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Jung K, Kim JG, Shin S, Roh EY, Hong YJ, Song EY. Allele and haplotype frequencies of 11 HLA loci in Koreans by next-generation sequencing. HLA 2023; 101:602-612. [PMID: 36719349 DOI: 10.1111/tan.14980] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Revised: 12/24/2022] [Accepted: 01/27/2023] [Indexed: 02/01/2023]
Abstract
Data on HLA genotype distribution, including DQA1 and DPA1, in the Korean population are limited. We aimed to investigate the allele and haplotype frequencies of 11 HLA loci in 339 Korean subjects using next-generation sequencing (NGS)-based HLA typing. A total of 339 samples from unrelated healthy subjects were genotyped for HLA-A, -B, -C, -DRB1, -DRB3, -DRB4, -DRB5, -DQB1, -DQA1, -DPB1, and -DPA1 using two different NGS-based HLA typing kits (166 tested using the NGSgo-MX11-3 kit [GenDx, Netherlands] and 173 by the AllType NGS 11 Loci Amplification kit [One Lambda, USA]). PyPop software was used to estimate allele and haplotype frequencies and linkage disequilibrium between the loci. Additionally, a principal component analysis was performed to compare the allele distribution of Koreans with that of other populations. A total of 214 HLA alleles (97 class I and 117 class II alleles) were assigned. The most frequent alleles for each locus were A*24:02:01 (24.78%), B*15:01:01 (10.18%), C*01:02:01 (18.44%), DRB1*04:05:01 (9.59%), DRB3*02:02:01 (13.72%), DRB4*01:03:01 (25.81%), DRB5*01:01:01 (9.0%), DQA1*01:02:01 (16.96%), DQB1*03:01:01 (14.31%), DPA1*01:03:01 (44.4%), and DPB1*05:01:01 (35.1%), respectively. The most frequent haplotypes were A*33:03:01-C*03:02:02-B*58:01:01 for HLA class I (5.01%) and DRB1*04:05:01-DQA1*03:03:01-DQB1*04:01:01-DPA1*02:02:02-DPB1*05:01:01 for HLA class II (6.23%). The total allelic ambiguities by NGS were estimated to be minimal and considerably decreased compared with those by Sanger sequencing. The Japanese population had the most similar allele distribution to Koreans, followed by the Chinese population. Frequency data of 11 HLA loci in Koreans can provide essential data for population genetics and disease association studies.
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Affiliation(s)
- Kiwook Jung
- Department of Laboratory Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea
- Department of Laboratory Medicine, Chungbuk National University Hospital, Cheongju, Republic of Korea
| | - Jisoo G Kim
- Department of Laboratory Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Sue Shin
- Department of Laboratory Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea
- Department of Laboratory Medicine, Seoul National University Boramae Medical Center, Seoul, Republic of Korea
| | - Eun Youn Roh
- Department of Laboratory Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea
- Department of Laboratory Medicine, Seoul National University Boramae Medical Center, Seoul, Republic of Korea
| | - Yun Ji Hong
- Department of Laboratory Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea
- Department of Laboratory Medicine, Seoul National University Bundang Hospital, Seongnam, Republic of Korea
| | - Eun Young Song
- Department of Laboratory Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea
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2
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Li SS, Hickey A, Shangguan S, Ehrenberg PK, Geretz A, Butler L, Kundu G, Apps R, Creegan M, Clifford RJ, Pinyakorn S, Eller LA, Luechai P, Gilbert PB, Holtz TH, Chitwarakorn A, Sacdalan C, Kroon E, Phanuphak N, de Souza M, Ananworanich J, O'Connell RJ, Robb ML, Michael NL, Vasan S, Thomas R. HLA-B∗46 associates with rapid HIV disease progression in Asian cohorts and prominent differences in NK cell phenotype. Cell Host Microbe 2022; 30:1173-1185.e8. [PMID: 35841889 DOI: 10.1016/j.chom.2022.06.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [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: 11/30/2021] [Revised: 01/17/2022] [Accepted: 06/09/2022] [Indexed: 12/12/2022]
Abstract
Human leukocyte antigen (HLA) alleles have been linked to HIV disease progression and attributed to differences in cytotoxic T lymphocyte (CTL) epitope representation. These findings are largely based on treatment-naive individuals of European and African ancestry. We assessed HLA associations with HIV-1 outcomes in 1,318 individuals from Thailand and found HLA-B∗46:01 (B∗46) associated with accelerated disease in three independent cohorts. B∗46 had no detectable effect on HIV-specific T cell responses, but this allele is unusual in containing an HLA-C epitope that binds inhibitory receptors on natural killer (NK) cells. Unbiased transcriptomic screens showed increased NK cell activation in people with HIV, without B∗46, and simultaneous single-cell profiling of surface proteins and transcriptomes revealed a NK cell subset primed for increased responses in the absence of B∗46. These findings support a role for NK cells in HIV pathogenesis, revealed by the unique properties of the B∗46 allele common only in Asia.
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Affiliation(s)
- Shuying S Li
- Fred Hutchinson Cancer Center, Vaccine and Infectious Disease Division, Seattle, WA 98104, USA
| | - Andrew Hickey
- Division of HIV Prevention, U.S. Centers for Disease Control and Prevention, Atlanta, GA 30329, USA; Thailand Ministry of Public Health, U.S. Centers for Disease Control and Prevention Collaboration, Nonthaburi 11000, Thailand
| | - Shida Shangguan
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine Inc., Bethesda, MD 20817, USA
| | - Philip K Ehrenberg
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
| | - Aviva Geretz
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine Inc., Bethesda, MD 20817, USA
| | - Lauryn Butler
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine Inc., Bethesda, MD 20817, USA
| | - Gautam Kundu
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine Inc., Bethesda, MD 20817, USA
| | - Richard Apps
- Center for Human Immunology, National Institutes of Health, Bethesda, MD 20892, USA
| | - Matthew Creegan
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine Inc., Bethesda, MD 20817, USA
| | - Robert J Clifford
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine Inc., Bethesda, MD 20817, USA
| | - Suteeraporn Pinyakorn
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine Inc., Bethesda, MD 20817, USA
| | - Leigh Anne Eller
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine Inc., Bethesda, MD 20817, USA
| | - Pikunchai Luechai
- Division of HIV Prevention, U.S. Centers for Disease Control and Prevention, Atlanta, GA 30329, USA; Thailand Ministry of Public Health, U.S. Centers for Disease Control and Prevention Collaboration, Nonthaburi 11000, Thailand
| | - Peter B Gilbert
- Fred Hutchinson Cancer Center, Vaccine and Infectious Disease Division, Seattle, WA 98104, USA
| | - Timothy H Holtz
- Division of HIV Prevention, U.S. Centers for Disease Control and Prevention, Atlanta, GA 30329, USA; Thailand Ministry of Public Health, U.S. Centers for Disease Control and Prevention Collaboration, Nonthaburi 11000, Thailand; Office of AIDS Research, National Institutes of Health, Bethesda, MD 20892, USA
| | - Anupong Chitwarakorn
- Department of Disease Control, Thailand Ministry of Public Health, Nonthaburi 11000, Thailand
| | - Carlo Sacdalan
- Institute of HIV Research and Innovation, Bangkok 10330, Thailand
| | - Eugène Kroon
- Institute of HIV Research and Innovation, Bangkok 10330, Thailand
| | | | - Mark de Souza
- Institute of HIV Research and Innovation, Bangkok 10330, Thailand
| | - Jintanat Ananworanich
- Department of Global Health, Amsterdam Medical Center, University of Amsterdam, 1105 BP Amsterdam, the Netherlands
| | | | - Merlin L Robb
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine Inc., Bethesda, MD 20817, USA
| | - Nelson L Michael
- Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
| | - Sandhya Vasan
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine Inc., Bethesda, MD 20817, USA
| | - Rasmi Thomas
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA.
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Turner TR, Hayward DR, Gymer AW, Barker DJ, Leen G, Cambridge CA, Macpherson HL, Georgiou X, Cooper MA, Lucas JAM, Nadeem D, Robinson J, Mayor NP, Marsh SGE. Widespread non‐coding polymorphism in
HLA
class
II
genes of International
HLA
and Immunogenetics Workshop cell lines. HLA 2022; 99:328-356. [DOI: 10.1111/tan.14571] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 01/26/2022] [Accepted: 01/27/2022] [Indexed: 12/01/2022]
Affiliation(s)
- Thomas R. Turner
- Anthony Nolan Research Institute, Royal Free Hospital London UK
- UCL Cancer Institute, Royal Free Campus London UK
| | | | - Arthur W. Gymer
- Anthony Nolan Research Institute, Royal Free Hospital London UK
| | | | - Gayle Leen
- Anthony Nolan Research Institute, Royal Free Hospital London UK
- UCL Cancer Institute, Royal Free Campus London UK
| | | | | | - Xenia Georgiou
- Anthony Nolan Research Institute, Royal Free Hospital London UK
| | | | | | - Daud Nadeem
- Anthony Nolan Research Institute, Royal Free Hospital London UK
| | - James Robinson
- 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
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Thomas R, Chansinghakul D, Limkittikul K, Gilbert PB, Hattasingh W, Moodie Z, Shangguan S, Frago C, Dulyachai W, Li SS, Jarman RG, Geretz A, Bouckenooghe A, Sabchareon A, Juraska M, Ehrenberg P, Michael NL, Bailleux F, Bryant C, Gurunathan S. Associations of human leukocyte antigen with neutralizing antibody titers in a tetravalent dengue vaccine phase 2 efficacy trial in Thailand. Hum Immunol 2022; 83:53-60. [PMID: 34635391 PMCID: PMC10536818 DOI: 10.1016/j.humimm.2021.09.006] [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: 03/01/2021] [Revised: 08/12/2021] [Accepted: 09/20/2021] [Indexed: 11/04/2022]
Abstract
The recombinant, live, attenuated, tetravalent dengue vaccine CYD-TDV has shown efficacy against all four dengue serotypes. In this exploratory study (CYD59, NCT02827162), we evaluated potential associations of host human leukocyte antigen (HLA) alleles with dengue antibody responses, CYD-TDV vaccine efficacy, and virologically-confirmed dengue (VCD) cases. Children 4-11 years old, who previously completed a phase 2b efficacy study of CYD-TDV in a single center in Thailand, were included in the study. Genotyping of HLA class I and II loci was performed by next-generation sequencing from DNA obtained from 335 saliva samples. Dengue neutralizing antibody titers (NAb) were assessed as a correlate of risk and protection. Regression analyses were used to assess associations between HLA alleles and NAb responses, vaccine efficacy, and dengue outcomes. Month 13 NAb log geometric mean titers (GMTs) were associated with decreased risk of VCD. In the vaccine group, HLA-DRB1*11 was significantly associated with higher NAb log GMT levels (beta: 0.76; p = 0.002, q = 0.13). Additionally, in the absence of vaccination, HLA associations were observed between the presence of DPB1*03:01 and increased NAb log GMT levels (beta: 1.24; p = 0.005, q = 0.17), and between DPB1*05:01 and reduced NAb log GMT levels (beta: -1.1; p = 0.001, q = 0.07). This study suggests associations of HLA alleles with NAb titers in the context of dengue outcomes. This study was registered with clinicaltrials.gov: NCT02827162.
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Affiliation(s)
- Rasmi Thomas
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
| | | | - Kriengsak Limkittikul
- Department of Tropical Pediatrics, Faculty of Tropical Medicine, Mahidol University, Bangkok 73170, Thailand
| | - Peter B Gilbert
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109-1024, USA
| | - Weerawan Hattasingh
- Department of Tropical Pediatrics, Faculty of Tropical Medicine, Mahidol University, Bangkok 73170, Thailand
| | - Zoe Moodie
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109-1024, USA
| | - Shida Shangguan
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD 20817, USA
| | - Carina Frago
- Global Clinical Sciences, Sanofi Pasteur, 048580, Singapore
| | - Wut Dulyachai
- Ratchaburi Hospital, Amphoe Muang Ratchaburi, 70000, Thailand
| | - Shuying Sue Li
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109-1024, USA
| | - Richard G Jarman
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
| | - Aviva Geretz
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD 20817, USA
| | | | - Arunee Sabchareon
- Department of Tropical Pediatrics, Faculty of Tropical Medicine, Mahidol University, Bangkok 73170, Thailand
| | - Michal Juraska
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109-1024, USA
| | - Philip Ehrenberg
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
| | - Nelson L Michael
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
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Gustiananda M, Sulistyo BP, Agustriawan D, Andarini S. Immunoinformatics Analysis of SARS-CoV-2 ORF1ab Polyproteins to Identify Promiscuous and Highly Conserved T-Cell Epitopes to Formulate Vaccine for Indonesia and the World Population. Vaccines (Basel) 2021; 9:1459. [PMID: 34960205 PMCID: PMC8704007 DOI: 10.3390/vaccines9121459] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 11/28/2021] [Accepted: 11/30/2021] [Indexed: 12/20/2022] Open
Abstract
SARS-CoV-2 and its variants caused the COVID-19 pandemic. Vaccines that target conserved regions of SARS-CoV-2 and stimulate protective T-cell responses are important for reducing symptoms and limiting the infection. Seven cytotoxic (CTL) and five helper T-cells (HTL) epitopes from ORF1ab were identified using NetCTLpan and NetMHCIIpan algorithms, respectively. These epitopes were generated from ORF1ab regions that are evolutionary stable as reflected by zero Shannon's entropy and are presented by 56 human leukocyte antigen (HLA) Class I and 22 HLA Class II, ensuring good coverage for the Indonesian and world population. Having fulfilled other criteria such as immunogenicity, IFNγ inducing ability, and non-homology to human and microbiome peptides, the epitopes were assembled into a vaccine construct (VC) together with β-defensin as adjuvant and appropriate linkers. The VC was shown to have good physicochemical characteristics and capability of inducing CTL as well as HTL responses, which stem from the engagement of the vaccine with toll-like receptor 4 (TLR4) as revealed by docking simulations. The most promiscuous peptide 899WSMATYYLF907 was shown via docking simulation to interact well with HLA-A*24:07, the most predominant allele in Indonesia. The data presented here will contribute to the in vitro study of T-cell epitope mapping and vaccine design in Indonesia.
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Affiliation(s)
- Marsia Gustiananda
- Department of Biomedicine, School of Life Sciences, Indonesia International Institute for Life Sciences, Jl. Pulomas Barat Kav 88, Jakarta 13210, Indonesia;
| | - Bobby Prabowo Sulistyo
- Department of Biomedicine, School of Life Sciences, Indonesia International Institute for Life Sciences, Jl. Pulomas Barat Kav 88, Jakarta 13210, Indonesia;
| | - David Agustriawan
- Department of Bioinformatics, School of Life Sciences, Indonesia International Institute for Life Sciences, Jl. Pulomas Barat Kav 88, Jakarta 13210, Indonesia;
| | - Sita Andarini
- Department of Pulmonology and Respiratory Medicine, Faculty of Medicine University of Indonesia, Persahabatan Hospital, Jl Persahabatan Raya 1, Jakarta 13230, Indonesia;
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Jekarl DW, Lee GD, Yoo JB, Kim JR, Yu H, Yoo J, Lim J, Kim M, Kim Y. HLA-A, -B, -C, -DRB1 allele and haplotype frequencies of the Korean population and performance characteristics of HLA typing by next-generation sequencing. HLA 2021; 97:188-197. [PMID: 33314756 DOI: 10.1111/tan.14167] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [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: 07/31/2019] [Revised: 10/06/2020] [Accepted: 12/07/2020] [Indexed: 01/10/2023]
Abstract
INTRODUCTION Human leukocyte antigen (HLA) identification at the allelic level is important for haematopoietic stem cell transplantation (HSCT). Next-generation sequencing (NGS) resolves ambiguous alleles by determining the phase of the polymorphisms. The aim of this study was to validate the software for HLA-SBT (sequence-based typing), assess Korean allele frequency, and characterise the performance of NGS-HLA typing. METHODS From the 2009 to 2016 registry, 1293 unrelated healthy donors with a complete dataset of previously characterised HLA-A, -B, -C, and -DRB1 loci were selected and assessed for frequency, haplotype inference, and relative linkage disequilibrium. For performance characteristics of NGS-HLA, alleles included in 1293 cases and ambiguous or alleles assigned as new by SBT-HLA software, or unassigned alleles were included. A total of 91 and 41 quality control samples resulted in 1056 alleles (132 samples × 4 loci × 2 diploid) for analysis. The GenDx NGSgo kit was used for NGS-HLA typing using the Illumina MiSeq platform. RESULTS A panel of 132 samples covered 231 alleles, including 53 HLA-A, 80 HLA-B, 43 HLA-C, and 55 HLA-DRB1 by HLA-SBT typing. Comparison of SBT-HLA and NGS-HLA typing showed 99.7% (1053/1056) concordance and discrepant cases were resolved by manual evaluation. Typing by NGS resulted in 67 HLA-A, 112 HLA-B, 71 HLA-C, and 72 HLA-DRB1 alleles. A total of 132 ambiguous, 4 new, and 1 unassigned alleles by HLA-SBT were resolved by NGS-HLA typing. CONCLUSIONS NGS-HLA typing provided robust and conclusive results without ambiguities, and its implementation could support HSCT in clinical settings.
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Affiliation(s)
- Dong Wook Jekarl
- Department of Laboratory Medicine, College of Medicine, Seoul St. Mary's Hospital, The Catholic University of Korea, Seoul, Republic of Korea.,Department of Laboratory Medicine, Seoul St. Mary's Hospital, The Catholic University of Korea Seoul, Republic of Korea
| | - Gun Dong Lee
- Department of Laboratory Medicine, Seoul St. Mary's Hospital, The Catholic University of Korea Seoul, Republic of Korea
| | - Jae Bin Yoo
- Department of Laboratory Medicine, Seoul St. Mary's Hospital, The Catholic University of Korea Seoul, Republic of Korea
| | - Jung Rok Kim
- Department of Laboratory Medicine, Eunpyeong St. Mary's Hospital, The Catholic University of Korea, Seoul, Republic of Korea
| | - Haein Yu
- Department of Laboratory Medicine, Seoul St. Mary's Hospital, The Catholic University of Korea Seoul, Republic of Korea
| | - Jaeeun Yoo
- Department of Laboratory Medicine, College of Medicine, Incheon St. Mary's Hospital, The Catholic University of Korea, Seoul, Republic of Korea
| | - Jihyang Lim
- Department of Laboratory Medicine, College of Medicine, Eunpyeong St. Mary's Hospital, The Catholic University of Korea, Seoul, Republic of Korea
| | - Myungshin Kim
- Department of Laboratory Medicine, College of Medicine, Seoul St. Mary's Hospital, The Catholic University of Korea, Seoul, Republic of Korea.,Department of Laboratory Medicine, Seoul St. Mary's Hospital, The Catholic University of Korea Seoul, Republic of Korea.,Catholic Genetic Laboratory Center, College of Medicine, Seoul St. Mary's Hospital, The Catholic University of Korea, Seoul, Republic of Korea
| | - Yonggoo Kim
- Department of Laboratory Medicine, College of Medicine, Seoul St. Mary's Hospital, The Catholic University of Korea, Seoul, Republic of Korea.,Department of Laboratory Medicine, Seoul St. Mary's Hospital, The Catholic University of Korea Seoul, Republic of Korea.,Catholic Genetic Laboratory Center, College of Medicine, Seoul St. Mary's Hospital, The Catholic University of Korea, Seoul, Republic of Korea
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7
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Chiowchanwisawakit P, Pithukpakorn M, Luangtrakool K, Permpikul P. HLA-B*27:04 associated with enthesitis and younger age of onset, and HLA-B allele profile in patients with ankylosing spondylitis in Thailand: A cross-sectional study. Int J Rheum Dis 2021; 24:411-417. [PMID: 33448675 DOI: 10.1111/1756-185x.14055] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 11/19/2020] [Accepted: 12/17/2020] [Indexed: 11/28/2022]
Abstract
AIM The aims of this study were to estimate human leukocyte antigen (HLA)-B allele frequency, to identify alleles associated with ankylosing spondylitis (AS), and to explore manifestations in various HLA-B*27 in Thai AS patients. METHODS This was a cross-sectional study. Thai patients older than 18 years with diagnosed AS according to modified New York criteria who visited Siriraj Hospital (Bangkok, Thailand) were consecutively enrolled. HLA-B alleles were determined by reverse sequence-specific oligonucleotide assays, and were assigned at a 4-digit resolution. HLA-B alleles of 334 unrelated healthy Thai donors who participated in a previous phase 2b dengue vaccine clinical trial were included as controls. Odds ratio (OR) and Fisher's exact test were used to estimate association between allele and AS. The P value significance threshold was calculated according to Bonferroni. RESULTS Among the 88 patients who were recruited, 34 HLA-B alleles were identified, and all patients were heterozygous. The prevalence of HLA-B*27 was 89.8%, and 4 alleles of HLA-B*27 were identified. HLA-B*27:04 (OR: 39.4, P < .0001) and HLA-B*27:05 (OR: 13.8, P = .0011) were associated with AS. In contrast, HLA-B*27:06 was not found to be associated with AS (OR: 0.4, P = .241). AS patients carrying HLA-B*27:04 were more likely to have enthesitis and younger age at onset than those carrying HLA-B*27:05. CONCLUSIONS HLA-B*27:04 and HLA-B*27:05 were both found to be strongly associated with Thai AS. HLA-B*27:06 showed a neutral allele for Thai AS. AS patients with HLA-B*27:04 had more enthesitis and younger age at onset than those with HLA-B*27:05.
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Affiliation(s)
- Praveena Chiowchanwisawakit
- Division of Rheumatology, Department of Medicine, Faculty of Medicine, Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Manop Pithukpakorn
- Division of Medical Genetics, Department of Medicine, Faculty of Medicine, Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Komon Luangtrakool
- Department of Transfusion Medicine, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Parichart Permpikul
- Department of Transfusion Medicine, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
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8
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Geretz A, Cofer L, Ehrenberg PK, Currier JR, Yoon IK, Alera MTP, Jarman R, Rothman AL, Thomas R. Next-generation sequencing of 11 HLA loci in a large dengue vaccine cohort from the Philippines. Hum Immunol 2020; 81:437-444. [PMID: 32654962 DOI: 10.1016/j.humimm.2020.06.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [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: 02/20/2020] [Revised: 05/27/2020] [Accepted: 06/17/2020] [Indexed: 01/25/2023]
Abstract
HLA genotyping by next-generation sequencing (NGS) has evolved with significant advancements in the last decade. Here we describe full-length HLA genotyping of 11 loci in 612 individuals comprising a dengue vaccine cohort from Cebu province in the Philippines. The multi-locus individual tagging NGS (MIT-NGS) method that we developed initially for genotyping 4-6 loci in one MiSeq run was expanded to 11 loci including HLA-A, B, C, DPA1, DPB1, DQA1, DQB1, DRB1, and DRB3/4/5. This change did not affect the overall coverage or depth of the sequencing reads. HLA alleles with frequencies greater than 10% were A*11:01:01, A*24:02:01, A*24:07:01, A*34:01:01, B*38:02:01, B*15:35, B*35:05:01, C*07:02:01, C*04:01:01, DPA1*02:02:02, DPB1*05:01:01, DPB1*01:01:01, DQA1*01:02:01, DQA1*06:01:01, DQB1*05:02:01, DQB1*03:01:01, DRB1*15:02:01, DRB1*12:02:01, DRB3*03:01:03, DRB4*01:03:01, and DRB5*01:01:01. Improvements in sequencing library preparation provide uniform and even coverage across all exons and introns. This has led to a marked reduction in allele imbalance and dropout. Furthermore, including more loci, such as DRB3/4/5, decreases cross-mapping and incorrect allele assignment at the DRB1 locus. The increased number of loci sequenced for each sample does not reduce the number of samples that can be multiplexed on a single MiSeq run and is therefore more cost-efficient. We believe that such improvements will help HLA genotyping by NGS to gain momentum over other conventional methods by increasing confidence in the calls.
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Affiliation(s)
- Aviva Geretz
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | - Lauryn Cofer
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | - Philip K Ehrenberg
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Jeffrey R Currier
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - In-Kyu Yoon
- Department of Virology, Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Maria T P Alera
- Philippines-AFRIMS Virology Research Unit, Cebu City, Philippines
| | - Richard Jarman
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Alan L Rothman
- Institute for Immunology and Informatics and Department of Cell and Molecular Biology, University of Rhode Island, Providence, RI, USA
| | - Rasmi Thomas
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA.
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Do MD, Le LGH, Nguyen VT, Dang TN, Nguyen NH, Vu HA, Mai TP. High-Resolution HLA Typing of HLA-A, -B, -C, -DRB1, and -DQB1 in Kinh Vietnamese by Using Next-Generation Sequencing. Front Genet 2020; 11:383. [PMID: 32425978 PMCID: PMC7204072 DOI: 10.3389/fgene.2020.00383] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [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: 11/07/2019] [Accepted: 03/27/2020] [Indexed: 12/19/2022] Open
Abstract
Human leukocyte antigen (HLA) genotyping displays the particular characteristics of HLA alleles and haplotype frequencies in each population. Although it is considered the current gold standard for HLA typing, high-resolution sequence-based HLA typing is currently unavailable in Kinh Vietnamese populations. In this study, high-resolution sequence-based HLA typing (3-field) was performed using an amplicon-based next-generation sequencing platform to identify the HLA-A, -B, -C, -DRB1, and -DQB1 alleles of 101 unrelated healthy Kinh Vietnamese individuals from southern Vietnam. A total of 28 HLA-A, 41 HLA-B, 21 HLA-C, 26 HLA-DRB1, and 25 HLA-DQB1 alleles were identified. The most frequently occurring HLA alleles were A∗11:01:01, B∗15:02:01, C∗07:02:01, DRB1∗12:02:01, and DQB1∗03:01:01. Haplotype calculation showed that A∗29:01:01∼B∗07:05:01, DRB1∗12:02:01∼DQB1∗3:01:01, A∗29:01:01∼C∗15:05:02∼B∗07:05:01, A∗33:03:01∼B∗58:01:01∼DRB1∗03:01:01, and A∗29:01:01∼C∗15:05:02∼B∗07:05:01∼DRB1∗10:01:01∼DQB1∗05:01:01 were the most common haplotypes in the southern Kinh Vietnamese population. Allele distribution and haplotype analyses demonstrated that the Vietnamese population shares HLA features with South-East Asians but retains unique characteristics. Data from this study will be potentially applicable in medicine and anthropology.
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Affiliation(s)
- Minh Duc Do
- Center for Molecular Biomedicine, University of Medicine and Pharmacy at Ho Chi Minh City, Ho Chi Minh City, Vietnam
| | - Linh Gia Hoang Le
- Center for Molecular Biomedicine, University of Medicine and Pharmacy at Ho Chi Minh City, Ho Chi Minh City, Vietnam
| | - Vinh The Nguyen
- Center for Molecular Biomedicine, University of Medicine and Pharmacy at Ho Chi Minh City, Ho Chi Minh City, Vietnam
| | - Tran Ngoc Dang
- Faculty of Public Health, University of Medicine and Pharmacy at Ho Chi Minh City, Ho Chi Minh City, Vietnam
| | - Nghia Hoai Nguyen
- Center for Molecular Biomedicine, University of Medicine and Pharmacy at Ho Chi Minh City, Ho Chi Minh City, Vietnam
| | - Hoang Anh Vu
- Center for Molecular Biomedicine, University of Medicine and Pharmacy at Ho Chi Minh City, Ho Chi Minh City, Vietnam
| | - Thao Phuong Mai
- Department of Physiology, Pathophysiology and Immunology, Faculty of Medicine, University of Medicine and Pharmacy at Ho Chi Minh City, Ho Chi Minh City, Vietnam
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Affiliation(s)
- Tamara A Vayntrub
- Histocompatibility, Immunogenetics, and Disease Profiling Laboratory, Stanford Blood Center, Palo Alto, CA, USA.
| | - Steven J Mack
- Center for Genetics, Children's Hospital Oakland Research Institute, Oakland, CA, USA.
| | - Marcelo A Fernandez-Viña
- Histocompatibility, Immunogenetics, and Disease Profiling Laboratory, Stanford Blood Center, Palo Alto, CA, USA; Department of Pathology, Stanford University Medical Center, Stanford, CA, USA.
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