Skip to main content

Advertisement

Log in

Identification of a novel MSH6 germline variant in a family with multiple gastro-intestinal malignancies by next generation sequencing

  • Original Article
  • Published:
Familial Cancer Aims and scope Submit manuscript

Abstract

The identification of germline variants that predispose to cancer is important to further our understanding of tumorigenesis, guide patient management, prevent disease in unaffected relatives, and inform best practice for health care. We describe a kindred with multiple gastrointestinal malignancies where a novel MSH6 germline susceptibility variant was identified by exome sequencing after eluding serial routine testing in multiple affected members. This case fosters discussion of our current understanding of DNA mismatch repair deficiency, the management of Lynch Syndrome, and the emerging role of next generation sequencing in laboratory medicine to identify rare pathogenic germline variants in a comprehensive, unbiased fashion.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Fig. 1
Fig. 2
Fig. 3

Similar content being viewed by others

References

  1. Al-Sukhni W, Aronson M, Gallinger S (2008) Hereditary colorectal cancer syndromes: familial adenomatous polyposis and lynch syndrome. Surg Clin North Am 88(4):819–844. doi:10.1016/j.suc.2008.04.012

    Article  PubMed  Google Scholar 

  2. Shia J (2008) Immunohistochemistry versus microsatellite instability testing for screening colorectal cancer patients at risk for hereditary nonpolyposis colorectal cancer syndrome. Part I. The utility of immunohistochemistry. J Mol Diagn 10(4):293–300. doi:10.2353/jmoldx.2008.080031

    Article  PubMed Central  PubMed  Google Scholar 

  3. Zhang L (2008) Immunohistochemistry versus microsatellite instability testing for screening colorectal cancer patients at risk for hereditary nonpolyposis colorectal cancer syndrome. Part II. The utility of microsatellite instability testing. J Mol Diagn 10(4):301–307. doi:10.2353/jmoldx.2008.080062

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  4. Evaluation of Genomic Applications in Practice and Prevention (EGAPP) Working Group (2009) Recommendations from the EGAPP Working Group: genetic testing strategies in newly diagnosed individuals with colorectal cancer aimed at reducing morbidity and mortality from Lynch syndrome in relatives. Genet Med 11(1):35–41. doi:10.1097/GIM.0b013e31818fa2ff

    Article  Google Scholar 

  5. Cicek MS, Lindor NM, Gallinger S, Bapat B, Hopper JL, Jenkins MA, Young J, Buchanan D, Walsh MD, Le Marchand L, Burnett T, Newcomb PA, Grady WM, Haile RW, Casey G, Plummer SJ, Krumroy LA, Baron JA, Thibodeau SN (2011) Quality assessment and correlation of microsatellite instability and immunohistochemical markers among population- and clinic-based colorectal tumors results from the Colon Cancer Family Registry. J Mol Diagn 13(3):271–281. doi:10.1016/j.jmoldx.2010.12.004

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  6. Moreira L, Balaguer F, Lindor N, de la Chapelle A, Hampel H, Aaltonen LA, Hopper JL, Le Marchand L, Gallinger S, Newcomb PA, Haile R, Thibodeau SN, Gunawardena S, Jenkins MA, Buchanan DD, Potter JD, Baron JA, Ahnen DJ, Moreno V, Andreu M, Ponz de Leon M, Rustgi AK, Castells A, EPICOLON Consortium (2012) Identification of Lynch syndrome among patients with colorectal cancer. JAMA 308(15):1555–1565. doi:10.1001/jama.2012.13088

    Article  CAS  PubMed  Google Scholar 

  7. Tanskanen T, Gylfe AE, Katainen R, Taipale M, Renkonen-Sinisalo L, Mecklin JP, Järvinen H, Tuupanen S, Kilpivaara O, Vahteristo P, Aaltonen LA (2013) Exome sequencing in diagnostic evaluation of colorectal cancer predisposition in young patients. Scand J Gastroenterol 48(6):672–678. doi:10.3109/00365521.2013.783102

    Article  CAS  PubMed  Google Scholar 

  8. Link DC, Schuettpelz LG, Shen D, Wang J, Walter MJ, Kulkarni S, Payton JE, Ivanovich J, Goodfellow PJ, Le Beau M, Koboldt DC, Dooling DJ, Fulton RS, Bender RH, Fulton LL, Delehaunty KD, Fronick CC, Appelbaum EL, Schmidt H, Abbott R, O’Laughlin M, Chen K, McLellan MD, Varghese N, Nagarajan R, Heath S, Graubert TA, Ding L, Ley TJ, Zambetti GP, Wilson RK, Mardis ER (2011) Identification of a novel TP53 cancer susceptibility mutation through whole-genome sequencing of a patient with therapy-related AML. JAMA 305(15):1568–1576. doi:10.1001/jama.2011.473

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  9. Pritchard CC, Smith C, Salipante SJ, Lee MK, Thornton AM, Nord AS, Gulden C, Kupfer SS, Swisher EM, Bennett RL, Novetsky AP, Jarvik GP, Olopade OI, Goodfellow PJ, King MC, Tait JF, Walsh T (2012) ColoSeq provides comprehensive lynch and polyposis syndrome mutational analysis using massively parallel sequencing. J Mol Diagn 14(4):357–366. doi:10.1016/j.jmoldx.2012.03.002

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  10. Yang Y, Muzny DM, Reid JG, Bainbridge MN, Willis A, Ward PA, Braxton A, Beuten J, Xia F, Niu Z, Hardison M, Person R, Bekheirnia MR, Leduc MS, Kirby A, Pham P, Scull J, Wang M, Ding Y, Plon SE, Lupski JR, Beaudet AL, Gibbs RA, Eng CM (2013) Clinical whole-exome sequencing for the diagnosis of mendelian disorders. N Engl J Med 369(16):1502–1511. doi:10.1056/NEJMoa1306555

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  11. Jacob HJ (2013) Next-generation sequencing for clinical diagnostics. N Engl J Med 369(16):1557–1558. doi:10.1056/NEJMe1310846

    Article  CAS  PubMed  Google Scholar 

  12. Cotterchio M, McKeown-Eyssen G, Sutherland H, Buchan G, Aronson M, Easson AM, Macey J, Holowaty E, Gallinger S (2000) Ontario familial colon cancer registry: methods and first-year response rates. Chronic Dis Can 21(2):81–86

    CAS  PubMed  Google Scholar 

  13. Li H, Durbin R (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25(14):1754–1760. doi:10.1093/bioinformatics/btp324

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  14. McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, Kernytsky A, Garimella K, Altshuler D, Gabriel S, Daly M, DePristo MA (2010) The genome analysis toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res 20(9):1297–1303. doi:10.1101/gr.107524.110

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  15. Wang K, Li M, Hakonarson H (2010) ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data. Nucleic Acids Res 38(16):e164. doi:10.1093/nar/gkq603

    Article  PubMed Central  PubMed  Google Scholar 

  16. Jiang YH, Yuen RK, Jin X, Wang M, Chen N, Wu X, Ju J, Mei J, Shi Y, He M, Wang G, Liang J, Wang Z, Cao D, Carter MT, Chrysler C, Drmic IE, Howe JL, Lau L, Marshall CR, Merico D, Nalpathamkalam T, Thiruvahindrapuram B, Thompson A, Uddin M, Walker S, Luo J, Anagnostou E, Zwaigenbaum L, Ring RH, Wang J, Lajonchere C, Wang J, Shih A, Szatmari P, Yang H, Dawson G, Li Y, Scherer SW (2013) Detection of clinically relevant genetic variants in autism spectrum disorder by whole-genome sequencing. Am J Hum Genet 93(2):249–263. doi:10.1016/j.ajhg.2013.06.012

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  17. Rehm HL (2013) Disease-targeted sequencing: a cornerstone in the clinic. Nat Rev Genet 14(4):295–300. doi:10.1038/nrg3463

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  18. Thompson BA, Spurdle AB, Plazzer JP, Greenblatt MS, Akagi K, Al-Mulla F, Bapat B, Bernstein I, Capellá G, den Dunnen JT, du Sart D, Fabre A, Farrell MP, Farrington SM, Frayling IM, Frebourg T, Goldgar DE, Heinen CD, Holinski-Feder E, Kohonen-Corish M, Robinson KL, Leung SY, Martins A, Moller P, Morak M, Nystrom M, Peltomaki P, Pineda M, Qi M, Ramesar R, Rasmussen LJ, Royer-Pokora B, Scott RJ, Sijmons R, Tavtigian SV, Tops CM, Weber T, Wijnen J, Woods MO, Macrae F, Genuardi M, InSiGHT (2014) Application of a 5-tiered scheme for standardized classification of 2,360 unique mismatch repair gene variants in the InSiGHT locus-specific database. Nat Genet 46(2):107–115. doi:10.1038/ng.2854

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  19. Richards CS, Bale S, Bellissimo DB, Das S, Grody WW, Hegde MR, Lyon E, Ward BE, Molecular Subcommittee of the ACMG Laboratory Quality Assurance Committee (2008) ACMG recommendations for standards for interpretation and reporting of sequence variations: revisions 2007. Genet Med 10(4):294–300. doi:10.1097/GIM.0b013e31816b5cae

    Article  CAS  PubMed  Google Scholar 

  20. Baglietto L, Lindor NM, Dowty JG, White DM, Wagner A, Gomez Garcia EB, Vriends AH, Dutch Lynch Syndrome Study Group, Cartwright NR, Barnetson RA, Farrington SM, Tenesa A, Hampel H, Buchanan D, Arnold S, Young J, Walsh MD, Jass J, Macrae F, Antill Y, Winship IM, Giles GG, Goldblatt J, Parry S, Suthers G, Leggett B, Butz M, Aronson M, Poynter JN, Baron JA, Le Marchand L, Haile R, Gallinger S, Hopper JL, Potter J, de la Chapelle A, Vasen HF, Dunlop MG, Thibodeau SN, Jenkins MA (2010) Risks of lynch syndrome cancers for MSH6 mutation carriers. J Natl Cancer Inst 102(3):193–201. doi:10.1093/jnci/djp473

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  21. Schulmann K, Brasch FE, Kunstmann E, Engel C, Pagenstecher C, Vogelsang H, Krüger S, Vogel T, Knaebel HP, Rüschoff J, Hahn SA, Knebel-Doeberitz MV, Moeslein G, Meltzer SJ, Schackert HK, Tympner C, Mangold E, Schmiegel W, German HNPCC Consortium (2005) HNPCC-associated small bowel cancer: clinical and molecular characteristics. Gastroenterology 128(3):590–599

    Article  CAS  PubMed  Google Scholar 

  22. Watson P, Vasen HF, Mecklin JP, Bernstein I, Aarnio M, Järvinen HJ, Myrhøj T, Sunde L, Wijnen JT, Lynch HT (2008) The risk of extra-colonic, extra-endometrial cancer in the Lynch syndrome. Int J Cancer 123(2):444–449. doi:10.1002/ijc.23508

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  23. Church J, Simmang C, Standards Task Force, American Society of Colon and Rectal Surgeons, Collaborative Group of the Americas on Inherited Colorectal Cancer and the Standards Committee of The American Society of Colon and Rectal Surgeons (2003) Practice parameters for the treatment of patients with dominantly inherited colorectal cancer (familial adenomatous polyposis and hereditary nonpolyposis colorectal cancer). Dis Colon Rectum 46(8):1001–1012

    Article  PubMed  Google Scholar 

  24. Ribic CM, Sargent DJ, Moore MJ, Thibodeau SN, French AJ, Goldberg RM, Hamilton SR, Laurent-Puig P, Gryfe R, Shepherd LE, Tu D, Redston M, Gallinger S (2003) Tumor microsatellite-instability status as a predictor of benefit from fluorouracil-based adjuvant chemotherapy for colon cancer. N Engl J Med 349(3):247–257

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  25. Sargent DJ, Marsoni S, Monges G, Thibodeau SN, Labianca R, Hamilton SR, French AJ, Kabat B, Foster NR, Torri V, Ribic C, Grothey A, Moore M, Zaniboni A, Seitz JF, Sinicrope F, Gallinger S (2010) Defective mismatch repair as a predictive marker for lack of efficacy of fluorouracil-based adjuvant therapy in colon cancer. J Clin Oncol 28(20):3219–3226. doi:10.1200/JCO.2009.27.1825

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  26. Fallik D, Borrini F, Boige V, Viguier J, Jacob S, Miquel C, Sabourin JC, Ducreux M, Praz F (2003) Microsatellite instability is a predictive factor of the tumor response to irinotecan in patients with advanced colorectal cancer. Cancer Res 63(18):5738–5744

    CAS  PubMed  Google Scholar 

  27. Win AK, Jenkins MA, Buchanan DD, Clendenning M, Young JP, Giles GG, Goldblatt J, Leggett BA, Hopper JL, Thibodeau SN, Lindor NM (2011) Determining the frequency of de novo germline mutations in DNA mismatch repair genes. J Med Genet 48(8):530–534. doi:10.1136/jmedgenet-2011-100082

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  28. Hegde M, Ferber M, Mao R, Samowitz W, Ganguly A, Working Group of the American College of Medical Genetics and Genomics (ACMG) Laboratory Quality Assurance Committee (2014) ACMG technical standards and guidelines for genetic testing for inherited colorectal cancer (Lynch syndrome, familial adenomatous polyposis, and MYH-associated polyposis). Genet Med 16(1):101–116. doi:10.1038/gim.2013.166

    Article  CAS  PubMed  Google Scholar 

  29. Dubé C, Rostom A, Lewin G, Tsertsvadze A, Barrowman N, Code C, Sampson M, Moher D, U.S. Preventive Services Task Force (2007) The use of aspirin for primary prevention of colorectal cancer: a systematic review prepared for the U.S. Preventive Services Task Force. Ann Intern Med 146(5):365–375

    Article  PubMed  Google Scholar 

  30. Johnston JJ, Rubinstein WS, Facio FM, Ng D, Singh LN, Teer JK, Mullikin JC, Biesecker LG (2012) Secondary variants in individuals undergoing exome sequencing: screening of 572 individuals identifies high-penetrance mutations in cancer-susceptibility genes. Am J Hum Genet 91(1):97–108. doi:10.1016/j.ajhg.2012.05.021

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  31. Dewey FE, Grove ME, Pan C, Goldstein BA, Bernstein JA, Chaib H, Merker JD, Goldfeder RL, Enns GM, David SP, Pakdaman N, Ormond KE, Caleshu C, Kingham K, Klein TE, Whirl-Carrillo M, Sakamoto K, Wheeler MT, Butte AJ, Ford JM, Boxer L, Ioannidis JP, Yeung AC, Altman RB, Assimes TL, Snyder M, Ashley EA, Quertermous T (2014) Clinical interpretation and implications of whole-genome sequencing. JAMA 311(10):1035–1045. doi:10.1001/jama.2014.1717

    Article  CAS  PubMed  Google Scholar 

  32. Green RC, Berg JS, Grody WW, Kalia SS, Korf BR, Martin CL, McGuire AL, Nussbaum RL, O’Daniel JM, Ormond KE, Rehm HL, Watson MS, Williams MS, Biesecker LG, American College of Medical Genetics and Genomics (2013) ACMG recommendations for reporting of incidental findings in clinical exome and genome sequencing. Genet Med 15(7):565–574. doi:10.1038/gim.2013.73

    Article  PubMed Central  CAS  PubMed  Google Scholar 

Download references

Acknowledgments

This study was supported by a McLaughlin Accelerator Grant and by funding from the GeneCure Foundation and the Canadian Institute for Health Research.

Conflicts of interests

We have no financial or personal conflicts of interests to declare.

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Jordan Lerner-Ellis.

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Connor, A.A., Katzov-Eckert, H., Whelan, T. et al. Identification of a novel MSH6 germline variant in a family with multiple gastro-intestinal malignancies by next generation sequencing. Familial Cancer 14, 69–75 (2015). https://doi.org/10.1007/s10689-014-9765-9

Download citation

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s10689-014-9765-9

Keywords

Navigation