Statistics – Methodology
Scientific paper
2010-10-25
Statistical Science 2009, Vol. 24, No. 4, 547-560
Statistics
Methodology
Published in at http://dx.doi.org/10.1214/09-STS286 the Statistical Science (http://www.imstat.org/sts/) by the Institute of M
Scientific paper
10.1214/09-STS286
Combining data from several case-control genome-wide association (GWA) studies can yield greater efficiency for detecting associations of disease with single nucleotide polymorphisms (SNPs) than separate analyses of the component studies. We compared several procedures to combine GWA study data both in terms of the power to detect a disease-associated SNP while controlling the genome-wide significance level, and in terms of the detection probability ($\mathit{DP}$). The $\mathit{DP}$ is the probability that a particular disease-associated SNP will be among the $T$ most promising SNPs selected on the basis of low $p$-values. We studied both fixed effects and random effects models in which associations varied across studies. In settings of practical relevance, meta-analytic approaches that focus on a single degree of freedom had higher power and $\mathit{DP}$ than global tests such as summing chi-square test-statistics across studies, Fisher's combination of $p$-values, and forming a combined list of the best SNPs from within each study.
Gail Mitchell H.
Pee David
Pfeiffer Ruth M.
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