POWERFUL TEST BASED ON CONDITIONAL EFFECTS FOR GENOME-WIDE SCREENING.

ABSTRACT: This paper considers testing procedures for screening large genome-wide data, where we examine hundreds of thousands of genetic variants, e.g., single nucleotide polymorphisms (SNP), on a quantitative phenotype. We screen the whole genome by SNP sets and propose a new test that is based on conditional effects from multiple SNPs. The test statistic is developed for weak genetic effects and incorporates correlations among genetic variables, which may be very high due to linkage disequilibrium. The limiting null distribution of the test statistic and the power of the test are derived. Under appropriate conditions, the test is shown to be more powerful than the minimum p-value method, which is based on marginal SNP effects and is the most commonly used method in genome-wide screening. The prop

SUBMITTER: Liu Y 

PROVIDER: S-EPMC5931742 | biostudies-literature | 2018 Mar

REPOSITORIES: biostudies-literature