Empirical Bayes Correction for the Winner's Curse in Genetic Association Studies

John P. Ferguson, Judy H. Cho, Can Yang, Hongyu Zhao

Research output: Contribution to journalArticlepeer-review

22 Scopus citations

Abstract

We consider an Empirical Bayes method to correct for the Winner's Curse phenomenon in genome-wide association studies. Our method utilizes the collective distribution of all odds ratios (ORs) to determine the appropriate correction for a particular single-nucleotide polymorphism (SNP). We can show that this approach is squared error optimal provided that this collective distribution is accurately estimated in its tails. To improve the performance when correcting the OR estimates for the most highly associated SNPs, we develop a second estimator that adaptively combines the Empirical Bayes estimator with a previously considered Conditional Likelihood estimator. The applications of these methods to both simulated and real data suggest improved performance in reducing selection bias.

Original languageEnglish
Pages (from-to)60-68
Number of pages9
JournalGenetic Epidemiology
Volume37
Issue number1
DOIs
StatePublished - Jan 2013
Externally publishedYes

Keywords

  • GWAS, Empirical Bayes
  • Winner's Curse

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