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Chou WH, Chen LC, Wong HSC, Chao CH, Chu HW, Chang WC. Phenomic landscape and pharmacogenomic implications for HLA region in a Taiwan Han Chinese population. Biomark Res 2024; 12:46. [PMID: 38702819 PMCID: PMC11067262 DOI: 10.1186/s40364-024-00591-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Accepted: 04/18/2024] [Indexed: 05/06/2024] Open
Abstract
BACKGROUND The human leukocyte antigen (HLA) genes, exhibiting significant genetic diversity, are associated with susceptibility to various clinical diseases and diverse in drug responses. High costs of HLA sequencing and the population-specific architecture of this genetic region necessitate the establishment of a population-specific HLA imputation reference panel. Moreover, there is a lack of understanding about the genetic and phenotypic landscape of HLA variations within the Taiwanese population. METHODS We created models for a Taiwanese-specific HLA imputation reference panel. These models were trained with the array genotype data and HLA sequencing data from 845 Taiwanese subjects. HLA imputation was applied for 59,448 Taiwanese subjects to characterize the HLA allele and haplotype frequencies. Additionally, a phenome-wide association study (PheWAS) was conducted to identify the phenotypes associated with HLA variations. The association of the biallelic HLA variants with the binary and quantitative traits were evaluated with additive logistic and linear regression models, respectively. Furthermore, an omnibus test with likelihood-ratio test was applied for each HLA amino acid position in the multiallelic HLA amino acid polymorphisms to compare the difference between a fitted model and a null model following a χ2 distribution of n-1 degree of freedom at a position with n residues. Finally, we estimated the prevalence of adverse drug reactions (ADR)-related HLA alleles in the Taiwanese population. RESULTS In this study, the reference panel models displayed remarkable accuracy, with averages of 99.3%, 98.9%, and 99.1% for 2-, 4-, 6-digit alleles of the eight classical HLA genes, respectively. For PheWAS, a total of 18,136 significant associations with HLA variants across 26 phenotypes are identified (p < 5×10-8), highlighting the pleiotropy feature of the HLA region. Among the independent signals, 15 are novel, including the association of HLA-B pos 138 variation with ankylosing spondylitis (AS), and rs9266290 and rs9266292 with allergy. Through an analysis spanning the entire HLA region, we identified clusters of phenotype correlations. Finally, the carriers of pharmacogenomic related HLA alleles, including HLA-C*01:02 (35.86%), HLA-B*58:01 (20.9%), and HLA-B*15:02 (8.38%), were characterized in the Taiwanese general population. CONCLUSIONS We successfully delivered the HLA imputation for 59,448 Taiwanese subjects and characterized the genetic and phenotypic landscapes of the HLA variations. In addition, we quantified the estimated prevalence of the ADR-related HLA alleles in the Taiwanese population. The developed HLA imputation reference panel could be used for estimation of population HLA allele frequencies, which can facilitate further studies in the role of HLA variants in a wider range of phenotypes in the population.
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Affiliation(s)
- Wan-Hsuan Chou
- Department of Clinical Pharmacy, School of Pharmacy, Taipei Medical University, Taipei, Taiwan
| | - Lu-Chun Chen
- Department of Clinical Pharmacy, School of Pharmacy, Taipei Medical University, Taipei, Taiwan
| | - Henry Sung-Ching Wong
- Department of Clinical Pharmacy, School of Pharmacy, Taipei Medical University, Taipei, Taiwan
| | - Ching-Hsuan Chao
- Department of Clinical Pharmacy, School of Pharmacy, Taipei Medical University, Taipei, Taiwan
| | - Hou-Wei Chu
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Wei-Chiao Chang
- Department of Clinical Pharmacy, School of Pharmacy, Taipei Medical University, Taipei, Taiwan.
- Master Program in Clinical Genomics and Proteomics, School of Pharmacy, Taipei Medical University, Taipei, Taiwan.
- Integrative Research Center for Critical Care, Wan Fang Hospital, Taipei Medical University, Taipei, Taiwan.
- Department of Pharmacy, Wan Fang Hospital, Taipei Medical University, Taipei, Taiwan.
- Department of Pharmacology, National Defense Medical Center, Taipei, Taiwan.
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Liao WL, Liu TY, Cheng CF, Chou YP, Wang TY, Chang YW, Chen SY, Tsai FJ. Analysis of HLA Variants and Graves' Disease and Its Comorbidities Using a High Resolution Imputation System to Examine Electronic Medical Health Records. Front Endocrinol (Lausanne) 2022; 13:842673. [PMID: 35321340 PMCID: PMC8936090 DOI: 10.3389/fendo.2022.842673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Accepted: 02/04/2022] [Indexed: 11/13/2022] Open
Abstract
Hyperthyroidism is a prevalent endocrine disorder, and genetics play a major role in the development of thyroid-associated diseases. In particular, the inheritance of HLA has been demonstrated to induce the highest susceptibility to Graves' disease (GD). However, thus far, no studies have reported the contribution of HLA to the development of GD and the complications that follow. Thus, in the present study, to the best of our knowledge, for the first time, a powerful imputation method, HIBAG, was used to predict the HLA subtypes among populations with available genome-wide SNP array data from the China Medical University Hospital (CMUH). The disease status was extracted from the CMUH electronic medical records; a total of 2,998 subjects with GD were identified as the cases to be tested and 29,083 subjects without any diagnosis of thyroid disorders were randomly selected as the controls. A total of 12 HLA class I genotypes (HLA-A*02:07-*11:01, HLA-B*40:01-*46:01 and *46:01-*46:01, and HLA-C*01:02-*01:02, *01:02-*03:04, and *01:02-*07:02) and 17 HLA class II genotypes (HLA-DPA1*02:02-*02:02, HLA-DPB1*02:01-*05:01, *02:02-*05:01, and *04:01-*05:01, HLA-DQA1*03:02, HLA-DRB1*09:01-*15:01, and *09:01-*09:01) were found to be associated with GD in the Taiwanese population. Moreover, the HLA subtypes HLA-A*11:01, HLA-B*46:01, HLA-DPA1*01:03, and HLA-DPB1*05:01 were found to be associated with heart disease, stroke, diabetes, and hypertension among subjects with GD. Our data suggest that several HLA alleles are markedly associated with GD and its comorbidities, including heart disease, hypertension, and diabetes.
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Affiliation(s)
- Wen-Ling Liao
- Graduate Institute of Integrated Medicine, College of Chinese Medicine, China Medical University, Taichung, Taiwan
- Center for Personalized Medicine, China Medical University Hospital, Taichung, Taiwan
| | - Ting-Yuan Liu
- Center for Precision Medicine, China Medical University Hospital, Taichung, Taiwan
| | - Chi-Fung Cheng
- Genetic Center, Department of Medical Research, China Medical University Hospital, Taichung, Taiwan
| | - Yu-Pao Chou
- Center for Precision Medicine, China Medical University Hospital, Taichung, Taiwan
- Department of Laboratory Medicine, China Medical University Hospital, Taichung, Taiwan
| | - Tzu-Yuan Wang
- Division of Endocrine and Metabolism, China Medical University Hospital, Taichung, Taiwan
| | - Ya-Wen Chang
- Graduate Institute of Integrated Medicine, College of Chinese Medicine, China Medical University, Taichung, Taiwan
- Genetic Center, Department of Medical Research, China Medical University Hospital, Taichung, Taiwan
| | - Shih-Yin Chen
- Genetic Center, Department of Medical Research, China Medical University Hospital, Taichung, Taiwan
- School of Chinese Medicine, China Medical University, Taichung, Taiwan
- *Correspondence: Shih-Yin Chen, ; Fuu-Jen Tsai,
| | - Fuu-Jen Tsai
- Genetic Center, Department of Medical Research, China Medical University Hospital, Taichung, Taiwan
- School of Chinese Medicine, China Medical University, Taichung, Taiwan
- *Correspondence: Shih-Yin Chen, ; Fuu-Jen Tsai,
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Ueta M. Findings by an International Collaboration on SJS/TEN With Severe Ocular Complications. Front Med (Lausanne) 2021; 8:649661. [PMID: 34926478 PMCID: PMC8672139 DOI: 10.3389/fmed.2021.649661] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Accepted: 11/04/2021] [Indexed: 12/19/2022] Open
Abstract
Stevens-Johnson Syndrome (SJS) is an acute inflammatory vesiculobullous reaction of the skin and mucosa, e.g., the ocular surface, oral cavity, and genitals. In patients with extensive skin detachment and a poor prognosis, the condition is called toxic epidermal necrolysis (TEN). Not all, but some patients with SJS/TEN manifest severe ocular lesions. Approximately 50% of SJS/TEN patients diagnosed by dermatologists and in burn units suffer from severe ocular complications (SOC) such as severe conjunctivitis with pseudomembrane and ocular surface epithelial defects in the acute stage. In the chronic stage, this results in sequelae such as severe dry eye and visual disturbance. Before 2005, our group of Japanese scientists started focusing on ophthalmic SJS/TEN with SOC. We found that cold medicines were the main causative drugs of SJS/TEN with SOC and that in Japanese patients, HLA-A * 02:06 and HLA-B * 44:03 were significantly associated with cold medicine-related SJS/TEN with SOC (CM-SJS/TEN with SOC). We expanded our studies and joined scientists from Korea, Brazil, India, Taiwan, Thailand, and the United Kingdom in an international collaboration to detect the genetic predisposition for SJS/TEN with SOC. This collaboration suggested that in Japanese patients, cold medicines, including NSAIDs, were the main causative drugs, and that HLA-A * 02:06 was implicated in Japanese and Korean patients and HLA-B * 44:03 in Japanese-, Indian-, and European ancestry Brazilian patients. Our joint findings reveal that there are ethnic differences in the HLA types associated with SJS/TEN with SOC.
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Affiliation(s)
- Mayumi Ueta
- Department of Ophthalmology, Kyoto Prefectural University of Medicine, Kyoto, Japan
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Ma KSK, Chung WH, Hsueh YJ, Chen SY, Tokunaga K, Kinoshita S, Ma DHK, Ueta M. Human leucocyte antigen association of patients with Stevens-Johnson syndrome/toxic epidermal necrolysis with severe ocular complications in Han Chinese. Br J Ophthalmol 2021; 106:610-615. [PMID: 33441319 DOI: 10.1136/bjophthalmol-2020-317105] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Revised: 12/15/2020] [Accepted: 12/19/2020] [Indexed: 12/17/2022]
Abstract
BACKGROUND/AIMS Stevens-Johnson syndrome/toxic epidermal necrolysis (SJS/TEN) induced by cold medicine (CM) may result in severe ocular complications (SOCs). The purpose of this study was to investigate the human leucocyte antigen (HLA) polymorphism pattern in CM-induced patients with SJS/TEN developing SOCs. METHODS All participants, including patients with SJS/TEN (n=33) and control patients (n=98), were enrolled through visits to the clinic from 2016 to 2017. SOCs were diagnosed (n=26) via a chart review or eye examination. Patient saliva was collected with commercialised kits and genotyped with PCR assays followed by hybridisation with sequence-specific oligonucleotide (SSO) probes (PCR-SSO) using commercial bead-based typing kits. RESULTS In all patients with SJS/TEN with SOCs, the HLA-A*02:07 carrier frequency was significantly higher than that in controls (OR=3.24, 95% CI=1.09 to 9.60, p=0.049), as was the genotype frequency (OR=3.89, 95% CI=1.49 to 10.16, p=0.007). In patients with CM-SJS/TEN with SOCs, the HLA-A*02:07 carrier frequency was higher than that in controls (OR=5.56, 95% CI=1.52 to 20.00, p=0.016), as was the allele frequency (OR=6.67, 95% CI=2.33 to 20.00, p=0.001). In patients with CM-SJS/TEN with SOCs, the HLA-B*46:01 allele frequency was significantly higher than that in controls (OR=3.85, 95% CI=1.52 to 10.00, p=0.008). CONCLUSIONS The HLA-A*02:07 and HLA-B*46:01 alleles were significantly associated with SOCs among Han Chinese patients with CM-SJS/TEN. These findings demonstrate the genetic diversity in SJS pathogenesis among different ethnic groups.
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Affiliation(s)
- Kevin Sheng-Kai Ma
- Department of Life Science, National Taiwan University, Taipei, Taiwan.,Limbal Stem Cell Laboratory, Department of Ophthalmology, Chang Gung Memorial Hospital Linkou Main Branch, Taoyuan, Taiwan
| | - Wen Hung Chung
- Department of Dermatology, Chang Gung Memorial Hospital Linkou Main Branch, Taoyuan, Taiwan.,Department of Dermatology, Xiamen Chang Gung Hospital, Xiamen, Fujian, China.,Drug Hypersensitivity Clinical and Research Center, Chang Gung Memorial Hospital, Linkou, Taoyuan, Taiwan.,Graduate Institute of Clinical Medical Sciences, College of Medicine, Chang Gung University, Kwei-Shan, Taoyuan, Taiwan.,Cancer Vaccine and Immune Cell Therapy Core Laboratory, Chang Gung Memorial Hospital, Linkou, Taoyuan, Taiwan.,Immune-Oncology Center of Excellence, Chang Gung Memorial Hospital, Linkou, Taoyuan, Taiwan
| | - Yi-Jen Hsueh
- Limbal Stem Cell Laboratory, Department of Ophthalmology, Chang Gung Memorial Hospital Linkou Main Branch, Taoyuan, Taiwan
| | - Shin-Yi Chen
- Department of Ophthalmology, Keelung Chang Gung Memorial Hospital of the CGMF, Keelung, Taiwan
| | - Katsushi Tokunaga
- Department of Human Genetics, The University of Tokyo Graduate School of Medicine Faculty of Medicine, Bunkyo-ku, Tokyo, Japan
| | - Shigeru Kinoshita
- Department of Ophthalmology, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - David H K Ma
- Limbal Stem Cell Laboratory, Department of Ophthalmology, Chang Gung Memorial Hospital Linkou Main Branch, Taoyuan, Taiwan .,Department of Ophthalmology, Xiamen Chang Gung Hospital, Xiamen, Fujian, China.,Department of Chinese Medicine, College of Medicine, Chang Gung University, Kwei-Shan, Taoyuan, Taiwan.,Center for Tissue Engineering, Chang Gung Memorial Hospital, Linkou, Taoyuan, Taiwan
| | - Mayumi Ueta
- Department of Frontier Medical Science and Technology for Ophthalmology, Kyoto Prefectural University of Medicine, Kyoto, Japan
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Huang YH, Khor SS, Zheng X, Chen HY, Chang YH, Chu HW, Wu PE, Lin YJ, Liao SF, Shen CY, Tokunaga K, Lee MH. A high-resolution HLA imputation system for the Taiwanese population: a study of the Taiwan Biobank. THE PHARMACOGENOMICS JOURNAL 2020; 20:695-704. [PMID: 32042094 DOI: 10.1038/s41397-020-0156-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Revised: 01/22/2020] [Accepted: 01/27/2020] [Indexed: 12/24/2022]
Abstract
An imputation algorithm for human leukocyte antigen (HLA) is helpful for exploring novel disease associations. However, population-specific HLA imputation references are essential for achieving high imputation accuracy. In this study, a subset of 1012 individuals from the Taiwan Biobank (TWB) who underwent both whole-genome SNP array and NGS-based HLA typing were used to establish Taiwanese HLA imputation references. The HIBAG package was used to generate the imputation references for eight HLA loci at a two- and three-field resolution. Internal validation was carried out to evaluate the call threshold and accuracy for each HLA gene. HLA class II genes found to be associated with rheumatoid arthritis (RA) were validated in this study by the imputed HLA alleles. Our Taiwanese population-specific references achieved average HLA imputation accuracies of 98.11% for two-field and 98.08% for three-field resolution. The frequency distribution of imputed HLA alleles among 23,972 TWB subjects were comparable with PCR-based HLA alleles in general Taiwanese reported in the allele frequency net database. We replicated four common HLA alleles (HLA-DRB1*03:01, DRB1*04:05, DQA1*03:03, and DQB1*04:01) significantly associated with RA. The population-specific references provide an informative tool to investigate the associations of HLA variants and human diseases in large-scale population-based studies.
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Affiliation(s)
- Yu-Han Huang
- Institute of Clinical Medicine, National Yang-Ming University, Taipei, Taiwan
| | - Seik-Soon Khor
- Department of Human Genetics, Graduate School of Medicine, the University of Tokyo, Toyo, Japan
| | - Xiuwen Zheng
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Hsuan-Yu Chen
- Institute of Statistical Science, Academia Sinica, Taipei, Taiwan
| | - Ya-Hsuan Chang
- Institute of Statistical Science, Academia Sinica, Taipei, Taiwan
| | - Hou-Wei Chu
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Pei-Ei Wu
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Yu-Ju Lin
- Institute of Clinical Medicine, National Yang-Ming University, Taipei, Taiwan
| | - Shu-Fen Liao
- Institute of Clinical Medicine, National Yang-Ming University, Taipei, Taiwan.,Institute of Statistical Science, Academia Sinica, Taipei, Taiwan
| | - Chen-Yang Shen
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Katsushi Tokunaga
- Department of Human Genetics, Graduate School of Medicine, the University of Tokyo, Toyo, Japan.
| | - Mei-Hsuan Lee
- Institute of Clinical Medicine, National Yang-Ming University, Taipei, Taiwan.
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HLA concordance between hematopoietic stem cell transplantation patients and umbilical cord blood units: Implications for cord blood banking in admixed populations. Hum Immunol 2019; 80:714-722. [PMID: 31101373 DOI: 10.1016/j.humimm.2019.05.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Revised: 05/01/2019] [Accepted: 05/10/2019] [Indexed: 11/22/2022]
Abstract
Umbilical cord blood stem cell transplantation is an important choice for treating a variety of hematopoietic, neoplastic, and genetic disorders. The optimal size for a cord blood bank to provide matching units for 80% of patients requiring a stem cell transplantation procedure depends on the particular characteristics of each population. In this study, we analyzed the immunogenetic diversity of a sample set of Mexican patients suffering from blood, hematopoietic, and immunological diseases, to assess the best strategy for cord blood banking. For achieving that, we analyzed HLA-A, HLA-B, HLA-DRB1, and HLA-DQB1 genotype and allele frequencies of both units from the bioarchive of the Umbilical Cord Blood Bank from La Raza and patients requiring a stem cell transplant and compared these variables with data from the same geographic and genetic context. We were able to detect significant differences for at least half of the alleles were observed for HLA class I and class II genes between units and patients. Five Native American haplotypes had lower frequencies in patients sample than in the cord blood units. Genetic admixture estimations for both groups showed a higher contribution of Native American component in the cord blood units. Differences in ancestral components in the Umbilical Cord Blood Bank from La Raza and six virtual banks modeled from a pool of Mexican mixed ancestry individuals show that genetic background is important in cord blood collection. In conclusion, increasing diversity over quantity of new cord blood units will improve the cost effectiveness of cord blood banking and health policies regarding hematopoietic stem cell transplantation in admixed populations such as those present in Latin American countries.
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Zhou S, Skaar DJ, Jacobson PA, Huang RS. Pharmacogenomics of Medications Commonly Used in the Intensive Care Unit. Front Pharmacol 2018; 9:1436. [PMID: 30564130 PMCID: PMC6289166 DOI: 10.3389/fphar.2018.01436] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Accepted: 11/20/2018] [Indexed: 12/11/2022] Open
Abstract
In the intensive care unit (ICU) setting, where highly variable and insufficient drug efficacies, as well as frequent and unpredictable adverse drug reactions (ADRs) occur, pharmacogenomics (PGx) offers an opportunity to improve health outcomes. However, PGx has not been fully evaluated in the ICU, partly due to lack of knowledge of how genetic markers may affect drug therapy. To fill in this gap, we conducted a review to summarize the PGx information for the medications commonly encountered in the ICU.
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Affiliation(s)
- Shuqin Zhou
- Department of Emergency and Critical Care Medicine, Shanghai Tenth People's Hospital, Tongji University, Shanghai, China.,Department of Experimental and Clinical Pharmacology, College of Pharmacy, University of Minnesota, Minneapolis, MN, United States
| | - Debra J Skaar
- Department of Experimental and Clinical Pharmacology, College of Pharmacy, University of Minnesota, Minneapolis, MN, United States
| | - Pamala A Jacobson
- Department of Experimental and Clinical Pharmacology, College of Pharmacy, University of Minnesota, Minneapolis, MN, United States
| | - R Stephanie Huang
- Department of Experimental and Clinical Pharmacology, College of Pharmacy, University of Minnesota, Minneapolis, MN, United States
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Yang KL, Zheng ZZ. Deduced probable human leukocyte antigen haplotypes associated with human leukocyte antigen DRB1*04:36 identified by case analysis of Taiwanese individuals. Tzu Chi Med J 2017; 29:12-17. [PMID: 28757758 PMCID: PMC5509187 DOI: 10.4103/tcmj.tcmj_8_17] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
Objective: Human leukocyte antigen (HLA) DRB1*04:36 is a low-frequency HLA-DRB1 allele. The aim here is to report the ethnicity of DRB1*04:36 and its associated HLA haplotypes among Taiwanese individuals. Materials and Methods: A sequence-based typing method was employed to confirm this low incidence allele. Polymerase chain reaction was performed to amplify exons 2 and 3 of the HLA-A and HLA-B loci and exon 2 of the HLA-DRB1 locus using group-specific primer sets. The amplicons were sequenced in both directions using BigDye Terminator Cycle Sequencing Ready Reaction kits and the manufacturer's protocols. One group of unrelated blood donors used in this study consists of randomized individuals with Taiwanese ethnicity who participate in the Tzu Chi Bone Marrow Donor Registry and the other group are randomized unrelated individuals from mainland China. The family members in the family part of the study are volunteer blood donors. Results: In exon 2, the DNA sequence of DRB1*04:36 is identical to DRB1*04:03:01 except for a nucleotide segment from residue 286 to residue 308. The nucleotide segment from residue 286 to residue 308, incidentally, is identical to that of DRB1*11:01:01:01. These observations suggest that DRB1*04:36 may have been derived through a gene recombination event involving DRB1*04:03:01 and DRB1*11:01:01:01. Our family study indicated that the HLA haplotype in association with DRB1*04:36 can be deduced to be A*24:02-B*39:01-DRB1*04:36. A randomized population study using Taiwanese suggests that additional DRB1*04:36 associated HLA haplotypes seem to exist. Conclusion: The information on the ethnicity of the DRB1**04:36 allele, and the deduced probable HLA haplotypes associated with the low incidence DRB1*04:36 allele that we report here, is of value to HLA testing laboratories for reference purposes. In addition, they can be used by stem cell transplantation donor search coordinators to aid the creation of strategy for finding compatible donors who are part of unrelated bone marrow donor registries when a patient carries this uncommon HLA allele.
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Affiliation(s)
- Kuo-Liang Yang
- Laboratory of Immunogenetics, Tzu Chi Cord Blood Bank and Buddhist Tzu Chi Marrow Donor Registry, Buddhist Tzu Chi Stem Cells Centre, Hualien Tzu Chi Hospital, Hualien, Taiwan.,Department of Laboratory Medicine, Buddhist Tzu Chi University, Hualien, Taiwan
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Yang KL, Chen HB. Using high-resolution human leukocyte antigen typing of 11,423 randomized unrelated individuals to determine allelic varieties, deduce probable human leukocyte antigen haplotypes, and observe linkage disequilibria between human leukocyte antigen-B and-C and human leukocyte antigen-DRB1 and-DQB1 alleles in the Taiwanese Chinese population. CI JI YI XUE ZA ZHI = TZU-CHI MEDICAL JOURNAL 2017; 29:84-90. [PMID: 28757772 PMCID: PMC5509198 DOI: 10.4103/tcmj.tcmj_35_17] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Objective: We report here the human leukocyte antigen (HLA) allelic variety and haplotype composition in a cohort of the Taiwanese Chinese population and their patterns of linkage disequilibria on HLA-B: HLA-C alleles and HLA-DRB1: HLA-DQB1 alleles at a high-resolution level. Materials and Methods: Peripheral whole blood from 11,423 Taiwanese Chinese unrelated individuals was collected in acid citrate dextrose. Genomic DNA was extracted using the QIAamp DNA Blood Mini Kit. The DNA material was subjected to HLA genotyping for HLA-A,-B,-C,-DRB1, and-DQB1 loci using a commercial polymerase chain reaction-sequence-based typing (PCR-SBT) kit, the SeCore® A/B/C/DRB1/DQB1 Locus Sequencing kit. High-resolution allelic sequencing was performed as previously described. Results: The number of individual HLA-B alleles detected was greater than the number of alleles recognized in the both the HLA-A and-DRB1 loci. Several novel alleles were discovered as a result of employing the SBT method and the high number of donors tested. In addition, we observed a genetic polymorphic feature of association between HLA-A and-B, HLA-B and-C, and HLA-DRB1 and-DQB1 alleles. Further, the homozygous haplotype frequencies of HLA-A and-B; HLA-A,-C, and-B; HLA-A,-C,-B, and-DRB1; and HLA-A,-C,-B,-DRB1, and-DQB1 in Taiwanese Chinese population are presented. Conclusion: As increasing number of HLA alleles are being discovered, periodic HLA profile investigation in a given population is essential to recognize the HLA complexity in that population. Population study can also provide an up-to-date strategic plan for future needs in terms of compatibility measurement for HLA matching between transplant donors and patients.
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Affiliation(s)
- Kuo-Liang Yang
- Laboratory of Immunogenetics, Tzu Chi Cord Blood Bank and Buddhist Tzu Chi Marrow Donor Registry, Buddhist Tzu Chi Stem Cells Centre, Hualien Tzu Chi Hospital, Hualien, Taiwan.,Department of Laboratory Medicine, Buddhist Tzu Chi University, Hualien, Taiwan
| | - Hsee-Bin Chen
- Laboratory of Immunogenetics, Tzu Chi Cord Blood Bank and Buddhist Tzu Chi Marrow Donor Registry, Buddhist Tzu Chi Stem Cells Centre, Hualien Tzu Chi Hospital, Hualien, Taiwan
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Yang KL, Zheng ZZ. Deduced probable human leukocyte antigen haplotypes associated with HLA-A*11:256Q and HLA-A*02:621 identified by case analyses of Taiwanese individuals. Tzu Chi Med J 2017; 29:197-200. [PMID: 29296047 PMCID: PMC5740691 DOI: 10.4103/tcmj.tcmj_124_17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Objective: HLA-A*11:256Q and HLA-A*02:621 are two low-frequency HLA-A alleles. The aim here is to report the ethnicity of A*11:256Q and A*02:621 and associated human leukocyte antigen (HLA) haplotypes among Taiwanese individuals. Materials and Methods: HLA data from randomized Taiwanese registered in the Tzu Chi Stem Cells Centre and China Shanghai Tissuebank Diagnostics were analyzed. HLA typing of the donors was carried out using a sequence-based typing method to confirm the two low-incidence alleles. Polymerase chain reaction was performed to amplify exons 2 and 3 of the HLA-A and HLA-B loci and exon 2 of the HLA-DRB1 locus using group-specific primer sets. The amplicons were sequenced in both directions using BigDye Terminator Cycle Sequencing Ready Reaction kits and the manufacturer's protocols. Exon 1 and exons 4-8 of the A*11:256Q allele were also sequenced and analyzed. Results: The Taiwanese ethnicity for both A*11:256Q and A*02:621 alleles was confirmed in this study. Further, the DNA sequence of A* 11:256Q was confirmed to be identical to A*11:02:01from exon 1 to exon 8 except for the residues from 409 to 417 where a segment of nine nucleotides (TACCGGCAG) is deleted in A*11:256Q. The HLA haplotype associated with A*11:256Q was deduced as A*11:256Q-B*27-DRB1*12. In exons 2 and 3, the DNA sequence of A*02:621 is identical to A*02:01:01:01 except at residue 169 where T of A*02:01:01:01 is replaced by C in A*02:621 (at codon 33; TTC->CTC). The HLA haplotype in association with A*02:621 was deduced as A*02:621-B*15:18-DRB1*12:02. Conclusion: The information on the ethnicity of the A*11:256Q and A*02:621 alleles and the deduced probable HLA haplotypes associated with the two low-incidence alleles reported here are valuable to HLA testing laboratories for reference purposes. In addition, they can be used by stem cell transplantation donor search coordinators to aid in finding compatible donors in unrelated bone marrow donor registries when a patient carries these uncommon HLA alleles.
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Affiliation(s)
- Kuo-Liang Yang
- Laboratory of Immunogenetics, Tzu Chi Cord Blood Bank and Buddhist Tzu Chi Marrow Donor Registry, Buddhist Tzu Chi Stem Cells Centre, Hualien Tzu Chi Hospital, Hualien, Taiwan.,Department of Laboratory Medicine, Tzu Chi University, Hualien, Taiwan
| | - Zheng-Zhong Zheng
- Department of Research, China Shanghai Tissuebank Diagnostics, Shanghai, China
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Chen YY, Chang JR, Huang WF, Hsu CH, Cheng HY, Sun JR, Kuo SC, Su IJ, Lin MS, Chen W, Dou HY. Genetic diversity of the Mycobacterium tuberculosis East African-Indian family in three tropical Asian countries. JOURNAL OF MICROBIOLOGY, IMMUNOLOGY, AND INFECTION = WEI MIAN YU GAN RAN ZA ZHI 2015; 50:886-892. [PMID: 26922173 DOI: 10.1016/j.jmii.2015.10.012] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2015] [Revised: 09/29/2015] [Accepted: 10/22/2015] [Indexed: 10/22/2022]
Abstract
BACKGROUND The Beijing lineage of Mycobacterium tuberculosis (MTB) is the most predominant MTB strain in Asian countries and is spreading worldwide, however, the East African-Indian (EAI) lineage is also particularly prevalent in many tropical Asian countries. The evolutionary relationships among MTB EAI isolates from Taiwan and those of tropical Asian countries remain unknown. METHODS The EAI strains collected from patients in Taiwan were analyzed using spacer oligonucleotide typing and mycobacterial interspersed repetitive unit-variable number of tandem repeats (MIRU-VNTR) typing, and compared with published profiles from Cambodia and Singapore to investigate potential epidemiological linkages. RESULTS Among the three countries, the EAI lineage was most prevalent in Cambodia (60%; Singapore, 25.62%; and Taiwan, 21.85%), having also the highest rates of multidrug resistance and lowest rates of clustering of MTB isolates. We describe a convenient method using seven selected MIRU-VNTR loci for first-line typing to discriminate Beijing and EAI lineages. A potential epidemiological linkage in these tropical Asian countries is also discussed based on a minimum-spanning tree constructed using 24 MIRU-VNTR loci of MTB EAI strains. CONCLUSION This study identified evolutionary relationships among MTB EAI isolates from Taiwan and those of two other tropical Asian countries, Cambodia and Singapore.
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Affiliation(s)
- Yih-Yuan Chen
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Zhunan, Miaoli, Taiwan, ROC; Department of Internal Medicine, Ditmanson Medical Foundation Chia-Yi Christian Hospital, Chia-Yi, Taiwan, ROC.
| | - Jia-Ru Chang
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Zhunan, Miaoli, Taiwan, ROC
| | - Wei-Feng Huang
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Zhunan, Miaoli, Taiwan, ROC
| | - Chih-Hao Hsu
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Zhunan, Miaoli, Taiwan, ROC
| | - Han-Yin Cheng
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Zhunan, Miaoli, Taiwan, ROC
| | - Jun-Ren Sun
- Division of Clinical Pathology, Department of Pathology, Tri-Service General Hospital and National Defense Medical Center, Taipei, Taiwan, ROC
| | - Shu-Chen Kuo
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Zhunan, Miaoli, Taiwan, ROC
| | - Ih-Jen Su
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Zhunan, Miaoli, Taiwan, ROC
| | - Ming-Shian Lin
- Department of Internal Medicine, Ditmanson Medical Foundation Chia-Yi Christian Hospital, Chia-Yi, Taiwan, ROC
| | - Wei Chen
- Department of Internal Medicine, Ditmanson Medical Foundation Chia-Yi Christian Hospital, Chia-Yi, Taiwan, ROC
| | - Horng-Yunn Dou
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Zhunan, Miaoli, Taiwan, ROC.
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Yang L, Chen X, Liu H, Chen Y, Zhao Y, Bu D, Zhu P. Donors with HLA-B*58:01/TNFα −308A haplotype are unfavorable to haploidentical hematopoietic stem cell transplantation in acute lymphoblastic leukemia. Transpl Immunol 2015; 32:92-8. [DOI: 10.1016/j.trim.2014.12.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2014] [Revised: 12/17/2014] [Accepted: 12/17/2014] [Indexed: 01/28/2023]
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13
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Ikeda N, Kojima H, Nishikawa M, Hayashi K, Futagami T, Tsujino T, Kusunoki Y, Fujii N, Suegami S, Miyazaki Y, Middleton D, Tanaka H, Saji H. Determination of HLA-A, -C, -B, -DRB1 allele and haplotype frequency in Japanese population based on family study. ACTA ACUST UNITED AC 2015; 85:252-9. [PMID: 25789826 PMCID: PMC5054903 DOI: 10.1111/tan.12536] [Citation(s) in RCA: 124] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2014] [Revised: 01/14/2015] [Accepted: 02/03/2015] [Indexed: 12/15/2022]
Abstract
The present study investigates the human leucocyte antigen (HLA) allele and haplotype frequencies in Japanese population. We carried out the frequency analysis in 5824 families living across Japanese archipelago. The studied population has mainly been typed for the purpose of transplant, especially the hematopoietic stem cell transplantation (HSCT). We determined HLA class I (A, B, and C) and HLA class II (DRB1) using Luminex technology. The haplotypes were directly counted by segregation. A total of 44 HLA‐A, 29 HLA‐C, 75 HLA‐B, and 42 HLA‐DRB1 alleles were identified. In the HLA haplotypes of A‐C‐B‐DRB1 and C‐B, the pattern of linkage disequilibrium peculiar to Japanese population has been confirmed. Moreover, the haplotype frequencies based on family study was compared with the frequencies estimated by maximum likelihood estimation (MLE), and the equivalent results were obtained. The allele and haplotype frequencies obtained in this study could be useful for anthropology, transplantation therapy, and disease association studies.
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Affiliation(s)
- N Ikeda
- HLA Foundation Laboratory, Kyoto, Japan
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14
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Genin E, Chen DP, Hung SI, Sekula P, Schumacher M, Chang PY, Tsai SH, Wu TL, Bellón T, Tamouza R, Fortier C, Toubert A, Charron D, Hovnanian A, Wolkenstein P, Chung WH, Mockenhaupt M, Roujeau JC. HLA-A*31:01 and different types of carbamazepine-induced severe cutaneous adverse reactions: an international study and meta-analysis. THE PHARMACOGENOMICS JOURNAL 2013; 14:281-8. [DOI: 10.1038/tpj.2013.40] [Citation(s) in RCA: 154] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2013] [Revised: 10/18/2013] [Accepted: 10/29/2013] [Indexed: 01/22/2023]
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15
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Zúñiga J, Yu N, Barquera R, Alosco S, Ohashi M, Lebedeva T, Acuña-Alonzo V, Yunis M, Granados-Montiel J, Cruz-Lagunas A, Vargas-Alarcón G, Rodríguez-Reyna TS, Fernandez-Viña M, Granados J, Yunis EJ. HLA class I and class II conserved extended haplotypes and their fragments or blocks in Mexicans: implications for the study of genetic diversity in admixed populations. PLoS One 2013; 8:e74442. [PMID: 24086347 PMCID: PMC3781075 DOI: 10.1371/journal.pone.0074442] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2013] [Accepted: 07/31/2013] [Indexed: 01/03/2023] Open
Abstract
Major histocompatibility complex (MHC) genes are highly polymorphic and informative in disease association, transplantation, and population genetics studies with particular importance in the understanding of human population diversity and evolution. The aim of this study was to describe the HLA diversity in Mexican admixed individuals. We studied the polymorphism of MHC class I (HLA-A, -B, -C), and class II (HLA-DRB1, -DQB1) genes using high-resolution sequence based typing (SBT) method and we structured the blocks and conserved extended haplotypes (CEHs) in 234 non-related admixed Mexican individuals (468 haplotypes) by a maximum likelihood method. We found that HLA blocks and CEHs are primarily from Amerindian and Caucasian origin, with smaller participation of African and recent Asian ancestry, demonstrating a great diversity of HLA blocks and CEHs in Mexicans from the central area of Mexico. We also analyzed the degree of admixture in this group using short tandem repeats (STRs) and HLA-B that correlated with the frequency of most probable ancestral HLA-C/−B and -DRB1/−DQB1 blocks and CEHs. Our results contribute to the analysis of the diversity and ancestral contribution of HLA class I and HLA class II alleles and haplotypes of Mexican admixed individuals from Mexico City. This work will help as a reference to improve future studies in Mexicans regarding allotransplantation, immune responses and disease associations.
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Affiliation(s)
- Joaquín Zúñiga
- Department of Immunology, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Mexico City, Mexico
| | - Neng Yu
- HLA Laboratory, The American Red Cross Northeast Division, Dedham, Massachusetts, United States of America
| | - Rodrigo Barquera
- Molecular Genetics Laboratory, National School of Anthropology and History, Mexico City, Mexico
| | - Sharon Alosco
- HLA Laboratory, The American Red Cross Northeast Division, Dedham, Massachusetts, United States of America
| | - Marina Ohashi
- HLA Laboratory, The American Red Cross Northeast Division, Dedham, Massachusetts, United States of America
| | - Tatiana Lebedeva
- HLA Laboratory, The American Red Cross Northeast Division, Dedham, Massachusetts, United States of America
| | - Víctor Acuña-Alonzo
- Molecular Genetics Laboratory, National School of Anthropology and History, Mexico City, Mexico
| | - María Yunis
- Department of Cancer Immunology and AIDS, Dana Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Julio Granados-Montiel
- Tissue Engineering, Cell Therapy and Regenerative Medicine Research Unit, Instituto Nacional de Rehabilitación, Mexico City, Mexico
| | - Alfredo Cruz-Lagunas
- Department of Immunology, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Mexico City, Mexico
| | - Gilberto Vargas-Alarcón
- Laboratory of Genomics, Instituto Nacional de Cardiología Ignacio Chavez, Mexico City, Mexico
| | - Tatiana S. Rodríguez-Reyna
- Department of Immunology and Rheumatology, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, Mexico
| | - Marcelo Fernandez-Viña
- Department of Pathology, Stanford University, Stanford, California, United States of America
| | - Julio Granados
- Department of Transplantation, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, Mexico
- * E-mail: (EJY); (JG)
| | - Edmond J. Yunis
- Department of Cancer Immunology and AIDS, Dana Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, United States of America
- * E-mail: (EJY); (JG)
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Wang F, He J, Chen S, Qin F, Dai B, Zhang W, Zhu FM, Lv HJ. HLA-A, HLA-B, HLA-DRB1 allele and haplotype frequencies in 6384 umbilical cord blood units and transplantation matching and engraftment statistics in the Zhejiang cord blood bank of China. Int J Immunogenet 2013; 41:13-9. [PMID: 23731569 DOI: 10.1111/iji.12064] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2012] [Revised: 03/21/2013] [Accepted: 05/15/2013] [Indexed: 11/30/2022]
Abstract
Umbilical cord blood (UCB) is a widely accepted source of progenitor cells, and now, many cord blood banks were established. Here, we analysed the HLA-A, HLA-B and HLA-DRB1 allele and haplotype frequencies, HLA matching possibilities for searching potential donors and outcome of UCB transplantations in Zhejiang cord blood bank of China. A total of 6384 UCB units were characterized for 17 HLA-A, 30 HLA-B and 13 HLA-DRB1 alleles at the first field resolution level. Additionally, B*14, B*15 and B*40 were typed to the second field level. A total of 1372 distinct A-B-DRB1 haplotypes were identified. The frequencies of 7 haplotypes were more than 1%, and 439 haplotypes were <0.01%. A*02-B*46-DRB1*09, A*33-B*58-DRB1*03 and A*30-B*13-DRB1*07 were the most common haplotypes, with frequencies of 4.4%, 3.3%, and 2.9%, respectively. Linkage disequilibrium(LD) analysis showed that there were 83 A-B, 106 B-DRB1, 54 A-DRB1 haplotypes with positive LD, in which 51 A-B, 60 B-DRB1, 32 A-DRB1 haplotypes exhibited a significant LD (P < 0.05). In 682 search requests, 12.9%, 40.0% and 42.7% of patients were found to have 6 of 6, 5 of 6 and 4 of 6 HLA-A, HLA-B and HLA-DRB1 matching donors, respectively. A total of 30 UCB units were transplanted to 24 patients (3 patients not evaluated due to early death); 14 of 21 patients (66.7%) engrafted. This study reveals the HLA distribution and its transplantation application in the cord blood bank of Zhejiang province. These data can help to select potential UCB donors for transplantation and used to assess the scale of new cord blood banking endeavours.
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Affiliation(s)
- F Wang
- Blood Center of Zhejiang Province, Hangzhou, Zhejiang, China; Key laboratory of blood safety research, Ministry of Health, Hangzhou, Zhejiang, China
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Yang KL, Lee SK, Lin PY. Probable HLA haplotypes in association with the uncommon HLA-C*03:36, -C*03:56, and -C*03:86 alleles in a Taiwanese population. Tzu Chi Med J 2013. [DOI: 10.1016/j.tcmj.2013.02.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
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18
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Yao Y, Shi L, Tao Y, Kulski JK, Lin K, Huang X, Xiang H, Chu J, Shi L. Distinct HLA allele and haplotype distributions in four ethnic groups of China. ACTA ACUST UNITED AC 2013; 80:452-61. [PMID: 23020309 DOI: 10.1111/tan.12007] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Distinct human leukocyte antigen (HLA) allele and haplotype distributions occur in the northern and southern Han populations of China. However, different ethnic groups in China show limited regional distributions for many HLA alleles and haplotypes. Therefore, it is necessary and meaningful to study the differences in HLA allele and haplotype distribution for northern and southern ethnic groups of China. A total of 428 unrelated individuals from the Lisu, Nu, Tu and Yugur ethnic populations were genotyped for HLA-A, -B, -C and -DRB1 alleles using the PCR-Luminex typing method. The frequencies of HLA alleles and statistically inferred haplotypes were calculated. A total of 29 HLA-A, 54 HLA-B, 27 HLA-C and 41 HLA-DRB1 alleles were spread throughout these four populations with distinct allele and deduced haplotype frequencies between populations. Some alleles and deduced haplotypes exhibited significantly different distributions between northern (Tu and Yugur) and southern groups (Lisu and Nu). A phylogenetic tree and principal component analysis were used to compare the HLA polymorphism between our dataset and 19 other eastern and southeastern Asian populations. This analysis showed that Lisu and Nu belong to a cluster of southern ethnic groups, while Tu and Yugur are most closely related to other northern groups. Thus, distinct ethnic population histories were revealed by analyzing HLA allelic polymorphisms with the HLA profiles of the Lisu and Nu southern Chinese ethnic groups clearly different from the Tu and Yugur northern ethnic groups. The results will be useful for future association studies of infectious disease and contribute toward a more efficient search of organ/tissue matches for transplantation.
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Affiliation(s)
- Y Yao
- Institute of Medical Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Kunming, 650118, China
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19
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Yang KL, Lee SK, Lin PY. Discovery of the rare HLA-B*39:77 allele in an unrelated Taiwanese bone marrow stem cell donor using the sequence-based typing method. Int J Immunogenet 2013; 40:331-4. [PMID: 23289951 DOI: 10.1111/iji.12036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2012] [Revised: 11/27/2012] [Accepted: 12/12/2012] [Indexed: 11/29/2022]
Abstract
We detected a rare HLA-B locus allele, B*39:77, in a Taiwanese unrelated marrow stem cell donor in our routine HLA sequence-based typing (SBT) exercise for a possible haematopoietic stem cell donation. In exons 2, 3 and 4, the DNA sequence of B*39:77 is identical to the sequence of B*39:01:01:01 except one nucleotide at nucleotide position 733 (G->A) in exon 4. The nucleotide variation caused one amino acid alteration at residue 221 (Gly->Ser). B*39:77 was probably derived from a nucleotide substitution event involving B*39:01:01:01. The probable HLA-A, -B, -C, -DRB1 and -DQB1 haplotype in association with B*39:77 may be deduced as A*02:01-B*39:77-C*07:02-DRB1*08:03-DQB1*06:01. Our discovery of B*39:77 in Taiwanese adds further polymorphism of B*39 variants in Taiwanese population.
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Affiliation(s)
- K L Yang
- Laboratory of Immunogenetics and Cord Blood Bank, Buddhist Tzu Chi Stem Cells Centre and Marrow Donor Registry, Buddhist Tzu Chi General Hospital, Buddhist Compassion Relief Tzu Chi Foundation, Hualien, Taiwan.
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20
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Liu Y, Zhao Z, Li T, Liao Q, Kushner N, Touzjian NY, Shao Y, Sun Y, Strong AJ, Lu Y. High resolution human leukocyte antigen class I allele frequencies and HIV-1 infection associations in Chinese Han and Uyghur cohorts. PLoS One 2012; 7:e50656. [PMID: 23251376 PMCID: PMC3520934 DOI: 10.1371/journal.pone.0050656] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2012] [Accepted: 10/24/2012] [Indexed: 12/19/2022] Open
Abstract
Background Host immunogenetic factors such as HLA class I polymorphism are important to HIV-1 infection risk and AIDS progression. Previous studies using high-resolution HLA class I profile data of Chinese populations appeared insufficient to provide information for HIV-1 vaccine development and clinical trial design. Here we reported HLA class I association with HIV-1 susceptibility in a Chinese Han and a Chinese Uyghur cohort. Methodology/Principal Findings Our cohort included 327 Han and 161 Uyghur ethnic individuals. Each cohort included HIV-1 seropositive and HIV-1 seronegative subjects. Four-digit HLA class I typing was performed by sequencing-based typing and high-resolution PCR-sequence specific primer. We compared the HLA class I allele and inferred haplotype frequencies between HIV-1 seropositive and seronegative groups. A neighbor-joining tree between our cohorts and other populations was constructed based on allele frequencies of HLA-A and HLA-B loci. We identified 58 HLA-A, 75 HLA-B, and 32 HLA-Cw distinct alleles from our cohort and no novel alleles. The frequency of HLA-B*5201 and A*0301 was significantly higher in the Han HIV-1 negative group. The frequency of HLA-B*5101 was significantly higher in the Uyghur HIV-1 negative group. We observed statistically significant increases in expectation-maximization (EM) algorithm predicted haplotype frequencies of HLA-A*0201-B*5101 in the Uyghur HIV-1 negative group, and of Cw*0304-B*4001 in the Han HIV-1 negative group. The B62s supertype frequency was found to be significantly higher in the Han HIV-1 negative group than in the Han HIV-1 positive group. Conclusions At the four-digit level, several HLA class I alleles and haplotypes were associated with lower HIV-1 susceptibility. Homogeneity of HLA class I and Bw4/Bw6 heterozygosity were not associated with HIV-1 susceptibility in our cohort. These observations contribute to the Chinese HLA database and could prove useful in the development of HIV-1 vaccine candidates.
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Affiliation(s)
- Yanhou Liu
- Vaccine Laboratory, Nankai University, Tianjin, China
| | | | - Tianyi Li
- Vaccine Laboratory, Nankai University, Tianjin, China
| | - Qi Liao
- Vaccine Laboratory, Nankai University, Tianjin, China
| | - Nicholas Kushner
- Vaccine Technologies Inc., Wellesley, Massachusetts, United States of America
| | - Neal Y. Touzjian
- Vaccine Technologies Inc., Wellesley, Massachusetts, United States of America
| | - Yiming Shao
- National Center for AIDS Prevention and Control, Beijing, China
| | - Yongtao Sun
- Fourth Military Medical University, Tangdu Hospital, Xi'an, China
| | - Amie J. Strong
- Vaccine Technologies Inc., Wellesley, Massachusetts, United States of America
| | - Yichen Lu
- Vaccine Technologies Inc., Wellesley, Massachusetts, United States of America
- Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, Massachusetts, United States of America
- * E-mail:
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Yang KL, Lee SK, Lin PY. Identification of the novel HLA-B*40:221 allele in a Taiwanese hematopoietic stem cell donor using a sequence-based typing method. Int J Immunogenet 2012; 40:320-1. [PMID: 23130842 DOI: 10.1111/iji.12003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2012] [Accepted: 09/20/2012] [Indexed: 11/29/2022]
Abstract
Using DNA sequence-based typing method, we found a new HLA-B*40 variant, B*40:221, in a Taiwanese hematopoietic stem cell donor. The allele sequence of B*40:221 is identical to the sequence of B*40:01:01 in exons 2, 3 and 4 except the nucleotides at codon 265 (GGG→AGG). The sequence variation caused one amino acid exchange at residue 265 where Gly was replaced by Arg. The probable HLA-A, -B, -C, -DRB1 and -DQB1 haplotype in association with B*40:221 may be deduced as HLA-A*11:01-B*40:221-C*03:04-DRB1*14:54-DQB1*05:02. The generation of B*40:221 is thought as a result of a nucleotide point mutation involving B*40:01:01. Our discovery of B*40:221 increases the polymorphism of B*40 in Taiwanese.
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Affiliation(s)
- K L Yang
- Laboratory of Immunogenetics and Cord Blood Bank, Buddhist Tzu Chi Stem Cells Centre and Marrow Donor Registry, Buddhist Tzu Chi General Hospital, Buddhist Compassion Relief Tzu Chi Foundation, Hualien, Taiwan.
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22
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Yang KL, Lee SK, Kao RH, Lin CL, Lin PY. Discovery of the novel HLA-DRB1*04:05:14 allele in a Taiwanese unrelated haematopoietic stem cell donor by a sequence-based typing method. Int J Immunogenet 2012; 40:326-7. [DOI: 10.1111/iji.12010] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2012] [Revised: 07/09/2012] [Accepted: 09/26/2012] [Indexed: 11/27/2022]
Affiliation(s)
| | - S. K. Lee
- Laboratory of Immunogenetics and Cord Blood Bank; Buddhist Tzu Chi Stem Cells Centre and Marrow Donor Registry; Buddhist Tzu Chi General Hospital; Buddhist Compassion Relief Tzu Chi Foundation; Hualien; Taiwan
| | - R. H. Kao
- Laboratory of Immunogenetics and Cord Blood Bank; Buddhist Tzu Chi Stem Cells Centre and Marrow Donor Registry; Buddhist Tzu Chi General Hospital; Buddhist Compassion Relief Tzu Chi Foundation; Hualien; Taiwan
| | - C. L. Lin
- Laboratory of Immunogenetics and Cord Blood Bank; Buddhist Tzu Chi Stem Cells Centre and Marrow Donor Registry; Buddhist Tzu Chi General Hospital; Buddhist Compassion Relief Tzu Chi Foundation; Hualien; Taiwan
| | - P. Y. Lin
- Laboratory of Immunogenetics and Cord Blood Bank; Buddhist Tzu Chi Stem Cells Centre and Marrow Donor Registry; Buddhist Tzu Chi General Hospital; Buddhist Compassion Relief Tzu Chi Foundation; Hualien; Taiwan
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23
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Sun C, Wei L, Luo F, Li Y, Li J, Zhu F, Kang P, Xu R, Xiao L, Liu Z, Xu P. HLA-DRB1 alleles are associated with the susceptibility to sporadic Parkinson's disease in Chinese Han population. PLoS One 2012; 7:e48594. [PMID: 23139797 PMCID: PMC3490875 DOI: 10.1371/journal.pone.0048594] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2012] [Accepted: 09/26/2012] [Indexed: 12/19/2022] Open
Abstract
Immune disorders may play an important role in the pathogenesis of Parkinson's disease (PD). Recently, polymorphisms in the HLA-DR region have been found to be associated with sporadic PD in European ancestry populations. However, polymorphisms in the HLA complex are highly variable with ethnic and geographic origin. To explore the relationships between polymorphisms of the HLA-DR region and sporadic PD in Chinese Han population, we genotyped 567 sporadic PD patients and 746 healthy controls in two independent series for the HLA-DRB1 locus with Polymerase chain reaction-sequence based typing(PCR-SBT). The χ(2) test was used to evaluate the distribution of allele frequencies between the patients and healthy controls. The impact of HLA-DRB1 alleles on PD risk was estimated by unconditional logistic regression. We found a significant higher frequency of HLA-DRB1*0301 in sporadic PD patients than in healthy controls and a positive association, which was independent of onset age, between HLA-DRB1*0301 and PD risk. Conversely, a lower frequency of HLA-DRB1*0406 was found in sporadic PD patients than in healthy controls, with a negative association between HLA-DRB1*0406 and PD risk. Furthermore, a meta-analysis involving 195205 individuals was conducted to summarize the frequencies of these two alleles in populations from various ethnic regions, we found a higher frequency of HLA-DRB1*0301, but a lower frequency of HLA-DRB1*0406 in European ancestry populations than that in Asians, this was consistent with the higher prevalence of sporadic PD in European ancestry populations. Based on these results, we speculate that HLA-DRB1 alleles are associated with the susceptibility to sporadic PD in Chinese Han population, among them HLA-DRB1*0301 is a risk allele while the effect of HLA-DRB1*0406 deserves debate.
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Affiliation(s)
- Congcong Sun
- Department of Neurology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, People’s Republic of China
| | - Lei Wei
- Department of Neurology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, People’s Republic of China
- Department of Neurology, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, People’s Republic of China
| | - Feifei Luo
- Department of Neurology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, People’s Republic of China
- Department of Neurology, The Third People’s Hospital of Chengdu, Chengdu, People’s Republic of China
| | - Yi Li
- Department of Neurology, Department of Neurology, Red-Cross Hospital in Guangzhou, Guangzhou, People’s Republic of China
| | - Jiaobiao Li
- Department of Neurology, HeYuan City Hospital, Guangdong, People’s Republic of China
| | - Feiqi Zhu
- Department of Neurology, Yuebei People's Hospital of Shantou University Medical College, Guangdong, People’s Republic of China
| | - Ping Kang
- Department of Neurology, The First People’s Hospital of Shaoguan, Guangdong, People’s Republic of China
| | - Rensi Xu
- Department of Neurology, The First Affiliated Hospital of NanChang University, NanChang, People’s Republic of China
| | - LuLu Xiao
- Department of Tissue Typing Center, Nanfang Hospital of Southern Medical University, Guangzhou, People’s Republic of China
| | - Zhuolin Liu
- Department of Neurology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, People’s Republic of China
| | - Pingyi Xu
- Department of Neurology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, People’s Republic of China
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Yang KL, Lee SK, Yang SY, Kao RH, Lin CL, Lin PY. Discovery of HLA-DRB1*03:20 allele in a Taiwanese volunteer hematopoietic stem cell donor and the probable HLA-A, -B, -C and -DRB1 haplotype in association with DRB1*03:20. Int J Immunogenet 2012; 40:243-5. [PMID: 22925692 DOI: 10.1111/j.1744-313x.2012.01151.x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2012] [Revised: 07/23/2012] [Accepted: 07/25/2012] [Indexed: 11/29/2022]
Abstract
The allele HLA-DRB1*03:20, a variant of DRB1*03, was first reported to the IMGT HLA database in April 2001 without indication on the ethnicity of the blood donor (Cell ID: HC 125775). We found a Taiwanese volunteer hematopoietic stem cell donor carries DRB1*03:20 by a sequence-based typing (SBT) method. The DNA sequence of DRB1*03:20 is identical to the sequence of DRB1*03:01:01 in exon 2, except a nucleotide substitution at position 341(T→C) (GTT→GCT at codon 85). The nucleotide replacement produced an amino acid variation at residue 85 (V→A). We hypothesize that DRB1*03:20 was probably derived from DRB1*03:01:01 via a nucleotide point mutation event. The probable HLA haplotype in association with DRB1*03:20 was deduced as A*11:02-B*58:01-C*07:02-DRB1*03:20. We here report the Taiwanese/Chinese ethnicity of DRB1*03:20.
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Affiliation(s)
- K L Yang
- Laboratory of Immunogenetics and Cord Blood Bank, Buddhist Tzu Chi Stem Cells Centre and Marrow Donor Registry, Buddhist Tzu Chi General Hospital, Buddhist Compassion Relief Tzu Chi Foundation, Hualien, Taiwan.
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Yang KL, Lee SK, Lin PY. Identification of the novel HLA-B*13:02:13 allele in a Taiwanese haematopoietic stem cell donor and the probable HLA haplotype in association with B*13:02:13. Int J Immunogenet 2012; 40:241-2. [PMID: 22913841 DOI: 10.1111/j.1744-313x.2012.01154.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2012] [Revised: 07/23/2012] [Accepted: 07/25/2012] [Indexed: 11/27/2022]
Abstract
Using sequence-based typing method, we found a new HLA-B*13:02 variant, B*13:02:13, in a Taiwanese haematopoietic stem cell donor. The DNA sequence of B*13:02:13 is identical to the sequence of B*13:02:01 in exons 2 and 3 except the nucleotide at position 588 where G is replaced by T (codon 172; CTG→CTT). The DNA sequence variation did not alter the amino acid sequence of B*13:02:01. The generation of B*13:02:13 is thought to derive from B*13:02:01 as a result of a silence mutation. The probable HLA-A, HLA-B and HLA-DRB1 haplotype in association with B*13:02:1 may be deduced as HLA-A*24-B*13:02:13-DRB1*07:01 or HLA-A*02-B*13:02:13-DRB1*07:01. The discovery of B*13:02:13 furthers the polymorphism of HLA-B*13 and HLA-B*13:02.
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Affiliation(s)
- K L Yang
- Laboratory of Immunogenetics and Cord Blood Bank, Buddhist Tzu Chi Stem Cells Centre and Marrow Donor Registry, Buddhist Tzu Chi General Hospital, Buddhist Compassion Relief Tzu Chi Foundation, Hualien, Taiwan.
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Yang KL, Lee SK, Kao RH, Lin CL, Lin PY. Recognition of a Caucasoid HLA-B locus allele, B*44:55, in a Taiwanese/Chinese bone marrow stem cell donor. Int J Immunogenet 2012; 40:154-5. [PMID: 22862996 DOI: 10.1111/j.1744-313x.2012.01146.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2012] [Revised: 06/18/2012] [Accepted: 07/04/2012] [Indexed: 11/30/2022]
Abstract
We detected a Caucasoid HLA-B allele, HLA-B*44:55, in a potential Taiwanese/Chinese bone marrow hematopoietic stem cell donor during our routine HLA SBT (sequence-based typing) practice. The sequence of B*44:55 varies with B*44:02:01:01 with one nucleotide in exon 2 at position 97 (T->C), while it differs from B*44:03:01 with one nucleotide in exon 2 at position 97 (T->C) and three nucleotides in exon 3 at residues 538-540 (CTG->GAC). The nucleotide replacements caused one amino acid variation with B*44:02:01:01 at residue 9 (Y->H) and two amino acid variations with B*44:03:01 at residue 9 (Y->H) and residue 156 (L->D). The formation of B*44:55 is probably the result of a nucleotide substitution involving B*44:02:01:01 at position 97 (T->C). The Taiwanese/Chinese donor with B*44:55 claims having no kinship with Caucasian. Our speculations on the origin of the Taiwanese/Chinese B*44:55 will be presented.
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Affiliation(s)
- K L Yang
- Laboratory of Immunogenetics and Cord Blood Bank, Buddhist Tzu Chi Stem Cells Centre and Marrow Donor Registry, Buddhist Tzu Chi General Hospital, Buddhist Compassion Relief Tzu Chi Foundation, Hualien, Taiwan.
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Yang KL, Lee SK, Yang SY, Kao RH, Lin CL, Lin PY. Discovery of the novel HLA-DRB1*09:01:08 allele in a Taiwanese volunteer bone marrow donor and identification of the probable HLA-A, HLA-B and HLA-DRB1 haplotype in association with DRB1*09:01:08. Int J Immunogenet 2012; 40:149-50. [DOI: 10.1111/j.1744-313x.2012.01143.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2012] [Accepted: 06/28/2012] [Indexed: 11/30/2022]
Affiliation(s)
| | - S. K. Lee
- Laboratory of Immunogenetics and Cord Blood Bank; Buddhist Tzu Chi Stem Cells Centre and Marrow Donor Registry; Buddhist Tzu Chi General Hospital; Buddhist Compassion Relief Tzu Chi Foundation; Hualien; Taiwan
| | - S. Y. Yang
- Laboratory of Immunogenetics and Cord Blood Bank; Buddhist Tzu Chi Stem Cells Centre and Marrow Donor Registry; Buddhist Tzu Chi General Hospital; Buddhist Compassion Relief Tzu Chi Foundation; Hualien; Taiwan
| | - R. H. Kao
- Laboratory of Immunogenetics and Cord Blood Bank; Buddhist Tzu Chi Stem Cells Centre and Marrow Donor Registry; Buddhist Tzu Chi General Hospital; Buddhist Compassion Relief Tzu Chi Foundation; Hualien; Taiwan
| | - C. L. Lin
- Laboratory of Immunogenetics and Cord Blood Bank; Buddhist Tzu Chi Stem Cells Centre and Marrow Donor Registry; Buddhist Tzu Chi General Hospital; Buddhist Compassion Relief Tzu Chi Foundation; Hualien; Taiwan
| | - P. Y. Lin
- Laboratory of Immunogenetics and Cord Blood Bank; Buddhist Tzu Chi Stem Cells Centre and Marrow Donor Registry; Buddhist Tzu Chi General Hospital; Buddhist Compassion Relief Tzu Chi Foundation; Hualien; Taiwan
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Yang KL, Lee SK, Kao RH, Lin CL, Lin PY. Detection of the rare HLA-B*40:97 allele in an unrelated Taiwanese bone marrow donor. Int J Immunogenet 2012; 39:527-9. [PMID: 22672657 DOI: 10.1111/j.1744-313x.2012.01133.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2012] [Accepted: 05/13/2012] [Indexed: 11/29/2022]
Abstract
We detected a rare HLA-B locus allele, B*40:97, in a Taiwanese unrelated donor in our routine HLA SBT (sequence-based typing) exercise for a possible hematopoietic stem cell donation. In exons 2, 3 and 4, the sequence of B*40:97 is identical to the sequence of B*40:02:01 except one nucleotide at nucleotide position 760 (C->T) in exon 4. The nucleotide variation caused one amino acid alteration at residue 230 (L->F). B*40:97 was probably derived from a nucleotide substitution event where C was replaced by T at nucleotide 760 involving B*40:02:01. The HLA-A, HLA-B, HLA-C, HLA-DRB1 and HLA-DQB1 haplotype in association with B*40:97 may be deduced as A*26:01-B*40:97-C*03:03-DRB1*11:01-DQB1*03:03. Our recognition of B*40:97 in Taiwanese helps to fill the void of ethnic information for the allele B*40:97 reported to the IMGT/HLA Database.
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Affiliation(s)
- K L Yang
- Laboratory of Immunogenetics and Cord Blood Bank, Buddhist Tzu Chi Stem Cells Centre and Marrow Donor Registry, Buddhist Tzu Chi General Hospital, Buddhist Compassion Relief Tzu Chi Foundation, Hualien, Taiwan
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Yang KL, Lee SK, Kao RH, Lin CL, Lin PY. Recognition of HLA-A*24:137 allele in a Taiwanese unrelated bone marrow stem cell donor and the plausible HLA haplotype associated with A*24:137. Int J Immunogenet 2012; 39:530-1. [PMID: 22672687 DOI: 10.1111/j.1744-313x.2012.01134.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2012] [Accepted: 05/13/2012] [Indexed: 11/27/2022]
Abstract
We detected a rare HLA-A*24:137 allele in an unrelated Taiwanese haematopoietic stem cell donor during a routine SBT (sequence-based typing) HLA typing exercise. The DNA sequence of A*24:137 is identical to the sequence of A*24:02:01:01 in exons 2 and 3 except at codon 21 where CGC was replaced with CAA. The DNA variation caused an amino acid alteration at amino acid residue 21 (R->Q). The HLA haplotype in association with A*24:137 may be deduced as A*24:137-B*15-DRB1*14. The formation of A*24:137 was probably the result of a nucleotide point mutation involving A*24:02:01:01. It remains to be determined whether A*24:137 is restricted to Taiwanese/Chinese ethnicity.
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Affiliation(s)
- K L Yang
- Laboratory of Immunogenetics and Cord Blood Bank, Buddhist Tzu Chi Stem Cells Centre and Marrow Donor Registry, Buddhist Tzu Chi General Hospital, Buddhist Compassion Relief Tzu Chi Foundation, Hualien, Taiwan.
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Yang KL, Lee SK, Lin PY. Identification of the novel HLA allele, HLA-B*40:159, in a Taiwanese hematopoietic stem cell donor and the probable HLA haplotype in an association with B*40:159. Int J Immunogenet 2012; 39:520-3. [PMID: 22646321 DOI: 10.1111/j.1744-313x.2012.01130.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2012] [Revised: 04/02/2012] [Accepted: 05/03/2012] [Indexed: 11/28/2022]
Abstract
Using a sequence-based typing method, we found a new HLA-B*40 variant, B*40:159, in a Taiwanese hematopoietic stem cell donor. The sequence of B*40:159 is identical to the sequence of B*40:06:01:01 in exons 2 and 3 except the nucleotides at positions 412 (A → G) and 429 (A → C). The sequence variation caused two amino acid exchanges at residue 114 (N → D) and residue 116 (Y → S). The probable HLA-A, HLA-B, HLA-C and HLA-DRB1 haplotype in association with B*40:159 may be deduced as HLA-A*02:06-B*40:159-C*08:01-DRB1*08:03. The generation of B*40:159 is thought as the result of a sequence recombination event where B*46:01:01:01, B*15:01:01 or B*15:02:01 donated a minimum length of the DNA sequence from residue 412 to residue 419 to the recipient sequence of B*40:06:01:01.
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Affiliation(s)
- K L Yang
- Laboratory of Immunogenetics and Cord Blood Bank, Buddhist Tzu Chi Stem Cells Centre and Marrow Donor Registry, Buddhist Tzu Chi General Hospital, Buddhist Compassion Relief Tzu Chi Foundation, Hualien, Taiwan.
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Yang KL, Lee SK, Kao RH, Lin CL, Lin PY. Discovery of the novel HLA-DRB1*03:77 allele in a Taiwanese unrelated hematopoietic stem cell donor by a sequence-based typing method and identification of the probable HLA haplotype in association with DRB1*03:77. Int J Immunogenet 2012; 39:442-4. [PMID: 22486852 DOI: 10.1111/j.1744-313x.2012.01110.x] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Here, we report a novel human leucocyte antigen (HLA)-DRB1 allele, DRB1*03:77, discovered in a Taiwanese unrelated volunteer hematopoietic stem cell donor by a sequence-based typing (SBT) method. The DNA sequence of DRB1*03:77 is identical to the DNA sequence of DRB1*03:01:01 in exon 2 except one nucleotide at position 223 (G→C). The nucleotide substitution caused an amino acid replacement at residue 46 (E→Q). The formation of DRB1*03:77 was thought as the result of a nucleotide point mutation. The probable HLA-A, HLA-B and HLA-DRB1 haplotype in association with DRB1*03:77 may be deduced as A*33-B*58-DRB1*03:77. The donor was a Minna Taiwanese whose ancestors came from mainland China.
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Affiliation(s)
- K L Yang
- Laboratory of Immunogenetics and Cord Blood Bank, Buddhist Tzu Chi Stem Cells Centre and Marrow Donor Registry, Buddhist Tzu Chi General Hospital, Buddhist Compassion Relief Tzu Chi Foundation, Hualien, Taiwan.
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Yang KL, Lee SK, Kao RH, Lin CL, Lin PY. Discovery of the novel HLA-DRB1*16:16 allele in a Taiwanese unrelated bone marrow stem cell donor by a sequence-based typing method and the probable haplotype associated with DRB1*16:16. Int J Immunogenet 2012; 39:445-7. [PMID: 22486893 DOI: 10.1111/j.1744-313x.2012.01111.x] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
We report here a de novo HLA-DRB1 allele, DRB1*16:16, discovered in a Taiwanese unrelated volunteer bone marrow stem cell donor by a sequence-based typing (SBT) method. In exon 2, the DNA sequence of DRB1*16:16 is identical to the sequence of DRB1*16:02:01 except the nucleotides at positions 258 (C→T), 260 (C→A) and 261 (T→G). The nucleotide substitution produced an amino acid replacement at residue 58 (A→E). The formation of DRB1*16:16 was probably generated by a DNA sequence recombination event involving DRB1*11:01:01 and DRB1*16:02:01. The probable HLA-A, -B and -DRB1 haplotype in association with DRB1*16:16 may be deduced as A*02-B*38-DRB1*16:16.
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Affiliation(s)
- K L Yang
- Laboratory of Immunogenetics and Cord Blood Bank, Buddhist Tzu Chi Stem Cells Centre and Marrow Donor Registry, Buddhist Tzu Chi General Hospital, Buddhist Compassion Relief Tzu Chi Foundation, Hualien, Taiwan.
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Yang KL, Lee SK, Lin PY. Discovery of a novel HLA-B*51 variant, B*51:112, in a Taiwanese bone marrow donor and identification of the plausible HLA haplotype in association with B*51:112. Int J Immunogenet 2012; 39:451-3. [PMID: 22420902 DOI: 10.1111/j.1744-313x.2012.01108.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The sequence of B*51:112 is identical to the sequence of B*51:01:01 in exons 2, 3 and 4, except the nucleotides at positions 206 (C→A) and 213 (C→G). The nucleotide replacement caused one amino acid substitution at residue 45 (T→K). The plausible HLA-A, -B and -DRB1 haplotype in association with B*51:112 may be deduced as HLA-A*02-B*51:112-DRB1*12. The generation of B*51:112 was probably as the result of a DNA recombination event where B*40:01:01 acted as a sequence donor donating a segment of the DNA sequence to the recipient sequence B*51:01:01. The donor carrying B*51:112 was a Minna Taiwanese whose ancestor came to Taiwan from the southern region of China.
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Affiliation(s)
- K L Yang
- Laboratory of Immunogenetics and Cord Blood Bank, Buddhist Tzu Chi Stem Cells Centre and Marrow Donor Registry, Buddhist Tzu Chi General Hospital, Buddhist Compassion Relief Tzu Chi Foundation, Hualien, Taiwan.
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Kurose K, Sugiyama E, Saito Y. Population differences in major functional polymorphisms of pharmacokinetics/pharmacodynamics-related genes in Eastern Asians and Europeans: implications in the clinical trials for novel drug development. Drug Metab Pharmacokinet 2011; 27:9-54. [PMID: 22123129 DOI: 10.2133/dmpk.dmpk-11-rv-111] [Citation(s) in RCA: 181] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Drug lag, recently discussed extensively in Japan, can be divided into two phases: clinical development time and application review time. The former factor is still an important problem that might be improved by promoting multi-regional clinical trials and considering the results from other similar populations with Japanese, such as Koreans and Chinese. In this review, we compare the allelic or genotype frequencies of 30 relatively common functional alleles mainly between Eastern Asians and Europeans as well as among 3 major populations in Eastern Asian countries, Japan, Korea, and China, in 12 pharmacokinetics (PK)/pharmacodynamics (PD)-related genes; CYP2C9 (*2 and *3), CYP2C19 (*2, *3 and *17), 13 CYP2D6 haplotypes including *4, *5 and *10, CYP3A5 (*3), UGT1A1 (*28 and *6), NAT2 (*5, *6 and *7), GSTM1 and GSTT1 null genotypes, SLCO1B1 521T>C, ABCG2 421C>A, and HLA-A*31:01 and HLA-B*58:01. In this review, differences in allele frequencies (AFs) or genotype frequencies (GFs) less than 0.1 (in the cases of highest AF (GF) ≥0.1) or less than 0.05 (in the cases of lowest AF (GF) <0.1) were regarded as similar. Between Eastern Asians and Europeans, AFs (or GFs) are regarded as being different for many alleles such as CYP2C9 (*2), CYP2C19 (*2, *3 and *17), CYP2D6 (*4 and *10), CYP3A5 (*3), UGT1A1 (*28 and *6), NAT2 (*5*7), GSTT1 null and ABCG2 421C>A. Among the 3 Eastern Asian populations, however, only AFs of CYP2C19*3, CYP2D6*10, HLA-A*31:01 and HLA-B*58:01 are regarded as dissimilar. For CYP2C19*3, the total functional impact on CYP2C19 could be small if the frequencies of the two null alleles CYP2C19*2 and *3 are combined. Regarding CYP2D6*10, frequency difference over 0.1 is observed only between Japanese and Chinese (0.147). Although environmental factors should be considered for PK/PD differences, we could propose that among Japan, Korea, and China, genetic differences are very small for the analyzed common PK-related gene polymorphisms. On the other hand, AFs of the two HLA alleles important for cutaneous adverse drug reactions are diverse even among Eastern Asians and thus should be taken into account.
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Affiliation(s)
- Kouichi Kurose
- Division of Medicinal Safety Science, National Institute of Health Sciences, Tokyo, Japan
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Shi L, Huang XQ, Shi L, Tao YF, Yao YF, Yu L, Lin KQ, Yi W, Sun H, Tokunaga K, Chu JY. HLA polymorphism of the Zhuang population reflects the common HLA characteristics among Zhuang-Dong language-speaking populations. J Zhejiang Univ Sci B 2011; 12:428-35. [PMID: 21634035 DOI: 10.1631/jzus.b1000285] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
A study of the human leukocyte antigen (HLA) genetic characteristics in the Zhuang, the largest ethnic population in China, would provide insight into Zhuang history and give a useful tool for disease associations, transplantation, and anthropology. In the present study, we report the comprehensive HLA-A, HLA-B, HLA-C, and HLA-DRB1 alleles and haplotypes in the Zhuang population of southern China for the first time. A total of 13 HLA-A, 24 HLA-B, 22 HLA-C, and 18 HLA-DRB1 were identified in 104 Zhuang individuals. The frequencies of HLA-A*11:01, A*02:07, A*24:02, A*02:03, and A*33:03 on A loci, B*15:02, B*58:01, B*46:01, and B*13:01 on B loci, C*03:04, C*08:01, C*01:02, C*03:02, and C*07:02 on C loci, and DRB1*15:01, DRB1*16:02, DRB1*14:01, DRB1*15:02, and DRB1*03:01 on the DRB1 loci were >10%. The A*33:03-C*03:02-B*58:01-DRB1*03:01 and A*02:07-C*01:02-B*46:01-DRB1*14:01 haplotypes were predominant in the Zhuang. The phylogenetic tree, as well as the analysis of haplotypes, suggested that the Zhuang are genetically similar to southern Chinese populations, especially the Zhuang-Dong language-speaking populations, such as the Bouyei, Dai, and Maonan. Even though the Zhuang and southern Chinese populations shared common alleles and haplotypes, the Zhuang has maintained its unique genetic characteristics.
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Affiliation(s)
- Li Shi
- Institute of Medical Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Kunming 650118, China
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Yang KL, Lee SK, Lin CC, Jiang S, Chiu HM, Lin S, Chen YC, Yang SY, Jian YF, Shyr MH, Lin CL, Lin PY. Discovery of two novel HLA-B alleles, B*46:13:03 and B*15:189, in two Taiwanese volunteer bone marrow donors by sequence-based typing. Int J Immunogenet 2011; 38:539-42. [PMID: 21819546 DOI: 10.1111/j.1744-313x.2011.01030.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We report here two novel HLA-B alleles, B*46:13:03 and B*15:189, discovered in two Taiwanese volunteer bone marrow donors. The sequence of B*15:189 has a nucleotide sequence possibly derived from a recombination event between HLA-B*39:01:01 and B*15:01:01:01, while the origin of the sequence B*46:13:03 was less obvious to postulate, considering the low frequency of B*46:13 in the general population and the silent mutations involved. Our report here adds further HLA polymorphism to the growing lists of HLA-B*46 and HLA-B*15 and provides an additional HLA information for donor search programme for patients undergoing transplant.
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Affiliation(s)
- K L Yang
- Laboratory of Immunogenetics, Buddhist Tzu Chi University, Buddhist Compassion Relief Tzu Chi Foundation, Hualien, Taiwan.
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Shi L, Shi L, Yao YF, Matsushita M, Yu L, Huang XQ, Yi W, Oka T, Tokunaga K, Chu JY. Genetic link among Hani, Bulang and other Southeast Asian populations: evidence from HLA -A, -B, -C, -DRB1 genes and haplotypes distribution. Int J Immunogenet 2011; 37:467-75. [PMID: 20637045 DOI: 10.1111/j.1744-313x.2010.00949.x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
Human leucocyte antigen (HLA) genetic characteristic of different ethnic minorities would be useful for tracing the origin of modern human HLA matching in transplantation and disease associations. In this study, we reported HLA-A, -B, -C and -DRB1 alleles and haplotypes in the Bulang and Hani populations of southwestern China using a high-resolution polymerase chain reaction-Luminex (PCR-Luminex) typing method. A total of nine HLA-A, 22 HLA-B, 13 HLA-C and 18 HLA-DRB1 alleles were identified in the Bulang population, and 11 HLA-A, 25 HLA-B, 14 HLA-C and 19 HLA-DRB1 alleles were in the Hani population. Compared with other populations, the predominant A*1101-B*1502-DRB1*1202 haplotype in the Bulang and Hani populations was also common in Jinuo, Wa, Dai, Maonan and Vietnamese populations. The distribution of HLA genes indicate that Bulang and Hani populations belong to the Southeast Asia group and they have maintained their original genetic characteristics and kept a long genetic distance from other populations owing to founder effects and subsequent geographic isolation. In addition, the close relationship among ethnic groups in Yunnan province and the Thai and Vietnamese populations were confirmed, whereas the Mon-Kmer-speaking populations shared other common HLA alleles and haplotypes compared with other linguistic groups.
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Affiliation(s)
- L Shi
- Institute of Medical Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Kunming, China
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McCormack M, Alfirevic A, Bourgeois S, Farrell JJ, Kasperavičiūtė D, Carrington M, Sills GJ, Marson T, Jia X, de Bakker PIW, Chinthapalli K, Molokhia M, Johnson MR, O'Connor GD, Chaila E, Alhusaini S, Shianna KV, Radtke RA, Heinzen EL, Walley N, Pandolfo M, Pichler W, Park BK, Depondt C, Sisodiya SM, Goldstein DB, Deloukas P, Delanty N, Cavalleri GL, Pirmohamed M. HLA-A*3101 and carbamazepine-induced hypersensitivity reactions in Europeans. N Engl J Med 2011; 364:1134-43. [PMID: 21428769 PMCID: PMC3113609 DOI: 10.1056/nejmoa1013297] [Citation(s) in RCA: 621] [Impact Index Per Article: 47.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
BACKGROUND Carbamazepine causes various forms of hypersensitivity reactions, ranging from maculopapular exanthema to severe blistering reactions. The HLA-B*1502 allele has been shown to be strongly correlated with carbamazepine-induced Stevens-Johnson syndrome and toxic epidermal necrolysis (SJS-TEN) in the Han Chinese and other Asian populations but not in European populations. METHODS We performed a genomewide association study of samples obtained from 22 subjects with carbamazepine-induced hypersensitivity syndrome, 43 subjects with carbamazepine-induced maculopapular exanthema, and 3987 control subjects, all of European descent. We tested for an association between disease and HLA alleles through proxy single-nucleotide polymorphisms and imputation, confirming associations by high-resolution sequence-based HLA typing. We replicated the associations in samples from 145 subjects with carbamazepine-induced hypersensitivity reactions. RESULTS The HLA-A*3101 allele, which has a prevalence of 2 to 5% in Northern European populations, was significantly associated with the hypersensitivity syndrome (P=3.5×10(-8)). An independent genomewide association study of samples from subjects with maculopapular exanthema also showed an association with the HLA-A*3101 allele (P=1.1×10(-6)). Follow-up genotyping confirmed the variant as a risk factor for the hypersensitivity syndrome (odds ratio, 12.41; 95% confidence interval [CI], 1.27 to 121.03), maculopapular exanthema (odds ratio, 8.33; 95% CI, 3.59 to 19.36), and SJS-TEN (odds ratio, 25.93; 95% CI, 4.93 to 116.18). CONCLUSIONS The presence of the HLA-A*3101 allele was associated with carbamazepine-induced hypersensitivity reactions among subjects of Northern European ancestry. The presence of the allele increased the risk from 5.0% to 26.0%, whereas its absence reduced the risk from 5.0% to 3.8%. (Funded by the U.K. Department of Health and others.).
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Affiliation(s)
- Mark McCormack
- Molecular and Cellular Therapeutics, the Royal College of Surgeons in Ireland, Dublin, Ireland
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Yang KL, Lee SK, Chu CC, Lin CC, Jiang S, Chiu HM, Lin S, Chen YC, Chen MJ, Jian YF, Yang CF, Yang SY, Shyr MH, Lin CL, Lin PY. Identification of two novel HLA-B*40 alleles, B*40:137 and B*40:158, in Taiwanese individuals. Int J Immunogenet 2011; 38:277-80. [DOI: 10.1111/j.1744-313x.2011.01001.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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41
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Yang KL, Chen MJ, Shyr MH, Lin CL, Lin PY. Rare HLA alleles and their predicted haplotypes in Tzu Chi Taiwanese marrow donor registry. Int J Immunogenet 2011; 38:263-7. [DOI: 10.1111/j.1744-313x.2010.00992.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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42
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Shen CM, Zhu BF, Deng YJ, Ye SH, Yan JW, Yang G, Wang HD, Qin HX, Huang QZ, Zhang JJ. Allele polymorphism and haplotype diversity of HLA-A, -B and -DRB1 loci in sequence-based typing for Chinese Uyghur ethnic group. PLoS One 2010; 5:e13458. [PMID: 21079793 PMCID: PMC2973946 DOI: 10.1371/journal.pone.0013458] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2010] [Accepted: 09/09/2010] [Indexed: 11/18/2022] Open
Abstract
Background Previous studies indicate that the frequency distributions of HLA alleles and haplotypes vary from one ethnic group to another or between the members of the same ethnic group living in different geographic areas. It is necessary and meaningful to study the high-resolution allelic and haplotypic distributions of HLA loci in different groups. Methodology/Principal Findings High-resolution HLA typing for the Uyghur ethnic minority group using polymerase chain reaction-sequence-based-typing method was first reported. HLA-A, -B and -DRB1 allelic distributions were determined in 104 unrelated healthy Uyghur individuals and haplotypic frequencies and linkage disequilibrium parameters for HLA loci were estimated using the maximum-likelihood method. A total of 35 HLA-A, 51 HLA-B and 33 HLA-DRB1 alleles were identified at the four-digit level in the population. High frequency alleles were HLA-A*1101 (13.46%), A*0201 (12.50%), A*0301 (10.10%); HLA-B*5101(8.17%), B*3501(6.73%), B*5001 (6.25%); HLA-DRB1*0701 (16.35%), DRB1*1501 (8.65%) and DRB1*0301 (7.69%). The two-locus haplotypes at the highest frequency were HLA-A*3001-B*1302 (2.88%), A*2402-B*5101 (2.86%); HLA-B*5001-DRB1*0701 (4.14%) and B*0702-DRB1*1501 (3.37%). The three-locus haplotype at the highest frequency was HLA-A*3001-B*1302-DRB1*0701(2.40%). Significantly high linkage disequilibrium was observed in six two-locus haplotypes, with their corresponding relative linkage disequilibrium parameters equal to 1. Neighbor-joining phylogenetic tree between the Uyghur group and other previously reported populations was constructed on the basis of standard genetic distances among the populations calculated using the four-digit sequence-level allelic frequencies at HLA-A, HLA-B and HLA-DRB1 loci. The phylogenetic analyses reveal that the Uyghur group belongs to the northwestern Chinese populations and is most closely related to the Xibe group, and then to Kirgiz, Hui, Mongolian and Northern Han. Conclusions/Significance The present findings could be useful to elucidate the genetic background of the population and to provide valuable data for HLA matching in clinical bone marrow transplantation, HLA-linked disease-association studies, population genetics, human identification and paternity tests in forensic sciences.
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Affiliation(s)
- Chun-mei Shen
- The Key Laboratory of Environment and Gene Related to Diseases, Xi'an Jiaotong University, Ministry of Education, Xi'an, Shaanxi, People's Republic of China
- Blood Center of Shaanxi Province, Xi'an, Shaanxi, People's Republic of China
- The Key Laboratory of Ministry of Health for Forensic Sciences, School of Medicine, Xi'an Jiaotong University, Xi'an, Shaanxi, People's Republic of China
| | - Bo-feng Zhu
- The Key Laboratory of Environment and Gene Related to Diseases, Xi'an Jiaotong University, Ministry of Education, Xi'an, Shaanxi, People's Republic of China
- Blood Center of Shaanxi Province, Xi'an, Shaanxi, People's Republic of China
- The Key Laboratory of Ministry of Health for Forensic Sciences, School of Medicine, Xi'an Jiaotong University, Xi'an, Shaanxi, People's Republic of China
- Department of Forensic Sciences, School of Medicine, Xi'an Jiaotong University, Xi'an, Shaanxi, People's Republic of China
- * E-mail:
| | - Ya-jun Deng
- Center of Forensic Sciences, Beijing Genomics Institute, Beijing, People's Republic of China
| | - Shi-hui Ye
- Blood Center of Shaanxi Province, Xi'an, Shaanxi, People's Republic of China
| | - Jiang-wei Yan
- Beijing Institute of Genomics, Chinese Academy of Science, Beijing, People's Republic of China
| | - Guang Yang
- Vascular Biology Center, Medical College of Georgia, Augusta, Georgia, United States of America
| | - Hong-dan Wang
- The Key Laboratory of Environment and Gene Related to Diseases, Xi'an Jiaotong University, Ministry of Education, Xi'an, Shaanxi, People's Republic of China
- The Key Laboratory of Ministry of Health for Forensic Sciences, School of Medicine, Xi'an Jiaotong University, Xi'an, Shaanxi, People's Republic of China
- Department of Forensic Sciences, School of Medicine, Xi'an Jiaotong University, Xi'an, Shaanxi, People's Republic of China
| | - Hai-xia Qin
- Institute of Molecular Medicine and Genetics, Medical College of Georgia, Augusta, Georgia, United States of America
| | - Qi-zhao Huang
- The Second Team of Students Brigade, Third Military Medical University, Chongqing, People's Republic of China
| | - Jing-Jing Zhang
- Beijing Genomics Institute, Beijing, People's Republic of China
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Yang KL, Lee SK, Lin CC, Jiang S, Chiu HM, Lin S, Chen YC, Jian YF, Chen MJ, Shyr MH, Lin CL, Lin PY. Identification of a novel HLA-A allele, A*11:60, in a Taiwanese family. Int J Immunogenet 2010; 38:167-9. [DOI: 10.1111/j.1744-313x.2010.00974.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Yang KL, Lee SK, Chu CC, Lin CC, Jiang S, Chiu HM, Lin S, Chen YC, Chen MJ, Jian YF, Yang CF, Yang SY, Shyr MJ, Lin CL, Lin PY. An HLA-A*02:01-B*13:01-DRB1*14:01:03 haplotype conserved in Taiwanese and a possible close relationship between DRB1*14:01:03 and DRB1*14:54. Int J Immunogenet 2010; 38:69-71. [DOI: 10.1111/j.1744-313x.2010.00970.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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45
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Lai MJ, Wen SH, Lin YH, Shyr MH, Lin PY, Yang KL. Distributions of human leukocyte antigen–A, –B, and –DRB1 alleles and haplotypes based on 46,915 Taiwanese donors. Hum Immunol 2010; 71:777-82. [DOI: 10.1016/j.humimm.2010.05.013] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2010] [Revised: 05/04/2010] [Accepted: 05/12/2010] [Indexed: 11/28/2022]
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46
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Zhang HB, Wei SG, Zheng HB, Yu B, Lai JH. Distribution of human leukocyte antigen alleles and haplotypes in Oroqen and Ewenki nationality minority in Inner Mongolia Autonomous Region of China. Int J Immunogenet 2010; 37:337-44. [PMID: 20518845 DOI: 10.1111/j.1744-313x.2010.00930.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The frequencies of the human leukocyte antigen alleles HLA-A,-B, DRB1 and the A-B, A-DRB1, B-DRB1, A-B-DRB1 haplotypes were investigated through means of PCR-based reverse line-strip sequence specific oligonucleotide hybridization on 108 Oroqen and 104 Ewenki nationality unrelated healthy individuals from the Inner Mongolia Autonomous Region of China. A total of thirteen different HLA-A alleles, 21 different HLA-B alleles and 13 different HLA-DRB1 alleles were detected in the Oroqen ethnic group and the most frequent HLA alleles found were A*24(35.65%), B*15(17.92%), and DRB1*09(17.59%), respectively. The common HLA-A-B-DRB1 haplotypes were A*24-B*40-DRB1*09(5.09%), A*24-B*48-DRB1*12(2.78%) and A*24-B*51-DRB1*04(2.78%); and the HLA-A*33-B*58, A*30-B*13, A*01-B*37, A*33-DRB1*03, A*01-DRB1*10, A*30-DRB1*07, B*37-DRB1*10, B*58-DRB1*03, B*38-DRB1*08, B*13-DRB1*07 were significant positive linkage disequilibrium in the Oroqen nationality group. In total, 14 different HLA-A alleles, 27 B alleles and 12 DRB1 alleles were found in Ewenki nationality group, and the most frequent HLA alleles found were A*24(24.49%), B*40(17.35%), and DRB1*04(14.80%), respectively. The common HLA-A-B-DRB1 haplotypes were A*33-B*58-DRB1*03(6.25%), A*01-B*51-DRB1*11(2.88%) and A*24-B*40-DRB1*09(2.88%); the HLA-A*33-B*58, A*29-B*44, A*03-B*52, A*33-DRB1*03, A*29-DRB1*07, A*24-DRB1*09, B*58-DRB1*03, B*08-DRB1*03, B*46-DRB1*09 were significant positive linkage disequilibrium in Ewenki nationality group. The distribution of HLA A,-B, DRB1, alleles haplotypes frequencies and phylogenetic tree indicated that the Oroqen and Ewenki population groups belongs to northern group of China, together as a group cluster.
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Affiliation(s)
- H B Zhang
- Key Laboratory of Ministry of Health for Forensic Sciences, School of Medicine, Xi'an Jiaotong University
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47
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Zhu BF, Yang G, Shen CM, Qin HX, Liu SZ, Deng YJ, Fan SL, Deng LB, Chen F, Zhang P, Fang J, Chen LP, Wang HD, Wang ZY, Lucas R. Distributions of HLA-A and -B alleles and haplotypes in the Yi ethnic minority of Yunnan, China: relationship to other populations. J Zhejiang Univ Sci B 2010; 11:127-35. [PMID: 20104647 PMCID: PMC2816316 DOI: 10.1631/jzus.b0900232] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
Abstract
Objective: To investigate the distributions of human leukocyte antigen (HLA)-A and -B alleles and HLA-A-B haplotypes in the Yi ethnic minority of the Yunnan Province, situated in southwestern China. Methods: DNA typing for HLA-A and -B loci was performed using the polymerase chain reaction-sequence-based typing (PCR-SBT) method on 114 randomly selected healthy individuals of the Yi population. The allelic frequencies of HLA-A and -B loci were calculated by direct counting and HLA-A-B haplotypes were estimated using the expectation maximization algorithm. Results: A total of 17 HLA-A and 38 HLA-B alleles were found in the Yi population. The most frequent alleles were A*2402 (32.46%), A*1101 (26.32%), and A*0203 (10.09%) at the HLA-A locus and B*4601 (12.28%), B*1525 (10.09%), B*4001 (8.77%), and B*3802 (7.89%) at the HLA-B locus. The predominant HLA-A-B haplotypes were A*2402-B*1525 (7.86%) and A*0203-B*3802 (5.64%), followed by A*1101-B*4001 (4.69%). Phylogenetic analysis indicates that the Yi population in the Honghe, Yunnan Province of China basically belongs to groups of southeastern Asian origin, but shares some characteristics with northeastern Asian groups. Conclusion: The present study may add to the understanding of HLA polymorphism in the Yi ethnic group that was poorly defined previously, and provide useful information for bone marrow transplantation, anthropological research, and forensic sciences as well as for disease-association studies.
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Affiliation(s)
- Bo-feng Zhu
- Department of Forensic Medicine, School of Medicine, Xi'an Jiaotong University, Xi'an 710061, China
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Yang G, Deng YJ, Qin H, Zhu BF, Chen F, Shen CM, Sun ZM, Chen LP, Wu J, Mu HF, Lucas R. HLA-B*15 subtypes distribution in Han population in Beijing, China, as compared with those of other populations. Int J Immunogenet 2010; 37:205-12. [DOI: 10.1111/j.1744-313x.2010.00910.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Shi L, Yao YF, Shi L, Matsushita M, Yu L, Lin QK, Tao YF, Oka T, Chu JY, Tokunaga K. HLA alleles and haplotypes distribution in Dai population in Yunnan province, Southwest China. ACTA ACUST UNITED AC 2009; 75:159-65. [PMID: 20003137 DOI: 10.1111/j.1399-0039.2009.01407.x] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Human leukocyte antigen (HLA) analysis would be a useful tool to trace the origin of modern humans. In this study, we provided the first four digital HLA-A, -B, -C and -DRB1 allele and haplotype data in the Dai ethnic population, which is a unique and representative Kam-Tai-speaking ethnic minority living in the Yunnan province of Southwestern China. Our results showed that the Dai population has unique HLA characteristic that are most closely related to the Southeastern Asia group and similar to the Kam-Tai speaking populations in China and Thailand.
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Affiliation(s)
- L Shi
- Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming, China
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Chen MJ, Chu CC, Shyr MH, Lin CL, Lin PY, Yang KL. A novel HLA-B allele, B*5214, detected in a Taiwanese volunteer bone marrow donor using a sequence-based typing method. Int J Immunogenet 2009; 37:39-41. [PMID: 19735312 DOI: 10.1111/j.1744-313x.2009.00876.x] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
HLA-B*5214, a novel rare allele of HLA-B*52 variant, was found in a Taiwanese volunteer bone marrow donor by sequence-based typing method. The sequence of B*5214 is identical to that of B*520101 in exon 2 but differs from B*520101 in exon 3 at nucleotide positions 419 A-->T and 435 A-->G. Alteration of these two nucleotides resulted an amino acid substitution at amino acid residue 116 Y-->F ( TAC-->TTC) and a silent exchange at residue 121 K-->K (AAA-->AAG).
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Affiliation(s)
- M J Chen
- Buddhist Tzu Chi Stem Cells Centre, Buddhist Tzu Chi Medical Centre, Buddhist Compassion Relief Tzu Chi Foundation, Hualien, Taiwan
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