A list of candidate genes for a particular disease can be gleaned from published association studies, gene expression studies, disease pathways and the specific interests of an investigator. Such lists may be very large, so we first filter the list against GWAS results as shown in Figure 1. We use SNPs that have genotype data in dbSNP as our source of SNPs in and near a gene (for a user-specified flanking region around the gene). We keep a gene if it has at least one small P-value SNP (less than or equal to a user-specified threshold, T1) in the GWAS. We also keep genes that were not adequately represented by SNPs in the GWAS panel. The percent of common SNPs (within a gene and flanking region) in high LD (pairwise r2 ≥ a user-specified threshold) with any GWAS SNP (including GWAS SNPs outside the gene and flanking region) is calculated and genes with coverage less than a user-specified cutoff A% are retained. Genes that do not have SNPs with small P-value but do have sufficient coverage by GWAS SNPs are excluded from further analysis.
