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Next-Generation Sequencing for Genetic Diagnosis of Hereditary Colorectal Cancer and Polyposis Syndrome

  • Hidetaka EguchiEmail author
  • Yasushi Okazaki
Chapter

Abstract

Approximately 5% of the total colorectal cancers are thought to be the hereditary ones. Phenotypes of the hereditary colorectal cancer and polyposis syndromes (HCCPS) as represented mainly by the Lynch syndrome and familial adenomatous polyposis overlap each other to some extent, making it difficult to provide a definite diagnosis, solely by the clinicopathological features. In order to cope with this issue, the genetic testing based on the next-generation sequencing techniques gathers much attention to the field of the HCCPS in recent years. In this chapter, the utility of the next-generation sequencing techniques and some tasks to be solved are discussed.

Keywords

Next-generation sequencing Hereditary gastrointestinal cancer syndromes Pathogenicity Causative genes Incidental/secondary findings 

References

  1. 1.
    Kanth P, Grimmett J, Champine M, Burt R, Samadder NJ. Hereditary colorectal polyposis and cancer syndromes: a primer on diagnosis and management. Am J Gastroenterol. 2017;112(10):1509–25.CrossRefGoogle Scholar
  2. 2.
    Yurgelun MB, Kulke MH, Fuchs CS, Allen BA, Uno H, Hornick JL, Ukaegbu CI, Brais LK, McNamara PG, Mayer RJ, Schrag D, Meyerhardt JA, Ng K, Kidd J, Singh N, Hartman AR, Wenstrup RJ, Syngal S. Cancer susceptibility gene mutations in individuals with colorectal cancer. J Clin Oncol. 2017;35(10):1086–95.CrossRefGoogle Scholar
  3. 3.
    Metzker ML. Sequencing technologies - the next generation. Nat Rev Genet. 2010;11(1):31–46.CrossRefGoogle Scholar
  4. 4.
    Bahassi el M, Stambrook PJ. Next-generation sequencing technologies: breaking the sound barrier of human genetics. Mutagenesis. 2014;29(5):303–10.CrossRefGoogle Scholar
  5. 5.
    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. ColoSeq provides comprehensive lynch and polyposis syndrome mutational analysis using massively parallel sequencing. J Mol Diagn. 2012;14(4):357–66.CrossRefGoogle Scholar
  6. 6.
    Cragun D, Radford C, Dolinsky JS, Caldwell M, Chao E, Pal T. Panel-based testing for inherited colorectal cancer: a descriptive study of clinical testing performed by a US laboratory. Clin Genet. 2014;86(6):510–20.CrossRefGoogle Scholar
  7. 7.
    Kohda M, Kumamoto K, Eguchi H, Hirata T, Tada Y, Tanakaya K, Akagi K, Takenoshita S, Iwama T, Ishida H, Okazaki Y. Rapid detection of germline mutations for hereditary gastrointestinal polyposis/cancers using HaloPlex target enrichment and high-throughput sequencing technologies. Fam Cancer. 2016;15(4):553–62.CrossRefGoogle Scholar
  8. 8.
    Simbolo M, Mafficini A, Agostini M, Pedrazzani C, Bedin C, Urso ED, Nitti D, Turri G, Scardoni M, Fassan M, Scarpa A. Next-generation sequencing for genetic testing of familial colorectal cancer syndromes. Hered Cancer Clin Pract. 2015;13(1):18.CrossRefGoogle Scholar
  9. 9.
    Yurgelun MB, Allen B, Kaldate RR, Bowles KR, Judkins T, Kaushik P, Roa BB, Wenstrup RJ, Hartman AR, Syngal S. Identification of a variety of mutations in cancer predisposition genes in patients with suspected lynch syndrome. Gastroenterology. 2015;149(3):604–13.CrossRefGoogle Scholar
  10. 10.
    Palles C, Cazier JB, Howarth KM, Domingo E, Jones AM, Broderick P, Kemp Z, Spain SL, Guarino E, Salguero I, Sherborne A, Chubb D, Carvajal-Carmona LG, Ma Y, Kaur K, Dobbins S, Barclay E, Gorman M, Martin L, Kovac MB, Humphray S, CORGI Consortium, WGS500 Consortium, Lucassen A, Holmes CC, Bentley D, Donnelly P, Taylor J, Petridis C, Roylance R, Sawyer EJ, Kerr DJ, Clark S, Grimes J, Kearsey SE, Thomas HJ, McVean G, Houlston RS, Tomlinson I. Germline mutations affecting the proofreading domains of POLE and POLD1 predispose to colorectal adenomas and carcinomas. Nat Genet. 2013;45(2):136–44.CrossRefGoogle Scholar
  11. 11.
    Briggs S, Tomlinson I. Germline and somatic polymerase ε and δ mutations define a new class of hypermutated colorectal and endometrial cancers. J Pathol. 2013;230(2):148–53.CrossRefGoogle Scholar
  12. 12.
    Bourdais R, Rousseau B, Pujals A, Boussion H, Joly C, Guillemin A, Baumgaertner I, Neuzillet C, Tournigand C. Polymerase proofreading domain mutations: New opportunities for immunotherapy in hypermutated colorectal cancer beyond MMR deficiency. Crit Rev Oncol Hematol. 2017;113:242–8.CrossRefGoogle Scholar
  13. 13.
    Weren RD, Ligtenberg MJ, Kets CM, de Voer RM, Verwiel ET, Spruijt L, van Zelst-Stams WA, Jongmans MC, Gilissen C, Hehir-Kwa JY, Hoischen A, Shendure J, Boyle EA, Kamping EJ, Nagtegaal ID, Tops BB, Nagengast FM, Geurts van Kessel A, van Krieken JH, Kuiper RP, Hoogerbrugge N. A germline homozygous mutation in the base-excision repair gene NTHL1 causes adenomatous polyposis and colorectal cancer. Nat Genet. 2015;47(6):668–71.CrossRefGoogle Scholar
  14. 14.
    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(2):337–51.CrossRefGoogle Scholar
  15. 15.
    Yan HHN, Lai JCW, Ho SL, Leung WK, Law WL, Lee JFY, Chan AKW, Tsui WY, Chan ASY, Lee BCH, Yue SSK, Man AHY, Clevers H, Yuen ST, Leung SY. RNF43 germline and somatic mutation in serrated neoplasia pathway and its association with BRAF mutation. Gut. 2017;66(9):1645–56.CrossRefGoogle Scholar
  16. 16.
    Seguí N, Mina LB, Lázaro C, Sanz-Pamplona R, Pons T, Navarro M, Bellido F, López-Doriga A, Valdés-Mas R, Pineda M, Guinó E, Vidal A, Soto JL, Caldés T, Durán M, Urioste M, Rueda D, Brunet J, Balbín M, Blay P, Iglesias S, Garré P, Lastra E, Sánchez-Heras AB, Valencia A, Moreno V, Pujana MÁ, Villanueva A, Blanco I, Capellá G, Surrallés J, Puente XS, Valle L. Germline mutations in FAN1 cause hereditary colorectal cancer by impairing DNA repair. Gastroenterology. 2015;149(3):563–6.CrossRefGoogle Scholar
  17. 17.
    Esteban-Jurado C, Vila-Casadesús M, Garre P, Lozano JJ, Pristoupilova A, Beltran S, Muñoz J, Ocaña T, Balaguer F, López-Cerón M, Cuatrecasas M, Franch-Expósito S, Piqué JM, Castells A, Carracedo A, Ruiz-Ponte C, Abulí A, Bessa X, Andreu M, Bujanda L, Caldés T, Castellví-Bel S. Whole-exome sequencing identifies rare pathogenic variants in new predisposition genes for familial colorectal cancer. Genet Med. 2015;17(2):131–42.CrossRefGoogle Scholar
  18. 18.
    Esteban-Jurado C, Franch-Expósito S, Muñoz J, Ocaña T, Carballal S, López-Cerón M, Cuatrecasas M, Vila-Casadesús M, Lozano JJ, Serra E, Beltran S, Brea-Fernández A, Ruiz-Ponte C, Castells A, Bujanda L, Garre P, Caldés T, Cubiella J, Balaguer F, Castellví-Bel S. The Fanconi anemia DNA damage repair pathway in the spotlight for germline predisposition to colorectal cancer. Eur J Hum Genet. 2016;24(10):1501–5.CrossRefGoogle Scholar
  19. 19.
    Nieminen TT, O’Donohue MF, Wu Y, Lohi H, Scherer SW, Paterson AD, Ellonen P, Abdel-Rahman WM, Valo S, Mecklin JP, Järvinen HJ, Gleizes PE, Peltomäki P. Germline mutation of RPS20, encoding a ribosomal protein, causes predisposition to hereditary nonpolyposis colorectal carcinoma without DNA mismatch repair deficiency. Gastroenterology. 2014;147(3):595–8.CrossRefGoogle Scholar
  20. 20.
    de Voer RM, Geurts van Kessel A, Weren RD, Ligtenberg MJ, Smeets D, Fu L, Vreede L, Kamping EJ, Verwiel ET, Hahn MM, Ariaans M, Spruijt L, van Essen T, Houge G, Schackert HK, Sheng JQ, Venselaar H, van Ravenswaaij-Arts CM, van Krieken JH, Hoogerbrugge N, Kuiper RP. Germline mutations in the spindle assembly checkpoint genes BUB1 and BUB3 are risk factors for colorectal cancer. Gastroenterology. 2013;145(3):544–7.CrossRefGoogle Scholar
  21. 21.
    Hahn MM, Vreede L, Bemelmans SA, van der Looij E, van Kessel AG, Schackert HK, Ligtenberg MJ, Hoogerbrugge N, Kuiper RP, de Voer RM. Prevalence of germline mutations in the spindle assembly checkpoint gene BUB1B in individuals with early-onset colorectal cancer. Genes Chromosomes Cancer. 2016;55(11):855–63.CrossRefGoogle Scholar
  22. 22.
    Aretz S, Stienen D, Friedrichs N, Stemmler S, Uhlhaas S, Rahner N, Propping P, Friedl W. Somatic APC mosaicism: a frequent cause of familial adenomatous polyposis (FAP). Hum Mutat. 2007;28:985–92.CrossRefGoogle Scholar
  23. 23.
    Schwab AL, Tuohy TM, Condie M, Neklason DW, Burt RW. Gonadal mosaicism and familial adenomatous polyposis. Fam Cancer. 2008;7:173–7.CrossRefGoogle Scholar
  24. 24.
    Yamaguchi K, Komura M, Yamaguchi R, Imoto S, Shimizu E, Kasuya S, Shibuya T, Hatakeyama S, Takahashi N, Ikenoue T, Hata K, Tsurita G, Shinozaki M, Suzuki Y, Sugano S, Miyano S, Furukawa Y. Detection of APC mosaicism by next-generation sequencing in an FAP patient. J Hum Genet. 2015;60:227–31.CrossRefGoogle Scholar
  25. 25.
    Spier I, Drichel D, Kerick M, Kirfel J, Horpaopan S, Laner A, Holzapfel S, Peters S, Adam R, Zhao B, Becker T, Lifton RP, Perner S, Hoffmann P, Kristiansen G, Timmermann B, Nöthen MM, Holinski-Feder E, Schweiger MR, Aretz S. Low-level APC mutational mosaicism is the underlying cause in a substantial fraction of unexplained colorectal adenomatous polyposis cases. J Med Genet. 2016;53(3):172–9.CrossRefGoogle Scholar
  26. 26.
    Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL, ACMG Laboratory Quality Assurance Committee. Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology. Genet Med. 2015;17(5):405–24.CrossRefGoogle Scholar
  27. 27.
    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. 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. 2014;46(2):107–15.CrossRefGoogle Scholar
  28. 28.
    Tricarico R, Kasela M, Mareni C, Thompson BA, Drouet A, Staderini L, Gorelli G, Crucianelli F, Ingrosso V, Kantelinen J, Papi L, De Angioletti M, Berardi M, Gaildrat P, Soukarieh O, Turchetti D, Martins A, Spurdle AB, Nyström M, Genuardi M, InSiGHT Variant Interpretation Committee. Assessment of the InSiGHT interpretation criteria for the clinical classification of 24 MLH1 and MSH2 gene variants. Hum Mutat. 2017;38(1):64–77.CrossRefGoogle Scholar

Copyright information

© Springer Nature Singapore Pte Ltd. 2019

Authors and Affiliations

  1. 1.Diagnosis and Therapeutics of Intractable DiseasesJuntendo University Graduate School of MedicineBunkyo-ku, TokyoJapan

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