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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] [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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Londono J, Santos AM, Peña P, Calvo E, Espinosa LR, Reveille JD, Vargas-Alarcon G, Jaramillo CA, Valle-Oñate R, Avila M, Romero C, Medina JF. Analysis of HLA-B15 and HLA-B27 in spondyloarthritis with peripheral and axial clinical patterns. BMJ Open 2015; 5:e009092. [PMID: 26560062 PMCID: PMC4654353 DOI: 10.1136/bmjopen-2015-009092] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
OBJECTIVE Human leucocyte antigen (HLA) B27 and HLA-B15 are associated with spondyloarthritis (SpA). Recent Assessment of SpondyloArthritis international Society (ASAS) criteria emphasise a distinction between SpA with axial and peripheral patterns. We analysed whether HLA-A, HLA-B and HLA-DRB1 alleles could associate with these patterns. METHODS We studied 100 healthy individuals and 178 patients with SpA according to European Spondyloarthropathy Study Group (ESSG) criteria. Patients were then classified according to ASAS criteria, the axial spondyloarthritis pattern (axSpA) being defined by ascertained sacroiliitis and the peripheral pattern (pSpA) by enthesitis and/or arthritis in extremities. A combined ax/p pattern was also considered. RESULTS Only HLA-B27 and HLA-B15 alleles were associated with SpA. ASAS criteria for axSpA were met in 152 patients (12 with isolated axSpA and 140 with a combined ax/p patterns). When the ASAS peripheral criteria were applied, 161 patients met these criteria (13 with isolated pSpA and 148 with a combined ax/p pattern). HLA-B27 was found in 83% of patients with axSpA and 43% of ax/pSpA patients according to axASAS. HLA-B27 occurred in 7% controls but not in any patient with isolated pSpA. HLA-B15 was encountered in 31% of patients with isolated pSpA and 20% of ax/pSpA patients according to pASAS criteria. Moreover, 2 healthy controls, but none of our patients with isolated axSpA were positive for HLA-B15. CONCLUSIONS Our data suggest that the presence of HLA-B15 favours the development of isolated/combined peripheral rather than isolated axSpA, while HLA-B27 promotes an isolated/combined axial disease and excludes a peripheral pattern. HLA-B15 should be considered in addition to HLA-B27 when diagnosing patients with SpA according to ASAS criteria.
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Affiliation(s)
- John Londono
- Department of Rheumatology, University of La Sabana, Chia, Cundinamarca, Colombia
| | - Ana Maria Santos
- Department of Rheumatology, University of La Sabana, Chia, Cundinamarca, Colombia
| | - Paola Peña
- Department of Rheumatology, University of La Sabana, Chia, Cundinamarca, Colombia
| | - Enrique Calvo
- Department of Radiology, National University of Colombia, Bogota, Colombia
| | - Luis R Espinosa
- LSU Health Sciences Center, Louisiana State University, New Orleans, Louisiana, USA
| | - John D Reveille
- Division of Rheumatology and Clinical Immunogenetics, Department of Internal Medicine, University of Texas Health Science Center, Houston, Texas, USA
| | - Gilberto Vargas-Alarcon
- Interventional Genetic Study Group in Cardiovascular Diseases, Department of Molecular Biology, National Institute of Cardiology Ignacio Chávez, Mexico DF, Mexico
| | - Carlos A Jaramillo
- Department of Biological Sciences, University of Los Andes, Bogota, Colombia
| | - Rafael Valle-Oñate
- Rheumatology and Immunology Unit, Department of Internal Medicine, Hospital Militar Central, Bogota, Colombia
| | - Mabel Avila
- Department of Rheumatology, University of La Sabana, Chia, Cundinamarca, Colombia
- Rheumatology and Immunology Unit, Department of Internal Medicine, Hospital Militar Central, Bogota, Colombia
| | - Consuelo Romero
- Rheumatology and Immunology Unit, Department of Internal Medicine, Hospital Militar Central, Bogota, Colombia
| | - Juan F Medina
- Department of Internal Medicine, School of Medicine, University of Navarra and Ciberehd, Pamplona, Spain
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Osoegawa K, Mack SJ, Udell J, Noonan DA, Ozanne S, Trachtenberg E, Prestegaard M. HLA Haplotype Validator for quality assessments of HLA typing. Hum Immunol 2015; 77:273-282. [PMID: 26546873 DOI: 10.1016/j.humimm.2015.10.018] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2015] [Revised: 08/29/2015] [Accepted: 10/29/2015] [Indexed: 11/15/2022]
Abstract
HLA alleles are observed in specific haplotypes, due to Linkage Disequilibrium (LD) between particular alleles. Haplotype frequencies for alleles in strong LD have been established for specific ethnic groups and racial categories. Application of high-resolution HLA typing using Next Generation Sequencing (NGS) is becoming a common practice in research and clinical laboratory settings. HLA typing errors using NGS occasionally occur due to allelic sequence imbalance or misalignment. Manual inspection of HLA genotypes is labor intensive and requires an in-depth knowledge of HLA alleles and haplotypes. We developed the "HLA Haplotype Validator (HLAHapV)" software, which inspects an HLA genotype for both the presence of common and well-documented alleles and observed haplotypes. The software also reports warnings when rare alleles, or alleles that do not belong to recognized haplotypes, are found. The software validates observable haplotypes in genotype data, providing increased confidence regarding the accuracy of the HLA typing, and thus reducing the effort involved in correcting potential HLA typing errors. The HLAHapV software is a powerful tool for quality control of HLA genotypes prior to the application of downstream analyses. We demonstrate the use of the HLAHapV software for identifying unusual haplotypes, which can lead to finding potential HLA typing errors.
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Affiliation(s)
- Kazutoyo Osoegawa
- Department of Pathology, Stanford University, Stanford, CA, USA; Children's Hospital Oakland Research Institute, Oakland, CA, USA.
| | - Steven J Mack
- Children's Hospital Oakland Research Institute, Oakland, CA, USA
| | - Julia Udell
- Children's Hospital Oakland Research Institute, Oakland, CA, USA
| | - David A Noonan
- Children's Hospital Oakland Research Institute, Oakland, CA, USA
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Cervera I, Herraiz MA, Vidart J, Ortega S, Martínez-Laso J. Different patterns of A*80:01:01:01 allele generation based on exon or intron sequences. ACTA ACUST UNITED AC 2014; 85:58-67. [PMID: 25515742 DOI: 10.1111/tan.12496] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2014] [Revised: 11/24/2014] [Accepted: 11/30/2014] [Indexed: 11/27/2022]
Abstract
Generation of the HLA-A*80:01:01:01 allele has been analysed using its complete sequence. Direct comparison of the sequences and phylogenetic trees using the human leukocyte antigen (HLA)-A representative alleles and the major histocompatibility complex (MHC)-A sequences of non-human primates has been made. Results based on exon sequences confirm previously published, but considering only the sequences of the introns, two distinct regions can be differentiated. The first one comprises from the 5' untranslated region region to the first part of intron 3 sequence (shared with A2 family), and the second one includes the sequence from the end of intron 3 to intron 7 (shared with A1/A3/A11/A36/A30 family). Each of them clusters with Gorilla and Chimpanzee MHC-A sequences, respectively, suggesting an origin coming from a common ancestor to Gorilla and Chimpanzee.
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Affiliation(s)
- I Cervera
- Unidad de Inmunogenetica, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain
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Chen NY, Zhang W, He J, Zhu FM, Lv HJ. Genomic full-length sequence of a novel HLA-B*39:01:01:03 allele was identified in a Chinese individual. ACTA ACUST UNITED AC 2014; 83:132-4. [PMID: 24372507 DOI: 10.1111/tan.12267] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2013] [Accepted: 11/15/2013] [Indexed: 11/28/2022]
Abstract
HLA-B*39:01:01:03 allele differs from HLA-B*39:01:01:01 allele by a single nucleotide substitution.
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Affiliation(s)
- N-Y Chen
- HLA Typing Laboratory, Blood Center of Zhejiang Province, Hangzhou, China; Key Laboratory of Blood Safety Research, Ministry of Health, Hangzhou, China
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