We analyzed genome-wide data in 5,001 schizophrenia cases and 6,243 controls from a population-based sampling frame in Sweden (N=11,244, Table 1). Most subjects (57.4%) have never been previously reported. Following genotyping and imputation with the 1000 Genomes Project Phase 1 reference panel, the genetic data consisted of allelic dosages for 9,871,789 high-quality polymorphic SNPs. Given that this imputation panel is based on >800 chromosomes of European ancestry and includes the detail afforded by genome sequencing, we anticipated increased power in finding and describing association signals. Indeed, we observed 10,201 SNPs and 187 genomic regions with P < 1×10−5 using 1000 Genomes imputation compared with 1,594 SNPs and 133 regions for HapMap3 imputation (counts include only one region from the MHC).
