A SIMPLE, CONSISTENT ESTIMATOR OF SNP HERITABILITY FROM GENOME-WIDE ASSOCIATION STUDIES

• 成果类型: Article
• 署名作者: Schwartzman, Armin; Schork, Andrew J.; Zablocki, Rong; Thompson, Wesley K.
• 署名单位: University of California System; University of California San Diego; University of California System; University of California San Diego
• 刊物名称: ANNALS OF APPLIED STATISTICS
• ISSN/ISSBN: 1932-6157
• DOI: 10.1214/19-AOAS1291
• 发表日期: 2019
• 页码: 2509-2538
• 关键词: variance-estimation; explanation; loci

摘要

Analysis of genome-wide association studies (GWAS) is characterized by a large number of univariate regressions where a quantitative trait is regressed on hundreds of thousands to millions of single-nucleotide polymorphism (SNP) allele counts, one at a time. This article proposes an estimator of the SNP heritability of the trait, defined here as the fraction of the variance of the trait explained by the SNPs in the study. The proposed GWAS heritability (GWASH) estimator is easy to compute, highly interpretable and is consistent as the number of SNPs and the sample size increase. More importantly, it can be computed from summary statistics typically reported in GWAS, not requiring access to the original data. The estimator takes full account of the linkage disequilibrium (LD) or correlation between the SNPs in the study through moments of the LD matrix, estimable from auxiliary datasets. Unlike other proposed estimators in the literature, we establish the theoretical properties of the GWASH estimator and obtain analytical estimates of the precision, allowing for power and sample size calculations for SNP heritability estimates and forming a firm foundation for future methodological development.