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Saxena A, Sharma G, Tyagi S, Mourya M, Coshic P, Tiwari PK, Mehra NK, Kanga U. HLA-A*02 repertoires in three defined population groups from North and Central India: Punjabi Khatries, Kashmiri Brahmins and Sahariya Tribe. HLA 2018; 93:16-23. [PMID: 30516033 DOI: 10.1111/tan.13447] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Revised: 11/26/2018] [Accepted: 11/29/2018] [Indexed: 01/30/2023]
Abstract
The allelic family of HLA-A*02 with a repertoire of approximately 1022 alleles represents the predominant and most heterogeneous group at the HLA-A locus. This remarkable diversity signifies its evolutionary relevance. Its population-specific diversity is attributed to environmental factors and pathogen pressure and can be harnessed in biology and medicine, particularly in disease association and for HLA-based vaccination approaches. We therefore investigated the HLA-A*02 repertoire in two North Indian caste populations, viz Punjabi Khatries (PK, N = 250), Kashmiri Brahmins (KB, N = 160) and a Central Indian tribe Sahariya (ST, N = 100) using Luminex-based high-resolution rSSO method. When required, results were confirmed with high-resolution PCR-SSP and/or next-generation sequencing (NGS). In the three populations evaluated, HLA-A*02 was observed with an overall high phenotypic/allelic frequency, however, A*02 repertoire differed among them. A total of six alleles were observed (A*02:01, *02:03, *02:05, *02:06, *02:07 and *02:11) in the caste groups, compared with four (except *02:05 and *02:07) in the tribals. Our striking observation was the high occurrence of A*02:11 at the repertoire level (80.6% in ST, 39% in PK, 31.8% in KB). Globally, this allele is rare, observed with low frequencies in limited ethnic groups. The primordial A*02:01 allele, representative A*02 allele in most ethnicities was observed as the second predominant allele (PK = 27.3%, KB = 31.8% and ST = 11.9%). Extremely high occurrence of A*02:11 in ST may be representation of ancient Austro-Asiatic genetic pool. In caste populations, the observed A*02 repertoire may be a consequence of natural selection and/or admixture from different populations.
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Affiliation(s)
- Abhishweta Saxena
- Department of Transplant Immunology and Immunogenetics, All India Institute of Medical Sciences, New Delhi, India
| | - Gaurav Sharma
- Department of Transplant Immunology and Immunogenetics, All India Institute of Medical Sciences, New Delhi, India
| | - Shweta Tyagi
- Department of Transplant Immunology and Immunogenetics, All India Institute of Medical Sciences, New Delhi, India
| | - Manish Mourya
- Department of Transplant Immunology and Immunogenetics, All India Institute of Medical Sciences, New Delhi, India
| | - Poonam Coshic
- Department of Transfusion Medicine (Blood Bank), All India Institute of Medical Sciences, New Delhi, India
| | - Pramod K Tiwari
- Centre for Genomics Molecular and Human Genetics, School of studies in Zoology, Jiwaji University, Gwalior, India
| | - Narinder K Mehra
- Dr C.G Pandit National Chair and Former Dean (Research), All India Institute of Medical Sciences, New Delhi, India
| | - Uma Kanga
- Department of Transplant Immunology and Immunogenetics, All India Institute of Medical Sciences, New Delhi, India
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Kwok J, Guo M, Yang W, Ip P, Chan GC, Ho J, Lee C, Middleton D, Lu L. Estimation of optimal donor number in Bone Marrow Donor Registry: Hong Kong’s experience. Hum Immunol 2017; 78:610-613. [DOI: 10.1016/j.humimm.2017.08.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2016] [Revised: 07/18/2017] [Accepted: 08/29/2017] [Indexed: 02/07/2023]
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Kwok J, Guo M, Yang W, Lee CK, Ho J, Tang WH, Chan YS, Middleton D, Lu LW, Chan GCF. HLA-A, -B, -C, and -DRB1 genotyping and haplotype frequencies for a Hong Kong Chinese population of 7595 individuals. Hum Immunol 2016; 77:1111-1112. [PMID: 27769748 DOI: 10.1016/j.humimm.2016.10.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Revised: 10/12/2016] [Accepted: 10/17/2016] [Indexed: 10/20/2022]
Abstract
HLA-A, -B, -C and -DRB1 gene and haplotype frequencies have been calculated from 7595 southern Chinese unrelated donors in a Hong Kong Bone Marrow Donor Registry. This is the first large-scale paper to report the distribution of A-C-B-DRB1 alleles in Hong Kong Chinese. This information is important for phylogenetic, comparative studies and estimating the optimal and cost-effective donor size and likelihood of obtaining appropriately matched donors for Chinese patients awaiting haematopoietic stem cell transplantation. The allele and haplotype data are available in the Allele Frequencies Net Database under the population name ''Hong Kong Chinese BMDR'' and the identifier (AFND003357).
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Affiliation(s)
- Janette Kwok
- Division of Transplantation and Immunogenetics, Queen Mary Hospital, Hong Kong.
| | - Mengbiao Guo
- Department of Paediatrics and Adolescent Medicine, The University of Hong Kong, Hong Kong
| | - Wanling Yang
- Department of Paediatrics and Adolescent Medicine, The University of Hong Kong, Hong Kong
| | - C K Lee
- Hong Kong Red Cross Blood Transfusion Services, Hong Kong
| | - Jenny Ho
- Division of Transplantation and Immunogenetics, Queen Mary Hospital, Hong Kong
| | - W H Tang
- Division of Transplantation and Immunogenetics, Queen Mary Hospital, Hong Kong
| | - Y S Chan
- Division of Transplantation and Immunogenetics, Queen Mary Hospital, Hong Kong
| | - Derek Middleton
- Transplant Immunology, Royal Liverpool Hospital, Liverpool, UK
| | - L W Lu
- Department of Pathology, The University of Hong Kong, Hong Kong
| | - Godfrey C F Chan
- Department of Paediatrics and Adolescent Medicine, The University of Hong Kong, Hong Kong
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Kwok J, Guo M, Yang W, Lee CK, Chan NK, Ho J, Tang WH, Chan YS, Middleton D, Lu LW, Chan GCF. HLA-A, -B and -DRB1 genotyping and haplotype frequencies of 3892 cord blood units in the Hong Kong Chinese Cord Blood Registry. Hum Immunol 2016; 77:1109-1110. [PMID: 27769747 DOI: 10.1016/j.humimm.2016.10.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2016] [Revised: 10/12/2016] [Accepted: 10/17/2016] [Indexed: 11/25/2022]
Abstract
HLA-A, -B and -DRB1 gene and haplotype frequencies have been calculated from 3892 southern Chinese unrelated cord blood units in a Hong Kong Cord Blood Registry. This is the first large-scale paper to report the distribution of A-B-DRB1 alleles in Hong Kong Chinese Cord Blood Units. This information is important for estimating the optimal and economically cost-effective donor size and likelihood of obtaining appropriately matched cord blood units for Chinese patients awaiting haematopoietic stem cell transplantation. The data are available in the Allele Frequencies Net Database under the population name ''Hong Kong Chinese Cord Blood Registry'' and the identifier (AFND003358).
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Affiliation(s)
- Janette Kwok
- Division of Transplantation and Immunogenetics, Queen Mary Hospital, Hong Kong.
| | - Mengbiao Guo
- Department of Paediatrics and Adolescent Medicine, The University of Hong Kong, Hong Kong
| | - Wanling Yang
- Department of Paediatrics and Adolescent Medicine, The University of Hong Kong, Hong Kong
| | - C K Lee
- Hong Kong Red Cross Blood Transfusion Service, Hong Kong
| | - N K Chan
- Hong Kong Red Cross Blood Transfusion Service, Hong Kong
| | - Jenny Ho
- Division of Transplantation and Immunogenetics, Queen Mary Hospital, Hong Kong
| | - W H Tang
- Division of Transplantation and Immunogenetics, Queen Mary Hospital, Hong Kong
| | - Y S Chan
- Division of Transplantation and Immunogenetics, Queen Mary Hospital, Hong Kong
| | - Derek Middleton
- Transplant Immunology, Royal Liverpool Hospital, Liverpool, UK
| | - L W Lu
- Department of Pathology, The University of Hong Kong, Hong Kong
| | - Godfrey C F Chan
- Department of Paediatrics and Adolescent Medicine, The University of Hong Kong, Hong Kong
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Abstract
Disease association studies involving highly polymorphic immunogenetic data may involve analyses at one or many units of analysis, including amino acid, allele, genotype and haplotype levels, as well as consideration of gene-gene or gene-environment interactions. The selection of the appropriate statistical tests is critical and will be dependent on the nature of the dataset (e.g., case-control vs. family data) as well as the specific research hypotheses being tested. This paper describes the various study and analysis categories used for such analyses, including the advantages and limitations of such techniques.
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Castelli EC, Mendes-Junior CT, Veiga-Castelli LC, Pereira NF, Petzl-Erler ML, Donadi EA. Evaluation of computational methods for the reconstruction of HLA haplotypes. ACTA ACUST UNITED AC 2010; 76:459-66. [DOI: 10.1111/j.1399-0039.2010.01539.x] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Lee MTM, Hung SI, Wei CY, Chen YT. Pharmacogenetics of toxic epidermal necrolysis. Expert Opin Pharmacother 2010; 11:2153-62. [DOI: 10.1517/14656566.2010.495120] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Ming Ta Michael Lee
- Institute of Biomedical Sciences, Academia Sinica, 128 Academia Road, Section 2, Nankang, 11529 Taipei, Taiwan ;
- National Genotyping Center, Academia Sinica, Taipei, Taiwan
- China Medical University, Graduate Institute of Graduate Medical Science, Taichung, Taiwan
| | - Shuen-Iu Hung
- Institute of Biomedical Sciences, Academia Sinica, 128 Academia Road, Section 2, Nankang, 11529 Taipei, Taiwan ;
- National Yang-Ming University, School of Medicine, Institute of Pharmacology, Taipei, Taiwan
| | - Chun-Yu Wei
- Taiwan International Graduate Program, Molecular Medicine Program, Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
- Institute of Biochemistry and Molecular Biology, School of Life Sciences National Yang-Ming University, Taipei, Taiwan
| | - Yuan-Tsong Chen
- Institute of Biomedical Sciences, Academia Sinica, 128 Academia Road, Section 2, Nankang, 11529 Taipei, Taiwan ;
- Duke University Medical Center, Department of Pediatrics, Durham, NC, USA
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Kupatawintu P, Pheancharoen S, Srisuddee A, Tanaka H, Tadokoro K, Nathalang O. HLA-A, -B, -DR haplotype frequencies in the Thai Stem Cell Donor Registry. ACTA ACUST UNITED AC 2010; 75:730-6. [DOI: 10.1111/j.1399-0039.2010.01450.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Romphruk AV, Romphruk A, Kongmaroeng C, Klumkrathok K, Paupairoj C, Leelayuwat C. HLA class I and II alleles and haplotypes in ethnic Northeast Thais. ACTA ACUST UNITED AC 2010; 75:701-11. [DOI: 10.1111/j.1399-0039.2010.01448.x] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Hei AL, Li W, Deng ZH, He J, Jin WM, Du D, Zhou XY, Xiao Y, Zhang ZX, Cai JP. Analysis of high-resolution HLA-A, -B, -Cw, -DRB1, and -DQB1 alleles and haplotypes in 718 Chinese marrow donors based on donor-recipient confirmatory typings. Int J Immunogenet 2009; 36:275-82. [PMID: 19674163 DOI: 10.1111/j.1744-313x.2009.00866.x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
High-resolution human leucocyte antigen (HLA)-A, -B, -Cw, -DRB1, and -DQB1 alleles and haplotype frequencies were analysed from 718 Chinese healthy donors selected from the Chinese Marrow Donor Program registry based on HLA donor-recipient confirmatory typings. A total of 28 HLA-A, 61 HLA-B, 30 HLA-Cw, 40 HLA-DRB1 and 18 HLA-DQB1 alleles were identified, and HLA-A*1101, A*2402, A*0201, B*4001, Cw*0702, Cw*0102, Cw*0304, DRB1*0901, DRB1*1501, DQB1*0301, DQB1*0303 and DQB1*0601 were found with frequencies higher than 10% in this study population. Multiple-locus haplotype analysis by the maximum-likelihood method revealed 45 A-B, 38 Cw-B, 47 B-DRB1, 29 DRB1-DQB1, 24 A-B-DRB1, 38 A-Cw-B, 23 A-Cw-B-DRB1, 33 Cw-B-DRB1-DQB1 and 22 A-Cw-B-DRB1-DQB1 haplotypes with frequencies >0.5%. The most common two-, three-, four- and five-locus haplotypes in this population were: A*0207-B*4601 (7.34%), Cw*0102-B*4601 (8.71%), B*1302-DRB1*0701 (6.19%), DRB1*0901-DQB1*0303 (14.27%), A*3001-B*1302-DRB1*0701 (5.36%), A*0207-Cw*0102-B*4601 (7.06%), A*3001-Cw*0602-B*1302-DRB1*0701 (5.36%), Cw*0602-B*1302-DRB1*0701-DQB1*0202 (6.12%) and A*3001-Cw*0602-B*1302-DRB1*0701-DQB1*0202 (5.29%). Presentation of the high-resolution alleles and haplotypes data at HLA-A, -B, -Cw, -DRB1 and -DQB1 loci will be useful for HLA matching in transplantation as well as for other medical and anthropological applications in the Chinese population.
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Affiliation(s)
- A-L Hei
- The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics & Beijing Hospital, Ministry of Health, Beijing 100730, China
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Wen SH, Lai MJ, Yang KL. Human leukocyte antigen-A, -B, and -DRB1 haplotypes of cord blood units in the Tzu Chi Taiwan Cord Blood Bank. Hum Immunol 2008; 69:430-6. [DOI: 10.1016/j.humimm.2008.05.012] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2007] [Revised: 05/15/2008] [Accepted: 05/27/2008] [Indexed: 11/15/2022]
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