Subjects were recruited for 15 different studies belonging to the Gene Environment Association Studies (GENEVA) consortium16 (Table 1). Each study was approved by the institutional review board of the study investigator’s institution, and all subjects provided written informed consent for participation in the study. The Supplementary Note describes the phenotypes. Each study was genotyped on one of five different Illumina array types at the Center for Inherited Disease Research (CIDR), the Broad Institute Center for Genotyping and Analysis, or the University of Southern California (Supplementary Table 1). DNA samples were derived from blood (92%) or saliva/buccal swabs (8%). No lymphoblastoid cell line or whole-genome amplified samples were included in the analyses described here. Because cell lines may have artifactual mosaic anomalies47, mis-identification of DNA source is a concern. However, only the Addiction study had both cell line and non-cell line samples and the non-cell line samples analyzed here did not have an unusual frequency of mosaic anomalies. Genotypic data cleaning and calculation of BAF and LRR are described in the Supplementary Note. Sample sizes for analyses vary (as stated in Results) because a small proportion of the subjects are missing data for age at DNA sampling or other variables.
