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- Title
Genetic variance estimation with imputed variants finds negligible missing heritability for human height and body mass index.
- Authors
Perry, John R B; Nolte, Ilja M; Snieder, Harold; Milani, Lili; Mägi, Reedik; Hamsten, Anders; Esko, Tonu; Metspalu, Andres; Ingelsson, Erik; Soranzo, Nicole; Keller, Matthew C; Goddard, Michael E; Visscher, Peter M; Bakshi, Andrew; Zhu, Zhihong; Vinkhuyzen, Anna A E; Robinson, Matthew R; Wray, Naomi R; Magnusson, Patrik K E; Pedersen, Nancy L
- 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.
- Subjects
HERITABILITY; BODY mass index; GENOME editing; STATURE; HUMAN genetics
- Publication
Nature Genetics, 2015, Vol 47, Issue 10, p1114
- ISSN
1061-4036
- Publication type
Article
- DOI
10.1038/ng.3390