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Title: Implications of simplified linkage equilibrium SNP simulation
Contributor(s): Lee, Sang Hong  (author)
Publication Date: 2015
DOI: 10.1073/pnas.1502868112
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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).
Publication Type: Journal Article
Grant Details: NHMRC/APP1080157
Source of Publication: Proceedings of the National Academy of Sciences, 112(40), p. E5449-E5451
Publisher: National Academy of Sciences
Place of Publication: United States of America
ISSN: 1091-6490
Fields of Research (FoR) 2008: 070201 Animal Breeding
060408 Genomics
060412 Quantitative Genetics (incl. Disease and Trait Mapping Genetics)
Fields of Research (FoR) 2020: 300305 Animal reproduction and breeding
310509 Genomics
310506 Gene mapping
Socio-Economic Objective (SEO) 2008: 970108 Expanding Knowledge in the Information and Computing Sciences
970106 Expanding Knowledge in the Biological Sciences
970107 Expanding Knowledge in the Agricultural and Veterinary Sciences
Socio-Economic Objective (SEO) 2020: 280115 Expanding knowledge in the information and computing sciences
280102 Expanding knowledge in the biological sciences
280101 Expanding knowledge in the agricultural, food and veterinary sciences
HERDC Category Description: C4 Letter of Note
Appears in Collections:Journal Article
School of Environmental and Rural Science

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