Polygenic background modifies penetrance of monogenic variants conferring risk for coronary artery disease, breast cancer, or colorectal cancer

ABSTRACT Background Genetic variation can predispose to disease both through (i) monogenic risk variants in specific genes that disrupt a specific physiologic pathway and have a large effect on disease risk and (ii) polygenic risk that involves large numbers of variants of small effect that affect many different pathways. Few studies have explored the interaction between monogenic risk variants and polygenic risk. Methods We identified monogenic risk variants and calculated polygenic scores for three diseases, coronary artery disease, breast cancer, and colorectal cancer, in three study populations — case-control cohorts for coronary artery disease (UK Biobank; N=12,879) and breast cancer (Color Genomics; N=19,264), and an independent cohort of 49,738 additional UK Biobank participants. Results In the coronary artery disease case-control cohort, increased risk for carriers of a monogenic variant ranged from 1.3-fold for those in the lowest polygenic score quintile to 12.6-fold for those in the highest. For breast cancer, increased risk ranged from 2.4 to 6.9-fold across polygenic score quintiles. Among the 49,738 UK Biobank participants who carried a monogenic risk variant, the probability of disease at age 75 years was strongly modified by polygenic risk. Across individuals in the lowest to highest percentiles of polygenic risk, the probability of disease ranged from 17% to 78% for coronary artery disease; 13% to 76% for breast cancer; and 11% to 80% for colon cancer. Conclusions For three important genomic conditions, polygenic risk powerfully modifies the risk conferred by monogenic risk variants.