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Genetic variance estimation with imputed variants finds negligible missing heritability for human height and body mass index
Univ Queensland, Queensland Brain Inst, Brisbane, Qld, Australia.;Univ Queensland, Diamantina Inst, Translat Res Inst, Brisbane, Qld, Australia..
Univ Queensland, Queensland Brain Inst, Brisbane, Qld, Australia..
Univ Queensland, Queensland Brain Inst, Brisbane, Qld, Australia..
Univ Queensland, Queensland Brain Inst, Brisbane, Qld, Australia.;Univ Bristol, Sch Social & Community Med, IEU, MRC, Bristol, Avon, England..
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2015 (English)In: Nature Genetics, ISSN 1061-4036, E-ISSN 1546-1718, Vol. 47, no 10, 1114-1120 p.Article in journal (Refereed) Published
Abstract [en]

We propose a method (GREML-LDMS) to estimate heritability for human complex traits in unrelated individuals using whole-genome sequencing data. We demonstrate using simulations based on whole-genome sequencing data that similar to 97% and similar to 68% of variation at common and rare variants, respectively, can be captured by imputation. Using the GREML-LDMS method, we estimate from 44,126 unrelated individuals that all similar to 17 million imputed variants explain 56% (standard error (s.e.) = 2.3%) of variance for height and 27% (s.e. = 2.5%) of variance for body mass index (BMI), and we find evidence that height- and BMI-associated variants have been under natural selection. Considering the imperfect tagging of imputation and potential overestimation of heritability from previous family-based studies, heritability is likely to be 60-70% for height and 30-40% for BMI. Therefore, the missing heritability is small for both traits. For further discovery of genes associated with complex traits, a study design with SNP arrays followed by imputation is more cost-effective than whole-genome sequencing at current prices.

Place, publisher, year, edition, pages
2015. Vol. 47, no 10, 1114-1120 p.
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Medical Genetics
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URN: urn:nbn:se:uu:diva-265693DOI: 10.1038/ng.3390ISI: 000361969900006PubMedID: 26323059OAI: oai:DiVA.org:uu-265693DiVA: diva2:866946
Funder
NIH (National Institute of Health), R01MH100141
Available from: 2015-11-04 Created: 2015-11-02 Last updated: 2017-12-01Bibliographically approved

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Ingelsson, Erik

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