details of mgs subject recruitment and sample characteristics are provided in the online full methods ( section a1 ) . samples ( 5.3% ) were excluded for high missing data rates , outlier proportions of heterozygous genotypes , incorrect sex or genotypic relatedness to other subjects . snps ( 7% for african american , 25% for european - ancestry and 27% for combined analyses ) were excluded for minor allele frequencies less than 1% , high missing data rates , hardy - weinberg deviation ( controls ) , or excessive mendelian errors ( trios ) , discordant genotypes ( duplicate samples ) or large allele frequency differences among dna plates . principal component scores reflecting continental and within - europe ancestries of each subject were computed and outliers excluded . genomic control  values for autosomes after qc were 1.042 for african american and 1.087 for the larger european - ancestry and combined analyses . for mgs , association of single snps to schizophrenia was tested by logistic regression ( trend test ) using plink10 , separately for european - ancestry , african american and combined datasets , correcting for principal component scores that reflected geographical gradients or that differed between cases and controls , and for sex for chromosome x and pseudoautosomal snps . genotypic data were imputed for 192 regions surrounding the best findings , and for additional regions selected for meta - analysis.11 detailed results are available in supplementary datafiles 1 and 2 , and complete results from dbgap ( www.ncbi.nlm.nih.gov/sites/entrez?db=gap ) . meta - analysis of the mgs , isc and sgene datasets was carried out by combining p - values for all snps ( in the selected regions ) for which genotyped or imputed data were available for all datasets , with weights computed from case - control sample sizes .