Table 1.
Clinical characteristics of the Vietnamese individuals included in leprosy per se, leprosy subtype polarization and type-1 reaction association analyses with HLA genes.
Table 2.
HLA alleles significantly associated with risk or protection from leprosy per se in Vietnam.
Fig 1.
HLA class I and class II alleles with study-wide significance for association with leprosy.
A schematic representation of the MHC/HLA region highlighting the genes sequenced in the present study is shown on top. The four-digit HLA alleles associated with risk and protection from leprosy per se are shown in orange and green, respectively. The HLA-DRB1 allele with suggestive significance captured by the alleles in signal #2 is indicated by a box with lighter color. Odds ratios (OR) and P-values presented in the boxes refer to the results of univariable association analyses under an additive model (Table 2 and S1 Table). HLA alleles that belong to the same association signal based on the forward and pairwise conditional analyses are connected by lines (S2 and S3 Tables). The signals indicated common haplotypes of the corresponding alleles (S1 Fig).
Fig 2.
Forward conditional analysis of HLA amino acids with study-wide significance for association with leprosy.
The figure presents the results for the genotypic association test under an additive model adjusted for gender and A) unconditioned for any marker (univariable analysis, S4 Table), B) conditioned on HLA-DRβ1 57D (forward step 1), C) conditioned on HLA-DRβ1 57D and HLA-DRβ1 13F (forward step 2) and D) conditioned on HLA-DRβ1 57D, HLA-DRβ1 13F and HLA-B 63E (forward step 3). A schematic representation of the MHC/HLA region highlighting the genes sequenced in the present study is shown on top. In the graphs, the y axes indicate the negative log10 of the P-value for association of amino acids with leprosy per se and the x axes correspond to the amino acid position in the mature HLA proteins. The results for each HLA gene are shown by column and the dots represent single amino acids. The HLA loci and amino acid markers are ordered based on their genomic positions. The red line corresponds to the significance P-value threshold for multiple-testing of amino acid markers (P = 2.81 × 10−4) in the univariable analysis (A) and the blue lines represent a Pconditional of 0.01 in the multivariable analyses (B-D). Dots shown in black reached the multiple testing P-value threshold in the univariable analysis while grey dots were not significant (A). Only amino acids significantly associated in the univariable step (A) were included in the multivariable analyses (B-D). The most significant association signal at each step is indicated by the name of the amino acid(s) shown in blue. Borderline-associated HLA-A 19K is presented in black in step (A). The locations of the markers used for stepwise conditioning are indicated by red arrows.
Table 3.
Comparison of HLA allele-based and HLA amino acid-based models using the Akaike Information Criterion (AIC).
Fig 3.
HLA-DRβ1 13F~ 57D~ HLA-B 63N/E haplotypes correlated with the associated HLA-DRB1 and HLA-B alleles.
A) Distribution of phased haplotypes of the risk amino acids HLA-DRβ1 13F and 57D among HLA-DRB1 alleles. The left column presents the 39 four-digit HLA-DRB1 alleles genotyped in the present Vietnamese sample. Rare (< 1%) and common (≥ 1%) alleles are indicated by r and c, respectively. The middle column presents the amino acid residues at HLA-DRβ1 positions 13 and 57 for each HLA allele. In the left and middle columns, the HLA alleles and amino acids with P < 0.01 are colored in orange or green if their presence corresponded to risk or protection from leprosy, respectively (S1 and S4 Tables). Markers with multiple-testing significance in the univariable analysis are indicated by a darker orange/green. In the right column, HLA alleles are grouped based on the haplotype of the presence/absence of HLA-DRβ1 13F and 57D. B) Contribution of the HLA-B 63N/E biallelic amino acid polymorphism to the association of HLA-DRβ1 13F present~ 57D present and HLA-DRβ1 13F absent ~ 57D absent with leprosy. The results of the four estimated phased haplotypes are presented by columns. Odds ratios (OR), 95% confidence intervals (95% CI) and P Chi-square were determined for the four haplotypes using the pool of remaining haplotypes as reference (44.7% in cases and 40.4% in controls), except haplotypes with missing data (0.7% in cases and 0.3% in controls). Four-digit HLA-B~ HLA-DRB1 haplotypes belonging to each group and presenting counts higher or equal to ten chromosomes in cases and/or controls are listed at the bottom. HLA alleles and single amino acids that as binary markers presented P < 0.01 in the genotypic univariable analysis are colored in red and green when associated with risk or protection from leprosy, respectively. Markers that reached the multiple-testing thresholds are indicated in bold (S1 and S4 Tables).