between groups. This testing could potentially be done simultaneously with frequency differences at other individual loci or among other collapsed sets using a summary distance-based Hotelling’s T-Squared statistic.28, 38 The CMC statistic has desirable properties in that it appropriately controls type I error rates even when non-functional variants are included in the set of variants to be tested, and has better power than the standard CAST method. In addition, the CMC statistic can be implemented in a regression modeling framework as discussed later.
