In their meta-analysis, the PGC conducted imputation using 1000 Genomes phase 1, the standard reference panel available at that time. In the present study, we used 1000 Genomes phase 3 as our imputation reference panel, as phase 3 is an improvement over phase 1. Imputation was conducted using Minimac3 (Das et al. 2016) on an imputation webserver (https://imputationserver.sph.umich.edu). In total, 45 994 018 variants were imputed, including 124 of the 128 PGC genome-wide significant variants. Imputation quality is shown in online Supplementary Table S2. Of these 124 variants, 90% had a Minimac R2 (RSQ) higher than 0.9. The four remaining variants failed because they did not exist in 1000 Genomes phase 3. According to the 1000 Genomes Project Consortium, a total of 2.3 million variants were present in phase 1 but absent from phase 3 (http://www.1000genomes.org/faq/why-are-phase-1-sites-missing-phase-3-dataset/). Differences between phase 1 and 3 are due to platform differences, a few samples from phase 1 not included in phase 3, and improved variant calling pipelines.
