We sequenced 1542 Caucasians from Scotland comprising 240 cases of SZ, 221 cases of BD, 192 cases of rMDD and, as controls, 889 members of the Lothian Birth Cohort 1936 (LBC1936), which have been extensively phenotyped.60 Each sample was sequenced to >80% coverage at a minimum of 30-fold read depth by long-range PCR and sequencing on either Illumina GAII or HiSeq 2000 sequencers. To ensure a robust data set, all variants within repetitive regions were removed. Final quality score thresholds for the data were derived from capillary sequence validation of 10% of the remaining variants. All variants with an MAF <1% were validated by ABI3730 sequencing. After quality control, there was no evidence for sequencing bias between cases and controls (Supplementary Figure S1). Allele frequencies from our sample showed strong concordance to those from the European subset of the 1000 Genomes Project61 (Supplementary Figure S2). We report 2718 SNPs in the 1542 samples analysed, 708 at ⩾1% and 2010 at <1% MAF (Supplementary Table S1). Only 1027 of the 2718 SNPs (38%) were previously reported in the European subset of the 1000 Genomes Project.61
