illustrates the location of rs2040410 (R2
*0301 = 0.872) (8
) and rs7454108 (R2
*0302 = 1.0) (8
) in relation to classical HLA genes. The rs2040410 A allele is associated with DRB1
*0301, and the rs7454108 C allele is associated with DQB1
*0302. We hypothesized that subjects with HLA genotype DR3/4-DQ8 would have the SNP genotype AG/CT. Of 6,641 T1DGC subjects, 5,019 (75.6%) had HLA genotyping and data for the SNPs of interest. Of the 1,191 subjects with DR3/4-DQ8, 1,121 (94.1%) had AG/CT and 52 (4.6%) had AA/CT. Of the 3,828 subjects that were not DR3/4-DQ8, only 12 (0.3%) had the genotype AG/CT and 1 (0.03%) had the genotype AA/CT. Using the two genotypes AG/CT and AA/CT as markers of the DR3/4-DQ8 genotype, we identified subjects with DR3/4-DQ8 with 98.5% sensitivity and 99.7% specificity (). Of the 13 false-positives, 4 (30.8%) were DRB1
*0301 and DQB1
*0302 but not DR4-DQ8 (Online Appendix [available at http://dx.doi.org/10.2337/db08-0605
Location of SNPs (♦) in relation to classical HLA loci (A) and HLA-DRB1 and -DQB1 loci (B). Numbers are distance in megabase (Mb) pairs from the telomere.
TABLE 2 Evaluation of rs2040410 and rs7454108 in subjects participating in the British Diabetic Association, Denmark, Human Biological Data Interchange, Poland, and U.K. T1DGC cohorts and in subjects in the DAISY population analyzed by restriction digest and (more ...)
In analysis of the British Diabetic Association cohort with DR3/4-DQ8, 87.4% (376 of 429) of subjects had the genotype AG/CT and 10.0% (43 of 429) had the genotype AA/CT, compared with 97.8% (745 of 762) and 1.18% (9 of 762), respectively, in the other cohorts (P < 0.0001). The unique frequency of the AA genotype of rs2040410 with the DR3/4-DQ8 genotype in this population suggests population differences within the U.K., as the U.K. cohort did not have increased frequency of the AA rs2040410 genotype.
Of the 2,162 parents in the T1DGC population, 200 were DR3/4-DQ8 and 97.0% (194 of 200) were AA/CT or AG/CT, while 99.7% (1,956 of 1,962) of subjects that were not DR3/4-DQ8 were not AA/CT or AG/CT. There were 2,283 probands in this population; 99.0% (901 of 910) of DR3/4-DQ8 probands were AA/CT or AG/CT, and 99.5% (1,366 of 1,373) of non–DR3/4-DQ8 probands were not AA/CT or AG/CT.
We evaluated 143 subjects in the DAISY study, 69 with DR3/4-DQ8. Subjects were chosen to represent a wide range of HLA genotypes, with a focus on DR3/4-DQ8 individuals (Online Appendix Table 2). All 69 subjects with DR3/4-DQ8 were AG/CT, and none of the subjects without DR3/4-DQ8 were AG/CT or AA/CT. Using the two genotypes AG/CT and AA/CT as markers of the DR3/4-DQ8 genotype, we identified subjects with DR3/4-DQ8 with 100% sensitivity and specificity ().
Overall, the sensitivity of the test was 98.57% and the specificity was 99.67% (). The rs2040410 A allele was present in 2,921 of the 3,018 (96.8%) individuals with DRB1*0301. The rs7454108 C allele was present in 3,315 of the 3,353 (98.9%) individuals with DQB1*0302.