Evaluating the Calibration and Power of Three Gene-Based Association Tests of Rare Variants for the X Chromosome.

ABSTRACT: Although genome-wide association studies (GWAS) have identified thousands of trait-associated genetic variants, there are relatively few findings on the X chromosome. For analysis of low-frequency variants (minor allele frequency <5%), investigators can use region- or gene-based tests where multiple variants are analyzed jointly to increase power. To date, there are no gene-based tests designed for association testing of low-frequency variants on the X chromosome. Here we propose three gene-based tests for the X chromosome: burden, sequence kernel association test (SKAT), and optimal unified SKAT (SKAT-O). Using simulated case-control and quantitative trait (QT) data, we evaluate the calibration and power of these tests as a function of (1) male:female sample size ratio; and (2) coding of

SUBMITTER: Ma C 

PROVIDER: S-EPMC4609297 | biostudies-literature | 2015 Nov

REPOSITORIES: biostudies-literature