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Re-evaluation of SNP heritability in complex human traits

View ORCID ProfileDoug Speed, View ORCID ProfileNa Cai, The UCLEB Consortium, Michael R. Johnson, View ORCID ProfileSergey Nejentsev, View ORCID ProfileDavid J Balding
doi: https://doi.org/10.1101/074310
Doug Speed
1UCL Genetics Institute, University College London, United Kingdom
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  • For correspondence: doug.speed@ucl.ac.uk
Na Cai
2Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
3European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
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Michael R. Johnson
5Division of Brain Science, Imperial College London, United Kingdom
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Sergey Nejentsev
6Department of Medicine, University of Cambridge, United Kingdom
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David J Balding
1UCL Genetics Institute, University College London, United Kingdom
7Centre for Systems Genomics, School of BioSciences and School of Mathematics & Statistics, University of Melbourne, Australia
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Abstract

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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  • ↵4 A full list of members and afñliations appears in the Supplementary Material

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted January 15, 2017.
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Re-evaluation of SNP heritability in complex human traits
Doug Speed, Na Cai, The UCLEB Consortium, Michael R. Johnson, Sergey Nejentsev, David J Balding
bioRxiv 074310; doi: https://doi.org/10.1101/074310
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Re-evaluation of SNP heritability in complex human traits
Doug Speed, Na Cai, The UCLEB Consortium, Michael R. Johnson, Sergey Nejentsev, David J Balding
bioRxiv 074310; doi: https://doi.org/10.1101/074310

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