RT Journal Article
SR Electronic
T1 Re-evaluation of SNP heritability in complex human traits
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 074310
DO 10.1101/074310
A1 Doug Speed
A1 Na Cai
A1 The UCLEB Consortium
A1 Michael R. Johnson
A1 Sergey Nejentsev
A1 David J Balding
YR 2017
UL http://biorxiv.org/content/early/2017/01/15/074310.abstract
AB 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%.