To examine if schizophrenia PRS was predictive of symptom and cognitive variables in chronic schizophrenia we first performed imputation on the genotyped data. Autosomes were imputed using 1000 Genomes Project Phase 3 data as the reference set. Imputation was done in following steps: (1) Applied strict quality filters using thresholds for hwe 1e-06 and removed individuals who had >2% missing data after which 721 subjects and 421,802 SNPs remained. (2) Pre-phased the filtered data in SHAPEIT software package by first checking for strand alignment issues, removing strand inconsistencies and then estimating haplotypes (Howie et al., 2012). (3) Conducted imputation in chunks of 5 million bases (Mb) using IMPUTE2 software package (Marchini and Howie, 2010). (4) Applied post imputation quality control filters (the same filters used in the Psychiatric Genomics Consortium analysis: maf 0.1 and info score cutoff of 0.9) to select the list of markers (Ripke et al., 2014).
