Genotype imputation was performed using the pre-phasing/imputation stepwise approach implemented in IMPUTE2 / SHAPEIT (chunk size of 3 Mb and default parameters). 91,92 The imputation reference set consisted of 2,186 phased haplotypes from the full 1000Genomes Project dataset (March 2012, 40,318,245 variants). Evaluation of λGC led to the removal of SNPs with control allele frequencies < 0.005 or > 0.995, imputation “info” values < 0.2, or that were genotyped only in the smallest sample set (Sw1). Given that male sex is a risk factor for schizophrenia, 93 chromosome X imputation was conducted for subjects passing QC for the autosomal analysis (excluding chrX SNPs with missingness ≥ 0.05 or HWE P < 10−6 in females). Imputation was performed separately for males and females, gene dosages tested for association under an additive logistic regression model using the same covariates as for the autosomal analysis. All genomic locations are given in NCBI build 37/UCSC hg19 coordinates.
