in heparinized tubes. We added 500 μL whole blood to a flask containing 9 mL RPMI 1640 (Gibco) with 10% FCS, 5 mg/L phytohemagglutinin (Gibco), 100 000 U/L penicillin, and 100 mg/L streptomycin. Cultures were set up in duplicate and incubated at 37 °C for 72 h. We harvested cells after colcemid treatment (0.4 mg/L) for 20 min and then performed FISH. Briefly, we used 7 different probes from chromosome 5q22 to cytogenetically clone the deletion breakpoints RP11-809J10, RP11-619D6, RP11-616C24, RP11-389E12, and RP11-145D17 (ordered from the centromere to the telomere and covering approximately 1 Mb). All probes were obtained from the 32K BAC Rearray of the Children’s Hospital Oakland Research Institute (www.chori.org/bccpcc) and kindly provided by Luis Pérez-Jurado. Probes (1 μg of each) were directly labeled by a standard nick translation reaction, hybridized in pairs, and detected according to standard protocols (18). The FISH analysis was performed under an Olympus BX60 fluorescence microscope equipped with the appropriate filter set, and images were captured using the Cytovision software (Applied Imaging).

development and validation of the semiquantitative multiplex pcr

To determine whether the assay was optimal for the screening of genomic copy number alterations in the subset of polyposis patients, we analyzed 23 negative controls and 1 positive control (the cytogenetical deletion at 5q). Using numerical cumulative comparison, the R′ (SD; range) of the 23 negative controls was 1.00 (0.08; 0.83–1.21) taking into account all exons and samples (Fig. 1A⇓ ). Most of the outlier values within the 23 control intensities belonged to a single control. The positive control showed an R′ of 0.55 (0.06; 0.47–0.67) (Fig. 1A⇓ ). Using numerical sample-to-control comparison (Fig. 1B⇓ ), R values for the deleted control were 0.55 (0.07; 0.39–0.77). The variability was concentrated in a few amplicons evenly distributed along the 3 multiplex PCR reactions, making it unlikely that the robustness of the technique was affected. Visual sample-to-control comparison revealed a 2-fold reduction of peak intensity when superimposing the deleted control on a negative control in all APC amplicons (see Supplemental Fig. 1 in the online Data Supplement). No reduction was observed when comparing the different negative controls (data not shown).

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Figure 1.

Validation screening of APC gene in 23 nondeleted individuals and 1 whole-gene deletion carrier.

(A), Intersample variability of 23 wt controls assessed by numerical cumulative comparison. The y axis represents ratios (R′) of relative allele dosage. Amplicons spanning all APC gene exons are represented in the x axis. White, gray, and dashed boxes show the multiplex PCR in which each exon is amplified (multiplex1, multiplex2, and multiplex3, respectively). The black line inside the box represents the median of the ratio. The bottom and top edges of the boxes represent the 25th and 75th percentiles. Outlier values are shown as circles outside the boxes. Black squares correspond to ratios (R′) from the deleted control. (B), Numerical sample-to-control comparison. Ratios (R) were obtained by numerically superimposing the deleted control on all 23 negative controls analyzed within the same experiment, one by one.

We assayed 10 replicates of both a negative control and the deleted control in the same experiment to assess the intraexperimental variability (Supplemental Data Fig. 2A). Using the cumulative comparison, mean R′ values of 1 (0.09; 0.73–1.25) and 0.52 (0.05; 0.38–0.71) were obtained for the normal and the deleted controls, respectively. As in the previous assay, the variability was concentrated in a few amplicons, and more extreme values appeared in only 1 or 2 amplicons of a replicate, thus reducing the likelihood of interpretation errors. Finally, interexperimental variability was studied in 13 independent QMPSF assays using the deleted control. Numerical cumulative comparison with the 23 HNPCC patients yielded R′ values of 0.45 (0.10; 0.14–0.69) (see Supplemental Fig. 2B in the online Data Supplement). There was no overlap between any of the wt and deleted control ratios.

Thus, QMPSF was able to detect the loss of 1 copy of the gene for all fragments analyzed, with an acceptable amount of intra- and interexperimental variability.

deletion screening in patients

We used the above data to establish the following experimental design incorporating 2 duplicates of 2 wt controls in each run and a single sample of the deleted control. The run was disregarded when the ratio between replicates of wt controls was >1.2 or <0.8. Once a copy number variation was observed, the experiments were independently replicated at least twice using independent DNA aliquots. Deletions were detected in 3 of the 13 (23%) selected APC/MUTYH mutation-negative classic FAP families (see Supplemental Table 2 and Supplemental Fig. 3 in the online Data Supplement). Two of these deletions were partial, and the other encompassed the entire gene. The partial deletions encompassed exons 9 and 10 and from exon 11 to all amplicons of exon 15, respectively. The MLPA analyses performed for the 13 classic FAP families confirmed the QMPSF results. No gross rearrangements were detected in the 32 AFAP mutation-negative families.

Regarding genotype-phenotype correlation in classic FAP families, carriers of gross deletions (n = 4, including the cytogenetically deleted control) were diagnosed at an earlier age [23.25 (7.09) years] than APC/MUTYH mutation-negative index cases [36.9 (7.84) years; n = 10; P = 0.028, Wilcoxon rank-sum test] (see Supplemental Table 2 and Supplemental Fig. 3 in the online Data Supplement). Differences were detected with respect to other APC gene mutation carriers [29.28 (13.39) years; n = 57], although the differences were not significant, possibly owing to the low number of deletion carriers. In contrast, no differences were observed in the number of colorectal polyps, the presence of extracolonic manifestations, or family history.

molecular characterization of the partial apc deletions

We confirmed all 3 of the observed deletions by replicating QMPSF assays and using MLPA. Further characterization was carried out in partial deletion carriers, which provided insight into the molecular nature of these aberrations.

In an index case, QMPSF analysis showed a deletion removing exons 9 and 10 (Fig. 2⇓ , A and B). Genomic DNA PCR encompassing exons 8–11 revealed the amplification of an abnormal fragment of approximately 4 kb in the affected patient, corresponding to the junction fragment comprising the deleted region (Fig. 2⇓ , A and C). Sequence analysis revealed that the first 3007 bp of intron 8 were fused to the last 496 bp of intron 10, deleting a 8011-bp fragment of the gene (g.80715_88725del8011; NC_000005.8; GI:51511721) (Fig. 2D⇓ ). Alignment of intronic sequences using the RepeatMasker program revealed that the recombination did not involve any flanking repeat elements, suggesting a nonhomologous recombination process (Fig. 2D⇓ ).

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Figure 2.

Characterization of APC deletion involving exons 9 and 10 (g.80715_88725del8011; NC_000005.8; GI:51511721).

(A), Schematic representation of the APC rearrangement. Black boxes represent exons. Alu repeats present in this region and their orientation are shown by gray boxes. The primers used for the amplification of the deleted fragment and sequencing of the breakpoint are shown as black and open arrows, respectively. The lengths of expected wt and deleted PCR products are also indicated above by 2-headed gray arrows. The approximately 8-kb deleted region is delimited by broken lines. (B), QMPSF of APC showing the heterozygous deletion of exons 9 and 10. Electropherograms from a control (in blue) and the deletion carrier (in red) were superimposed using HMBS as the internal control. A 2-fold reduction of exon 9 and 10 peaks (bold letters) is observed in the patient profile. (C), PCR of the deleted fragment in the mutation carrier. Primers (black arrows in A) amplified an approximately 4-kb product corresponding to the deleted allele. This product was not present in a control DNA sample. (D), Sequencing of the breakpoint was performed using open arrow primers in A. Sequence alignment of the region encompassing the breakpoint (“patient” to the left of the sequence) and the parental strands mediating the deletion (numbers of their nucleotides shown to the left of the sequences). Sequence identities are indicated by vertical bars. The breakpoint is indicated by the letters in bold.

Fig. 3⇓ shows a schematic representation of molecular studies done in an index case carrying a deletion of exon 11 to all fragments of exon 15. A QMPSF pattern showing 2-fold reduction of intensities of these exons was detected in the index case (Fig. 4A⇓ ) and in another affected relative (data not shown). To further characterize the 3′ extension of the deletion, genomic DNA QRT-PCR was performed on eight fragments up to 400 kb downstream of the deleted area using exon 5 of the APC gene as a reference for normalization (Fig. 3⇓ , Fig. 4A⇓ ; see Supplemental Table 1 in the online Data Supplement). Samples from an affected member and a healthy relative were compared with control DNA. The 3′ breakpoint was located within a region of approximately 83 kb encompassed by fragments REEP5_e3 and DCP2_e2 in the affected subject (Fig. 3⇓ , Fig. 4B⇓ ). FISH analysis using 5 probes covering 835 kb also confirmed the approximate location of the breakpoint (Fig. 3⇓ , Fig. 4C⇓ ). Probes corresponding to RP11-809J10, RP11-619D06, RP11-389E12, and RP11-145D17 clones yielded a double signal concordant with the QMPSF and QRT-PCR results. Although approximately half of the area covered by RP11-619D06 was deleted, the nondeleted area was sufficient to hybridize and identify the corresponding fluorescent signal. Only the RP11-616C24 probe yielded a single signal. No attempt was made to sequence the 5′ breakpoint.

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Figure 3.

Schematic representation of the region studied for the characterization of exon 11–15 deletion (ranging from 111925202 to 112760819 nucleotides from NC_000005).

Genes are represented as open boxes. The positions of fragments analyzed by QRT-PCR are shown by circles, each with a corresponding letter below (a to i, see Fig. 4B⇓ ). A 2-headed broken arrow depicts the region in which the 3′ breakpoint is placed. The probes used for FISH assays are represented below as black boxes (labeled with green fluorophore) and gray boxes (labeled with red fluorophore). Open and closed circles represent the deleted and nondeleted fragments analyzed by QRT-PCR.

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Figure 4.

Characterization of gross deletion involving exons 11–15 of the APC gene.

(A), QMPSF of APC showing the heterozygous deletion encompassing the region from exon 11 to the last amplicon of exon 15. Electropherograms from a control (in blue) and the carrier of the deletion (in red) were superimposed using HMBS as the internal control. (B), QRT-PCR results from analysis of fragments shown in Fig. 3⇑ (the names are indicated in the first column of the table). The ratios shown were calculated by taking the APC_e5 fragment as the reference (ratio = 1) for a healthy (wt subject) and a mutated (deleted subject) individual compared with a control DNA sample. Ratio approximately 1 means that the fragment is not deleted and ratio approximately 0.5 indicates the deletion of the fragment. (C), All FISH probes were hybridized over deleted patient metaphases. The presence of fluorescence in only one chromosome 5 depicts the deletion of the covered region. Probes span the following regions: RP11-809J10 (111925202–112128672), RP11-619D06 (112120960–112271440), RP11-616C245 (112223260–112387360), RP11-389E12 (112408900–112557640) and RP11-145D17 (112557148–112760819). A control probe from the 5q region was also used. The magnification shows the deletion of probe RP11-616C245 (in green) in one of the homolog chromosomes 5 and the overlapping signals (RP11-616C245, in green, and RP11-389E12, in red) in the other nondeleted homolog.