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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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Zhou Y, Song L, Li H. Full resolution HLA and KIR genes annotation for human genome assemblies. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.20.576452. [PMID: 38328160 PMCID: PMC10849470 DOI: 10.1101/2024.01.20.576452] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Abstract
The HLA (Human Leukocyte Antigen) genes and the KIR (Killer cell Immunoglobulin-like Receptor) genes are critical to immune responses and are associated with many immune-related diseases. Located in highly polymorphic regions, they are hard to be studied with traditional short-read alignment-based methods. Although modern long-read assemblers can often assemble these genes, using existing tools to annotate HLA and KIR genes in these assemblies remains a non-trivial task. Here, we describe Immuannot, a new computation tool to annotate the gene structures of HLA and KIR genes and to type the allele of each gene. Applying Immuannot to 56 regional and 212 whole-genome assemblies from previous studies, we annotated 9,931 HLA and KIR genes and found that almost half of these genes, 4,068, had novel sequences compared to the current Immuno Polymorphism Database (IPD). These novel gene sequences were represented by 2,664 distinct alleles, some of which contained non-synonymous variations resulting in 92 novel protein sequences. We demonstrated the complex haplotype structures at the two loci and reported the linkage between HLA/KIR haplotypes and gene alleles. We anticipate that Immuannot will speed up the discovery of new HLA/KIR alleles and enable the association of HLA/KIR haplotype structures with clinical outcomes in the future.
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Affiliation(s)
- Ying Zhou
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, 02115, USA
| | - Li Song
- Department of Biomedical Data Science, Dartmouth College, Hanover, NH, 03755, USA
| | - Heng Li
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, 02115, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, 02115, USA
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Klussmeier A, Putke K, Klasberg S, Kohler M, Sauter J, Schefzyk D, Schöfl G, Massalski C, Schäfer G, Schmidt AH, Roers A, Lange V. High population frequencies of MICA copy number variations originate from independent recombination events. Front Immunol 2023; 14:1297589. [PMID: 38035108 PMCID: PMC10684724 DOI: 10.3389/fimmu.2023.1297589] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Accepted: 10/24/2023] [Indexed: 12/02/2023] Open
Abstract
MICA is a stress-induced ligand of the NKG2D receptor that stimulates NK and T cell responses and was identified as a key determinant of anti-tumor immunity. The MICA gene is located inside the MHC complex and is in strong linkage disequilibrium with HLA-B. While an HLA-B*48-linked MICA deletion-haplotype was previously described in Asian populations, little is known about other MICA copy number variations. Here, we report the genotyping of more than two million individuals revealing high frequencies of MICA duplications (1%) and MICA deletions (0.4%). Their prevalence differs between ethnic groups and can rise to 2.8% (Croatia) and 9.2% (Mexico), respectively. Targeted sequencing of more than 70 samples indicates that these copy number variations originate from independent nonallelic homologous recombination events between segmental duplications upstream of MICA and MICB. Overall, our data warrant further investigation of disease associations and consideration of MICA copy number data in oncological study protocols.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Axel Roers
- Institute for Immunology, Medical Faculty Carl Gustav Carus, University of Technology (TU) Dresden, Dresden, Germany
- Institute for Immunology, University Hospital Heidelberg, Heidelberg, Germany
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Laufer VA, Glover TW, Wilson TE. Applications of advanced technologies for detecting genomic structural variation. MUTATION RESEARCH. REVIEWS IN MUTATION RESEARCH 2023; 792:108475. [PMID: 37931775 PMCID: PMC10792551 DOI: 10.1016/j.mrrev.2023.108475] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 09/07/2023] [Accepted: 11/02/2023] [Indexed: 11/08/2023]
Abstract
Chromosomal structural variation (SV) encompasses a heterogenous class of genetic variants that exerts strong influences on human health and disease. Despite their importance, many structural variants (SVs) have remained poorly characterized at even a basic level, a discrepancy predicated upon the technical limitations of prior genomic assays. However, recent advances in genomic technology can identify and localize SVs accurately, opening new questions regarding SV risk factors and their impacts in humans. Here, we first define and classify human SVs and their generative mechanisms, highlighting characteristics leveraged by various SV assays. We next examine the first-ever gapless assembly of the human genome and the technical process of assembling it, which required third-generation sequencing technologies to resolve structurally complex loci. The new portions of that "telomere-to-telomere" and subsequent pangenome assemblies highlight aspects of SV biology likely to develop in the near-term. We consider the strengths and limitations of the most promising new SV technologies and when they or longstanding approaches are best suited to meeting salient goals in the study of human SV in population-scale genomics research, clinical, and public health contexts. It is a watershed time in our understanding of human SV when new approaches are expected to fundamentally change genomic applications.
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Affiliation(s)
- Vincent A Laufer
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI 48109, USA.
| | - Thomas W Glover
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI 48109, USA; Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI 48109, USA.
| | - Thomas E Wilson
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI 48109, USA; Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI 48109, USA.
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