Simultaneous Detection of Signal Regions Using Quadratic Scan Statistics With Applications to Whole Genome Association Studies

Abstract

We consider in this article detection of signal regions associated with disease outcomes in whole genome association studies. Gene- or region-based methods have become increasingly popular in whole genome association analysis as a complementary approach to traditional individual variant analysis. However, these methods test for the association between an outcome and the genetic variants in a prespecified region, for example, a gene. In view of massive intergenic regions in whole genome sequencing (WGS) studies, we propose a computationally efficient quadratic scan (Q-SCAN) statistic based method to detect the existence and the locations of signal regions by scanning the genome continuously. The proposed method accounts for the correlation (linkage disequilibrium) among genetic variants, and allows for signal regions to have both causal and neutral variants, and the effects of signal variants to be in different directions. We study the asymptotic properties of the proposed Q-SCAN statistics. We derive an empirical threshold that controls for the family-wise error rate, and show that under regularity conditions the proposed method consistently selects the true signal regions. We perform simulation studies to evaluate the finite sample performance of the proposed method. Our simulation results show that the proposed procedure outperforms the existing methods, especially when signal regions have causal variants whose effects are in different directions, or are contaminated with neutral variants. We illustrate Q-SCAN by analyzing the WGS data from the Atherosclerosis Risk in Communities study. Supplementary materials for this article are available online.