In summary, we have developed a new SNP-based method, called SNP Set Enrichment Analysis (SSEA), for pathway analysis of GWAS data. SSEA selects a multiple and varying number of SNPs to represent each gene using an adaptive truncated product statistic. The selected SNPs are then ranked and enrichment of pathways is tested using a weighted Kolmogorov-Smirnov test. We tested SSEA in two genetically distinct GWAS studies of schizophrenia with large samples, and discovered 22 significant pathways in the European-American sample and 11 significant pathways in the African-American sample. Eight important pathways were found in both distinct samples providing support for our method.
