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Schoech, Armin P; Jordan, Daniel M; Loh, Po-Ru; Gazal, Steven; O'Connor, Luke J; Balick, Daniel J; Palamara, Pier F; Finucane, Hilary K; Sunyaev, Shamil R; Price, Alkes L
Nature communications, 02/2019, Letnik: 10, Številka: 1Journal Article
Understanding the role of rare variants is important in elucidating the genetic basis of human disease. Negative selection can cause rare variants to have larger per-allele effect sizes than common variants. Here, we develop a method to estimate the minor allele frequency (MAF) dependence of SNP effect sizes. We use a model in which per-allele effect sizes have variance proportional to p(1 - p) , where p is the MAF and negative values of α imply larger effect sizes for rare variants. We estimate α for 25 UK Biobank diseases and complex traits. All traits produce negative α estimates, with best-fit mean of -0.38 (s.e. 0.02) across traits. Despite larger rare variant effect sizes, rare variants (MAF < 1%) explain less than 10% of total SNP-heritability for most traits analyzed. Using evolutionary modeling and forward simulations, we validate the α model of MAF-dependent trait effects and assess plausible values of relevant evolutionary parameters.
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JCR | SNIP | JCR | SNIP | JCR | SNIP | JCR | SNIP |
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