Confirmation of novel type 1 diabetes risk loci in families

Aims/hypothesis Over 50 regions of the genome have been associated with type 1 diabetes risk, mainly using large case/control collections. In a recent genome-wide association (GWA) study, 18 novel susceptibility loci were identified and replicated, including replication evidence from 2,319 families. Here, we, the Type 1Diabetes Genetics Consortium(T1DGC), aimed to exclude the possibility that any of the 18 loci were false-positives due to population stratification by significantly increasing the statistical power of our family study. Methods We genotyped the most disease-predicting singlenucleotide polymorphisms at the 18 susceptibility loci in 3,108 families and used existing genotype data for 2,319 families from the original study, providing 7,013 parent-child trios for analysis. We tested for association using the transmission disequilibrium test. Results Seventeen of the 18 susceptibility loci reached nominal levels of significance (p<0.05) in the expanded family collection, with 14q24.1 just falling short (p=0.055). When we allowed for multiple testing, ten of the 17 nominally significant loci reached the required level of significance (p< 2.8×10 ^-3). All susceptibility loci had consistent direction of effects with the original study. Conclusions/interpretation The results for the novel GWA study-identified loci are genuine and not due to population stratification. The next step, namely correlation of the most disease-associated genotypes with phenotypes, such as RNA and protein expression analyses for the candidate genes within or near each of the susceptibility regions, can now proceed.