Power estimation and sample size determination for replication studies of genome-wide association studies

BMC Genomics
Wei Jiang, Weichuan Yu

Abstract

Replication study is a commonly used verification method to filter out false positives in genome-wide association studies (GWAS). If an association can be confirmed in a replication study, it will have a high confidence to be true positive. To design a replication study, traditional approaches calculate power by treating replication study as another independent primary study. These approaches do not use the information given by primary study. Besides, they need to specify a minimum detectable effect size, which may be subjective. One may think to replace the minimum effect size with the observed effect sizes in the power calculation. However, this approach will make the designed replication study underpowered since we are only interested in the positive associations from the primary study and the problem of the "winner's curse" will occur. An Empirical Bayes (EB) based method is proposed to estimate the power of replication study for each association. The corresponding credible interval is estimated in the proposed approach. Simulation experiments show that our method is better than other plug-in based estimators in terms of overcoming the winner's curse and providing higher estimation accuracy. The coverage probability of give...Continue Reading

References

Oct 11, 2001·American Journal of Human Genetics·H H GöringJ Blangero
Jul 29, 2003·Proceedings of the National Academy of Sciences of the United States of America·John D Storey, Robert Tibshirani
Jun 1, 1955·Annals of Human Genetics·B WOOLF
Sep 20, 2006·Nature Reviews. Genetics·David J Balding
Mar 16, 2007·American Journal of Human Genetics·Sebastian Zollner, Jonathan K Pritchard
Jun 8, 2007·Nature·UNKNOWN NCI-NHGRI Working Group on Replication in Association StudiesFrancis S Collins
Jun 8, 2007·Nature·UNKNOWN Wellcome Trust Case Control Consortium
Apr 22, 2008·American Journal of Human Genetics·Arpita GhoshFred A Wright
Jul 18, 2008·Epidemiology·John P A Ioannidis
May 11, 2010·Statistical Science : a Review Journal of the Institute of Mathematical Statistics·Peter KraftJohn P A Ioannidis
Jun 22, 2010·Nature Genetics·Jian YangPeter M Visscher
Oct 14, 2010·Nature Reviews. Genetics·Vikas BansalNicholas J Schork
Jan 20, 2011·Human Genetics·Lei SunShelley B Bull
Aug 14, 2012·Nature Genetics·Andrew P MorrisUNKNOWN DIAbetes Genetics Replication And Meta-analysis (DIAGRAM) Consortium
Sep 27, 2012·Genetic Epidemiology·John P FergusonHongyu Zhao

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Citations

Jun 15, 2016·Hypertension·Ani ManichaikulPaula Q Barrett
Nov 28, 2017·Journal of Biopharmaceutical Statistics·Weidong ZhangSandeep Menon

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