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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] [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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Que TN, Khanh NB, Tung PD, Hang PTL, Van Anh NT, Thang ND. Frequency and distribution of HLA-DQB1 alleles from 2076 cord blood samples of the Vietnamese cohort. Int J Immunogenet 2022; 49:340-344. [PMID: 35916345 DOI: 10.1111/iji.12592] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 07/21/2022] [Accepted: 07/22/2022] [Indexed: 11/28/2022]
Abstract
Human leucocyte antigen (HLA) alleles are very diverse and characterized by ethnicity. To date, information about the frequencies and distributions of HLA alleles among the Vietnamese population is still limited. In this study, HLA-DQB1 alleles of 2076 cord blood units from individuals belonging to Vietnam's Kinh ethnic people were genotyped using Luminex-based polymerase chain reaction sequence-specific oligonucleotide. The results of the study demonstrated that there were 23 alleles on the locus HLA-DQB1. Among those, there were six alleles with high frequencies of over 5%, including DQB1* 03:01 (35.9%), DQB1* 05:01 (12.8%), DQB1* 03:03 (12.2%); DQB1* 06:01 (7.20%), DQB1* 05:02 (6.62%) and DQB1* 02:01 (5.30%) and five rare alleles with low frequencies of below 0.1%. More importantly, this study for the first time reported the presence of two new rare alleles including DQB1* 01:01 and DQB1* 01:02. Conclusively, this study provided significant information about HLA-DQB1 alleles for further investigations and clinical applications.
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Affiliation(s)
- Tran Ngoc Que
- Stem Cell Bank, National Institute of Hematology and Blood Transfusion, Hanoi, Vietnam.,Department of Hematology, Hanoi Medical University, Hanoi, Vietnam
| | - Nguyen Ba Khanh
- Stem Cell Bank, National Institute of Hematology and Blood Transfusion, Hanoi, Vietnam.,Department of Hematology, Hanoi Medical University, Hanoi, Vietnam
| | - Pham Dinh Tung
- Department of Probability and Statistics, Faculty of Mathematics-Mechanics-Informatics, VNU University of Science, Vietnam National University, Hanoi, Vietnam
| | - Pham Thi Luong Hang
- Faculty of Biology, VNU University of Science, Vietnam National University-Hanoi, Hanoi, Vietnam
| | - Nguyen Thi Van Anh
- Key Laboratory of Enzyme and Protein Technology, VNU University of Science, Vietnam National University-Hanoi, Hanoi, Vietnam
| | - Nguyen Dinh Thang
- Faculty of Biology, VNU University of Science, Vietnam National University-Hanoi, Hanoi, Vietnam
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3
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Que TN, Khanh NB, Khanh BQ, Van Son C, Van Anh NT, Anh TTT, Tung PD, Thang ND. Allele and Haplotype Frequencies of HLA-A, -B, -C, and -DRB1 Genes in 3,750 Cord Blood Units From a Kinh Vietnamese Population. Front Immunol 2022; 13:875283. [PMID: 35844516 PMCID: PMC9277059 DOI: 10.3389/fimmu.2022.875283] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 05/30/2022] [Indexed: 11/13/2022] Open
Abstract
The frequencies and diversities of human leukocyte antigen (HLA) alleles and haplotypes are representative of ethnicities. Matching HLA alleles is essential for many clinical applications, including blood transfusion, stem cell transplantation, and tissue/organ transplantation. To date, the information about the frequencies and distributions of HLA alleles and haplotypes among the Kinh Vietnamese population is limited because of the small sample size. In this study, more than 3,750 cord blood units from individuals belonging to the Kinh Vietnamese population were genotyped using PCR sequence-specific oligonucleotide (PCR-SSO) for HLA testing. The results of the study demonstrated that the most frequently occurring HLA-A, -B, -C, and -DRB1 alleles were A*11:01 (25%), A*24:02 (12.3%), A*02:01 (11.2); A*03:03 (8.95%), A*02:03 (7.81%), A*29:01 (7.03%); B*15:02 (15.1%), B*46:01 (10.7%), B*58:01 (7.65%), B*38:02 (7.29%); C*08:01 (17.2), C*07:02 (16.2%), C*01:02 (15.2), C*03:02 (8.3%), C*15:05 (6.13); DRB1*12:02 (31.0%), DRB1*09:01 (10.47%), DRB1*15:02 (7.54%); DRB1*07:01 (6.68%), DRB1*10:01 (6.63%), respectively, with the highest allele diversity level observed in locus B (93 alleles). The most frequent haplotypes of two-locus combinations of HLA-A–B, HLA-A–C, HLA-A–DRB1, HLA-B–C, HLA-B–DRB1, and HLA-C–DRB1 haplotypes were A*11:01–B*15:02 (7.63%), A*11:01–C*08:01 (7.98%), A*11:01–DRB1*12:02 (10.56%), B*15:02–C*08:01 (14.0%), B*15:02–DRB1*12:02 (10.47%), and C*08:01–DRB1*12:02 (11.38%), respectively. In addition, the most frequent haplotypes of three- and four-locus sets of HLA-A–B–C, HLA-A–B–DRB1, HLA-A–C–DRB1, HLA-B–C–DRB1, and HLA-A–B–C–DRB1 were A*11:01–B*15:02–C*08:01 (7.57%), A*11:01–B*15:02–DRB1*12:02 (5.39%), A*11:01–C*08:01–DRB1*12:02 (5.54%), B*15:02–C*08:01–DRB1*12:02 (10.21%), and A*11:01–B*15:02–C*08:01–DRB1*12:02 (5.45%), respectively. This study provides critical information on the frequencies and distributions of HLA alleles and haplotypes in the Kinh Vietnamese population, accounting for more than 85% of Vietnamese citizens. It paves the way to establish an umbilical cord blood bank for cord blood transplantation programs in Vietnam.
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Affiliation(s)
- Tran Ngoc Que
- Stem Cell Bank, National Institute of Hematology and Blood Transfusion, Pham Van Bach, Cau Giay, Hanoi, Vietnam
- Department of Hematology, Hanoi Medical University, 1 Ton That Tung, Dong Da, Hanoi, Vietnam
| | - Nguyen Ba Khanh
- Stem Cell Bank, National Institute of Hematology and Blood Transfusion, Pham Van Bach, Cau Giay, Hanoi, Vietnam
- Department of Hematology, Hanoi Medical University, 1 Ton That Tung, Dong Da, Hanoi, Vietnam
| | - Bach Quoc Khanh
- Stem Cell Bank, National Institute of Hematology and Blood Transfusion, Pham Van Bach, Cau Giay, Hanoi, Vietnam
- Department of Hematology, Hanoi Medical University, 1 Ton That Tung, Dong Da, Hanoi, Vietnam
| | - Chu Van Son
- Key Laboratory of Enzyme and Protein Technology, VNU University of Science, Vietnam National University-Hanoi, 334 Nguyen Trai, Thanh Xuan, Hanoi, Vietnam
| | - Nguyen Thi Van Anh
- Key Laboratory of Enzyme and Protein Technology, VNU University of Science, Vietnam National University-Hanoi, 334 Nguyen Trai, Thanh Xuan, Hanoi, Vietnam
| | - Tran Thi Thuy Anh
- Faculty of Biology, VNU University of Science, Vietnam National University-Hanoi, 334 Nguyen Trai, Thanh Xuan, Hanoi, Vietnam
| | - Pham Dinh Tung
- Department of Probability and Statistics, Faculty of Mathematics–Mechanics–Informatics, VNU University of Science, Vietnam National University, 334 Nguyen Trai, Thanh Xuan, Hanoi, Vietnam
| | - Nguyen Dinh Thang
- Faculty of Biology, VNU University of Science, Vietnam National University-Hanoi, 334 Nguyen Trai, Thanh Xuan, Hanoi, Vietnam
- *Correspondence: Nguyen Dinh Thang,
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Khan A, Shin JY, So MK, Na JH, Justesen S, Ansari AA, Ko BJ, Ahn SM. Characterization of HLA-A*33:03 epitopes via immunoprecipitation and LC-MS/MS. Proteomics 2021; 22:e2100171. [PMID: 34561969 DOI: 10.1002/pmic.202100171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 08/29/2021] [Accepted: 09/22/2021] [Indexed: 11/06/2022]
Abstract
Human leukocyte antigen (HLA) class I has more than 18,000 alleles, each of which binds to a set of unique peptides from the cellular degradome. Deciphering the interaction between antigenic peptides and HLA proteins is crucial for understanding immune responses in autoimmune diseases and cancer. In this study, we aimed to characterize the peptidome that binds to HLA-A*33:03, which is one of the most prevalent HLA-A alleles in the Northeast Asian population, but poorly studied. For this purpose, we analyzed the HLA-A*33:03 monoallelic B cell line using immunoprecipitation of HLA-A and peptide complexes, followed by liquid chromatography-tandem mass spectrometry (LC-MS/MS). In this study, we identified 5731 unique peptides that were associated with HLA A*33:03, and experimentally validated the affinity of 40 peptides for HLA-A*33:03 and their stability in HLA A*33:03-peptides complexes. To our knowledge, this study represents the largest dataset of peptides associated with HLA-A*33:03. Also, this is the first study in which HLA A*33:03-associated peptides were experimentally validated.
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Affiliation(s)
- Amir Khan
- Department of Health Sciences and Technology, GAIHST, Gachon University, Incheon, Republic of Korea.,Department of Genome Medicine and Science, College of Medicine, Gachon University, Incheon, Republic of Korea
| | - Ji-Yon Shin
- Department of Health Sciences and Technology, GAIHST, Gachon University, Incheon, Republic of Korea
| | - Min Kyung So
- New Drug Development Center, Osong Medical Innovation Foundation, Cheongju-si, Republic of Korea
| | - Jung-Hyun Na
- Department of Pharmaceutical Engineering, Sangji University, Wonju, Republic of Korea
| | | | - Adnan Ahmad Ansari
- National Center for Bioinformatics, Quaid-i-Azam University, Islamabad, Pakistan
| | - Byoung Joon Ko
- School of Biopharmaceutical and Medical Sciences, Sungshin Women's University, Seoul, Republic of Korea
| | - Sung-Min Ahn
- Department of Health Sciences and Technology, GAIHST, Gachon University, Incheon, Republic of Korea.,Department of Genome Medicine and Science, College of Medicine, Gachon University, Incheon, Republic of Korea
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Ahmed AF, Sukasem C, Sabbah MA, Musa NF, Mohamed Noor DA, Daud NAA. Genetic Determinants in HLA and Cytochrome P450 Genes in the Risk of Aromatic Antiepileptic-Induced Severe Cutaneous Adverse Reactions. J Pers Med 2021; 11:383. [PMID: 34067134 PMCID: PMC8150699 DOI: 10.3390/jpm11050383] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 04/20/2021] [Accepted: 04/28/2021] [Indexed: 12/19/2022] Open
Abstract
Adverse drug reaction (ADR) is a pressing health problem, and one of the main reasons for treatment failure with antiepileptic drugs. This has become apparent in the event of severe cutaneous adverse reactions (SCARs), which can be life-threatening. In this review, four hypotheses were identified to describe how the immune system is triggered in the development of SCARs, which predominantly involve the human leukocyte antigen (HLA) proteins. Several genetic variations in HLA genes have been shown to be strongly associated with the susceptibility to developing SCARs when prescribed carbamazepine or phenytoin. These genetic variations were also shown to be prevalent in certain populations. Apart from the HLA genes, other genes proposed to affect the risk of SCARs are genes encoding for CYP450 drug-metabolising enzymes, which are involved in the pharmacokinetics of offending drugs. Genetic variants in CYP2C9 and CYPC19 enzymes were also suggested to modulate the risk of SCARs in some populations. This review summarizes the literature on the manifestation and aetiology of antiepileptic-induced SCARs, updates on pharmacogenetic markers associated with this reaction and the implementation of pre-emptive testing as a preventive strategy for SCARs.
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Affiliation(s)
- Ali Fadhel Ahmed
- Discipline of Clinical Pharmacy, School of Pharmaceutical Sciences, Universiti Sains Malaysia, Pulau Pinang 11800, Malaysia or (A.F.A.); (D.A.M.N.)
| | - Chonlaphat Sukasem
- Department of Pathology, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok 10400, Thailand;
- Laboratory for Pharmacogenomics, Somdech Phra Debaratana Medical Center (SDMC), Ramathibodi Hospital, Bangkok 10400, Thailand
- The Thai Severe Cutaneous Adverse Drug Reaction (THAI-SCAR) Research Group, Chulalongkorn University, Bangkok 10330, Thailand
- Advanced Research and Development Laboratory, Bumrungrad International Hospital, Bangkok 10110, Thailand
| | - Majeed Arsheed Sabbah
- Forensic DNA for Research and Training Centre, Alnahrain University, Baghdad 64074, Iraq;
| | - Nur Fadhlina Musa
- Human Genome Center, School of Medical Sciences, Universiti Sains Malaysia, Kubang Kerian, Kota Bharu 16150, Malaysia;
| | - Dzul Azri Mohamed Noor
- Discipline of Clinical Pharmacy, School of Pharmaceutical Sciences, Universiti Sains Malaysia, Pulau Pinang 11800, Malaysia or (A.F.A.); (D.A.M.N.)
| | - Nur Aizati Athirah Daud
- Discipline of Clinical Pharmacy, School of Pharmaceutical Sciences, Universiti Sains Malaysia, Pulau Pinang 11800, Malaysia or (A.F.A.); (D.A.M.N.)
- Human Genome Center, School of Medical Sciences, Universiti Sains Malaysia, Kubang Kerian, Kota Bharu 16150, Malaysia;
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Baek IC, Choi EJ, Shin DH, Kim HJ, Choi H, Kim TG. Distributions of HLA-A, -B, and -DRB1 alleles typed by amplicon-based next generation sequencing in Korean volunteer donors for unrelated hematopoietic stem cell transplantation. HLA 2021; 97:112-126. [PMID: 33179442 DOI: 10.1111/tan.14134] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 09/23/2020] [Accepted: 11/04/2020] [Indexed: 01/20/2023]
Abstract
HLA genes play a pivotal role for successful hematopoietic stem cell transplantation (HSCT). There is an increasing need for sophisticated screening of donor HLA genotypes for unrelated HSCT. Next generation sequencing (NGS) has emerged as an alternative for classical Sanger sequence for HLA typing. In this study, HLA-A, -B, and -DRB1 alleles were genotyped at the allelic (6-digit) level using MiSeqDx in 26,202 volunteers from the Korean Network for Organ Sharing. Exon 2 and 3 of HLA-A and -B and exon 2 of HLA-DRB1 were amplified by polymerase chain reaction (PCR) and each allele was determined by matching the targeted exons and the reference sequence consisting of the IPD-IMGT/HLA Database. Seventy alleles of HLA-A, 102 alleles of HLA-B, and 69 alleles of HLA-DRB1 were identified. According to common and well-documented catalogs, 34 alleles in HLA-A, 61 in HLA-B, and 45 in HLA-DRB1 locus were common alleles, and 12, 14, and 11 kinds, were well-documented alleles, respectively. Thirteen novel alleles including 3 alleles in HLA-A, 8 alleles in HLA-B, and 2 alleles in HLA-DRB1 loci were found. Ten haplotypes with a frequency of more than 1.0% accounted for 22.4% of the total haplotype frequencies. Cis/trans ambiguities of HLA-A and -B loci by combination of exons 2 and 3 were analyzed to be 0.17% of 3 and 3.95% of 22 genotypes, respectively. This information on rare and novel alleles found by accurate HLA typing with NGS may be helpful for unrelated HSCT among Koreans.
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Affiliation(s)
- In-Cheol Baek
- Hematopoietic Stem Cell Bank, College of Medicine, The Catholic University of Korea, Seoul, South Korea
| | - Eun-Jeong Choi
- Hematopoietic Stem Cell Bank, College of Medicine, The Catholic University of Korea, Seoul, South Korea
| | - Dong-Hwan Shin
- Hematopoietic Stem Cell Bank, College of Medicine, The Catholic University of Korea, Seoul, South Korea
| | - Hyoung-Jae Kim
- Hematopoietic Stem Cell Bank, College of Medicine, The Catholic University of Korea, Seoul, South Korea
| | - Haeyoun Choi
- Department of Microbiology, College of Medicine, The Catholic University of Korea, Seoul, South Korea
| | - Tai-Gyu Kim
- Hematopoietic Stem Cell Bank, College of Medicine, The Catholic University of Korea, Seoul, South Korea.,Department of Microbiology, College of Medicine, The Catholic University of Korea, Seoul, South Korea
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McGill JR, Yogurtcu ON, Verthelyi D, Yang H, Sauna ZE. SampPick: Selection of a Cohort of Subjects Matching a Population HLA Distribution. Front Immunol 2019; 10:2894. [PMID: 31921155 PMCID: PMC6933600 DOI: 10.3389/fimmu.2019.02894] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Accepted: 11/26/2019] [Indexed: 11/21/2022] Open
Abstract
Immune responses to therapeutic proteins and peptides can adversely affect their safety and efficacy; consequently, immunogenicity risk-assessments are part of the development, licensure and clinical use of these products. In most cases the development of anti-drug antibodies is mediated by T cells which requires antigen presentation by Major Histocompatibility Complex Class II (MHCII) molecules (also called Human Leucocyte Antigen, HLA in humans). Immune responses to many protein therapeutics are thus HLA-restricted and it is important that the distribution of HLA variants used in the immunogenicity assessments provides adequate coverage of the target population. Due to biases inherent to the collection of samples in a blood bank or donor pool, simple random sampling will not achieve a truly representative sample of the population of interest. To help select a donor cohort we introduce SampPick, an implementation of simulated annealing which optimizes cohort selection to closely match the frequency distribution of a target population or subpopulation. With inputs of a target background frequency distribution for a population and a set of available, HLA-typed donors, the algorithm will iteratively create a cohort of donors of a user selected size that will closely match the target population rather than a random sample. In addition to optimizing the HLA types of donor cohorts, the software presented can be used to optimize donor cohorts for any other biallelic or monoallelic trait.
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Affiliation(s)
- Joseph R McGill
- Hemostasis Branch, Division of Plasma Protein Therapeutics, Office of Tissues and Advanced Therapies, Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, MD, United States
| | - Osman N Yogurtcu
- Office of Biostatistics & Epidemiology, Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, MD, United States
| | - Daniela Verthelyi
- Office of Biotechnology Products, Office of Product Quality, Center for Drugs Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, MD, United States
| | - Hong Yang
- Office of Biostatistics & Epidemiology, Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, MD, United States
| | - Zuben E Sauna
- Hemostasis Branch, Division of Plasma Protein Therapeutics, Office of Tissues and Advanced Therapies, Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, MD, United States
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Yang JJ, Hwang SH, Ko DH, Seo EJ, Oh HB. Tri-allelic expression of HLA gene in 46,XX/46,XY chimerism. Transpl Immunol 2018; 53:38-42. [PMID: 30579837 DOI: 10.1016/j.trim.2018.12.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Revised: 12/18/2018] [Accepted: 12/19/2018] [Indexed: 10/27/2022]
Abstract
INTRODUCTION Chimerism is defined as coexistence of different cell lines in an individual. 46,XX/46,XY chimerism is very rare and exhibits broad range of clinical phenotypes. Most cases are detected at infancy or younger age due to disorders of sex development, while phenotypically normal cases are incidentally discovered through abnormal blood grouping results or multiple genotypes in HLA. OBJECTIVE Aim was to determine the genetic expression of numerous HLA alleles detected in phenotypically normal 46,XX/46,XY chimerism. MATERIALS AND METHODS A patient was admitted for lung transplantation due to end-stage pulmonary disease. Pre-transplantation work-up included blood group typing and HLA DNA typing analyses. Peripheral blood and hair follicle specimens were used to confirm unusual tri-allelic results by high-resolution PCR-SBT. Cytogenetic analyses of karyotyping, FISH and chromosomal microarray were done. Flowcytometry crossmatch analysis was conducted using lymphocytes and anti-HLA sera defined by Luminex panel reactive antibody test (One Lambda, Inc., Canoga Park, CA), to determine antigen expression of HLA alleles. RESULTS 46,XX/46,XY chimerism was confirmed through series of cytogenetic analyses. HLA typing of the patient revealed three alleles from HLA-A, -B and -DRB1 loci. Antigen expression of all 3 HLA alleles was confirmed by flow cytometry crossmatch. DISCUSSION A case of normal phenotype 46,XX/46,XY chimerism was detected for the first time in Korean patient admitted for lung transplantation. Cytogenetic results were confirmatory for chimerism and HLA typing using PCR-SBT method was able to detect the presence of 3 HLA alleles. Flowcytometry crossmatch was proven sensitive for detecting antigen expression of different cell lines of small proportions.
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Affiliation(s)
- John Jeongseok Yang
- Department of Laboratory Medicine, University of Ulsan College of Medicine and Asan Medical Center, Seoul, Republic of Korea
| | - Sang-Hyun Hwang
- Department of Laboratory Medicine, University of Ulsan College of Medicine and Asan Medical Center, Seoul, Republic of Korea
| | - Dae-Hyun Ko
- Department of Laboratory Medicine, University of Ulsan College of Medicine and Asan Medical Center, Seoul, Republic of Korea
| | - Eul-Ju Seo
- Department of Laboratory Medicine, University of Ulsan College of Medicine and Asan Medical Center, Seoul, Republic of Korea
| | - Heung-Bum Oh
- Department of Laboratory Medicine, University of Ulsan College of Medicine and Asan Medical Center, Seoul, Republic of Korea.
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Lee S, Huh JY, Turner DM, Lee S, Robinson J, Stein JE, Shim SH, Hong CP, Kang MS, Nakagawa M, Kaneko S, Nakanishi M, Rao MS, Kurtz A, Stacey GN, Marsh SGE, Turner ML, Song J. Repurposing the Cord Blood Bank for Haplobanking of HLA-Homozygous iPSCs and Their Usefulness to Multiple Populations. Stem Cells 2018; 36:1552-1566. [PMID: 30004605 DOI: 10.1002/stem.2865] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Revised: 06/17/2018] [Accepted: 05/02/2018] [Indexed: 01/26/2023]
Abstract
Although autologous induced pluripotent stem cells (iPSCs) can potentially be useful for treating patients without immune rejection, in reality it will be extremely expensive and labor-intensive to make iPSCs to realize personalized medicine. An alternative approach is to make use of human leukocyte antigen (HLA) haplotype homozygous donors to provide HLA matched iPSC products to significant numbers of patients. To establish a haplobank of iPSCs, we repurposed the cord blood bank by screening ∼4,200 high resolution HLA typed cord blood samples, and selected those homozygous for the 10 most frequent HLA-A,-B,-DRB1 haplotypes in the Korean population. Following the generation of 10 iPSC lines, we conducted a comprehensive characterization, including morphology, expression of pluripotent markers and cell surface antigens, three-germ layer formation, vector clearance, mycoplasma/microbiological/viral contamination, endotoxin, and short tandem repeat (STR) assays. Various genomic analyses using microarray and comparative genomic hybridization (aCGH)-based single nucleotide polymorphism (SNP) and copy number variation (CNV) were also conducted. These 10 HLA-homozygous iPSC lines match 41.07% of the Korean population. Comparative analysis of HLA population data shows that they are also of use in other Asian populations, such as Japan, with some limited utility in ethnically diverse populations, such as the UK. Taken together, the generation of the 10 most frequent Korean HLA-homozygous iPSC lines serves as a useful pointer for the development of optimal methods for iPSC generation and quality control and indicates the benefits and limitations of collaborative HLA driven selection of donors for future stocking of worldwide iPSC haplobanks. Stem Cells 2018;36:1552-1566.
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Affiliation(s)
- Suji Lee
- Department of Biomedical Science, CHA Stem Cell Institute, CHA University, Seongnam-si, Gyeonggi-do, Republic of Korea
| | - Ji Young Huh
- Department of Laboratory Medicine, CHA Bundang Medical Center, CHA University, Seongnam-si, Gyeonggi-do, Republic of Korea
| | - David M Turner
- Histocompatibility and Immunogenetics Laboratory, Royal Infirmary of Edinburgh, Edinburgh, UK
- Advanced Therapeutics, Scottish National Blood Transfusion Service, Edinburgh, UK
| | - Soohyeon Lee
- Department of Biomedical Science, CHA Stem Cell Institute, CHA University, Seongnam-si, Gyeonggi-do, Republic of Korea
| | - James Robinson
- HLA Informatics Group, Anthony Nolan Research Institute, Royal Free Campus, London, UK
- UCL Cancer Institute, University College London, London, UK
| | - Jeremy E Stein
- HLA Informatics Group, Anthony Nolan Research Institute, Royal Free Campus, London, UK
| | - Sung Han Shim
- Department of Biomedical Science, CHA Stem Cell Institute, CHA University, Seongnam-si, Gyeonggi-do, Republic of Korea
| | - Chang Pyo Hong
- Bioinformatics Team, Theragen Etex Bio Institute, Suwon-si, Gyeonggi-do, Republic of Korea
| | - Myung Seo Kang
- Department of Laboratory Medicine, CHA Bundang Medical Center, CHA University, Seongnam-si, Gyeonggi-do, Republic of Korea
| | - Masato Nakagawa
- Center for iPS Cell Research and Application, Kyoto University, Kyoto, Japan
| | - Shin Kaneko
- Center for iPS Cell Research and Application, Kyoto University, Kyoto, Japan
| | - Mahito Nakanishi
- Biotechnology Research Institute for Drug Discovery, National Institute of Advanced Industrial Science and Technology, Ibaraki, Japan
| | - Mahendra S Rao
- New York Stem Cell Foundation Research Institute, New York, New York, USA
| | - Andreas Kurtz
- Berlin-Brandenburg Center for Regenerative Therapies, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Glyn N Stacey
- International Stem Cell Banking Initiative, Hertfordshire, UK
| | - Steven G E Marsh
- HLA Informatics Group, Anthony Nolan Research Institute, Royal Free Campus, London, UK
- UCL Cancer Institute, University College London, London, UK
| | - Marc L Turner
- Advanced Therapeutics, Scottish National Blood Transfusion Service, Edinburgh, UK
- Global Alliance for iPSC Therapies, The Jack Copland Centre, Edinburgh, UK
| | - Jihwan Song
- Department of Biomedical Science, CHA Stem Cell Institute, CHA University, Seongnam-si, Gyeonggi-do, Republic of Korea
- Global Alliance for iPSC Therapies, The Jack Copland Centre, Edinburgh, UK
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10
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Jia X, Horinouchi T, Hitomi Y, Shono A, Khor SS, Omae Y, Kojima K, Kawai Y, Nagasaki M, Kaku Y, Okamoto T, Ohwada Y, Ohta K, Okuda Y, Fujimaru R, Hatae K, Kumagai N, Sawanobori E, Nakazato H, Ohtsuka Y, Nakanishi K, Shima Y, Tanaka R, Ashida A, Kamei K, Ishikura K, Nozu K, Tokunaga K, Iijima K. Strong Association of the HLA-DR/DQ Locus with Childhood Steroid-Sensitive Nephrotic Syndrome in the Japanese Population. J Am Soc Nephrol 2018; 29:2189-2199. [PMID: 30012571 DOI: 10.1681/asn.2017080859] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Accepted: 05/11/2018] [Indexed: 12/26/2022] Open
Abstract
Background Nephrotic syndrome is the most common cause of chronic glomerular disease in children. Most of these patients develop steroid-sensitive nephrotic syndrome (SSNS), but the loci conferring susceptibility to childhood SSNS are mainly unknown.Methods We conducted a genome-wide association study (GWAS) in the Japanese population; 224 patients with childhood SSNS and 419 adult healthy controls were genotyped using the Affymetrix Japonica Array in the discovery stage. Imputation for six HLA genes (HLA-A, -C, -B, -DRB1, -DQB1, and -DPB1) was conducted on the basis of Japanese-specific references. We performed genotyping for HLA-DRB1/-DQB1 using a sequence-specific oligonucleotide-probing method on a Luminex platform. Whole-genome imputation was conducted using a phased reference panel of 2049 healthy Japanese individuals. Replication was performed in an independent Japanese sample set including 216 patients and 719 healthy controls. We genotyped candidate single-nucleotide polymorphisms using the DigiTag2 assay.Results The most significant association was detected in the HLA-DR/DQ region and replicated (rs4642516 [minor allele G], combined Pallelic=7.84×10-23; odds ratio [OR], 0.33; 95% confidence interval [95% CI], 0.26 to 0.41; rs3134996 [minor allele A], combined Pallelic=1.72×10-25; OR, 0.29; 95% CI, 0.23 to 0.37). HLA-DRB1*08:02 (Pc=1.82×10-9; OR, 2.62; 95% CI, 1.94 to 3.54) and HLA-DQB1*06:04 (Pc=2.09×10-12; OR, 0.10; 95% CI, 0.05 to 0.21) were considered primary HLA alleles associated with childhood SSNS. HLA-DRB1*08:02-DQB1*03:02 (Pc=7.01×10-11; OR, 3.60; 95% CI, 2.46 to 5.29) was identified as the most significant genetic susceptibility factor.Conclusions The most significant association with childhood SSNS was detected in the HLA-DR/DQ region. Further HLA allele/haplotype analyses should enhance our understanding of molecular mechanisms underlying SSNS.
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Affiliation(s)
- Xiaoyuan Jia
- Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Tomoko Horinouchi
- Department of Pediatrics, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Yuki Hitomi
- Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Akemi Shono
- Department of Pediatrics, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Seik-Soon Khor
- Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Yosuke Omae
- Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Kaname Kojima
- Department of Integrative Genomics, Tohoku Medical Megabank Organization.,Graduate School of Medicine, and.,Graduate School of Information Sciences, Tohoku University, Sendai, Japan
| | - Yosuke Kawai
- Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.,Department of Integrative Genomics, Tohoku Medical Megabank Organization
| | - Masao Nagasaki
- Department of Integrative Genomics, Tohoku Medical Megabank Organization.,Graduate School of Medicine, and.,Graduate School of Information Sciences, Tohoku University, Sendai, Japan
| | - Yoshitsugu Kaku
- Department of Nephrology, Fukuoka Children's Hospital, Fukuoka, Japan
| | - Takayuki Okamoto
- Department of Pediatrics, Hokkaido University Hospital, Sapporo, Japan
| | - Yoko Ohwada
- Department of Pediatrics, Dokkyo Medical University School of Medicine, Tochigi, Japan
| | - Kazuhide Ohta
- Department of Pediatrics, Kanazawa Medical Center, Kanazawa, Japan
| | - Yusuke Okuda
- Department of Pediatrics, Shiga University of Medical Science, Shiga, Japan
| | - Rika Fujimaru
- Department of Pediatrics, Osaka City General Hospital, Osaka, Japan
| | - Ken Hatae
- Department of Pediatrics, Japanese Red Cross Fukuoka Hospital, Fukuoka, Japan
| | - Naonori Kumagai
- Department of Pediatrics, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Emi Sawanobori
- Department of Pediatrics, Faculty of Medicine, University of Yamanashi, Yamanashi, Japan
| | - Hitoshi Nakazato
- Department of Pediatrics, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan
| | - Yasufumi Ohtsuka
- Department of Pediatrics, Faculty of Medicine, Saga University, Saga, Japan
| | - Koichi Nakanishi
- Department of Pediatrics, Wakayama Medical University, Wakayama, Japan
| | - Yuko Shima
- Department of Pediatrics, Wakayama Medical University, Wakayama, Japan
| | - Ryojiro Tanaka
- Department of Nephrology, Hyogo Prefectural Kobe Children's Hospital, Kobe, Japan
| | - Akira Ashida
- Department of Pediatrics, Osaka Medical College, Osaka, Japan; and
| | - Koichi Kamei
- Division of Nephrology and Rheumatology, National Center for Child Health and Development, Tokyo, Japan
| | - Kenji Ishikura
- Division of Nephrology and Rheumatology, National Center for Child Health and Development, Tokyo, Japan
| | - Kandai Nozu
- Department of Pediatrics, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Katsushi Tokunaga
- Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan;
| | - Kazumoto Iijima
- Department of Pediatrics, Kobe University Graduate School of Medicine, Kobe, Japan;
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11
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Murakoshi H, Zou C, Kuse N, Akahoshi T, Chikata T, Gatanaga H, Oka S, Hanke T, Takiguchi M. CD8 + T cells specific for conserved, cross-reactive Gag epitopes with strong ability to suppress HIV-1 replication. Retrovirology 2018; 15:46. [PMID: 29970102 PMCID: PMC6029025 DOI: 10.1186/s12977-018-0429-y] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Accepted: 06/25/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Development of AIDS vaccines for effective prevention of circulating HIV-1 is required, but no trial has demonstrated definitive effects on the prevention. Several recent T-cell vaccine trials showed no protection against HIV-1 acquisition although the vaccines induced HIV-1-specific T-cell responses, suggesting that the vaccine-induced T cells have insufficient capacities to suppress HIV-1 replication and/or cross-recognize circulating HIV-1. Therefore, it is necessary to develop T-cell vaccines that elicit T cells recognizing shared protective epitopes with strong ability to suppress HIV-1. We recently designed T-cell mosaic vaccine immunogens tHIVconsvX composed of 6 conserved Gag and Pol regions and demonstrated that the T-cell responses to peptides derived from the vaccine immunogens were significantly associated with lower plasma viral load (pVL) and higher CD4+ T-cell count (CD4 count) in HIV-1-infected, treatment-naive Japanese individuals. However, it remains unknown T cells of which specificities have the ability to suppress HIV-1 replication. In the present study, we sought to identify more T cells specific for protective Gag epitopes in the vaccine immunogens, and analyze their abilities to suppress HIV-1 replication and recognize epitope variants in circulating HIV-1. RESULTS We determined 17 optimal Gag epitopes and their HLA restriction, and found that T-cell responses to 9 were associated significantly with lower pVL and/or higher CD4 count. T-cells recognizing 5 of these Gag peptides remained associated with good clinical outcome in 221 HIV-1-infected individuals even when comparing responders and non-responders with the same restricting HLA alleles. Although it was known previously that T cells specific for 3 of these protective epitopes had strong abilities to suppress HIV-1 replication in vivo, here we demonstrated equivalent abilities for the 2 novel epitopes. Furthermore, T cells against all 5 Gag epitopes cross-recognized variants in majority of circulating HIV-1. CONCLUSIONS We demonstrated that T cells specific for 5 Gag conserved epitopes in the tHIVconsvX have ability to suppress replication of circulating HIV-1 in HIV-1-infected individuals. Therefore, the tHIVconsvX vaccines have the right specificity to contribute to prevention of HIV-1 infection and eradication of latently infected cells following HIV-1 reactivation.
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Affiliation(s)
- Hayato Murakoshi
- Center for AIDS Research, Kumamoto University, 2-2-1 Honjo, Chuo-ku, Kumamoto, 860-0811, Japan
| | - Chengcheng Zou
- Center for AIDS Research, Kumamoto University, 2-2-1 Honjo, Chuo-ku, Kumamoto, 860-0811, Japan
| | - Nozomi Kuse
- Center for AIDS Research, Kumamoto University, 2-2-1 Honjo, Chuo-ku, Kumamoto, 860-0811, Japan
| | - Tomohiro Akahoshi
- Center for AIDS Research, Kumamoto University, 2-2-1 Honjo, Chuo-ku, Kumamoto, 860-0811, Japan
| | - Takayuki Chikata
- Center for AIDS Research, Kumamoto University, 2-2-1 Honjo, Chuo-ku, Kumamoto, 860-0811, Japan
| | - Hiroyuki Gatanaga
- Center for AIDS Research, Kumamoto University, 2-2-1 Honjo, Chuo-ku, Kumamoto, 860-0811, Japan.,AIDS Clinical Center, National Center for Global Health and Medicine, Tokyo, Japan
| | - Shinichi Oka
- Center for AIDS Research, Kumamoto University, 2-2-1 Honjo, Chuo-ku, Kumamoto, 860-0811, Japan.,AIDS Clinical Center, National Center for Global Health and Medicine, Tokyo, Japan
| | - Tomáš Hanke
- International Research Center of Medical Sciences, Kumamoto University, Kumamoto, Japan.,The Jenner Institute, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford, UK
| | - Masafumi Takiguchi
- Center for AIDS Research, Kumamoto University, 2-2-1 Honjo, Chuo-ku, Kumamoto, 860-0811, Japan.
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12
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da Silva-Malta MCF, Rodrigues PS, Zuccherato LW, de Souza FCB, Domingues EMFL, Souza VR, Tarazona-Santos E, Martins ML. Human leukocyte antigen distribution and genomic ancestry in Brazilian patients with sickle cell disease. HLA 2017; 90:211-218. [DOI: 10.1111/tan.13102] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Revised: 06/13/2017] [Accepted: 07/18/2017] [Indexed: 12/11/2022]
Affiliation(s)
- M. C. F. da Silva-Malta
- Fundação Centro de Hematologia e Hemoterapia de Minas Gerais - Hemominas; Belo Horizonte Brazil
| | - P. S. Rodrigues
- Fundação Centro de Hematologia e Hemoterapia de Minas Gerais - Hemominas; Belo Horizonte Brazil
| | - L. W. Zuccherato
- Departamento de Biologia Geral, Instituto de Ciências Biológicas; Universidade Federal de Minas Gerais; Belo Horizonte Brazil
| | - F. C. B. de Souza
- Fundação Centro de Hematologia e Hemoterapia de Minas Gerais - Hemominas; Belo Horizonte Brazil
| | - E. M. F. L. Domingues
- Fundação Centro de Hematologia e Hemoterapia de Minas Gerais - Hemominas; Belo Horizonte Brazil
| | - V. R. Souza
- Fundação Centro de Hematologia e Hemoterapia de Minas Gerais - Hemominas; Belo Horizonte Brazil
| | - E. Tarazona-Santos
- Departamento de Biologia Geral, Instituto de Ciências Biológicas; Universidade Federal de Minas Gerais; Belo Horizonte Brazil
| | - M. L. Martins
- Fundação Centro de Hematologia e Hemoterapia de Minas Gerais - Hemominas; Belo Horizonte Brazil
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13
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Kim KM, Han OJ, Kang MS, Huh JY. HLA-A*02:687, a novel allele identified by sequence-based typing in cord blood from a Korean woman. HLA 2017; 90:246-247. [PMID: 28686327 DOI: 10.1111/tan.13088] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2017] [Revised: 06/28/2017] [Accepted: 06/28/2017] [Indexed: 11/29/2022]
Abstract
A*02:687 showed one nucleotide difference with A*02:01:01:01 resulting in an amino acid change.
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Affiliation(s)
- K M Kim
- Department of Laboratory Medicine, CHA Bundang Medical Center, CHA University, Seongnam, South Korea
| | - O J Han
- Department of Laboratory Medicine, CHA Bundang Medical Center, CHA University, Seongnam, South Korea
| | - M S Kang
- Department of Laboratory Medicine, CHA Bundang Medical Center, CHA University, Seongnam, South Korea
| | - J Y Huh
- Department of Laboratory Medicine, CHA Bundang Medical Center, CHA University, Seongnam, South Korea
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14
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Ka S, Lee S, Hong J, Cho Y, Sung J, Kim HN, Kim HL, Jung J. HLAscan: genotyping of the HLA region using next-generation sequencing data. BMC Bioinformatics 2017; 18:258. [PMID: 28499414 PMCID: PMC5427585 DOI: 10.1186/s12859-017-1671-3] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2016] [Accepted: 05/03/2017] [Indexed: 12/30/2022] Open
Abstract
Background Several recent studies showed that next-generation sequencing (NGS)-based human leukocyte antigen (HLA) typing is a feasible and promising technique for variant calling of highly polymorphic regions. To date, however, no method with sufficient read depth has completely solved the allele phasing issue. In this study, we developed a new method (HLAscan) for HLA genotyping using NGS data. Results HLAscan performs alignment of reads to HLA sequences from the international ImMunoGeneTics project/human leukocyte antigen (IMGT/HLA) database. The distribution of aligned reads was used to calculate a score function to determine correctly phased alleles by progressively removing false-positive alleles. Comparative HLA typing tests using public datasets from the 1000 Genomes Project and the International HapMap Project demonstrated that HLAscan could perform HLA typing more accurately than previously reported NGS-based methods such as HLAreporter and PHLAT. In addition, the results of HLA-A, −B, and -DRB1 typing by HLAscan using data generated by NextGen were identical to those obtained using a Sanger sequencing–based method. We also applied HLAscan to a family dataset with various coverage depths generated on the Illumina HiSeq X-TEN platform. HLAscan identified allele types of HLA-A, −B, −C, −DQB1, and -DRB1 with 100% accuracy for sequences at ≥ 90× depth, and the overall accuracy was 96.9%. Conclusions HLAscan, an alignment-based program that takes read distribution into account to determine true allele types, outperformed previously developed HLA typing tools. Therefore, HLAscan can be reliably applied for determination of HLA type across the whole-genome, exome, and target sequences. Electronic supplementary material The online version of this article (doi:10.1186/s12859-017-1671-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Sojeong Ka
- R&D center, Syntekabio, Inc., 5 Hwarang-ro 14-gil, Seongbuk-gu, Seoul, 02792, South Korea
| | - Sunho Lee
- Main office, Syntekabio, Inc., 187 Techno 2-ro, Yuseong-gu, Daejeon, 34025, South Korea
| | - Jonghee Hong
- R&D center, Syntekabio, Inc., 5 Hwarang-ro 14-gil, Seongbuk-gu, Seoul, 02792, South Korea
| | - Yangrae Cho
- Main office, Syntekabio, Inc., 187 Techno 2-ro, Yuseong-gu, Daejeon, 34025, South Korea
| | - Joohon Sung
- Complex Disease and Genome Epidemiology Branch, Department of Epidemiology, School of Public Health, Seoul National University, Seoul, 08826, South Korea
| | - Han-Na Kim
- Department of Biochemistry, School of Medicine, Ewha Womans University, Seoul, 07985, South Korea
| | - Hyung-Lae Kim
- Department of Biochemistry, School of Medicine, Ewha Womans University, Seoul, 07985, South Korea.
| | - Jongsun Jung
- Main office, Syntekabio, Inc., 187 Techno 2-ro, Yuseong-gu, Daejeon, 34025, South Korea.
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15
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Arnaiz-Villena A, Muñiz E, del Palacio-Gruber J, Campos C, Alonso-Rubio J, Gomez-Casado E, Lopez-Pacheco F, Martin-Villa M, Silvera C. Ancestry of Amerindians and its Impact in Anthropology, Transplantation, HLA Pharmacogenomics and Epidemiology by HLA Study in Wiwa Colombian Population. ACTA ACUST UNITED AC 2016. [DOI: 10.2174/1874220301603010269] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Background:HLA autosomic genes are unique because they conform the most polymorphic human system. Importance of this system is recognized in Medicine for Transplantation, Epidemiology (HLA and disease linkage), Pharmacogenomics (HLA linked to drug side effects) and for defining the origin of populations in both male and female lineages.Objectives:Studying HLA profile of a isolated Amerindian group from North Colombia (Wiwa) in order to draw conclusions about its Preventive Medicine, the genetic relationship with Worldwide populations and America peopling, since this last issue is hotly debated.Methodology:A total of 14,660 HLA chromosomes were included. Peripheral blood was obtained from volunteer blood donors belonging to Wiwa (also named Arsario) ethnic group. HLA-A, -B, -C, -DRB1 and -DQB1 genes were analyzed by standard methods. Wiwa Amerindians relationships with others were calculated by using Arlequin, Dispan and Vista software computer packages.Results:Extended HLA, -A, -B, -C, -DRB1 and -DQB1 haplotypes have been studied for the first time in this population. Classical Amerindian haplotypes have been found and also new Wiwa (Arsario) Amerindian haplotypes. New haplotypes are A*68:01 - B*15:01 - C*03:03 - DRB1*14:02 - DQB1*03:02, A*11:01 - B*07:02 - C*07:02 - DRB1*15:03 - DQB1*06:02 and A*68:01 - B*15:01 - C*03:04 - DRB1*14:02 - DQB1*03:01.Conclusion:They have been reached after exhaustive comparisons of Wiwa with other Amerindians and Worldwide populations by using genetic distances, Neighbor Joining trees, correspondence analysis and specific group of alleles which are common and frequent in both Amerindians and Pacific Islanders. They are: 1) The Americas First Inhabitants have been probably come through Bering Strait and also through Pacific (from Austronesia and Asia) and Atlantic (from Europe) routes. A bidirectional gene flow is not discarded. 2) Genetic HLA Amerindian profile is separated from that of other Worldwide populations. 3) Amerindians geographical proximity groups’ relatedness is not concordant with HLA genetic relatedness, neither with language. This may be explained by a substantial population decrease that occurred after Europeans invaded America in 1492 and carried new pathogens and epidemics. 4) Our results are also useful for Wiwa and other Amerindians future preventive medicine (HLA linked diseases), HLA pharmacogenomics and transplantation regional programs.
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16
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Park H, Lee YJ, Song EY, Park MH. HLA-A, HLA-B and HLA-DRB1 allele and haplotype frequencies of 10 918 Koreans from bone marrow donor registry in Korea. Int J Immunogenet 2016; 43:287-96. [PMID: 27511726 DOI: 10.1111/iji.12288] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2016] [Accepted: 07/25/2016] [Indexed: 01/19/2023]
Abstract
The human leucocyte antigen (HLA) system is the most polymorphic genetic system in humans, and HLA matching is crucial in organ transplantation, especially in hematopoietic stem cell transplantation. We investigated HLA-A, HLA-B and HLA-DRB1 allele and haplotype frequencies at allelic level in 10 918 Koreans from bone marrow donor registry in Korea. Intermediate resolution HLA typing was performed using Luminex technology (Wakunaga, Japan), and additional allelic level typing was performed using PCR-single-strand conformation polymorphism method and/or sequence-based typing (Abbott Molecular, USA). Allele and haplotype frequencies were calculated by direct counting and maximum likelihood methods, respectively. A total of 39 HLA-A, 66 HLA-B and 47 HLA-DRB1 alleles were identified. High-frequency alleles found at a frequency of ≥5% were 6 HLA-A (A*02:01, *02:06, *11:01, *24:02, *31:01 and *33:03), 6 HLA-B (B*15:01, *35:01, *44:03, *51:01, 54:01 and *58:01) and 8 HLA-DRB1 (DRB1*01:01, *04:05, *04:06, *07:01, *08:03, *09:01, *13:02 and *15:01) alleles. At each locus, A*02, B*15 and DRB1*14 generic groups were most diverse at allelic level, consisting of 9, 12 and 11 different alleles, respectively. A total of 366, 197 and 21 different HLA-A-B-DRB1 haplotypes were estimated with frequencies of ≥0.05%, ≥0.1% and ≥0.5%, respectively. The five most common haplotypes with frequencies of ≥2.0% were A*33:03-B*44:03-DRB1*13:02 (4.97%), A*33:03-B*58:01-DRB1*13:02, A*33:03-B*44:03-DRB1*07:01, A*24:02-B*07:02-DRB1*01:01 and A*24:02-B*52:01-DRB1*15:02. Among 34 serologic HLA-A-B-DR haplotypes with frequencies of ≥0.5%, 17 haplotypes revealed allele-level diversity and majority of the allelic variation was arising from A2, A26, B61, B62, DR4 and DR14 specificities. Haplotype diversity obtained in this study is the most comprehensive data thus far reported in Koreans, and the information will be useful for unrelated stem cell transplantation as well as for disease association studies.
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Affiliation(s)
- H Park
- Department of Laboratory Medicine, Seegene Medical Foundation, Seoul, Korea
| | - Y-J Lee
- Department of Laboratory Medicine, Seoul National University College of Medicine, Seoul, Korea
| | - E Y Song
- Department of Laboratory Medicine, Seoul National University College of Medicine, Seoul, Korea
| | - M H Park
- Department of Laboratory Medicine, Seoul National University College of Medicine, Seoul, Korea.,Korea Organ Donation Agency Laboratory, Seoul, Korea
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17
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Chung HY, Song EY, Yoon JA, Suh DH, Lee SC, Kim YC, Park MH. Association of human leukocyte antigen with postherpetic neuralgia in Koreans. APMIS 2016; 124:865-71. [DOI: 10.1111/apm.12575] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2016] [Accepted: 06/09/2016] [Indexed: 11/27/2022]
Affiliation(s)
- Hye Yoon Chung
- Department of Laboratory Medicine; Seoul National University College of Medicine; Seoul Korea
| | - Eun Young Song
- Department of Laboratory Medicine; Seoul National University College of Medicine; Seoul Korea
| | - Jung Ah Yoon
- Department of Laboratory Medicine; Seoul National University College of Medicine; Seoul Korea
| | - Dae Hun Suh
- Department of Dermatology; Seoul National University College of Medicine; Seoul Korea
| | - Sang Chul Lee
- Department of Anesthesiology; Seoul National University College of Medicine; Seoul Korea
| | - Yong Chul Kim
- Department of Anesthesiology; Seoul National University College of Medicine; Seoul Korea
| | - Myoung Hee Park
- Department of Laboratory Medicine; Seoul National University College of Medicine; Seoul Korea
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18
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Kim KM, Han O, Kang MS, Huh JY. HLA-A*33:102, a novel allele identified by sequence-based typing in cord blood from a Korean woman. HLA 2016; 87:391-2. [DOI: 10.1111/tan.12772] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Revised: 02/16/2016] [Accepted: 02/17/2016] [Indexed: 11/30/2022]
Affiliation(s)
- K. M. Kim
- Department of Laboratory Medicine, CHA Bundang Medical Center; CHA University; Seongnam South Korea
| | - O.J. Han
- Department of Laboratory Medicine, CHA Bundang Medical Center; CHA University; Seongnam South Korea
| | - M. S. Kang
- Department of Laboratory Medicine, CHA Bundang Medical Center; CHA University; Seongnam South Korea
| | - J. Y. Huh
- Department of Laboratory Medicine, CHA Bundang Medical Center; CHA University; Seongnam South Korea
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19
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He Y, Zhang W, Chen N, Wang W, He J, Han Z, Tao S, Dong L, He J, Zhu F, Lv H. HLA-A, -B and -DRB1 allele and haplotype frequencies of 8333 Chinese Han from the Zhejiang province, China. Int J Immunogenet 2016; 43:86-95. [PMID: 26919533 DOI: 10.1111/iji.12254] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Revised: 01/05/2016] [Accepted: 01/31/2016] [Indexed: 11/30/2022]
Abstract
The distribution of human leucocyte antigen (HLA) allele and haplotype is varied among different ethnic populations. In this study, HLA-A, -B and -DRB1 allele and haplotype frequencies were determined in 8333 volunteer bone marrow donors of Zhejiang Han population using the polymerase chain reaction sequence-based typing. A total of 52 HLA-A, 96 HLA-B and 61 HLA-DRB1 alleles were found. Of these, the top three frequent alleles in HLA-A, HLA-B and HLA-DRB1 loci, respectively, were A*11:01 (24.53%), A*24:02 (17.35%), A*02:01 (11.58%); B*40:01 (15.67%), B*46:01 (11.87%), B*58:01 (9.05%); DRB1*09:01 (17.54%),DRB1*12:02 (9.64%) and DRB1*08:03 (8.65%). A total of 171 A-B-DRB1 haplotypes with a frequency of >0.1% were presented and the five most common haplotypes were A*33:03-B*58:01- DRB1*03:01, A*02:07-B*46:01-DRB1*09:01, A*30:01-B*13:02-DRB1*07:01, A*33:03-B*58:01-RB1*13:02 and A*11:01-B*15:02-DRB1*12:02. The information will be useful for selecting unrelated bone marrow donors and for anthropology studies and pharmacogenomics analysis.
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Affiliation(s)
- Y He
- Blood Center of Zhejiang Province, Hangzhou, Zhejiang, China.,Key Laboratory of Blood Safety Research, Ministry of Health, Hangzhou, Zhejiang, China.,Zhejiang Provincial Key Laboratory of Blood Safety Research, Hangzhou, Zhejiang, China
| | - W Zhang
- Blood Center of Zhejiang Province, Hangzhou, Zhejiang, China.,Key Laboratory of Blood Safety Research, Ministry of Health, Hangzhou, Zhejiang, China.,Zhejiang Provincial Key Laboratory of Blood Safety Research, Hangzhou, Zhejiang, China
| | - N Chen
- Blood Center of Zhejiang Province, Hangzhou, Zhejiang, China.,Key Laboratory of Blood Safety Research, Ministry of Health, Hangzhou, Zhejiang, China
| | - W Wang
- Blood Center of Zhejiang Province, Hangzhou, Zhejiang, China.,Key Laboratory of Blood Safety Research, Ministry of Health, Hangzhou, Zhejiang, China
| | - J He
- Blood Center of Zhejiang Province, Hangzhou, Zhejiang, China.,Key Laboratory of Blood Safety Research, Ministry of Health, Hangzhou, Zhejiang, China.,Zhejiang Provincial Key Laboratory of Blood Safety Research, Hangzhou, Zhejiang, China
| | - Z Han
- Blood Center of Zhejiang Province, Hangzhou, Zhejiang, China.,Key Laboratory of Blood Safety Research, Ministry of Health, Hangzhou, Zhejiang, China
| | - S Tao
- Blood Center of Zhejiang Province, Hangzhou, Zhejiang, China.,Key Laboratory of Blood Safety Research, Ministry of Health, Hangzhou, Zhejiang, China.,Zhejiang Provincial Key Laboratory of Blood Safety Research, Hangzhou, Zhejiang, China
| | - L Dong
- Blood Center of Zhejiang Province, Hangzhou, Zhejiang, China.,Key Laboratory of Blood Safety Research, Ministry of Health, Hangzhou, Zhejiang, China
| | - J He
- Blood Center of Zhejiang Province, Hangzhou, Zhejiang, China.,Key Laboratory of Blood Safety Research, Ministry of Health, Hangzhou, Zhejiang, China.,Zhejiang Provincial Key Laboratory of Blood Safety Research, Hangzhou, Zhejiang, China
| | - F Zhu
- Blood Center of Zhejiang Province, Hangzhou, Zhejiang, China.,Key Laboratory of Blood Safety Research, Ministry of Health, Hangzhou, Zhejiang, China.,Zhejiang Provincial Key Laboratory of Blood Safety Research, Hangzhou, Zhejiang, China
| | - H Lv
- Blood Center of Zhejiang Province, Hangzhou, Zhejiang, China.,Key Laboratory of Blood Safety Research, Ministry of Health, Hangzhou, Zhejiang, China.,Zhejiang Provincial Key Laboratory of Blood Safety Research, Hangzhou, Zhejiang, China
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20
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Park HJ, Kim YJ, Kim DH, Kim J, Park KH, Park JW, Lee JH. HLA Allele Frequencies in 5802 Koreans: Varied Allele Types Associated with SJS/TEN According to Culprit Drugs. Yonsei Med J 2016; 57:118-26. [PMID: 26632391 PMCID: PMC4696942 DOI: 10.3349/ymj.2016.57.1.118] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/11/2015] [Revised: 06/30/2015] [Accepted: 07/02/2015] [Indexed: 11/27/2022] Open
Abstract
PURPOSE Stevens-Johnson syndrome (SJS) and toxic epidermal necrolysis (TEN) are very serious forms of drug-induced cutaneous adverse reaction. SJS/TEN induced by certain drug is well known to be associated with some human leukocyte antigen (HLA) gene type. We aimed to explore HLA allele frequencies and their association with SJS/TEN according to culprit drugs in Korea. MATERIALS AND METHODS We enrolled 5802 subjects who had results of HLA typing test from August 2005 to July 2014. Total 28 SJS/TEN patients were categorized based on culprit drugs (allopurinol, lamotrigine, carbamazepine) and identified the presence of HLA-B*58:01, HLA-B*44:03, HLA-B*15:02, and HLA-A*31:01. RESULTS HLA-A*24:02 (20.5%), HLA-B*44:03 (10.0%), and HLA-Cw*01:02 (17.1%) were the most frequent type in HLA-A, -B, and -C genes, respectively. Allele frequencies of HLA-B*58:01, HLA-B*44:03, HLA-A*31:01, and HLA-B*15:02 were 7.0%, 10.0%, 5.0%, and 0.3%, respectively. In 958 allopurinol users, 9 subjects (0.9%) were diagnosed with SJS/TEN. Among them, 8 subjects possessed HLA-B*58:01 allele. SJS/TEN induced by allopurinol was more frequently developed in subjects with HLA-B*58:01 than in subjects without it [odds ratio: 57.4; confidence interval (CI) 7.12-463.50; p<0.001]. Allopurinol treatment, based on screening by HLA-B*58:01 genotyping, could be more cost-effective than that not based on screening. HLA-B*44:03 may be associated with lamotrigine-induced SJS/TEN (odds ratio: 12.75; CI 1.03-157.14; p=0.053). Among carbamazepine users, only two patients experienced SJS/TEN and possessed neither HLA-B*15:02 nor HLA-A*31:03. CONCLUSION HLA gene frequencies varied in Korea. Screening of HLA-B*58:01 before the use of allopurinol might be needed to anticipate probability of SJS/TEN.
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Affiliation(s)
- Hye Jung Park
- Division of Allergy and Immunology, Department of Internal Medicine, Institute of Allergy, Yonsei University College of Medicine, Seoul, Korea
| | - Young Joo Kim
- Division of Allergy and Immunology, Department of Internal Medicine, Institute of Allergy, Yonsei University College of Medicine, Seoul, Korea
| | - Dong Hyun Kim
- Division of Allergy and Immunology, Department of Internal Medicine, Institute of Allergy, Yonsei University College of Medicine, Seoul, Korea
| | - Junho Kim
- Division of Allergy and Immunology, Department of Internal Medicine, Institute of Allergy, Yonsei University College of Medicine, Seoul, Korea
| | - Kyung Hee Park
- Division of Allergy and Immunology, Department of Internal Medicine, Institute of Allergy, Yonsei University College of Medicine, Seoul, Korea
| | - Jung Won Park
- Division of Allergy and Immunology, Department of Internal Medicine, Institute of Allergy, Yonsei University College of Medicine, Seoul, Korea
| | - Jae Hyun Lee
- Division of Allergy and Immunology, Department of Internal Medicine, Institute of Allergy, Yonsei University College of Medicine, Seoul, Korea.
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21
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Zhou XY, Zhu FM, Li JP, Mao W, Zhang DM, Liu ML, Hei AL, Dai DP, Jiang P, Shan XY, Zhang BW, Zhu CF, Shen J, Deng ZH, Wang ZL, Yu WJ, Chen Q, Qiao YH, Zhu XM, Lv R, Li GY, Li GL, Li HC, Zhang X, Pei B, Jiao LX, Shen G, Liu Y, Feng ZH, Su YP, Xu ZX, Di WY, Jiang YQ, Fu HL, Liu XJ, Liu X, Zhou MZ, Du D, Liu Q, Han Y, Zhang ZX, Cai JP. High-Resolution Analyses of Human Leukocyte Antigens Allele and Haplotype Frequencies Based on 169,995 Volunteers from the China Bone Marrow Donor Registry Program. PLoS One 2015; 10:e0139485. [PMID: 26421847 PMCID: PMC4589403 DOI: 10.1371/journal.pone.0139485] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2015] [Accepted: 09/13/2015] [Indexed: 11/18/2022] Open
Abstract
Allogeneic hematopoietic stem cell transplantation is a widely used and effective therapy for hematopoietic malignant diseases and numerous other disorders. High-resolution human leukocyte antigen (HLA) haplotype frequency distributions not only facilitate individual donor searches but also determine the probability with which a particular patient can find HLA-matched donors in a registry. The frequencies of the HLA-A, -B, -C, -DRB1, and -DQB1 alleles and haplotypes were estimated among 169,995 Chinese volunteers using the sequencing-based typing (SBT) method. Totals of 191 HLA-A, 244 HLA-B, 146 HLA-C, 143 HLA-DRB1 and 47 HLA-DQB1 alleles were observed, which accounted for 6.98%, 7.06%, 6.46%, 9.11% and 7.91%, respectively, of the alleles in each locus in the world (IMGT 3.16 Release, Apr. 2014). Among the 100 most common haplotypes from the 169,995 individuals, nine distinct haplotypes displayed significant regionally specific distributions. Among these, three were predominant in the South China region (i.e., the 20th, 31st, and 81sthaplotypes), another three were predominant in the Southwest China region (i.e., the 68th, 79th, and 95th haplotypes), one was predominant in the South and Southwest China regions (the 18th haplotype), one was relatively common in the Northeast and North China regions (the 94th haplotype), and one was common in the Northeast, North and Northwest China (the 40th haplotype). In conclusion, this is the first to analyze high-resolution HLA diversities across the entire country of China, based on a detailed and complete data set that covered 31 provinces, autonomous regions, and municipalities. Specifically, we also evaluated the HLA matching probabilities within and between geographic regions and analyzed the regional differences in the HLA diversities in China. We believe that the data presented in this study might be useful for unrelated HLA-matched donor searches, donor registry planning, population genetic studies, and anthropogenesis studies.
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Affiliation(s)
- Xiao-Yang Zhou
- The Key Laboratory of Geriatrics, Beijing hospital & Beijing Institute of Geriatrics, Ministry of Health, Beijing, China
- Quality control laboratory, China Bone Marrow Program, Beijing, China
| | - Fa-Ming Zhu
- HLA Laboratory, Zhejiang Blood Center, Hangzhou, Zhejiang, China
| | - Jian-Ping Li
- HLA Laboratory, Liaoning Blood Center, Shenyang, Liaoning, China
| | - Wei Mao
- HLA Laboratory, Chongqing Blood Center, Chongqing, China
| | - De-Mei Zhang
- HLA Laboratory, Taiyuan Red Cross Blood Center, Taiyuan, Shanxi, China
| | - Meng-Li Liu
- HLA Laboratory, Shaanxi Blood Center, Xi’an, Shaanxi, China
| | - Ai-Lian Hei
- The Key Laboratory of Geriatrics, Beijing hospital & Beijing Institute of Geriatrics, Ministry of Health, Beijing, China
- Quality control laboratory, China Bone Marrow Program, Beijing, China
| | - Da-Peng Dai
- The Key Laboratory of Geriatrics, Beijing hospital & Beijing Institute of Geriatrics, Ministry of Health, Beijing, China
- Quality control laboratory, China Bone Marrow Program, Beijing, China
| | - Ping Jiang
- The Key Laboratory of Geriatrics, Beijing hospital & Beijing Institute of Geriatrics, Ministry of Health, Beijing, China
- Quality control laboratory, China Bone Marrow Program, Beijing, China
| | - Xiao-Yan Shan
- HLA Laboratory, Beijing Red Cross Blood Center, Beijing, China
| | - Bo-Wei Zhang
- HLA Laboratory, Henan Blood Center, Zhengzhou, Henan, China
| | - Chuan-Fu Zhu
- HLA Laboratory, Shandong Blood Center, Jinan, Shandong
| | - Jie Shen
- HLA Laboratory, the First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Zhi-Hui Deng
- The Key Laboratory of Histocompatibility and Immunogenetics, Shenzhen Blood Center, Shenzhen, Guangdong, China
| | - Zheng-Lei Wang
- HLA Laboratory, Hebei Blood Center, Shijiazhuang, Hebei, China
| | - Wei-Jian Yu
- HLA Laboratory, Dalian Red Cross Blood Center, Dalian, Liaoning, China
| | - Qiang Chen
- HLA Laboratory, Institute of Blood Transfusion, Chinese Academy of Medical Sciences & Peking Union Medical College, Chengdu, Sichuan, China
| | - Yan-Hui Qiao
- HLA Laboratory, Xinjiang Blood Center, Urumchi, Xinjiang, China
| | - Xiang-Ming Zhu
- HLA Laboratory, Kunming Blood Center, Kunming, Yunnan, China
| | - Rong Lv
- HLA Laboratory, Hefei Red Cross Blood Center, Hefei, Anhui, China
| | - Guo-Ying Li
- HLA Laboratory, Gansu Red Cross Blood Center, Lanzhou, Gansu, China
| | - Guo-Liang Li
- HLA Laboratory, Jiangxi Blood Center, Nanchang, Jiangxi, China
| | - Heng-Cong Li
- HLA Laboratory, Nanning Blood Center, Nanning, Guangxi, China
| | - Xu Zhang
- HLA Laboratory, Liaoning Blood Center, Shenyang, Liaoning, China
| | - Bin Pei
- HLA Laboratory, Xiamen Blood Center, Xiamen, Fujian, China
| | - Li-Xin Jiao
- HLA Laboratory, Changchun Blood Center, Changchun, Jilin, China
| | - Gang Shen
- HLA Laboratory, Wuhan Blood Center, Wuhan, Hubei, China
| | - Ying Liu
- HLA Laboratory, Harbin Red Cross Blood Center, Harbin, Heilongjiang, China
| | - Zhi-Hui Feng
- HLA Laboratory, Qingdao Blood Center, Qingdao, Shandong, China
| | - Yu-Ping Su
- HLA Laboratory, Yueyang Red Cross Blood Center, Yueyang, Hunan, China
| | - Zhao-Xia Xu
- HLA Laboratory, Changsha Blood Center, Changsha, Hunan, China
| | - Wen-Ying Di
- HLA Laboratory, Soochow Red Cross Blood Center, Suzhou, Jiangsu, China
| | - Yao-Qin Jiang
- HLA Laboratory, Shanghai Blood Center, Shanghai, China
| | - Hong-Lei Fu
- HLA Laboratory, BFR Transplant Diagnostic Service Center, Beijing China
| | - Xiang-Jun Liu
- HLA Laboratory, BFR Transplant Diagnostic Service Center, Beijing China
| | - Xiang Liu
- HLA Laboratory, CapitalBio Corporation, Beijing, China
| | - Mei-Zhen Zhou
- HLA Laboratory, Beijing Genomics Institute, Shenzhen, Guangdong, China
| | - Dan Du
- Department of HLA Technology, China Bone Marrow Program, Beijing, China
| | - Qi Liu
- Department of HLA Technology, China Bone Marrow Program, Beijing, China
| | - Ying Han
- Department of HLA Technology, China Bone Marrow Program, Beijing, China
| | - Zhi-Xin Zhang
- The Key Laboratory of Geriatrics, Beijing hospital & Beijing Institute of Geriatrics, Ministry of Health, Beijing, China
- Quality control laboratory, China Bone Marrow Program, Beijing, China
- * E-mail: (ZXZ); (JPC)
| | - Jian-Ping Cai
- The Key Laboratory of Geriatrics, Beijing hospital & Beijing Institute of Geriatrics, Ministry of Health, Beijing, China
- Quality control laboratory, China Bone Marrow Program, Beijing, China
- * E-mail: (ZXZ); (JPC)
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22
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Hong SS, Han OJ, Kang MS, Huh JY. HLA-B*59:09, a novel allele identified by sequence-based typing in a cord blood donated by a Korean woman. ACTA ACUST UNITED AC 2015; 86:146-7. [DOI: 10.1111/tan.12592] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2015] [Accepted: 05/12/2015] [Indexed: 11/27/2022]
Affiliation(s)
- S. S. Hong
- Department of Laboratory Medicine, CHA Bundang Medical Center; CHA University; Seongnam South Korea
| | - O. J. Han
- Department of Laboratory Medicine, CHA Bundang Medical Center; CHA University; Seongnam South Korea
| | - M. S. Kang
- Department of Laboratory Medicine, CHA Bundang Medical Center; CHA University; Seongnam South Korea
| | - J. Y. Huh
- Department of Laboratory Medicine, CHA Bundang Medical Center; CHA University; Seongnam South Korea
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23
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In JW, Roh EY, Oh S, Shin S, Park KU, Song EY. Allele and Haplotype Frequencies of Human Leukocyte Antigen-A, -B, -C, -DRB1, and -DQB1 From Sequence-Based DNA Typing Data in Koreans. Ann Lab Med 2015; 35:429-35. [PMID: 26131415 PMCID: PMC4446582 DOI: 10.3343/alm.2015.35.4.429] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2014] [Revised: 12/19/2014] [Accepted: 04/01/2015] [Indexed: 11/19/2022] Open
Abstract
Background Data on allele frequencies (AFs) and haplotype frequencies (HFs) of HLA-C and -DQB1 are limited in Koreans. We investigated AFs and HFs of HLA-A, -B, -C, -DRB1, and -DQB1 in Koreans by high-resolution sequence-based typing (SBT). Methods Hematopoietic stem cells were obtained from 613 healthy, unrelated donors to analyze HLA-A, -B, -C, -DRB1, and -DQB1 genotypes by using AlleleSEQR HLA-A, -B, -C, -DRB1, and -DQB1 SBT kits (Abbott Molecular, USA), respectively. Alleles belonging to HLA-C*07:01/07:06 group were further discriminated by using PCR-sequence specific primer analysis. AFs and HFs were calculated by direct counting and maximum likelihood method, respectively. Results In all, 24 HLA-A, 46 HLA-B, 24 HLA-C, 29 HLA-DRB1, and 15 HLA-DQB1 alleles were identified. AFs and HFs of HLA-A, -B, and -DRB1 were similar to those reported previously. For the HLA-C locus, C*01:02 was the most common allele, followed by C*03:03, C*03:04, C*14:02, C*03:02, and C*07:02 (AF ≥7%). AFs of C*07:01 and C*07:06 were 0.16% and 3.18%, respectively. For the HLA-DQB1 locus, DQB1*03:01 was the most common allele, followed by DQB1*03:03, *03:02, *06:01, *05:01, *04:01, and *06:02 (AF ≥7%). AFs of DQB1*02:01 and DQB1*02:02 were 2.12% and 6.69%, respectively. HFs of A*33:03-C*07:06 and C*07:06-B*44:03 were 3.09% and 3.10%, respectively, while those of DRB1*07:01-DQB1*02:02 and DRB1*03:01-DQB1*02:01 were 6.61% and 2.04%, respectively. Conclusions This study reported AFs and HFs of HLA, including HLA-C and -DQB1, in Koreans by using high-resolution SBT. These data can be used to resolve ambiguous results of HLA typing for organ and hematopoietic stem cell transplantations.
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Affiliation(s)
- Ji Won In
- Department of Laboratory Medicine, Seoul National University College of Medicine, Seoul, Korea
| | - Eun Youn Roh
- Department of Laboratory Medicine, Seoul National University College of Medicine, Seoul, Korea
| | - Sohee Oh
- Department of Biostatistics, Seoul National University Boramae Medical Center, Seoul, Korea
| | - Sue Shin
- Department of Laboratory Medicine, Seoul National University College of Medicine, Seoul, Korea
| | - Kyoung Un Park
- Department of Laboratory Medicine, Seoul National University College of Medicine, Seoul, Korea
| | - Eun Young Song
- Department of Laboratory Medicine, Seoul National University College of Medicine, Seoul, Korea. ; Department of Molecular Medicine and Biopharmaceutical Sciences, Graduate School of Convergence Science and Technology and College of Medicine, Medical Research Center, Seoul National University, Seoul, Korea
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24
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Park BG, Park Y, Yoon CE, Kwon OJ, Kim HS. A new HLA-B*15 allele, HLA-B*15:263, identified in a Korean individual. ACTA ACUST UNITED AC 2015; 86:58-9. [PMID: 25964089 DOI: 10.1111/tan.12582] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2015] [Revised: 04/01/2015] [Accepted: 04/21/2015] [Indexed: 11/30/2022]
Abstract
HLA-B*15:263 differs from HLA-B*15:18:01 by a single nucleotide exchange at position 824, C>G (codon 251 TCT>TGT).
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Affiliation(s)
- B G Park
- Department of Laboratory Medicine, Severance Hospital, Yonsei University College of Medicine, Seoul, South Korea
| | - Y Park
- Department of Laboratory Medicine, National Health Insurance Service Ilsan Hospital, Yonsei University College of Medicine, Goyang, Korea
| | - C E Yoon
- Biowithus Life Science Institute, Seoul, Korea
| | - O-J Kwon
- Biowithus Life Science Institute, Seoul, Korea
| | - H-S Kim
- Department of Laboratory Medicine, Severance Hospital, Yonsei University College of Medicine, Seoul, South Korea
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25
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Yoon YA, Kim JS, Yoon CE, Jang JH, Kang ES. A new HLA-A*30 allele, A*30:81, identified by sequence-based typing. ACTA ACUST UNITED AC 2014; 84:582-3. [PMID: 25302674 DOI: 10.1111/tan.12435] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2014] [Revised: 07/21/2014] [Accepted: 08/05/2014] [Indexed: 11/29/2022]
Abstract
The new allele, HLA-A*30:81, differs from A*30:01:01 by one nucleotide substitution at codon 272 (CTG→ATG).
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Affiliation(s)
- Y A Yoon
- Division of Chronic Disease Control, Korea Centers for Disease Control and Prevention, Cheongju, Korea
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26
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Jun JH, Hwang K, Kim SK, Oh HB, Cho MC, Lee KJ. Estimation of the 6-digit level allele and haplotype frequencies of HLA-A, -B, and -C in Koreans using ambiguity-solving DNA typing. ACTA ACUST UNITED AC 2014; 84:277-84. [PMID: 24851935 DOI: 10.1111/tan.12368] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2013] [Revised: 03/31/2014] [Accepted: 04/15/2014] [Indexed: 01/20/2023]
Abstract
Because Korean society is fast becoming multi-ethnic, the determination of ambiguous human leukocyte antigen (HLA) types using HLA allele frequencies is becoming less applicable. In this study, we focused on the development of new technical methods to directly resolve the ambiguities arising from HLA genotyping. One hundred and fifty unrelated healthy Korean adults were included in this study. All alleles from each HLA locus were first divided into 2-4 groups, with each group amplified in a single PCR tube (multi-group-specific amplification, MGSA). To resolve phase ambiguities, some allele groups were also amplified separately in small group-specific amplification (SGSA) tubes. In order to then resolve incomplete sequence ambiguities, primers for MGSA and SGSA were initially designed to cover additional exons. If needed, a heterozygous ambiguity resolving primer (HARP) or sequence specific primer (SSP) was also used. When MGSA and SGSA methods were applied, the rate of phase ambiguity was greatly reduced to an average of 6% (1.3% in HLA-A, 15.7% in -B, and 2.0% in -C). Additional HARP and SSP methods could resolve all the phase ambiguities. Using our proposed method, we also detected three alleles that have not been previously reported in Korea, C*04:82, C*07:18, and C*08:22, and report 6-digit level HLA allele and haplotype frequencies among Koreans. In conclusion, the use of MGSA/SGSA for the initial amplification step is a cost-effective method facilitating timely and accurate reporting, given the continuing increase in the ethnic diversity of the Korean population. The MGSA described here can be applicable to various populations and thus could be shared by the majority of HLA typing laboratories. However, efforts to solve HLA ambiguity should continue, because SGSA, HARPs and SSPs would be specific to a particular population.
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Affiliation(s)
- J-H Jun
- Life Science Institute of Biowithus, Seoul, South Korea
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27
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Lee HS. Association of Human Leukocyte Antigen-DRB1 with Juvenile Idiopathic Arthritis. JOURNAL OF RHEUMATIC DISEASES 2014. [DOI: 10.4078/jrd.2014.21.5.225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
- Hye-Soon Lee
- Division of Rheumatology, Hanyang University Guri Hospital, Department of Internal Medicine, Hanyang University College of Medicine, Guri, Korea
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