Testing the role of predicted gene knockouts in human anthropometric trait variation.
Lessard S., Manning AK., Low-Kam C., Auer PL., Giri A., Graff M., Schurmann C., Yaghootkar H., Luan J., Esko T., Karaderi T., NHLBI GO Exome Sequence Project None., GOT2D None., T2D-GENES None., GIANT Consortium None., Bottinger EP., Lu Y., Carlson C., Caulfield M., Dubé MP., Jackson RD., Kooperberg C., McKnight B., Mongrain I., Peters U., Reiner AP., Rhainds D., Sotoodehnia N., Hirschhorn JN., Scott RA., Munroe PB., Frayling TM., Loos RJ., North KE., Edwards TL., Tardif JC., Lindgren CM., Lettre G.
Although the role of complete gene inactivation by two loss-of-function mutations inherited in trans is well-established in recessive Mendelian diseases, we have not yet explored how such gene knockouts (KOs) could influence complex human phenotypes. Here, we developed a statistical framework to test the association between gene KOs and quantitative human traits. Our method is flexible, publicly available, and compatible with common genotype format files (e.g. PLINK and vcf). We characterized gene KOs in 4498 participants from the NHLBI Exome Sequence Project (ESP) sequenced at high coverage (>100×), 1976 French Canadians from the Montreal Heart Institute Biobank sequenced at low coverage (5.7×), and >100 000 participants from the Genetic Investigation of ANthropometric Traits (GIANT) Consortium genotyped on an exome array. We tested associations between gene KOs and three anthropometric traits: body mass index (BMI), height and BMI-adjusted waist-to-hip ratio (WHR). Despite our large sample size and multiple datasets available, we could not detect robust associations between specific gene KOs and quantitative anthropometric traits. Our results highlight several limitations and challenges for future gene KO studies in humans, in particular when there is no prior knowledge on the phenotypes that might be affected by the tested gene KOs. They also suggest that gene KOs identified with current DNA sequencing methodologies probably do not strongly influence normal variation in BMI, height, and WHR in the general human population.