Genetic variation in HLA-DR and HLA-DQ genes appears to be critical in expression of islet autoantibodies and progression/risk to type 1 diabetes, with contributions from other type 1 diabetes-associated genes (PTPN22, UBASH3A, IFIH1, INS, PTPN2)8–11; however, in these studies only a small subset of genetic variants (those most strongly associated with type 1 diabetes risk from case–control studies) have been examined, overlooking the vast majority of the human genome. This evidence concerns the gene PTPN22 and type 1 diabetes mellitus.