An empirical evaluation of the common disease-common variant hypothesis

While genome-wide linkage studies have been successful in mapping variants underlying rare monogenic disorders, genome-wide association studies may be more appropriate for detecting common variants of modest effects that underlie common disorders. To this end, we were interested in determining whether genetic variants associated with a phenotype differed depending on whether they were within or outside of regions linked to the phenotype. In particular, we compared allele frequencies and effect sizes between associated single-nucleotide polymorphisms within and outside of linkage regions using the Genetic Analysis Workshop 15 Problem 1. We did not find any statistically significant differences between these two sets. However, our power calculations show that these results may be inconclusive.