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Pollock NR, Farias TDJ, Kichula KM, Sauter J, Scholz S, Nii-Trebi NI, Khor SS, Tokunaga K, Voorter CE, Groeneweg M, Augusto DG, Arrieta-Bolaños E, Mayor NP, Edinur HA, ElGhazali G, Issler HC, Petzl-Erler ML, Oksenberg JR, Marin WM, Hollenbach JA, Gendzekhadze K, Cita R, Stelet V, Rajalingam R, Koskela S, Clancy J, Chatzistamatiou T, Houwaart T, Kulski J, Guethlein LA, Parham P, Schmidt AH, Dilthey A, Norman PJ. The 18th International HLA & Immunogenetics workshop project report: Creating fully representative MHC reference haplotypes. HLA 2024; 103:e15568. [PMID: 38923286 PMCID: PMC11210686 DOI: 10.1111/tan.15568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Revised: 04/25/2024] [Accepted: 05/29/2024] [Indexed: 06/28/2024]
Abstract
A fundamental endeavor of the International Histocompatibility and Immunogenetics Workshop (IHIW) was assembling a collection of DNA samples homozygous through the MHC genomic region. This collection proved invaluable for assay development in the histocompatibility and immunogenetics field, for generating the human reference genome, and furthered our understanding of MHC diversity. Defined by their HLA-A, -B, -C and -DRB1 alleles, the combined frequency of the haplotypes from these individuals is ~20% in Europe. Thus, a significant proportion of MHC haplotypes, both common and rare throughout the world, and including many associated with disease, are not yet represented. In this workshop component, we are collecting the next generation of MHC -homozygous samples, to expand, diversify and modernize this critical community resource that has been foundational to the field. We asked laboratories worldwide to identify samples homozygous through all HLA class I and/or HLA class II genes, or through whole-genome SNP genotyping or sequencing, to have extensive homozygosity tracts within the MHC region. The focus is non-Europeans or those having HLA haplotypes less common in Europeans. Through this effort, we have obtained samples from 537 individuals representing 294 distinct haplotypes, as determined by their HLA class I and II alleles, and an additional 50 haplotypes distinct in HLA class I or II alleles. Although we have expanded the diversity, many populations remain underrepresented, particularly from Africa, and we encourage further participation. The data will serve as a resource for investigators seeking to characterize variation across the MHC genomic region for disease and population studies.
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Affiliation(s)
- Nicholas R. Pollock
- Department of Biomedical Informatics, University of Colorado School of Medicine, Aurora, Colorado, USA
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Ticiana D. J. Farias
- Department of Biomedical Informatics, University of Colorado School of Medicine, Aurora, Colorado, USA
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Katherine M. Kichula
- Department of Biomedical Informatics, University of Colorado School of Medicine, Aurora, Colorado, USA
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Jürgen Sauter
- DKMS Group, Tübingen, Germany; DKMS Life Science Lab, Dresden, Germany
| | - Stephan Scholz
- Institute of Medical Microbiology and Hospital Hygiene, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Nicholas I. Nii-Trebi
- Department of Medical Laboratory Sciences, School of Biomedical & Allied Health Sciences, College of Health Sciences, University of Ghana, Accra 00233, Ghana
| | - Seik-Soon Khor
- Genome Medical Science Project, National Center for Global Health and Medicine Hospital, Tokyo, Japan
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
| | - Katsushi Tokunaga
- Genome Medical Science Project, National Center for Global Health and Medicine Hospital, Tokyo, Japan
| | - Christina E. Voorter
- Department of Transplantation Immunology, Tissue Typing Laboratory, Maastricht University Medical Center, Maastricht, Netherlands
| | - Mathijs Groeneweg
- Department of Transplantation Immunology, Tissue Typing Laboratory, Maastricht University Medical Center, Maastricht, Netherlands
| | - Danillo G. Augusto
- Department of Biological Sciences, The University of North Carolina at Charlotte, Charlotte, NC, USA
| | - Esteban Arrieta-Bolaños
- Institute for Experimental Cellular Therapy, University Hospital Essen, Essen, Germany
- German Cancer Consortium (DKTK), partner site Essen/Düsseldorf, Heidelberg, Germany
| | - Neema P. Mayor
- Anthony Nolan Research Institute, Royal Free Hospital, London, UK
- UCL Cancer Institute, Royal Free Campus, London, UK
| | - Hisham Atan Edinur
- School of Health Sciences, Universiti Sains Malaysia, Health Campus, Kelantan, Malaysia
| | - Gehad ElGhazali
- Immunology laboratory, Sheikh Khalifa Medical City- Purelab, Purehealth, Abu Dhabi and College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates
| | - Hellen C. Issler
- Laboratory of Human Molecular Genetics, Postgraduate Program in Genetics, Department of Genetics, Federal University of Paraná (UFPR), Curitiba 81531-980, Brazil
| | - Maria Luiza Petzl-Erler
- Laboratory of Human Molecular Genetics, Postgraduate Program in Genetics, Department of Genetics, Federal University of Paraná (UFPR), Curitiba 81531-980, Brazil
| | - Jorge R. Oksenberg
- Weill Institute for Neurosciences, Department of Neurology, University of California San Francisco, San Francisco, CA, 94158, USA
| | - Wesley M. Marin
- Weill Institute for Neurosciences, Department of Neurology, University of California San Francisco, San Francisco, CA, 94158, USA
| | - Jill A. Hollenbach
- Weill Institute for Neurosciences, Department of Neurology, University of California San Francisco, San Francisco, CA, 94158, USA
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA, 94158, USA
| | - Ketevan Gendzekhadze
- HLA Laboratory, Department of Hematology and HCT, City of Hope National Medical Center, Duarte, CA
| | - Rafael Cita
- Transplant Immunology Laboratory, Pio XII Foundation, Barretos, Brazil
| | - Vinícius Stelet
- Immunogenetics Laboratory, National Cancer Institute, Rio de Janeiro, Brazil
| | - Raja Rajalingam
- Immunogenetics and Transplantation Laboratory, Department of Surgery, University of California San Francisco, San Francisco, CA, USA
| | - Satu Koskela
- Finnish Red Cross Blood Service; Biobank, 01730 Vantaa, Finland
| | - Jonna Clancy
- Finnish Red Cross Blood Service; Biobank, 01730 Vantaa, Finland
| | - Theofanis Chatzistamatiou
- Histocompatibility & Immunogenetics Laboratory, Hellenic Cord Blood Bank, Biomedical Research Foundation, Academy of Athens,11528 Athens, Greece
| | - Torsten Houwaart
- Department of Medical Laboratory Sciences, School of Biomedical & Allied Health Sciences, College of Health Sciences, University of Ghana, Accra 00233, Ghana
| | - Jerzy Kulski
- Department of Molecular Life Science, Tokai University School of Medicine, Isehara, Kanagawa, Japan
| | - Lisbeth A. Guethlein
- Department of Structural Biology and Department of Microbiology and Immunology, Stanford University School of Medicine, USA
| | - Peter Parham
- Department of Structural Biology and Department of Microbiology and Immunology, Stanford University School of Medicine, USA
| | | | - Alexander Dilthey
- Department of Medical Laboratory Sciences, School of Biomedical & Allied Health Sciences, College of Health Sciences, University of Ghana, Accra 00233, Ghana
| | - Paul J. Norman
- Department of Biomedical Informatics, University of Colorado School of Medicine, Aurora, Colorado, USA
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, Colorado, USA
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2
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Houwaart T, Scholz S, Pollock NR, Palmer WH, Kichula KM, Strelow D, Le DB, Belick D, Hülse L, Lautwein T, Wachtmeister T, Wollenweber TE, Henrich B, Köhrer K, Parham P, Guethlein LA, Norman PJ, Dilthey AT. Complete sequences of six major histocompatibility complex haplotypes, including all the major MHC class II structures. HLA 2023; 102:28-43. [PMID: 36932816 PMCID: PMC10986641 DOI: 10.1111/tan.15020] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 02/10/2023] [Accepted: 02/24/2023] [Indexed: 03/19/2023]
Abstract
Accurate and comprehensive immunogenetic reference panels are key to the successful implementation of population-scale immunogenomics. The 5Mbp Major Histocompatibility Complex (MHC) is the most polymorphic region of the human genome and associated with multiple immune-mediated diseases, transplant matching and therapy responses. Analysis of MHC genetic variation is severely complicated by complex patterns of sequence variation, linkage disequilibrium and a lack of fully resolved MHC reference haplotypes, increasing the risk of spurious findings on analyzing this medically important region. Integrating Illumina, ultra-long Nanopore, and PacBio HiFi sequencing as well as bespoke bioinformatics, we completed five of the alternative MHC reference haplotypes of the current (GRCh38/hg38) build of the human reference genome and added one other. The six assembled MHC haplotypes encompass the DR1 and DR4 haplotype structures in addition to the previously completed DR2 and DR3, as well as six distinct classes of the structurally variable C4 region. Analysis of the assembled haplotypes showed that MHC class II sequence structures, including repeat element positions, are generally conserved within the DR haplotype supergroups, and that sequence diversity peaks in three regions around HLA-A, HLA-B+C, and the HLA class II genes. Demonstrating the potential for improved short-read analysis, the number of proper read pairs recruited to the MHC was found to be increased by 0.06%-0.49% in a 1000 Genomes Project read remapping experiment with seven diverse samples. Furthermore, the assembled haplotypes can serve as references for the community and provide the basis of a structurally accurate genotyping graph of the complete MHC region.
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Affiliation(s)
- Torsten Houwaart
- Institute of Medical Microbiology and Hospital HygieneHeinrich Heine University DüsseldorfDüsseldorfGermany
| | - Stephan Scholz
- Institute of Medical Microbiology and Hospital HygieneHeinrich Heine University DüsseldorfDüsseldorfGermany
| | - Nicholas R. Pollock
- Department of Biomedical InformaticsAnschutz Medical Campus, University of ColoradoAuroraColoradoUSA
- Department of Immunology and MicrobiologyAnschutz Medical Campus, University of ColoradoAuroraColoradoUSA
| | - William H. Palmer
- Department of Biomedical InformaticsAnschutz Medical Campus, University of ColoradoAuroraColoradoUSA
- Department of Immunology and MicrobiologyAnschutz Medical Campus, University of ColoradoAuroraColoradoUSA
| | - Katherine M. Kichula
- Department of Biomedical InformaticsAnschutz Medical Campus, University of ColoradoAuroraColoradoUSA
- Department of Immunology and MicrobiologyAnschutz Medical Campus, University of ColoradoAuroraColoradoUSA
| | - Daniel Strelow
- Institute of Medical Microbiology and Hospital HygieneHeinrich Heine University DüsseldorfDüsseldorfGermany
| | - Duyen B. Le
- Institute of Medical Microbiology and Hospital HygieneHeinrich Heine University DüsseldorfDüsseldorfGermany
| | - Dana Belick
- Institute of Medical Microbiology and Hospital HygieneHeinrich Heine University DüsseldorfDüsseldorfGermany
| | - Lisanna Hülse
- Institute of Medical Microbiology and Hospital HygieneHeinrich Heine University DüsseldorfDüsseldorfGermany
| | - Tobias Lautwein
- Biologisch‐Medizinisches‐Forschungszentrum (BMFZ)Genomics & Transcriptomics Laboratory, Heinrich Heine University DüsseldorfDüsseldorfGermany
| | - Thorsten Wachtmeister
- Biologisch‐Medizinisches‐Forschungszentrum (BMFZ)Genomics & Transcriptomics Laboratory, Heinrich Heine University DüsseldorfDüsseldorfGermany
| | - Tassilo E. Wollenweber
- Biologisch‐Medizinisches‐Forschungszentrum (BMFZ)Genomics & Transcriptomics Laboratory, Heinrich Heine University DüsseldorfDüsseldorfGermany
| | - Birgit Henrich
- Institute of Medical Microbiology and Hospital HygieneHeinrich Heine University DüsseldorfDüsseldorfGermany
| | - Karl Köhrer
- Biologisch‐Medizinisches‐Forschungszentrum (BMFZ)Genomics & Transcriptomics Laboratory, Heinrich Heine University DüsseldorfDüsseldorfGermany
| | - Peter Parham
- Department of Structural Biology, and Department of Microbiology and ImmunologyStanford UniversityStanfordCaliforniaUSA
| | - Lisbeth A. Guethlein
- Department of Structural Biology, and Department of Microbiology and ImmunologyStanford UniversityStanfordCaliforniaUSA
| | - Paul J. Norman
- Department of Biomedical InformaticsAnschutz Medical Campus, University of ColoradoAuroraColoradoUSA
- Department of Immunology and MicrobiologyAnschutz Medical Campus, University of ColoradoAuroraColoradoUSA
| | - Alexander T. Dilthey
- Institute of Medical Microbiology and Hospital HygieneHeinrich Heine University DüsseldorfDüsseldorfGermany
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3
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Creary LE, Guerra SG, Chong W, Brown CJ, Turner TR, Robinson J, Bultitude WP, Mayor NP, Marsh SGE, Saito K, Lam K, Duke JL, Mosbruger TL, Ferriola D, Monos D, Willis A, Askar M, Fischer G, Saw CL, Ragoussis J, Petrek M, Serra-Pagés C, Juan M, Stavropoulos-Giokas C, Dinou A, Ameen R, Al Shemmari S, Spierings E, Gendzekhadze K, Morris GP, Zhang Q, Kashi Z, Hsu S, Gangavarapu S, Mallempati KC, Yamamoto F, Osoegawa K, Vayntrub T, Chang CJ, Hansen JA, Fernández-Viňa MA. Next-generation HLA typing of 382 International Histocompatibility Working Group reference B-lymphoblastoid cell lines: Report from the 17th International HLA and Immunogenetics Workshop. Hum Immunol 2019; 80:449-460. [PMID: 30844424 DOI: 10.1016/j.humimm.2019.03.001] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Revised: 02/09/2019] [Accepted: 03/01/2019] [Indexed: 10/27/2022]
Abstract
Extended molecular characterization of HLA genes in the IHWG reference B-lymphoblastoid cell lines (B-LCLs) was one of the major goals for the 17th International HLA and Immunogenetics Workshop (IHIW). Although reference B-LCLs have been examined extensively in previous workshops complete high-resolution typing was not completed for all the classical class I and class II HLA genes. To address this, we conducted a single-blind study where select panels of B-LCL genomic DNA samples were distributed to multiple laboratories for HLA genotyping by next-generation sequencing methods. Identical cell panels comprised of 24 and 346 samples were distributed and typed by at least four laboratories in order to derive accurate consensus HLA genotypes. Overall concordance rates calculated at both 2- and 4-field allele-level resolutions ranged from 90.4% to 100%. Concordance for the class I genes ranged from 91.7 to 100%, whereas concordance for class II genes was variable; the lowest observed at HLA-DRB3 (84.2%). At the maximum allele-resolution 78 B-LCLs were defined as homozygous for all 11 loci. We identified 11 novel exon polymorphisms in the entire cell panel. A comparison of the B-LCLs NGS HLA genotypes with the HLA genotypes catalogued in the IPD-IMGT/HLA Database Cell Repository, revealed an overall allele match at 68.4%. Typing discrepancies between the two datasets were mostly due to the lower-resolution historical typing methods resulting in incomplete HLA genotypes for some samples listed in the IPD-IMGT/HLA Database Cell Repository. Our approach of multiple-laboratory NGS HLA typing of the B-LCLs has provided accurate genotyping data. The data generated by the tremendous collaborative efforts of the 17th IHIW participants is useful for updating the current cell and sequence databases and will be a valuable resource for future studies.
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Affiliation(s)
- Lisa E Creary
- Department of Pathology, Stanford University School of Medicine, Palo Alto, CA, USA; Histocompatibility, Immunogenetics and Disease Profiling Laboratory, Stanford Blood Center, Palo Alto, CA, USA.
| | - Sandra G Guerra
- Histocompatibility and Immunogenetics Service Development Laboratory, NHS Blood and Transplant, London, UK
| | - Winnie Chong
- Histocompatibility and Immunogenetics Service Development Laboratory, NHS Blood and Transplant, London, UK
| | - Colin J Brown
- Department of Histocompatibility and Immunogenetics, NHS Blood and Transplant, London, UK
| | - Thomas R Turner
- Anthony Nolan Research Institute, Royal Free Hospital, London, UK; UCL Cancer Institute, Royal Free Campus, London, UK
| | - James Robinson
- Anthony Nolan Research Institute, Royal Free Hospital, London, UK; UCL Cancer Institute, Royal Free Campus, London, UK
| | - Will P Bultitude
- Anthony Nolan Research Institute, Royal Free Hospital, London, UK; UCL Cancer Institute, Royal Free Campus, London, UK
| | - Neema P Mayor
- Anthony Nolan Research Institute, Royal Free Hospital, London, UK; UCL Cancer Institute, Royal Free Campus, London, UK
| | - Steven G E Marsh
- Anthony Nolan Research Institute, Royal Free Hospital, London, UK; UCL Cancer Institute, Royal Free Campus, London, UK
| | - Katsuyuki Saito
- Molecular Biology Research Department, One Lambda, Thermo Fisher Scientific, Canoga Park, CA, USA
| | - Kevin Lam
- Molecular Biology Research Department, One Lambda, Thermo Fisher Scientific, Canoga Park, CA, USA
| | - Jamie L Duke
- Immunogenetics Laboratory, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Timothy L Mosbruger
- Immunogenetics Laboratory, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Deborah Ferriola
- Immunogenetics Laboratory, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Dimitrios Monos
- Immunogenetics Laboratory, The Children's Hospital of Philadelphia, Philadelphia, PA, USA; Department of Pathology and Lab Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Amanda Willis
- Department of Pathology and Laboratory Medicine, Baylor University Medical Center, Dallas, USA
| | - Medhat Askar
- Department of Pathology and Laboratory Medicine, Baylor University Medical Center, Dallas, USA
| | - Gottfried Fischer
- Department for Blood Group Serology and Transfusion Medicine, Medical University of Vienna, Vienna, Austria
| | - Chee Loong Saw
- HLA Laboratory, Division of Haematology, McGill University Health Centre, Montreal, Canada
| | - Jiannis Ragoussis
- Department of Human Genetics, McGill University & McGill University and Genome Quèbec Innovation Centre, Montreal, Canada
| | - Martin Petrek
- Department of Pathological Physiology and Immunogenomics, IMTM, Faculty of Medicine and Dentistry, Palacky University, Olomouc, Czech Republic
| | - Carles Serra-Pagés
- Immunology Department, Hospital Clinic de Barcelona, University of Barcelona, IDIBAPS, Barcelona, Spain
| | - Manel Juan
- Immunology Department, Hospital Clinic de Barcelona, University of Barcelona, IDIBAPS, Barcelona, Spain
| | | | - Amalia Dinou
- Biomedical Research Foundation Academy of Athens, Hellenic Cord Blood Bank, Athens, Greece
| | - Reem Ameen
- Health Sciences Center, Kuwait University, Kuwait
| | | | - Eric Spierings
- Laboratory of Translational Immunology, UMC Utrecht, Utrecht, Netherlands
| | | | - Gerald P Morris
- Department of Pathology, University of California San Diego, La Jolla, CA, USA
| | - Qiuheng Zhang
- Department of Pathology and Laboratory Medicine, UCLA Immunogenetics Center, Los Angeles, CA, USA
| | - Zahra Kashi
- HLA Department, Kashi Clinical Laboratories, Inc., Portland, OR, USA
| | - Susan Hsu
- HLA Laboratory, American Red Cross, Philadelphia, PA, USA
| | - Sridevi Gangavarapu
- Histocompatibility, Immunogenetics and Disease Profiling Laboratory, Stanford Blood Center, Palo Alto, CA, USA
| | - Kalyan C Mallempati
- Histocompatibility, Immunogenetics and Disease Profiling Laboratory, Stanford Blood Center, Palo Alto, CA, USA
| | - Fumiko Yamamoto
- Histocompatibility, Immunogenetics and Disease Profiling Laboratory, Stanford Blood Center, Palo Alto, CA, USA
| | - Kazutoyo Osoegawa
- Histocompatibility, Immunogenetics and Disease Profiling Laboratory, Stanford Blood Center, Palo Alto, CA, USA
| | - Tamara Vayntrub
- Histocompatibility, Immunogenetics and Disease Profiling Laboratory, Stanford Blood Center, Palo Alto, CA, USA
| | | | - John A Hansen
- Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Marcelo A Fernández-Viňa
- Department of Pathology, Stanford University School of Medicine, Palo Alto, CA, USA; Histocompatibility, Immunogenetics and Disease Profiling Laboratory, Stanford Blood Center, Palo Alto, CA, USA
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4
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Kelly A, Trowsdale J. Introduction: MHC/KIR and governance of specificity. Immunogenetics 2017; 69:481-488. [PMID: 28695288 PMCID: PMC5537316 DOI: 10.1007/s00251-017-0986-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Accepted: 04/12/2017] [Indexed: 12/02/2022]
Abstract
The MHC controls specificity, to ensure that appropriate immune responses are mounted to invading pathogens whilst maintaining tolerance to the host. It encodes molecules that act as sentinels, providing a snapshot of the health of the interior and exterior of the cell for immune surveillance. To maintain the ability to respond appropriately to any disease requires a delicate balance of expression and function, and many subtleties of the system have been described at the gene, individual and population level. The main players are the highly polymorphic classical MHC class I and class II molecules, as well as some non-classical loci of both types. Transporter associated with antigen processing (TAP) peptide transporters, proteasome components and Tapasin, encoded within the MHC, are also involved in selection of peptide for presentation. The plethora of mechanisms microorganisms use to subvert immune recognition, through blocking these antigen processing and presentation pathways, attests to the importance of HLA in resistance to infection. There is continued interest in MHC genetics in its own right, as well as in relation to KIR, to transplantation, infection, autoimmunity and reproduction. Also of topical interest, cancer immunotherapy through checkpoint inhibition depends on highly specific recognition of cancer peptide antigen and continued expression of HLA molecules. Here, we briefly introduce some background to the MHC/KIR axis in man. This special issue of immunogenetics expands on these topics, in humans and other model species.
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Affiliation(s)
- Adrian Kelly
- Department of Pathology, University of Cambridge, Cambridge, CB21QP, UK
| | - John Trowsdale
- Department of Pathology, University of Cambridge, Cambridge, CB21QP, UK.
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5
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Petersdorf EW. Role of major histocompatibility complex variation in graft-versus-host disease after hematopoietic cell transplantation. F1000Res 2017; 6:617. [PMID: 28529723 PMCID: PMC5419254 DOI: 10.12688/f1000research.10990.1] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 04/25/2017] [Indexed: 01/01/2023] Open
Abstract
Graft-versus-host disease (GVHD) remains a significant potentially life-threatening complication of allogeneic hematopoietic cell transplantation (HCT). Since the discovery of the human leukocyte antigen (HLA) system over 50 years ago, significant advances have clarified the nature of HLA variation between transplant recipients and donors as a chief etiology of GVHD. New information on coding and non-coding gene variation and GVHD risk provides clinicians with options to consider selected mismatched donors when matched donors are not available. These advances have increased the availability of unrelated donors for patients in need of a transplant and have lowered the overall morbidity and mortality of HCT.
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6
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Norman PJ, Norberg SJ, Guethlein LA, Nemat-Gorgani N, Royce T, Wroblewski EE, Dunn T, Mann T, Alicata C, Hollenbach JA, Chang W, Shults Won M, Gunderson KL, Abi-Rached L, Ronaghi M, Parham P. Sequences of 95 human MHC haplotypes reveal extreme coding variation in genes other than highly polymorphic HLA class I and II. Genome Res 2017; 27:813-823. [PMID: 28360230 PMCID: PMC5411776 DOI: 10.1101/gr.213538.116] [Citation(s) in RCA: 69] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Accepted: 02/10/2017] [Indexed: 12/26/2022]
Abstract
The most polymorphic part of the human genome, the MHC, encodes over 160 proteins of diverse function. Half of them, including the HLA class I and II genes, are directly involved in immune responses. Consequently, the MHC region strongly associates with numerous diseases and clinical therapies. Notoriously, the MHC region has been intractable to high-throughput analysis at complete sequence resolution, and current reference haplotypes are inadequate for large-scale studies. To address these challenges, we developed a method that specifically captures and sequences the 4.8-Mbp MHC region from genomic DNA. For 95 MHC homozygous cell lines we assembled, de novo, a set of high-fidelity contigs and a sequence scaffold, representing a mean 98% of the target region. Included are six alternative MHC reference sequences of the human genome that we completed and refined. Characterization of the sequence and structural diversity of the MHC region shows the approach accurately determines the sequences of the highly polymorphic HLA class I and HLA class II genes and the complex structural diversity of complement factor C4A/C4B. It has also uncovered extensive and unexpected diversity in other MHC genes; an example is MUC22, which encodes a lung mucin and exhibits more coding sequence alleles than any HLA class I or II gene studied here. More than 60% of the coding sequence alleles analyzed were previously uncharacterized. We have created a substantial database of robust reference MHC haplotype sequences that will enable future population scale studies of this complicated and clinically important region of the human genome.
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Affiliation(s)
- Paul J Norman
- Departments of Structural Biology and Microbiology & Immunology, Stanford University School of Medicine, Stanford, California 94305, USA
| | | | - Lisbeth A Guethlein
- Departments of Structural Biology and Microbiology & Immunology, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Neda Nemat-Gorgani
- Departments of Structural Biology and Microbiology & Immunology, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Thomas Royce
- Illumina Incorporated, San Diego, California 92122, USA
| | - Emily E Wroblewski
- Departments of Structural Biology and Microbiology & Immunology, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Tamsen Dunn
- Illumina Incorporated, San Diego, California 92122, USA
| | - Tobias Mann
- Illumina Incorporated, San Diego, California 92122, USA
| | - Claudia Alicata
- Departments of Structural Biology and Microbiology & Immunology, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Jill A Hollenbach
- Department of Neurology, University of California San Francisco School of Medicine, San Francisco, California 94158, USA
| | - Weihua Chang
- Illumina Incorporated, San Diego, California 92122, USA
| | | | | | - Laurent Abi-Rached
- Departments of Structural Biology and Microbiology & Immunology, Stanford University School of Medicine, Stanford, California 94305, USA
| | | | - Peter Parham
- Departments of Structural Biology and Microbiology & Immunology, Stanford University School of Medicine, Stanford, California 94305, USA
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7
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Ashouri E, Norman PJ, Guethlein LA, Han AS, Nemat-Gorgani N, Norberg SJ, Ghaderi A, Parham P. HLA class I variation in Iranian Lur and Kurd populations: high haplotype and allotype diversity with an abundance of KIR ligands. HLA 2016; 88:87-99. [PMID: 27558013 DOI: 10.1111/tan.12852] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Revised: 07/10/2016] [Accepted: 07/21/2016] [Indexed: 11/30/2022]
Abstract
HLA-A, -B and -C alleles of 285 individuals, representing three Iranian Lur populations and one Iranian Kurd population were sequenced completely, yielding human leukocyte antigen (HLA) class I genotypes at high resolution and filling four fields of the official HLA nomenclature. Each population has 87-99 alleles, evenly distributed between the three HLA class I genes, 145 alleles being identified in total. These alleles were already known, named and deposited in the HLA database. The alleles form 316 different HLA A-B-C haplotypes, with each population having between 80 and 112 haplotypes. The four Iranian populations form a related group that is distinguished from other populations, including other Iranians. All four KIR ligands - the A3/11, Bw4, C1 and C2 epitopes - are well represented, particularly Bw4, which is carried by three high-frequency allotypes: HLA-A*24:02, HLA-A*32:01 and HLA-B*51:01. In the Lur and Kurd populations, between 82% and 94% of individuals have the Bw4 epitope, the ligand for KIR3DL1. HLA-B*51:01 is likely of Neandertal origin and associated with Behcet's disease, also known as the Silk Road disease. The Lordegan Lur have the highest frequency of HLA-B*51:01 in the world. This allele is present on 46 Lur and Kurd haplotypes. Present at lower frequency is HLA-B*51:08, which is also associated with Behcet's disease. In the four Iranian populations, 31 haplotypes encode both Bw4(+) HLA-A and Bw4(+) HLA-B, a dual combination of Bw4 epitopes that is relatively rare in other populations, worldwide. This study both demonstrates and emphasizes the value of studying HLA class I polymorphism at highest resolution in anthropologically well-defined populations.
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Affiliation(s)
- E Ashouri
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA.,Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA.,Endocrinology and Metabolism Research Center, Namazi Hospital, Shiraz University of Medical Sciences, Shiraz, Iran
| | - P J Norman
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA.,Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - L A Guethlein
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA.,Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - A S Han
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA.,Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - N Nemat-Gorgani
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA.,Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | | | - A Ghaderi
- Shiraz Institute for Cancer Research, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - P Parham
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA.,Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
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Norman P, Hollenbach J, Nemat-Gorgani N, Marin W, Norberg S, Ashouri E, Jayaraman J, Wroblewski E, Trowsdale J, Rajalingam R, Oksenberg J, Chiaroni J, Guethlein L, Traherne J, Ronaghi M, Parham P. Defining KIR and HLA Class I Genotypes at Highest Resolution via High-Throughput Sequencing. Am J Hum Genet 2016; 99:375-91. [PMID: 27486779 DOI: 10.1016/j.ajhg.2016.06.023] [Citation(s) in RCA: 113] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2016] [Accepted: 06/23/2016] [Indexed: 12/12/2022] Open
Abstract
The physiological functions of natural killer (NK) cells in human immunity and reproduction depend upon diverse interactions between killer cell immunoglobulin-like receptors (KIRs) and their HLA class I ligands: HLA-A, HLA-B, and HLA-C. The genomic regions containing the KIR and HLA class I genes are unlinked, structurally complex, and highly polymorphic. They are also strongly associated with a wide spectrum of diseases, including infections, autoimmune disorders, cancers, and pregnancy disorders, as well as the efficacy of transplantation and other immunotherapies. To facilitate study of these extraordinary genes, we developed a method that captures, sequences, and analyzes the 13 KIR genes and HLA-A, HLA-B, and HLA-C from genomic DNA. We also devised a bioinformatics pipeline that attributes sequencing reads to specific KIR genes, determines copy number by read depth, and calls high-resolution genotypes for each KIR gene. We validated this method by using DNA from well-characterized cell lines, comparing it to established methods of HLA and KIR genotyping, and determining KIR genotypes from 1000 Genomes sequence data. This identified 116 previously uncharacterized KIR alleles, which were all demonstrated to be authentic by sequencing from source DNA via standard methods. Analysis of just two KIR genes showed that 22% of the 1000 Genomes individuals have a previously uncharacterized allele or a structural variant. The method we describe is suited to the large-scale analyses that are needed for characterizing human populations and defining the precise HLA and KIR factors associated with disease. The methods are applicable to other highly polymorphic genes.
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