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GWAS significance thresholds for deep phenotyping studies can depend upon minor allele frequencies and sample size by Huma Asif; Ney Alliey-Rodriguez; Sarah Keedy; Carol A. Tamminga; John A. Sweeney; Godfrey Pearlson; Brett A. Clementz; Matcheri S. Keshavan; Peter Buckley; Chunyu Liu; Benjamin Neale; Elliot S. Gershon is a Neuroscience article available to read on EtoBox.
What is GWAS significance thresholds for deep phenotyping studies can depend upon minor allele frequencies and sample size about?
An important issue affecting genome-wide association studies with deep phenotyping (multiple correlated phenotypes) is determining the suitable family-wise significance threshold. Straightforward family-wise correction (Bonferroni) of p < 0.05 for 4.3 million genotypes and 335 phenotypes would give a threshold of p 0.1), the permutation family-wise threshold was in close agreement with spectral decomposition methods. However, for less common SNPs (0.05 < MAF ≤ 0.1), the permutation threshold calculated over all SNPs was off by orders of magnitude. This applies to the number of individuals studied (here 777) but not to very much larger numbers. Based on these findings, we propose that the threshold to find a particular level of family-wise significance may need to be established using separate permutations of the actual data for several MAF bins.
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- Author
- Huma Asif; Ney Alliey-Rodriguez; Sarah Keedy; Carol A. Tamminga; John A. Sweeney; Godfrey Pearlson; Brett A. Clementz; Matcheri S. Keshavan; Peter Buckley; Chunyu Liu; Benjamin Neale; Elliot S. Gershon
- Publisher
- Nature Publishing Group; Springer Science and Business Media LLC; Society for Mining, Metallurgy and Exploration Inc. (ISSN 1359-4184)
- Published
- 2020
- Language
- EN
- Field
- Neuroscience (Life Sciences)