1
|
Use of sanger and next-generation sequencing to screen for mosaic and intronic APC variants in unexplained colorectal polyposis patients. Fam Cancer 2021; 21:79-83. [PMID: 33683519 PMCID: PMC8799582 DOI: 10.1007/s10689-021-00236-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Accepted: 02/16/2021] [Indexed: 12/12/2022]
Abstract
In addition to classic germline APC gene variants, APC mosaicism and deep intronic germline APC variants have also been reported to be causes of adenomatous polyposis. In this study, we investigated 80 unexplained colorectal polyposis patients without germline pathogenic variants in known polyposis predisposing genes to detect mosaic and deep intronic APC variants. All patients developed more than 50 colorectal polyps, with adenomas being predominantly observed. To detect APC mosaicism, we performed next-generation sequencing (NGS) in leukocyte DNA. Furthermore, using Sanger sequencing, the cohort was screened for the following previously reported deep intronic pathogenic germline APC variants: c.1408 + 731C > T, p.(Gly471Serfs*55), c.1408 + 735A > T, p.(Gly471Serfs*55), c.1408 + 729A > G, p.(Gly471Serfs*55) and c.532-941G > A, p.(Phe178Argfs*22). We did not detect mosaic or intronic APC variants in the screened unexplained colorectal polyposis patients. The results of this study indicate that the deep intronic APC variants investigated in this study are not a cause of colorectal polyposis in this Dutch population. In addition, NGS did not detect any further mosaic variants in our cohort.
Collapse
|
2
|
Sullivan BA, Qin X, Redding TS, Gellad ZF, Stone A, Weiss D, Madison AN, Sims KJ, Williams CD, Lieberman D, Hauser ER, Provenzale D. Genetic Colorectal Cancer and Adenoma Risk Variants Are Associated with Increasing Cumulative Adenoma Counts. Cancer Epidemiol Biomarkers Prev 2020; 29:2269-2276. [PMID: 32928932 DOI: 10.1158/1055-9965.epi-20-0465] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 06/25/2020] [Accepted: 09/04/2020] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND The genetic basis for most individuals with high cumulative lifetime colonic adenomas is unknown. We investigated associations between known colorectal cancer-risk single-nucleotide polymorphisms (SNP) and increasing cumulative adenoma counts. METHODS The Cooperative Studies Program #380 screening colonoscopy cohort includes 612 selected participants age 50 to 75 with genotyped blood samples and 10 years of clinical follow-up. We evaluated 41 published "colorectal cancer-risk SNPs" for associations with individual cumulative adenoma counts or having ≥10 cumulative adenomas. SNPs were analyzed singly or combined in a polygenic risk score (PRS). The PRS was constructed from eight published SNPs associated with multiple adenomas, termed "adenoma-risk SNPs." RESULTS Four colorectal cancer-risk SNPs were associated with increasing cumulative adenoma counts (P < 0.05): rs12241008 (gene: VTI1A), rs2423279 (BMP2/HAO1), rs3184504 (SH2B3), and rs961253 (FERMT1/BMP2), with risk allele risk ratios of 1.31, 1.29, 1.24, and 1.23, respectively. Three colorectal cancer-risk SNPs were associated with ≥10 cumulative adenomas (P < 0.05), with risk allele odds ratios of 2.09 (rs3184504), 2.30 (rs961253), and 1.94 (rs3217901). A weighted PRS comprised of adenoma-risk SNPs was associated with higher cumulative adenomas (weighted rate ratio = 1.57; P = 0.03). CONCLUSIONS In this mostly male veteran colorectal cancer screening cohort, several known colorectal cancer-risk SNPs were associated with increasing cumulative adenoma counts and the finding of ≥10 cumulative adenomas. In addition, an increasing burden of adenoma-risk SNPs, measured by a weighted PRS, was associated with higher cumulative adenomas. IMPACT Future work will seek to validate these findings in different populations and then augment current colorectal cancer risk prediction tools with precancerous, adenoma genetic data.
Collapse
Affiliation(s)
- Brian A Sullivan
- Cooperative Studies Program Epidemiology Center, Durham VA Health Care System, Durham, North Carolina.,Department of Medicine, Duke University, Durham, North Carolina
| | - Xuejun Qin
- Cooperative Studies Program Epidemiology Center, Durham VA Health Care System, Durham, North Carolina.,Department of Biostatistics and Bioinformatics, Duke University, Durham, North Carolina
| | - Thomas S Redding
- Cooperative Studies Program Epidemiology Center, Durham VA Health Care System, Durham, North Carolina
| | - Ziad F Gellad
- Cooperative Studies Program Epidemiology Center, Durham VA Health Care System, Durham, North Carolina.,Department of Medicine, Duke University, Durham, North Carolina
| | - Anjanette Stone
- Cooperative Studies Program Pharmacogenomics Analysis Laboratory, Central Arkansas Veterans Health System, Little Rock, Arkansas
| | - David Weiss
- Perry Point Cooperative Studies Program Coordinating Center, Perry Point VA Medical Center, Perry Point, Maryland
| | - Ashton N Madison
- Cooperative Studies Program Epidemiology Center, Durham VA Health Care System, Durham, North Carolina
| | - Kellie J Sims
- Cooperative Studies Program Epidemiology Center, Durham VA Health Care System, Durham, North Carolina
| | - Christina D Williams
- Cooperative Studies Program Epidemiology Center, Durham VA Health Care System, Durham, North Carolina.,Department of Medicine, Duke University, Durham, North Carolina
| | - David Lieberman
- Division of Gastroenterology and Hepatology, School of Medicine, Oregon Health & Science University, Portland, Oregon.,VA Portland Health Care System, Portland, Oregon
| | - Elizabeth R Hauser
- Cooperative Studies Program Epidemiology Center, Durham VA Health Care System, Durham, North Carolina.,Department of Biostatistics and Bioinformatics, Duke University, Durham, North Carolina
| | - Dawn Provenzale
- Cooperative Studies Program Epidemiology Center, Durham VA Health Care System, Durham, North Carolina. .,Department of Medicine, Duke University, Durham, North Carolina
| |
Collapse
|
3
|
Terlouw D, Suerink M, Singh SS, Gille HJJP, Hes FJ, Langers AMJ, Morreau H, Vasen HFA, Vos YJ, van Wezel T, Tops CM, Ten Broeke SW, Nielsen M. Declining detection rates for APC and biallelic MUTYH variants in polyposis patients, implications for DNA testing policy. Eur J Hum Genet 2019; 28:222-230. [PMID: 31527860 DOI: 10.1038/s41431-019-0509-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Revised: 08/22/2019] [Accepted: 08/29/2019] [Indexed: 12/16/2022] Open
Abstract
This study aimed to determine the prevalence of APC-associated familial adenomatous polyposis (FAP) and MUTYH-associated polyposis (MAP) in a large cohort, taking into account factors as adenoma count and year of diagnosis. All application forms used to send patients in for APC and MUTYH variant analysis between 1992 and 2017 were collected (n = 2082). Using the data provided on the application form, the APC and biallelic MUTYH prevalence was determined and possible predictive factors were examined using multivariate multinomial logistic regression analysis in SPSS. The prevalence of disease causing variants in the APC gene significantly increases with adenoma count while MAP shows a peak prevalence in individuals with 50-99 adenomas. Logistic regression analysis shows significant odds ratios for adenoma count, age at diagnosis, and, interestingly, a decline in the chance of finding a variant in either gene over time. Moreover, in 22% (43/200) of patients with FAP-related extracolonic manifestations a variant was identified. The overall detection rates are above 10% for patients with >10 adenomas aged <60 and >20 adenomas aged <70. Patients with variants outside these criteria had FAP-related extracolonic manifestations, colorectal cancer aged <40, somatic KRAS c.34G > T variant in the tumor or a first-degree relative with >10 adenomas. Therefore, APC and MUTYH testing in patients with >10 adenomas aged <60 and with >20 adenomas aged <70 is advised. Almost all FAP and MAP patients not meeting these criteria showed other characteristics that can be used as an indication to prompt genetic testing.
Collapse
Affiliation(s)
- Diantha Terlouw
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, the Netherlands
| | - Manon Suerink
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, the Netherlands
| | - Sunny S Singh
- Department of Internal Medicine, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Hans J J P Gille
- Department of Clinical Genetics, VUMC, Amsterdam, the Netherlands
| | - Frederik J Hes
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, the Netherlands
| | - Alexandra M J Langers
- Department of Gastroenterology and Hepatology, Leiden University Medical Center, Leiden, the Netherlands
| | - Hans Morreau
- Department of Pathology, Leiden University Medical Center, Leiden, the Netherlands
| | - Hans F A Vasen
- Department of Gastroenterology and Hepatology, Leiden University Medical Center, Leiden, the Netherlands.,The Netherlands Foundation for the Detection of Hereditary Tumours, Leiden, the Netherlands
| | - Yvonne J Vos
- Department of Clinical Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Tom van Wezel
- Department of Pathology, Leiden University Medical Center, Leiden, the Netherlands
| | - Carli M Tops
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, the Netherlands
| | - Sanne W Ten Broeke
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, the Netherlands.,Department of Clinical Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Maartje Nielsen
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, the Netherlands.
| |
Collapse
|
4
|
Rosenthal EA, Shirts BH, Amendola LM, Horike-Pyne M, Robertson PD, Hisama FM, Bennett RL, Dorschner MO, Nickerson DA, Stanaway IB, Nassir R, Vickers KT, Li C, Grady WM, Peters U, Jarvik GP. Rare loss of function variants in candidate genes and risk of colorectal cancer. Hum Genet 2018; 137:795-806. [PMID: 30267214 PMCID: PMC6283057 DOI: 10.1007/s00439-018-1938-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Accepted: 09/18/2018] [Indexed: 02/07/2023]
Abstract
Although ~ 25% of colorectal cancer or polyp (CRC/P) cases show familial aggregation, current germline genetic testing identifies a causal genotype in the 16 major genes associated with high penetrance CRC/P in only 20% of these cases. As there are likely other genes underlying heritable CRC/P, we evaluated the association of variation at novel loci with CRC/P. We evaluated 158 a priori selected candidate genes by comparing the number of rare potentially disruptive variants (PDVs) found in 84 CRC/P cases without an identified CRC/P risk-associated variant and 2440 controls. We repeated this analysis using an additional 73 CRC/P cases. We also compared the frequency of PDVs in select genes among CRC/P cases with two publicly available data sets. We found a significant enrichment of PDVs in cases vs. controls: 20% of cases vs. 11.5% of controls with ≥ 1 PDV (OR = 1.9, p = 0.01) in the original set of cases. Among the second cohort of CRC/P cases, 18% had a PDV, significantly different from 11.5% (p = 0.02). Logistic regression, adjusting for ancestry and multiple testing, indicated association between CRC/P and PDVs in NTHL1 (p = 0.0001), BRCA2 (p = 0.01) and BRIP1 (p = 0.04). However, there was no significant difference in the frequency of PDVs at each of these genes between all 157 CRC/P cases and two publicly available data sets. These results suggest an increased presence of PDVs in CRC/P cases and support further investigation of the association of NTHL1, BRCA2 and BRIP1 variation with CRC/P.
Collapse
Affiliation(s)
- Elisabeth A Rosenthal
- Division of Medical Genetics, School of Medicine, University of Washington Medical Center, Seattle, WA, USA.
| | - Brian H Shirts
- Department of Laboratory Medicine, School of Medicine, University of Washington, Seattle, WA, USA
| | - Laura M Amendola
- Division of Medical Genetics, School of Medicine, University of Washington Medical Center, Seattle, WA, USA
| | - Martha Horike-Pyne
- Division of Medical Genetics, School of Medicine, University of Washington Medical Center, Seattle, WA, USA
| | - Peggy D Robertson
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Fuki M Hisama
- Division of Medical Genetics, School of Medicine, University of Washington Medical Center, Seattle, WA, USA
- Department of Neurology, School of Medicine, University of Washington, Seattle, WA, USA
| | - Robin L Bennett
- Division of Medical Genetics, School of Medicine, University of Washington Medical Center, Seattle, WA, USA
| | - Michael O Dorschner
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Department of Pathology, School of Medicine, University of Washington, Seattle, WA, USA
- Department of Psychiatry and Behavioral Sciences, School of Medicine, University of Washington, Seattle, WA, USA
| | | | - Ian B Stanaway
- Department of Biomedical Informatics and Medical Education, School of Medicine, University of Washington, Seattle, WA, USA
| | - Rami Nassir
- Department of Biochemistry and Molecular Medicine, University of California Davis, Davis, CA, USA
| | - Kathy T Vickers
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Christopher Li
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - William M Grady
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Department of Medicine, University of Washington School of Medicine, Seattle, WA, USA
| | - Ulrike Peters
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Department of Epidemiology, School of Public Health, University of Washington, Seattle, WA, USA
| | - Gail P Jarvik
- Division of Medical Genetics, School of Medicine, University of Washington Medical Center, Seattle, WA, USA
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Department of Epidemiology, School of Public Health, University of Washington, Seattle, WA, USA
| |
Collapse
|
5
|
Risk of eighteen genome-wide association study-identified genetic variants for colorectal cancer and colorectal adenoma in Han Chinese. Oncotarget 2018; 7:77651-77663. [PMID: 27769063 PMCID: PMC5363611 DOI: 10.18632/oncotarget.12750] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2015] [Accepted: 10/01/2016] [Indexed: 01/20/2023] Open
Abstract
Background Recent genome-wide association studies (GWAS) identified eighteen single-nucleotide polymorphisms (SNPs) to be significantly associated with the risk of colorectal cancer (CRC). However, overall results of the following replications are inconsistent and little is known about whether these associations also exit in colorectal adenomas (CRA). Methods The SNP genotyping was performed using a Sequenom MassARRAY to investigate the association of these eighteen SNPs with colorectal neoplasm in a case-control study consisted of 1049 colorectal cancers, 283 adenomas, and 1030 controls. Results Two of these SNPs, rs10505477 and rs719725, showed evidence of an association in both CRC and CRA in our study population. Besides, seven SNPs (rs10808555, rs7014346, rs7837328, rs704017, rs11196172, rs4779584, and rs7229639) were significantly associated with CRC, and another one SNP rs11903757 was over-represented in CRA compared with controls. The strongest association was provided by rs11196172 (OR = 2.02, 95% CI = 1.66 - 2.46, P < 0.0001) and rs11903757 (OR = 1.96, 95% CI = 1.28 - 3.00, P = 0.0026). Conclusion These results suggest that some previously reported SNP associations also have impact on CRC and CRA predispositions in the Han Chinese population. A part of genetic risk to CRC is possibly mediated by susceptibility to adenomas.
Collapse
|
6
|
Ghorbanoghli Z, Nieuwenhuis MH, Houwing-Duistermaat JJ, Jagmohan-Changur S, Hes FJ, Tops CM, Wagner A, Aalfs CM, Verhoef S, Gómez García EB, Sijmons RH, Menko FH, Letteboer TG, Hoogerbrugge N, van Wezel T, Vasen HFA, Wijnen JT. Colorectal cancer risk variants at 8q23.3 and 11q23.1 are associated with disease phenotype in APC mutation carriers. Fam Cancer 2017; 15:563-70. [PMID: 26880076 PMCID: PMC5010832 DOI: 10.1007/s10689-016-9877-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Familial adenomatous polyposis (FAP) is a dominantly inherited syndrome caused by germline mutations in the APC gene and characterized by the development of multiple colorectal adenomas and a high risk of developing colorectal cancer (CRC). The severity of polyposis is correlated with the site of the APC mutation. However, there is also phenotypic variability within families with the same underlying APC mutation, suggesting that additional factors influence the severity of polyposis. Genome-wide association studies identified several single nucleotide polymorphisms (SNPs) that are associated with CRC. We assessed whether these SNPs are associated with polyp multiplicity in proven APC mutation carriers. Sixteen CRC-associated SNPs were analysed in a cohort of 419 APC germline mutation carriers from 182 families. Clinical data were retrieved from the Dutch Polyposis Registry. Allele frequencies of the SNPs were compared for patients with <100 colorectal adenomas versus patients with ≥100 adenomas, using generalized estimating equations with the APC genotype as a covariate. We found a trend of association of two of the tested SNPs with the ≥100 adenoma phenotype: the C alleles of rs16892766 at 8q23.3 (OR 1.71, 95 % CI 1.05-2.76, p = 0.03, dominant model) and rs3802842 at 11q23.1 (OR 1.51, 95 % CI 1.03-2.22, p = 0.04, dominant model). We identified two risk variants that are associated with a more severe phenotype in APC mutation carriers. These risk variants may partly explain the phenotypic variability in families with the same APC gene defect. Further studies with a larger sample size are recommended to evaluate and confirm the phenotypic effect of these SNPs in FAP.
Collapse
Affiliation(s)
- Z Ghorbanoghli
- Netherlands Foundation for the Detetion of Hereditary Tumors, Leiden, The Netherlands.
- Department of Gastroenterology and Hepatology, Leiden University Medical Centre, Rijnsburgerweg 10, 2333 AA, Leiden, The Netherlands.
| | - M H Nieuwenhuis
- Netherlands Foundation for the Detetion of Hereditary Tumors, Leiden, The Netherlands
| | - J J Houwing-Duistermaat
- Department of Medical Statistics and Bioinformatics, Leiden University Medical Center, Leiden, The Netherlands
| | - S Jagmohan-Changur
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - F J Hes
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - C M Tops
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - A Wagner
- Department of Clinical Genetics, Erasmus Medical Center, Rotterdam, The Netherlands
| | - C M Aalfs
- Department of Clinical Genetics, Amsterdam Medical Centre, Amsterdam, The Netherlands
| | - S Verhoef
- Family Cancer Clinic, the Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - E B Gómez García
- Department of Clinical Genetics, University of Maastricht, Maastricht, The Netherlands
| | - R H Sijmons
- Department of Genetics, University Medical Centre Groningen, University of Groningen, Groningen, The Netherlands
| | - F H Menko
- Department of Clinical Genetics, VU University Medical Center, Amsterdam, The Netherlands
| | - T G Letteboer
- Department of Medical Genetics, University Medical Centre Utrecht, Utrecht, The Netherlands
| | - N Hoogerbrugge
- Department of Human Genetics, Radboud University Nijmegen Medical Center, Nijmegen, The Netherlands
| | - T van Wezel
- Departments of Pathology, Leiden University Medical Center, Leiden, The Netherlands
| | - H F A Vasen
- Netherlands Foundation for the Detetion of Hereditary Tumors, Leiden, The Netherlands
- Department of Gastroenterology and Hepatology, Leiden University Medical Centre, Rijnsburgerweg 10, 2333 AA, Leiden, The Netherlands
| | - J T Wijnen
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
| |
Collapse
|
7
|
Schubert SA, Ruano D, Elsayed FA, Boot A, Crobach S, Sarasqueta AF, Wolffenbuttel B, van der Klauw MM, Oosting J, Tops CM, van Eijk R, Vasen HFA, Vossen RHAM, Nielsen M, Castellví-Bel S, Ruiz-Ponte C, Tomlinson I, Dunlop MG, Vodicka P, Wijnen JT, Hes FJ, Morreau H, de Miranda NFCC, Sijmons RH, van Wezel T. Evidence for genetic association between chromosome 1q loci and predisposition to colorectal neoplasia. Br J Cancer 2017; 117:1215-1223. [PMID: 28742792 PMCID: PMC5589990 DOI: 10.1038/bjc.2017.240] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Revised: 05/31/2017] [Accepted: 06/30/2017] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND A substantial fraction of familial colorectal cancer (CRC) and polyposis heritability remains unexplained. This study aimed to identify predisposing loci in patients with these disorders. METHODS Homozygosity mapping was performed using 222 563 SNPs in 302 index patients with various colorectal neoplasms and 3367 controls. Linkage analysis, exome and whole-genome sequencing were performed in a family affected by microsatellite stable CRCs. Candidate variants were genotyped in 10 554 cases and 21 480 controls. Gene expression was assessed at the mRNA and protein level. RESULTS Homozygosity mapping revealed a disease-associated region at 1q32.3 which was part of the linkage region 1q32.2-42.2 identified in the CRC family. This includes a region previously associated with risk of CRC. Sequencing identified the p.Asp1432Glu variant in the MIA3 gene (known as TANGO1 or TANGO) and 472 additional rare, shared variants within the linkage region. In both cases and controls the population frequency was 0.02% for this MIA3 variant. The MIA3 mutant allele showed predominant mRNA expression in normal, cancer and precancerous tissues. Furthermore, immunohistochemistry revealed increased expression of MIA3 in adenomatous tissues. CONCLUSIONS Taken together, our two independent strategies associate genetic variations in chromosome 1q loci and predisposition to familial CRC and polyps, which warrants further investigation.
Collapse
Affiliation(s)
- Stephanie A Schubert
- Department of Pathology, Leiden University Medical Center, Leiden University, Leiden 2300 RC, The Netherlands
| | - Dina Ruano
- Department of Pathology, Leiden University Medical Center, Leiden University, Leiden 2300 RC, The Netherlands
| | - Fadwa A Elsayed
- Department of Pathology, Leiden University Medical Center, Leiden University, Leiden 2300 RC, The Netherlands
| | - Arnoud Boot
- Department of Pathology, Leiden University Medical Center, Leiden University, Leiden 2300 RC, The Netherlands
| | - Stijn Crobach
- Department of Pathology, Leiden University Medical Center, Leiden University, Leiden 2300 RC, The Netherlands
| | - Arantza Farina Sarasqueta
- Department of Pathology, Leiden University Medical Center, Leiden University, Leiden 2300 RC, The Netherlands
| | - Bruce Wolffenbuttel
- Department of Endocrinology, University of Groningen, University Medical Center Groningen, Groningen 9700 RB, The Netherlands
| | - Melanie M van der Klauw
- Department of Endocrinology, University of Groningen, University Medical Center Groningen, Groningen 9700 RB, The Netherlands
| | - Jan Oosting
- Department of Pathology, Leiden University Medical Center, Leiden University, Leiden 2300 RC, The Netherlands
| | - Carli M Tops
- Department of Clinical Genetics, Leiden University Medical Center, Leiden University, Leiden 2300 RC, The Netherlands
| | - Ronald van Eijk
- Department of Pathology, Leiden University Medical Center, Leiden University, Leiden 2300 RC, The Netherlands
| | - Hans FA Vasen
- Department of Gastroenterology and Hepatology, Leiden University Medical Center, Leiden University, Leiden 2300 RC, The Netherlands
| | - Rolf HAM Vossen
- Department of Human Genetics, Leiden University Medical Center, Leiden University, Leiden 2300 RC, The Netherlands
| | - Maartje Nielsen
- Department of Clinical Genetics, Leiden University Medical Center, Leiden University, Leiden 2300 RC, The Netherlands
| | - Sergi Castellví-Bel
- Department of Gastroenterology, Hospital Clínic, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), University of Barcelona, Barcelona, Catalonia 08036, Spain
| | - Clara Ruiz-Ponte
- Fundación Pública Galega de Medicina Xenómica (FPGMX)-SERGAS, Grupo de Medicina Xenómica-USC, Instituto de Investigación Sanitaria de Santiago (IDIS), Centro de Investigación en Red de Enfermedades Raras (CIBERER), Santiago de Compostela 15706, Spain
| | - Ian Tomlinson
- Oxford Centre for Cancer Gene Research, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Malcolm G Dunlop
- Colon Cancer Genetics Group, MRC Human Genetics Unit, The University of Edinburgh, Western General Hospital, Edinburgh EH4 2XU, UK
| | - Pavel Vodicka
- Institute of Experimental Medicine, Institute of Biology and Medical Genetics, Prague 142 00, Czech Republic
| | - Juul T Wijnen
- Department of Clinical Genetics, Leiden University Medical Center, Leiden University, Leiden 2300 RC, The Netherlands
| | - Frederik J Hes
- Department of Clinical Genetics, Leiden University Medical Center, Leiden University, Leiden 2300 RC, The Netherlands
| | - Hans Morreau
- Department of Pathology, Leiden University Medical Center, Leiden University, Leiden 2300 RC, The Netherlands
| | - Noel FCC de Miranda
- Department of Pathology, Leiden University Medical Center, Leiden University, Leiden 2300 RC, The Netherlands
| | - Rolf H Sijmons
- Department of Genetics, University of Groningen, University Medical Centre Groningen, Groningen 9700 RB, The Netherlands
| | - Tom van Wezel
- Department of Pathology, Leiden University Medical Center, Leiden University, Leiden 2300 RC, The Netherlands
| |
Collapse
|
8
|
Jansen AML, Crobach S, Geurts-Giele WRR, van den Akker BEWM, Garcia MV, Ruano D, Nielsen M, Tops CMJ, Wijnen JT, Hes FJ, van Wezel T, Dinjens WNM, Morreau H. Distinct Patterns of Somatic Mosaicism in the APC Gene in Neoplasms From Patients With Unexplained Adenomatous Polyposis. Gastroenterology 2017; 152:546-549.e3. [PMID: 27816598 DOI: 10.1053/j.gastro.2016.10.040] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Revised: 10/21/2016] [Accepted: 10/23/2016] [Indexed: 12/02/2022]
Abstract
We investigated the presence and patterns of mosaicism in the APC gene in patients with colon neoplasms not associated with any other genetic variants; we performed deep sequence analysis of APC in at least 2 adenomas or carcinomas per patient. We identified mosaic variants in APC in adenomas from 9 of the 18 patients with 21 to approximately 100 adenomas. Mosaic variants of APC were variably detected in leukocyte DNA and/or non-neoplastic intestinal mucosa of these patients. In a comprehensive sequence analysis of 1 patient, we found no evidence for mosaicism in APC in non-neoplastic intestinal mucosa. One patient was found to carry a mosaic c.4666dupA APC variant in only 10 of 16 adenomas, indicating the importance of screening 2 or more adenomas for genetic variants.
Collapse
Affiliation(s)
- Anne M L Jansen
- Department of Pathology, Leiden University Medical Centre, Leiden, The Netherlands; Department of Human Genetics, Leiden University Medical Centre, Leiden, The Netherlands
| | - Stijn Crobach
- Department of Pathology, Leiden University Medical Centre, Leiden, The Netherlands
| | - Willemina R R Geurts-Giele
- Department of Pathology, Erasmus MC Cancer Institute, University Medical Centre Rotterdam, The Netherlands
| | | | | | - Dina Ruano
- Department of Pathology, Leiden University Medical Centre, Leiden, The Netherlands
| | - Maartje Nielsen
- Department of Clinical Genetics, Leiden University Medical Centre, Leiden, The Netherlands
| | - Carli M J Tops
- Department of Clinical Genetics, Leiden University Medical Centre, Leiden, The Netherlands
| | - Juul T Wijnen
- Department of Human Genetics, Leiden University Medical Centre, Leiden, The Netherlands; Department of Clinical Genetics, Leiden University Medical Centre, Leiden, The Netherlands
| | - Frederik J Hes
- Department of Clinical Genetics, Leiden University Medical Centre, Leiden, The Netherlands
| | - Tom van Wezel
- Department of Pathology, Leiden University Medical Centre, Leiden, The Netherlands
| | - Winand N M Dinjens
- Department of Pathology, Erasmus MC Cancer Institute, University Medical Centre Rotterdam, The Netherlands
| | - Hans Morreau
- Department of Pathology, Leiden University Medical Centre, Leiden, The Netherlands.
| |
Collapse
|
9
|
Arriba M, García JL, Rueda D, Pérez J, Brandariz L, Nutu OA, Alonso L, Rodríguez Y, Urioste M, González-Sarmiento R, Perea J. Unsupervised Analysis of Array Comparative Genomic Hybridization Data from Early-Onset Colorectal Cancer Reveals Equivalence with Molecular Classification and Phenotypes. Neoplasia 2016; 19:28-34. [PMID: 27987438 PMCID: PMC5166699 DOI: 10.1016/j.neo.2016.11.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2016] [Revised: 11/02/2016] [Accepted: 11/07/2016] [Indexed: 02/07/2023] Open
Abstract
AIM To investigate whether chromosomal instability (CIN) is associated with tumor phenotypes and/or with global genomic status based on MSI (microsatellite instability) and CIMP (CpG island methylator phenotype) in early-onset colorectal cancer (EOCRC). METHODS Taking as a starting point our previous work in which tumors from 60 EOCRC cases (≤45 years at the time of diagnosis) were analyzed by array comparative genomic hybridization (aCGH), in the present study we performed an unsupervised hierarchical clustering analysis of those aCGH data in order to unveil possible associations between the CIN profile and the clinical features of the tumors. In addition, we evaluated the MSI and the CIMP statuses of the samples with the aim of investigating a possible relationship between copy number alterations (CNAs) and the MSI/CIMP condition in EOCRC. RESULTS Based on the similarity of the CNAs detected, the unsupervised analysis stratified samples into two main clusters (A, B) and four secondary clusters (A1, A2, B3, B4). The different subgroups showed a certain correspondence with the molecular classification of colorectal cancer (CRC), which enabled us to outline an algorithm to categorize tumors according to their CIMP status. Interestingly, each subcluster showed some distinctive clinicopathological features. But more interestingly, the CIN of each subcluster mainly affected particular chromosomes, allowing us to define chromosomal regions more specifically affected depending on the CIMP/MSI status of the samples. CONCLUSIONS Our findings may provide a basis for a new form of classifying EOCRC according to the genomic status of the tumors.
Collapse
Affiliation(s)
- María Arriba
- Centre for Biomedical Research of the 12 de Octubre University Hospital, Avda. de Córdoba, S/N, 28041, Madrid, Spain
| | - Juan L García
- Biomedical Research Institute of Salamanca (IBSAL). University Hospital of Salamanca-USAL-CSIC, P° de San Vicente, 58-182, 37007, Salamanca, Spain; Institute of Molecular and Cellular Biology of Cancer (IBMCC), University of Salamanca-CSIC, Campus Miguel de Unamuno, 37007, Salamanca, Spain
| | - Daniel Rueda
- Molecular Biology Laboratory, 12 de Octubre University Hospital, Avda. de Córdoba, S/N, 28041, Madrid, Spain
| | - Jessica Pérez
- Biomedical Research Institute of Salamanca (IBSAL). University Hospital of Salamanca-USAL-CSIC, P° de San Vicente, 58-182, 37007, Salamanca, Spain; Institute of Molecular and Cellular Biology of Cancer (IBMCC), University of Salamanca-CSIC, Campus Miguel de Unamuno, 37007, Salamanca, Spain
| | - Lorena Brandariz
- Department of Surgery, 12 de Octubre University Hospital. Avda. de Córdoba, S/N, 28041, Madrid, Spain
| | - Oana A Nutu
- Department of Surgery, 12 de Octubre University Hospital. Avda. de Córdoba, S/N, 28041, Madrid, Spain
| | - Laura Alonso
- Department of Surgery, 12 de Octubre University Hospital. Avda. de Córdoba, S/N, 28041, Madrid, Spain
| | - Yolanda Rodríguez
- Department of Pathology, 12 de Octubre University Hospital, Avda. de Córdoba, S/N, 28041, Madrid, Spain
| | - Miguel Urioste
- Familial Cancer Clinical Unit, Human Cancer Genetics Program. Spanish National Cancer Research Centre (CNIO), C/Melchor Fernández Almagro, 3, 28029, Madrid, Spain; Center for Biomedical Network Research on Rare Diseases (CIBERER), Institute of Health Carlos III, C/Monforte de Lemos 3-5, Pabellón 11, 28029, Madrid, Spain
| | - Rogelio González-Sarmiento
- Biomedical Research Institute of Salamanca (IBSAL). University Hospital of Salamanca-USAL-CSIC, P° de San Vicente, 58-182, 37007, Salamanca, Spain; Institute of Molecular and Cellular Biology of Cancer (IBMCC), University of Salamanca-CSIC, Campus Miguel de Unamuno, 37007, Salamanca, Spain
| | - José Perea
- Centre for Biomedical Research of the 12 de Octubre University Hospital, Avda. de Córdoba, S/N, 28041, Madrid, Spain; Department of Surgery, 12 de Octubre University Hospital. Avda. de Córdoba, S/N, 28041, Madrid, Spain.
| |
Collapse
|
10
|
Marabelli M, Molinaro V, Abou Khouzam R, Berrino E, Panero M, Balsamo A, Venesio T, Ranzani GN. Colorectal Adenomatous Polyposis: Heterogeneity of Susceptibility Gene Mutations and Phenotypes in a Cohort of Italian Patients. Genet Test Mol Biomarkers 2016; 20:777-785. [PMID: 27705013 DOI: 10.1089/gtmb.2016.0198] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
AIMS Colorectal adenomatous polyposis entailing cancer predisposition is caused by constitutional mutations in different genes. APC is associated with the familial adenomatous polyposis (FAP/AFAP) and MUTYH with the MUTYH-associated polyposis (MAP), while POLE and POLD1 mutations cause the polymerase proofreading-associated polyposis (PPAP). METHODS We screened for mutations in patients with multiple adenomas/FAP: 121 patients were analyzed for APC and MUTYH mutations, and 36 patients were also evaluated for POLE and POLD1 gene mutations. RESULTS We found 20 FAP/AFAP, 15 MAP, and no PPAP subjects: pathogenic mutations proved to be heterogeneous, and included 5 APC and 1 MUTYH novel mutations. The mutation detection rate was significantly different between patients with 5-100 polyps and those with >100 polyps (p = 8.154 × 10-7), with APC mutations being associated with an aggressive phenotype (p = 1.279 × 10-9). Mean age at diagnosis was lower in FAP/AFAP compared to MAP (p = 3.055 × 10-4). Mutation-negative probands showed a mean age at diagnosis that was significantly higher than FAP/AFAP (p = 3.46986 × 10-7) and included 45.3% of patients with <30 polyps and 70.9% of patients with no family history. CONCLUSIONS This study enlarges the APC and MUTYH mutational spectra, and also evaluated variants of uncertain significance, including the MUTYH p.Gln338His mutation. Moreover this study underscores the phenotypic heterogeneity and genotype-phenotype correlations in a cohort of Italian patients.
Collapse
Affiliation(s)
- Monica Marabelli
- 1 Department of Biology and Biotechnology, University of Pavia , Pavia, Italy
| | - Valeria Molinaro
- 1 Department of Biology and Biotechnology, University of Pavia , Pavia, Italy
| | - Raefa Abou Khouzam
- 1 Department of Biology and Biotechnology, University of Pavia , Pavia, Italy
| | | | - Mara Panero
- 2 Candiolo Cancer Institute , FPO-IRCCS, Torino, Italy
| | | | | | | |
Collapse
|
11
|
Adam R, Spier I, Zhao B, Kloth M, Marquez J, Hinrichsen I, Kirfel J, Tafazzoli A, Horpaopan S, Uhlhaas S, Stienen D, Friedrichs N, Altmüller J, Laner A, Holzapfel S, Peters S, Kayser K, Thiele H, Holinski-Feder E, Marra G, Kristiansen G, Nöthen MM, Büttner R, Möslein G, Betz RC, Brieger A, Lifton RP, Aretz S. Exome Sequencing Identifies Biallelic MSH3 Germline Mutations as a Recessive Subtype of Colorectal Adenomatous Polyposis. Am J Hum Genet 2016; 99:337-51. [PMID: 27476653 DOI: 10.1016/j.ajhg.2016.06.015] [Citation(s) in RCA: 161] [Impact Index Per Article: 20.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Accepted: 06/14/2016] [Indexed: 12/20/2022] Open
Abstract
In ∼30% of families affected by colorectal adenomatous polyposis, no germline mutations have been identified in the previously implicated genes APC, MUTYH, POLE, POLD1, and NTHL1, although a hereditary etiology is likely. To uncover further genes with high-penetrance causative mutations, we performed exome sequencing of leukocyte DNA from 102 unrelated individuals with unexplained adenomatous polyposis. We identified two unrelated individuals with differing compound-heterozygous loss-of-function (LoF) germline mutations in the mismatch-repair gene MSH3. The impact of the MSH3 mutations (c.1148delA, c.2319-1G>A, c.2760delC, and c.3001-2A>C) was indicated at the RNA and protein levels. Analysis of the diseased individuals' tumor tissue demonstrated high microsatellite instability of di- and tetranucleotides (EMAST), and immunohistochemical staining illustrated a complete loss of nuclear MSH3 in normal and tumor tissue, confirming the LoF effect and causal relevance of the mutations. The pedigrees, genotypes, and frequency of MSH3 mutations in the general population are consistent with an autosomal-recessive mode of inheritance. Both index persons have an affected sibling carrying the same mutations. The tumor spectrum in these four persons comprised colorectal and duodenal adenomas, colorectal cancer, gastric cancer, and an early-onset astrocytoma. Additionally, we detected one unrelated individual with biallelic PMS2 germline mutations, representing constitutional mismatch-repair deficiency. Potentially causative variants in 14 more candidate genes identified in 26 other individuals require further workup. In the present study, we identified biallelic germline MSH3 mutations in individuals with a suspected hereditary tumor syndrome. Our data suggest that MSH3 mutations represent an additional recessive subtype of colorectal adenomatous polyposis.
Collapse
Affiliation(s)
- Ronja Adam
- Institute of Human Genetics, University of Bonn, 53127 Bonn, Germany; Center for Hereditary Tumor Syndromes, University of Bonn, 53127 Bonn, Germany
| | - Isabel Spier
- Institute of Human Genetics, University of Bonn, 53127 Bonn, Germany; Center for Hereditary Tumor Syndromes, University of Bonn, 53127 Bonn, Germany
| | - Bixiao Zhao
- Department of Genetics, Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, CT 06520-8005, USA
| | - Michael Kloth
- Institute of Pathology, University of Cologne, 50937 Cologne, Germany
| | - Jonathan Marquez
- Department of Genetics, Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, CT 06520-8005, USA
| | - Inga Hinrichsen
- Medical Clinic 1, Biomedical Research Laboratory, Goethe-University Frankfurt, 60590 Frankfurt, Germany
| | - Jutta Kirfel
- Institute of Pathology, University of Bonn, 53127 Bonn, Germany
| | - Aylar Tafazzoli
- Institute of Human Genetics, University of Bonn, 53127 Bonn, Germany; Department of Genomics, Life & Brain Center, University of Bonn, 53127 Bonn, Germany
| | - Sukanya Horpaopan
- Institute of Human Genetics, University of Bonn, 53127 Bonn, Germany; Department of Anatomy, Faculty of Medical Science, Naresuan University, Phitsanulok, Chiang Mai 50200, Thailand
| | - Siegfried Uhlhaas
- Institute of Human Genetics, University of Bonn, 53127 Bonn, Germany
| | - Dietlinde Stienen
- Institute of Human Genetics, University of Bonn, 53127 Bonn, Germany
| | | | - Janine Altmüller
- Cologne Center for Genomics, University of Cologne, 50937 Cologne, Germany; Institute of Human Genetics, University of Cologne, 50937 Cologne, Germany
| | - Andreas Laner
- Medizinische Klinik und Poliklinik IV, Ludwig-Maximilians-University, 80336 Munich, Germany; Medical Genetics Center, 80335 Munich, Germany
| | - Stefanie Holzapfel
- Institute of Human Genetics, University of Bonn, 53127 Bonn, Germany; Center for Hereditary Tumor Syndromes, University of Bonn, 53127 Bonn, Germany
| | - Sophia Peters
- Institute of Human Genetics, University of Bonn, 53127 Bonn, Germany
| | - Katrin Kayser
- Institute of Human Genetics, University of Bonn, 53127 Bonn, Germany
| | - Holger Thiele
- Cologne Center for Genomics, University of Cologne, 50937 Cologne, Germany
| | - Elke Holinski-Feder
- Medizinische Klinik und Poliklinik IV, Ludwig-Maximilians-University, 80336 Munich, Germany; Medical Genetics Center, 80335 Munich, Germany
| | - Giancarlo Marra
- Institute of Molecular Cancer Research, University of Zurich, CH-8057 Zurich, Switzerland
| | | | - Markus M Nöthen
- Institute of Human Genetics, University of Bonn, 53127 Bonn, Germany; Department of Genomics, Life & Brain Center, University of Bonn, 53127 Bonn, Germany
| | - Reinhard Büttner
- Institute of Pathology, University of Cologne, 50937 Cologne, Germany
| | - Gabriela Möslein
- HELIOS Klinikum Wuppertal, University of Witten/Herdecke, 42283 Wuppertal, Germany
| | - Regina C Betz
- Institute of Human Genetics, University of Bonn, 53127 Bonn, Germany; Department of Genomics, Life & Brain Center, University of Bonn, 53127 Bonn, Germany
| | - Angela Brieger
- Medical Clinic 1, Biomedical Research Laboratory, Goethe-University Frankfurt, 60590 Frankfurt, Germany
| | - Richard P Lifton
- Department of Genetics, Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, CT 06520-8005, USA
| | - Stefan Aretz
- Institute of Human Genetics, University of Bonn, 53127 Bonn, Germany; Center for Hereditary Tumor Syndromes, University of Bonn, 53127 Bonn, Germany.
| |
Collapse
|
12
|
Copy number variants associated with 18p11.32, DCC and the promoter 1B region of APC in colorectal polyposis patients. Meta Gene 2015; 7:95-104. [PMID: 26909336 PMCID: PMC4733217 DOI: 10.1016/j.mgene.2015.12.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2015] [Revised: 12/16/2015] [Accepted: 12/21/2015] [Indexed: 01/05/2023] Open
Abstract
Familial Adenomatous Polyposis (FAP) is the second most common inherited predisposition to colorectal cancer (CRC) associated with the development of hundreds to thousands of adenomas in the colon and rectum. Mutations in APC are found in ~ 80% polyposis patients with FAP. In the remaining 20% no genetic diagnosis can be provided suggesting other genes or mechanisms that render APC inactive may be responsible. Copy number variants (CNVs) remain to be investigated in FAP and may account for disease in a proportion of polyposis patients. A cohort of 56 polyposis patients and 40 controls were screened for CNVs using the 2.7M microarray (Affymetrix) with data analysed using ChAS (Affymetrix). A total of 142 CNVs were identified unique to the polyposis cohort suggesting their involvement in CRC risk. We specifically identified CNVs in four unrelated polyposis patients among CRC susceptibility genes APC, DCC, MLH1 and CTNNB1 which are likely to have contributed to disease development in these patients. A recurrent deletion was observed at position 18p11.32 in 9% of the patients screened that was of particular interest. Further investigation is necessary to fully understand the role of these variants in CRC risk given the high prevalence among the patients screened.
Collapse
Key Words
- ALL, acute lymphoblastic leukaemia
- BH, Bengamini and Hochberg
- CHAS, Chromosome Analysis Suite
- CN, copy number
- CNV
- CNV, copy number variation
- COSMIC, Catalogue of Somatic Mutations in Cancer
- CRC, colorectal cancer
- Cancer
- DGV, Database of genomic variants
- DNA, deoxyribose nucleic acid
- FAP, familial adenomatous polyposis
- HMDD, human microRNA disease database
- KEGG, Kyoto Encyclopaedia of Genes and Genomes
- Kb, kilobase
- LOH, loss of heterozygosity
- MLPA, multiplex ligation-dependant probe amplification
- MMR, mismatch repair
- NTC, no template control
- QC, quality control
- RNA, ribose nucleic acid
- SNP, single nucleotide polymorphism
- TAM, Tool for the annotation of microRNAs
- TCGA, The Cancer Genome Atlas
- UCSC, University of California, Santa Cruz
- diagnostic testing
- lncRNA, link RNA
- long non-coding RNAs
- mapd, median absolute pairwise difference
- miR, microRNA
- ng, nanogram
- polyposis
Collapse
|
13
|
Weren RDA, Venkatachalam R, Cazier JB, Farin HF, Kets CM, de Voer RM, Vreede L, Verwiel ETP, van Asseldonk M, Kamping EJ, Kiemeney LA, Neveling K, Aben KKH, Carvajal-Carmona L, Nagtegaal ID, Schackert HK, Clevers H, van de Wetering M, Tomlinson IP, Ligtenberg MJL, Hoogerbrugge N, Geurts van Kessel A, Kuiper RP. Germline deletions in the tumour suppressor gene FOCAD are associated with polyposis and colorectal cancer development. J Pathol 2015; 236:155-64. [PMID: 25712196 PMCID: PMC6681464 DOI: 10.1002/path.4520] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2014] [Revised: 02/09/2015] [Accepted: 02/18/2015] [Indexed: 12/20/2022]
Abstract
Heritable genetic variants can significantly affect the lifetime risk of developing cancer, including polyposis and colorectal cancer (CRC). Variants in genes currently known to be associated with a high risk for polyposis or CRC, however, explain only a limited number of hereditary cases. The identification of additional genetic causes is, therefore, crucial to improve CRC prevention, detection and treatment. We have performed genome-wide and targeted DNA copy number profiling and resequencing in early-onset and familial polyposis/CRC patients, and show that deletions affecting the open reading frame of the tumour suppressor gene FOCAD are recurrent and significantly enriched in CRC patients compared with unaffected controls. All patients carrying FOCAD deletions exhibited a personal or family history of polyposis. RNA in situ hybridization revealed FOCAD expression in epithelial cells in the colonic crypt, the site of tumour initiation, as well as in colonic tumours and organoids. Our data suggest that monoallelic germline deletions in the tumour suppressor gene FOCAD underlie moderate genetic predisposition to the development of polyposis and CRC.
Collapse
Affiliation(s)
- Robbert D A Weren
- Department of Human Genetics, Radboud university medical center, Nijmegen, The Netherlands
| | | | | | - Henner F Farin
- Hubrecht Institute, University Medical Centre Utrecht, The Netherlands
| | - C Marleen Kets
- Department of Human Genetics, Radboud university medical center, Nijmegen, The Netherlands
| | - Richarda M de Voer
- Department of Human Genetics, Radboud university medical center, Nijmegen, The Netherlands
| | - Lilian Vreede
- Department of Human Genetics, Radboud university medical center, Nijmegen, The Netherlands
| | - Eugène T P Verwiel
- Department of Human Genetics, Radboud university medical center, Nijmegen, The Netherlands
| | - Monique van Asseldonk
- Department of Pathology, Radboud university medical center, Nijmegen, The Netherlands
| | - Eveline J Kamping
- Department of Human Genetics, Radboud university medical center, Nijmegen, The Netherlands
| | - Lambertus A Kiemeney
- Radboud Institute for Health Sciences, Radboud university medical center, Nijmegen, The Netherlands
| | - Kornelia Neveling
- Department of Human Genetics, Radboud university medical center, Nijmegen, The Netherlands
| | - Katja K H Aben
- Radboud Institute for Health Sciences, Radboud university medical center, Nijmegen, The Netherlands
- Netherlands Comprehensive Cancer Organization, Utrecht, The Netherlands
| | - Luis Carvajal-Carmona
- Genome Center and Department of Biochemistry and Molecular Medicine, School of Medicine, University of California at Davis, CA, USA
| | - Iris D Nagtegaal
- Department of Pathology, Radboud university medical center, Nijmegen, The Netherlands
| | - Hans K Schackert
- Department of Surgical Research, Universitätsklinikum Carl Gustav Carus, Technische Universität Dresden, Germany
| | - Hans Clevers
- Hubrecht Institute, University Medical Centre Utrecht, The Netherlands
| | | | - Ian P Tomlinson
- Wellcome Trust Centre for Human Genetics University of Oxford, UK
| | - Marjolijn J L Ligtenberg
- Department of Human Genetics, Radboud university medical center, Nijmegen, The Netherlands
- Department of Pathology, Radboud university medical center, Nijmegen, The Netherlands
| | - Nicoline Hoogerbrugge
- Department of Human Genetics, Radboud university medical center, Nijmegen, The Netherlands
| | - Ad Geurts van Kessel
- Department of Human Genetics, Radboud university medical center, Nijmegen, The Netherlands
| | - Roland P Kuiper
- Department of Human Genetics, Radboud university medical center, Nijmegen, The Netherlands
| |
Collapse
|
14
|
Baert-Desurmont S, Charbonnier F, Houivet E, Ippolito L, Mauillon J, Bougeard M, Abadie C, Malka D, Duffour J, Desseigne F, Colas C, Pujol P, Lejeune S, Dugast C, Buecher B, Faivre L, Leroux D, Gesta P, Coupier I, Guimbaud R, Berthet P, Manouvrier S, Cauchin E, Prieur F, Laurent-Puig P, Lebrun M, Jonveaux P, Chiesa J, Caron O, Morin-Meschin ME, Polycarpe-Osaer F, Giraud S, Zaanan A, Bonnet D, Mansuy L, Bonadona V, El Chehadeh S, Duhoux F, Gauthier-Villars M, Saurin JC, Collonge-Rame MA, Brugières L, Wang Q, Bressac-de Paillerets B, Rey JM, Toulas C, Buisine MP, Bronner M, Sokolowska J, Hardouin A, Cailleux AF, Sebaoui H, Blot J, Tinat J, Benichou J, Frebourg T. Clinical relevance of 8q23, 15q13 and 18q21 SNP genotyping to evaluate colorectal cancer risk. Eur J Hum Genet 2015; 24:99-105. [PMID: 25873010 PMCID: PMC4795220 DOI: 10.1038/ejhg.2015.72] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2014] [Revised: 01/19/2015] [Accepted: 01/27/2015] [Indexed: 01/13/2023] Open
Abstract
To determine if the at-risk single-nucleotide polymorphism (SNP) alleles for colorectal cancer (CRC) could contribute to clinical situations suggestive of an increased genetic risk for CRC, we performed a prospective national case–control study based on highly selected patients (CRC in two first-degree relatives, one before 61 years of age; or CRC diagnosed before 51 years of age; or multiple primary CRCs, the first before 61 years of age; exclusion of Lynch syndrome and polyposes) and controls without personal or familial history of CRC. SNPs were genotyped using SNaPshot, and statistical analyses were performed using Pearson's χ2 test, Cochran–Armitage test of trend and logistic regression. We included 1029 patients and 350 controls. We confirmed the association of CRC risk with four SNPs, with odds ratio (OR) higher than previously reported: rs16892766 on 8q23.3 (OR: 1.88, 95% confidence interval (CI): 1.30–2.72; P=0.0007); rs4779584 on 15q13.3 (OR: 1.42, CI: 1.11–1.83; P=0.0061) and rs4939827 and rs58920878/Novel 1 on 18q21.1 (OR: 1.49, CI: 1.13–1.98; P=0.007 and OR: 1.49, CI: 1.14–1.95; P=0.0035). We found a significant (P<0.0001) cumulative effect of the at-risk alleles or genotypes with OR at 1.62 (CI: 1.10–2.37), 2.09 (CI: 1.43–3.07), 2.87 (CI: 1.76–4.70) and 3.88 (CI: 1.72–8.76) for 1, 2, 3 and at least 4 at-risk alleles, respectively, and OR at 1.71 (CI: 1.18–2.46), 2.29 (CI: 1.55–3.38) and 6.21 (CI: 2.67–14.42) for 1, 2 and 3 at-risk genotypes, respectively. Combination of SNPs may therefore explain a fraction of clinical situations suggestive of an increased risk for CRC.
Collapse
Affiliation(s)
- Stéphanie Baert-Desurmont
- Inserm U1079, University of Rouen, Institute for Research and Innovation in Biomedicine, Rouen, France.,Department of Genetics, University Hospital, Rouen, France.,Cancéropôle Nord-Ouest, France
| | - Françoise Charbonnier
- Inserm U1079, University of Rouen, Institute for Research and Innovation in Biomedicine, Rouen, France.,Department of Genetics, University Hospital, Rouen, France.,Cancéropôle Nord-Ouest, France
| | - Estelle Houivet
- Department of Biostatistics, University Hospital and Inserm U657, University of Rouen, Institute for Research and Innovation in Biomedicine, Rouen, France.,Centre d'Investigation Clinique, University Hospital, Rouen, France
| | - Lorena Ippolito
- Inserm U1079, University of Rouen, Institute for Research and Innovation in Biomedicine, Rouen, France.,Cancéropôle Nord-Ouest, France
| | | | - Marion Bougeard
- Inserm U1079, University of Rouen, Institute for Research and Innovation in Biomedicine, Rouen, France
| | - Caroline Abadie
- Inserm U1079, University of Rouen, Institute for Research and Innovation in Biomedicine, Rouen, France.,Department of Genetics, Comprehensive Cancer Center Eugène Marquis, Rennes, France
| | - David Malka
- Department of Genetics, Institut Gustave Roussy, Villejuif, France
| | - Jacqueline Duffour
- Department of Genetics, Comprehensive Cancer Center Val d'Aurelle, Montpellier, France
| | - Françoise Desseigne
- Department of Genetics, Comprehensive Cancer Center Léon Bérard, Lyon, France
| | - Chrystelle Colas
- Department of Genetics, AP-HP, Hôpital Saint Antoine, Paris, France
| | - Pascal Pujol
- Department of Genetics, University Hospital, Montpellier, France
| | - Sophie Lejeune
- Department of Genetics, University Hospital, Lille, France
| | - Catherine Dugast
- Department of Genetics, Comprehensive Cancer Center Eugène Marquis, Rennes, France
| | - Bruno Buecher
- Department of Genetics, Institut Curie, Paris, France
| | - Laurence Faivre
- Department of Genetics, University Hospital and Comprehensive Cancer Center Georges-François Leclerc, Dijon, France
| | | | - Paul Gesta
- Department of Genetics, Hospital, Niort, France
| | - Isabelle Coupier
- Department of Genetics, University Hospital, Montpellier, France
| | - Rosine Guimbaud
- Department of Genetics, Comprehensive Cancer Center Claudius Regaud, Toulouse, France
| | - Pascaline Berthet
- Department of Genetics, Comprehensive Cancer Center François Baclesse, Caen, France
| | | | | | - Fabienne Prieur
- Department of Genetics, University Hospital, Saint Etienne, France
| | | | - Marine Lebrun
- Department of Genetics, University Hospital, Saint Etienne, France
| | | | - Jean Chiesa
- Department of Genetics, University Hospital, Nîmes, France
| | - Olivier Caron
- Department of Genetics, Institut Gustave Roussy, Villejuif, France
| | | | | | - Sophie Giraud
- Department of Genetics, University Hospital Edouard Herriot, Lyon, France
| | - Aziz Zaanan
- Department of Genetics, Hôpital Européen Georges Pompidou, Paris, France
| | - Delphine Bonnet
- Department of Genetics, University Hospital, Toulouse, France
| | - Ludovic Mansuy
- Department of Genetics, University Hospital, Nancy, France
| | - Valérie Bonadona
- Department of Genetics, Comprehensive Cancer Center Léon Bérard, Lyon, France
| | - Salima El Chehadeh
- Department of Genetics, University Hospital and Comprehensive Cancer Center Georges-François Leclerc, Dijon, France
| | - François Duhoux
- Department of Genetics, Cancer Centre, Cliniques Universitaires St Luc, Bruxelles, Belgium
| | | | | | | | | | - Qing Wang
- Department of Genetics, Comprehensive Cancer Center Léon Bérard, Lyon, France
| | | | - Jean-Marc Rey
- Department of Genetics, University Hospital, Montpellier, France
| | - Christine Toulas
- Department of Genetics, Comprehensive Cancer Center Claudius Regaud, Toulouse, France
| | | | - Myriam Bronner
- Department of Genetics, University Hospital, Nancy, France
| | | | - Agnès Hardouin
- Department of Genetics, Comprehensive Cancer Center François Baclesse, Caen, France
| | | | - Hakim Sebaoui
- Department of Clinical Research, University Hospital, Rouen, France
| | - Julien Blot
- Department of Clinical Research, University Hospital, Rouen, France
| | - Julie Tinat
- Inserm U1079, University of Rouen, Institute for Research and Innovation in Biomedicine, Rouen, France.,Department of Genetics, University Hospital, Rouen, France.,Cancéropôle Nord-Ouest, France
| | - Jacques Benichou
- Department of Biostatistics, University Hospital and Inserm U657, University of Rouen, Institute for Research and Innovation in Biomedicine, Rouen, France
| | - Thierry Frebourg
- Inserm U1079, University of Rouen, Institute for Research and Innovation in Biomedicine, Rouen, France.,Department of Genetics, University Hospital, Rouen, France.,Cancéropôle Nord-Ouest, France
| |
Collapse
|
15
|
Abstract
Hereditary factors are involved in the development of a substantial proportion of all cases of colorectal cancer. Inherited forms of colorectal cancer are usually subdivided into polyposis syndromes characterized by the development of multiple colorectal polyps and nonpolyposis syndromes characterized by the development of few or no polyps. Timely identification of hereditary colorectal cancer syndromes is vital because patient participation in early detection programmes prevents premature death due to cancer. Polyposis syndromes are fairly easy to recognize, but some patients might have characteristics that overlap with other clinically defined syndromes. Comprehensive analysis of the genes known to be associated with polyposis syndromes helps to establish the final diagnosis in these patients. Recognizing Lynch syndrome is more difficult than other polyposis syndromes owing to the absence of pathognomonic features. Most investigators therefore recommend performing systematic molecular analysis of all newly diagnosed colorectal cancer using immunohistochemical methods. The implementation in clinical practice of new high-throughput methods for molecular analysis might further increase the identification of individuals at risk of hereditary colorectal cancer. This Review describes the clinical management of the various hereditary colorectal cancer syndromes and demonstrates the advantage of using a classification based on the underlying gene defects.
Collapse
Affiliation(s)
- Hans F A Vasen
- Department of Gastroenterology, Leiden University Medical Centre, Rijnsburgerweg 10, 2333 AA Leiden, Netherlands
| | - Ian Tomlinson
- Wellcome Trust Centre for Human Genetics and NIHR Comprehensive Biomedical Research Centre, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Antoni Castells
- Department of Gastroenterology, Hospital Clinic, University of Barcelona, IDIBAPS, CIBERehd, Villaroel 170, 08036 Barcelona, Catalonia, Spain
| |
Collapse
|
16
|
Cheng THT, Gorman M, Martin L, Barclay E, Casey G, Saunders B, Thomas H, Clark S, Tomlinson I. Common colorectal cancer risk alleles contribute to the multiple colorectal adenoma phenotype, but do not influence colonic polyposis in FAP. Eur J Hum Genet 2015; 23:260-3. [PMID: 24801760 PMCID: PMC4140766 DOI: 10.1038/ejhg.2014.74] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2013] [Revised: 03/17/2014] [Accepted: 03/26/2014] [Indexed: 12/30/2022] Open
Abstract
The presence of multiple (5-100) colorectal adenomas suggests an inherited predisposition, but the genetic aetiology of this phenotype is undetermined if patients test negative for Mendelian polyposis syndromes such as familial adenomatous polyposis (FAP) and MUTYH-associated polyposis (MAP). We investigated whether 18 common colorectal cancer (CRC) predisposition single-nucleotide polymorphisms (SNPs) could help to explain some cases with multiple adenomas who phenocopied FAP or MAP, but had no pathogenic APC or MUTYH variant. No multiple adenoma case had an outlying number of CRC SNP risk alleles, but multiple adenoma patients did have a significantly higher number of risk alleles than population controls (P=5.7 × 10(-7)). The association was stronger in those with ≥10 adenomas. The CRC SNPs accounted for 4.3% of the variation in multiple adenoma risk, with three SNPs (rs6983267, rs10795668, rs3802842) explaining 3.0% of the variation. In FAP patients, the CRC risk score did not differ significantly from the controls, as we expected given the overwhelming effect of pathogenic germline APC variants on the phenotype of these cases. More unexpectedly, we found no evidence that the CRC SNPs act as modifier genes for the number of colorectal adenomas in FAP patients. In conclusion, common colorectal tumour risk alleles contribute to the development of multiple adenomas in patients without pathogenic germline APC or MUTYH variants. This phenotype may have 'polygenic' or monogenic origins. The risk of CRC in relatives of multiple adenoma cases is probably much lower for cases with polygenic disease, and this should be taken into account when counselling such patients.
Collapse
Affiliation(s)
- Timothy H T Cheng
- Molecular and Population Genetics Laboratory, Nuffield Department of Clinical Medicine, Wellcome Trust Centre for Human Genetics, Oxford, UK
| | - Maggie Gorman
- Molecular and Population Genetics Laboratory, Nuffield Department of Clinical Medicine, Wellcome Trust Centre for Human Genetics, Oxford, UK
| | - Lynn Martin
- Molecular and Population Genetics Laboratory, Nuffield Department of Clinical Medicine, Wellcome Trust Centre for Human Genetics, Oxford, UK
| | - Ella Barclay
- Molecular and Population Genetics Laboratory, Nuffield Department of Clinical Medicine, Wellcome Trust Centre for Human Genetics, Oxford, UK
| | - Graham Casey
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, USA
| | - Brian Saunders
- Wolfson Unit for Endoscopy, Imperial College School of Medicine, St Mark's Hospital, Harrow, UK
| | - Huw Thomas
- Family Cancer Registry, Imperial College School of Medicine, St Mark's Hospital, Harrow, UK
| | - Sue Clark
- Polyposis Registry, Imperial College School of Medicine, St Mark's Hospital, Harrow, UK
| | - Ian Tomlinson
- Molecular and Population Genetics Laboratory, Nuffield Department of Clinical Medicine, Wellcome Trust Centre for Human Genetics, Oxford, UK
- Oxford NIHR Comprehensive Biomedical Research Centre, Wellcome Trust Centre for Human Genetics, Oxford, UK
| |
Collapse
|
17
|
Spier I, Holzapfel S, Altmüller J, Zhao B, Horpaopan S, Vogt S, Chen S, Morak M, Raeder S, Kayser K, Stienen D, Adam R, Nürnberg P, Plotz G, Holinski-Feder E, Lifton RP, Thiele H, Hoffmann P, Steinke V, Aretz S. Frequency and phenotypic spectrum of germline mutations inPOLEand seven other polymerase genes in 266 patients with colorectal adenomas and carcinomas. Int J Cancer 2015; 137:320-31. [DOI: 10.1002/ijc.29396] [Citation(s) in RCA: 107] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2014] [Revised: 11/03/2014] [Accepted: 11/19/2014] [Indexed: 12/14/2022]
Affiliation(s)
- Isabel Spier
- Institute of Human Genetics, University of Bonn; Bonn Germany
| | | | - Janine Altmüller
- Cologne Center for Genomics, University of Cologne; Cologne Germany
- Institute of Human Genetics, University of Cologne; Cologne Germany
| | - Bixiao Zhao
- Department of Genetics; Howard Hughes Medical Institute, Yale University School of Medicine; New Haven USA
| | | | - Stefanie Vogt
- Institute of Human Genetics, University of Bonn; Bonn Germany
- MVZ Dr. Eberhard & Partner; Dortmund Germany
| | - Sophia Chen
- Department of Genetics; Howard Hughes Medical Institute, Yale University School of Medicine; New Haven USA
| | - Monika Morak
- Medizinische Klinik-Campus Innenstadt, Klinikum der LMU; Munich Germany
- MGZ-Center of Medical Genetics; Munich Germany
| | - Susanne Raeder
- Institute of Human Genetics, University of Bonn; Bonn Germany
| | - Katrin Kayser
- Institute of Human Genetics, University of Bonn; Bonn Germany
| | | | - Ronja Adam
- Institute of Human Genetics, University of Bonn; Bonn Germany
| | - Peter Nürnberg
- Cologne Center for Genomics, University of Cologne; Cologne Germany
| | - Guido Plotz
- Medizinische Klinik 1, Biomedical Research Laboratory, University of Frankfurt; Frankfurt Germany
| | - Elke Holinski-Feder
- Medizinische Klinik-Campus Innenstadt, Klinikum der LMU; Munich Germany
- MGZ-Center of Medical Genetics; Munich Germany
| | - Richard P. Lifton
- Department of Genetics; Howard Hughes Medical Institute, Yale University School of Medicine; New Haven USA
| | - Holger Thiele
- Cologne Center for Genomics, University of Cologne; Cologne Germany
| | - Per Hoffmann
- Institute of Human Genetics, University of Bonn; Bonn Germany
- Department of Genomics; Life & Brain Center, University of Bonn; Bonn Germany
- Division of Medical Genetics; University Hospital Basel and Department of Biomedicine, University of Basel; Basel Switzerland
| | - Verena Steinke
- Institute of Human Genetics, University of Bonn; Bonn Germany
| | - Stefan Aretz
- Institute of Human Genetics, University of Bonn; Bonn Germany
| |
Collapse
|
18
|
Common genetic variants (rs4779584 and rs10318) at 15q13.3 contributes to colorectal adenoma and colorectal cancer susceptibility: evidence based on 22 studies. Mol Genet Genomics 2014; 290:901-12. [PMID: 25475391 DOI: 10.1007/s00438-014-0970-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2014] [Accepted: 11/25/2014] [Indexed: 01/20/2023]
Abstract
Several genome-wide association studies on colorectal cancer (CRC) have reported similar findings of a new susceptibility locus, 15q13.3. After that, a number of studies have reported that the rs4779584 and rs10318 polymorphisms at chromosome 15q13.3 have been implicated in CRC and colorectal adenoma (CRA) risk; however, these studies have yielded inconsistent results. To investigate this inconsistency, we performed a meta-analysis of 22 studies involving a total of 48,468 CRC cases, 4,189 CRA cases, and 85,105 controls for the two polymorphisms to evaluate its effect on genetic susceptibility for CRC/CRA. Potential sources of heterogeneity and publication bias were also systematically explored. Overall, the summary odds ratio (OR) of rs4779584-T variant for CRC was 1.13 (95 % CI 1.09-1.16, P < 10(-5)) and 1.15 (95 % CI 1.04-1.28, P = 0.006) for CRA. After stratified by ethnicity, significantly increased CRC risks were found for rs4779584 polymorphism among East Asians and Caucasians, while no significant associations were detected among African American and other ethnic populations. A meta-analysis of studies on the rs10318 polymorphism also showed significant overall association with CRC, yielding a per-allele OR of 1.13 (95 % CI 1.02-1.24, P = 0.02). In the subgroup analysis by ethnicity, significantly increased CRC risks were found in Caucasians; whereas no significant associations were found among East Asians and African Americans. This meta-analysis demonstrated that the rs4779584 and rs10318 polymorphism at 15q13.3 is a risk factor associated with increased CRC/CRA susceptibility, but these associations vary in different ethnic populations.
Collapse
|
19
|
Germline variants in POLE are associated with early onset mismatch repair deficient colorectal cancer. Eur J Hum Genet 2014; 23:1080-4. [PMID: 25370038 DOI: 10.1038/ejhg.2014.242] [Citation(s) in RCA: 87] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2014] [Revised: 09/11/2014] [Accepted: 09/19/2014] [Indexed: 12/17/2022] Open
Abstract
Germline variants affecting the exonuclease domains of POLE and POLD1 predispose to multiple colorectal adenomas and/or colorectal cancer (CRC). The aim of this study was to estimate the prevalence of previously described heterozygous germline variants POLE c.1270C>G, p.(Leu424Val) and POLD1 c.1433G>A, p.(Ser478Asn) in a Dutch series of unexplained familial, early onset CRC and polyposis index cases. We examined 1188 familial CRC and polyposis index patients for POLE p.(Leu424Val) and POLD1 p.(Ser478Asn) variants using competitive allele-specific PCR. In addition, protein expression of the POLE and DNA mismatch repair genes was studied by immunohistochemistry in tumours from POLE carriers. Somatic mutations were screened using semiconductor sequencing. We detected three index patients (0.25%) with a POLE p.(Leu424Val) variant. In one patient, the variant was found to be de-novo. Tumours from three patients from two families were microsatellite instable, and immunohistochemistry showed MSH6/MSH2 deficiency suggestive of Lynch syndrome. Somatic mutations but no germline MSH6 and MSH2 variants were subsequently found, and one tumour displayed a hypermutator phenotype. None of the 1188 patients carried the POLD1 p.(Ser478Asn) variant. POLE germline variant carriers are also associated with a microsatellite instable CRC. POLE DNA analysis now seems warranted in microsatellite instable CRC, especially in the absence of a causative DNA mismatch repair gene germline variant.
Collapse
|
20
|
Horpaopan S, Spier I, Zink AM, Altmüller J, Holzapfel S, Laner A, Vogt S, Uhlhaas S, Heilmann S, Stienen D, Pasternack SM, Keppler K, Adam R, Kayser K, Moebus S, Draaken M, Degenhardt F, Engels H, Hofmann A, Nöthen MM, Steinke V, Perez-Bouza A, Herms S, Holinski-Feder E, Fröhlich H, Thiele H, Hoffmann P, Aretz S. Genome-wide CNV analysis in 221 unrelated patients and targeted high-throughput sequencing reveal novel causative candidate genes for colorectal adenomatous polyposis. Int J Cancer 2014; 136:E578-89. [PMID: 25219767 DOI: 10.1002/ijc.29215] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2014] [Revised: 08/04/2014] [Accepted: 09/03/2014] [Indexed: 12/27/2022]
Abstract
To uncover novel causative genes in patients with unexplained adenomatous polyposis, a model disease for colorectal cancer, we performed a genome-wide analysis of germline copy number variants (CNV) in a large, well characterized APC and MUTYH mutation negative patient cohort followed by a targeted next generation sequencing (NGS) approach. Genomic DNA from 221 unrelated German patients was genotyped on high-resolution SNP arrays. Putative CNVs were filtered according to stringent criteria, compared with those of 531 population-based German controls, and validated by qPCR. Candidate genes were prioritized using in silico, expression, and segregation analyses, data mining and enrichment analyses of genes and pathways. In 27% of the 221 unrelated patients, a total of 77 protein coding genes displayed rare, nonrecurrent, germline CNVs. The set included 26 candidates with molecular and cellular functions related to tumorigenesis. Targeted high-throughput sequencing found truncating point mutations in 12% (10/77) of the prioritized genes. No clear evidence was found for autosomal recessive subtypes. Six patients had potentially causative mutations in more than one of the 26 genes. Combined with data from recent studies of early-onset colorectal and breast cancer, recurrent potential loss-of-function alterations were detected in CNTN6, FOCAD (KIAA1797), HSPH1, KIF26B, MCM3AP, YBEY and in three genes from the ARHGAP family. In the canonical Wnt pathway oncogene CTNNB1 (β-catenin), two potential gain-of-function mutations were found. In conclusion, the present study identified a group of rarely affected genes which are likely to predispose to colorectal adenoma formation and confirmed previously published candidates for tumor predisposition as etiologically relevant.
Collapse
|