Estimating heritability and its enrichment in tissue-specific gene sets in admixed populations
Authors: Luo Yang , Li Xinyi , Wang Xin , Gazal Steven , Mercader Josep Maria ,   23andMe Research Team,   SIGMA Type 2 Diabetes Consortium, Neale Benjamin M. , Florez Jose C. , Auton Adam , Price Alkes L. , Finucane Hilary K. , Raychaudhuri Soumya 
Published: December 2018

The increasing size and diversity of genome-wide association studies provide an exciting opportunity to study how the genetics of complex traits vary among diverse populations. Here, we introduce covariate-adjusted LD score regression (cov-LDSC), a method to accurately estimate genetic heritability and its enrichment in both homogenous and admixed populations with summary statistics and in-sample LD estimates. In-sample LD can be estimated from a subset of the GWAS samples, allowing our method to be applied efficiently to very large cohorts. In simulations, we show that unadjusted LDSC underestimates by 10% − 60% in admixed populations; in contrast, cov-LDSC is robust to all simulation parameters. We apply cov-LDSC to genotyping data from approximately 170,000 Latino, 47,000 African American and 135,000 European individuals. We estimate and detect heritability enrichment in three quantitative and five dichotomous phenotypes respectively, making this, to our knowledge, the most comprehensive heritability-based analysis of admixed individuals. Our results show that most traits have high concordance of and consistent tissue-specific heritability enrichment among different populations. However, for age at menarche, we observe population-specific heritability estimates of . We observe consistent patterns of tissue-specific heritability enrichment across populations; for example, in the limbic system for BMI, the per-standardized-annotation effect size τ* is 0.16 ± 0.04, 0.28 ± 0.11 and 0.18 ± 0.03 in Latino, African American and European populations respectively. Our results demonstrate that our approach is a powerful way to analyze genetic data for complex traits from underrepresented populations.

Author summary

Admixed populations such as African Americans and Hispanic Americans bear a disproportionately high burden of disease but remain underrepresented in current genetic studies. It is important to extend current methodological advancements for understanding the genetic basis of complex traits in homogeneous populations to individuals with admixed genetic backgrounds. Here, we develop a computationally efficient method to answer two specific questions. First, does genetic variation contribute to the same amount of phenotypic variation (heritability) across diverse populations? Second, are the genetic mechanisms shared among different populations? To answer these questions, we use our novel method to conduct the first comprehensive heritability-based analysis of a large number of admixed individuals. We show that there is a high degree of concordance in total heritability and tissue-specific enrichment between different ancestral groups. However, traits such as age at menarche show a noticeable differences among populations. Our work provides a powerful way to analyze genetic data in admixed populations and may contribute to the applicability of genomic medicine to admixed population groups.