Comparison of false-discovery rate for genome-wide and fine mapping regionsReport as inadecuate

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BMC Proceedings

, 1:S148

First Online: 18 December 2007DOI: 10.1186-1753-6561-1-S1-S148

Cite this article as: Tabangin, M.E., Woo, J.G., Liu, C. et al. BMC Proc 2007 1Suppl 1: S148. doi:10.1186-1753-6561-1-S1-S148


With technological advances in high-throughput genotyping, it is not unusual to perform hundreds of thousands of tests for each phenotype. Thus, correction to control type I error is essential. The false-discovery rate FDR has been successfully used in genome-wide expression data. However, its performance has not been evaluated for association analysis. Our objective was to analyze the Genetic Analysis Workshop 15 simulated data set, with answers, to evaluate FDR for genome-wide association and fine mapping. In genome-wide analysis, FDR performed well, with good localization of positive results. However, in fine mapping, all tested methods performed poorly, producing a high proportion of significant results. Thus, caution should be used when employing FDR for fine mapping.

List of abbreviations usedFDRFalse Discovery Rate

FPFalse positive

LDLinkage Disequilibrium

RARheumatoid Arthritis

SNPSingle Nucleotide Polymorphism

TPTrue positive

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Author: Meredith E Tabangin - Jessica G Woo - Chunyan Liu - Todd G Nick - Lisa J Martin


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