alexa Rare-variant association testing for sequencing data with the sequence kernel association test.
Genetics & Molecular Biology

Genetics & Molecular Biology

Human Genetics & Embryology

Author(s): Wu MC, Lee S, Cai T, Li Y, Boehnke M,

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Abstract Sequencing studies are increasingly being conducted to identify rare variants associated with complex traits. The limited power of classical single-marker association analysis for rare variants poses a central challenge in such studies. We propose the sequence kernel association test (SKAT), a supervised, flexible, computationally efficient regression method to test for association between genetic variants (common and rare) in a region and a continuous or dichotomous trait while easily adjusting for covariates. As a score-based variance-component test, SKAT can quickly calculate p values analytically by fitting the null model containing only the covariates, and so can easily be applied to genome-wide data. Using SKAT to analyze a genome-wide sequencing study of 1000 individuals, by segmenting the whole genome into 30 kb regions, requires only 7 hr on a laptop. Through analysis of simulated data across a wide range of practical scenarios and triglyceride data from the Dallas Heart Study, we show that SKAT can substantially outperform several alternative rare-variant association tests. We also provide analytic power and sample-size calculations to help design candidate-gene, whole-exome, and whole-genome sequence association studies. Copyright © 2011 The American Society of Human Genetics. Published by Elsevier Inc. All rights reserved.
This article was published in Am J Hum Genet and referenced in Human Genetics & Embryology

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