Genetic Evaluation of Turkish patients with Colorectal Carcinoma in Terms of Lynch Syndrome by Targeted Next Generation Sequencing

Purpose: Lynch syndrome LS is a hereditary cancer disorder characterized by increased lifetime risk for various cancers. Colorectal cancer CRC is the most common cancer in LS. Germline testing of mismatch repair MMR genes is required for definitive diagnosis of LS. The purposes of this study was to report the results of the mutation analysis of MMR genes using targeted next generation sequencing NGS in patients with CRC for providing benefits to the diagnosing and management of LS as the first study from Turkey, to our knowledge. Patients and Methods: A total of 28 patients with CRC were evaluated for LS between 2016 and 2017 years. Sequencing analysis by using NGS was performed in MLH1, MSH2, and MSH6 genes and deletion/duplication analysis by using multiplex ligation-dependent probe amplification MLPA method were performed in MLH1, MSH2, MSH6, EPCAM genes in 28 patients. Results: A total of 9 variants were found in 28 patients 4 in MSH2, 4 in MLH1, 1 in MSH6 . The diagnosis of LS was confirmed in 9 patients 32%; 9/28 . Four variants were assessed as known variants, 5 variants as novel. Conclusion: The patients with CRC should be evaluated in terms of LS because of increased lifetime risk of developing various cancers. If there is an indication for LS after genetic counseling, germline testing for definitive diagnosis of LS should be performed

Keywords:

Colorectal cancer, Lynch syndrome, mismatches repair genes next generation sequencing, novel mutation,

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Moreira L, Balaguer F, Lindor N, et al. Identification of Lynch syndrome among patients with colorectal cancer. JAMA 2012;308:1555–1565. [CrossRef]
Hampel H, Bennett RL, Buchanan A, Pearlman R, Wiesner GL; for a Guideline Development Group of the American College of Medical Genetics and Genomics Professional Practice and Guidelines Committee and of the National Society of Genetic Counselors Practice Guidelines Committee. A practice guideline from the American College of Medical Genetics and Genomics and the National Society of Genetic Counselors: referral indications for cancer predisposition assessment. Genet Med 2015;17:70–87. [CrossRef]
National Comprehensive Cancer Network. NCCN Clinical Practice Guidelines in Oncology: Colorectal Cancer Screening. Version 2; 2012. http://www.nccn.org/professionals/physician_gls/PDF/colorectal_ screening.pdf
Giardiello FM, Allen JI, Axilbund JE, et al. Guidelines on genetic evaluation and management of Lynch syndrome: a consensus statement by the US Multi-society Task Force on colorectal cancer. Am J Gastroenterol 2014;109:1159–1179. [CrossRef]
Syngal S, Brand RE, Church JM, Giardiello FM, Hampel HL, Burt RW. ACG clinical guideline: Genetic testing and management of hereditary gastrointestinal cancer syndromes. Am J Gastroenterol 2015;110:223–262. [CrossRef]
Herzig DO, Buie WD, Weiser MR, et al. Clinical Practice Guidelines for the Surgical Treatment of Patients With Lynch Syndrome. Dis Colon Rectum 2017;60:137–143. [CrossRef]
Kastrinos F, Uno H, Ukaegbu C, et al. Development and Validation of the PREMM5 Model for Comprehensive Risk Assessment of Lynch Syndrome. J Clin Oncol 2017;35:2165–2172. [CrossRef]
Robinson JT, Thorvaldsdóttir H, Winckler W, et al. Integrative Genomics Viewer. Nat Biotechnol 2011;29:24–26. [CrossRef]
Thorvaldsdóttir H, Robinson JT, Mesirov JP. Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration. Brief Bioinform 2013;14:178–192. [CrossRef]
Richards S, Aziz N, Bale S, et al. 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;17:405–423. [CrossRef]
Thompson BA, Spurdle AB, Plazzer JP, et al. Application of a five-tiered scheme for standardized classification of 2, 360 unique mismatch repair gene variants lodged on the InSiGHT locus-specific database. Nat Genet 2014;46:107–115. [CrossRef]
Schwarz JM, Cooper DN, Schuelke M, Seelow D. MutationTaster2: mutation prediction for the deep-sequencing age. Nat Methods 2014;11:361–362. [CrossRef]
Adzhubei IA, Schmidt S, Peshkin L, et al. A method and server for predicting damaging missense mutations. Nat Methods 2010;7:248– 249. [CrossRef]
Kumar P, Henikoff S, Ng PC. Predicting the effects of coding non- synonymous variants on protein function using the SIFT algorithm. Nat Protoc 2009;4:1073–1081. [CrossRef]
Desmet FO, Hamroun D, Lalande M, Collod-Béroud G, Claustres M, Béroud C. Human Splicing Finder: an online bioinformatics tool to predict splicing signals. Nucleic Acids Res 2009;37:e67. [CrossRef]
Mİller P, Seppälä T, Bernstein I, et al. Incidence of and survival after subsequent cancers in carriers of pathogenic MMR variants with previous cancer: a report from the prospective Lynch syndrome database. Gut 2017;66:1657–1664. [CrossRef]
Bartley AN, Hamilton SR, Alsabeh R, et al. Members of the Cancer Biomarker Reporting Workgroup, College of American Pathologists. Template for reporting results of biomarker testing of specimens from patients with carcinoma of the colon and rectum. Arch Pathol Lab Med 2014;138:166–170. [CrossRef]
Tunca B, Pedroni M, Cecener G, et al. Analysis of mismatch repair gene mutations in Turkish HNPCC patients. Fam Cancer 2010;9:365– 376. [CrossRef]
Ziada-Bouchaar H, Sifi K, Filali T, Hammada T, Satta D, Abadi N. First description of mutational analysis of MLH1, MSH2 and MSH6 in Algerian families with suspected Lynch syndrome. Fam Cancer 2017;16:57–66. [CrossRef]
Soares BL, Brant AC, Gomes R, et al. Screening for germline mutations in mismatch repair genes in patients with Lynch syndrome by next generation sequencing. Fam Cancer 2018;17:387–394. [CrossRef]
Alqahtani M, Edwards C, Buzzacott N, et al. Screening for Lynch syndrome in young Saudi colorectal cancer patients using microsatellite instability testing and next generation sequencing. Fam Cancer 2018;17:197–203. [CrossRef]
Ben Sghaier R, Jansen AML, Bdioui A, et al. Targeted next generation sequencing screening of Lynch syndrome in Tunisian population. Fam Cancer 2019;18:343–348.[CrossRef]