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November 2009 Robust Tests in Genome-Wide Scans under Incomplete Linkage Disequilibrium
Gang Zheng, Jungnam Joo, Dmitri Zaykin, Colin Wu, Nancy Geller
Statist. Sci. 24(4): 503-516 (November 2009). DOI: 10.1214/09-STS314


Under complete linkage disequilibrium (LD), robust tests often have greater power than Pearson’s chi-square test and trend tests for the analysis of case-control genetic association studies. Robust statistics have been used in candidate-gene and genome-wide association studies (GWAS) when the genetic model is unknown. We consider here a more general incomplete LD model, and examine the impact of penetrances at the marker locus when the genetic models are defined at the disease locus. Robust statistics are then reviewed and their efficiency and robustness are compared through simulations in GWAS of 300,000 markers under the incomplete LD model. Applications of several robust tests to the Wellcome Trust Case-Control Consortium [Nature 447 (2007) 661–678] are presented.


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Gang Zheng. Jungnam Joo. Dmitri Zaykin. Colin Wu. Nancy Geller. "Robust Tests in Genome-Wide Scans under Incomplete Linkage Disequilibrium." Statist. Sci. 24 (4) 503 - 516, November 2009.


Published: November 2009
First available in Project Euclid: 20 April 2010

zbMATH: 1329.62440
MathSciNet: MR2779340
Digital Object Identifier: 10.1214/09-STS314

Rights: Copyright © 2009 Institute of Mathematical Statistics


Vol.24 • No. 4 • November 2009
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