UK BioCoin: Swift Trait-Specific Summary Statistics Regression for UK Biobank

Abstract

AbstractSummary statistics derived from large-scale biobanks facilitate the sharing of genetic discoveries while minimizing the risk of compromising individual-level data privacy. However, these summary statistics, such as those from the UK Biobank (UKB) provided by Neale’s lab, are often adjusted by a fixed set of covariates to all traits (12 covariates including 10 PCs, sex and age), preventing the exploration of trait-specific summary statistics. In this study, we present a novel computational device UK BioCoin (UKC), which is designed to provide an efficient framework for trait-specific adjustment for covariates. Without requiring access to individual-level data from UKB, UKC leverages summary statistics regression technique and resources from UKB (289 GB of 199 phenotypes and 10 million SNPs), to enable the generation of GWAS summary statistics adjusted by user-specified covariates. Through a comprehensive analysis of height under trait-specific adjustments, we demonstrate that the GWAS summary statistics generated by UKC closely mirror those generated from individual-level UKB GWAS (ρ ≥0.99 for effect sizes andρ ≥0.99 forp-values). Furthermore, we demonstrate the results for GWAS, SNP-heritability estimation, polygenic score, and Mendelian randomization, after various trait-specific covariate adjustments as allowed by UKC, indicating UKC a platform that harnesses in-depth exploration for researchers lacking access to UKB. The whole framework of UKC is portable for other biobank, as demonstrated in Westlake Biobank, which can equivalently be converted to a ‘UKC-like” platform and promote data sharing. UKC has its computational engine fully optimized, and the computational efficiency of UKC is about 70 times faster than that of UKB. We package UKC as a Docker image of 20 GB (https://github.com/Ttttt47/UKBioCoin), which can be easily deployed on an average computer (e.g. laptop).One sentence summaryWe develop UK BioCoin (UKC), which allows fine-tuning of covariates for each UK Biobank trait but does not relay on UK Biobank individual-level data. It will change the current landscape of GWAS and reshape its downstream analyses.