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Robinson J, Barker DJ, Marsh SGE. 25 years of the IPD-IMGT/HLA Database. HLA 2024; 103:e15549. [PMID: 38936817 DOI: 10.1111/tan.15549] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2024] [Revised: 05/03/2024] [Accepted: 05/16/2024] [Indexed: 06/29/2024]
Abstract
Twenty-five years ago, in 1998, the HLA Informatics Group of the Anthony Nolan Research Institute released the IMGT/HLA Database. Since this time, this online resource has acted as the repository for the numerous variant sequences of HLA alleles named by the WHO Nomenclature Committee for Factors of the HLA System. The IPD-IMGT/HLA Database has provided a stable, highly accessible, user-friendly repository for this work. During this time, the technology underlying HLA typing has undergone significant changes. Next generation sequencing (NGS) has superseded previous methodologies of HLA typing and can generate large amounts of high-resolution sequencing data. This has resulted in a drastic increase in the number and complexity of sequences submitted to the database. The challenge for the IPD-IMGT/HLA Database has been to maintain the highest standards of curation, while supporting the core set of tools and functionality to our users with increased numbers of submissions and sequences. Traditional methods of accessing and presenting data have been challenged and new methods utilising new computing technologies have had to be developed to keep pace and support a shifting user demographic.
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Affiliation(s)
- James Robinson
- Anthony Nolan Research Institute, Royal Free Hospital, London, UK
- UCL Cancer Institute, University College London (UCL), London, UK
| | - Dominic J Barker
- Anthony Nolan Research Institute, Royal Free Hospital, London, UK
- UCL Cancer Institute, University College London (UCL), London, UK
| | - Steven G E Marsh
- Anthony Nolan Research Institute, Royal Free Hospital, London, UK
- UCL Cancer Institute, University College London (UCL), London, UK
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Barker DJ, Maccari G, Georgiou X, Cooper MA, Flicek P, Robinson J, Marsh SGE. The IPD-IMGT/HLA Database. Nucleic Acids Res 2022; 51:D1053-D1060. [PMID: 36350643 PMCID: PMC9825470 DOI: 10.1093/nar/gkac1011] [Citation(s) in RCA: 904] [Impact Index Per Article: 301.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 10/14/2022] [Accepted: 10/21/2022] [Indexed: 11/10/2022] Open
Abstract
It is 24 years since the IPD-IMGT/HLA Database, http://www.ebi.ac.uk/ipd/imgt/hla/, was first released, providing the HLA community with a searchable repository of highly curated HLA sequences. The database now contains over 35 000 alleles of the human Major Histocompatibility Complex (MHC) named by the WHO Nomenclature Committee for Factors of the HLA System. This complex contains the most polymorphic genes in the human genome and is now considered hyperpolymorphic. The IPD-IMGT/HLA Database provides a stable and user-friendly repository for this information. Uptake of Next Generation Sequencing technology in recent years has driven an increase in the number of alleles and the length of sequences submitted. As the size of the database has grown the traditional methods of accessing and presenting this data have been challenged, in response, we have developed a suite of tools providing an enhanced user experience to our traditional web-based users while creating new programmatic access for our bioinformatics user base. This suite of tools is powered by the IPD-API, an Application Programming Interface (API), providing scalable and flexible access to the database. The IPD-API provides a stable platform for our future development allowing us to meet the future challenges of the HLA field and needs of the community.
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Affiliation(s)
- Dominic J Barker
- Anthony Nolan Research Institute, Royal Free Hospital, Pond Street, London, NW3 2QG, UK,UCL Cancer Institute, University College London (UCL), Royal Free Campus, Pond Street, London, NW3 2QG, UK
| | - Giuseppe Maccari
- Data Science for Health (DaScH) Lab, Fondazione Toscana Life Sciences, Siena, Italy
| | - Xenia Georgiou
- Anthony Nolan Research Institute, Royal Free Hospital, Pond Street, London, NW3 2QG, UK
| | - Michael A Cooper
- Anthony Nolan Research Institute, Royal Free Hospital, Pond Street, London, NW3 2QG, UK
| | - Paul Flicek
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - James Robinson
- To whom correspondence should be addressed. Tel: +44 20 7284 8307;
| | - Steven G E Marsh
- Correspondence may also be addressed to Steven G.E. Marsh. Tel: +44 20 7284 8321;
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Autoimmune Diseases of Digestive Organs-A Multidisciplinary Challenge: A Focus on Hepatopancreatobiliary Manifestation. J Clin Med 2021; 10:jcm10245796. [PMID: 34945093 PMCID: PMC8705412 DOI: 10.3390/jcm10245796] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 12/04/2021] [Accepted: 12/07/2021] [Indexed: 12/11/2022] Open
Abstract
It is well known that some pathological conditions, especially of autoimmune etiology, are associated with the HLA (human leukocyte antigen) phenotype. Among these diseases, we include celiac disease, inflammatory bowel disease, autoimmune enteropathy, autoimmune hepatitis, primary sclerosing cholangitis and primary biliary cholangitis. Immunoglobulin G4-related diseases (IgG4-related diseases) constitute a second group of autoimmune gastrointestinal, hepatobiliary and pancreatic illnesses. IgG4-related diseases are systemic and rare autoimmune illnesses. They often are connected with chronic inflammation and fibrotic reaction that can occur in any organ of the body. The most typical feature of these diseases is a mononuclear infiltrate with IgG4-positive plasma cells and self-sustaining inflammatory response. In this review, we focus especially upon the hepatopancreatobiliary system, autoimmune pancreatitis and IgG4-related sclerosing cholangitis. The cooperation of the gastroenterologist, radiologist, surgeon and histopathologist is crucial for establishing correct diagnoses and appropriate treatment, especially in IgG4 hepatopancreatobiliary diseases.
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Robinson J, Barker DJ, Georgiou X, Cooper MA, Flicek P, Marsh SGE. IPD-IMGT/HLA Database. Nucleic Acids Res 2020; 48:D948-D955. [PMID: 31667505 PMCID: PMC7145640 DOI: 10.1093/nar/gkz950] [Citation(s) in RCA: 331] [Impact Index Per Article: 66.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Revised: 10/03/2019] [Accepted: 10/29/2019] [Indexed: 11/14/2022] Open
Abstract
The IPD-IMGT/HLA Database, http://www.ebi.ac.uk/ipd/imgt/hla/, currently contains over 25 000 allele sequence for 45 genes, which are located within the Major Histocompatibility Complex (MHC) of the human genome. This region is the most polymorphic region of the human genome, and the levels of polymorphism seen exceed most other genes. Some of the genes have several thousand variants and are now termed hyperpolymorphic, rather than just simply polymorphic. The IPD-IMGT/HLA Database has provided a stable, highly accessible, user-friendly repository for this information, providing the scientific and medical community access to the many variant sequences of this gene system, that are critical for the successful outcome of transplantation. The number of currently known variants, and dramatic increase in the number of new variants being identified has necessitated a dedicated resource with custom tools for curation and publication. The challenge for the database is to continue to provide a highly curated database of sequence variants, while supporting the increased number of submissions and complexity of sequences. In order to do this, traditional methods of accessing and presenting data will be challenged, and new methods will need to be utilized to keep pace with new discoveries.
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Affiliation(s)
- James Robinson
- Anthony Nolan Research Institute, London, UK
- UCL Cancer Institute, University College London (UCL), London, UK
| | | | | | | | - Paul Flicek
- European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridge, UK
| | - Steven G E Marsh
- Anthony Nolan Research Institute, London, UK
- UCL Cancer Institute, University College London (UCL), London, UK
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Chang CJ, Osoegawa K, Milius RP, Maiers M, Xiao W, Fernandez-Viňa M, Mack SJ. Collection and storage of HLA NGS genotyping data for the 17th International HLA and Immunogenetics Workshop. Hum Immunol 2018; 79:77-86. [PMID: 29247682 PMCID: PMC5805642 DOI: 10.1016/j.humimm.2017.12.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Revised: 11/12/2017] [Accepted: 12/08/2017] [Indexed: 01/06/2023]
Abstract
For over 50 years, the International HLA and Immunogenetics Workshops (IHIW) have advanced the fields of histocompatibility and immunogenetics (H&I) via community sharing of technology, experience and reagents, and the establishment of ongoing collaborative projects. Held in the fall of 2017, the 17th IHIW focused on the application of next generation sequencing (NGS) technologies for clinical and research goals in the H&I fields. NGS technologies have the potential to allow dramatic insights and advances in these fields, but the scope and sheer quantity of data associated with NGS raise challenges for their analysis, collection, exchange and storage. The 17th IHIW adopted a centralized approach to these issues, and we developed the tools, services and systems to create an effective system for capturing and managing these NGS data. We worked with NGS platform and software developers to define a set of distinct but equivalent NGS typing reports that record NGS data in a uniform fashion. The 17th IHIW database applied our standards, tools and services to collect, validate and store those structured, multi-platform data in an automated fashion. We have created community resources to enable exploration of the vast store of curated sequence and allele-name data in the IPD-IMGT/HLA Database, with the goal of creating a long-term community resource that integrates these curated data with new NGS sequence and polymorphism data, for advanced analyses and applications.
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Affiliation(s)
| | - Kazutoyo Osoegawa
- Histocompatibility, Immunogenetics & Disease Profiling Laboratory, Stanford Blood Center, Palo Alto, CA, USA
| | - Robert P Milius
- Bioinformatics Research, National Marrow Donor Program, Minneapolis, MN, USA
| | - Martin Maiers
- Bioinformatics Research, National Marrow Donor Program, Minneapolis, MN, USA
| | - Wenzhong Xiao
- Stanford Genome Technology Center, Palo Alto, CA, USA; Massachusetts General Hospital and Shriners Hospital for Children, Boston, MA, USA
| | - Marcelo Fernandez-Viňa
- Histocompatibility, Immunogenetics & Disease Profiling Laboratory, Stanford Blood Center, Palo Alto, CA, USA; Department of Pathology, Stanford University Medical Center, Stanford, CA, USA
| | - Steven J Mack
- Center for Genetics, Children's Hospital Oakland Research Institute, Oakland, CA, USA.
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Siebert N, Jensen C, Troschke-Meurer S, Zumpe M, Jüttner M, Ehlert K, Kietz S, Müller I, Lode HN. Neuroblastoma patients with high-affinity FCGR2A, -3A and stimulatory KIR 2DS2 treated by long-term infusion of anti-GD 2 antibody ch14.18/CHO show higher ADCC levels and improved event-free survival. Oncoimmunology 2016; 5:e1235108. [PMID: 27999754 DOI: 10.1080/2162402x.2016.1235108] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Revised: 09/07/2016] [Accepted: 09/07/2016] [Indexed: 12/11/2022] Open
Abstract
Polymorphisms in Fc-gamma-receptor (FCGR) genes as well as killer cell immunoglobulin-like receptor (KIR) and KIR ligand (KIRL) repertoires may influence antitumor effects of monoclonal antibodies (mAb). Here, we systematically analyzed high- and low-affinity FCGR2A and -3A genotypes as well as stimulating and inhibitory KIR/KIRL combinations in 53 neuroblastoma (NB) patients treated by long-term infusion (LTI) of anti-GD2 IgG1 Ab ch14.18/CHO using validated real-time PCR methods. Patients with high-affinity FCGR2A and -3A genotypes showed a higher level of Ab-dependent cell-mediated cytotoxicity (ADCC) on day 8 after the start of ch14.18/CHO and superior event-free survival (EFS) compared to patients with low FCGR genotypes. Similar observations were made for patients with stimulatory KIR/KIRL haplotype B (combination of KIR genes including activating receptor genes) compared to inhibitory haplotype A (a fixed set of genes encoding for inhibitory receptors, except 2DS4) and stronger effects were found in patients when haplotype B and high-affinity FCGRs were combined. Surprisingly, independent analysis of KIRs showed a major role of activating KIR 2DS2 for high ADCC levels and prolongation of EFS. The greatest effect was observed in 2DS2-positive patients that also had high-affinity FCGR2A and -3A genotypes. In summary, the presence of the activating KIR 2DS2 has a major effect on ADCC levels and survival in NB patients treated by LTI of ch14.18/CHO and may therefore be a useful biomarker in combination with FCGR polymorphisms for Ab-based immunotherapies.
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Affiliation(s)
- Nikolai Siebert
- Department of Pediatric Oncology and Hematology, University Medicine Greifswald , Greifswald, Germany
| | - Christian Jensen
- Department of Pediatric Oncology and Hematology, University Medicine Greifswald , Greifswald, Germany
| | - Sascha Troschke-Meurer
- Department of Pediatric Oncology and Hematology, University Medicine Greifswald , Greifswald, Germany
| | - Maxi Zumpe
- Department of Pediatric Oncology and Hematology, University Medicine Greifswald , Greifswald, Germany
| | - Madlen Jüttner
- Department of Pediatric Oncology and Hematology, University Medicine Greifswald , Greifswald, Germany
| | - Karoline Ehlert
- Department of Pediatric Oncology and Hematology, University Medicine Greifswald , Greifswald, Germany
| | - Silke Kietz
- Department of Pediatric Oncology and Hematology, University Medicine Greifswald , Greifswald, Germany
| | - Ina Müller
- Department of Pediatric Oncology and Hematology, University Medicine Greifswald , Greifswald, Germany
| | - Holger N Lode
- Department of Pediatric Oncology and Hematology, University Medicine Greifswald , Greifswald, Germany
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Abstract
The IMGT/HLA Database (http://www.ebi.ac.uk/ipd/imgt/hla/) was first released over 15 years ago, providing the HLA community with a searchable repository of highly curated HLA sequences. The HLA complex is located within the 6p21.3 region of human chromosome 6 and contains more than 220 genes of diverse function. Many of the genes encode proteins of the immune system and are highly polymorphic, with some genes currently having over 3,000 known allelic variants. The Immuno Polymorphism Database (IPD) (http://www.ebi.ac.uk/ipd/) expands on this model, with a further set of specialist databases related to the study of polymorphic genes in the immune system. The IPD project works with specialist groups or nomenclature committees who provide and curate individual sections before they are submitted to IPD for online publication. IPD currently consists of four databases: IPD-KIR contains the allelic sequences of killer-cell immunoglobulin-like receptors; IPD-MHC is a database of sequences of the major histocompatibility complex of different species; IPD-HPA, alloantigens expressed only on platelets; and IPD-ESTDAB, which provides access to the European Searchable Tumour Cell-Line Database, a cell bank of immunologically characterized melanoma cell lines. Through the work of the HLA Informatics Group and in collaboration with the European Bioinformatics Institute we are able to provide public access to this data through the website http://www.ebi.ac.uk/ipd/.
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Affiliation(s)
- James Robinson
- Anthony Nolan Research Institute, Royal Free Hospital, Pond Street, Hampstead, London, NW3 2QG, UK
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Ayuk F, Bussmann L, Zabelina T, Veit R, Alchalby H, Wolschke C, Lellek H, Bacher U, Zander AR, Kröger N. Serum albumin level predicts survival of patients with gastrointestinal acute graft-versus-host disease after allogeneic stem cell transplantation. Ann Hematol 2013; 93:855-61. [PMID: 24248672 DOI: 10.1007/s00277-013-1957-0] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2013] [Accepted: 11/04/2013] [Indexed: 11/29/2022]
Abstract
In a retrospective single-centre study, we analysed the prognostic impact of factors identifiable at initial diagnosis of acute GVHD (aGVHD). We retrospectively analysed 495 adult patients of whom 308 (62 %) developed acute GVHD (I-IV) and were included in further analysis. Gut aGVHD was diagnosed in 163/308 cases (53 %). Conditioning was myeloablative conditioning (MAC) in 123 (39.9 %) and reduced intensity (RIC) in 185 (60.1 %) patients. Median serum albumin level at diagnosis of aGVHD was 34 g/l, which was used as cut-off for low vs. normal albumin levels. In patients with gut aGVHD, low albumin level at the time of diagnosis of aGVHD was associated with poorer overall survival (OS) which was 52 vs. 67 % at 1 year and 40 vs. 61 % at 3 years, p = 0.015. In patients with only skin aGVHD, 1- and 3-year OS of patients with low vs. normal albumin levels were 72 vs. 72 % and 59 vs. 57 %, respectively, p = 0.69. In multivariate analysis of patients with gut aGVHD, low serum albumin level ≤34 g/l (relative risk (RR) 2.13, p = 0.003), gut aGVHD grades 3-4 (RR 2.70, p = 0.001), RIC (RR 1.84, p = 0.024), matched unrelated donor (RR 1.86, p = 0.18) and mismatched unrelated donor (RR 2.76, p = 0.03) retained negative impact on OS. Subgroup analysis revealed that impact of albumin was restricted to patients with gut aGVHD after RIC. Low serum albumin levels are associated with poorer OS in patients with gut but not skin aGVHD after RIC but not MAC allogeneic stem cell transplantation.
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Affiliation(s)
- Francis Ayuk
- Clinic for stem cell transplantation, University Medical Center Hamburg-Eppendorf, Martinistr. 52, 20245, Hamburg, Germany,
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Kratzer W, Kibele M, Akinli A, Porzner M, Boehm BO, Koenig W, Oeztuerk S, Mason RA, Mao R, Haenle MH. Prevalence of celiac disease in Germany: A prospective follow-up study. World J Gastroenterol 2013; 19:2612-2620. [PMID: 23674868 PMCID: PMC3645379 DOI: 10.3748/wjg.v19.i17.2612] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/31/2012] [Revised: 11/28/2012] [Accepted: 02/06/2013] [Indexed: 02/06/2023] Open
Abstract
AIM: To determine the prevalence of celiac disease in a randomly selected population sample.
METHODS: A total of 2157 subjects (1036 males; 1121 females) participating in a population-based cross-sectional study underwent laboratory testing for tissue transglutaminase and antibodies to immunoglobulin A, endomysium and antigliadin. In a second step, all subjects who had been examined serologically were surveyed using a questionnaire that included questions specific to celiac disease. Subjects with positive antibody titers and those with histories positive for celiac disease then underwent biopsy. At the first follow up, antibody titers were again determined in these subjects and subjects were questioned regarding symptoms specific for celiac disease and disorders associated with celiac disease. The second follow up consisted of a telephone interview with subjects positive for celiac disease.
RESULTS: Antibody tests consistent with celiac disease were reported in eight subjects, corresponding to an overall prevalence of 1:270 (8/2157). The prevalence among women was 1:224 and 1:518 in men. Classical symptoms were observed in 62.5% of subjects. Atypical celiac disease was present in 25.0%, and transient celiac disease in 12.5%. False-negative test results were returned in three subjects. This yields a sensitivity and specificity of 62.5% and 50.0%, respectively, for tissue transglutaminase immunoglobulin-A antibody; of 62.5% and 71.4% respectively, for endomysium antibody; and of 62.5% and 71.4%, respectively, for antigliadin antibody.
CONCLUSION: The prevalence rate in our collective lies within the middle tertile of comparable studies in Europe. The use of a single antibody test for screening purposes must be called into question.
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Ayuk F, Zabelina T, Wortmann F, Alchalby H, Wolschke C, Lellek H, Bacher U, Zander A, Kröger N. Donor choice according to age for allo-SCT for AML in complete remission. Bone Marrow Transplant 2013; 48:1028-32. [PMID: 23419435 DOI: 10.1038/bmt.2013.14] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2012] [Revised: 12/30/2012] [Accepted: 01/15/2013] [Indexed: 11/09/2022]
Abstract
In a retrospective study of 168 patients with AML in CR who underwent allo-SCT, we compare the impact of young unrelated donors (UD) vs older matched related donors (MRD) on 5-year OS (5-yr OS). Median follow-up was 59 months and median donor age was 39 years, which was used as cutoff for young vs older donors. Kaplan-Meier-estimated 5-yr OS was better with UD ≤39 years vs MRD >39 years (66% vs 34%, P=0.001). In multivariate analysis, only donor age and cytogenetic risk impacted 5-yr OS. Compared with UD ≤39 years, both MRD >39 years (relative risk (RR): 4.31, P=0.001) and UD >39 years (RR: 2.14, P=0.03) were associated with poorer 5-yr OS. Standard-risk cytogenetics was associated with better 5-yr OS compared with bad-risk cytogenetics, (RR: 0.53, P=0.02). Subgroup analyses of patients ≥50 years (n=76) revealed similar results, with 5-yr OS of 62% for UD ≤39 yrs and 26% for MRD >39 yrs (P=0.022). In patients undergoing allo-HSCT for AML, young UD may improve outcome as compared with older MRD.
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Affiliation(s)
- F Ayuk
- Clinic for Stem Cell Transplantation, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.
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Hollenbach JA, Holcomb C, Hurley CK, Mabdouly A, Maiers M, Noble JA, Robinson J, Schmidt AH, Shi L, Turner V, Yao Y, Mack SJ. 16(th) IHIW: immunogenomic data-management methods. report from the immunogenomic data analysis working group (IDAWG). Int J Immunogenet 2012; 40:46-53. [PMID: 23280068 DOI: 10.1111/iji.12026] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2012] [Revised: 11/06/2012] [Accepted: 11/08/2012] [Indexed: 11/29/2022]
Abstract
SUMMARY The goal of the immunogenomic data analysis working group (IDAWG) is to facilitate the consistent analysis of HLA and KIR data, and the sharing of those data among the immunogenomic and larger genomic communities. However, the data management approaches currently applied by immunogenomic researchers are not widely discussed or reported in the literature, and the effect of different approaches on data analyses is not known. With ASHI's support, the IDAWG developed a 45 question survey on HLA and KIR data generation, data management and data analysis practices. Survey questions detailed the loci genotyped, typing systems used, nomenclature versions reported, computer operating systems and software used to manage and transmit data, the approaches applied to resolve HLA ambiguity and the methods used for basic population-level analyses. Respondents were invited to demonstrate their HLA ambiguity resolution approaches in simulated data sets. By May 2012, 156 respondents from 35 nations had completed the survey. These survey respondents represent a broad sampling of the Immunogenomic community; 52% were European, 30% North American, 10% Asian, 4% South American and 4% from the Pacific. The project will continue in conjunction with the 17th Workshop, with the aim of developing community data sharing standards, ambiguity resolution documentation formats, single-task data Management tools and novel data analysis methods and applications. While additional project details and plans for the 17th IHIW will be forthcoming, we welcome the input and participation in these projects from the histocompatibility and immunogenetics community.
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Affiliation(s)
- J A Hollenbach
- Children's Hospital Oakland Research Institute, Oakland, CA 94610, USA.
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12
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Robinson J, Halliwell JA, McWilliam H, Lopez R, Parham P, Marsh SGE. The IMGT/HLA database. Nucleic Acids Res 2012; 41:D1222-7. [PMID: 23080122 PMCID: PMC3531221 DOI: 10.1093/nar/gks949] [Citation(s) in RCA: 511] [Impact Index Per Article: 39.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
It is 14 years since the IMGT/HLA database was first released, providing the HLA community with a searchable repository of highly curated HLA sequences. The HLA complex is located within the 6p21.3 region of human chromosome 6 and contains more than 220 genes of diverse function. Of these, 21 genes encode proteins of the immune system that are highly polymorphic. The naming of these HLA genes and alleles and their quality control is the responsibility of the World Health Organization Nomenclature Committee for Factors of the HLA System. Through the work of the HLA Informatics Group and in collaboration with the European Bioinformatics Institute, we are able to provide public access to these data through the website http://www.ebi.ac.uk/imgt/hla/. Regular updates to the website ensure that new and confirmatory sequences are dispersed to the HLA community and the wider research and clinical communities. This article describes the latest updates and additional tools added to the IMGT/HLA project.
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Affiliation(s)
- James Robinson
- HLA Informatics Group, Anthony Nolan Research Institute, Royal Free Hospital, Pond Street, Hampstead, London NW3 2QG, UK
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13
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Gourraud PA, Hollenbach JA, Barnetche T, Single RM, Mack SJ. Standard methods for the management of immunogenetic data. Methods Mol Biol 2012; 882:197-213. [PMID: 22665236 PMCID: PMC4209945 DOI: 10.1007/978-1-61779-842-9_12] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2023]
Abstract
In this chapter, we outline some basic principles for the consistent management of immunogenetic data. These include the preparation of a single master data file that can serve as the basis for all subsequent analyses, a focus on the quality and homogeneity of the data to be analyzed, the documentation of the coding systems used to represent the data, and the application of nomenclature standards specific for each immunogenetic system being evaluated. The data management principles discussed here are intended to provide a foundation for the data analysis methods detailed in Chaps. 13 and 14 . The relationship between the data management and analysis methods covered in these three chapters is illustrated in Fig. 3.The application of these data management principles is a first step toward consistent and reproducible data analyses. While it may take extra time and effort to apply them, we feel that it is better to take this approach than to assume that low data quality can be compensated for by large sample sizes.In addition to their relevance for analytical reproducibility, it is important to consider these data management principles from an ethical perspective. The reliability of the data collected and generated as part of a research study should be as important a component of the ethical review of a research application as the security of those data. Finally, in addition to ensuring the integrity of the data from collection to publication, the application of these data management principles will provide a means to foster research integrity and to improve the potential for collaborative data sharing.
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14
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Huppmann P, Neurohr C, Leuschner S, Leuchte H, Baumgartner R, Zimmermann G, Meis T, von Wulffen W, Überfuhr P, Hatz R, Frey L, Behr J. The Munich-LTX-Score: predictor for survival after lung transplantation. Clin Transplant 2011; 26:173-83. [DOI: 10.1111/j.1399-0012.2011.01573.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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15
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Hollenbach JA, Mack SJ, Gourraud PA, Single RM, Maiers M, Middleton D, Thomson G, Marsh SGE, Varney MD. A community standard for immunogenomic data reporting and analysis: proposal for a STrengthening the REporting of Immunogenomic Studies statement. TISSUE ANTIGENS 2011; 78:333-44. [PMID: 21988720 PMCID: PMC3636772 DOI: 10.1111/j.1399-0039.2011.01777.x] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Modern high-throughput HLA and KIR typing technologies are generating a wealth of immunogenomic data with the potential to revolutionize the fields of histocompatibility and immune-related disease association and population genetic research, much as SNP-based approaches have revolutionized association research. The STrengthening the REporting of Genetic Association studies (STREGA) statement provides community-based data reporting and analysis standards for genomic disease-association studies, identifying specific areas in which adoption of reporting guidelines can improve the consistent interpretation of genetic studies. While aspects of STREGA can be applied to immunogenomic studies, HLA and KIR research requires additional consideration, as the high levels of polymorphism associated with immunogenomic data pose unique methodological and computational challenges to the synthesis of information across datasets. Here, we outline the principle challenges to consistency in immunogenomic studies, and propose that an immunogenomic-specific analog to the STREGA statement, a STrengthening the REporting of Immunogenomic Studies (STREIS) statement, be developed as part of the 16th International HLA and Immunogenetics Workshop. We propose that STREIS extends at least four of the 22 elements of the STREGA statement to specifically address issues pertinent to immunogenomic data: HLA and KIR nomenclature, data-validation, ambiguity resolution, and the analysis of highly polymorphic genetic systems. As with the STREGA guidelines, the intent behind STREIS is not to dictate the design of immunogenomic studies, but to ensure consistent and transparent reporting of research, facilitating the synthesis of HLA and KIR data across studies.
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Affiliation(s)
- J A Hollenbach
- Center for Genetics, Children's Hospital & Research Center Oakland, Oakland, CA, USA.
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Abstract
The Nomenclature Committee for Factors of the HLA System of the World Health Organization standardizes the nomenclature of the HLA system and meets regularly during the International Histocompatibility Workshops. During the 15th International Histocompatibility Workshop in Buzios (RJ), Brazil, in September 2008, there was a meeting of the nomenclature committee when new rules were established, which were implemented in April 2010.
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Affiliation(s)
- Margareth Afonso Torres
- Division of Histocompatibility, Clinical Pathology Deparment, Hospital Israelita Albert Einstein - HIAE, São Paulo, SP, BR
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Human immunodeficiency virus type 1 infection is associated with increased NK cell polyfunctionality and higher levels of KIR3DL1+ NK cells in ugandans carrying the HLA-B Bw4 motif. J Virol 2011; 85:4802-11. [PMID: 21411516 DOI: 10.1128/jvi.00111-11] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Natural killer (NK) cells are important innate effector cells controlled by an array of activating and inhibitory receptors. Some alleles of the inhibitory killer-cell immunoglobulin-like receptor KIR3DL1 in combination with its HLA class I ligand Bw4 have been genetically associated with slower HIV-1 disease progression. Here, we observed that the presence of HLA-B Bw4 was associated with elevated frequencies of KIR3DL1(+) CD56(dim) NK cells in chronically HIV-1-infected individuals from the rural district of Kayunga, Uganda. In contrast, levels of KIR2DL1(+) CD56(dim) NK cells were decreased, and levels of KIR2DL3(+) CD56(dim) NK cells were unchanged in infected subjects carrying their respective HLA-C ligands. Furthermore, the size of the KIR3DL1(+) NK cell subset correlated directly with viral load, and this effect occurred only in HLA-B Bw4(+) patients, suggesting that these cells expand in response to viral replication but may have relatively poor antiviral capacity. In contrast, no association with viral load was present for KIR2DL1(+) and KIR2DL3(+) NK cells. Interestingly, chronic HIV-1 infection was associated with an increased polyfunctional response in the NK cell compartment, and, upon further investigation, KIR3DL1(+) CD56(dim) NK cells exhibited a significantly increased functional response in the patients carrying HLA-B Bw4. These results indicate that chronic HIV-1 infection is associated with increased NK cell polyfunctionality and elevated levels of KIR3DL1(+) NK cells in Ugandans carrying the HLA-B Bw4 motif.
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Erikoglu M, Büyükdogan M, Cora T. The Relationship Between HLA Antigens and Blood Groups. ELECTRONIC JOURNAL OF GENERAL MEDICINE 2011. [DOI: 10.29333/ejgm/82699] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Mack SJ, Hollenbach JA. Allele Name Translation Tool and Update NomenCLature: software tools for the automated translation of HLA allele names between successive nomenclatures. ACTA ACUST UNITED AC 2010; 75:457-61. [PMID: 20412076 DOI: 10.1111/j.1399-0039.2010.01477.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
In this brief communication, we describe the Allele Name Translation Tool (antt) and Update NomenCLature (uncl), free programs developed to facilitate the translation of human leukocyte antigen (HLA) allele names recorded using the December 2002 version of the HLA allele nomenclature (e.g. A*01010101) to those recorded using the colon-delimited version of the HLA allele nomenclature (e.g. A*01:01:01:01) that was adopted in April 2010. In addition, the antt and uncl translate specific HLA allele-name changes (e.g. DPB1*0502 is translated to DPB1*104:01), as well as changes to the locus prefix for HLA-C (i.e. Cw* is translated to C*). The antt and uncl will also translate allele names that have been truncated to two, four, or six digits, as well as ambiguous allele strings. The antt is a locally installed and run application, while uncl is a web-based tool that requires only an Internet connection and a modern browser. The antt accepts a variety of HLA data-presentation and allele-name formats. In addition, the antt can translate using user-defined conversion settings (e.g. the names of alleles that encode identical peptide binding domains can be translated to a common 'P-code'), and can serve as a preliminary data-sanity tool. The antt is available for download, and uncl for use, at www.igdawg.org/software.
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Affiliation(s)
- S J Mack
- Children's Hospital Oakland Research Institute, Oakland, CA 94609, USA.
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20
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Lee KW, Park MH. New HLA Nomenclature (2010) and Its Clinical Application in Koreans. Ann Lab Med 2010; 30:203-17. [DOI: 10.3343/kjlm.2010.30.3.203] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Affiliation(s)
- Kyung Wha Lee
- Hallym Institution for Genome Application, Hallym University College of Medicine, Anyang, Korea
| | - Myoung Hee Park
- Department of Laboratory Medicine, Seoul National University College of Medicine, Seoul, Korea
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21
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Marsh SGE, Albert ED, Bodmer WF, Bontrop RE, Dupont B, Erlich HA, Fernández-Viña M, Geraghty DE, Holdsworth R, Hurley CK, Lau M, Lee KW, Mach B, Maiers M, Mayr WR, Müller CR, Parham P, Petersdorf EW, Sasazuki T, Strominger JL, Svejgaard A, Terasaki PI, Tiercy JM, Trowsdale J. Nomenclature for factors of the HLA system, 2010. TISSUE ANTIGENS 2010. [PMID: 20356336 DOI: 10.1111/j.1399‐0039.2010.01466.x] [Citation(s) in RCA: 268] [Impact Index Per Article: 17.9] [Reference Citation Analysis] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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22
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Marsh SGE, Albert ED, Bodmer WF, Bontrop RE, Dupont B, Erlich HA, Fernández-Viña M, Geraghty DE, Holdsworth R, Hurley CK, Lau M, Lee KW, Mach B, Maiers M, Mayr WR, Müller CR, Parham P, Petersdorf EW, Sasazuki T, Strominger JL, Svejgaard A, Terasaki PI, Tiercy JM, Trowsdale J. Nomenclature for factors of the HLA system, 2010. TISSUE ANTIGENS 2010; 75:291-455. [PMID: 20356336 PMCID: PMC2848993 DOI: 10.1111/j.1399-0039.2010.01466.x] [Citation(s) in RCA: 3308] [Impact Index Per Article: 220.5] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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Abstract
The WHO Nomenclature Committee for Factors of the HLA System met during the 15th International Histocompatibility and Immunogenetics Workshop in Buzios, Brazil in September 2008. This update is an extract of the main report that documents the additions and revisions to the nomenclature of human leukocyte antigen (HLA) specificities following the principles established in previous reports.
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Delgado-Vega AM, Castiblanco J, Gómez LM, Diaz-Gallo LM, Rojas-Villarraga A, Anaya JM. Bcl-2 antagonist killer 1 (BAK1) polymorphisms influence the risk of developing autoimmune rheumatic diseases in women. Ann Rheum Dis 2010; 69:462-5. [PMID: 19282307 DOI: 10.1136/ard.2008.100818] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
OBJECTIVE Bcl-2 antagonist killer 1 (BAK1) is a Bcl-2 family proapoptotic member suggested as a candidate gene for autoimmune diseases. The influence of BAK1 polymorphisms on the risk of developing autoimmune rheumatic diseases (AIRDs) in women was investigated. METHODS A total of 719 Colombian women were included in the present study: 209 had systemic lupus erythematosus, 99 primary Sjögren syndrome, 159 rheumatoid arthritis and 252 were healthy matched controls. Tag single nucleotide polymorphisms (SNPs) and potentially functional variants were typed by TaqMan allele discrimination assays. HLA-DRB1 and HLA-DQB1 typing was performed by reverse dot-blot hybridisation and linkage disequilibrium (LD) with BAK1 SNPs was assessed. RESULTS SNPs rs513349 (odds ratio (OR) 0.57, 95% CI 0.46 to 0.72, p = <0.001) and rs5745582 (OR 1.61, 95% CI 1.26 to 2.04, p = <0.001) were associated with the AIRDs included in this study. There was a significant increase of the rs513349G-rs561276C-rs5745582A (GCA) haplotype in each patient cohort as compared to controls (OR 1.95, 95% CI 1.50 to 2.54, p = <0.001). These SNPs were not in LD with HLA-DRB1 or HLA-DQB1 genes. CONCLUSIONS The results indicate that the BAK1 polymorphisms influence the risk of acquiring AIRDs in the population studied and are consistent with the paradigm that autoimmune diseases are likely to share common susceptibility variants.
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Affiliation(s)
- A M Delgado-Vega
- Center for Autoimmune Diseases Research, Rosario University, Bogotá, Colombia
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25
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Moonsamy P, Bonella P, Goodwin G, Dolan L, Erlich HA. The identification of a new HLA-DPB1 allele (*1302) in one family and the detection of a recombination event between the DR and the DQ regions in another Caucasian T1DGC family. ACTA ACUST UNITED AC 2009; 74:268-70. [PMID: 19691641 DOI: 10.1111/j.1399-0039.2009.01308.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The analysis of families collected by the T1DGC and typed at high resolution for the HLA class I and class II loci provided an opportunity for identifying new alleles and rare recombination events. In one American Caucasian family, a novel allele (HLA-DPB1*1302), detected as an unusual pattern of probe binding, was identified in the mother and in one child. Amplicons from both individuals were sequenced and a new variant of DPB1*1301 with an A->T mutation [TAC to TTC in codon 64, (amino acid 35); Y to F] was confirmed. In another American Caucasian family, one child inherited an unusual haplotype, DRB1*1501-DQA1*0102-DQB1*0609-DPA1*0103-DPB1*0601 resulting from a recombination between the DRB1 loci on the maternal chromosomes DRB1*1501-DQA1*0102-DQB1*0602-DPA1*0103-DPB1*0401 and DRB1*1302-DQA1*0102-DQB1*0609-DPA1*0103-DPB1*0601.
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Affiliation(s)
- P Moonsamy
- Human Genetics, Roche Molecular Systems Inc., Pleasanton, CA 94588, USA.
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26
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Cassinotti A, Birindelli S, Clerici M, Trabattoni D, Lazzaroni M, Ardizzone S, Colombo R, Rossi E, Porro GB. HLA and autoimmune digestive disease: a clinically oriented review for gastroenterologists. Am J Gastroenterol 2009; 104:195-217; quiz 194, 218. [PMID: 19098870 DOI: 10.1038/ajg.2008.10] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
OBJECTIVES The human leukocyte antigen (HLA) system includes genes involved in graft-vs-host rejection and in immune response. The discovery that HLAs are associated with several diseases led to appealing developments both in basic biomedical research and in clinical medicine, and offered the opportunity to improve the understanding of pathogenesis and classification of diseases, as well as to provide diagnostic and prognostic indicators. The aim of this article is to review the association between HLA alleles and autoimmune digestive disease and its current relationship with modern HLA nomenclature and clinical practice. METHODS Articles dealing with the association between HLAs and autoimmune digestive disease (including celiac disease, inflammatory bowel disease, autoimmune hepatitis, sclerosing cholangitis and primary biliary cirrhosis) were searched for using Pubmed and SCOPUS databases from earliest records to January 2008. RESULTS The review has provided two sections. In the first, we explain the basic principles of HLA structure, function, and nomenclature, as an introduction to the second section, which describes current associations between HLA alleles and digestive diseases. The clinical implications of each HLA association are critically discussed. Actually, a clinical role for HLA typing is suggested for only a few conditions, e.g., celiac disease. CONCLUSIONS The knowledge of current HLA nomenclature and of its association with some digestive diseases such as celiac disease can be useful in clinical practice for diagnostic and prognostic purposes. This can avoid improper HLA typing as well as stressing the need for further studies on other possible clinical applications.
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Affiliation(s)
- Andrea Cassinotti
- Department of Clinical Science, Division of Gastroenterology, L. Sacco University Hospital, via G.B.Grassi 74, Milan, Italy.
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27
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Abstract
We describe the identification of a new DRB1*14 allele, DRB1*1461, found in a Chinese individual. The novel allele has been identified in routine polymerase chain reaction-sequence-specific oligonucleotide and sequence-based typing. The nucleotide sequence of DRB1*1461 is identical to DRB1*1404 except for a single substitution in codon 16 (TAT-->CAT), leading to a change from Tyr to His.
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Affiliation(s)
- Z Wang
- HLA Laboratory, Beijing Red Cross Blood Center, Beijing, China.
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28
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Comparison of Two Doses of Antithymocyte Globulin in Patients Undergoing Matched Unrelated Donor Allogeneic Stem Cell Transplantation. Biol Blood Marrow Transplant 2008; 14:913-9. [DOI: 10.1016/j.bbmt.2008.05.023] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2008] [Accepted: 05/28/2008] [Indexed: 11/19/2022]
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29
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Ayuk F, Diyachenko G, Zabelina T, Panse J, Wolschke C, Eiermann T, Binder T, Fehse B, Erttmann R, Kabisch H. Anti-thymocyte globulin overcomes the negative impact of HLA mismatching in transplantation from unrelated donors. Exp Hematol 2008; 36:1047-54. [DOI: 10.1016/j.exphem.2008.03.011] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2007] [Revised: 01/31/2008] [Accepted: 03/03/2008] [Indexed: 10/22/2022]
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30
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Holland OJ, Cowan PE, Gleeson DM, Chamley LW. Novel alleles in classical major histocompatibility complex class II loci of the brushtail possum (Trichosurus vulpecula). Immunogenetics 2008; 60:449-60. [PMID: 18548245 DOI: 10.1007/s00251-008-0300-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2008] [Accepted: 04/21/2008] [Indexed: 10/22/2022]
Abstract
We have investigated the diversity of class II major histocompatibility complex (MHC) loci in the brushtail possum (Trichosurus vulpecula), an important marsupial pest species in New Zealand. Immunocontraceptive vaccines, a method of fertility control that employs the immune system to attack reproductive cells or proteins, are currently being researched as a means of population control for the possum. Variation has been observed in the immune response of individual possums to immunocontraceptives. If this variability is under genetic control, it could compromise vaccine efficacy through preferential selection of animals that fail to mount a significant immune response and remain fertile. The MHC is an important immune region for antigen presentation and as such may influence the response to immunocontraceptives. We used known marsupial MHC sequences to design polymerase chain reaction primers to screen for possum MHC loci. Alpha and beta chains from two class II families, DA and DB, were found in possums throughout New Zealand. Forty new class II MHC alleles were identified in the possum, and the levels of variability in the MHC of this marsupial appear to be comparable to those of eutherian species. Preliminary population surveys showed evidence of clustering/variability in the distribution of MHC alleles in geographically separate locations. The extensive variation demonstrated in possums reinforces the need for further research to assess the risk that such MHC variation poses for long-term immunocontraceptive vaccine efficacy.
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Affiliation(s)
- Olivia J Holland
- National Research Centre for Possum Biocontrol, Landcare Research, Auckland, New Zealand.
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31
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Xiong P, Zeng X, Song MS, Jia SW, Zhong MH, Xiao LL, Lan W, Cai C, Wu XW, Gong FL, Wang W. Lack of association between HLA-A, -B and -DRB1 alleles and the development of SARS: a cohort of 95 SARS-recovered individuals in a population of Guangdong, southern China. Int J Immunogenet 2008; 35:69-74. [PMID: 18186801 PMCID: PMC7165669 DOI: 10.1111/j.1744-313x.2007.00741.x] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Severe acute respiratory syndrome (SARS), caused by infection with a novel coronavirus (SARS‐CoV), was the first major novel infectious disease at the beginning of the 21st century, with China especially affected. SARS was characterized by high infectivity, morbidity and mortality, and the confined pattern of the disease spreading among the countries of South‐East and East Asia suggested the existence of susceptible factor(s) in these populations. Studies in the populations of Hong Kong and Taiwan showed an association of human leucocyte antigen (HLA) polymorphisms with the development and/or severity of SARS, respectively. The aim of the present study was to define the genotypic patterns of HLA‐A, ‐B and ‐DRB1 loci in SARS patients and a co‐resident population of Guangdong province, southern China, where the first SARS case was reported. The samples comprised 95 cases of recovered SARS patients and 403 unrelated healthy controls. HLA ‐A, ‐B and ‐DRB1 alleles were genotyped using polymerase chain reaction with sequence‐specific primers. The severity of the disease was assessed according to the history of lung infiltration, usage of assisted ventilation and occurrence of lymphocytopenia. Although the allelic frequencies of A23, A34, B60, DRB1*12 in the SARS group were slightly higher, and A33, ‐B58 and ‐B61 were lower than in the controls, no statistical significance was found when the Pc value was considered. Similarly, no association of HLA alleles with the severity of the disease was detected. Thus, variations in the major histocompatibility complex are unlikely to have contributed significantly to either the susceptibility or the severity of SARS in the population of Guangdong.
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Affiliation(s)
- P Xiong
- Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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32
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Castaño-Rodríguez N, Diaz-Gallo LM, Pineda-Tamayo R, Rojas-Villarraga A, Anaya JM. Meta-analysis of HLA-DRB1 and HLA-DQB1 polymorphisms in Latin American patients with systemic lupus erythematosus. Autoimmun Rev 2008; 7:322-30. [PMID: 18295738 DOI: 10.1016/j.autrev.2007.12.002] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2007] [Accepted: 12/10/2007] [Indexed: 10/22/2022]
Abstract
OBJECTIVE To estimate the common effect size of HLA-DRB1 and -DQB1 alleles on systemic lupus erythematosus (SLE) susceptibility across Latin America populations through a meta-analysis. METHODS Case-control studies on HLA class II association with SLE in Latin America were searched up to August 2007. The effect summary odds ratios (ORs) and 95% confidence intervals (CIs) were obtained by means of the random effect model. RESULTS Eleven studies were selected, which included 747 cases and 1180 controls. Associations with SLE susceptibility were found for HLA-DR2 (OR: 1.75; 95% CI: 1.40-2.19) and -DR3 (OR: 2.02; 95% CI: 1.44-2.83) groups. HLA-DRB1*0301 allele disclosed the strongest association (OR: 2.14; 95% CI: 1.28-3.56). HLA-DR3-DQ2 haplotype was a risk factor (OR: 2.92; 95% CI: 1.66-5.14). A protective effect was found for the HLA-DR5 group (OR: 0.43; 95% CI: 0.27-0.67), mainly due to a negative association between HLA-DRB1*1101 allele and disease (OR: 0.21; 95% CI: 0.06-0.72). Functional analysis of susceptibility and protective alleles revealed physicochemical differences of critical amino acids shaping the peptide-binding groove at DRbeta chain allowing us to infer an approach to understand the role of HLA in SLE. No significant association was established for HLA-DQB1 alleles. CONCLUSIONS HLA-DRB1 gene is a mayor factor for development of SLE in Latin Americans.
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Affiliation(s)
- Natalia Castaño-Rodríguez
- Cellular Biology and Immunogenetics Unit, Corporación para Investigaciones Biológicas, Medellín, Colombia
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Alves C, Veiga S, Toralles MBP, Lopes ACV. O papel do complexo principal de histocompatibilidade na fisiologia da gravidez e na patogênese de complicações obstétricas. REVISTA BRASILEIRA DE SAÚDE MATERNO INFANTIL 2007. [DOI: 10.1590/s1519-38292007000400002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Este trabalho tem por objetivo discutir a estrutura e função dos Antígenos Leucocitários Humanos (HLA), seus métodos de detecção, nomenclatura e os mecanismos imunopatológicos que o associam com a fisiologia da gestação e morbidades obstétricas. Sabe-se que o equilíbrio imunológico entre mãe e concepto é imprescindível na manutenção da gravidez. Moléculas do HLA - notadamente o HLA-G expresso na interface materno-fetal - exercem função importante na tolerância imunológica materna, evitando rejeição fetal e algumas complicações obstétricas. Além disso, o HLA permeia diversas etapas do desenvolvimento conceptual como clivagem, formação do trofoblasto e implantação. Para revisão, foram pesquisados os bancos de dados MEDLINE e LILACS, utilizando os descritores: "HLA antigens"; "pregnancy"; "embryonic development"; "pregnancy complication"; "abortion, habitual"; "pre-eclampsia". O conhecimento sobre a influência do HLA na gravidez é necessário para melhor manejo da gestação e patologias obstétricas auto-imunes, favorecendo intervenções precoces e terapêutica específica, reduzindo a morbimortalidade materna e perinatal.
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Tang TF, Hou L, Tu B, Hwang WYK, Yeoh AEJ, Ng J, Hurley CK. Identification of nine new HLA class I alleles in volunteers from the Singapore stem cell donor registries. ACTA ACUST UNITED AC 2007; 68:518-20. [PMID: 17176443 DOI: 10.1111/j.1399-0039.2006.00707.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Based on unusual probe hybridization patterns, two human leukocyte antigen (HLA)-A, five HLA-B, and two HLA-C alleles (A*240208, A*3211Q; B*1822, B*3938Q, B*4606, B*4607N, B*5139; Cw*0321, Cw*0734) were identified in individuals from the Singapore Bone Marrow Donor Program and Singapore Cord Blood Bank. Eight of the nine alleles encode amino acid substitutions altering the antigen-binding region including three alleles with changes altering a cysteine at codon 164 (A*3211Q, B*3938Q, B*4607N). This substitution either eliminates a key disulfide bond or results in a stop codon, both likely affecting the expression of the HLA molecules. Only one allele (A*240208) carries a synonymous substitution.
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Affiliation(s)
- T F Tang
- Department of Pediatrics, Georgetown University Medical Center, Washington, DC, USA
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35
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Krasowska-Kwiecień A, Sancewicz-Pach K, Moczulska A. Idiopathic nephrotic syndrome in Polish children - its variants and associations with HLA. Pediatr Nephrol 2006; 21:1837-46. [PMID: 16967287 DOI: 10.1007/s00467-006-0271-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/12/2006] [Revised: 07/07/2006] [Accepted: 07/11/2006] [Indexed: 10/24/2022]
Abstract
HLA-DR and HLA-DQ antigens were investigated in 127 Polish children with idiopathic nephrotic syndrome (INS) followed-up for the median time of 11 years (minimum 7 years). HLA typing was performed using the polymerase chain reaction sequence-specific oligonucleotide probing technique and the microlymphocytotoxicity test. Histopathologic INS categories and a response to therapy were analyzed according to particular HLA associations. The results were compared with 330 healthy individuals. In INS children, we observed an increased frequency of HLA-DR7, DR3/7, DQ2 and DQ8, whereas HLA-DR13, DR15, DQ5 and DQ6 were decreased. In minimal change nephrotic syndrome, a relationship with HLA-DR3, DR7, DR3/7 and DQ2 was found. Evolved from minimal changes, focal segmental glomerulosclerosis was associated with HLA-DR7, while primary focal segmental glomerulosclerosis with HLA-DR4 and DQ8. In steroid-dependence and secondary steroid-resistance, an increased frequency of HLA-DR3, DR7, DR3/7 and DQ2 was documented. In contrast, primary steroid-resistant nephrotic syndrome was associated with HLA-DR4 and DQ8. Steroid-dependent patients bearing HLA-DR3 achieved longer remissions after chlorambucil therapy compared with HLA-DR3-negative. In steroid-resistant focal segmental glomerulosclerosis, a reduced response to cyclosporine A was associated with HLA-DR4. Associations with HLA differentiate between pathoanatomic entities of INS and may influence a response to immunosuppressive therapy.
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Affiliation(s)
- Aleksandra Krasowska-Kwiecień
- Department of Transplantation, Polish-American Institute of Pediatrics, Jagiellonian University, 265 Wielicka St., 30-663 Cracow, Poland.
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36
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Lee LC, Zachary AA, Leffell MS, Newschaffer CJ, Matteson KJ, Tyler JD, Zimmerman AW. HLA-DR4 in families with autism. Pediatr Neurol 2006; 35:303-7. [PMID: 17074598 DOI: 10.1016/j.pediatrneurol.2006.06.006] [Citation(s) in RCA: 86] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/23/2005] [Revised: 05/04/2006] [Accepted: 06/19/2005] [Indexed: 01/02/2023]
Abstract
Autoimmune disorders are observed with increased frequency among parents of individuals with autism, particularly mothers. Because there is evidence supporting an association between autoimmune disorders and specific alleles of the human leukocyte antigen (HLA) system, we examined HLA types and subtypes in families with autism. Two groups were studied: 16 families selected from a geographically defined area in eastern Tennessee have males with a diagnosis of autism; and 33 families selected across all regions in the United States have multiple males having autism diagnosis. The HLA-DR4 frequencies of mothers, fathers, and children in these two groups were compared with a reference series of 475 normal, unrelated Caucasians. Results of HLA typing indicated that mothers and their sons in the geographically defined group had a significantly higher frequency of DR4 than normal control subjects (odds ratio = 5.54, 95% confidence interval = 1.74-18.67 and odds ratio = 4.20, 95% confidence interval = 1.37-13.27, respectively). No significant difference in the distribution of HLA alleles was evident between the United States-all region group and control subjects. Findings of this study are consistent with a hypothesis that prenatal maternal-fetal immune interaction can affect fetal brain development in a population residing in a geographically defined region. Such immune interactions may involve HLA and related genes in both genetic and epigenetic mechanisms during pregnancy.
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Affiliation(s)
- Li-Ching Lee
- Center for Autism and Developmental Disabilities Epidemiology, Department of Epidemiology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, Maryland 21205, USA.
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37
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Aureli A, Piancatelli D, Ozzella G, Liberatore G, Piazza A, Adorno D. B*3812: a new HLA-B38 variant identified by sequence-based typing. ACTA ACUST UNITED AC 2006; 68:91-3. [PMID: 16774549 DOI: 10.1111/j.1399-0039.2006.00602.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- A Aureli
- C.N.R. Institute for Organ Transplantation and Immunocytology, Piazzale Collemaggio, 67100 L'Aquila, Italy.
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38
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Piancatelli D, Del Beato T, Aureli A, Papola F, Adorno D. A new HLA-CW*14 allele, Cw*140204, identified by allele-specific DNA amplification and sequencing. ACTA ACUST UNITED AC 2006; 68:93-5. [PMID: 16774550 DOI: 10.1111/j.1399-0039.2006.00619.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- D Piancatelli
- C.N.R. Institute for Organ Transplantation and Immunocytology, Piazzale Collemaggio, 67100 L'Aquila, Italy.
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39
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Danzer M, Polin H, Faé I, Fischer GF, Gabriel C. Exon 1-4 sequence analysis of a novel HLA-A allele, HLA-A*2458. ACTA ACUST UNITED AC 2006; 68:177-8. [PMID: 16866891 DOI: 10.1111/j.1399-0039.2006.00634.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- M Danzer
- Red Cross Transfusion Service of Upper Austria, Linz, Austria.
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40
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Bordner AJ, Abagyan R. Ab initio prediction of peptide-MHC binding geometry for diverse class I MHC allotypes. Proteins 2006; 63:512-26. [PMID: 16470819 DOI: 10.1002/prot.20831] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Since determining the crystallographic structure of all peptide-MHC complexes is infeasible, an accurate prediction of the conformation is a critical computational problem. These models can be useful for determining binding energetics, predicting the structures of specific ternary complexes with T-cell receptors, and designing new molecules interacting with these complexes. The main difficulties are (1) adequate sampling of the large number of conformational degrees of freedom for the flexible peptide, (2) predicting subtle changes in the MHC interface geometry upon binding, and (3) building models for numerous MHC allotypes without known structures. Whereas previous studies have approached the sampling problem by dividing the conformational variables into different sets and predicting them separately, we have refined the Biased-Probability Monte Carlo docking protocol in internal coordinates to optimize a physical energy function for all peptide variables simultaneously. We also imitated the induced fit by docking into a more permissive smooth grid representation of the MHC followed by refinement and reranking using an all-atom MHC model. Our method was tested by a comparison of the results of cross-docking 14 peptides into HLA-A*0201 and 9 peptides into H-2K(b) as well as docking peptides into homology models for five different HLA allotypes with a comprehensive set of experimental structures. The surprisingly accurate prediction (0.75 A backbone RMSD) for cross-docking of a highly flexible decapeptide, dissimilar to the original bound peptide, as well as docking predictions using homology models for two allotypes with low average backbone RMSDs of less than 1.0 A illustrate the method's effectiveness. Finally, energy terms calculated using the predicted structures were combined with supervised learning on a large data set to classify peptides as either HLA-A*0201 binders or nonbinders. In contrast with sequence-based prediction methods, this model was also able to predict the binding affinity for peptides to a different MHC allotype (H-2K(b)), not used for training, with comparable prediction accuracy.
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Affiliation(s)
- Andrew J Bordner
- Department of Molecular Biology, The Scripps Research Institute, San Diego, California, USA.
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41
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Shan X, Gao G, He X, Wu G, Zhang Z. Identification of a novel HLA-B allele HLA-B*4059 in Chinese bone marrow donors. ACTA ACUST UNITED AC 2006; 67:339-40. [PMID: 16634873 DOI: 10.1111/j.1399-0039.2006.00568.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- X Shan
- Beijing Red Cross Blood Center, Beijing 100088, China.
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42
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Hoelsch K, Lenggeler I, Knabe H, Hartel K, Klein HG, Woelpl A. Identification of a novel HLA-B*44 variant (B*4441) in three unrelated Caucasian individuals. ACTA ACUST UNITED AC 2006; 67:247-9. [PMID: 16573564 DOI: 10.1111/j.1399-0039.2006.00563.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Here, we report the identification of a new human leukocyte antigen (HLA)-B*44 allele found almost simultaneous in three DNA samples which were part of routine bone marrow donor typing by order of the German registry 'Aktion Knochenmarkspende Bayern'. The samples appeared noticeable in different polymerase chain reactions using sequence-specific primers (PCR-SSP) or sequence-specific oligonucleotides (PCR-SSO). Sequence-based typing revealed a novel allele officially designated as B*4441*. This sequence differs from HLA-B*44020101/4427 by two nucleotide positions at the beginning of exon 3: by position 353 (T to C) and by position 355 (A to C). These differences in sequence result in deviant amino acids at codon 94 (Ile94Thr) and codon 95 (Ile95Leu).
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Affiliation(s)
- K Hoelsch
- Laboratory for Medical Genetics, Dr Klein, Martinsried, Munich, Germany
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43
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Heo YS, Hwang SH, Kwon OJ, Hur SS, Oh HB. Structural aspect of novel HLA-A*02 allele, A*0286, identified by sequence-based typing. ACTA ACUST UNITED AC 2006; 67:84-5. [PMID: 16451209 DOI: 10.1111/j.1399-0039.2005.00502.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Y-S Heo
- Division of Drug Discovery, CrystalGenomics, Seoul, South Korea
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44
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Affiliation(s)
- K Ludajic
- Clinical Department for Blood Group Serology,Medical University of Vienna, Austria.
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45
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Alkharsah KR, Dedicoat M, DeLuca DS, Schulz TF, Blasczyk R. Identification of two new HLA-A variants, HLA-A*2911 and HLA-A*6827+. ACTA ACUST UNITED AC 2006; 67:170-2. [PMID: 16441495 DOI: 10.1111/j.1399-0039.2006.00505.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- K R Alkharsah
- Institute of Virology, Hannover Medical School, Hannover, Germany
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46
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Ozzella G, Monaco PI, Tessitore A, Piazza A, Piancatelli D, Adorno D. Identification of a novel HLA-DRB1*11 allele: DRB1*1152. ACTA ACUST UNITED AC 2006; 67:180-2. [PMID: 16441502 DOI: 10.1111/j.1399-0039.2006.00534.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- G Ozzella
- Organ Transplant and Immunocitology, C.N.R. Institute, Rome, Italy.
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47
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Thude H, Hardt C, Schorner U, Ferencik S, Helfricht C, Barz D. Identification of a new HLA-B allele, HLA-B*4443, in a German family. ACTA ACUST UNITED AC 2006; 66:696-9. [PMID: 16305687 DOI: 10.1111/j.1399-0039.2005.00490.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
A novel human leukocyte antigen (HLA)-B allele is described. The allele was identified in a German blood donor of Caucasian origin. Because high-resolution HLA-typing using sequence-specific primers gave inconclusive results, sequence-based typing was performed. Nucleotide sequences of exons 2 and 3 most closely match with HLA-B*4417 and HLA-B*440301 (99.5% identity). The predicted protein sequence revealed a single amino acid substitution (D156L) compared with the HLA-B*4417 allele but two substitutions (Y113H, D116S) compared with the HLA-B*440301 allele. Therefore, the novel allele has been officially assigned HLA-B*4443 by the WHO Nomenclature Committee. The HLA-B*4443 allele was found with the A*2301, Cw*0401, B*4443, DRB1*0701, DRB4*0107, and DQB1*0202 haplotype.
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Affiliation(s)
- H Thude
- Institute for Transfusion Medicine, University Hospital of Jena, Germany.
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48
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Horn PA, DeLuca DS, Blasczyk R. An amino acid contributing to pockets A, B, and D of the peptide-binding groove is altered in A*0315. ACTA ACUST UNITED AC 2006; 66:703-4. [PMID: 16305690 DOI: 10.1111/j.1399-0039.2005.00488.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- P A Horn
- Institute for Transfusion Medicine, Hannover Medical School, Carl-Neuberg-Str. 1, 30625 Hannover, Germany
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49
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Kwon OJ, Hwang SH, Lee MN, Oh HB. A novel HLA-A*2601 variant, A*260102, identified by sequence-based typing. ACTA ACUST UNITED AC 2006; 66:704-5. [PMID: 16305691 DOI: 10.1111/j.1399-0039.2005.00487.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- O-J Kwon
- BioSewoom Institute of Bioscience & Biotechnology, Seoul, Republic of Korea
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50
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Smith DM, Lunney JK, Ho CS, Martens GW, Ando A, Lee JH, Schook L, Renard C, Chardon P. Nomenclature for factors of the swine leukocyte antigen class II system, 2005. ACTA ACUST UNITED AC 2006; 66:623-39. [PMID: 16305679 DOI: 10.1111/j.1399-0039.2005.00492.x] [Citation(s) in RCA: 77] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A systematic nomenclature for the genes and alleles of the swine major histocompatibility complex (MHC) is essential to the development and communication of research in swine immunology. The Swine Leukocyte Antigen (SLA) Nomenclature Committee of the International Society for Animal Genetics (ISAG) has reviewed all of the DNA-sequence information for MHC class II genes, available in GenBank/EMBL/DDBJ databases, and the associated published reports to develop such a systematic nomenclature. This article summarizes the proposed nomenclature, which parallels the World Health Organization's nomenclature for factors of the human MHC. The SLA class II genes expressed on the cell membrane will be noted as SLA-DRA, SLA-DRB1, SLA-DQA, and SLA-DQB1. Nomenclature assignments for all SLA class II GenBank sequences are now noted. The committee will add new SLA class II allele designations, as they are discovered, and will maintain a publicly available list of all recognized genes and alleles using the Immuno Polymorphism Database (IPD). The sequences will be available from the IPD-MHC section of the database which contains non-human MHC sequences (http://www.ebi.ac.uk/ipd/mhc/sla/).
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Affiliation(s)
- D M Smith
- Baylor University Medical Center, Dallas, TX, USA.
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