Distinctive DNA mismatch repair and APC rare variants in African Americans with colorectal neoplasia

// Hassan Ashktorab 1 , Hamed Azimi 1 , Sudhir Varma 3 , Payaam Tavakoli 1 , Michael L. Nickerson 4 and Hassan Brim 2 1 Department of Medicine and Cancer Center, Washington, DC, USA 2 Department of Pathology, Howard University College of Medicine, Washington, DC, USA 3 Hithru LLC, Silver Spring, MD, USA 4 Laboratory of Translational Genomics, National Cancer Institute, Bethesda, MD, USA Correspondence to: Hassan Ashktorab, email: hashktorab@howard.edu Michael L. Nickerson, email: nickersonml@mail.nih.gov Keywords: targeted exome sequencing; colon; African Americans Received: January 25, 2017     Accepted: May 23, 2017     Published: October 07, 2017 ABSTRACT Purpose: African Americans have a higher incidence and mortality from colorectal cancer. This disparity might be due, in part, to the type of mutations in driver genes. In this study, we examined alterations specific to APC , MSH3 , and MSH6 genes using targeted exome sequencing to determine distinctive variants in the course of neoplastic transformation. Experimental Design: A total of 140 African American colon samples (30 normal, 21 adenomas, 33 advanced adenomas and 56 cancers) were used as our discovery set on an Ion Torrent platform. A 36 samples subset was resequenced on an Illumina platform for variants’ validation. Bioinformatics analyses were performed and novel validated variants are reported. Results: Two novel MSH6 variants were validated and mapped to the MutS-V region near the MSH2 binding site. For MSH3, 4 known variants were validated and were located in exon 10 (3 non-synonymous) and exon 18 (1 synonymous). As for APC , 20 variants were validated with 4 novel variants: 3 stopgain and 1 non-synonymous. These variants mapped prior to and on the Armadillo repeats region, to the 15-amino acid repeat region, and to the 20-amino acid repeats region, respectively. Conclusion: We defined novel variants that target DNA mismatch repair and APC genes in African Americans with colorectal lesions. A greater frequency of variants in genes encoding DNA mismatch repair functions and APC likely plays major roles in colorectal cancer initiation and higher incidence of the disease in African Americans.