Novel genetic analysis for case-control genome-wide association studies: quantification of power and genomic prediction accuracy
Date
2013
Authors
Lee, S.H.
Wray, N.R.
Editors
Zaykin, D.
Advisors
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Journal article
Citation
PLoS ONE, 2013; 8(8, article no. e71494):1-7
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Abstract
Genome-wide association studies (GWAS) are routinely conducted for both quantitative and binary (disease) traits. We present two analytical tools for use in the experimental design of GWAS. Firstly, we present power calculations quantifying power in a unified framework for a range of scenarios. In this context we consider the utility of quantitative scores (e.g. endophenotypes) that may be available on cases only or both cases and controls.
Secondly, we consider, the accuracy of prediction of genetic risk from genome-wide SNPs and derive an expression for genomic prediction accuracy using a liability threshold model for disease traits in a case-control design. The expected values based on our derived equations for both power and prediction accuracy agree well with observed estimates from simulations.
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Dissertation Note
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Data source: Supporting information, https://doi.org/10.1371/journal.pone.0071494
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Copyright 2013 Lee, Wray. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited (http://creativecommons.org/licenses/by/4.0)