Multitrait genome association analysis identifies new susceptibility genes for human anthropometric variation in the GCAT cohort

• Published in: Journal of medical genetics Vol. 55; no. 11; pp. 765 - 778
• Main Authors: Galván-Femenía, Iván, Obón-Santacana, Mireia, Piñeyro, David, Guindo-Martinez, Marta, Duran, Xavier, Carreras, Anna, Pluvinet, Raquel, Velasco, Juan, Ramos, Laia, Aussó, Susanna, Mercader, J M, Puig, Lluis, Perucho, Manuel, Torrents, David, Moreno, Victor, Sumoy, Lauro, de Cid, Rafael
• Format: Journal Article Publication
• Language: English
• Published: England BMJ Publishing Group 01.11.2018
• Series: Original article
• Subjects: Complex Traits; Enginyeria biomèdica; Genetic phenotypes; Genome; Genome signal detection; Genomes; Àrees temàtiques de la UPC; cohort; complex traits; gwas; phenome; multitrait
• ISSN: 0022-2593; 1468-6244
• DOI: 10.1136/jmedgenet-2018-105437

BackgroundHeritability estimates have revealed an important contribution of SNP variants for most common traits; however, SNP analysis by single-trait genome-wide association studies (GWAS) has failed to uncover their impact. In this study, we applied a multitrait GWAS approach to discover additional factor of the missing heritability of human anthropometric variation.MethodsWe analysed 205 traits, including diseases identified at baseline in the GCAT cohort (Genomes For Life- Cohort study of the Genomes of Catalonia) (n=4988), a Mediterranean adult population-based cohort study from the south of Europe. We estimated SNP heritability contribution and single-trait GWAS for all traits from 15 million SNP variants. Then, we applied a multitrait-related approach to study genome-wide association to anthropometric measures in a two-stage meta-analysis with the UK Biobank cohort (n=336 107).ResultsHeritability estimates (eg, skin colour, alcohol consumption, smoking habit, body mass index, educational level or height) revealed an important contribution of SNP variants, ranging from 18% to 77%. Single-trait analysis identified 1785 SNPs with genome-wide significance threshold. From these, several previously reported single-trait hits were confirmed in our sample with LINC01432 (p=1.9×10−9) variants associated with male baldness, LDLR variants with hyperlipidaemia (ICD-9:272) (p=9.4×10−10) and variants in IRF4 (p=2.8×10−57), SLC45A2 (p=2.2×10−130), HERC2 (p=2.8×10−176), OCA2 (p=2.4×10−121) and MC1R (p=7.7×10−22) associated with hair, eye and skin colour, freckling, tanning capacity and sun burning sensitivity and the Fitzpatrick phototype score, all highly correlated cross-phenotypes. Multitrait meta-analysis of anthropometric variation validated 27 loci in a two-stage meta-analysis with a large British ancestry cohort, six of which are newly reported here (p value threshold <5×10−9) at ZRANB2-AS2, PIK3R1, EPHA7, MAD1L1, CACUL1 and MAP3K9.ConclusionConsidering multiple-related genetic phenotypes improve associated genome signal detection. These results indicate the potential value of data-driven multivariate phenotyping for genetic studies in large population-based cohorts to contribute to knowledge of complex traits.