Exome-Wide Association Study of Pancreatic Cancer Risk

Abstract

We conducted a case-control exome-wide association study to discover germline variants in coding regions that affect risk for pancreatic cancer, combining data from 5 studies. We analyzed exome and genome sequencing data from 437 patients with pancreatic cancer (cases) and 1922 individuals not known to have cancer (controls). In the primary analysis, BRCA2 had the strongest enrichment for rare inactivating variants (17/437 cases vs 3/1922 controls) (P = 3.27x10^-6; exome-wide statistical significance threshold P < 2.5x10^-6). Cases had more rare inactivating variants in DNA repair genes than controls, even after excluding 13 genes known to predispose to pancreatic cancer (adjusted odds ratio, 1.35; P = .045). At the suggestive threshold (P < .001), 6 genes were enriched for rare damaging variants (UHMK1, AP1G2, DNTA, CHST6, FGFR3, and EPHA1) and 7 genes had associations with pancreatic cancer risk, based on the sequence-kernel association test. We confirmed variants in BRCA2 as the most common high-penetrant genetic factor associated with pancreatic cancer and we also identified candidate pancreatic cancer genes. Large collaborations and novel approaches are needed to overcome the genetic heterogeneity of pancreatic cancer predisposition.

Keywords: Familial Cancer; Inherited Cancer; Pancreas; Rare Variant Burden Tests.

Figure 1

Power to detect a gene enriched for rare inactivating variants based on an empirical “spike-in” procedure. 1a) Power at the exome-wide significance level P<2.5×10⁻⁶. 1b) Power at the suggestive significance level P<.001.

Figure 2

Manhattan plots and quantile-quantile plots for gene-based case-control association analyses. 2a) Rare inactivating variants. 2b) Rare damaging variants.