Novel genetic analysis for case-control genome-wide association studies: quantification of power and genomic prediction accuracy.

Sang Hong Lee, Naomi R. Wray

Research output: Contribution to journalArticlepeer-review

20 Citations (Scopus)


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.

Original languageEnglish
Article numbere71494
JournalPloS one
Issue number8
Publication statusPublished or Issued - 2013
Externally publishedYes

ASJC Scopus subject areas

  • Biochemistry, Genetics and Molecular Biology(all)
  • Agricultural and Biological Sciences(all)
  • General

Cite this