Rare Variants in the DNA Repair Pathway and the Risk of Colorectal Cancer

Abstract

Background. Inherited susceptibility is an important contributor to colorectal cancer (CRC) risk and rare variants in key genes or pathways could account in part for the missing proportion of CRC heritability. Methods. We conducted an exome-wide association study including 2,327 cases and 2,966 controls of European ancestry from three large epidemiologic studies. Single variant associations were tested using logistic regression models adjusting for appropriate study-specific covariates. In addition, we examined the aggregate effects of rare coding variation at the gene and pathway levels using Bayesian model uncertainty techniques. Results. In an exome-wide gene-level analysis, we identified ST6GALNAC2 as the top associated gene based on the Bayesian Risk Index (BRI) method (summary Bayes Factor[BF]BRI= 2604.23). A rare coding variant in this gene, rs139401613, was the top associated variant (P=1.01x10-6) in an exome-wide single variant analysis. Pathway-level association analyses based on the integrative Bayesian Risk Index (iBRI) method found extreme evidence of association with the DNA repair pathway (BFiBRI=17852.4), specifically with the non-homologous end joining (NHEJ, BFiBRI=437.95) and nucleotide excision repair (NER, BFiBRI=36.96) subpathways. The iBRI method also identified RPA2, PRKDC, ERCC5, ERCC8 as the top associated DNA repair genes (summary BFiBRI{greater than or equal to}10), with rs28988897, rs8178232, rs141369732, rs201642761 being the most likely associated variants in these genes, respectively. Conclusion. We identified novel variants and genes associated with CRC risk and provided additional evidence for a role of DNA repair in CRC tumorigenesis. Impact. This study provides new insights into the genetic predisposition to CRC which has potential for translation into improved risk prediction.