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Marzouka NAD, Alnaqbi H, Al-Aamri A, Tay G, Alsafar H. Investigating the genetic makeup of the major histocompatibility complex (MHC) in the United Arab Emirates population through next-generation sequencing. Sci Rep 2024; 14:3392. [PMID: 38337023 PMCID: PMC10858242 DOI: 10.1038/s41598-024-53986-1] [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: 11/26/2023] [Accepted: 02/07/2024] [Indexed: 02/12/2024] Open
Abstract
The Human leukocyte antigen (HLA) molecules are central to immune response and have associations with the phenotypes of various diseases and induced drug toxicity. Further, the role of HLA molecules in presenting antigens significantly affects the transplantation outcome. The objective of this study was to examine the extent of the diversity of HLA alleles in the population of the United Arab Emirates (UAE) using Next-Generation Sequencing methodologies and encompassing a larger cohort of individuals. A cohort of 570 unrelated healthy citizens of the UAE volunteered to provide samples for Whole Genome Sequencing and Whole Exome Sequencing. The definition of the HLA alleles was achieved through the application of the bioinformatics tools, HLA-LA and xHLA. Subsequently, the findings from this study were compared with other local and international datasets. A broad range of HLA alleles in the UAE population, of which some were previously unreported, was identified. A comparison with other populations confirmed the current population's unique intertwined genetic heritage while highlighting similarities with populations from the Middle East region. Some disease-associated HLA alleles were detected at a frequency of > 5%, such as HLA-B*51:01, HLA-DRB1*03:01, HLA-DRB1*15:01, and HLA-DQB1*02:01. The increase in allele homozygosity, especially for HLA class I genes, was identified in samples with a higher level of genome-wide homozygosity. This highlights a possible effect of consanguinity on the HLA homozygosity. The HLA allele distribution in the UAE population showcases a unique profile, underscoring the need for tailored databases for traditional activities such as unrelated transplant matching and for newer initiatives in precision medicine based on specific populations. This research is part of a concerted effort to improve the knowledge base, particularly in the fields of transplant medicine and investigating disease associations as well as in understanding human migration patterns within the Arabian Peninsula and surrounding regions.
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Affiliation(s)
- Nour Al Dain Marzouka
- Center for Biotechnology, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
| | - Halima Alnaqbi
- Center for Biotechnology, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
| | - Amira Al-Aamri
- Center for Biotechnology, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
| | - Guan Tay
- Division of Psychiatry, Faculty of Health and Medical Sciences, Medical School, The University of Western Australia, Crawley, WA, Australia
- School of Medical and Health Sciences, Edith Cowan University, Joondalup, WA, Australia
| | - Habiba Alsafar
- Center for Biotechnology, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates.
- College of Medicine and Health Sciences, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates.
- Department of Biomedical Engineering, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates.
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2
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Shiina T, Kulski JK. HLA Genetics for the Human Diseases. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2024; 1444:237-258. [PMID: 38467984 DOI: 10.1007/978-981-99-9781-7_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/13/2024]
Abstract
Highly polymorphic human leukocyte antigen (HLA) molecules (alleles) expressed by different classical HLA class I and class II genes have crucial roles in the regulation of innate and adaptive immune responses, transplant rejection and in the pathogenesis of numerous infectious and autoimmune diseases. To date, over 35,000 HLA alleles have been published from the IPD-IMGT/HLA database, and specific HLA alleles and HLA haplotypes have been reported to be associated with more than 100 different diseases and phenotypes. Next generation sequencing (NGS) technology developed in recent years has provided breakthroughs in various HLA genomic/gene studies and transplant medicine. In this chapter, we review the current information on the HLA genomic structure and polymorphisms, as well as the genetic context in which numerous disease associations have been identified in this region.
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Affiliation(s)
| | - Jerzy K Kulski
- Tokai University School of Medicine, Isehara, Japan
- School of Biomedical Sciences, The University of Western Australia, Nedlands, Western Australia, Australia
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3
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Human leukocyte antigen super-locus: nexus of genomic supergenes, SNPs, indels, transcripts, and haplotypes. Hum Genome Var 2022; 9:49. [PMID: 36543786 PMCID: PMC9772353 DOI: 10.1038/s41439-022-00226-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 11/08/2022] [Accepted: 11/15/2022] [Indexed: 12/24/2022] Open
Abstract
The human Major Histocompatibility Complex (MHC) or Human Leukocyte Antigen (HLA) super-locus is a highly polymorphic genomic region that encodes more than 140 coding genes including the transplantation and immune regulatory molecules. It receives special attention for genetic investigation because of its important role in the regulation of innate and adaptive immune responses and its strong association with numerous infectious and/or autoimmune diseases. In recent years, MHC genotyping and haplotyping using Sanger sequencing and next-generation sequencing (NGS) methods have produced many hundreds of genomic sequences of the HLA super-locus for comparative studies of the genetic architecture and diversity between the same and different haplotypes. In this special issue on 'The Current Landscape of HLA Genomics and Genetics', we provide a short review of some of the recent analytical developments used to investigate the SNP polymorphisms, structural variants (indels), transcription and haplotypes of the HLA super-locus. This review highlights the importance of using reference cell-lines, population studies, and NGS methods to improve and update our understanding of the mechanisms, architectural structures and combinations of human MHC genomic alleles (SNPs and indels) that better define and characterise haplotypes and their association with various phenotypes and diseases.
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4
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Sun Y, Yuan F, Wang L, Dai D, Zhang Z, Liang F, Liu N, Long J, Zhao X, Xi Y. Recombination and mutation shape variations in the major histocompatibility complex. J Genet Genomics 2022; 49:1151-1161. [PMID: 35358716 DOI: 10.1016/j.jgg.2022.03.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2021] [Revised: 03/07/2022] [Accepted: 03/08/2022] [Indexed: 01/14/2023]
Abstract
The major histocompatibility complex (MHC) is closely associated with numerous diseases, but its high degree of polymorphism complicates the discovery of disease-associated variants. In principle, recombination and de novo mutations are two critical factors responsible for MHC polymorphisms. However, direct evidence for this hypothesis is lacking. Here, we report the generation of fine-scale MHC recombination and de novo mutation maps of ∼5 Mb by deep sequencing (> 100×) of the MHC genome for 17 MHC recombination and 30 non-recombination Han Chinese families (a total of 190 individuals). Recombination hotspots and Han-specific breakpoints are located in close proximity at haplotype block boundaries. The average MHC de novo mutation rate is higher than the genome-wide de novo mutation rate, particularly in MHC recombinant individuals. Notably, mutation and recombination generated polymorphisms are located within and outside linkage disequilibrium regions of the MHC, respectively, and evolution of the MHC locus was mainly controlled by positive selection. These findings provide insights on the evolutionary causes of the MHC diversity and may facilitate the identification of disease-associated genetic variants.
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Affiliation(s)
- Yuying Sun
- Department of Immunology and National Immunoassay Laboratory, Fifth Medical Center of Chinese PLA General Hospital, Beijing 100071, China; Institute of Beijing 307 Hospital, Anhui Medical University, Hefei, Anhui 230032, China.
| | - Fang Yuan
- Department of Immunology and National Immunoassay Laboratory, Fifth Medical Center of Chinese PLA General Hospital, Beijing 100071, China
| | - Ling Wang
- Department of Immunology and National Immunoassay Laboratory, Fifth Medical Center of Chinese PLA General Hospital, Beijing 100071, China; Institute of Beijing 307 Hospital, Anhui Medical University, Hefei, Anhui 230032, China
| | - Dongfa Dai
- Department of Immunology and National Immunoassay Laboratory, Fifth Medical Center of Chinese PLA General Hospital, Beijing 100071, China; Institute of Beijing 307 Hospital, Anhui Medical University, Hefei, Anhui 230032, China
| | - Zhijian Zhang
- Department of Immunology and National Immunoassay Laboratory, Fifth Medical Center of Chinese PLA General Hospital, Beijing 100071, China; Institute of Beijing 307 Hospital, Anhui Medical University, Hefei, Anhui 230032, China
| | - Fei Liang
- Department of Immunology and National Immunoassay Laboratory, Fifth Medical Center of Chinese PLA General Hospital, Beijing 100071, China
| | - Nan Liu
- Department of Immunology and National Immunoassay Laboratory, Fifth Medical Center of Chinese PLA General Hospital, Beijing 100071, China
| | - Juan Long
- Department of Immunology and National Immunoassay Laboratory, Fifth Medical Center of Chinese PLA General Hospital, Beijing 100071, China
| | - Xiao Zhao
- Department of Immunology and National Immunoassay Laboratory, Fifth Medical Center of Chinese PLA General Hospital, Beijing 100071, China
| | - Yongzhi Xi
- Department of Immunology and National Immunoassay Laboratory, Fifth Medical Center of Chinese PLA General Hospital, Beijing 100071, China.
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5
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Timofeeva OA, Philogene MC, Zhang QJ. Current donor selection strategies for allogeneic hematopoietic cell transplantation. Hum Immunol 2022; 83:674-686. [PMID: 36038413 DOI: 10.1016/j.humimm.2022.08.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Revised: 08/11/2022] [Accepted: 08/12/2022] [Indexed: 12/27/2022]
Abstract
Since the first allogeneic hematopoietic stem cell transplantation (HCT) was performed by Dr. E. Donnall Thomas in 1957, the field has advanced with new stem cell sources, immune suppressive regimens, and transplant protocols. Stem cells may be collected from bone marrow, peripheral or cord blood from an identical twin, a sibling, or a related or unrelated donor, which can be human leukocyte antigen (HLA) matched, mismatched, or haploidentical. Although HLA matching is one of the most important criteria for successful allogeneic HCT (allo-HCT) to minimize graft vs host disease (GVHD), prevent relapse, and improve overall survival, the novel immunosuppressive protocols for GVHD prophylaxis offered improved outcomes in haploidentical HCT (haplo-HCT), expanding donor availability for the majority of HCT candidates. These immunosuppressive protocols are currently being tested with the HLA-matched and mismatched donors to improve HCT outcomes further. In addition, fine-tuning the DPB1 mismatching and discovering the B leader genotype and mismatching may offer further optimization of donor selection and transplant outcomes. While the decision about a donor type largely depends on the patient's characteristics, disease status, and the transplant protocols utilized by an individual transplant center, there are general approaches to donor selection dictated by donor-recipient histocompatibility and the urgency for HCT. This review highlights recent advances in understanding critical factors in donor selection strategies for allo-HCT. It uses clinical vignettes to demonstrate the importance of making timely decisions for HCT candidates.
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Affiliation(s)
- Olga A Timofeeva
- Department of Pathology and Laboratory Medicine, MedStar Georgetown University Hospital, Georgetown University School of Medicine, Georgetown University Medical Center, Washington, DC 20007, United States.
| | - Mary Carmelle Philogene
- Histocompatibility Laboratory Services, American Red Cross, Penn-Jersey Region, Philadelphia, PA 19123, United States.
| | - Qiuheng Jennifer Zhang
- UCLA Immunogenetics Center, Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles 90095, United States.
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Mytilineos D, Tsamadou C, Neuchel C, Platzbecker U, Bunjes D, Schub N, Wagner-Drouet E, Wulf G, Kröger N, Murawski N, Einsele H, Schaefer-Eckart K, Freitag S, Casper J, Kaufmann M, Dürholt M, Hertenstein B, Klein S, Ringhoffer M, Mueller CR, Frank S, Schrezenmeier H, Fuerst D, Mytilineos J. The Human Leukocyte Antigen-DPB1 Degree of Compatibility Is Determined by Its Expression Level and Mismatch Permissiveness: A German Multicenter Analysis. Front Immunol 2021; 11:614976. [PMID: 33569061 PMCID: PMC7868530 DOI: 10.3389/fimmu.2020.614976] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Accepted: 12/10/2020] [Indexed: 11/17/2022] Open
Abstract
T-cell epitope matching according to the TCE3 algorithm classifies HLA-DPB1 mismatches in permissive and non-permissive. This classification has been shown to be predictive for mortality and acute GvHD (aGvHD) events in large international cohorts. We retrospectively genotyped HLA-DPB1 in 3523 patients transplanted in Germany between 2000 and 2014 and in their unrelated donors using an Illumina amplicon-NGS based assay. Aim of the study was to evaluate DP-compatibility beyond the established TCE3 algorithm by assessing the combined effect of several DP-mismatch parameters on post-transplant outcome. We implemented an extended DP-mismatch assessment model where TCE3, DP allotype expression with respect to rs9277534, mismatch vector and number of mismatches were conjointly taken into consideration. In this model, non-permissive HLA-DPB1 mismatches showed significantly increased aGvHD risk if they were accompanied by two HLA-DPB1 mismatches in GvH direction (HR: 1.46) or one mismatched highly expressed patient allotype (HR: 1.53). As previously reported, non-permissive HLA-DPB1 mismatches associated with a significantly higher risk of aGvHD and non-relapse mortality (HR 1.36 and 1.21, respectively), which in turn translated into worse GvHD and relapse free survival (HR 1.13). Effects on GvL and GvHD appeared strongest in GvH-directed non-permissive mismatches. Our study results support the consideration of additional HLA-DPB1 mismatch parameters along with the established TCE3 matching algorithm for refinement of future donor selection. In particular, our findings suggest that DP non-permissiveness associated with two HLA-DPB1 mismatches or at least on highly expressed mismatched patient allotype should be avoided.
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Affiliation(s)
- Daphne Mytilineos
- Institute of Clinical Transfusion Medicine and Immunogenetics Ulm, German Red Cross Blood Transfusion Service, Baden Wuerttemberg-Hessen, and University Hospital Ulm, Ulm, Germany.,Institute of Transfusion Medicine, University of Ulm, Ulm, Germany.,Department of Otorhinolaryngology, Head and Neck Surgery, University of Ulm, Ulm, Germany
| | - Chrysanthi Tsamadou
- Institute of Clinical Transfusion Medicine and Immunogenetics Ulm, German Red Cross Blood Transfusion Service, Baden Wuerttemberg-Hessen, and University Hospital Ulm, Ulm, Germany.,Institute of Transfusion Medicine, University of Ulm, Ulm, Germany
| | - Christine Neuchel
- Institute of Clinical Transfusion Medicine and Immunogenetics Ulm, German Red Cross Blood Transfusion Service, Baden Wuerttemberg-Hessen, and University Hospital Ulm, Ulm, Germany.,Institute of Transfusion Medicine, University of Ulm, Ulm, Germany
| | - Uwe Platzbecker
- Department of Hematology/Oncology, University of Leipzig, Leipzig, Germany
| | - Donald Bunjes
- Department of Internal Medicine III, University of Ulm, Ulm, Germany
| | - Natalie Schub
- Division of Stem Cell Transplantation and Immunotherapy, 2nd Department of Medicine, University of Kiel, Kiel, Germany
| | - Eva Wagner-Drouet
- Department of Medicine III, Johannes Gutenberg-University Mainz, Mainz, Germany
| | - Gerald Wulf
- Department of Hematology/Oncology, Georg-August-University Göttingen, Göttingen, Germany
| | - Nicolaus Kröger
- Department of Stem Cell Transplantation, University Hospital Hamburg Eppendorf, Hamburg, Germany
| | - Niels Murawski
- Department Internal Medicine I, Universitätsklinikum des Saarlandes, Homburg, Germany
| | - Hermann Einsele
- Department of Internal Medicine II, University Hospital Würzburg, Würzburg, Germany
| | - Kerstin Schaefer-Eckart
- Medizinische Klinik 5, Klinikum Nürnberg, Paracelsus Medizinische Privatuniversität, Nürnberg, Germany
| | - Sebastian Freitag
- Department of Medicine III, Hematology/Oncology/Palliative Care, Rostock University Medical Center, Rostock, Germany
| | - Jochen Casper
- Division of Hematology and Oncology, Oldenburg Clinic, University of Oldenburg, Oldenburg, Germany
| | - Martin Kaufmann
- 2nd Department of Internal Medicine, Oncology and Hematology, Robert Bosch Hospital Stuttgart, Stuttgart, Germany
| | - Mareike Dürholt
- Department of Hematology/Oncology and Stem Cell Transplantation, Evangelisches Krankenhaus Essen-Werden, Essen, Germany
| | - Bernd Hertenstein
- Department of Hematology/Oncology, Klinikum Bremen-Mitte, Bremen, Germany
| | - Stefan Klein
- Medizinische Klinik III, Universitäts Medizin Mannheim, Mannheim, Germany
| | - Mark Ringhoffer
- Medizinische Klinik III, Städtisches Klinikum Karlsruhe, Karlsruhe, Germany
| | - Carlheinz R Mueller
- ZKRD - Zentrales Knochenmarkspender-Register für Deutschland, German National Bone Marrow Donor Registry, Ulm, Germany.,DRST - German Registry for Stem Cell Transplantation, Ulm, Germany
| | - Sandra Frank
- DRST - German Registry for Stem Cell Transplantation, Ulm, Germany
| | - Hubert Schrezenmeier
- Institute of Clinical Transfusion Medicine and Immunogenetics Ulm, German Red Cross Blood Transfusion Service, Baden Wuerttemberg-Hessen, and University Hospital Ulm, Ulm, Germany.,Institute of Transfusion Medicine, University of Ulm, Ulm, Germany
| | - Daniel Fuerst
- Institute of Clinical Transfusion Medicine and Immunogenetics Ulm, German Red Cross Blood Transfusion Service, Baden Wuerttemberg-Hessen, and University Hospital Ulm, Ulm, Germany.,Institute of Transfusion Medicine, University of Ulm, Ulm, Germany
| | - Joannis Mytilineos
- Institute of Clinical Transfusion Medicine and Immunogenetics Ulm, German Red Cross Blood Transfusion Service, Baden Wuerttemberg-Hessen, and University Hospital Ulm, Ulm, Germany.,Institute of Transfusion Medicine, University of Ulm, Ulm, Germany.,DRST - German Registry for Stem Cell Transplantation, Ulm, Germany
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7
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Partanen J, Hyvärinen K, Bickeböller H, Bogunia-Kubik K, Crossland RE, Ivanova M, Perutelli F, Dressel R. Review of Genetic Variation as a Predictive Biomarker for Chronic Graft-Versus-Host-Disease After Allogeneic Stem Cell Transplantation. Front Immunol 2020; 11:575492. [PMID: 33193367 PMCID: PMC7604383 DOI: 10.3389/fimmu.2020.575492] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Accepted: 09/28/2020] [Indexed: 12/11/2022] Open
Abstract
Chronic graft-versus-host disease (cGvHD) is one of the major complications of allogeneic stem cell transplantation (HSCT). cGvHD is an autoimmune-like disorder affecting multiple organs and involves a dermatological rash, tissue inflammation and fibrosis. The incidence of cGvHD has been reported to be as high as 30% to 60% and there are currently no reliable tools for predicting the occurrence of cGvHD. There is therefore an important unmet clinical need for predictive biomarkers. The present review summarizes the state of the art for genetic variation as a predictive biomarker for cGvHD. We discuss three different modes of action for genetic variation in transplantation: genetic associations, genetic matching, and pharmacogenetics. The results indicate that currently, there are no genetic polymorphisms or genetic tools that can be reliably used as validated biomarkers for predicting cGvHD. A number of recommendations for future studies can be drawn. The majority of studies to date have been under-powered and included too few patients and genetic markers. Like in all complex multifactorial diseases, large collaborative genome-level studies are now needed to achieve reliable and unbiased results. Some of the candidate genes, in particular, CTLA4, HSPE, IL1R1, CCR6, FGFR1OP, and IL10, and some non-HLA variants in the HLA gene region have been replicated to be associated with cGvHD risk in independent studies. These associations should now be confirmed in large well-characterized cohorts with fine mapping. Some patients develop cGvHD despite very extensive immunosuppression and other treatments, indicating that the current therapeutic regimens may not always be effective enough. Hence, more studies on pharmacogenetics are also required. Moreover, all of these studies should be adjusted for diagnostic and clinical features of cGvHD. We conclude that future studies should focus on modern genome-level tools, such as machine learning, polygenic risk scores and genome-wide association study-transcription meta-analyses, instead of focusing on just single variants. The risk of cGvHD may be related to the summary level of immunogenetic differences, or whole genome histocompatibility between each donor-recipient pair. As the number of genome-wide analyses in HSCT is increasing, we are approaching an era where there will be sufficient data to incorporate these approaches in the near future.
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Affiliation(s)
- Jukka Partanen
- Finnish Red Cross Blood Service, Research and Development, Helsinki, Finland
| | - Kati Hyvärinen
- Finnish Red Cross Blood Service, Research and Development, Helsinki, Finland
| | - Heike Bickeböller
- Department of Genetic Epidemiology, University Medical Center Göttingen, Göttingen, Germany
| | - Katarzyna Bogunia-Kubik
- Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Wroclaw, Poland
| | - Rachel E Crossland
- Haematological Sciences, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Milena Ivanova
- Medical University, University Hospital Alexandrovska, Sofia, Bulgaria
| | - Francesca Perutelli
- Haematological Sciences, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, United Kingdom.,Section of Hematology, Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
| | - Ralf Dressel
- Institute of Cellular and Molecular Immunology, University Medical Center Göttingen, Göttingen, Germany
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8
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Ritari J, Hyvärinen K, Clancy J, Partanen J, Koskela S. Increasing accuracy of HLA imputation by a population-specific reference panel in a FinnGen biobank cohort. NAR Genom Bioinform 2020; 2:lqaa030. [PMID: 33575586 PMCID: PMC7671345 DOI: 10.1093/nargab/lqaa030] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Revised: 04/20/2020] [Accepted: 04/26/2020] [Indexed: 01/02/2023] Open
Abstract
The HLA genes, the most polymorphic genes in the human genome, constitute the strongest single genetic susceptibility factor for autoimmune diseases, transplantation alloimmunity and infections. HLA imputation via statistical inference of alleles based on single-nucleotide polymorphisms (SNPs) in linkage disequilibrium (LD) with alleles is a powerful first-step screening tool. Due to different LD structures between populations, the accuracy of HLA imputation may benefit from matching the imputation reference with the study population. To evaluate the potential advantage of using population-specific reference in HLA imputation, we constructed an HLA reference panel consisting of 1150 Finns with 5365 major histocompatibility complex region SNPs consistent between genome builds. We evaluated the accuracy of the panel against a European panel in an independent test set of 213 Finnish subjects. We show that the Finnish panel yields a lower imputation error rate (1.24% versus 1.79%). More than 30% of imputation errors occurred in haplotypes enriched in Finland. The frequencies of imputed HLA alleles were highly correlated with clinical-grade HLA allele frequencies and allowed accurate replication of established HLA–disease associations in ∼102 000 biobank participants. The results show that a population-specific reference increases imputation accuracy in a relatively isolated population within Europe and can be successfully applied to biobank-scale genome data collections.
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Affiliation(s)
- Jarmo Ritari
- Research and Development, Finnish Red Cross Blood Service, Kivihaantie 7, 00310 Helsinki, Finland
| | - Kati Hyvärinen
- Research and Development, Finnish Red Cross Blood Service, Kivihaantie 7, 00310 Helsinki, Finland
| | - Jonna Clancy
- Research and Development, Finnish Red Cross Blood Service, Kivihaantie 7, 00310 Helsinki, Finland
| | | | - Jukka Partanen
- Research and Development, Finnish Red Cross Blood Service, Kivihaantie 7, 00310 Helsinki, Finland
| | - Satu Koskela
- Research and Development, Finnish Red Cross Blood Service, Kivihaantie 7, 00310 Helsinki, Finland
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9
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Ritari J, Hyvärinen K, Koskela S, Niittyvuopio R, Nihtinen A, Salmenniemi U, Putkonen M, Volin L, Kwan T, Pastinen T, Itälä-Remes M, Partanen J. Computational Analysis of HLA-presentation of Non-synonymous Recipient Mismatches Indicates Effect on the Risk of Chronic Graft-vs.-Host Disease After Allogeneic HSCT. Front Immunol 2019; 10:1625. [PMID: 31379830 PMCID: PMC6646417 DOI: 10.3389/fimmu.2019.01625] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Accepted: 07/01/2019] [Indexed: 12/20/2022] Open
Abstract
Genetic mismatches in protein coding genes between allogeneic hematopoietic stem cell transplantation (allo-HSCT) recipient and donor can elicit an alloimmunity response via peptides presented by the recipient HLA receptors as minor histocompatibility antigens (mHAs). While the impact of individual mHAs on allo-HSCT outcome such as graft-vs.-host and graft-vs.-leukemia effects has been demonstrated, it is likely that established mHAs constitute only a small fraction of all immunogenic non-synonymous variants. In the present study, we have analyzed the genetic mismatching in 157 exome-sequenced sibling allo-HSCT pairs to evaluate the significance of polymorphic HLA class I associated peptides on clinical outcome. We applied computational mismatch estimation approaches based on experimentally verified HLA ligands available in public repositories, published mHAs, and predicted HLA-peptide affinites, and analyzed their associations with chronic graft-vs.-host disease (cGvHD) grades. We found that higher estimated recipient mismatching consistently increased the risk of severe cGvHD, suggesting that HLA-presented mismatching influences the likelihood of long-term complications in the patient. Furthermore, computational approaches focusing on estimation of HLA-presentation instead of all non-synonymous mismatches indiscriminately may be beneficial for analysis sensitivity and could help identify novel mHAs.
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Affiliation(s)
- Jarmo Ritari
- Finnish Red Cross Blood Service, Helsinki, Finland
| | | | - Satu Koskela
- Finnish Red Cross Blood Service, Helsinki, Finland
| | - Riitta Niittyvuopio
- Stem Cell Transplantation Unit, Department of Hematology, Comprehensive Cancer Center, Helsinki University Hospital, Helsinki, Finland
| | - Anne Nihtinen
- Stem Cell Transplantation Unit, Department of Hematology, Comprehensive Cancer Center, Helsinki University Hospital, Helsinki, Finland
| | - Urpu Salmenniemi
- Stem Cell Transplantation Unit, Division of Medicine, Department of Hematology, Turku University Hospital, Turku, Finland
| | - Mervi Putkonen
- Stem Cell Transplantation Unit, Division of Medicine, Department of Hematology, Turku University Hospital, Turku, Finland
| | - Liisa Volin
- Stem Cell Transplantation Unit, Department of Hematology, Comprehensive Cancer Center, Helsinki University Hospital, Helsinki, Finland
| | - Tony Kwan
- Department of Human Genetics, McGill University and Genome Quebec Innovation Centre, McGill University, Montreal, QC, Canada
| | - Tomi Pastinen
- Department of Human Genetics, McGill University and Genome Quebec Innovation Centre, McGill University, Montreal, QC, Canada.,Center for Pediatric Genomic Medicine, Children's Mercy, Kansas City, MO, United States
| | - Maija Itälä-Remes
- Stem Cell Transplantation Unit, Division of Medicine, Department of Hematology, Turku University Hospital, Turku, Finland
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10
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Increased MHC Matching by C4 Gene Compatibility in Unrelated Donor Hematopoietic Stem Cell Transplantation. Biol Blood Marrow Transplant 2019; 25:891-898. [DOI: 10.1016/j.bbmt.2018.12.759] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Accepted: 12/19/2018] [Indexed: 12/22/2022]
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