replaced them with N1*β subjects randomly chosen from the T2D population. Similarly, we analyzed T2D data, replacing N2*β T2D with T1D cases. For each of T1D and T2D, 100 alternate samples were created at each 10% increment of β. Association analyses were then run using the χ2 test in PLINK [25] on each alternate phenotype file. We took the −log (p-value) from each of the 100 association analyses at each β level, and then calculated the arithmetic mean of the −log (p-value). The scripts developed for the analyses presented in the study are available at the following URL: http://web.cs.dal.ca/~cullis/heterogeneity/.
