Human Leukocyte Antigen Amino Acid Research Articles

Phenomic landscape and pharmacogenomic implications for HLA region in a Taiwan Han Chinese population

BackgroundThe human leukocyte antigen (HLA) genes, exhibiting significant genetic diversity, are associated with susceptibility to various clinical diseases and diverse in drug responses. High costs of HLA sequencing and the population-specific architecture of this genetic region necessitate the establishment of a population-specific HLA imputation reference panel. Moreover, there is a lack of understanding about the genetic and phenotypic landscape of HLA variations within the Taiwanese population.MethodsWe created models for a Taiwanese-specific HLA imputation reference panel. These models were trained with the array genotype data and HLA sequencing data from 845 Taiwanese subjects. HLA imputation was applied for 59,448 Taiwanese subjects to characterize the HLA allele and haplotype frequencies. Additionally, a phenome-wide association study (PheWAS) was conducted to identify the phenotypes associated with HLA variations. The association of the biallelic HLA variants with the binary and quantitative traits were evaluated with additive logistic and linear regression models, respectively. Furthermore, an omnibus test with likelihood-ratio test was applied for each HLA amino acid position in the multiallelic HLA amino acid polymorphisms to compare the difference between a fitted model and a null model following a χ2 distribution of n-1 degree of freedom at a position with n residues. Finally, we estimated the prevalence of adverse drug reactions (ADR)-related HLA alleles in the Taiwanese population.ResultsIn this study, the reference panel models displayed remarkable accuracy, with averages of 99.3%, 98.9%, and 99.1% for 2-, 4-, 6-digit alleles of the eight classical HLA genes, respectively. For PheWAS, a total of 18,136 significant associations with HLA variants across 26 phenotypes are identified (p < 5×10-8), highlighting the pleiotropy feature of the HLA region. Among the independent signals, 15 are novel, including the association of HLA-B pos 138 variation with ankylosing spondylitis (AS), and rs9266290 and rs9266292 with allergy. Through an analysis spanning the entire HLA region, we identified clusters of phenotype correlations. Finally, the carriers of pharmacogenomic related HLA alleles, including HLA-C*01:02 (35.86%), HLA-B*58:01 (20.9%), and HLA-B*15:02 (8.38%), were characterized in the Taiwanese general population.ConclusionsWe successfully delivered the HLA imputation for 59,448 Taiwanese subjects and characterized the genetic and phenotypic landscapes of the HLA variations. In addition, we quantified the estimated prevalence of the ADR-related HLA alleles in the Taiwanese population. The developed HLA imputation reference panel could be used for estimation of population HLA allele frequencies, which can facilitate further studies in the role of HLA variants in a wider range of phenotypes in the population.

Genome-Wide Association Study Identifies IFIH1 and HLA-DQB1*05:02 Loci Associated With Anti-NMDAR Encephalitis.

Anti-N-methyl-d-aspartate receptor (NMDAR) encephalitis is a rare autoimmune neurologic disorder, the genetic etiology of which remains poorly understood. Our study aims to investigate the genetic basis of this disease in the Chinese Han population. We performed a genome-wide association study and fine-mapping study within the major histocompatibility complex (MHC) region of 413 Chinese patients with anti-NMDAR encephalitis recruited from 6 large tertiary hospitals and 7,127 healthy controls. Our genome-wide association analysis identified a strong association at the IFIH1 locus on chromosome 2q24.2 (rs3747517, p = 1.06 × 10-8, OR = 1.55, 95% CI, 1.34-1.80), outside of the human leukocyte antigen (HLA) region. Furthermore, through a fine-mapping study of the MHC region, we discovered associations for 3 specific HLA class I and II alleles. Notably, HLA-DQB1*05:02 (p = 1.43 × 10-12; OR, 2.10; 95% CI 1.70-2.59) demonstrates the strongest association among classical HLA alleles, closely followed by HLA-A*11:01 (p = 4.36 × 10-7; OR, 1.52; 95% CI 1.29-1.79) and HLA-A*02:07 (p = 1.28 × 10-8; OR, 1.87; 95% CI 1.50-2.31). In addition, we uncovered 2 main HLA amino acid variation associated with anti-NMDAR encephalitis including HLA-DQβ1-126H (p = 1.43 × 10-12; OR, 2.10; 95% CI 1.70-2.59), exhibiting a predisposing effect, and HLA-B-97R (p = 3.40 × 10-8; OR, 0.63; 95% CI 0.53-0.74), conferring a protective effect. Computational docking analysis suggested a close relationship between the NR1 subunit of NMDAR and DQB1*05:02. Our findings indicate that genetic variation in IFIH1, involved in the type I interferon signaling pathway and innate immunity, along with variations in the HLA class I and class II genes, has substantial implications for the susceptibility to anti-NMDAR encephalitis in the Chinese Han population.

Association study of human leukocyte antigen variants and idiopathic pulmonary fibrosis.

Idiopathic pulmonary fibrosis (IPF) is a chronic interstitial pneumonia marked by progressive lung fibrosis and a poor prognosis. Recent studies have highlighted the potential role of infection in the pathogenesis of IPF, and a prior association of the HLA-DQB1 gene with idiopathic fibrotic interstitial pneumonia (including IPF) has been reported. Owing to the important role that the human leukocyte antigen (HLA) region plays in the immune response, here we evaluated if HLA genetic variation was associated specifically with IPF risk. We performed a meta-analysis of associations of the HLA region with IPF risk in individuals of European ancestry from seven independent case-control studies of IPF (comprising 5159 cases and 27 459 controls, including a prior study of fibrotic interstitial pneumonia). Single nucleotide polymorphisms, classical HLA alleles and amino acids were analysed and signals meeting a region-wide association threshold of p<4.5×10-4 and a posterior probability of replication >90% were considered significant. We sought to replicate the previously reported HLA-DQB1 association in the subset of studies independent of the original report. The meta-analysis of all seven studies identified four significant independent single nucleotide polymorphisms associated with IPF risk. However, none met the posterior probability for replication criterion. The HLA-DQB1 association was not replicated in the independent IPF studies. Variation in the HLA region was not consistently associated with risk in studies of IPF. However, this does not preclude the possibility that other genomic regions linked to the immune response may be involved in the aetiology of IPF.

Tutorial: a statistical genetics guide to identifying HLA alleles driving complex disease.

The human leukocyte antigen (HLA) locus is associated with more complex diseases than any other locus in the human genome. In many diseases, HLA explains more heritability than all other known loci combined. In silico HLA imputation methods enable rapid and accurate estimation of HLA alleles in the millions of individuals that are already genotyped on microarrays. HLA imputation has been used to define causal variation in autoimmune diseases, such as type I diabetes, and in human immunodeficiency virus infection control. However, there are few guidelines on performing HLA imputation, association testing, and fine mapping. Here, we present a comprehensive tutorial to impute HLA alleles from genotype data. We provide detailed guidance on performing standard quality control measures for input genotyping data and describe options to impute HLA alleles and amino acids either locally or using the web-based Michigan Imputation Server, which hosts a multi-ancestry HLA imputation reference panel. We also offer best practice recommendations to conduct association tests to define the alleles, amino acids, and haplotypes that affect human traits. Along with the pipeline, we provide a step-by-step online guide with scripts and available software ( https://github.com/immunogenomics/HLA_analyses_tutorial ). This tutorial will be broadly applicable to large-scale genotyping data and will contribute to defining the role of HLA in human diseases across global populations.

Association of Human Leukocyte Antigen Variants with Progression of Monoclonal Gammopathy of Undetermined Significance to Multiple Myeloma

Background: Multiple Myeloma (MM), a neoplasm of terminally differentiated plasma cells that produce a monoclonal immunoglobulin, represents 10% of hematologic malignancies. Virtually all MM arises from monoclonal gammopathy of undetermined significance (MGUS), an asymptomatic premalignant phase, at a rate of progression of about 1% annually. However, the risk of progression is not uniform as some individuals with MGUS could have progression rates as high as 58% in 20 years. Novel predictive markers are critically needed to accurately identify MGUS patients at high-risk of malignant transformation, so that early intervention can be implemented to prevent end-organ damage associated with frank myeloma. Genome-wide association studies (GWAS) have repeatedly identified loci at the major histocompatibility complex (MHC) that are associated with the risk of many cancers including MM. However, the impact of specific MHC loci on the MGUS-to-MM progression risk has not been elucidated. Methods: We used the Illumina Infinium Global Screening Array to scan the buffy coat samples of 259 MGUS and 654 MM patients enrolled from the Medical College of Wisconsin (MCW) Tissue Bank. All MGUS and MM patients have been chart reviewed and confirmed diagnosis. After a standard quality control (QC), 249 MGUS and 619 MM patients with 11,882 genotyped single nucleotide polymorphisms (SNPs) in the MHC region (20 to 40 mb at chromosome 6) were used for analysis. The SNP2HLA v1.0.3 software and HLA*IMP:03 were applied to impute classical human leukocyte antigen (HLA) alleles at a four-digit resolution based on SNP genotyping. SNP2HLA uses Beagle to impute all missing SNPs, classical HLA alleles, and amino acid polymorphisms to the HapMap reference panel. HLA*IMP:03 uses the Michigan Imputation Server to impute phased haplotypes to a multi-ethnic panel of 10,561 individuals with SNP genotype data and lab-based typing of alleles at 11 HLA genes. A post-imputation QC was conducted to remove variants with low imputation quality score (R2 < 0.3). Logistic regression analysis was performed using PLINK, a whole genome association analysis toolset, which adjusted for age, race, sex, and top principal components. Results: As evidenced by the quantile-quantile (QQ) plot (Figure 1), there was no evidence for hidden substructure or cryptic relatedness in the GWAS (λ=1.02). The final set of imputed variants from both tools used in association analysis were of high quality (R2 ≥0.9). Although we did not observe any HLA variants showing associations with the progression of MGUS to MM at Bonferroni adjusted significance level for SNP2HLA (P = 0.05/5865 = 8.53 × 10-6) and for HLA*IMP:03 (P = 0.05/215 = 2.33 × 10-4), we found 4 classical HLA alleles and 30 HLA Amino Acids were associated with MGUS progression at a P-value of < 0.05 via association analysis with SNP2HLA. Association analysis for HLA*IMP:03 imputation data identified 8 classical HLA alleles were associated with MGUS progression at P value < 0.05. Among them, two classical HLA alleles were identified in both tools, they are HLA_B*08:01 (odds ratio, OR=0.38, 95% confidence interval, CI =0.19-0.77 and OR=0.43, 95% CI=0.21-0.86 for SNP2HLA and HLA*IMP:03, respectively) and HLA_C*07:01 (OR=0.61, 95% CI=0.41-0.89 and OR=0.63, 95% CI=0.41-0.98 for SNP2HLA and HLA*IMP:03, respectively) (Table 1). Conclusions: These results implicate that HLA alleles may contribute to the progression of MGUS to MM. Further studies are needed to validate our findings with larger sample sizes and explore the biological mechanisms. Figure 1View largeDownload PPTFigure 1View largeDownload PPT Close modal

Human Leukocyte Antigen Fine-Mapping and Correlation Analysis of Han and Minority Leprosy Patients in Southern China.

Backround: Leprosy is very prevalent in many populations around the world, which is well known that both alleles for human leukocyte antigen (HLA) as well as single nucleotide polymorphisms (SNPs) in the HLA region are common in leprosy patients. Previous studies have identified leprosy-associated susceptibility genes that explain only part of disease risk and heritability. In view of the complicated characteristics of the major histocompatibility complex (MHC) region, this study aimed to explore the development and variation of HLA in leprosy and its possible mechanism. Methods: Previous genome-wide association data were extracted from Han and minority populations in southern China for HLA fine-mapping studies. Insertion and deletion (INDEL), SNP, and copy number variation (CNV) imputation were determined by using the Thousand People Database (1KGP Phase 3 Dataset) as a reference panel. The HAN-MHC database was used to input the HLA classical alleles and amino acids in the MHC region, and further step-regression analysis was performed to analyze independent variation signals associated with leprosy. Results: The most significant locus rs75324027 (the same locus as rs602875 in the HLA-DR region) [p = 7.49E-09, OR= 0.62, 95%,CI: 0.52–0.73] in the intergene region between HLA-DQA1 and HLA-DRB1 was related with leprosy in M-S(Han leprosy patients in south China)disease. In M-SM (Leprosy patients of ethnic minorities in south China)disease, one of the most significant loci of the HLA-DQB1 gene was 6-32626438-A-T (p = 4.49E-08, OR = 0.36, 95%,CI: 0.25–0.52). Therefore, rs75324027 is a locus in M-S disease, and 6-32626438-a-T may be a new locus in M-SM disease. The interaction between 6 and 32626438-A-T and RS75324027 was analyzed, and A significant interaction relationship was found. In the optimal model, the accuracy of prediction was 0.5974, cross-validation Consistency:10, p = 0.0107. Conclusion: In conclusion, this study is the first to assess the association between HLA and leprosy susceptibility in Han and other minority populations in southern China using the Thousand Population database and the Han MHC database. In addition, our analysis validated the previously reported locus rs602875 in the HLA-DR region and for the first time identified an unreported independent locus in leprosy among ethnic minorities in southern China.

O01 Genetic risk factors associated with increased risk of uveitis in patients with juvenile idiopathic arthritis

Abstract Background/Aims Juvenile idiopathic arthritis (JIA) is a childhood-onset rheumatic disease, which is associated with increased risk of uveitis. Approximately 80% of childhood chronic anterior uveitis cases are JIA-associated (JIAU), where it is considered a serious complication with the potential to lead to permanent blindness. Studies have reported associations of increased risk of JIAU to genetic variation within human leukocyte antigen (HLA) genes, in particular amino acid positions of HLA-DRB1. Here we report the results of the largest fine-mapping study of HLA genes in JIAU to date. Methods Genotyping was performed using Illumina Infinium CoreExome and Infinium OnmiExpress arrays. Samples were excluded with a call rate &amp;lt;0.98, discrepancy between genetically inferred sex and database records, inferred relatedness (Identity-by-decent), or ancestral outlier based on principal component analysis (PCA). SNPs were excluded with a call rate &amp;lt;0.98 or a minor allele frequency (MAF) &amp;lt;0.01. HLA alleles, amino acids, and SNPs were imputed using SNP2HLA. Analysis was performed on markers with an information score &amp;gt;0.9 and MAF &amp;gt; 0.01 using logistic regression, or omnibus test for multi-allelic markers, including 3 PCs as covariates. Independent effects were identified using forward stepwise logistic regression by inclusion of previously identified variants as covariates. Results We analysed 7,425 markers across the HLA region in 450 JIAU cases and 2,024 JIA cases. We defined study-wide significance at a Bonferroni corrected threshold of 6.7x10-6. The most significant association was at amino acid position 13 of DRB1 (p-value = 3.0x10-30) where the presence of serine (OR 1.7, 95% CI 1.4-1.9) or glycine (OR 2.0, 95% CI 1.6-2.5) were associated with increased risk of uveitis. Conditioning on DRB1 position 13, found a further association to amino acid position 67 of DRB1 (p-value = 2.4x10-6, unconditioned p-value = 3.2x10-23). The presence of isoleucine (OR 1.5, 95% CI 1.2-1.9) and phenylalanine (OR 1.8 95%, CI 1.4-2.2) at position 67 were associated with increased risk. No further study-wide associations were found at DRB1. Conditioning on all HLA-DRB1 alleles identified an independent effect at amino acid position 69 in DPB1 (p-value = 5.3x10-7, unconditioned p-value = 1.1x10-10). The presence of glutamic acid was associated with increased risk (OR 1.7, 95% CI 1.4-2.0). Conclusion This is the largest genetic study of HLA regions in JIAU and further resolves the genetic risk factors in this key susceptibility region. The analysis in this study has independently validated the association signal at position 13 of HLA-DRB1 (highly correlated with position 11) that had been reported in a previous study. Conditional analysis of HLA-DRB1 revealed a novel secondary association signal at DRB1 to amino acid position 67. Conditional analysis on all DRB1 alleles confirmed association to position 69 of HLA-DPB1 where previous reports of this signal had been only modestly associated. Disclosure M. Tordoff: None. S.L. Smith: None. E. Lopez-Isac: None. A. Morris: None. S. Eyre: None. W. Thomson: None. J. Bowes: None.

The spectrum of association in HLA region with rheumatoid arthritis in a diverse Asian population: evidence from the MyEIRA case-control study

BackgroundFine-mapping of human leukocyte antigen (HLA) region for rheumatoid arthritis (RA) risk factors has identified several HLA alleles and its corresponding amino acid residues as independent signals (i.e., HLA-A, HLA-B, HLA-DPB1, and HLA-DQA1 genes), in addition to the well-established genetic factor in HLA-DRB1 gene. However, this was mainly performed in the Caucasian and East Asian populations, and data from different Asian regions is less represented. We aimed to evaluate whether there are independent RA risk variants in both anti-citrullinated protein antibody (ACPA)-positive and ACPA-negative RA patients from the multi-ethnic Malaysian population, using the fine-mapping of HLA region strategy.MethodsWe imputed the classical HLA alleles, amino acids, and haplotypes using the Immunochip genotyping data of 1260 RA cases (i.e., 530 Malays, 259 Chinese, 412 Indians, and 59 mixed ethnicities) and 1571 controls (i.e., 981 Malays, 205 Chinese, 297 Indians, and 87 mixed ethnicities) from the Malaysian Epidemiological Investigation of Rheumatoid Arthritis (MyEIRA) population-based case-control study. Stepwise logistic regression was performed to identify the independent genetic risk factors for RA within the HLA region.ResultsWe confirmed that the HLA-DRB1 amino acid at position 11 with valine residue conferred the strongest risk effect for ACPA-positive RA (OR = 4.26, 95% CI = 3.30–5.49, PGWAS = 7.22 × 10−29) in the Malays. Our study also revealed that HLA-DRB1 amino acid at position 96 with histidine residue was negatively associated with the risk of developing ACPA-positive RA in the Indians (OR = 0.48, 95% CI = 0.37–0.62, PGWAS = 2.58 × 10−08). Interestingly, we observed that HLA-DQB1*03:02 allele was inversely related to the risk of developing ACPA-positive RA in the Malays (OR = 0.17, 95% CI = 0.09–0.30, PGWAS = 1.60 × 10−09). No association was observed between the HLA variants and risk of developing ACPA-negative RA in any of the three major ethnic groups in Malaysia.ConclusionsOur results demonstrate that the RA-associated genetic factors in the multi-ethnic Malaysian population are similar to those in the Caucasian population, despite significant differences in the genetic architecture of HLA region across populations. A novel and distinct independent association between the HLA-DQB1*03:02 allele and ACPA-positive RA was observed in the Malays. In common with the Caucasian population, there is little risk from HLA region for ACPA-negative RA.

Low Hydrophobic Mismatch Scores Calculated for HLA-A/B/DR/DQ Loci Improve Kidney Allograft Survival.

We evaluated the impact of human leukocyte antigen (HLA) disparity (immunogenicity; IM) on long-term kidney allograft survival. The IM was quantified based on physicochemical properties of the polymorphic linear donor/recipient HLA amino acids (the Cambridge algorithm) as a hydrophobic, electrostatic, amino acid mismatch scores (HMS\\AMS\\EMS) or eplet mismatch (EpMM) load. High-resolution HLA-A/B/DRB1/DQB1 types were imputed to calculate HMS for primary/re-transplant recipients of deceased donor transplants. The multiple Cox regression showed the association of HMS with graft survival and other confounders. The HMS integer 0–10 scale showed the most survival benefit between HMS 0 and 3. The Kaplan–Meier analysis showed that: the HMS=0 group had 18.1-year median graft survival, a 5-year benefit over HMS>0 group; HMS ≤ 3.0 had 16.7-year graft survival, a 3.8-year better than HMS>3.0 group; and, HMS ≤ 7.8 had 14.3-year grafts survival, a 1.8-year improvement over HMS>7.8 group. Stratification based on EMS, AMS or EpMM produced similar results. Additionally, the importance of HLA-DR with/without -DQ IM for graft survival was shown. In our simulation of 1,000 random donor/recipient pairs, 75% with HMS>3.0 were re-matched into HMS ≤ 3.0 and the remaining 25% into HMS≥7.8: after re-matching, the 13.5 years graft survival would increase to 16.3 years. This approach matches donors to recipients with low/medium IM donors thus preventing transplants with high IM donors.

Fine Mapping of the Major Histocompatibility Complex Region and Association of the HLA-B*52:01 Allele With Cervical Cancer in Japanese Women

Understanding the genetic contribution of the major histocompatibility complex (MHC) region to the risk of cervical cancer (CC) will help understand how immune responses to infection with human papillomaviruses are associated with CC. To determine whether the HLA-B*52:01 allele is associated with CC in Japanese women. This was a multicenter genetic association study. Genotype and phenotype data were obtained from BioBank Japan Project. Additional patients with CC were enrolled from the Aichi Cancer Center Research Institute. An MHC fine-mapping study was conducted on CC risk in the Japanese population by applying a human leukocyte antigen (HLA) imputation method to the large-scale CC genome-wide association study data of using the Japanese population-specific HLA reference panel. Participants included 540 women in BioBank Japan Project with CC or 39 829 women without gynecologic diseases, malignant neoplasms, and MHC-related diseases as controls. An additional 168 patients with CC were recruited from Aichi Cancer Center Research Institute. Histopathological subtypes and clinical stages were not considered. Participants with low genotype call rate, closely related participants, and outliers in the principal component analysis were excluded. Data analysis was performed from August 2018 to January 2020. Loci within the MHC region associated with CC risk, and the direction and size of association. A total of 704 CC cases and 39 556 controls were analyzed. All participants were Japanese women with a median (range) age of 67 (18 to 100) years. One of the class I HLA alleles of HLA-B*52:01 was significantly associated with CC risk (odds ratio, 1.60; 95% CI, 1.38-1.86; P = 7.4 × 10-10). Allele frequency spectra of HLA-B*52:01 are heterogeneous among worldwide populations with high frequency in Japanese populations (0.109 in controls), suggesting its population-specific risk associated with CC. The conditional analysis suggested that HLA-B*52:01 could explain most of the MHC risk associated with CC because no other HLA alleles remained significant after conditioning on the HLA-B*52:01. The HLA amino acid residue-based analysis suggested that HLA-B p.Tyr171His located in the peptide-binding groove was associated with the most significant CC risk (odds ratio, 1.47; 95% CI, 1.30-1.66; P = 1.2 × 10-9). The results of this study contribute to understanding of the genetic background of CC. The results suggest that immune responses mediated by class I HLA molecules are associated with susceptibility to CC.

994 Risk and association of HLA alleles with methimazole induced cutaneous adverse reactions in Chinese Han population

Background: Methimazole (MMI), a common prescribed medication for hyperthyroidism caused by Graves’ disease (GD), is a frequent cause of cutaneous adverse drug reactions (cADRs). Currently, no tests are available to predict the risk of the MMI induced cADRs. Identification of the susceptibility locus of MMI induced cADRs is important for clinical management. The aim of this study was to analyze the association of human leukocyte antigen (HLA) alleles with MMI induced cADRs in the Chinese, and evaluate their predictive ability and potential clinical implications. Methods: A total of 15 MMI induced cADRs patients were analyzed for HLA-A, -B, -C and -DRB1 alleles by using a polymerase chain reaction sequence-specific oligonucleotides method (PCR-SSO). General Chinese Han population and 48 MMI tolerant patients were typed as controls respectively. Risk alleles and amino acid residues were analyzed between cases and controls. Molecular docking was conducted to probe the direct interactions between the HLA proteins and MMI. Results: Among all tested HLA alleles, HLA-DRB1*04:03 was significantly enriched in MMI induced cADRs patients compared with population controls (corrected P = 8.0×10-8, OR = 23.63, 95%CI: 10.44-53.47). The frequency of HLA-DRB1*04:03 carriers was 53.3% (8/15) in MMI induced cADRs cases compared with none in 48 MMI tolerants (corrected P= 1.0× 10–5, OR = 109.93, 95%CI: 5.73-2108.85). The analysis of associations with HLA amino acid positions found that His42, Tyr66 and Val115 might be the risk amino acid residues for cADRs. Molecular dynamics simulations revealed these three residues located at the core binding site of HLA-A*04:03 with peptides. In contrast to other alleles, the binding site of MMI in HLA-DRB1*04:03 helix is less conflicted with peptide. Conclusions: HLA-DRB1*04:03 allele was strongly associated with MMI induced cADRs in Chinese and could be used as a valid pharmacogenetic marker for prediction of MMI induced cADRs.

Amino acid position 37 of HLA-DRβ1 affects susceptibility to Crohn's disease in Asians.

Crohn's disease (CD) and ulcerative colitis (UC) are the major types of chronic inflammatory bowel disease (IBD) characterized by recurring episodes of inflammation of the gastrointestinal tract. Although it is well established that human leukocyte antigen (HLA) is a major risk factor for IBD, it is yet to be determined which HLA alleles or amino acids drive the risks of CD and UC in Asians. To define the roles of HLA for IBD in Asians, we fine-mapped HLA in 12568 individuals from Korea and Japan (3294 patients with CD, 1522 patients with UC and 7752 controls). We identified that the amino acid position 37 of HLA-DRβ1 plays a key role in the susceptibility to CD (presence of serine being protective, P=3.6×10-67, OR=0.48 [0.45-0.52]). For UC, we confirmed the known association of the haplotype spanning HLA-C*12:02, HLA-B*52:01 and HLA-DRB1*1502 (P=1.2×10-28, OR=4.01 [3.14-5.12]).

OR13 Human leukocyte antigen analysis using high resolution SNP data: Imputation, association and amino acid binding pocket residues investigation in IgAD patients

Background Genetic variation at human leukocyte antigen (HLA) alleles influences many phenotypes and mediate susceptibility to a wide range of human diseases include Immunoglobulin A Deficiency (IgAD). The high resolution SNP genotyping has enabled large cohort studies in this complex region. Aim To Investigate the HLA association of IgAD using high resolution SNP data and to identify the combinations of biologically relevant amino acid (AA) residues directly involved in disease. Methods HLA imputation was performed in 1046 samples including 758 IgAD individual and 288 ethnically matched controls. The imputation results were further confirmed by high resolution typing. Subsequently, multiple tools include SKDM HLA tools, SNP2HLA and Plink were used to investigate the amino acid binding pocket association in IgAD cohorts. Finally, 3D visualization of the predicted HLA amino acid sequence was performed using RaptorX. Results Strong IgAD association were observed in HLA-B*0801 ( p = 5.364 ∗ 10 −14 ), HLA-B*1402 ( p = 0.0016), HLA-DRB1*0301 ( p = 3.276 ∗ 10 −12 ), HLA-DRB1*0102 ( p = 0.001 ∗ 10 −12 ), HLA-DRB1*1201 ( p = 1.684 ∗ 10 −4 ), HLA-DQB1*0201 ( p = 1.835 ∗ 10 −12 ). Conversely, HLA-B*1501 ( p = 1.358 ∗ 10 −5 ), HLA-B*0702 ( p = 5.662 ∗ 10 −7 ), HLA-DRB1*1501 ( p = 6.34 ∗ 10 −23 ), HLA-DQB1*0402 ( p = 0.004) and HLA-DQB1*0602 ( p = 9.396 ∗ 10 −23 ) showed strong protection against IgAD. In addition, most significant AA residues in different HLA region associated with IgAD are: HLA-B ((AA 9, Asp, pockets 2 and 3, p = 8.047 ∗ 10 −14 ); (AA 156, Asp, pockets 4 and 5, p = 4.396 ∗ 10 −13 )); HLA-DRB1 ((AA 26, Tyr, pocket 4, p = 8.249 ∗ 10 −10 ); (AA 67, Leu, pocket 7, p = 5.236 ∗ 10 −8 )); HLA-DQB1 ((AA 38, Val, pocket 9, p = 4.894 ∗ 10 −10 ); (AA 37, Ile, pocket 9, p = 8.216 ∗ 10 −9 ), (AA 28 Ser and AA 47 Phe, pocket 7, p = 8.216 ∗ 10 −9 ); (AA 30, Ser, pocket 6, p = 8.216 ∗ 10 −9 ); (AA 71, Lys, pockets 4 and 7, p = 8.216 ∗ 10 −9 )). Conclusion The results suggested that certain peptide-binding residues of the HLA class I and class II molecule is associated with susceptibility to IgAD.

Association of HLA Genotype and Fulminant Type 1 Diabetes in Koreans.

Fulminant type 1 diabetes (T1DM) is a distinct subtype of T1DM that is characterized by rapid onset hyperglycemia, ketoacidosis, absolute insulin deficiency, and near normal levels of glycated hemoglobin at initial presentation. Although it has been reported that class II human leukocyte antigen (HLA) genotype is associated with fulminant T1DM, the genetic predisposition is not fully understood. In this study we investigated the HLA genotype and haplotype in 11 Korean cases of fulminant T1DM using imputation of whole exome sequencing data and compared its frequencies with 413 participants of the Korean Reference Panel. The HLA-DRB1*04:05–HLA-DQB1*04:01 haplotype was significantly associated with increased risk of fulminant T1DM in Fisher's exact test (odds ratio [OR], 4.11; 95% confidence interval [CI], 1.56 to 10.86; p = 0.009). A histidine residue at HLA-DRβ1 position 13 was marginally associated with increased risk of fulminant T1DM (OR, 2.45; 95% CI ,1.01 to 5.94; p = 0.054). Although we had limited statistical power, we provide evidence that HLA haplotype and amino acid change can be a genetic risk factor of fulminant T1DM in Koreans. Further large-scale research is required to confirm these findings.

Construction and application of a Korean reference panel for imputing classical alleles and amino acids of human leukocyte antigen genes.

Genetic variations of human leukocyte antigen (HLA) genes within the major histocompatibility complex (MHC) locus are strongly associated with disease susceptibility and prognosis for many diseases, including many autoimmune diseases. In this study, we developed a Korean HLA reference panel for imputing classical alleles and amino acid residues of several HLA genes. An HLA reference panel has potential for use in identifying and fine-mapping disease associations with the MHC locus in East Asian populations, including Koreans. A total of 413 unrelated Korean subjects were analyzed for single nucleotide polymorphisms (SNPs) at the MHC locus and six HLA genes, including HLA-A, -B, -C, -DRB1, -DPB1, and -DQB1. The HLA reference panel was constructed by phasing the 5,858 MHC SNPs, 233 classical HLA alleles, and 1,387 amino acid residue markers from 1,025 amino acid positions as binary variables. The imputation accuracy of the HLA reference panel was assessed by measuring concordance rates between imputed and genotyped alleles of the HLA genes from a subset of the study subjects and East Asian HapMap individuals. Average concordance rates were 95.6% and 91.1% at 2-digit and 4-digit allele resolutions, respectively. The imputation accuracy was minimally affected by SNP density of a test dataset for imputation. In conclusion, the Korean HLA reference panel we developed was highly suitable for imputing HLA alleles and amino acids from MHC SNPs in East Asians, including Koreans.

Fine Mapping Seronegative and Seropositive Rheumatoid Arthritis to Shared and Distinct HLA Alleles by Adjusting for the Effects of Heterogeneity

Despite progress in defining human leukocyte antigen (HLA) alleles for anti-citrullinated-protein-autoantibody-positive (ACPA(+)) rheumatoid arthritis (RA), identifying HLA alleles for ACPA-negative (ACPA(-)) RA has been challenging because of clinical heterogeneity within clinical cohorts. We imputed 8,961 classical HLA alleles, amino acids, and SNPs from Immunochip data in a discovery set of 2,406 ACPA(-) RA case and 13,930 control individuals. We developed a statistical approach to identify and adjust for clinical heterogeneity within ACPA(-) RA and observed independent associations for serine and leucine at position 11 in HLA-DRβ1 (p = 1.4 × 10(-13), odds ratio [OR] = 1.30) and for aspartate at position 9 in HLA-B (p = 2.7 × 10(-12), OR = 1.39) within the peptide binding grooves. These amino acid positions induced associations at HLA-DRB1(∗)03 (encoding serine at 11) and HLA-B(∗)08 (encoding aspartate at 9). We validated these findings in an independent set of 427 ACPA(-) case subjects, carefully phenotyped with a highly sensitive ACPA assay, and 1,691 control subjects (HLA-DRβ1 Ser11+Leu11: p = 5.8 × 10(-4), OR = 1.28; HLA-B Asp9: p = 2.6 × 10(-3), OR = 1.34). Although both amino acid sites drove risk of ACPA(+) and ACPA(-) disease, the effects of individual residues at HLA-DRβ1 position 11 were distinct (p < 2.9 × 10(-107)). We also identified an association with ACPA(+) RA at HLA-A position 77 (p = 2.7 × 10(-8), OR = 0.85) in 7,279 ACPA(+) RA case and 15,870 control subjects. These results contribute to mounting evidence that ACPA(+) and ACPA(-) RA are genetically distinct and potentially have separate autoantigens contributing to pathogenesis. We expect that our approach might have broad applications in analyzing clinical conditions with heterogeneity at both major histocompatibility complex (MHC) and non-MHC regions.

MHC associations with clinical and autoantibody manifestations in European SLE

Systemic lupus erythematosus (SLE) is a clinically heterogeneous disease affecting multiple organ systems and characterized by autoantibody formation to nuclear components. Although genetic variation within the major histocompatibility complex (MHC) is associated with SLE, its role in the development of clinical manifestations and autoantibody production is not well defined. We conducted a meta-analysis of four independent European SLE case collections for associations between SLE sub-phenotypes and MHC single-nucleotide polymorphism genotypes, human leukocyte antigen (HLA) alleles and variant HLA amino acids. Of the 11 American College of Rheumatology criteria and 7 autoantibody sub-phenotypes examined, anti-Ro/SSA and anti-La/SSB antibody subsets exhibited the highest number and most statistically significant associations. HLA-DRB1*03:01 was significantly associated with both sub-phenotypes. We found evidence of associations independent of MHC class II variants in the anti-Ro subset alone. Conditional analyses showed that anti-Ro and anti-La subsets are independently associated with HLA-DRB1*0301, and that the HLA-DRB1*03:01 association with SLE is largely but not completely driven by the association of this allele with these sub-phenotypes. Our results provide strong evidence for a multilevel risk model for HLA-DRB1*03:01 in SLE, where the association with anti-Ro and anti-La antibody-positive SLE is much stronger than SLE without these autoantibodies.

Integrating peptides' sequence and energy of contact residues information improves prediction of peptide and HLA-I binding with unknown alleles

BackgroundThe HLA (human leukocyte antigen) class I is a kind of molecule encoded by a large family of genes and is characteristic of high polymorphism. Now the number of the registered HLA-I molecules has exceeded 3000. Slight differences in the amino acid sequences of HLAs would make them bind to different sets of peptides. In the past decades, although many methods have been proposed to predict the binding between peptides and HLA-I molecules and achieved good performance, most experimental data used by them is limited to the HLAs with a small number of alleles. Thus they are inclined to obtain high prediction accuracy only for data with similar alleles. Because the peptides and HLAs together determine the binding, it's necessary to consider their contribution meanwhile.ResultsBy taking into account the features of the peptides sequence and the energy of contact residues, in this paper a method based on the artificial neural network is proposed to predict the binding of peptides and HLA-I even when the HLAs' potential alleles are unknown. Two experiments in the allele-specific and super-type cases are performed respectively to validate our method. In the first case, we collect 14 HLA-A and 14 HLA-B molecules on Bjoern Peters dataset, and compare our method with the ARB, SMM, NetMHC and other 16 online methods. Our method gets the best average AUC (Area under the ROC) value as 0.909. In the second one, we use leave one out cross validation on MHC-peptide binding data that has different alleles but shares the common super-type. Compared to gold standard methods like NetMHC and NetMHCpan, our method again achieves the best average AUC value as 0.847.ConclusionsOur method achieves satisfactory results. Whenever it's tested on the HLA-I with single definite gene or with super-type gene locus, it gets better classification accuracy. Especially, when the training set is small, our method still works better than the other methods in the comparison. Therefore, we could make a conclusion that by combining the peptides' information, HLAs amino acid residues' interaction information and contact energy, our method really could improve prediction of the peptide HLA-I binding even when there aren't the prior experimental dataset for HLAs with various alleles.

Classical HLA-DRB1 and DPB1 alleles account for HLA associations with primary biliary cirrhosis

Susceptibility to primary biliary cirrhosis (PBC) is strongly associated with HLA region polymorphisms. To determine if associations can be explained by classical HLA determinants we studied Italian 676 cases and 1440 controls with genotyped with dense single nucleotide polymorphisms (SNPs) for which classical HLA alleles and amino acids were imputed. Although previous genome-wide association studies and our results show stronger SNP associations near DQB1, we demonstrate that the HLA signals can be attributed to classical DRB1 and DPB1 genes. Strong support for the predominant role of DRB1 is provided by our conditional analyses. We also demonstrate an independent association of DPB1. Specific HLA-DRB1 genes (*08, *11 and *14) account for most of the DRB1 association signal. Consistent with previous studies, DRB1*08 (p = 1.59 × 10−11) was the strongest predisposing allele where as DRB1*11 (p = 1.42 × 10−10) was protective. Additionally DRB1*14 and the DPB1 association (DPB1*03:01) (p = 9.18 × 10−7) were predisposing risk alleles. No signal was observed in the HLA class 1 or class 3 regions. These findings better define the association of PBC with HLA and specifically support the role of classical HLA-DRB1 and DPB1 genes and alleles in susceptibility to PBC.

Human leukocyte antigen Class II amino acid epitopes: susceptibility and progression markers for beryllium hypersensitivity.

Chronic beryllium disease (CBD) is a hypersensitivity granulomatosis characterized by beryllium hypersensitivity (BH) and mediated by CD4+ T cells. However, all individuals with BH may not develop CBD. To examine the role of the three different human leukocyte antigen (HLA) Class II isotypes in BH with (CBD) and without clinical disease (BHWCD), we performed DNA-based typing of HLA-DPB1, HLA-DQB1, and HLA-DRB1 loci on 55 subjects with BH (25 with established CBD and 30 with BHWCD), and compared this with the results for 82 beryllium-exposed workers with no evidence of BH. The allele distribution was utilized to identify candidate amino acid epitopes that differed between the study groups. HLA-DPB1-E69 was the most important marker for BH, and did not differentiate BHWCD from CBD. A significant association with CBD was observed with HLA-DQB1-G86 (p(corr) < 0.04), and HLA-DRB1-S11 was significantly increased in CBD as compared with BHWCD (p < 0.03). These observations suggest that HLA-DPB1-E69 is a marker for susceptibility to BH and not just a progression marker for CBD. In addition, HLA amino acid epitopes on HLA-DRB1 and -DQB1, in concert with or independently of HLA-DPB1-E69, may be associated with progression to CBD.