Detection of sequence variations in the adenomatous polyposis coli (APC) gene using denaturing high-performance liquid chromatography

Gene mapping and molecular analysis of hereditarynon-polyposis colorectal cancer (Lynch Syndrome)using systems biological approaches

Hereditary non-polyposis colorectal cancer (HNPCC) also known as Lynch Syndrome (LS), is a hereditary form of colorectal cancer (CRC). LSis caused by mutations in the mismatch repair (MMR) genes, mostly in MLH1, MSH2, MSH6 and PMS2. Identification of these gene mutations is essential to diagnose CRC, especially at a young age to increase the survival rate. Using open target platform, we have performed genetic association studies to analyze the different genes involved in the LS and to obtain target for disease evidence. We have also analyzed upstream regulators as target molecules in the data sets. We discovered that MLH1, MSH2, MSH6, PMS2, MLH3, EPCAM, TGFBR2, FBXO11 and PRSS58 were showing most association in LS. Our findings may further enhance the understanding of the hereditaryform of CRC.

Genetic Testing for Hereditary Nonpolyposis Colorectal Cancer (HNPCC)

Hereditary nonpolyposis colorectal cancer (HNPCC), also called Lynch syndrome, is an autosomal dominant cancer syndrome that confers an elevated risk of early-onset colorectal cancer (CRC) and increased lifetime risk for other cancers of the endometrium, stomach, small intestine, hepatobiliary system, kidney, ureter, and ovary. Lynch syndrome accounts for up to 3% of all CRC, making it the most common hereditary colorectal cancer syndrome. Germline mutations in methyl-directed mismatch repair (MMR) genes give rise to microsatellite instability (MSI) in tumor DNA. Lynch syndrome is most frequently caused by pathogrenic variants in the mismatch repair genes MLH1, MSH2, MSH6, and PMS2. Germline mutations in MLH1 and MSH2 account for approximately 90% of detected mutations in families with Lynch syndrome. Pathogenic vatiants in MSH6 have been reported in approximately 7-10% of families with Lynch syndrome. Pathogenic variants in PMS2 account for fewer than 5% of mutations in families with Lynch syndrome. This unit presents a comprehensive molecular genetic testing strategy for Lynch syndrome including MSI analysis, next generation sequencing (NGS)-based targeted sequence analysis, PCR-based Sanger sequencing and microarray-based comparative genomic hybridization (array-CGH). © 2017 by John Wiley & Sons, Inc.

Detecting APC Gene Mutations in Familial Adenomatous Polyposis (FAP)

Hereditary forms of colorectal cancer (CRC) account for up to 5% of total cases. Familial adenomatous polyposis (FAP) is an autosomal dominant condition affecting nearly 1 in 5000 people and accounts for only about 1% of all CRCs. It is characterized by the progressive development of hundreds to thousands of adenomatous colon polyps. The gene associated with FAP (APC) contains 15 coding exons. The mutation spectrum of the APC gene is broad in that 87% of causative mutations are point mutations (including other sequence variants) and around 10% to 15% are intragenic deletions and duplications. The strategy for molecular diagnostic testing for FAP involves initial full sequence analysis of APC for sequence variants followed by screening for deletion/duplications using microarray-based comparative genomic hybridization (array CGH) or Multiplex Ligation-dependent Probe Amplification (MLPA). Recently, next generation sequencing (NGS)-based targeted gene analysis has become clinically available for detection of point mutations and other sequence variants. This unit discusses detailed protocols for an NGS-based sequencing assay, PCR-based Sanger sequencing, and array CGH. © 2017 by John Wiley & Sons, Inc.

Contribution of APC and MUTYH mutations to familial adenomatous polyposis susceptibility in Hungary

Familial adenomatous polyposis (FAP) is a colorectal cancer predisposition syndrome with considerable genetic and phenotypic heterogeneity, defined by the development of multiple adenomas throughout the colorectum. FAP is caused either by monoallelic mutations in the adenomatous polyposis coli gene APC, or by biallelic germline mutations of MUTYH, this latter usually presenting with milder phenotype. The aim of the present study was to characterize the genotype and phenotype of Hungarian FAP patients. Mutation screening of 87 unrelated probands from FAP families (21 of them presented as the attenuated variant of the disease, showing <100 polyps) was performed using DNA sequencing and multiplex ligation-dependent probe amplification. Twenty-four different pathogenic mutations in APC were identified in 65 patients (75 %), including nine cases (37.5 %) with large genomic alterations. Twelve of the point mutations were novel. In addition, APC-negative samples were also tested for MUTYH mutations and we were able to identify biallelic pathogenic mutations in 23 % of these cases (5/22). Correlations between the localization of APC mutations and the clinical manifestations of the disease were observed, cases with a mutation in the codon 1200-1400 region showing earlier age of disease onset (p < 0.003). There were only a few, but definitive dissimilarities between APC- and MUTYH-associated FAP in our cohort: the age at onset of polyposis was significantly delayed for biallelic MUTYH mutation carriers as compared to patients with an APC mutation. Our data represent the first comprehensive study delineating the mutation spectra of both APC and MUTYH in Hungarian FAP families, and underscore the overlap between the clinical characteristics of APC- and MUTYH-associated phenotypes, necessitating a more appropriate clinical characterization of FAP families.

Targeting tumor suppressor networks for cancer therapeutics

Cancer is a consequence of mutations in genes that control cell proliferation, differentiation and cellular homeostasis. These genes are classified into two categories: oncogenes and tumor suppressor genes. Together, overexpression of oncogenes and loss of tumor suppressors are the dominant driving forces for tumorigenesis. Hence, targeting oncogenes and tumor suppressors hold tremendous therapeutic potential for cancer treatment. In the last decade, the predominant cancer drug discovery strategy has relied on a traditional reductionist approach of dissecting molecular signaling pathways and designing inhibitors for the selected oncogenic targets. Remarkable therapies have been developed using this approach; however, targeting oncogenes is only part of the picture. Our understanding of the importance of tumor suppressors in preventing tumorigenesis has also advanced significantly and provides a new therapeutic window of opportunity. Given that tumor suppressors are frequently mutated, deleted, or silenced with loss-of-function, restoring their normal functions to treat cancer holds tremendous therapeutic potential. With the rapid expansion in our knowledge of cancer over the last several decades, developing effective anticancer regimens against tumor suppressor pathways has never been more promising. In this article, we will review the concept of tumor suppression, and outline the major therapeutic strategies and challenges of targeting tumor suppressor networks for cancer therapeutics.

Deep sequencing with intronic capture enables identification of an APC exon 10 inversion in a patient with polyposis

PURPOSE

Single-exon inversions have rarely been described in clinical syndromes and are challenging to detect using Sanger sequencing. We report the case of a 40-year-old woman with adenomatous colon polyps too numerous to count and who had a complex inversion spanning the entire exon 10 in APC (the gene encoding for adenomatous polyposis coli), causing exon skipping and resulting in a frameshift and premature protein truncation.

METHODS

In this study, we employed complete APC gene sequencing using high-coverage next-generation sequencing by ColoSeq, analysis with BreakDancer and SLOPE software, and confirmatory transcript analysis.

RESULTS

ColoSeq identified a complex small genomic rearrangement consisting of an inversion that results in translational skipping of exon 10 in the APC gene. This mutation would not have been detected by traditional sequencing or gene-dosage methods.

CONCLUSION

We report a case of adenomatous polyposis resulting from a complex single-exon inversion. Our report highlights the benefits of large-scale sequencing methods that capture intronic sequences with high enough depth of coverage-as well as the use of informatics tools-to enable detection of small pathogenic structural rearrangements.

Precancerous lesions in colorectal cancer

Colorectal cancer (CRC) is the third most common cause of cancer death in the world. The incidence rate (ASR) and age distribution of this disease differ between most of African-Middle-Eastern (AMAGE) and North America and Europe for many reasons. However, in all areas, "CRC" is considered as one of the most preventable cancers, because it might develop from variant processes like polyps and IBD in addition to the genetic pathogenesis which became very well known in this disease. We tried in this paper to review all the possible reasons of the differences in incidence and age between the west and AMAGE. Also we reviewed all the mutations that lead to the hereditary and familiar clustering of this disease with the correlations with the surrounding food and environment of different areas. Then, we focused on the precancerous pathology of this disease with special focusing on early detection depending on new endoscopy technology and most important genetic studies. We lastly reviewed the evidence of some of the surveillance and put suggestions about future surveillance programs and how important those programs are on the psychological aspect of the patients and their families.

Crystal structures of the armadillo repeat domain of adenomatous polyposis coli and its complex with the tyrosine-rich domain of Sam68

Adenomatous polyposis coli (APC) is a tumor suppressor protein commonly mutated in colorectal tumors. APC plays important roles in Wnt signaling and other cellular processes. Here, we present the crystal structure of the armadillo repeat (Arm) domain of APC, which facilitates the binding of APC to various proteins. APC-Arm forms a superhelix with a positively charged groove. We also determined the structure of the complex of APC-Arm with the tyrosine-rich (YY) domain of the Src-associated in mitosis, 68 kDa protein (Sam68), which regulates TCF-1 alternative splicing. Sam68-YY forms numerous interactions with the residues on the groove and is thereby fixed in a bent conformation. We assessed the effects of mutations and phosphorylation on complex formation between APC-Arm and Sam68-YY. Structural comparisons revealed different modes of ligand recognition between the Arm domains of APC and other Arm-containing proteins.

Increased variance in germline allele-specific expression of APC associates with colorectal cancer

BACKGROUND & AIMS

Germline variations in allele-specific expression (ASE) are associated with highly penetrant familial cancers, but their role in common sporadic cancers is unclear. ASE of adenomatous polyposis coli (APC) is associated with pathogenesis of familial adenomatous polyposis. We investigated whether moderate variations in ASE of APC contribute to common forms of colorectal cancer (CRC).

METHODS

Denaturing high-performance liquid chromatography was used to analyze germline ASE of APC in blood samples from patients with CRC (cases, n = 53) and controls (n = 68). Means, medians, and variances of ASE were compared. Variants in the APC gene region also were analyzed.

RESULTS

The distribution of ASE differed significantly between groups; cases had significantly larger amounts of variance than controls (P = .0004). Risk for CRC increased proportionally with the degree of deviation from the mean. The odds ratio for individuals with levels of ASE that deviated more than 1 standard deviation from the mean was 3.97 (95% confidence interval, 1.71-9.24; P = .001); for those with levels greater than 1.645 standard deviations, the odds ratio was 13.46 (95% confidence interval, 1.76-609.40; P = .005). Sequence analysis revealed that a patient with a high level of ASE who did not have a family history of CRC carried a nonsense mutation in APC (p.Arg216X). Genotype analysis of APC associated multiple single-nucleotide polymorphisms with ASE values and/or variance among cases, but not controls. Cis variants, therefore, might account for some of the variance in ASE of APC.

CONCLUSIONS

Patients with CRC have a larger variance in germline levels of ASE in APC than controls; large distances from the mean ASE were associated with risk for common forms of CRC.

The intestinal nuclear receptor signature with epithelial localization patterns and expression modulation in tumors

BACKGROUND & AIMS

The WNT-adenomatous polyposis coli system controls cell fate in the intestinal epithelium, where compartment-specific genes tightly regulate proliferation, migration, and differentiation. Nuclear receptors are transcription factors functioning as sensors of hormones and nutrients that are known to contribute to colon cancer progression. Here we mapped the messenger RNA (mRNA) abundance and the epithelial localization of the entire nuclear receptor family in mouse and human intestine.

METHODS

We used complementary high-resolution in situ hybridization and systematic real-time quantitative polymerase chain reaction in samples of normal distal ileum and proximal colon mucosa and tumors obtained from mouse and human adenomatous polyposis coli-initiated tumor models (ie, Apc(Min/+) mice and familial adenomatous polyposis patients) and in cellular models of human colon cancer.

RESULTS

We first defined for each receptor an expression pattern based on its transcript localization in the distal ileum and the proximal colon. Then, we compared the mRNA levels between normal intestinal epithelium and neoplastic intestinal tissue. After analyzing the correspondence between mouse and human tumor samples plus genetically modified human colon cancer cells, we used complementary graphic and statistical approaches to present a comprehensive overview with several classification trees for the nuclear hormone receptor intestinal transcriptome.

CONCLUSIONS

We defined the intestinal nuclear hormone receptor map, which indicates that the localization pattern of a receptor in normal intestine predicts the modulation of its expression in tumors. Our results are useful to select those nuclear receptors that could be used eventually as early diagnostic markers or targeted for clinical intervention in intestinal polyposis and cancer.

Genetic testing for hereditary nonpolyposis colorectal cancer (HNPCC)

Hereditary nonpolyposis colorectal cancer (HNPCC) is an autosomal dominant cancer syndrome that confers an elevated risk of early-onset colorectal cancer (CRC) and increased lifetime risk for other cancers of the endometrium, stomach, small intestine, hepatobiliary system, kidney, ureter, and ovary. HNPCC accounts for up to 5% of all CRC, making it the most common hereditary colorectal cancer syndrome. Germline mutations in methyl-directed mismatch repair (MMR) genes give rise to microsatellite instability (MSI) in tumor DNA. HNPCC is most often associated with mutations in the MLH1 gene on 3p21, the MSH2 gene on 2p21, and to a lesser extent MSH6 on 2p16. This unit presents a comprehensive molecular and genetic screening strategy for HNPCC mutations in the MLH1, MSH2, and MSH6 genes, including analysis of MSI, mutation scanning by denaturing high-pressure liquid chromatography (DHPLC), and DNA sequencing analysis.

APC mutation spectrum of Norwegian familial adenomatous polyposis families: high ratio of novel mutations. J Cancer Res Clin Oncol. 2009;135:1463-1470. [PMID: 19444466 DOI: 10.1007/s00432-009-0594-4]

INTRODUCTION

Familial adenomatous polyposis (FAP) is an autosomal dominantly inherited disease caused by mutations in the adenomatous polyposis coli (APC) gene. Massive formation of colorectal adenomas, of which some will inevitably develop into adenocarcinomas, is the hallmark of the disease. Characterization of causative APC mutations allows presymptomatic diagnosis, close follow-up and prophylactic intervention in families. To date more than 900 different germline mutations have been characterized worldwide demonstrating allelic heterogeneity.

PURPOSE

The germline mutation spectrum of APC identified in 69 apparently unrelated Norwegian FAP families are presented and discussed with reference to clinical phenotype and novel mutation rate.

METHODS

Different methods have been used over the years. However, all mutations were confirmed detectable by an implemented denaturing high-performance liquid chromatography screening approach. Multiplex ligation-dependent probe amplification analysis was employed for potential gross rearrangements.

RESULTS

Fifty-three distinctive mutations were detected, of which 22 have been detected in Norway exclusively. Except for two major deletion mutations encompassing the entire APC, all mutations resulted in premature truncation of translation caused by non-sense (31%) or change in reading frame (69%).

CONCLUSION

A high ratio of novel APC mutations continues to contribute to APC mutation heterogeneity causing FAP. This is the first comprehensive report of APC germline mutation spectrum in Norway.

NF2 mutation screening by denaturing high-performance liquid chromatography and high-resolution melting analysis

Neurofibromatosis type 2 (NF2) is an autosomal-dominant disorder caused by mutations in the NF2 gene and predisposing to the development of nervous system. Identification of germline mutations is essential to provide appropriate genetic counseling in NF2 patients, but it represents an extremely challenging task because the vast majority of mutations are unique and spread over the entire coding sequence. Moreover, about 30% of de novo patients are indeed mosaic, and direct sequencing can undetect mutated alleles present in a minority of cells. As most screening techniques do not meet the requirements for efficient NF2 testing, we have developed a semi-automated denaturing high-performance liquid chromatography (DHPLC) method for point mutation detection combined with a multiplex ligation-dependent probe amplification approach to screen for gene rearrangements. In addition, we have evaluated high-resolution melting analysis (HRMA) as an exon scanning procedure to identify point mutations in the NF2 gene. The results obtained in 92 NF2 patients expand the NF2 mutational spectrum and indicate DHPLC and HRMA as good systems to screen for point mutations in diseases with a heterogeneous spectrum of alterations.

DHPLC analysis of adenomatous polyposis coli (APC) mutations using ready-to-use APC plates: simple detection of multiple base pair deletion mutations

The adenomatous polyposis coli (APC), which is the susceptible gene for familial adenomatous polyposis (FAP) and sporadic colorectal cancer, spans 15 exons. The open reading frame of APC is 8529 bp, which encodes 2843 amino acids. Conventional genetic screening involves extensive time as well as high cost and labor. Thus, we developed a novel APC ready-to-use plate for high-throughput mutational analysis by denaturing high performance liquid chromatography (DHPLC). To prepare the ready-to-use APC plate, all 38 primer pairs and PCR mixtures were aliquoted into individual wells of a 96-well plate, and frozen at -20 degrees C until use. All 38 PCR primers were designed to be amplified at the same temperature (52 degrees C). We examined a total of 27 FAP patient samples with APC germline mutations (17 for multiple bp deletions, 1 for 1 bp deletion, 9 for nonsense mutations) and 50 APC-negative noncarriers. All 17 multiple bp deletion mutations were detected during the initial 50 degrees C running analysis and thus ruled out for further analyses. All other mutations were clearly detected under specific optimized conditions. More than 50% of the APC germline mutations were multiple base pair deletions and efficiently selected by omitting time-consuming partial denaturing conditions.

Identification of a novel duplication in the APC gene using multiple ligation probe amplification in a patient with familial adenomatous polyposis

Germline mutations in the adenomatous polyposis coli (APC) gene cause familial adenomatous polyposis (FAP), an autosomal dominant disease characterized by hundreds to thousands of adenomatous polyps in the colon and rectum, with progression to colorectal cancer. The majority of APC mutations are nucleotide substitutions and frameshift mutations that result in truncated proteins. Recently, large genomic alterations of the APC gene have been reported in FAP. DNA from 15 FAP patients, in whom no APC germline mutations were detected with denaturing high performance liquid chromatography, was analyzed with multiplex ligation-dependent probe amplification (MLPA) to evaluate gross genomic alterations in the APC gene. In one case, MLPA identified a novel duplication of exons 2-6 in one copy of the APC gene. Reverse transcriptase-polymerase chain reaction revealed that the mutant allele contained an in-frame multiexon duplication including 18 nucleotides located in exon 2, upstream of the ATG initiation codon. The presence of a premature stop codon in the duplicated sequence leads to the synthesis of a truncated APC polypeptide. These findings highlight the utility of evaluating infrequent APC mutation events in FAP patients using MLPA.

Detecting mutations in the APC gene in familial adenomatous polyposis (FAP)

Hereditary forms of colorectal cancer (CRC) account for up to 5% of total cases. Familial adenomatous polyposis (FAP) is an autosomal dominant condition affecting nearly 1 in 5000 people and accounts for only about 1% of all CRCs. It is characterized by the progressive development of hundreds to thousands of adenomatous colon polyps. The gene associated with FAP (APC) contains 15 exons in the coding region. A scanning approach for large genes is reasonable, but some standard techniques have limited analytical sensitivity. The method described here, using DHPLC as mutation scanning approach for medium-throughput DNA sequence analysis, is largely considered to be the gold standard for point mutation analysis, and can be optimized for high-throughput testing. Detection of deletion and duplication mutations refractory to sequencing have been described using real-time quantitative PCR for dosage analysis. Technical strategies for mutation detection in the APC gene are presented in this chapter.

Screening for melanocortin-4 receptor mutations in a cohort of Belgian morbidly obese adults and children

OBJECTIVE

To investigate whether pathogenic melanocortin-4 receptor (MC4R) mutations are a common cause of obesity in Belgium.

DESIGN

Cross-sectional mutation analysis.

SUBJECTS

In total, 95 morbidly obese adults (mean age 44.02+/-11.35 years; mean BMI 47.87+/-4.17 kg/m2 and 123 obese children and adolescents were screened for mutations in MC4R (mean age 16.56+/-2.58 years; BMI>95th percentile for age and sex; mean % overweight 170.86 +/- 23.63).

MEASUREMENTS

A series of anthropometric (e.g. weight, height, waist, hip), biochemical and clinical measurements were performed on all subjects. The entire coding region of MC4R was screened using DHPLC, a highly sensitive and specific method for mutation analysis. Direct sequencing was performed when the chromatogram deviated from the WT pattern.

RESULTS

Mutation screening of a cohort of Belgian obese adults and children did not detect any pathogenic mutations as only the previously described polymorphisms Val103Ile, Thr112Met and Ile251Leu were detected.

CONCLUSION

Pathogenic mutations in MC4R are not a common cause of obesity in a Belgian population of obese adults, children and adolescents.

Congenital hypertrophy of the retinal pigment epithelium (CHRPE) in familial colorectal cancer

BACKGROUND AND AIM

Congenital hypertrophy of the retinal pigment epithelium (CHRPE) is a pigmented fundus lesion associated with familial adenomatous polyposis (FAP). CHRPE prevalence has been reported to be increased in subjects with familial or sporadic non-polyposis colorectal cancer (CRC), suggesting that some individuals with non-polyposis CRC have an attenuated form of FAP. Other studies have not confirmed these clinical observations and have failed to identify mutations in the gene responsible for FAP, but the reason for the discrepancy in relation to CHRPE prevalence has not been resolved. We determined the prevalence of CHRPE in subjects without CRC (negative control cohort), subjects with FAP (positive control cohort), and subjects with familial non-polyposis CRC (test cohort).

METHOD

A cohort study consisting of 37 negative control subjects, 9 positive control subjects with documented APC gene mutations, and 36 test subjects with familial non-polyposis CRC but no identified pathogenic APC gene mutation. The diagnosis of hereditary non-polyposis colon cancer was excluded in the test cohort by testing for microsatellite instability in tumour tissue.

RESULTS

None of the 37 people in the negative control group had CHRPE. Five of nine (56%) patients with FAP had multiple CHRPE lesions. None of the 36 subjects in the test cohort had CHRPE lesions.

CONCLUSIONS

Ophthalmoscopy may contribute to risk assessment in families with FAP but not in familial non-polyposis CRC. Care must be exercised when interpreting pigmented fundus lesions because 8-13% of subjects in each of the cohorts had pigmented retinal lesions that were not CHRPE. Bilateral lesions and lesions with a depigmented halo were the hallmarks of CHRPE associated with FAP.

Genetic mutations in von Willebrand disease identified by DHPLC and DNA sequence analysis

Von Willebrand disease (VWD) is a common inherited bleeding disorder caused by quantitative (types 1 and 3) and qualitative (type 2) defects in von Willebrand factor (VWF). The VWF gene is a large gene containing 52 exons; except for type 2 VWD, the majority of mutations causing VWD are not localized to specific exons. We have used denaturing high performance liquid chromatography (DHPLC) to scan the coding region of the VWF gene for sequence variations. Primers were designed to amplify all 52 exons while avoiding amplification of the VWF pseudogene. Exon-specific primers were designed with sequencing primers, allowing direct sequencing of each VWF exon. Sequence variations in 33 previously characterized von Willebrand disease (VWD) samples were all detected using DHPLC demonstrating the high sensitivity of this technique. In addition, we analyzed 42 patients or family members with VWD. Thirty-two novel sequence variations were identified (2 deletions, 2 nonsense, 15 missense, 6 silent, and 7 intronic), some with clear functional consequences. A previously described deletion in exon 18, 2435delC, was also found in two unrelated type 3 patients. This DHPLC and DNA sequencing technique will enable the full length assessment of the VWF gene necessary to detect mutations causing types 1 and 3 VWD.

Attenuated familial adenomatous polyposis: a case report with mixed features and review of genotype-phenotype correlation

Familial adenomatous polyposis represents approximately 1% of all colorectal cancers and is caused by germline mutations in the adenomatous polyposis coli (APC) gene. Most mutations are located within the first 2000 codons, and several mutational hot spots have been identified. The relative location of the mutation may be associated with the number of polyps and partially predicts specific phenotypic expression. Mutations associated with the attenuated phenotype are found predominantly in the 5' region of the gene or in the last third. We describe a patient with a mutation in codon 161 of the APC gene, which displays a phenotype most closely resembling the attenuated form of familial adenomatous polyposis, and review the literature, the implications of this mutation, and the importance of the molecular testing in the proper and more complete characterization of these patients. Differences in the APC mutation sites alone cannot completely account for intrafamilial and interfamilial variation in the polyposis phenotypes.

Assay validation for identification of hereditary nonpolyposis colon cancer-causing mutations in mismatch repair genes MLH1, MSH2, and MSH6

Hereditary nonpolyposis colon cancer (HNPCC, Online Mendelian Inheritance in Man (OMIM) 114500) is an autosomal dominant disorder that is genetically heterogeneous because of underlying mutations in mismatch repair genes, primarily MLH1, MSH2, and MSH6. One challenge to correctly diagnosing HNPCC is that the large size of the causative genes makes identification of mutations both labor intensive and expensive. We evaluated the usefulness of denaturing high performance liquid chromatography (DHPLC) for scanning mismatch repair genes (MLH1, MSH2, and MSH6) for point mutations, small deletions, and insertions. Our assay consisted of 51 sets of primers designed to amplify all exons of these genes. All polymerase chain reaction reactions were amplified simultaneously using the same reaction conditions in a 96-well format. The amplified products were analyzed by DHPLC across a range of optimum temperatures for partial fragment denaturation based on the melting profile of each specific fragment. DNA specimens from 23 previously studied HNPCC patients were analyzed by DHPLC, and all mutations were correctly identified and confirmed by sequence analysis. Here, we present our validation studies of the DHPLC platform for HNPCC mutation analysis and compare its merits with other scanning technologies. This approach provides greater sensitivity and more directed molecular analysis for clinical testing in HNPCC.

Identification of APC gene mutations in colorectal cancer using universal microarray-based combinatorial sequencing-by-hybridization

Familial adenomatous polyposis (FAP) is an autosomal dominant inherited form of colorectal cancer, caused mostly by mutations in the APC gene. Due to the wide variety of mutations found and the large size of the APC gene, several methods of mutation detection are used, which can be time consuming and costly. Here we demonstrate a new method of mutation detection in the APC gene using an array-based approach termed combinatorial sequencing-by-hybridization (cSBH). In cSBH, a universal probe set is attached to a support and a second one is in solution. Two-probe ligation occurs when a DNA strand from the target PCR product consecutively anneals to both unlabeled array-bound and solution-phase dye-labeled probe, creating all target-complementary long-labeled probes attached to the surface. A standard array reader scores fluorescent signals at each array position. Cell lines and patient DNA with known APC gene mutations were analyzed using a cSBH-based HyChip trade mark product. Results show that this universal hexamer (6-mer) chip can successfully detect a range of mutations. Results are very robust for a continuous readout of 3.6 kb from a PCR target, with 99.97% accuracy on a single HyChip trade mark slide. cSBH is a fast, cost-efficient method for first stage mutation screening in the APC or any other gene.

Molecular analysis of GISTs: evaluation of sequencing and dHPLC

Gastrointestinal stromal tumors (GISTs) are the most common mesenchymal tumors of the gastrointestinal tract and are characterized by mutations in the proto-oncogene KIT (c-kit). To date, the detection of genomic alterations of the c-kit gene has been based mostly on direct sequencing. However, sequencing is an expensive and time-consuming approach. Since the technology of WAVE DNA Fragment Analysis System (Transgenomic, Inc., Worcester, MA) (dHPLC) is available in our laboratory, we decided to evaluate its use. Sixteen patients with small/large intestine, stomach tumors were included in the study. Immunohistochemical evaluation was performed on formalin-fixed, paraffin-embedded specimens with the polyclonal antibody CD117 for the KIT protein. After DNA extraction and isolation from paraffin-embedded sections, a nested PCR approach was applied to amplify sequences of exon 11 of the c-kit gene. dHPLC and the ABI Prism 310 Genetic Analyzer (Applied Biosystems, Bedford, MA) were used respectively for screening and identification of genomic alterations. Immunohistochemical analysis revealed strong and diffuse KIT expression in each of the 16 paraffin-embedded sections examined. dHPLC analysis in two temperatures showed the presence of genomic alterations in 8 out of 16 (50%) samples examined. Subsequently, sequence analysis of exon 11 in those samples revealed c-kit alterations in only 8 out of 16 (50%) samples. These were five deletions, one of which was an in-frame deletion one-point mutation and one insertion. Furthermore, the sensitivity of both methods was compared by using different mixtures of a wild-type and a sample with a deletion in exon 11. dHPLC was shown to be able to detect genomic alterations in all four different sample mixtures, whereas with sequence analysis genomic alterations were detected only in the 1:2 and 1:4 sample mixtures. In conclusion, we showed that dHPLC is an efficient and accurate, as well as a more sensitive, method for screening of genomic alterations in exon 11 of the c-kit gene, compared to sequence analysis.

Genetic analysis of the APC gene in Taiwanese familial adenomatous polyposis

Colorectal cancer has become the third leading cause of death from cancer in Taiwan. Familial adenomatous polyposis (FAP) is an autosomal dominant inherited disease characterized by the presence of multiple adenomatous polyps in the colon and rectum. The gene responsible for FAP (APC) was cloned in 1991. Extensive analyses of the mutation spectra in FAP kindreds have been performed in different countries, but the results have been highly variable (30-80%). In this study, we used denaturing high-performance liquid chromatography (DHPLC) followed by automatic sequencing in an effort to establish the mutation spectrum of APC from DNA of peripheral blood cells. Among the 6 FAP probands analyzed, mutations were detected in 3 (50%), 2 of which were novel. The first novel mutation was at codon 2166, with a C to T transition, resulting in a stop codon. The second novel mutation was at codon 1971, with a C to G transversion, resulting in an amino acid change from serine to cysteine. The third mutation involved an A insertion in the sequence of -AAAAAA- at codons 1554-1556, which created a downstream stop codon (codon 1558). This study is the first to report mutation analysis in Taiwanese FAP probands.

The use of denaturing high-performance liquid chromatography (DHPLC) for the analysis of genetic variations: impact for diagnostics and pharmacogenetics

Over the past five years, denaturing high-performance liquid chromatography (DHPLC) has emerged as one of the most versatile technologies for the analysis of genetic variations. With the benefit of novel polymer chemistries used for separation, the accuracy, sensitivity, and the throughput of DHPLC for DNA and RNA analysis have greatly improved. DHPLC has been adopted in many laboratories for the screening of mutations and single-nucleotide polymorphisms (SNPs). The ability of DHPLC to detect known and unknown mutations simultaneously has put this technology at the forefront of genetic analysis for a wide variety of diseases. In addition, the high sensitivity of DHPLC combined with the accuracy of the heteroduplex analysis has allowed the development of applications beyond the scope of traditional sequencing or genotyping, e.g., the early detection of cancer. This article reviews the methods, which made DHPLC a widely used tool for diagnosis in molecular genetics and pharmacogenetics. The article provides an overview of current applications in these fields and points to novel applications in areas like epigenetics and the analysis of heteroplasmic mitochondrial DNA, in which DHPLC is becoming the leading technology.

Mutation searching in colorectal cancer studies: experience with a denaturing high-pressure liquid chromatography system for exon-by-exon scanning of tumour suppressor genes

AIMS

In hereditary colorectal cancer (CRC) disorders such as familial adenomatous polyposis and hereditary non-polyposis colon cancer, the identification of germline mutations greatly assists in the clinical management of families. In addition, study of somatic mutations in the cancers themselves (both hereditary and sporadic) has been fundamental in the elucidation of the initiation and progression of CRC. Many of the genes underlying CRC development are large; hence mutation screening is a time-consuming and labour-intensive process requiring a rapid and accurate alternative to gel-based systems such as single-strand confirmational polymorphism (SSCP) or denaturing gradient gel electrophoresis (DGGE). Here we report our progress using denaturing gradient high-pressure liquid chromatography (DHPLC) in the screening of the mismatch repair genes MLH1 and MSH2 and in screening the APC and HPP1 tumour suppressor genes for mutations.

METHODS

Genomic DNA was amplified using intronic primer sets spanning individual exons in the gene(s) under study. PCR products were subjected to DHPLC and the resultant chromatographs were compared with those of normal controls and aberrant peaks identified. Amplified products with aberrant peaks in the study samples underwent manual sequencing to confirm the presence of sequence variants.

RESULTS

The proportion of amplified fragments showing aberrant peaks (hits) ranged from 18 to 30% and in the case of every gene, more than 80% of these could be confirmed as a sequence variant by manual sequencing. The highest rate was found in HPP1, where all hits were found to be sequence variants, and the lowest rate was found in MSH2, where manual sequencing failed to find a sequence variant in 17% of the hits attained. Mutations varied in their nature from directly truncating through splice variants to missense and deletion mutations. Traces for each mutation displayed unique shapes and both deletions and single base changes were equally dramatic. During the mutation scanning many polymorphisms presented as aberrant peaks, as would be expected. Importantly, the same polymorphism gave an identical chromatographic tracing between individuals, opening the possibility to identify common polymorphisms on pattern recognition alone. There remains, though, the possibility that rare pathogenic variants may assume an identical shape.

CONCLUSIONS

The results indicate that DHPLC is a sensitive and efficient technique for screening of DNA for sequence variants. Given that polymorphisms comprised the largest proportion of variants found in each gene (66-100%), excluding these by pattern recognition would markedly reduce the amount of sequencing required.