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Recovery of trait heritability from whole genome sequence data

By Pierrick Wainschtein, Deepti P Jain, Zhili Zheng, TOPMed Anthropometry Working Group, Trans-Omics for Precision Medicine Consortium, L. Adrienne Cupples, Aladdin H Shadyab, Barbara McKnight, Benjamin M Shoemaker, Braxton D Mitchell, Bruce M Psaty, Charles Kooperberg, Ching-Ti Liu, Christine M Albert, Dan Roden, Daniel I. Chasman, Dawood Darbar, Donald M Lloyd-Jones, Donna K Arnett, Elizabeth A Regan, Eric Boerwinkle, Jerome Rotter, Jeffrey R O'Connell, Lisa R Yanek, Mariza de Andrade, Matthew A Allison, Merry-Lynn N McDonald, Mina K Chung, Myriam Fornage, Nathalie Chami, Nicholas L Smith, Patrick T Ellinor, Ramachandran S. Vasan, Rasika A. Mathias, Ruth JF Loos, Stephen Rich, Steven A. Lubitz, Susan R. Heckbert, Susan Redline, Xiuqing Guo, Y-D Ida Chen, Cecelia A. Laurie, Ryan D Hernandez, Stephen T. McGarvey, Michael E Goddard, Cathy C Laurie, Kari E North, Leslie A Lange, Bruce S. Weir, Loic Yengo, Jian Yang, Peter M Visscher

Posted 25 Mar 2019
bioRxiv DOI: 10.1101/588020 (published DOI: 10.1530/ey.16.14.15)

Heritability, the proportion of phenotypic variance explained by genetic factors, can be estimated from pedigree data, but such estimates are uninformative with respect to the underlying genetic architecture. Analyses of data from genome-wide association studies (GWAS) on unrelated individuals have shown that for human traits and disease, approximately one-third to two-thirds of heritability is captured by common SNPs. It is not known whether the remaining heritability is due to the imperfect tagging of causal variants by common SNPs, in particular if the causal variants are rare, or other reasons such as over-estimation of heritability from pedigree data. Here we show that pedigree heritability for height and body mass index (BMI) appears to be largely recovered from whole-genome sequence (WGS) data on 25,465 unrelated individuals of European ancestry. We assigned 33.7 million genetic variants to groups based upon their minor allele frequencies (MAF) and linkage disequilibrium (LD) with variants nearby, and estimated and partitioned genetic variance accordingly. The estimated heritability was 0.68 (SE 0.10) for height and 0.30 (SE 0.10) for BMI, with a range of ~0.60 - 0.71 for height and ~0.25 - 0.35 for BMI, depending on quality control and analysis strategies. Low-MAF variants in low LD with neighbouring variants were enriched for heritability, to a greater extent for protein-altering variants, consistent with negative selection thereon. Cumulatively variants with 0.0001 < MAF < 0.1 explained 0.47 (SE 0.07) and 0.30 (SE 0.10) of heritability for height and BMI, respectively. Our results imply that rare variants, in particular those in regions of low LD, is a major source of the still missing heritability of complex traits and disease.

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