The lack of specific hypotheses in traditional genome-wide association studies has a disadvantage - it greatly limits the statistical power, ensuring that only the strongest signals can be detected, even with very large numbers of subjects.
Gene set hypothesis testing (GSHT) enables investigators to take a biological hypothesis and test it using GWAS data. For example, in our paper, we tested the hypothesis that failure to downregulate inflammatory signals during macrophage maturation is a key mechanism in the pathogenesis of Crohn's disease. We defined search criteria to find inflammatory genes that are downregulated during macrophage differentiation, and then empirically tested the hypothesis that these genes are likely to be associated with Crohn's disease.Baillie, J. K. et al. PLOS Genetics 13, e1006641 (Mar. 6, 2017).
We are very grateful to recieve funding from the following sources: Wellcome Trust, BBSRC, Intensive Care Society, MRC, NIH.