Genotyping was conducted using the Human670-QuadCustom Illumina BeadChip at the Wellcome Trust Sanger Institute [36]. Quality control steps included removing SNPs with minor allele frequency (MAF) < 1%, genotyping success rate < 95%, or Hardy–Weinberg equilibrium P < 1 × 10−6, and removing individuals with genotyping success rate < 95%, a mismatch between phenotypical and genotypical gender, excess relatedness (outside known families) and heterozygosity outliers. Genotypes were imputed to the 1000 Genomes Phase 3 reference panel [44] using ShapeIT [45] for phasing and IMPUTE2 [46] for imputation, resulting in 13 688 418 autosomal SNPs for analyses. Prior analyses indicated a single dimension of ancestry in the sample [47]. Although a single dimension of ancestry does not preclude variation along this dimension, we note that fine-scale population substructure is less of an issue for common variants (versus rare variants), especially in the present sample, given the relatively longer LD blocks that make the Finnish population more homogeneous than other populations of mixed European ancestry.
