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Devriese M, Da Silva S, Le Mene M, Rouquie J, Allain V, Kolesar L, Rigo K, Creary LE, Lauterbach N, Usureau C, Dewez M, Caillat-Zucman S, Werner G, Taupin JL. Two-field resolution on-call HLA typing for deceased donors using nanopore sequencing. HLA 2024; 103:e15441. [PMID: 38507216 DOI: 10.1111/tan.15441] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 02/21/2024] [Accepted: 03/01/2024] [Indexed: 03/22/2024]
Abstract
The current practice of HLA genotyping in deceased donors poses challenges due to limited resolution within time constraints. Nevertheless, the assessment of compatibility between anti-HLA sensitized recipients and mismatched donors remains a critical medical need, particularly when dealing with allele-specific (second field genotyping level) donor-specific antibodies. In this study, we present a customized protocol based on the NanoTYPE® HLA typing kit, employing the MinION® sequencer, which enables rapid HLA typing of deceased donors within a short timeframe of 3.75 h on average at a three-field resolution with almost no residual ambiguities. Through a prospective real-time analysis of HLA typing in 18 donors, we demonstrated the efficacy and precision of our nanopore-based method in comparison to the conventional approach and without delaying organ allocation. Indeed, this duration was consistent with the deceased donor organ donation procedure leading to organ allocation via the French Biomedicine Agency. The improved resolution achieved with our protocol enhances the security of organ allocation, particularly benefiting highly sensitized recipients who often present intricate HLA antibody profiles. By overcoming technical challenges and providing comprehensive genotyping data, this approach holds the potential to significantly impact deceased donor HLA genotyping, thereby facilitating optimal organ allocation strategies.
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Affiliation(s)
- Magali Devriese
- Laboratoire d'Immunologie et Histocompatibilité, Hôpital Saint Louis, Paris, France
- INSERM UMR976, Institut de Recherche Saint-Louis, Université de Paris, Paris, France
| | - Sephora Da Silva
- Laboratoire d'Immunologie et Histocompatibilité, Hôpital Saint Louis, Paris, France
| | - Melchior Le Mene
- Laboratoire d'Immunologie et Histocompatibilité, Hôpital Saint Louis, Paris, France
| | - Julien Rouquie
- Laboratoire d'Immunologie et Histocompatibilité, Hôpital Saint Louis, Paris, France
| | - Vincent Allain
- Laboratoire d'Immunologie et Histocompatibilité, Hôpital Saint Louis, Paris, France
| | | | | | | | | | - Cedric Usureau
- Laboratoire d'Immunologie et Histocompatibilité, Hôpital Saint Louis, Paris, France
- INSERM UMR976, Institut de Recherche Saint-Louis, Université de Paris, Paris, France
| | | | - Sophie Caillat-Zucman
- Laboratoire d'Immunologie et Histocompatibilité, Hôpital Saint Louis, Paris, France
- INSERM UMR976, Institut de Recherche Saint-Louis, Université de Paris, Paris, France
| | | | - Jean-Luc Taupin
- Laboratoire d'Immunologie et Histocompatibilité, Hôpital Saint Louis, Paris, France
- INSERM UMR976, Institut de Recherche Saint-Louis, Université de Paris, Paris, France
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2
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Hajdarevic R, Lande A, Rekeland I, Rydland A, Strand EB, Sosa DD, Creary LE, Mella O, Egeland T, Saugstad OD, Fluge Ø, Lie BA, Viken MK. Fine mapping of the major histocompatibility complex (MHC) in myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) suggests involvement of both HLA class I and class II loci. Brain Behav Immun 2021; 98:101-109. [PMID: 34403736 DOI: 10.1016/j.bbi.2021.08.219] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 08/04/2021] [Accepted: 08/09/2021] [Indexed: 10/20/2022] Open
Abstract
The etiology of myalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS) is unknown, but involvement of the immune system is one of the proposed underlying mechanisms. Human leukocyte antigen (HLA) associations are hallmarks of immune-mediated and autoimmune diseases. We have previously performed high resolution HLA genotyping and detected associations between ME/CFS and certain HLA class I and class II alleles. However, the HLA complex harbors numerous genes of immunological importance, and there is extensive and complex linkage disequilibrium across the region. In the current study, we aimed to fine map the association signals in the HLA complex by genotyping five additional classical HLA loci and 5,342 SNPs in 427 Norwegian ME/CFS patients, diagnosed according to the Canadian Consensus Criteria, and 480 healthy Norwegian controls. SNP association analysis revealed two distinct and independent association signals (p ≤ 0.001) tagged by rs4711249 in the HLA class I region and rs9275582 in the HLA class II region. Furthermore, the primary association signal in the HLA class II region was located within the HLA-DQ gene region, most likely due to HLA-DQB1, particularly the amino acid position 57 (aspartic acid/alanine) in the peptide binding groove, or an intergenic SNP upstream of HLA-DQB1. In the HLA class I region, the putative causal locus might map outside the classical HLA genes as the association signal spans several genes (DDR1, GTF2H4, VARS2, SFTA2 and DPCR1) with expression levels influenced by the ME/CFS associated SNP genotype. Taken together, our results implicate the involvement of the MHC, and in particular the HLA-DQB1 gene, in ME/CFS. These findings should be replicated in larger cohorts, particularly to verify the putative involvement of HLA-DQB1, a gene important for antigen-presentation to T cells and known to harbor alleles providing the largest risk for well-established autoimmune diseases.
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Affiliation(s)
- Riad Hajdarevic
- Department of Medical Genetics, University of Oslo and Oslo University Hospital, Oslo, Norway; Institute of Clinical Medicine, University of Oslo, Oslo, Norway.
| | - Asgeir Lande
- Department of Medical Genetics, University of Oslo and Oslo University Hospital, Oslo, Norway; Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Ingrid Rekeland
- Department of Oncology and Medical Physics, Haukeland University Hospital, Bergen, Norway
| | - Anne Rydland
- Department of Medical Genetics, University of Oslo and Oslo University Hospital, Oslo, Norway; Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Elin B Strand
- CFS/ME Center, Oslo University Hospital, Oslo, Norway; Faculty of Health, VID Specialized University, Stavanger, Norway
| | - Daisy D Sosa
- CFS/ME Center, Oslo University Hospital, Oslo, Norway; National Advisory Unit on CFS/ME, Oslo, Norway
| | - Lisa E Creary
- Department of Pathology, Stanford University, School of Medicine, Palo Alto, CA, USA; Histocompatibility and Immunogenetics Laboratory, Stanford Blood Center, Palo Alto, CA, USA
| | - Olav Mella
- Department of Oncology and Medical Physics, Haukeland University Hospital, Bergen, Norway; Department of Clinical Science, University of Bergen, Norway
| | - Torstein Egeland
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway; Department of Immunology, Oslo University Hospital, Oslo, Norway
| | - Ola D Saugstad
- Department of Pediatric Research, Oslo University Hospital, University of Oslo, Oslo, Norway
| | - Øystein Fluge
- Department of Oncology and Medical Physics, Haukeland University Hospital, Bergen, Norway; Department of Clinical Science, University of Bergen, Norway
| | - Benedicte A Lie
- Department of Medical Genetics, University of Oslo and Oslo University Hospital, Oslo, Norway; Institute of Clinical Medicine, University of Oslo, Oslo, Norway; Department of Immunology, Oslo University Hospital, Oslo, Norway
| | - Marte K Viken
- Department of Medical Genetics, University of Oslo and Oslo University Hospital, Oslo, Norway; Department of Immunology, Oslo University Hospital, Oslo, Norway.
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3
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Creary LE, Gangavarapu S, Caillier SJ, Cavalcante P, Frangiamore R, Lie BA, Bengtsson M, Harbo HF, Brauner S, Hollenbach JA, Oksenberg JR, Bernasconi P, Maniaol AH, Hammarström L, Mantegazza R, Fernández-Viña MA. Next-Generation Sequencing Identifies Extended HLA Class I and II Haplotypes Associated With Early-Onset and Late-Onset Myasthenia Gravis in Italian, Norwegian, and Swedish Populations. Front Immunol 2021; 12:667336. [PMID: 34163474 PMCID: PMC8215161 DOI: 10.3389/fimmu.2021.667336] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Accepted: 04/27/2021] [Indexed: 11/13/2022] Open
Abstract
Genetic susceptibility to myasthenia gravis (MG) associates with specific HLA alleles and haplotypes at the class I and II regions in various populations. Previous studies have only examined alleles at a limited number of HLA loci that defined only broad serotypes or alleles defined at the protein sequence level. Consequently, genetic variants in noncoding and untranslated HLA gene segments have not been fully explored but could also be important determinants for MG. To gain further insight into the role of HLA in MG, we applied next-generation sequencing to analyze sequence variation at eleven HLA genes in early-onset (EO) and late-onset (LO) non-thymomatous MG patients positive for the acetylcholine receptor (AChR) antibodies and ethnically matched controls from Italy, Norway, and Sweden. For all three populations, alleles and haplotype blocks present on the ancestral haplotype AH8.1 were associated with risk in AChR-EOMG patients. HLA-B*08:01:01:01 was the dominant risk allele in Italians (OR = 3.28, P = 1.83E-05), Norwegians (OR = 3.52, P = 4.41E-16), and in Swedes HLA-B*08:01 was the primary risk allele (OR = 4.24, P <2.2E-16). Protective alleles and haplotype blocks were identified on the HLA-DRB7, and HLA-DRB13.1 class II haplotypes in Italians and Norwegians, whereas in Swedes HLA-DRB7 exhibited the main protective effect. For AChR-LOMG patients, the HLA-DRB15.1 haplotype and associated alleles were significantly associated with susceptibility in all groups. The HLA-DR13-HLA-DR-HLA-DQ haplotype was associated with protection in all AChR-LOMG groups. This study has confirmed and extended previous findings that the immunogenetic predisposition profiles for EOMG and LOMG are distinct. In addition, the results are consistent with a role for non-coding HLA genetic variants in the pathogenesis of MG.
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Affiliation(s)
- Lisa E Creary
- Department of Pathology, Stanford University School of Medicine, Palo Alto, CA, United States.,Histocompatibility, Immunogenetics and Disease Profiling Laboratory, Stanford Blood Center, Palo Alto, CA, United States
| | - Sridevi Gangavarapu
- Histocompatibility, Immunogenetics and Disease Profiling Laboratory, Stanford Blood Center, Palo Alto, CA, United States
| | - Stacy J Caillier
- Department of Neurology, School of Medicine, University of California San Francisco, San Francisco, CA, United States
| | - Paola Cavalcante
- Neurology IV Unit Neuroimmunology and Neuromuscular Diseases, Fondazione I.R.C.C.S Istituto Neurologico Carlo Besta (INCB), Milan, Italy
| | - Rita Frangiamore
- Neurology IV Unit Neuroimmunology and Neuromuscular Diseases, Fondazione I.R.C.C.S Istituto Neurologico Carlo Besta (INCB), Milan, Italy
| | - Benedicte A Lie
- Department of Immunology and Transfusion Medicine, Oslo University Hospital, Oslo, Norway.,Institute of Clinical Medicine, University of Oslo, Oslo, Norway.,Department of Medical Genetics, University of Oslo and Oslo University Hospital, Oslo, Norway
| | - Mats Bengtsson
- Department of Immunology, Genetics and Pathology (IGP), Rudbeck Laboratory, Uppsala University and University Hospital, Uppsala, Sweden
| | - Hanne Flinstad Harbo
- Department of Neurology, Oslo University Hospital and University of Oslo, Oslo, Norway
| | - Susanna Brauner
- Department of Clinical Neuroscience, Karolinska Institutet, Stockholm, Sweden
| | - Jill A Hollenbach
- Department of Neurology, School of Medicine, University of California San Francisco, San Francisco, CA, United States
| | - Jorge R Oksenberg
- Department of Neurology, School of Medicine, University of California San Francisco, San Francisco, CA, United States
| | - Pia Bernasconi
- Neurology IV Unit Neuroimmunology and Neuromuscular Diseases, Fondazione I.R.C.C.S Istituto Neurologico Carlo Besta (INCB), Milan, Italy
| | | | - Lennart Hammarström
- The Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Renato Mantegazza
- Neurology IV Unit Neuroimmunology and Neuromuscular Diseases, Fondazione I.R.C.C.S Istituto Neurologico Carlo Besta (INCB), Milan, Italy.,Department of Clinical Research and Innovation, Fondazione I.R.C.C.S Istituto Neurologico Carlo Besta (INCB), Milan, Italy
| | - Marcelo A Fernández-Viña
- Department of Pathology, Stanford University School of Medicine, Palo Alto, CA, United States.,Histocompatibility, Immunogenetics and Disease Profiling Laboratory, Stanford Blood Center, Palo Alto, CA, United States
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4
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Osoegawa K, Creary LE, Montero-Martín G, Mallempati KC, Gangavarapu S, Caillier SJ, Santaniello A, Isobe N, Hollenbach JA, Hauser SL, Oksenberg JR, Fernández-Viňa MA. High Resolution Haplotype Analyses of Classical HLA Genes in Families With Multiple Sclerosis Highlights the Role of HLA-DP Alleles in Disease Susceptibility. Front Immunol 2021; 12:644838. [PMID: 34211458 PMCID: PMC8240666 DOI: 10.3389/fimmu.2021.644838] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 05/10/2021] [Indexed: 11/13/2022] Open
Abstract
Multiple sclerosis (MS) susceptibility shows strong genetic associations with HLA alleles and haplotypes. We genotyped 11 HLA genes in 477 non-Hispanic European MS patients and their 954 unaffected parents using a validated next-generation sequencing (NGS) methodology. HLA haplotypes were assigned unequivocally by tracing HLA allele transmissions. We explored HLA haplotype/allele associations with MS using the genotypic transmission disequilibrium test (gTDT) and multiallelic TDT (mTDT). We also conducted a case-control (CC) study with all patients and 2029 healthy unrelated ethnically matched controls. We performed separate analyses of 54 extended multi-case families by reviewing transmission of haplotype blocks. The haplotype fragment including DRB5*01:01:01~DRB1*15:01:01:01 was significantly associated with predisposition (gTDT: p < 2.20e-16; mTDT: p =1.61e-07; CC: p < 2.22e-16) as reported previously. A second risk allele, DPB1*104:01 (gTDT: p = 3.69e-03; mTDT: p = 2.99e-03; CC: p = 1.00e-02), independent from the haplotype bearing DRB1*15:01 was newly identified. The allele DRB1*01:01:01 showed significant protection (gTDT: p = 8.68e-06; mTDT: p = 4.50e-03; CC: p = 1.96e-06). Two DQB1 alleles, DQB1*03:01 (gTDT: p = 2.86e-03; mTDT: p = 5.56e-02; CC: p = 4.08e-05) and DQB1*03:03 (gTDT: p = 1.17e-02; mTDT: p = 1.16e-02; CC: p = 1.21e-02), defined at two-field level also showed protective effects. The HLA class I block, A*02:01:01:01~C*03:04:01:01~B*40:01:02 (gTDT: p = 5.86e-03; mTDT: p = 3.65e-02; CC: p = 9.69e-03) and the alleles B*27:05 (gTDT: p = 6.28e-04; mTDT: p = 2.15e-03; CC: p = 1.47e-02) and B*38:01 (gTDT: p = 3.20e-03; mTDT: p = 6.14e-03; CC: p = 1.70e-02) showed moderately protective effects independently from each other and from the class II associated factors. By comparing statistical significance of 11 HLA loci and 19 haplotype segments with both untruncated and two-field allele names, we precisely mapped MS candidate alleles/haplotypes while eliminating false signals resulting from ‘hitchhiking’ alleles. We assessed genetic burden for the HLA allele/haplotype identified in this study. This family-based study including the highest-resolution of HLA alleles proved to be powerful and efficient for precise identification of HLA genotypes associated with both, susceptibility and protection to development of MS.
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Affiliation(s)
- Kazutoyo Osoegawa
- Histocompatibility & Immunogenetics Laboratory, Stanford Blood Center, Palo Alto, CA, United States
| | - Lisa E Creary
- Histocompatibility & Immunogenetics Laboratory, Stanford Blood Center, Palo Alto, CA, United States.,Department of Pathology, Stanford University School of Medicine, Palo Alto, CA, United States
| | - Gonzalo Montero-Martín
- Histocompatibility & Immunogenetics Laboratory, Stanford Blood Center, Palo Alto, CA, United States.,Department of Pathology, Stanford University School of Medicine, Palo Alto, CA, United States
| | - Kalyan C Mallempati
- Histocompatibility & Immunogenetics Laboratory, Stanford Blood Center, Palo Alto, CA, United States
| | - Sridevi Gangavarapu
- Histocompatibility & Immunogenetics Laboratory, Stanford Blood Center, Palo Alto, CA, United States
| | - Stacy J Caillier
- Weill Institute for Neurosciences, Department of Neurology, University of California San Francisco, San Francisco, CA, United States
| | - Adam Santaniello
- Weill Institute for Neurosciences, Department of Neurology, University of California San Francisco, San Francisco, CA, United States
| | - Noriko Isobe
- Department of Neurology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Jill A Hollenbach
- Weill Institute for Neurosciences, Department of Neurology, University of California San Francisco, San Francisco, CA, United States
| | - Stephen L Hauser
- Weill Institute for Neurosciences, Department of Neurology, University of California San Francisco, San Francisco, CA, United States
| | - Jorge R Oksenberg
- Weill Institute for Neurosciences, Department of Neurology, University of California San Francisco, San Francisco, CA, United States
| | - Marcelo A Fernández-Viňa
- Histocompatibility & Immunogenetics Laboratory, Stanford Blood Center, Palo Alto, CA, United States.,Department of Pathology, Stanford University School of Medicine, Palo Alto, CA, United States
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5
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Creary LE, Sacchi N, Mazzocco M, Morris GP, Montero-Martin G, Chong W, Brown CJ, Dinou A, Stavropoulos-Giokas C, Gorodezky C, Narayan S, Periathiruvadi S, Thomas R, De Santis D, Pepperall J, ElGhazali GE, Al Yafei Z, Askar M, Tyagi S, Kanga U, Marino SR, Planelles D, Chang CJ, Fernández-Viña MA. High-resolution HLA allele and haplotype frequencies in several unrelated populations determined by next generation sequencing: 17th International HLA and Immunogenetics Workshop joint report. Hum Immunol 2021; 82:505-522. [PMID: 34030896 DOI: 10.1016/j.humimm.2021.04.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 04/23/2021] [Accepted: 04/28/2021] [Indexed: 12/12/2022]
Abstract
The primary goal of the unrelated population HLA diversity (UPHD) component of the 17th International HLA and Immunogenetics Workshop was to characterize HLA alleles at maximum allelic-resolution in worldwide populations and re-evaluate patterns of HLA diversity across populations. The UPHD project included HLA genotype and sequence data, generated by various next-generation sequencing methods, from 4,240 individuals collated from 12 different countries. Population data included well-defined large datasets from the USA and smaller samples from Europe, Australia, and Western Asia. Allele and haplotype frequencies varied across populations from distant geographical regions. HLA genetic diversity estimated at 2- and 4-field allelic resolution revealed that diversity at the majority of loci, particularly for European-descent populations, was lower at the 2-field resolution. Several common alleles with identical protein sequences differing only by intronic substitutions were found in distinct haplotypes, revealing a more detailed characterization of linkage between variants within the HLA region. The examination of coding and non-coding nucleotide variation revealed many examples in which almost complete biunivocal relations between common alleles at different loci were observed resulting in higher linkage disequilibrium. Our reference data of HLA profiles characterized at maximum resolution from many populations is useful for anthropological studies, unrelated donor searches, transplantation, and disease association studies.
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Affiliation(s)
- Lisa E Creary
- Department of Pathology, Stanford University School of Medicine, Palo Alto, CA, USA; Histocompatibility and Immunogenetics Laboratory, Stanford Blood Center, Palo Alto CA, USA.
| | - Nicoletta Sacchi
- Italian Bone Marrow Donor Registry Tissue Typing Laboratory, E.O. Ospedali Galliera, Genova, Italy
| | - Michela Mazzocco
- Italian Bone Marrow Donor Registry Tissue Typing Laboratory, E.O. Ospedali Galliera, Genova, Italy
| | - Gerald P Morris
- Department of Pathology, University of California San Diego, La Jolla, CA, USA
| | - Gonzalo Montero-Martin
- Histocompatibility and Immunogenetics Laboratory, Stanford Blood Center, Palo Alto CA, USA
| | - 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; Faculty of Life Sciences and Medicine, King's College London, University of London, England, UK
| | - Amalia Dinou
- Biomedical Research Foundation Academy of Athens, Hellenic Cord Blood Bank, Athens, Greece
| | | | - Clara Gorodezky
- Laboratory of Immunology and Immunogenetics, Fundación Comparte Vida, A.C. Mexico City, Mexico
| | | | | | - Rasmi Thomas
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, USA
| | | | - Jennifer Pepperall
- Welsh Transplant and Immunogenetics Laboratory, Welsh Blood Service, Pontyclun, United Kingdom
| | - Gehad E ElGhazali
- Sheikh Khalifa Medical City-Union 71, Abu Dhabi and the Department of Immunology, College of Medicine and Health Sciences, UAE University, Al Ain, United Arab Emirates
| | - Zain Al Yafei
- Sheikh Khalifa Medical City-Union 71, Abu Dhabi and the Department of Immunology, College of Medicine and Health Sciences, UAE University, Al Ain, United Arab Emirates
| | - Medhat Askar
- Department of Pathology and Laboratory Medicine, Baylor University Medical center, Dallas, USA
| | - Shweta Tyagi
- Department of Transplant Immunology and Immunogenetics, All India Institute of Medical Sciences, New Delhi, India
| | - Uma Kanga
- Department of Transplant Immunology and Immunogenetics, All India Institute of Medical Sciences, New Delhi, India
| | - Susana R Marino
- Department of Pathology, The University of Chicago Medicine, Chicago, IL, USA
| | - Dolores Planelles
- Histocompatibility, Centro de Transfusión de la Comunidad Valenciana, Valencia, Spain; Grupo Español de Trabajo en Histocompatibilidad e Inmunología del Trasplante (GETHIT), Spanish Society for Immunology, Madrid, Spain
| | | | - Marcelo A Fernández-Viña
- Department of Pathology, Stanford University School of Medicine, Palo Alto, CA, USA; Histocompatibility and Immunogenetics Laboratory, Stanford Blood Center, Palo Alto CA, USA.
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6
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Anderson KM, Augusto DG, Dandekar R, Shams H, Zhao C, Yusufali T, Montero-Martín G, Marin WM, Nemat-Gorgani N, Creary LE, Caillier S, Mofrad MRK, Parham P, Fernández-Viña M, Oksenberg JR, Norman PJ, Hollenbach JA. Killer Cell Immunoglobulin-like Receptor Variants Are Associated with Protection from Symptoms Associated with More Severe Course in Parkinson Disease. J Immunol 2020; 205:1323-1330. [PMID: 32709660 DOI: 10.4049/jimmunol.2000144] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Accepted: 06/28/2020] [Indexed: 12/12/2022]
Abstract
Immune dysfunction plays a role in the development of Parkinson disease (PD). NK cells regulate immune functions and are modulated by killer cell immunoglobulin-like receptors (KIR). KIR are expressed on the surface of NK cells and interact with HLA class I ligands on the surface of all nucleated cells. We investigated KIR-allelic polymorphism to interrogate the role of NK cells in PD. We sequenced KIR genes from 1314 PD patients and 1978 controls using next-generation methods and identified KIR genotypes using custom bioinformatics. We examined associations of KIR with PD susceptibility and disease features, including age at disease onset and clinical symptoms. We identified two KIR3DL1 alleles encoding highly expressed inhibitory receptors associated with protection from PD clinical features in the presence of their cognate ligand: KIR3DL1*015/HLA-Bw4 from rigidity (p c = 0.02, odds ratio [OR] = 0.39, 95% confidence interval [CI] 0.23-0.69) and KIR3DL1*002/HLA-Bw4i from gait difficulties (p c = 0.05, OR = 0.62, 95% CI 0.44-0.88), as well as composite symptoms associated with more severe disease. We also developed a KIR3DL1/HLA interaction strength metric and found that weak KIR3DL1/HLA interactions were associated with rigidity (pc = 0.05, OR = 9.73, 95% CI 2.13-172.5). Highly expressed KIR3DL1 variants protect against more debilitating symptoms of PD, strongly implying a role of NK cells in PD progression and manifestation.
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Affiliation(s)
- Kirsten M Anderson
- Department of Neurology, Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA 94158
| | - Danillo G Augusto
- Department of Neurology, Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA 94158
| | - Ravi Dandekar
- Department of Neurology, Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA 94158
| | - Hengameh Shams
- Department of Neurology, Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA 94158
| | - Chao Zhao
- Department of Neurology, Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA 94158
| | - Tasneem Yusufali
- Department of Neurology, Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA 94158
| | | | - Wesley M Marin
- Department of Neurology, Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA 94158
| | - Neda Nemat-Gorgani
- Department of Structural Biology and Immunology, Stanford University, Palo Alto, CA 94305
| | - Lisa E Creary
- Department of Pathology, Stanford University School of Medicine, Palo Alto, CA 94304
| | - Stacy Caillier
- Department of Neurology, Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA 94158
| | - Mohammad R K Mofrad
- Molecular Cell Biomechanics Laboratory, Department of Bioengineering and Mechanical Engineering, University of California, Berkeley, CA 94720; and
| | - Peter Parham
- Department of Structural Biology and Immunology, Stanford University, Palo Alto, CA 94305
| | | | - Jorge R Oksenberg
- Department of Neurology, Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA 94158
| | - Paul J Norman
- Division of Biomedical Informatics and Personalized Medicine, Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, CO 80045
| | - Jill A Hollenbach
- Department of Neurology, Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA 94158;
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7
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Ivanova M, Creary LE, Al Hadra B, Lukanov T, Mazzocco M, Sacchi N, Ameen R, Al-Shemmari S, Moise A, Ursu LD, Constantinescu I, Vayntrub T, Fernández-Viňa MA, Shivarov V, Naumova E. 17th IHIW component "Immunogenetics of Ageing" - New NGS data. Hum Immunol 2019; 80:703-713. [PMID: 31331679 DOI: 10.1016/j.humimm.2019.07.287] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Revised: 07/08/2019] [Accepted: 07/12/2019] [Indexed: 12/14/2022]
Abstract
The 'Immunogenetics of Aging' project is a component introduced in the 14th International HLA and Immunogenetics Workshop (IHIW) and developed further within subsequent workshops. The aim was to determine the relevance of immunogenetic markers, focusing on HLA, cytokine genes, and some innate immunity genes, for successful aging and an increased capacity to reach the extreme limits of life-span. Within the 17th IHIW we applied Next Generation Sequencing methods to refine further HLA associations at allele level in longevity, and to extend our knowledge to additional loci such as HLA-DQA1, HLA-DPB1 and HLA-DPA1. Analysis of relatively small number of healthy elderly and young controls from four populations showed that some HLA class I and class II alleles were significantly positively associated with healthy aging. Additionally we observed statistically significant differences in HLA allele distribution when the analysis was performed separately in elderly females and males compared to sex-matched young controls. Haplotypes, probably associated with better control of viral and malignant diseases were increased in the elderly sample. These preliminary NGS data could confirm our hypotheses that survival and longevity might be associated with selection of HLA alleles and haplotypes conferring disease resistance or susceptibility. Therefore HLA alleles and haplotypes could be informative immunogenetic markers for successful ageing.
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Affiliation(s)
- Milena Ivanova
- Department of Clinical Immunology, University Hospital Alexandrovska, Medical University, Sofia, Bulgaria.
| | - 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
| | - Bushra Al Hadra
- Department of Clinical Immunology, University Hospital Alexandrovska, Medical University, Sofia, Bulgaria
| | - Tsvetelin Lukanov
- Department of Clinical Immunology, University Hospital Alexandrovska, Medical University, Sofia, Bulgaria
| | - Michela Mazzocco
- Italian Bone Marrow Donor Registry Tissue Typing Laboratory, E.O. Ospedali Galliera, Genova, Italy
| | - Nicoletta Sacchi
- Italian Bone Marrow Donor Registry Tissue Typing Laboratory, E.O. Ospedali Galliera, Genova, Italy
| | - Reem Ameen
- Medical Laboratory Sciences Department, Health Sciences Center, Kuwait University, Jabriya, Kuwait
| | - Salem Al-Shemmari
- Medical Laboratory Sciences Department, Health Sciences Center, Kuwait University, Jabriya, Kuwait
| | - Ana Moise
- Carol Davila University of Medicine and Pharmacy, Bucharest, Centre for Immunogenetics and Virology, Fundeni Clinical Institute, Bucharest, Romania
| | - Larisa Denisa Ursu
- Carol Davila University of Medicine and Pharmacy, Bucharest, Centre for Immunogenetics and Virology, Fundeni Clinical Institute, Bucharest, Romania
| | - Ileana Constantinescu
- Carol Davila University of Medicine and Pharmacy, Bucharest, Centre for Immunogenetics and Virology, Fundeni Clinical Institute, Bucharest, Romania
| | - Tamara Vayntrub
- Histocompatibility, Immunogenetics and Disease Profiling Laboratory, Stanford Blood Center, Palo Alto, CA, 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
| | - Velizar Shivarov
- Laboratory of Clinical Immunology, University Hospital Sofiamed, Sofia, Bulgaria; Department of Genetics, Faculty of Biology, Sofia University "St. Kliment Ohridski", Sofia, Bulgaria
| | - Elissaveta Naumova
- Department of Clinical Immunology, University Hospital Alexandrovska, Medical University, Sofia, Bulgaria
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8
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Osoegawa K, Mallempati KC, Gangavarapu S, Oki A, Gendzekhadze K, Marino SR, Brown NK, Bettinotti MP, Weimer ET, Montero-Martín G, Creary LE, Vayntrub TA, Chang CJ, Askar M, Mack SJ, Fernández-Viña MA. HLA alleles and haplotypes observed in 263 US families. Hum Immunol 2019; 80:644-660. [PMID: 31256909 DOI: 10.1016/j.humimm.2019.05.018] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2018] [Revised: 05/29/2019] [Accepted: 05/31/2019] [Indexed: 11/17/2022]
Abstract
The 17th International HLA and Immunogenetics Workshop (IHIW) conducted a project entitled "The Study of Haplotypes in Families by NGS HLA". We investigated the HLA haplotypes of 1017 subjects in 263 nuclear families sourced from five US clinical immunogenetics laboratories, primarily as part of the evaluation of related donor candidates for hematopoietic stem cell and solid organ transplantation. The parents in these families belonged to five broad groups - African (72 parents), Asian (115), European (210), Hispanic (118) and "Other" (11). High-resolution HLA genotypes were generated for each subject using next-generation sequencing (NGS) HLA typing systems. We identified the HLA haplotypes in each family using HaplObserve, software that builds haplotypes in families by reviewing HLA allele segregation from parents to children. We calculated haplotype frequencies within each broad group, by treating the parents in each family as unrelated individuals. We also calculated standard measures of global linkage disequilibrium (LD) and conditional asymmetric LD for each ethnic group, and used untruncated and two-field allele names to investigate LD patterns. Finally we demonstrated the utility of consensus DNA sequences in identifying novel variants, confirming them using HLA allele segregation at the DNA sequence level.
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Affiliation(s)
- Kazutoyo Osoegawa
- Histocompatibility, Immunogenetics & Disease Profiling Laboratory, Stanford Blood Center, Palo Alto, CA, USA.
| | - Kalyan C Mallempati
- Histocompatibility, Immunogenetics & Disease Profiling Laboratory, Stanford Blood Center, Palo Alto, CA, USA
| | - Sridevi Gangavarapu
- Histocompatibility, Immunogenetics & Disease Profiling Laboratory, Stanford Blood Center, Palo Alto, CA, USA
| | - Arisa Oki
- HLA Laboratory, City of Hope, Duarte, CA, USA
| | | | - Susana R Marino
- Transplant Immunology Laboratory, The University of Chicago Medicine, Chicago, IL, USA
| | - Nicholas K Brown
- Transplant Immunology Laboratory, The University of Chicago Medicine, Chicago, IL, USA
| | | | - Eric T Weimer
- Department of Pathology & Laboratory Medicine, UNC Chapel Hill School of Medicine, Chapel Hill, NC, USA
| | - Gonzalo Montero-Martín
- Histocompatibility, Immunogenetics & Disease Profiling Laboratory, Stanford Blood Center, Palo Alto, CA, USA; Department of Pathology, Stanford University School of Medicine, Palo Alto, CA, USA
| | - Lisa E Creary
- Histocompatibility, Immunogenetics & Disease Profiling Laboratory, Stanford Blood Center, Palo Alto, CA, USA; Department of Pathology, Stanford University School of Medicine, Palo Alto, CA, USA
| | - Tamara A Vayntrub
- Histocompatibility, Immunogenetics & Disease Profiling Laboratory, Stanford Blood Center, Palo Alto, CA, USA
| | | | - Medhat Askar
- Baylor University Medical Center, Dallas, TX, USA
| | - Steven J Mack
- Center for Genetics, Children's Hospital Oakland Research Institute, Oakland, CA, USA
| | - Marcelo A Fernández-Viña
- Histocompatibility, Immunogenetics & Disease Profiling Laboratory, Stanford Blood Center, Palo Alto, CA, USA; Department of Pathology, Stanford University School of Medicine, Palo Alto, CA, USA
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9
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Goeury T, Creary LE, Fernandez-Vina MA, Tiercy JM, Nunes JM, Sanchez-Mazas A. Mandenka from Senegal: Next Generation Sequencing typings reveal very high frequencies of particular HLA class II alleles and haplotypes. HLA 2019; 91:148-150. [PMID: 29280562 DOI: 10.1111/tan.13197] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Accepted: 12/19/2017] [Indexed: 01/10/2023]
Affiliation(s)
- T Goeury
- Department of Genetics and Evolution - Anthropology Unit, AGP Laboratory, University of Geneva, Geneva, Switzerland.,Institute of Genetics and Genomics in Geneva (IGE3), Geneva, Switzerland
| | - L E Creary
- Stanford University, School of Medicine, Palo Alto, California
| | | | - J-M Tiercy
- Transplantation Immunology Unit and National Reference Laboratory for Histocompatibility, Geneva University Hospital, Geneva, Switzerland.,Institute of Genetics and Genomics in Geneva (IGE3), Geneva, Switzerland
| | - J M Nunes
- Department of Genetics and Evolution - Anthropology Unit, AGP Laboratory, University of Geneva, Geneva, Switzerland.,Institute of Genetics and Genomics in Geneva (IGE3), Geneva, Switzerland
| | - A Sanchez-Mazas
- Department of Genetics and Evolution - Anthropology Unit, AGP Laboratory, University of Geneva, Geneva, Switzerland.,Institute of Genetics and Genomics in Geneva (IGE3), Geneva, Switzerland
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10
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Osoegawa K, Vayntrub TA, Wenda S, De Santis D, Barsakis K, Ivanova M, Hsu S, Barone J, Holdsworth R, Diviney M, Askar M, Willis A, Railton D, Laflin S, Gendzekhadze K, Oki A, Sacchi N, Mazzocco M, Andreani M, Ameen R, Stavropoulos-Giokas C, Dinou A, Torres M, Dos Santos Francisco R, Serra-Pages C, Goodridge D, Balladares S, Bettinotti MP, Iglehart B, Kashi Z, Martin R, Saw CL, Ragoussis J, Downing J, Navarrete C, Chong W, Saito K, Petrek M, Tokic S, Padros K, Beatriz Rodriguez M, Zakharova V, Shragina O, Marino SR, Brown NK, Shiina T, Suzuki S, Spierings E, Zhang Q, Yin Y, Morris GP, Hernandez A, Ruiz P, Khor SS, Tokunaga K, Geretz A, Thomas R, Yamamoto F, Mallempati KC, Gangavarapu S, Kanga U, Tyagi S, Marsh SGE, Bultitude WP, Liu X, Cao D, Penning M, Hurley CK, Cesbron A, Mueller C, Mytilineos J, Weimer ET, Bengtsson M, Fischer G, Hansen JA, Chang CJ, Mack SJ, Creary LE, Fernandez-Viña MA. Quality control project of NGS HLA genotyping for the 17th International HLA and Immunogenetics Workshop. Hum Immunol 2019; 80:228-236. [PMID: 30738112 PMCID: PMC6446570 DOI: 10.1016/j.humimm.2019.01.009] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Revised: 01/10/2019] [Accepted: 01/30/2019] [Indexed: 11/24/2022]
Abstract
The 17th International HLA and Immunogenetics Workshop (IHIW) organizers conducted a Pilot Study (PS) in which 13 laboratories (15 groups) participated to assess the performance of the various sequencing library preparation protocols, NGS platforms and software in use prior to the workshop. The organizers sent 50 cell lines to each of the 15 groups, scored the 15 independently generated sets of NGS HLA genotyping data, and generated "consensus" HLA genotypes for each of the 50 cell lines. Proficiency Testing (PT) was subsequently organized using four sets of 24 cell lines, selected from 48 of 50 PS cell lines, to validate the quality of NGS HLA typing data from the 34 participating IHIW laboratories. Completion of the PT program with a minimum score of 95% concordance at the HLA-A, HLA-B, HLA-C, HLA-DRB1 and HLA-DQB1 loci satisfied the requirements to submit NGS HLA typing data for the 17th IHIW projects. Together, these PS and PT efforts constituted the 17th IHIW Quality Control project. Overall PT concordance rates for HLA-A, HLA-B, HLA-C, HLA-DPA1, HLA-DPB1, HLA-DQA1, HLA-DQB1, HLA-DRB1, HLA-DRB3, HLA-DRB4 and HLA-DRB5 were 98.1%, 97.0% and 98.1%, 99.0%, 98.6%, 98.8%, 97.6%, 96.0%, 99.1%, 90.0% and 91.7%, respectively. Across all loci, the majority of the discordance was due to allele dropout. The high cost of NGS HLA genotyping per experiment likely prevented the retyping of initially failed HLA loci. Despite the high HLA genotype concordance rates of the software, there remains room for improvement in the assembly of more accurate consensus DNA sequences by NGS HLA genotyping software.
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Affiliation(s)
- Kazutoyo Osoegawa
- Histocompatibility, Immunogenetics, and Disease Profiling Laboratory, Stanford Blood Center, Palo Alto, CA, USA.
| | - Tamara A Vayntrub
- Histocompatibility, Immunogenetics, and Disease Profiling Laboratory, Stanford Blood Center, Palo Alto, CA, USA
| | - Sabine Wenda
- Department of Blood Group Serology and Transfusion Medicine, Medical University of Vienna, Vienna, Austria
| | | | - Konstantinos Barsakis
- Histocompatibility, Immunogenetics, and Disease Profiling Laboratory, Stanford Blood Center, Palo Alto, CA, USA; University of Crete, Biology Department, Heraklion, Greece; Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | | | - Susan Hsu
- Histocompatibility/Molecular Genetics, American Red Cross, Philadelphia, PA, USA
| | - Jonathan Barone
- Histocompatibility/Molecular Genetics, American Red Cross, Philadelphia, PA, USA
| | | | - Mary Diviney
- Australian Red Cross Blood Services, Melbourne, Australia
| | - Medhat Askar
- Baylor University Medical Center, Dallas, TX, USA
| | | | - Dawn Railton
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Sophie Laflin
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | | | - Arisa Oki
- City of Hope National Medical Center, Duarte, CA, USA
| | | | | | - Marco Andreani
- Fondazione I.M.E. Istituto Mediterraneo Di Ematologia, Rome, Italy
| | - Reem Ameen
- Health Sciences Center, Kuwait University, Jabriya, Kuwait
| | | | | | | | | | - Carles Serra-Pages
- Centro de Diagonóstico Biomédico, Hospital Clínic de Barcelona, Barcelona, Spain
| | | | | | | | - Brian Iglehart
- Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Zahra Kashi
- Kashi Clinical Laboratories, Inc., Portland, OR, USA
| | | | | | - Jiannis Ragoussis
- McGill University Health Centre, Montreal, QC, Canada; Department of Human Genetics, McGill University, Montreal, Quebec, Canada
| | | | - Cristina Navarrete
- National H&I Service Development Laboratory NHS Blood and Transplant, London, UK
| | - Winnie Chong
- National H&I Service Development Laboratory NHS Blood and Transplant, London, UK
| | | | - Martin Petrek
- Palacky University, Faculty of Medicine and Dentistry, Olomouc, Czech Republic
| | - Stana Tokic
- Palacky University, Faculty of Medicine and Dentistry, Olomouc, Czech Republic
| | - Karin Padros
- Primer Centro Argentino de Immunogenetica (PRICAI), Fundación Favaloro, CABA, Argentina
| | - Ma Beatriz Rodriguez
- Primer Centro Argentino de Immunogenetica (PRICAI), Fundación Favaloro, CABA, Argentina
| | - Viktoria Zakharova
- Rogachev Federal Research Centre of Pediatric Hematology,Oncology and Immunology, Moscow, Russian Federation
| | - Olga Shragina
- Rogachev Federal Research Centre of Pediatric Hematology,Oncology and Immunology, Moscow, Russian Federation
| | | | | | | | - Shingo Suzuki
- Tokai University School of Medicine, Kanagawa, Japan
| | | | - Qiuheng Zhang
- University of California, Los Angeles, Immunogenetics Center, Los Angeles, CA, USA
| | - Yuxin Yin
- University of California, Los Angeles, Immunogenetics Center, Los Angeles, CA, USA
| | | | | | - Phillip Ruiz
- University of Miami Miller School of Medicine, USA
| | | | | | - Aviva Geretz
- Walter Reed Army Institute of Research, Silver Spring, MD, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | - Rasmi Thomas
- Walter Reed Army Institute of Research, Silver Spring, MD, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | - Fumiko Yamamoto
- 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
| | - Sridevi Gangavarapu
- Histocompatibility, Immunogenetics, and Disease Profiling Laboratory, Stanford Blood Center, Palo Alto, CA, USA
| | - Uma Kanga
- All India Institute of Medical Sciences, New Delhi, India
| | - Shweta Tyagi
- All India Institute of Medical Sciences, New Delhi, India
| | - Steven G E Marsh
- Anthony Nolan Research Institute and UCL Cancer Institute, Royal Free Campus, London, UK
| | - Will P Bultitude
- Anthony Nolan Research Institute and UCL Cancer Institute, Royal Free Campus, London, UK
| | - Xiangjun Liu
- Bo Fu Rui (BFR) Transplant Diagnostics, Beijing, China
| | - Dajiang Cao
- Bo Fu Rui (BFR) Transplant Diagnostics, Beijing, China
| | | | | | - Anne Cesbron
- Histocompatibility and Immunogenetics Laboratory, Nantes, France
| | - Claudia Mueller
- Transplantation and Immunology, Universitat Tuebingen, Germany
| | | | - Eric T Weimer
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill School of Medicine, NC, USA
| | - Mats Bengtsson
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Gottfried Fischer
- Department of Blood Group Serology and Transfusion Medicine, Medical University of Vienna, Vienna, Austria
| | - John A Hansen
- Division of Clinical Research, Fred Hutchinson Cancer Research Center, Seattle, WA, USA; Department of Pediatrics, University of Washington School of Medicine, Seattle, WA, USA
| | | | - Steven J Mack
- Center for Genetics, Children's Hospital Oakland Research Institute, Oakland, CA, USA
| | - Lisa E Creary
- Histocompatibility, Immunogenetics, and Disease Profiling Laboratory, Stanford Blood Center, Palo Alto, CA, USA; Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Marcelo A Fernandez-Viña
- Histocompatibility, Immunogenetics, and Disease Profiling Laboratory, Stanford Blood Center, Palo Alto, CA, USA; Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
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11
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Goeury T, Creary LE, Brunet L, Galan M, Pasquier M, Kervaire B, Langaney A, Tiercy JM, Fernández-Viña MA, Nunes JM, Sanchez-Mazas A. Deciphering the fine nucleotide diversity of full HLA class I and class II genes in a well-documented population from sub-Saharan Africa. HLA 2019; 91:36-51. [PMID: 29160618 PMCID: PMC5767763 DOI: 10.1111/tan.13180] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Revised: 11/01/2017] [Accepted: 11/15/2017] [Indexed: 01/06/2023]
Abstract
With the aim to understand how next‐generation sequencing (NGS) improves both our assessment of genetic variation within populations and our knowledge on HLA molecular evolution, we sequenced and analysed 8 HLA loci in a well‐documented population from sub‐Saharan Africa (Mandenka). The results of full‐gene NGS‐MiSeq sequencing compared with those obtained by traditional typing techniques or limited sequencing strategies showed that segregating sites located outside exon 2 are crucial to describe not only class I but also class II population diversity. A comprehensive analysis of exons 2, 3, 4 and 5 nucleotide diversity at the 8 HLA loci revealed remarkable differences among these gene regions, notably a greater variation concentrated in the antigen recognition sites of class I exons 3 and some class II exons 2, likely associated with their peptide‐presentation function, a lower diversity of HLA‐C exon 3, possibly related to its role as a KIR ligand, and a peculiar molecular diversity of HLA‐A exon 2, revealing demographic signals. Based on full‐length HLA sequences, we also propose that the most frequent DRB1 allele in the studied population, DRB1*13:04, emerged from an allelic conversion involving 3 potential alleles as donors and DRB1*11:02:01 as recipient. Finally, our analysis revealed a high occurrence of the DRB1*13:04‐DQA1*05:05:01‐DQB1*03:19 haplotype, possibly resulting from a selective sweep due to protection to Onchorcerca volvulus, a prevalent pathogen in West Africa. This study unveils highly relevant information on the molecular evolution of HLA genes in relation to their immune function, calling for similar analyses in other populations living in contrasting environments.
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Affiliation(s)
- T Goeury
- Laboratory of Anthropology, Genetics and Peopling History, Department of Genetics and Evolution - Anthropology Unit, University of Geneva, Geneva, Switzerland.,Institute of Genetics and Genomics in Geneva, University of Geneva, Geneva, Switzerland
| | - L E Creary
- Department of Pathology, Stanford University School of Medicine, Palo Alto, California
| | - L Brunet
- Laboratory of Anthropology, Genetics and Peopling History, Department of Genetics and Evolution - Anthropology Unit, University of Geneva, Geneva, Switzerland.,Transplantation Immunology Unit and National Reference Laboratory for Histocompatibility (UIT/LNRH), Geneva University Hospital, Geneva, Switzerland
| | - M Galan
- INRA, UMR 1062 CBGP, avenue du Campus Agropolis, Montferrier sur Lez, France
| | - M Pasquier
- Laboratory of Anthropology, Genetics and Peopling History, Department of Genetics and Evolution - Anthropology Unit, University of Geneva, Geneva, Switzerland.,Institute of Genetics and Genomics in Geneva, University of Geneva, Geneva, Switzerland
| | - B Kervaire
- Laboratory of Anthropology, Genetics and Peopling History, Department of Genetics and Evolution - Anthropology Unit, University of Geneva, Geneva, Switzerland.,Transplantation Immunology Unit and National Reference Laboratory for Histocompatibility (UIT/LNRH), Geneva University Hospital, Geneva, Switzerland
| | - A Langaney
- Laboratory of Anthropology, Genetics and Peopling History, Department of Genetics and Evolution - Anthropology Unit, University of Geneva, Geneva, Switzerland
| | - J-M Tiercy
- Institute of Genetics and Genomics in Geneva, University of Geneva, Geneva, Switzerland.,Transplantation Immunology Unit and National Reference Laboratory for Histocompatibility (UIT/LNRH), Geneva University Hospital, Geneva, Switzerland
| | - M A Fernández-Viña
- Department of Pathology, Stanford University School of Medicine, Palo Alto, California
| | - J M Nunes
- Laboratory of Anthropology, Genetics and Peopling History, Department of Genetics and Evolution - Anthropology Unit, University of Geneva, Geneva, Switzerland.,Institute of Genetics and Genomics in Geneva, University of Geneva, Geneva, Switzerland
| | - A Sanchez-Mazas
- Laboratory of Anthropology, Genetics and Peopling History, Department of Genetics and Evolution - Anthropology Unit, University of Geneva, Geneva, Switzerland.,Institute of Genetics and Genomics in Geneva, University of Geneva, Geneva, Switzerland
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12
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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: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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13
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Montero-Martín G, Mallempati KC, Gangavarapu S, Sánchez-Gordo F, Herrero-Mata MJ, Balas A, Vicario JL, Sánchez-García F, González-Escribano MF, Muro M, Moya-Quiles MR, González-Fernández R, Ocejo-Vinyals JG, Marín L, Creary LE, Osoegawa K, Vayntrub T, Caro-Oleas JL, Vilches C, Planelles D, Fernández-Viña MA. High-resolution characterization of allelic and haplotypic HLA frequency distribution in a Spanish population using high-throughput next-generation sequencing. Hum Immunol 2019; 80:429-436. [PMID: 30763600 DOI: 10.1016/j.humimm.2019.02.005] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Revised: 02/07/2019] [Accepted: 02/09/2019] [Indexed: 12/25/2022]
Abstract
Next-generation sequencing (NGS) at the HLA-A, -B, -C, -DPA1, -DPB1, -DQA1, -DQB1, -DRB1 and -DRB3/4/5 loci was performed on 282 healthy unrelated individuals from different major regions of Spain. High-resolution HLA genotypes defined by full sequencing of class I loci and extended coverage of class II loci were obtained to determine allele frequencies and also to estimate extended haplotype frequencies. HLA alleles were typed at the highest resolution level (4-field level, 4FL); with exception of a minor deviation in HLA-DPA1, no statistically significant deviations from expected Hardy Weinberg Equilibrium (HWE) proportions were observed for all other HLA loci. This study provides new 4FL-allele and -haplotype frequencies estimated for the first time in the Spanish population. Furthermore, our results describe extended haplotypes (including the less frequently typed HLA-DPA1 and HLA-DQA1 loci) and show distinctive haplotype associations found at 4FL-allele definition in this Spanish population study. The distinctive allelic and haplotypic diversity found at the 4FL reveals the high level of heterozygosity and specific haplotypic associations displayed that were not apparent at 2-field level (2FL). Overall, these results may contribute as a useful reference source for future population studies, for HLA-disease association studies as a healthy control group dataset and for improving donor recruitment strategies of bone marrow registries. HLA genotyping data of this Spanish population cohort was also included in the 17th International Histocompatibility and Immunogenetics Workshop (IHIW) as part of the study of HLA diversity in unrelated worldwide populations using NGS.
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Affiliation(s)
| | - Kalyan C Mallempati
- Stanford Blood Center, Stanford University School of Medicine, Palo Alto, CA, USA
| | - Sridevi Gangavarapu
- Stanford Blood Center, Stanford University School of Medicine, Palo Alto, CA, USA
| | | | | | - Antonio Balas
- Histocompatibility, Centro de Transfusión de la Comunidad de Madrid, Madrid, Spain
| | - Jose L Vicario
- Histocompatibility, Centro de Transfusión de la Comunidad de Madrid, Madrid, Spain
| | | | | | - Manuel Muro
- Immunology, Hospital Clínico Universitario Virgen de la Arrixaca, Murcia, Spain
| | - Maria R Moya-Quiles
- Immunology, Hospital Clínico Universitario Virgen de la Arrixaca, Murcia, Spain
| | | | | | - Luis Marín
- Molecular Biology-Hematology, Hospital Clínico Universitario, Salamanca, Spain
| | - Lisa E Creary
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Kazutoyo Osoegawa
- Stanford Blood Center, Stanford University School of Medicine, Palo Alto, CA, USA
| | - Tamara Vayntrub
- Stanford Blood Center, Stanford University School of Medicine, Palo Alto, CA, USA
| | - Jose L Caro-Oleas
- Histocompatibility and Immunogenetics, Banc de Sang i Teixits, Barcelona, Spain
| | - Carlos Vilches
- Immunogenetics and Histocompatibility, Instituto de Investigación Sanitaria Puerta de Hierro, Madrid, Spain
| | - Dolores Planelles
- Histocompatibility, Centro de Transfusión de la Comunidad Valenciana, Valencia, Spain
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14
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González-Quezada BA, Creary LE, Munguia-Saldaña AJ, Flores-Aguilar H, Fernández-Viña MA, Gorodezky C. Exploring the ancestry and admixture of Mexican Oaxaca Mestizos from Southeast Mexico using next-generation sequencing of 11 HLA loci. Hum Immunol 2019; 80:157-162. [PMID: 30708029 DOI: 10.1016/j.humimm.2019.01.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Revised: 12/03/2018] [Accepted: 01/17/2019] [Indexed: 02/01/2023]
Abstract
The Mestizos of Oaxaca resulted from the admixture of Zapotecan Natives with Spaniards and Africans. We selected 112 donors from Oaxaca and applied next-generation sequencing to characterize exon and intron variants in complete or extended HLA genes. Some alleles found, are unique to Mexican Natives and most likely will be absent in most major ethnicities, namely: Caucasians, Africans or Asians. Among these are HLA-A*68:03:01, HLA-A*68:05:01, HLA-C*03:04:01:02, HLA-C*15:09, HLA-C*3:05, HLA-C*03:06:01, HLA-B*39:05:01, HLA-B*35:14:01, HLA-B*35:12:01, HLA-B*35:43:01, HLA-B*40:05, HLA-B:40:08, HLA-B*51:02:01, HLA-B*35:24:01 and HLA-B*39:08. HLA-DQA1*05:05:01:05 and some HLA-DRB1 alleles were only present in Amerindians/Mestizos. Three haplotypes are unique to Mexican Natives, five to Middle-Eastern and Sephardi-Jews. We detected a novel HLA-DQA1*04:01:01 exon 4 variant. Any novel allele may have been positively selected to enlarge the peptide-binding repertoire, and some, like HLA-B*39:02:02 and HLA-B*39:05:01 were found with unique haplotype associations, suggesting convergent evolution events and/or allele lineage diversification. The allele frequencies were fairly evenly distributed in most HLA loci with the exception of HLA-DPB1. The application of NGS in Oaxaca is novel and will lead to better use in the clinical setting. It offers deep knowledge on the population structure, origins, migration, and discovery of new alleles and haplotypes that other techniques did not achieve.
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Affiliation(s)
- B A González-Quezada
- Dept. of Immunology & Immunogenetics, InDRE, Secretary of Health, Mexico City, Mexico; Fundación Comparte Vida, A.C., Mexico City, Mexico.
| | - L E Creary
- Department of Pathology, Stanford University School of Medicine, Palo Alto, CA, USA.
| | - A J Munguia-Saldaña
- Dept. of Immunology & Immunogenetics, InDRE, Secretary of Health, Mexico City, Mexico.
| | - H Flores-Aguilar
- Dept. of Immunology & Immunogenetics, InDRE, Secretary of Health, Mexico City, Mexico; Fundación Comparte Vida, A.C., Mexico City, Mexico.
| | - M A Fernández-Viña
- Department of Pathology, Stanford University School of Medicine, Palo Alto, CA, USA.
| | - C Gorodezky
- Dept. of Immunology & Immunogenetics, InDRE, Secretary of Health, Mexico City, Mexico; Fundación Comparte Vida, A.C., Mexico City, Mexico.
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Askar MZ, Williams JD, Madbouly AS, Kang S, Kennedy S, Willis A, Knudsen T, Robinson J, Creary LE, Fernandez-Vina MA. P073The common uncommon extended HLA haplotype: Do two weak associations make it strong? Hum Immunol 2018. [DOI: 10.1016/j.humimm.2018.07.132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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16
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Osoegawa K, Creary LE, Mallempati K, Gangavarapu S, Caillier S, Hollenbach J, Oksenberg J, Fernandez-Vina M. OR4 High resolution haplotype analyses of classical HLA genes in families with multiple sclerosis. Hum Immunol 2018. [DOI: 10.1016/j.humimm.2018.07.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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17
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Creary LE, Galarza P, Chang CJ, Shields B, Maha GC, Cardozo MBR, Osoegawa K, Vayntrub TA, Fernandez-Vina MA. P083 The HLA genetic structure of an argentinian registry population reflect a divergent demographic history. Hum Immunol 2018. [DOI: 10.1016/j.humimm.2018.07.142] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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18
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Thorstenson YR, Creary LE, Huang H, Rozot V, Nguyen TT, Babrzadeh F, Kancharla S, Fukushima M, Kuehn R, Wang C, Li M, Krishnakumar S, Mindrinos M, Fernandez Viña MA, Scriba TJ, Davis MM. Allelic resolution NGS HLA typing of Class I and Class II loci and haplotypes in Cape Town, South Africa. Hum Immunol 2018; 79:839-847. [PMID: 30240896 DOI: 10.1016/j.humimm.2018.09.004] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2017] [Revised: 07/23/2018] [Accepted: 09/17/2018] [Indexed: 11/18/2022]
Abstract
The development of next-generation sequencing (NGS) methods for HLA genotyping has already had an impact on the scope and precision of HLA research. In this study, allelic resolution HLA typing was obtained for 402 individuals from Cape Town, South Africa. The data were produced by high-throughput NGS sequencing as part of a study of T-cell responses to Mycobacterium tuberculosis in collaboration with the University of Cape Town and Stanford University. All samples were genotyped for 11 HLA loci, namely HLA-A, -B, -C, -DPA1, -DPB1, -DQA1, -DQB1, -DRB1, -DRB3, -DRB4, and -DRB5. NGS HLA typing of samples from Cape Town inhabitants revealed a unique cohort, including unusual haplotypes, and 22 novel alleles not previously reported in the IPD-IMGT/HLA Database. Eight novel alleles were in Class I loci and 14 were in Class II. There were 62 different alleles of HLA-A, 72 of HLA-B, and 47 of HLA-C. Alleles A∗23:17, A∗43:01, A∗29:11, A∗68:27:01, A∗01:23, B∗14:01:01, B∗15:10:01, B∗39:10:01, B∗45:07, B∗82:02:01 and C∗08:04:01 were notably more frequent in Cape Town compared to other populations reported in the literature. Class II loci had 21 different alleles of DPA1, 46 of DPB1, 27 of DQA1, 26 of DQB1, 41 of DRB1, 5 of DRB3, 4 of DRB4 and 6 of DRB5. The Cape Town cohort exhibited high degrees of HLA diversity and relatively high heterozygosity at most loci. Genetic distances between Cape Town and five other sub-Saharan African populations were also calculated and compared to European Americans.
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Affiliation(s)
| | - Lisa E Creary
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Huang Huang
- Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA, USA
| | - Virginie Rozot
- South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease and Molecular Medicine, Division of Immunology, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | | | | | | | | | - Raquel Kuehn
- Immucor, Sirona Genomics, Mountain View, CA, USA
| | - Chunlin Wang
- Immucor, Sirona Genomics, Mountain View, CA, USA
| | - Ming Li
- Immucor, Sirona Genomics, Mountain View, CA, USA
| | | | | | | | - Thomas J Scriba
- South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease and Molecular Medicine, Division of Immunology, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Mark M Davis
- Stanford University and Howard Hughes Medical Institute, Stanford, CA
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19
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Creary LE, Mallempati KC, Gangavarapu S, Caillier SJ, Oksenberg JR, Fernández-Viňa MA. Deconstruction of HLA-DRB1*04:01:01 and HLA-DRB1*15:01:01 class II haplotypes using next-generation sequencing in European-Americans with multiple sclerosis. Mult Scler 2018; 25:772-782. [PMID: 29683085 DOI: 10.1177/1352458518770019] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
BACKGROUND The association between HLA-DRB1*15:01 with multiple sclerosis (MS) susceptibility is well established, but the contribution of the tightly associated HLA-DRB5*01:01 allele has not yet been completely ascertained. Similarly, the effects of HLA-DRB1*04:01 alleles and haplotypes, defined at the full-gene resolution level with MS risk remains to be elucidated. OBJECTIVES To characterize the molecular architecture of class II HLA-DR15 and HLA-DR4 haplotypes associated with MS. METHODS Next-generation sequencing was used to determine HLA-DQB1, HLA-DQA1, and HLA-DRB1/4/5 alleles in 1403 unrelated European-American patients and 1425 healthy unrelated controls. Effect sizes of HLA alleles and haplotypes on MS risk were measured by odds ratio (OR) with 95% confidence intervals. RESULTS HLA-DRB1*15:01:01:01SG (OR = 3.20, p < 2.2E-16), HLA-DRB5*01:01:01 (OR = 2.96, p < 2.2E-16), and HLA-DRB5*01:01:01v1_STR1 (OR = 8.18, p = 4.3E-05) alleles all occurred at significantly higher frequencies in MS patients compared to controls. The most significant predis-posing haplotypes were HLA-DQB1*06:02:01~ HLA-DQA1*01:02:01:01SG~HLA-DRB1*15:01:01:01SG~HLA-DRB5*01:01:01 and HLA-DQB1*06:02:01~HLA-DQA1*01:02:01:01SG~HLA-DRB1*15:01:01:01SG~HLA-DRB5*01:01:01v1_STR1 (OR = 3.19, p < 2.2E-16; OR = 9.30, p = 9.7E-05, respectively). Analyses of the HLA-DRB1*04 cohort in the absence of HLA-DRB1*15:01 haplotypes revealed that the HLA-DQB1*03:01:01:01~HLA-DQA1*03:03:01:01~HLA-DRB1*04:01:01:01SG~HLA-DRB4*01:03:01:01 haplotype was protective (OR = 0.64, p = 0.028), whereas the HLA-DQB1*03:02:01~HLA-DQA1*03:01:01~HLA-DRB1*04:01:01:01SG~HLA-DRB4*01:03:01:01 haplotype was associated with MS susceptibility (OR = 1.66, p = 4.9E-03). CONCLUSION HLA-DR15 haplotypes, including genomic variants of HLA-DRB5, and HLA-DR4 haplotypes affect MS risk.
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Affiliation(s)
- Lisa E Creary
- Department of Pathology, Stanford University School of Medicine, Palo Alto, CA, USA
| | - Kalyan C Mallempati
- Histocompatibility, Immunogenetics and Disease Profiling Laboratory, Stanford Blood Center, Palo Alto, CA, USA
| | - Sridevi Gangavarapu
- Histocompatibility, Immunogenetics and Disease Profiling Laboratory, Stanford Blood Center, Palo Alto, CA, USA
| | - Stacy J Caillier
- Department of Neurology, University of California, San Francisco, CA, USA
| | - Jorge R Oksenberg
- Department of Neurology, University of California, San Francisco, CA, USA
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20
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Creary LE, Krishnakumar S, Wang C, Li M, Sanchez-Mazas A, Nunes JM, Levinson DF, Mindrinos MN, Fernandez-Vina MA. P041 Next generation sequencing reveals HLA genomic and haplotype diversity in U.S. populations of European and African ancestry. Hum Immunol 2016. [DOI: 10.1016/j.humimm.2016.07.106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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21
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Munguía A, Creary LE, Flores-Aguilar H, Gonzalez BA, Gangavarapu S, Mindrino M, Fernandez-Vina M, Gorodezky C. P107 Next generation sequencing (NGS) of the MHC, in Mestizos from Oaxaca, belonging to the Mexican unrelated donor registry-DONORMO. Hum Immunol 2016. [DOI: 10.1016/j.humimm.2016.07.172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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22
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Creary LE, McKenzie CA, Menzel S, Hanchard NA, Taylor V, Hambleton I, Spector TD, Forrester TE, Thein SL. Ethnic differences in F cell levels in Jamaica: a potential tool for identifying new genetic loci controlling fetal haemoglobin. Br J Haematol 2009; 144:954-60. [DOI: 10.1111/j.1365-2141.2008.07532.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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23
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Lemnrau AG, Cardoso S, Creary LE, Brown C, Miretti M, Girdlestone J, Navarrete CV. Human platelet antigen typing of neonatal alloimmune thrombocytopenia patients using whole genome amplified DNA and a 5'-nuclease assay. Transfusion 2009; 49:953-8. [PMID: 19175554 DOI: 10.1111/j.1537-2995.2008.02064.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
BACKGROUND A serious constraint in the investigation of the human platelet antigen (HPA) status of potential neonatal alloimmune thrombocytopenia (NAIT) cases is the limited amount of DNA available from the neonates. Whole genome amplification (WGA) of these DNA samples could overcome this problem, but requires validation to ensure that it is sufficiently sensitive and accurate before its application in a clinical diagnostic setting. STUDY DESIGN AND METHODS This study has validated the use of WGA DNA for HPA-1, -2, -3, -4, -5, and -15 genotyping with a panel of six controls and 13 previously HPA-typed samples from neonates together with parental DNA, using a 5'-nuclease (TaqMan) assay. WGA was performed using titrated amounts of genomic and WGA DNA template. HPA typing was performed on genomic and amplified DNA using a 5'-nuclease assay or polymerase chain reaction with sequence-specific primers (PCR-SSP). RESULTS WGA DNA yields were in the suggested range of 400x to 800x, as assessed by spectrophotometry and gel analysis, and did not require further purification. HPA genotyping showed 100 percent concordance when using down to 5 ng of genomic or WGA template. CONCLUSION This study demonstrates that WGA can be used for HPA typing using PCR-SSP or plate-based 5'-nuclease assays. The use of WGA for HPA typing in clinical samples from NAIT patients was validated with 100 percent concordance, and it is suggested that this technology can be used for other analyses where DNA amounts are limited.
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Affiliation(s)
- Alina G Lemnrau
- Histocompatibility & Immunogenetics Department, NHSBT, London, UK
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Creary LE, Ulug P, Menzel S, McKenzie CA, Hanchard NA, Taylor V, Farrall M, Forrester TE, Thein SL. Genetic variation on chromosome 6 influences F cell levels in healthy individuals of African descent and HbF levels in sickle cell patients. PLoS One 2009; 4:e4218. [PMID: 19148297 PMCID: PMC2621086 DOI: 10.1371/journal.pone.0004218] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2008] [Accepted: 12/08/2008] [Indexed: 12/03/2022] Open
Abstract
Fetal haemoglobin (HbF) is a major ameliorating factor in sickle cell disease. We investigated if a quantitative trait locus on chromosome 6q23 was significantly associated with HbF and F cell levels in individuals of African descent. Single nucleotide polymorphisms (SNPs) in a 24-kb intergenic region, 33-kb upstream of the HBS1L gene and 80-kb upstream of the MYB gene, were typed in 177 healthy Afro-Caribbean subjects (AC) of approximately 7% European admixture, 631 healthy Afro-Germans (AG, a group of African and German descendents located in rural Jamaica with about 20% European admixture), 87 West African and Afro-Caribbean individuals with sickle cell anaemia (HbSS), as well as 75 Northern Europeans, which served as a contrasting population. Association with a tag SNP for the locus was detected in all four groups (AC, P = 0.005, AG, P = 0.002, HbSS patients, P = 0.019, Europeans, P = 1.5 x 10(-7)). The association signal varied across the interval in the African-descended groups, while it is more uniform in Europeans. The 6q QTL for HbF traits is present in populations of African origin and is also acting in sickle cell anaemia patients. We have started to distinguish effects originating from European and African ancestral populations in our admixed study populations.
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Affiliation(s)
- Lisa E. Creary
- King's College London School of Medicine, Division of Gene and Cell, Based Therapy, James Black Centre, Denmark Hill Campus, London, United Kingdom
| | - Pinar Ulug
- King's College London School of Medicine, Division of Gene and Cell, Based Therapy, James Black Centre, Denmark Hill Campus, London, United Kingdom
| | - Stephan Menzel
- King's College London School of Medicine, Division of Gene and Cell, Based Therapy, James Black Centre, Denmark Hill Campus, London, United Kingdom
| | - Colin A. McKenzie
- Tropical Metabolism Research Unit, Tropical Medicine Research Institute, University of the West Indies, Mona, Kingston, Jamaica
| | - Neil A. Hanchard
- Tropical Metabolism Research Unit, Tropical Medicine Research Institute, University of the West Indies, Mona, Kingston, Jamaica
| | | | - Martin Farrall
- Department of Cardiovascular Medicine, Wellcome Trust Centre for Human, Genetics, University of Oxford, Oxford, United Kingdom
| | - Terrence E. Forrester
- Tropical Metabolism Research Unit, Tropical Medicine Research Institute, University of the West Indies, Mona, Kingston, Jamaica
| | - Swee Lay Thein
- King's College London School of Medicine, Division of Gene and Cell, Based Therapy, James Black Centre, Denmark Hill Campus, London, United Kingdom
- King's College Hospital, Department of Haematological Medicine, Denmark Hill, London, United Kingdom
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Abstract
BACKGROUND The outcome of clinical transplantation and a number of disease susceptibilities show very strong associations with genetic variants within the major histocompatibility complex, particularly in the human leukocyte antigen (HLA) genes. A problem with many association studies is the lack of sufficient DNA to perform multiple genetic analyses, particularly with transplantation outcomes where donor and recipient DNA are often in short supply. This study assesses whether a multiple-strand displacement whole genome amplification (WGA) method could generate sufficient template of high quality to perform unbiased amplification for analysis of the HLA-A, -B, -C, -DRB1, and -DQB1 genes. STUDY DESIGN AND METHODS A panel of DNA samples from various biological sources was subjected to WGA reaction using Phi29 DNA polymerase. The HLA genotypes were subsequently determined using standard polymerase chain reaction (PCR)-based methods including sequence-specific oligonucleotide probes (PCR-SSOP, Luminex, Luminex Corp.) and sequence-based typing (PCR-SBT). WGA products and original DNA samples were used to determine the sensitivity of the Luminex assay; in addition, reamplified WGA products were also genotyped. RESULTS The WGA templates, as well as serially amplified DNA for two successive rounds, yielded HLA genotypes fully concordant with those determined for the original DNA samples. WGA products and original DNA gave reproducible HLA-DQB1 genotypes with 100 to 10 ng of template. Purification of the WGA products was required for successful PCR-SBT, but not for the PCR-SSOP method. CONCLUSION Our study suggests that WGA can be a reliable method for generating unlimited DNA for medium- or high-resolution HLA typing using the techniques described above.
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Affiliation(s)
- Lisa E Creary
- Histocompatibility and Immunogenetics Research Group, Department of Histocompatibility and Immunogenetics, Colindale Centre, NHSBT, NHSBT, London, UK
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