Addressing population-specific multiple testing burdens in genetic association studies.

ABSTRACT: The number of effectively independent tests performed in genome-wide association studies (GWAS) varies by population, making a universal P-value threshold inappropriate. We estimated the number of independent SNPs in Phase 3 HapMap samples by: (1) the LD-pruning function in PLINK, and (2) an autocorrelation-based approach. Autocorrelation was also used to estimate the number of independent SNPs in whole genome sequences from 1000 Genomes. Both approaches yielded consistent estimates of numbers of independent SNPs, which were used to calculate new population-specific thresholds for genome-wide significance. African populations had the most stringent thresholds (1.49 × 10(-7) for YRI at r(2) = 0.3), East Asian populations the least (3.75 × 10(-7) for JPT at r(2) = 0.3). We also assessed how

SUBMITTER: Sobota RS 

PROVIDER: S-EPMC4334751 | biostudies-literature | 2015 Mar

REPOSITORIES: biostudies-literature