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Montero-Martin G, Kichula KM, Misra MK, Vargas LB, Marin WM, Hollenbach JA, Fernández-Viña MA, Elfishawi S, Norman PJ. Exceptional diversity of KIR and HLA class I in Egypt. HLA 2024; 103:e15177. [PMID: 37528739 PMCID: PMC11068459 DOI: 10.1111/tan.15177] [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: 02/16/2023] [Revised: 05/25/2023] [Accepted: 07/14/2023] [Indexed: 08/03/2023]
Abstract
Genetically determined variation of killer cell immunoglobulin like receptors (KIR) and their HLA class I ligands affects multiple aspects of human health. Their extreme diversity is generated through complex interplay of natural selection for pathogen resistance and reproductive health, combined with demographic structure and dispersal. Despite significant importance to multiple health conditions of differential effect across populations, the nature and extent of immunogenetic diversity is under-studied for many geographic regions. Here, we describe the first high-resolution analysis of KIR and HLA class I combinatorial diversity in Northern Africa. Analysis of 125 healthy unrelated individuals from Cairo in Egypt yielded 186 KIR alleles arranged in 146 distinct centromeric and 79 distinct telomeric haplotypes. The most frequent haplotypes observed were KIR-A, encoding two inhibitory receptors specific for HLA-C, two that are specific for HLA-A and -B, and no activating receptors. Together with 141 alleles of HLA class I, 75 of which encode a KIR ligand, we identified a mean of six distinct interacting pairs of inhibitory KIR and HLA allotypes per individual. We additionally characterize 16 KIR alleles newly identified in the study population. Our findings place Egyptians as one of the most highly diverse populations worldwide, with important implications for transplant matching and studies of immune-mediated diseases.
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Affiliation(s)
| | - Katherine M. Kichula
- Department of Biomedical Informatics, University of Colorado School of Medicine, Aurora, CO, USA
| | - Maneesh K. Misra
- Department of Neurology, Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA, USA
- Department of Pathology, University of Chicago Medicine, Chicago, IL, USA
| | - Luciana B. Vargas
- Department of Biomedical Informatics, University of Colorado School of Medicine, Aurora, CO, USA
| | - Wesley M. Marin
- Department of Neurology, Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA, USA
| | - Jill A. Hollenbach
- Department of Neurology, Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA, USA
| | | | - Sally Elfishawi
- BMT lab unit, Clinical Pathology Dept., National Cancer Institute, Cairo University, Cairo, Egypt
| | - Paul J. Norman
- Department of Biomedical Informatics, University of Colorado School of Medicine, Aurora, CO, USA
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, CO, USA
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Ma Q, Augusto DG, Montero-Martin G, Caillier SJ, Osoegawa K, Cree BAC, Hauser SL, Didonna A, Hollenbach JA, Norman PJ, Fernandez-Vina M, Oksenberg JR. High-resolution DNA methylation screening of the major histocompatibility complex in multiple sclerosis. Front Neurol 2023; 14:1326738. [PMID: 38145128 PMCID: PMC10739394 DOI: 10.3389/fneur.2023.1326738] [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] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Accepted: 11/23/2023] [Indexed: 12/26/2023] Open
Abstract
Background The HLA-DRB1 gene in the major histocompatibility complex (MHC) region in chromosome 6p21 is the strongest genetic factor identified as influencing multiple sclerosis (MS) susceptibility. DNA methylation changes associated with MS have been consistently detected at the MHC region. However, understanding the full scope of epigenetic regulations of the MHC remains incomplete, due in part to the limited coverage of this region by standard whole genome bisulfite sequencing or array-based methods. Methods We developed and validated an MHC capture protocol coupled with bisulfite sequencing and conducted a comprehensive analysis of the MHC methylation landscape in blood samples from 147 treatment naïve MS study participants and 129 healthy controls. Results We identified 132 differentially methylated region (DMRs) within MHC region associated with disease status. The DMRs overlapped with established MS risk loci. Integration of the MHC methylome with human leukocyte antigen (HLA) genetic data indicate that the methylation changes are significantly associated with HLA genotypes. Using DNA methylation quantitative trait loci (mQTL) mapping and the causal inference test (CIT), we identified 643 cis-mQTL-DMRs paired associations, including 71 DMRs possibly mediating causal relationships between 55 single nucleotide polymorphisms (SNPs) and MS risk. Results The results describe MS-associated methylation changes in MHC region and highlight the association between HLA genotypes and methylation changes. Results from the mQTL and CIT analyses provide evidence linking MHC region variations, methylation changes, and disease risk for MS.
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Affiliation(s)
- Qin Ma
- Weill Institute for Neurosciences, Department of Neurology, University of California San Francisco, San Francisco, CA, United States
| | - Danillo G. Augusto
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, NC, United States
| | - Gonzalo Montero-Martin
- Histocompatibility and Immunogenetics Laboratory, Stanford Blood Center, Palo Alto, CA, United States
- Department of Pathology, Stanford University School of Medicine, Palo Alto, CA, United States
- HLA Histocompatibility and Immunogenetics Laboratory, Vitalant, Phoenix, AZ, United States
| | - Stacy J. Caillier
- Weill Institute for Neurosciences, Department of Neurology, University of California San Francisco, San Francisco, CA, United States
| | - Kazutoyo Osoegawa
- Histocompatibility and Immunogenetics Laboratory, Stanford Blood Center, Palo Alto, CA, United States
| | - Bruce A. C. Cree
- 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
| | - Alessandro Didonna
- Department of Anatomy and Cell Biology, Brody School of Medicine, East Carolina University, Greenville, NC, United States
| | - Jill A. Hollenbach
- Weill Institute for Neurosciences, Department of Neurology, University of California San Francisco, San Francisco, CA, United States
| | - Paul J. Norman
- Department of Biomedical Informatics and Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, CO, United States
| | - Marcelo Fernandez-Vina
- Histocompatibility and Immunogenetics Laboratory, Stanford Blood Center, Palo Alto, CA, United States
- Department of Pathology, Stanford University School of Medicine, Palo Alto, CA, United States
| | - Jorge R. Oksenberg
- Weill Institute for Neurosciences, Department of Neurology, University of California San Francisco, San Francisco, CA, United States
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Saper VE, Ombrello MJ, Tremoulet AH, Montero-Martin G, Prahalad S, Canna S, Shimizu C, Deutsch G, Tan SY, Remmers EF, Monos D, Hahn T, Phadke OK, Cassidy E, Ferguson I, Mallajosyula V, Xu J, Rosa Duque JS, Chua GT, Ghosh D, Szymanski AM, Rubin D, Burns JC, Tian L, Fernandez-Vina MA, Mellins ED, Hollenbach JA. Severe delayed hypersensitivity reactions to IL-1 and IL-6 inhibitors link to common HLA-DRB1*15 alleles. Ann Rheum Dis 2022; 81:406-415. [PMID: 34789453 PMCID: PMC10564446 DOI: 10.1136/annrheumdis-2021-220578] [Citation(s) in RCA: 43] [Impact Index Per Article: 21.5] [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: 04/27/2021] [Accepted: 09/29/2021] [Indexed: 12/11/2022]
Abstract
OBJECTIVES Drug reaction with eosinophilia and systemic symptoms (DRESS) is a severe, delayed hypersensitivity reaction (DHR). We observed DRESS to inhibitors of interleukin 1 (IL-1) or IL-6 in a small group of patients with Still's disease with atypical lung disease. We sought to characterise features of patients with Still's disease with DRESS compared with drug-tolerant Still's controls. We analysed human leucocyte antigen (HLA) alleles for association to inhibitor-related DHR, including in a small Kawasaki disease (KD) cohort. METHODS In a case/control study, we collected a multicentre series of patients with Still's disease with features of inhibitor-related DRESS (n=66) and drug-tolerant Still's controls (n=65). We retrospectively analysed clinical data from all Still's subjects and typed 94/131 for HLA. European Still's-DRESS cases were ancestry matched to International Childhood Arthritis Genetics Consortium paediatric Still's cases (n=550) and compared for HLA allele frequencies. HLA association also was analysed using Still's-DRESS cases (n=64) compared with drug-tolerant Still's controls (n=30). KD subjects (n=19) were similarly studied. RESULTS Still's-DRESS features included eosinophilia (89%), AST-ALT elevation (75%) and non-evanescent rash (95%; 88% involving face). Macrophage activation syndrome during treatment was frequent in Still's-DRESS (64%) versus drug-tolerant Still's (3%; p=1.2×10-14). We found striking enrichment for HLA-DRB1*15 haplotypes in Still's-DRESS cases versus INCHARGE Still's controls (p=7.5×10-13) and versus self-identified, ancestry-matched Still's controls (p=6.3×10-10). In the KD cohort, DRB1*15:01 was present only in those with suspected anakinra reactions. CONCLUSIONS DRESS-type reactions occur among patients treated with IL-1/IL-6 inhibitors and strongly associate with common HLA-DRB1*15 haplotypes. Consideration of preprescription HLA typing and vigilance for serious reactions to these drugs are warranted.
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Affiliation(s)
- Vivian E Saper
- Pediatrics, Stanford University, Stanford, California, USA
| | - Michael J Ombrello
- Translational Genetics and Genomics Unit, NIAMS, National Institutes of Health, Bethesda, Maryland, USA
| | | | - Gonzalo Montero-Martin
- Stanford Blood Center, Histocompatibility and Immunogenetics Laboratory, Stanford University, Stanford, California, USA
| | - Sampath Prahalad
- Children's Healthcare of Atlanta, Atlanta, Georgia, USA
- Pediatrics, Emory University, Atlanta, Georgia, USA
| | - Scott Canna
- Pediatrics, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Chisato Shimizu
- Pediatrics, University of California San Diego, La Jolla, California, USA
| | - Gail Deutsch
- Pathology, Seattle Children's Hospital, Seattle, Washington, USA
| | - Serena Y Tan
- Pathology, Stanford University, Stanford, California, USA
| | - Elaine F Remmers
- National Human Genome Research Institute, Bethesda, Maryland, USA
| | - Dimitri Monos
- Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Timothy Hahn
- Pediatrics, The Pennsylvania State University College of Medicine, Hershey, Pennsylvania, USA
| | | | - Elaine Cassidy
- Pediatrics, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Ian Ferguson
- Pediatrics, Yale University School of Medicine, New Haven, Connecticut, USA
| | | | - Jianpeng Xu
- Pediatrics, Stanford University, Stanford, California, USA
| | - Jaime S Rosa Duque
- Pediatrics, University of Hong Kong, Hong Kong Special Adminstrative District, China
| | - Gilbert T Chua
- Pediatrics, University of Hong Kong, Hong Kong Special Adminstrative District, China
| | - Debopam Ghosh
- Pediatrics, Stanford University, Stanford, California, USA
| | - Ann Marie Szymanski
- Translational Genetics and Genomics Unit, NIAMS, National Institutes of Health, Bethesda, Maryland, USA
| | - Danielle Rubin
- Translational Genetics and Genomics Unit, NIAMS, National Institutes of Health, Bethesda, Maryland, USA
| | - Jane C Burns
- Pediatrics, University of California San Diego, La Jolla, California, USA
| | - Lu Tian
- Biomedical Data Science, Stanford University, Stanford, California, USA
| | - Marcelo A Fernandez-Vina
- Stanford Blood Center, Histocompatibility and Immunogenetics Laboratory, Stanford University, Stanford, California, USA
| | | | - Jill A Hollenbach
- Neurology, University of California San Francisco, San Francisco, California, USA
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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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Amorim LM, Augusto DG, Nemat-Gorgani N, Montero-Martin G, Marin WM, Shams H, Dandekar R, Caillier S, Parham P, Fernández-Viña MA, Oksenberg JR, Norman PJ, Hollenbach JA. High-Resolution Characterization of KIR Genes in a Large North American Cohort Reveals Novel Details of Structural and Sequence Diversity. Front Immunol 2021; 12:674778. [PMID: 34025673 PMCID: PMC8137979 DOI: 10.3389/fimmu.2021.674778] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Accepted: 04/20/2021] [Indexed: 12/14/2022] Open
Abstract
The KIR (killer-cell immunoglobulin-like receptor) region is characterized by structural variation and high sequence similarity among genes, imposing technical difficulties for analysis. We undertook the most comprehensive study to date of KIR genetic diversity in a large population sample, applying next-generation sequencing in 2,130 United States European-descendant individuals. Data were analyzed using our custom bioinformatics pipeline specifically designed to address technical obstacles in determining KIR genotypes. Precise gene copy number determination allowed us to identify a set of uncommon gene-content KIR haplotypes accounting for 5.2% of structural variation. In this cohort, KIR2DL4 is the framework gene that most varies in copy number (6.5% of all individuals). We identified phased high-resolution alleles in large multi-locus insertions and also likely founder haplotypes from which they were deleted. Additionally, we observed 250 alleles at 5-digit resolution, of which 90 have frequencies ≥1%. We found sequence patterns that were consistent with the presence of novel alleles in 398 (18.7%) individuals and contextualized multiple orphan dbSNPs within the KIR complex. We also identified a novel KIR2DL1 variant, Pro151Arg, and demonstrated by molecular dynamics that this substitution is predicted to affect interaction with HLA-C. No previous studies have fully explored the full range of structural and sequence variation of KIR as we present here. We demonstrate that pairing high-throughput sequencing with state-of-art computational tools in a large cohort permits exploration of all aspects of KIR variation including determination of population-level haplotype diversity, improving understanding of the KIR system, and providing an important reference for future studies.
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Affiliation(s)
- Leonardo M. Amorim
- Programa de Pós-Graduação em Genética, Universidade Federal do Paraná, Curitiba, Brazil
| | - Danillo G. Augusto
- Department of Neurology, University of California, San Francisco, CA, United States
| | - Neda Nemat-Gorgani
- Department of Structural Biology, Stanford University, Palo Alto, CA, United States
| | - Gonzalo Montero-Martin
- Histocompatibility & Immunogenetics Laboratory, Stanford Blood Center, Palo Alto, CA, United States
| | - Wesley M. Marin
- Department of Neurology, University of California, San Francisco, CA, United States
| | - Hengameh Shams
- Department of Neurology, University of California, San Francisco, CA, United States
| | - Ravi Dandekar
- Department of Neurology, University of California, San Francisco, CA, United States
| | - Stacy Caillier
- Department of Neurology, University of California, San Francisco, CA, United States
| | - Peter Parham
- Department of Structural Biology, Stanford University, Palo Alto, CA, United States
| | | | - Jorge R. Oksenberg
- Department of Neurology, University of California, San Francisco, CA, United States
| | - Paul J. Norman
- Department of Structural Biology, Stanford University, Palo Alto, CA, United States
- Division of Biomedical Informatics and Personalized Medicine, University of Colorado, Denver, CO, United States
| | - Jill A. Hollenbach
- Department of Neurology, University of California, San Francisco, CA, United States
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Elfishawi M, Mossallam G, Augusto DG, Montero-Martin G, de Bruin H, Van de Pasch L, Norman PJ, Rozemuller E, Fernandez-Vina M, Abrudescu A, Hollenbach JA, Zaky K, Elfishawi S. Behçet disease, new insights in disease associations and manifestations: a next-generation sequencing study. Clin Exp Immunol 2021; 204:144-151. [PMID: 33421092 DOI: 10.1111/cei.13571] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [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: 11/21/2020] [Revised: 12/20/2020] [Accepted: 12/21/2020] [Indexed: 12/01/2022] Open
Abstract
Behçet disease is a multi-system disease associated with human leukocyte antigen (HLA) class I polymorphism. High-resolution next-generation sequencing (NGS) with haplotype analysis has not been performed previously for this disease. Sixty Egyptian patients diagnosed according to the International Study Group (ISG) criteria for Behçet disease and 160 healthy geographic and ethnic-matched controls were genotyped for HLA class I loci (HLA-A, B, C). For HLA class II loci (DRB1, DRB3/4/5, DQA1, DQB1, DPA1, DPB1), 40 control samples were genotyped. High-resolution HLA genotyping was performed using NGS and the results were analyzed. Clinical manifestations were oral ulcers (100%), genital ulcers (100%), eye (55%) and neurological (28%) and vascular involvement (35%). HLA-B*51:08 [odds ratio (OR) = 19·75, 95% confidence interval (CI) = 6·5-79; P < 0·0001], HLA-B*15:03 (OR = 12·15, 95% CI = 3·7-50·7; P < 0·0001), HLA-C*16:02 (OR = 6·53, 95% CI = 3-14; P < 0·0001), HLA-A*68:02 (OR = 3·14, 95% CI = 1·1-8·9; P < 0·01) were found to be associated with Behçet disease, as were HLA-DRB1*13:01 and HLA-DQB1*06:03 (OR = 3·39, 95% CI = 0·9-18·9; P = 0·04 for both). By contrast, HLA-A*03:01 (OR = 0·13, 95% CI = 0-0·8; P = 0·01) and HLA-DPB1*17:01 were found to be protective (OR = 0·27, 95% CI = 0·06-1·03; P = 0·02). We identified strong linkage disequilibrium between HLA-B*51:08 and C*16:02 and A*02:01 in a haplotype associated with Behçet disease. HLA-B*51:08 was significantly associated with legal blindness (OR = 2·98, 95% CI = 1·06-8·3; P = 0·01). In Egyptian Behçet patients, HLA-B*51:08 is the most common susceptibility allele and holds poor prognosis for eye involvement.
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Affiliation(s)
- M Elfishawi
- Division of Rheumatology, Mayo Clinic College of Medicine, Rochester, MN, USA
| | - G Mossallam
- BMT Lab Unit, Clinical Pathology Deptartment, National Cancer Institute, Cairo University, Cairo, Egypt
| | - D G Augusto
- Department of Neurology, University of California San Francisco, San Francisco, CA, USA
| | - G Montero-Martin
- Department of Pathology, Stanford University School of Medicine, Palo Alto, CA, USA
| | | | | | - P J Norman
- Division of Personalized Medicine and Department of Immunology and Microbiology, University of Colorado School of Medicine, Denver, CO, USA
| | | | - M Fernandez-Vina
- Department of Pathology, Stanford University School of Medicine, Palo Alto, CA, USA
| | - A Abrudescu
- Department of Medicine, New York City Health + Hospitals: Queens, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - J A Hollenbach
- Department of Neurology, University of California San Francisco, San Francisco, CA, USA
| | - K Zaky
- Rheumatology and Rehabilitation, Faculty of Medicine, Al-Azhar University, Cairo, Egypt
| | - S Elfishawi
- BMT Lab Unit, Clinical Pathology Deptartment, National Cancer Institute, Cairo University, Cairo, Egypt
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7
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Gorzynski JE, De Jong HN, Amar D, Hughes CR, Ioannidis A, Bierman R, Liu D, Tanigawa Y, Kistler A, Kamm J, Kim J, Cappello L, Neff NF, Rubinacci S, Delaneau O, Shoura MJ, Seo K, Kirillova A, Raja A, Sutton S, Huang C, Sahoo MK, Mallempati KC, Montero-Martin G, Osoegawa K, Jimenez-Morales D, Watson N, Hammond N, Joshi R, Fernandez-Vina M, Christle JW, Wheeler MT, Febbo P, Farh K, Schroth G, Desouza F, Palacios J, Salzman J, Pinsky BA, Rivas MA, Bustamante CD, Ashley EA, Parikh VN. High-throughput SARS-CoV-2 and host genome sequencing from single nasopharyngeal swabs. medRxiv 2020. [PMID: 32766602 DOI: 10.1101/2020.07.27.20163147] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
During COVID19 and other viral pandemics, rapid generation of host and pathogen genomic data is critical to tracking infection and informing therapies. There is an urgent need for efficient approaches to this data generation at scale. We have developed a scalable, high throughput approach to generate high fidelity low pass whole genome and HLA sequencing, viral genomes, and representation of human transcriptome from single nasopharyngeal swabs of COVID19 patients.
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Belbezier A, Joubert B, Montero-Martin G, Fernandez-Vina M, Fabien N, Rogemond V, Mignot E, Honnorat J. Multiplex family with GAD65-Abs neurologic syndromes. Neurol Neuroimmunol Neuroinflamm 2017; 5:e416. [PMID: 29379821 PMCID: PMC5778747 DOI: 10.1212/nxi.0000000000000416] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Accepted: 10/02/2017] [Indexed: 11/17/2022]
Abstract
Objective: Neurologic autoimmune syndromes associated with anti–glutamate acid decarboxylase 65 antibodies (GAD65-Abs) are rare and mostly sporadic. Methods: We describe a niece and her aunt with GAD65-Abs neurologic syndromes. High-resolution HLA typing of Class I and Class II alleles was performed using next-generation sequencing. Results: The proband had cerebellar ataxia and probable limbic encephalitis features, whereas her niece had stiff-person syndrome. Both had a high titer of GAD65-Abs in serum and CSF and showed signs of inflammation in CSF. Both affected members carried the same rare recombinant DRB1*15:01:01∼DQA1*01:02:01∼DQB1*05:02:01 haplotype, which may or may not be involved in disease susceptibility. Of interest, other unaffected members of the family either had the same HLA haplotype but normal serum GAD65-Abs or had different HLA types but a high titer of serum GAD65-Abs without neurologic symptoms, suggesting cumulative effects. Conclusions: This unique association strengthens the concept that hereditary factors, possibly including specific HLA haplotypes, play a role in neurologic syndromes associated with GAD65-Abs.
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Affiliation(s)
- Aude Belbezier
- French Reference Center on Paraneoplastic Neurological Syndrome (A.B., B.J., V.R., J.H.), Hospices Civils de Lyon, Hôpital Neurologique, Bron, France; Institut NeuroMyoGene INSERM U1217/CNRS UMR 5310 (A.B., B.J., V.R., J.H.), Université de Lyon-Université Claude Bernard Lyon 1, France; Stanford Blood Center (G.M.-M., M.F.-V., E.M.), Histocompatibility, Immunogenetics & Disease Profiling Laboratory, Palo Alto, CA; Immunology, Hospices Civils de Lyon (N.F.), Hôpital Lyon-Sud, France; and Stanford University Center for Sleep Sciences and Medicine (E.M), Palo Alto, CA
| | - Bastien Joubert
- French Reference Center on Paraneoplastic Neurological Syndrome (A.B., B.J., V.R., J.H.), Hospices Civils de Lyon, Hôpital Neurologique, Bron, France; Institut NeuroMyoGene INSERM U1217/CNRS UMR 5310 (A.B., B.J., V.R., J.H.), Université de Lyon-Université Claude Bernard Lyon 1, France; Stanford Blood Center (G.M.-M., M.F.-V., E.M.), Histocompatibility, Immunogenetics & Disease Profiling Laboratory, Palo Alto, CA; Immunology, Hospices Civils de Lyon (N.F.), Hôpital Lyon-Sud, France; and Stanford University Center for Sleep Sciences and Medicine (E.M), Palo Alto, CA
| | - Gonzalo Montero-Martin
- French Reference Center on Paraneoplastic Neurological Syndrome (A.B., B.J., V.R., J.H.), Hospices Civils de Lyon, Hôpital Neurologique, Bron, France; Institut NeuroMyoGene INSERM U1217/CNRS UMR 5310 (A.B., B.J., V.R., J.H.), Université de Lyon-Université Claude Bernard Lyon 1, France; Stanford Blood Center (G.M.-M., M.F.-V., E.M.), Histocompatibility, Immunogenetics & Disease Profiling Laboratory, Palo Alto, CA; Immunology, Hospices Civils de Lyon (N.F.), Hôpital Lyon-Sud, France; and Stanford University Center for Sleep Sciences and Medicine (E.M), Palo Alto, CA
| | - Marcelo Fernandez-Vina
- French Reference Center on Paraneoplastic Neurological Syndrome (A.B., B.J., V.R., J.H.), Hospices Civils de Lyon, Hôpital Neurologique, Bron, France; Institut NeuroMyoGene INSERM U1217/CNRS UMR 5310 (A.B., B.J., V.R., J.H.), Université de Lyon-Université Claude Bernard Lyon 1, France; Stanford Blood Center (G.M.-M., M.F.-V., E.M.), Histocompatibility, Immunogenetics & Disease Profiling Laboratory, Palo Alto, CA; Immunology, Hospices Civils de Lyon (N.F.), Hôpital Lyon-Sud, France; and Stanford University Center for Sleep Sciences and Medicine (E.M), Palo Alto, CA
| | - Nicole Fabien
- French Reference Center on Paraneoplastic Neurological Syndrome (A.B., B.J., V.R., J.H.), Hospices Civils de Lyon, Hôpital Neurologique, Bron, France; Institut NeuroMyoGene INSERM U1217/CNRS UMR 5310 (A.B., B.J., V.R., J.H.), Université de Lyon-Université Claude Bernard Lyon 1, France; Stanford Blood Center (G.M.-M., M.F.-V., E.M.), Histocompatibility, Immunogenetics & Disease Profiling Laboratory, Palo Alto, CA; Immunology, Hospices Civils de Lyon (N.F.), Hôpital Lyon-Sud, France; and Stanford University Center for Sleep Sciences and Medicine (E.M), Palo Alto, CA
| | - Véronique Rogemond
- French Reference Center on Paraneoplastic Neurological Syndrome (A.B., B.J., V.R., J.H.), Hospices Civils de Lyon, Hôpital Neurologique, Bron, France; Institut NeuroMyoGene INSERM U1217/CNRS UMR 5310 (A.B., B.J., V.R., J.H.), Université de Lyon-Université Claude Bernard Lyon 1, France; Stanford Blood Center (G.M.-M., M.F.-V., E.M.), Histocompatibility, Immunogenetics & Disease Profiling Laboratory, Palo Alto, CA; Immunology, Hospices Civils de Lyon (N.F.), Hôpital Lyon-Sud, France; and Stanford University Center for Sleep Sciences and Medicine (E.M), Palo Alto, CA
| | - Emmanuel Mignot
- French Reference Center on Paraneoplastic Neurological Syndrome (A.B., B.J., V.R., J.H.), Hospices Civils de Lyon, Hôpital Neurologique, Bron, France; Institut NeuroMyoGene INSERM U1217/CNRS UMR 5310 (A.B., B.J., V.R., J.H.), Université de Lyon-Université Claude Bernard Lyon 1, France; Stanford Blood Center (G.M.-M., M.F.-V., E.M.), Histocompatibility, Immunogenetics & Disease Profiling Laboratory, Palo Alto, CA; Immunology, Hospices Civils de Lyon (N.F.), Hôpital Lyon-Sud, France; and Stanford University Center for Sleep Sciences and Medicine (E.M), Palo Alto, CA
| | - Jérôme Honnorat
- French Reference Center on Paraneoplastic Neurological Syndrome (A.B., B.J., V.R., J.H.), Hospices Civils de Lyon, Hôpital Neurologique, Bron, France; Institut NeuroMyoGene INSERM U1217/CNRS UMR 5310 (A.B., B.J., V.R., J.H.), Université de Lyon-Université Claude Bernard Lyon 1, France; Stanford Blood Center (G.M.-M., M.F.-V., E.M.), Histocompatibility, Immunogenetics & Disease Profiling Laboratory, Palo Alto, CA; Immunology, Hospices Civils de Lyon (N.F.), Hôpital Lyon-Sud, France; and Stanford University Center for Sleep Sciences and Medicine (E.M), Palo Alto, CA
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