Table 4

Haplotypic association results with selected AAs from both α-chain and β-chain

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  • Estimated haplotype frequency (%) (out of 636 control subjects and 962 patients), estimated ORs, haplotype score, and P values from association analysis with T1D (in case-control study), with GADA level among patients, and with IA-2A level among patients. For given haplotypes, one or more DQA1-DQB1 haplotypes may be merged into haplotype groups. Estimated haplotype frequencies (%) among those with positive autoantibody, estimated ORs, z scores, and P value are listed: A) three motifs with effectively two AAs (α44, β57) among carriers of DQ8/9 haplotypes, B) three motifs with effectively two AAs (α44, β135) among carriers of DQ2, and C) six motifs with three AAs (α44, β57, β135) among carriers of DQ8/9 or DQ2. AAs (α44, α22, α23, α49, α51, α53, α54, α73, α184) in DQ8/9 mixture are in complete LD and can be represented by α44, and AAs (α22, α49, α51) are in complete LD in DQ2 mixture, and their polymorphisms are captured by α44. Further, (β135, α31, α37, α47, α48, α50, α72, α104, α153, α158, α160, α172, α212) are in complete LD with each other and thus represented by β135. Hence, three AAs (α44, β57, β135) capture all polymorphisms of their motifs in both DQ2 and DQ8/9 mixtures. Haplotype groups include haplotypes that share the same DQ motifs. DQ2.5 refers to DQA1*05:01-DQB1*02:01 (blue), and DQ8.1 includes either DQA1*03:01-DQB1*03:02 or DQA1*03:02-DQB1*03:02 (red). Risk and protective haplotypes are highlighted green and red, respectively, at the significance level of 5%. pos, positive.