scholarly journals HLA imputation and its application to genetic and molecular fine-mapping of the MHC region in autoimmune diseases

2021 ◽  
Author(s):  
Tatsuhiko Naito ◽  
Yukinori Okada
Keyword(s):  
Autoimmune Diseases ◽  
Fine Mapping ◽  
Disease Risk ◽  
Human Leukocyte ◽  
Nucleotide Polymorphisms ◽  
Imputation Methods ◽  
Leukocyte Antigen ◽  
Sequencing Technologies ◽  
Computational Performance ◽  
Causal Variants

AbstractVariations of human leukocyte antigen (HLA) genes in the major histocompatibility complex region (MHC) significantly affect the risk of various diseases, especially autoimmune diseases. Fine-mapping of causal variants in this region was challenging due to the difficulty in sequencing and its inapplicability to large cohorts. Thus, HLA imputation, a method to infer HLA types from regional single nucleotide polymorphisms, has been developed and has successfully contributed to MHC fine-mapping of various diseases. Different HLA imputation methods have been developed, each with its own advantages, and recent methods have been improved in terms of accuracy and computational performance. Additionally, advances in HLA reference panels by next-generation sequencing technologies have enabled higher resolution and a more reliable imputation, allowing a finer-grained evaluation of the association between sequence variations and disease risk. Risk-associated variants in the MHC region would affect disease susceptibility through complicated mechanisms including alterations in peripheral responses and central thymic selection of T cells. The cooperation of reliable HLA imputation methods, informative fine-mapping, and experimental validation of the functional significance of MHC variations would be essential for further understanding of the role of the MHC in the immunopathology of autoimmune diseases.

scholarly journals Shared HLA Class II in Six Autoimmune Diseases in Latin America: A Meta-Analysis

2012 ◽  
Vol 2012 ◽  
pp. 1-10 ◽  
Author(s):  
Paola Cruz-Tapias ◽  
Oscar M. Pérez-Fernández ◽  
Adriana Rojas-Villarraga ◽  
Alberto Rodríguez-Rodríguez ◽  
María-Teresa Arango ◽  
...  
Keyword(s):  
Risk Factor ◽  
Autoimmune Diseases ◽  
Lupus Erythematosus ◽  
Meta Analysis ◽  
Human Leukocyte ◽  
Class Ii ◽  
Hla Class Ii ◽  
Genetic Characteristics ◽  
Latin Americans ◽  
Leukocyte Antigen

The prevalence and genetic susceptibility of autoimmune diseases (ADs) may vary depending on latitudinal gradient and ethnicity. The aims of this study were to identify common human leukocyte antigen (HLA) class II alleles that contribute to susceptibility to six ADs in Latin Americans through a meta-analysis and to review additional clinical, immunological, and genetic characteristics of those ADs sharing HLA alleles. DRB1∗03:01 (OR: 4.04; 95%CI: 1.41–11.53) was found to be a risk factor for systemic lupus erythematosus (SLE), Sjögren's syndrome (SS), and type 1 diabetes mellitus (T1D). DRB1∗04:05 (OR: 4.64; 95%CI: 2.14–10.05) influences autoimmune hepatitis (AIH), rheumatoid arthritis (RA), and T1D; DRB1∗04:01 (OR: 3.86; 95%CI: 2.32–6.42) is a susceptibility factor for RA and T1D. Opposite associations were found between multiple sclerosis (MS) and T1D. DQB1∗06:02 and DRB1∗15 alleles were risk factors for MS but protective factors for T1D. Likewise, DQB1∗06:03 allele was a risk factor for AIH but a protective one for T1D. Several common autoantibodies and clinical associations as well as additional shared genes have been reported in these ADs, which are reviewed herein. These results indicate that in Latin Americans ADs share major loci and immune characteristics.

A Systematic Review and Meta-Analysis of HLA-Class-II Associations in Patients with IgG4 Autoimmunity

2021 ◽  
Author(s):  
Anja Panhuber ◽  
Giovanni Lamorte ◽  
Veronica Bruno ◽  
Hakan Cetin ◽  
Wolfgang Bauer ◽  
...  
Keyword(s):  
Systematic Review ◽  
Autoimmune Diseases ◽  
Genetic Risk ◽  
Meta Analysis ◽  
Human Leukocyte ◽  
Pemphigus Vulgaris ◽  
Case Control ◽  
Case Control Studies ◽  
Leukocyte Antigen ◽  
Susceptibility Factors

Abstract Autoimmune diseases caused by pathogenic IgG4 subclass autoantibodies (IgG4-AID) include diseases like MuSK myasthenia gravis, pemphigus vulgaris or thrombotic thrombocytopenic purpura. Their etiology is still unknown. Polymorphisms in the human leukocyte antigen (HLA) gene locus, particularly in HLA-DRB1, are known genetic susceptibility factors for autoimmune diseases. We hypothesized a similar role for HLA polymorphisms in IgG4-AID and conducted a systematic review and meta-analysis with case-control studies on IgG4-AID based on MOOSE/ HuGENet guidelines. Genotype (G) and allele (A) frequencies of HLA-DQB1*05 (G: OR 3.8; 95% CI 2.44-5.9; p < 0.00001; A: OR 2.54; 95% CI 1.82-3.55; p < 0.00001) and HLA-DRB1*14 (G: OR 4.31; 95% CI 2.82-6.59; p < 0.00001; A: OR 4.78; 95% CI 3.52-6.49; p < 0.00001) and the HLA-DRB1*14-DQB1*05 haplotype (OR 6.3; 95% CI 3.28-12.09; p < 0.00001 / OR 4.98; 95% CI 3.8-6.53; p < 0.00001) were increased while HLA-DRB1*13 (G: OR 0.48; 95% CI 0.34-0.68; p < 0.0001; A: OR 0.46; 95% CI 0.34-0.62; p < 0.00001) was decreased in IgG4-AID patients. In conclusion, the HLA-DQB1*05, HLA-DRB1*14 alleles and the HLA-DQB1*05-DRB1*14 haplotype could be genetic risk factors that predispose for the production of pathogenic IgG4 autoantibodies and the HLA-DRB1*13 allele may protect from IgG4 autoimmunity.

scholarly journals Combined genetic analysis of juvenile idiopathic arthritis clinical subtypes identifies novel risk loci, target genes and key regulatory mechanisms

2020 ◽  
pp. annrheumdis-2020-218481 ◽  
Author(s):  
Elena López-Isac ◽  
Samantha L Smith ◽  
Miranda C Marion ◽  
Abigail Wood ◽  
Marc Sudman ◽  
...  
Keyword(s):  
Juvenile Idiopathic Arthritis ◽  
Fine Mapping ◽  
Target Genes ◽  
Genome Wide Association Study ◽  
Disease Risk ◽  
Enrichment Analysis ◽  
Joint Analysis ◽  
Integrative Approach ◽  
Nucleotide Polymorphisms ◽  
A Genome

ObjectivesJuvenile idiopathic arthritis (JIA) is the most prevalent form of juvenile rheumatic disease. Our understanding of the genetic risk factors for this disease is limited due to low disease prevalence and extensive clinical heterogeneity. The objective of this research is to identify novel JIA susceptibility variants and link these variants to target genes, which is essential to facilitate the translation of genetic discoveries to clinical benefit.MethodsWe performed a genome-wide association study (GWAS) in 3305 patients and 9196 healthy controls, and used a Bayesian model selection approach to systematically investigate specificity and sharing of associated loci across JIA clinical subtypes. Suggestive signals were followed-up for meta-analysis with a previous GWAS (2751 cases/15 886 controls). We tested for enrichment of association signals in a broad range of functional annotations, and integrated statistical fine-mapping and experimental data to identify target genes.ResultsOur analysis provides evidence to support joint analysis of all JIA subtypes with the identification of five novel significant loci. Fine-mapping nominated causal single nucleotide polymorphisms with posterior inclusion probabilities ≥50% in five JIA loci. Enrichment analysis identified RELA and EBF1 as key transcription factors contributing to disease risk. Our integrative approach provided compelling evidence to prioritise target genes at six loci, highlighting mechanistic insights for the disease biology and IL6ST as a potential drug target.ConclusionsIn a large JIA GWAS, we identify five novel risk loci and describe potential function of JIA association signals that will be informative for future experimental works and therapeutic strategies.

scholarly journals HATK: HLA analysis toolkit

2020 ◽  
Author(s):  
Wanson Choi ◽  
Yang Luo ◽  
Soumya Raychaudhuri ◽  
Buhm Han
Keyword(s):  
Amino Acid ◽  
Fine Mapping ◽  
Disease Susceptibility ◽  
Human Leukocyte ◽  
Amino Acid Sequences ◽  
Hla Typing ◽  
Amino Acid Residues ◽  
Leukocyte Antigen ◽  
Mapping Analysis ◽  
Visualization Tools

Abstract Summary Fine-mapping human leukocyte antigen (HLA) genes involved in disease susceptibility to individual alleles or amino acid residues has been challenging. Using information regarding HLA alleles obtained from HLA typing, HLA imputation or HLA inference, our software expands the alleles to amino acid sequences using the most recent IMGT/HLA database and prepares a dataset suitable for fine-mapping analysis. Our software also provides useful functionalities, such as various association tests, visualization tools and nomenclature conversion. Availability and implementation https://github.com/WansonChoi/HATK.

Embryo Genome Profiling by Single-Cell Sequencing for Preimplantation Genetic Diagnosis in a β-Thalassemia Family

2015 ◽  
Vol 61 (4) ◽  
pp. 617-626 ◽  
Author(s):  
Yanwen Xu ◽  
Shengpei Chen ◽  
Xuyang Yin ◽  
Xiaoting Shen ◽  
Xiaoyu Pan ◽  
...  
Keyword(s):  
Single Cell ◽  
Preimplantation Genetic Diagnosis ◽  
Genetic Diagnosis ◽  
Human Leukocyte ◽  
Nucleotide Polymorphisms ◽  
Clinical Practices ◽  
Mendelian Disorder ◽  
Leukocyte Antigen ◽  
Single Cell Sequencing ◽  
Embryonic Genome

Abstract BACKGROUND The embryonic genome, including genotypes and haplotypes, contains all the information for preimplantation genetic diagnosis, representing great potential for mendelian disorder carriers to conceive healthy babies. METHODS We developed a strategy to obtain the full embryonic genome for a β-thalassemia–carrier couple to have a healthy second baby. We carried out sequencing for single blastomere cells and the family trio and further developed the analysis pipeline, including recovery of the missing alleles, removal of the majority of errors, and phasing of the embryonic genome. RESULTS The final accuracy for homozygous and heterozygous single-nucleotide polymorphisms reached 99.62% and 98.39%, respectively. The aneuploidies of embryos were detected as well. Based on the comprehensive embryonic genome, we effectively performed whole-genome mendelian disorder diagnosis and human leukocyte antigen matching tests. CONCLUSIONS This retrospective study in a β-thalassemia family demonstrates a method for embryo genome recovery through single-cell sequencing, which permits detection of genetic variations in preimplantation genetic diagnosis. It shows the potential of single-cell sequencing technology in preimplantation genetic diagnosis clinical practices.

scholarly journals Sharing information between related diseases using Bayesian joint fine mapping increases accuracy and identifies novel associations in six immune mediated diseases

2019 ◽  
Author(s):  
Jennifer L Asimit ◽  
Daniel B Rainbow ◽  
Mary D Fortune ◽  
Nastasiya F Grinberg ◽  
Linda S Wicker ◽  
...  
Keyword(s):  
Fine Mapping ◽  
Disease Risk ◽  
Computationally Efficient ◽  
Specific Expression ◽  
Immune Mediated ◽  
Allele Specific ◽  
Causal Variants ◽  
Molecular Phenotypes ◽  
Disease Analysis ◽  
Individual Disease

AbstractThousands of genetic variants have been associated with human disease risk, but linkage disequilibrium (LD) hinders fine-mapping the causal variants. We show that stepwise regression, and, to a lesser extent, stochastic search fine mapping can mis-identify as causal, SNPs which jointly tag distinct causal variants. Frequent sharing of causal variants between immune-mediated diseases (IMD) motivated us to develop a computationally efficient multinomial fine-mapping (MFM) approach that borrows information between diseases in a Bayesian framework. We show that MFM has greater accuracy than single disease analysis when shared causal variants exist, and negligible loss of precision otherwise. Applying MFM to data from six IMD revealed causal variants undetected in individual disease analysis, including in IL2RA where we confirm functional effects of multiple causal variants using allele-specific expression in sorted CD4+ T cells from genotype-selected individuals. MFM has the potential to increase fine-mapping resolution in related diseases enabling the identification of associated cellular and molecular phenotypes.

scholarly journals Unravelling the Roles Of susceptibility Loci for Autoimmune Diseases in the Post-GWAS Era

2018 ◽  
Author(s):  
Jody Ye ◽  
Kathleen Gillespie ◽  
Santiago Rodriguez
Keyword(s):  
Autoimmune Diseases ◽  
Disease Risk ◽  
Association Studies ◽  
Copy Number Variations ◽  
Genome Wide Association Studies ◽  
Nucleotide Polymorphisms ◽  
Susceptibility Loci ◽  
Single Nucleotide ◽  
Environmental Interactions ◽  
Genome Wide

Although genome-wide association studies (GWAS) have identified several hundred loci associated with autoimmune diseases, their mechanistic insights are still poorly understood. The human genome is more complex than common single nucleotide polymorphisms (SNPs) that are interrogated by GWAS arrays. Some structural variants such as insertions-deletions, copy number variations, and minisatellites that are not very well tagged by SNPs cannot be fully explored by GWAS. Therefore, it is possible that some of these loci may have large effects on autoimmune disease risk. In addition, other layers of regulations such as gene-gene interactions, epigenetic-determinants, gene and environmental interactions also contribute to the heritability of autoimmune diseases. This review focuses on discussing why studying these elements may allow us to gain a more comprehensive understanding of the aetiology of complex autoimmune traits.

scholarly journals Effective Detection of Human Leukocyte Antigen Risk Alleles in Celiac Disease Using Tag Single Nucleotide Polymorphisms

PLoS ONE ◽  
2008 ◽  
Vol 3 (5) ◽  
pp. e2270 ◽  
Author(s):  
Alienke J. Monsuur ◽  
Paul I. W. de Bakker ◽  
Alexandra Zhernakova ◽  
Dalila Pinto ◽  
Willem Verduijn ◽  
...  
Keyword(s):  
Celiac Disease ◽  
Single Nucleotide Polymorphisms ◽  
Human Leukocyte Antigen ◽  
Human Leukocyte ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Leukocyte Antigen ◽  
Risk Alleles

scholarly journals Donor human leukocyte antigen-G single nucleotide polymorphisms are associated with post-lung transplant mortality

2019 ◽  
Vol 54 (2) ◽  
pp. 1802126 ◽  
Author(s):  
Julieta Lazarte ◽  
Jin Ma ◽  
Tereza Martinu ◽  
Liran Levy ◽  
William Klement ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
Lung Transplantation ◽  
Human Leukocyte Antigen ◽  
Mortality Risk ◽  
Lung Transplant ◽  
Multivariable Analysis ◽  
Human Leukocyte ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Leukocyte Antigen

Human leukocyte antigen (HLA)-G is a non-classical HLA that inhibits immune responses. Its expression is modified by single nucleotide polymorphisms (SNPs), which are associated with transplant outcomes. Our aim was to investigate the association of donor and recipient HLA-G SNPs with chronic lung allograft dysfunction (CLAD) and mortality after lung transplantation.In this single-centre study, we examined 11 HLA-G SNPs in 345 consecutive recipients and 297 donors of a first bilateral lung transplant. A multivariable Cox proportional hazards model assessed associations of SNPs with death and CLAD. Transbronchial biopsies (TBBx) and bronchoalveolar lavage (BAL) samples were examined using quantitative PCR, ELISA and immunofluorescence.Over a median of 4.75 years, 142 patients (41%) developed CLAD; 170 (49%) died. Multivariable analysis revealed donor SNP +3142 (GG+CG versus CC) was associated with increased mortality (hazard ratio 1.78, 95% CI 1.12–2.84; p=0.015). In contrast, five donor SNPs, -201(CC), -716(TT), -56(CC), G*01:03(AA) and 14 bp INDEL, conferred reduced mortality risk. Specific donor–recipient SNP pairings reduced CLAD risk. Predominantly epithelial HLA-G expression was observed on TBBx without rejection. Soluble HLA-G was present in higher concentrations in the BAL samples of patients who later developed CLAD.Specific donor SNPs were associated with mortality risk after lung transplantation, while certain donor–recipient SNP pairings modulated CLAD risk. TBBx demonstrated predominantly epithelial, and therefore presumably donor-derived, HLA-G expression in keeping with these observations. This study is the first to demonstrate an effect of donor HLA-G SNPs on lung transplantation outcome.

scholarly journals HLA Immune Function Genes in Autism

2012 ◽  
Vol 2012 ◽  
pp. 1-13 ◽  
Author(s):  
Anthony R. Torres ◽  
Jonna B. Westover ◽  
Allen J. Rosenspire
Keyword(s):  
Immune Responses ◽  
Autoimmune Diseases ◽  
Human Leukocyte ◽  
Chromosome 6 ◽  
Genetic Studies ◽  
Leukocyte Antigen ◽  
Adaptive Immune ◽  
Hla Genes ◽  
Genetic Complexity ◽  
Antigen Presenting

The human leukocyte antigen (HLA) genes on chromosome 6 are instrumental in many innate and adaptive immune responses. The HLA genes/haplotypes can also be involved in immune dysfunction and autoimmune diseases. It is now becoming apparent that many of the non-antigen-presenting HLA genes make significant contributions to autoimmune diseases. Interestingly, it has been reported that autism subjects often have associations with HLA genes/haplotypes, suggesting an underlying dysregulation of the immune system mediated by HLA genes. Genetic studies have only succeeded in identifying autism-causing genes in a small number of subjects suggesting that the genome has not been adequately interrogated. Close examination of the HLA region in autism has been relatively ignored, largely due to extraordinary genetic complexity. It is our proposition that genetic polymorphisms in the HLA region, especially in the non-antigen-presenting regions, may be important in the etiology of autism in certain subjects.

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