Pathway analyses can utilize raw genotype data for individual subjects [6, 12, 13] or a list of p-values relating genes or SNPs to a phenotype [14–16]. Pathway-based tools for raw genotypes do not effectively include covariates but can naturally correct for linkage disequilibrium (LD) through permutation. In contrast, p-value distributions are readily accessible via other researchers and can be generated with application of covariates, but require corrections for LD based on reference populations. Investigators should consider their resources and study goals when selecting the most appropriate genomic data source.
