In this section, we describe the construction of single-trait input GWASs used in several of our downstream analyses, including as inputs for the single-trait and multi-trait PGIs. The single-trait input GWAS for a phenotype is obtained by meta-analysing summary statistics from up to three sources of information: analyses in UKB, analyses in 23andMe, and summary statistics from a previously published study of the phenotype5,42,49,50,52,60–73. The input GWAS for a phenotype is the same across most cohorts. However, when there is overlap between a Repository cohort and cohorts that contributed to summary statistics from previously published studies, or in order to construct a PGI for a UKB partition that is based on summary statistics including the rest of the UKB sample, we restrict the meta-analyses to summary statistics based on non-overlapping data. Details on the construction of single-trait input GWAS are in Supplementary Table 8.
