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Controlling the Rate of GWAS False Discoveries

Damian Brzyski, Christine B. Peterson, Piotr Sobczyk, Emmanuel J. Candés, Malgorzata Bogdan, Chiara Sabatti
doi: https://doi.org/10.1101/058230
Damian Brzyski
aJagiellonian University
bIndiana University
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Christine B. Peterson
cStanford University
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Piotr Sobczyk
dWroclaw University of Technology
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Emmanuel J. Candés
cStanford University
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Malgorzata Bogdan
eUniversity of Wroclaw
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Chiara Sabatti
cStanford University
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Abstract

With the rise of both the number and the complexity of traits of interest, control of the false discovery rate (FDR) in genetic association studies has become an increasingly appealing and accepted target for multiple comparison adjustment. While a number of robust FDR controlling strategies exist, the nature of this error rate is intimately tied to the precise way in which discoveries are counted, and the performance of FDR controlling procedures is satisfactory only if there is a one-to-one correspondence between what scientists describe as unique discoveries and the number of rejected hypotheses. The presence of linkage disequilibrium between markers in genome-wide association studies (GWAS) often leads researchers to consider the signal associated to multiple neighboring SNPs as indicating the existence of a single genomic locus with possible influence on the phenotype. This a posteriori aggregation of rejected hypotheses results in inflation of the relevant FDR. We propose a novel approach to FDR control that is based on pre-screening to identify the level of resolution of distinct hypotheses. We show how FDR controlling strategies can be adapted to account for this initial selection both with theoretical results and simulations that mimic the dependence structure to be expected in GWAS. We demonstrate that our approach is versatile and useful when the data are analyzed using both tests based on single marker and multivariate regression. We provide an R package that allows practitioners to apply our procedure on standard GWAS format data, and illustrate its performance on lipid traits in the NFBC66 cohort study.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted June 10, 2016.
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Controlling the Rate of GWAS False Discoveries
Damian Brzyski, Christine B. Peterson, Piotr Sobczyk, Emmanuel J. Candés, Malgorzata Bogdan, Chiara Sabatti
bioRxiv 058230; doi: https://doi.org/10.1101/058230
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Controlling the Rate of GWAS False Discoveries
Damian Brzyski, Christine B. Peterson, Piotr Sobczyk, Emmanuel J. Candés, Malgorzata Bogdan, Chiara Sabatti
bioRxiv 058230; doi: https://doi.org/10.1101/058230

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