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This article is part of the supplement: Genetic Analysis Workshop 17: Unraveling Human Exome Data

Open Access Proceedings

Gene-based multiple trait analysis for exome sequencing data

Jingyuan Zhao and Anbupalam Thalamuthu*

Author Affiliations

Human Genetics, Genome Institute of Singapore, 60 Biopolis Street 02-01, Singapore 138672

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BMC Proceedings 2011, 5(Suppl 9):S75  doi:10.1186/1753-6561-5-S9-S75

Published: 29 November 2011

Abstract

The common genetic variants identified through genome-wide association studies explain only a small proportion of the genetic risk for complex diseases. The advancement of next-generation sequencing technologies has enabled the detection of rare variants that are expected to contribute significantly to the missing heritability. Some genetic association studies provide multiple correlated traits for analysis. Multiple trait analysis has the potential to improve the power to detect pleiotropic genetic variants that influence multiple traits. We propose a gene-level association test for multiple traits that accounts for correlation among the traits. Gene- or region-level testing for association involves both common and rare variants. Statistical tests for common variants may have limited power for individual rare variants because of their low frequency and multiple testing issues. To address these concerns, we use the weighted-sum pooling method to test the joint association of multiple rare and common variants within a gene. The proposed method is applied to the Genetic Association Workshop 17 (GAW17) simulated mini-exome data to analyze multiple traits. Because of the nature of the GAW17 simulation model, increased power was not observed for multiple-trait analysis compared to single-trait analysis. However, multiple-trait analysis did not result in a substantial loss of power because of the testing of multiple traits. We conclude that this method would be useful for identifying pleiotropic genes.