Targeted sequencing of established and candidate colorectal cancer genes in the Colon Cancer Family Registry Cohort

// Leon Raskin 1 , Yan Guo 2 , Liping Du 2 , Mark Clendenning 3 , Christophe Rosty 3, 4, 5 , Colon Cancer Family Registry (CCFR), Noralane M. Lindor 6 , Stephen B. Gruber 7, 8 and Daniel D. Buchanan 3, 5, 9 1 Division of Epidemiology, School of Medicine, Vanderbilt University Medical Center and Vanderbilt Ingram Comprehensive Cancer Center, Nashville, TN, USA 2 Center for Quantitative Sciences, Vanderbilt University Medical Center and Vanderbilt Ingram Comprehensive Cancer Center, Nashville, TN, USA 3 Colorectal Oncogenomics Group, Genetic Epidemiology Laboratory, Department of Pathology, University of Melbourne, Parkville, Victoria, Australia 4 Envoi Specialist Pathologists, Herston, Queensland, Australia 5 University of Queensland, School of Medicine, Herston, Queensland, Australia 6 Department of Health Sciences Research, Mayo Clinic, Scottsdale, AZ, USA 7 USC Norris Comprehensive Cancer Center, Los Angeles, CA, USA 8 Department of Preventive Medicine, University of Southern California, Los Angeles, CA, USA 9 Genetic Medicine and Familial Cancer Centre, The Royal Melbourne Hospital, Parkville, Victoria, Australia Correspondence to: Leon Raskin, email: leon.raskin@gmail.com Keywords: targeted sequencing, DNA pooling, rare variants, hereditary colorectal cancer, Colon Cancer Family Registry Received: February 16, 2017 Accepted: April 19, 2017 Published: June 21, 2017 ABSTRACT The underlying genetic cause of colorectal cancer (CRC) can be identified for 5-10% of all cases, while at least 20% of CRC cases are thought to be due to inherited genetic factors. Screening for highly penetrant mutations in genes associated with Mendelian cancer syndromes using next-generation sequencing (NGS) can be prohibitively expensive for studies requiring large samples sizes. The aim of the study was to identify rare single nucleotide variants and small indels in 40 established or candidate CRC susceptibility genes in 1,046 familial CRC cases (including both MSS and MSI-H tumor subtypes) and 1,006 unrelated controls from the Colon Cancer Family Registry Cohort using a robust and cost-effective DNA pooling NGS strategy. We identified 264 variants in 38 genes that were observed only in cases, comprising either very rare (minor allele frequency <0.001) or not previously reported (n=90, 34%) in reference databases, including six stop-gain, three frameshift, and 255 non-synonymous variants predicted to be damaging. We found novel germline mutations in established CRC genes MLH1 , APC , and POLE, and likely pathogenic variants in cancer susceptibility genes BAP1, CDH1, CHEK2, ENG, and MSH3 . For the candidate CRC genes, we identified likely pathogenic variants in the helicase domain of POLQ and in the LRIG1 , SH2B3 , and NOS1 genes and present their clinicopathological characteristics. Using a DNA pooling NGS strategy, we identified novel germline mutations in established CRC susceptibility genes in familial CRC cases. Further studies are required to support the role of POLQ , LRIG1 , SH2B3 and NOS1 as CRC susceptibility genes.