Haplotypes for LMP2 exon3-LMP7 exon2-LMP7 intron6- DRB1*03:01 Number of haplotypes observed Observed haplotype frequency Pab Expected haplotype frequency (Pa X Pb) D= (Pab - Pa X Pb) D’=D/ Pa (1-Pb) r2=D2/Pa X Pb r =√r2 For T1D patients  2N=398 GCG-DRB1*03:01 148 0.3718 0.2964 0.0754 0.2273 0.0192 0.1385 GCG-DRB1*07:01 21 0.0527 0.0474 0.0054 0.00932 0.00062 0.0248 ACT-DRB1*03:01 33 0.0829 0.0746 0.0083 0.0998 0.00093 0.0305 ACT-DRB1*07:01 14 0.0352 0.0119 0.0233 0.1594 0.0455 0.2134 GCT-DRB1*03:01 30 0.0754 0.0472 0.02818 0.5337 0.0168 0.1297 GCT-DRB1*07:01 3 0.00754 0.00754 0 0 0 0 For healthy controls 2N=700 GCG-DRB1*03:01 51 0.0728 0.04437 0.02843 0.06337 0.01822 0.1349 GCG-DRB1*07:01 61 0.0871 0.0838 0.00329 0.008 0.00013 0.0114 ACT-DRB1*03:01 9 0.01286 0.0117 0.00116 0.0098 0.00012 0.0107 ACT-DRB1*07:01 16 0.0229 0.0221 0.0008 0.0074 2.896E-05 0.00538 GCT-DRB1*03:01 18 0.0257 0.01467 0.01103 0.07436 0.00829 0.0911 GCT-DRB1*07:01 39 0.0557 0.0277 0.028 0.207 0.0284 0.1685
Pab = Observed haplotype frequency counted directly and divided by 2N and the resulting haplotype frequencies were used to calculate D, Pa = haplotype frequency (hf) of GCG, ACT or GCT, Pb = gene frequency of DRB1*03:01. Haplotype frequency of (Pa) GCG=0.628, ACT=0.158, GCT=0.1, gf (Pb) of DRB1*03:01=0.472, DRB1*07:01=0.0754 in T1D. In controls hf frequency of GCG=0.493, ACT=0.13, GCT=0.163, gf of DRB1*03:01=0.09, DRB1*07:01=0.17
Table 6: Linkage disequilibrium analysis for LMP2 exon3-LMP7 exon2-LMP7 intron6 haplotypes with predisposing and protective HLA alleles