Assessing similarity of DNA profiles

Abstract

The genetic similarity of strains of a pathogen can be assessed by using a matrix of dissimilarities that is derived from bands in their DNA profile which are present or absent. The dependence between elements of the dissimilarity matrix, if not accounted for, results in underestimation of the variance in comparisons between groups of strains which are differentiated according to the possession of an attribute. We examine a previously proposed statistic for determining whether a group of strains is more similar than expected. We show the limitations of this statistic and propose a new statistic which better addresses the hypotheses that are usually considered in this field of study. The stat..