Summary statistics, including effect allele and other allele oriented to the + strand, effect allele frequency, chromosome and position (hg19), and imputation quality were uploaded to a secure site at the Brigham and Women’s Hospital/Channing Division of Network Medicine. Quality control assessments included assessing allele frequencies versus 1000 Genomes reference, standard error versus sample size, and quantile-quantile plots. Variants with an imputation quality metric of < 0.3 (provided a higher threshold for imputation quality was not already implemented), a minor allele count (MAC) of < 20 using the effective sample size or the number of cases and adjusted for imputation quality where applicable, were set to missing. Variants were included for meta-analysis if they were present in at least 13 studies (those with European ancestry and at least 7 million markers passing all quality control filters).
