GWAS and CNV studies capture only a proportion of genetic variation and do not allow for the effects of unmeasured genetic and environmental risk factors. In the future, the next generation of sequencing studies will go some way toward addressing some of these gaps. The pathway analysis using ALIGATOR relies on Gene Ontology, the Kyoto Encyclopedia of Genes and Genomes pathways, Mouse Genome Informatics, and PANTHER-defined functional categories (28). The ability to detect enriched pathways will depend on how well and how accurately biological processes are defined, and again, this knowledge will evolve over time.
