For OZ-ALC, most subjects (N=4601) were genotyped on the Illumina CNV370-Quadv3 (Illumina); genotyping on a small number of additional individuals was conducted on the Illumina 317 K (N=20) and 610 Quad v1 (N=517) platforms; data are available at dbGaP phs000181 (see the study by Medland et al.,26 for additional details). To account for the lower density of genotyped SNPs and variation in platform contents, imputation to HapMap (http://hapmap.ncbi.nlm.nih.gov) CEU I+II data (release 22, build 36) was conducted in MACH27 and best guess genotypes were selected based on Rsq⩾0.3 and imputation quality⩾0.9, resulting in 112 594 autosomal SNPs. Nuanced admixture was determined using EIGENSTRAT25 and outliers were removed, as outlined in the study by Heath et al.18
