Included in heritability theme

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Author: Doug Speed
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Research area: genetics
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Open peer-review

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Re-evaluation of SNP heritability in complex human traits


Created on 30th May 2017

This paper has been published in Nature genetics.

Doug Speed; Na Cai; The UCLEB Consortium; Michael Johnson; Sergey Nejentsev; David Balding;


SNP heritability, the proportion of phenotypic variance explained by SNPs, has been reported for many hundreds of traits. Its estimation requires strong prior assumptions about the distribution of heritability across the genome, but the assumptions in current use have not been thoroughly tested. By analyzing imputed data for a large number of human traits, we empirically derive a model that more accurately describes how heritability varies with minor allele frequency, linkage disequilibrium and genotype certainty. Across 19 traits, our improved model leads to estimates of common SNP heritability on average 43% (SD 3) higher than those obtained from the widely-used software GCTA, and 25% (SD 2) higher than those from the recently-proposed extension GCTA-LDMS. Previously, DNaseI hypersensitivity sites were reported to explain 79% of SNP heritability; using our improved heritability model their estimated contribution is only 24%.

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# Status Date
1 Completed 31 Oct 2016 View review
2 Completed 2 Jun 2017 View review