We present here the pre-planned principal analyses for this project. In order to advance knowledge of schizophrenia, a minority of samples were included in prior reports. Genotyping was conducted in six batches (denoted Sw1-Sw6) with total sample sizes of 464, 694, 1498, 2388, 4461, and 2345. Genotypes were generated as sufficient numbers of samples accumulated from the field work in Sweden. The 2009 International Schizophrenia Consortium report contained GWAS data from the Sw1-2 subjects (N=1158, 9.8% of the sample before quality control). 14. The 2011 PGC schizophrenia paper also contained GWAS data from the Sw1-2 subjects plus ∼80 SNPs from Sw3-4 in the replication phase. 17 The 2012 Bergen et al. paper had a particular focus contrasting schizophrenia with bipolar disorder and reported GWAS results from Sw1-4 (N=4044, 42.6% of the full sample). 75 Thus, of the total sample of 11,850 Swedish subjects before quality control (5,351 cases, 6,509 controls), 57.4% have never been reported previously.
