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Reevaluation of SNP heritability in complex human traits

Nature Genetics volume 49, pages 986–992 (2017)Cite this article

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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 current assumptions 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 (MAF), linkage disequilibrium (LD) and genotype certainty. Across 19 traits, our improved model leads to estimates of common SNP heritability on average 43% (s.d. 3%) higher than those obtained from the widely used software GCTA and 25% (s.d. 2%) higher than those from the recently proposed extension GCTA-LDMS. Previously, DNase I 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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Figure 1: Comparison of the GCTA and LDAK models.
Figure 2: Relationship between heritability and MAF.
Figure 3: Comparison of methods for estimating for real and simulated data.
Figure 4: Comparing the GCTA and LDAK models for the GWAS traits.
Figure 5: Enrichment of SNP classes.
Figure 6: Varying quality control for the UCLEB traits.

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Acknowledgements

Access to Wellcome Trust Case Control Consortium data was authorized as work related to the project “Genome-wide association study of susceptibility and clinical phenotypes in epilepsy,” while access to Children's Hospital of Philadelphia (CHOP) data was granted under Project 49228-1, “Assumptions underlying estimates of SNP heritability.” We thank A. Molloy, J. Mills and L. Brody for permission to use genotype data from the Trinity College Dublin Student Study and S. Langley for help accessing the CHOP data. This work is funded by the UK Medical Research Council under grant MR/L012561/1 (awarded to D.S.) and the British Heart Foundation under grant RG/10/12/28456 (the UCLEB Consortium) and is supported by researchers at the National Institute for Health Research (NIHR) University College London Hospitals Biomedical Research Centre. N.C. is an ESPOD Fellow from the European Molecular Biology Laboratory, European Bioinformatics Institute, and Wellcome Trust Sanger Institute. M.R.J. receives funding from the Imperial College NIHR Biomedical Research Centre (BRC) Scheme. S.N. is a Wellcome Trust Senior Research Fellow in Basic Biomedical Science and is also supported by the NIHR Cambridge Biomedical Research Centre. Analyses were performed with the use of the UCL Computer Science Cluster and the help of the CS Technical Support Group, as well as the use of the UCL Legion High-Performance Computing Facility (Legion@UCL) and associated support services.

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Authors and Affiliations

  1. UCL Genetics Institute, University College London, London, UK

    Doug Speed & David J Balding

  2. Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, UK

    Na Cai

  3. European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, UK

    Na Cai

  4. Division of Brain Science, Imperial College London, London, UK

    Michael R Johnson

  5. Department of Medicine, University of Cambridge, Cambridge, UK

    Sergey Nejentsev

  6. Centre for Systems Genomics, School of BioSciences, and School of Mathematics and Statistics, University of Melbourne, Melbourne, Victoria, Australia

    David J Balding

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D.S. and N.C. performed the analyses. D.S. and D.J.B. wrote the manuscript with assistance from N.C., M.R.J., S.N. and members of the UCLEB Consortium.

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Correspondence to Doug Speed.

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Speed, D., Cai, N., the UCLEB Consortium. et al. Reevaluation of SNP heritability in complex human traits. Nat Genet 49, 986–992 (2017). https://doi.org/10.1038/ng.3865

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