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Title: Genetic variance estimation with imputed variants finds negligible missing heritability for human height and body mass index
Contributor(s): Yang, Jian (author); Bakshi, Andrew (author); Snieder, Harold (author); The LifeLines Cohort Study, (author); Esko, Tonu (author); Milani, Lili (author); Magi, Reedik (author); Metspalu, Andres (author); Hamsten, Anders (author); Magnusson, Patrik K E (author); Pedersen, Nancy L (author); Ingelsson, Erik (author); Zhu, Zhihong (author); Soranzo, Nicole (author); Keller, Matthew C (author); Wray, Naomi R (author); Goddard, Michael E (author); Visscher, Peter M (author); Hemani, Gibran (author); Vinkhuyzen, Anna A E (author); Lee, Sang Hong  (author); Robinson, Matthew R (author); Perry, John R B (author); Nolte, Ilja M (author); van Vliet-Ostaptchouk, Jana V (author)
Publication Date: 2015
Open Access: Yes
DOI: 10.1038/ng.3390Open Access Link
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Abstract: 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 ~97% and ~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 ~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.
Publication Type: Journal Article
Source of Publication: Nature Genetics, 47(10), p. 1114-1120
Publisher: Nature Publishing Group
Place of Publication: United States of America
ISSN: 1546-1718
Fields of Research (FoR) 2008: 060408 Genomics
060412 Quantitative Genetics (incl. Disease and Trait Mapping Genetics)
070201 Animal Breeding
Fields of Research (FoR) 2020: 310509 Genomics
310506 Gene mapping
300305 Animal reproduction and breeding
Socio-Economic Objective (SEO) 2008: 970106 Expanding Knowledge in the Biological Sciences
970108 Expanding Knowledge in the Information and Computing Sciences
970107 Expanding Knowledge in the Agricultural and Veterinary Sciences
Socio-Economic Objective (SEO) 2020: 280102 Expanding knowledge in the biological sciences
280115 Expanding knowledge in the information and computing sciences
280101 Expanding knowledge in the agricultural, food and veterinary sciences
Peer Reviewed: Yes
HERDC Category Description: C1 Refereed Article in a Scholarly Journal
Appears in Collections:Journal Article

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