Implications of simplified linkage equilibrium SNP simulation

Title
Implications of simplified linkage equilibrium SNP simulation
Publication Date
2015
Author(s)
Lee, Sang Hong
Type of document
Journal Article
Language
en
Entity Type
Publication
Publisher
National Academy of Sciences
Place of publication
United States of America
DOI
10.1073/pnas.1502868112
UNE publication id
une:19006
Abstract
Golan et al. (1) report that restricted maximum likelihood (REML) seriously underestimates SNP heritability when using a case-control design. Their conclusions are based on results from simplified linkage equilibrium SNP simulation (SLES), which the authors acknowledge may be unrealistic. We simulated case-control data using the liability threshold model (1, 2), based on a real genome-wide association study (GWAS) of 800,000 SNPs from 64,000 samples, i.e., a genome-wide linkage disequilibrium SNP simulation (GLDS). Our simulation used a population disease risk of K = 0.01 and proportion of cases in the sample of P = 0.5 (therefore, there were 640 cases and 640 controls in the estimation analyses).
Link
Citation
Proceedings of the National Academy of Sciences, 112(40), p. E5449-E5451
ISSN
1091-6490
0027-8424
Start page
E5449
End page
E5451

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