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Singh P, Rajput R, Mehra N, Vajpayee M. Analysis of HLA association among North Indian HIV positive individuals with and without tuberculosis. Meta Gene 2020. [DOI: 10.1016/j.mgene.2020.100673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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Mehra NK. Defining genetic architecture of the populations in the Indian subcontinent: Impact of human leukocyte antigen diversity studies. INDIAN JOURNAL OF HUMAN GENETICS 2011; 16:105-7. [PMID: 21206695 PMCID: PMC3009418 DOI: 10.4103/0971-6866.73394] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- N K Mehra
- Department of Transplant Immunology and Immunogenetics, All India Institute of Medical Sciences, New Delhi - 110 029, India
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Gupta A, Kamal S, Gupta V, Bambery P, Kaura B. HLA Typing in Vogt-Koyanagi-Harada Syndrome in North Indian Patients. Ocul Immunol Inflamm 2009; 15:89-97. [PMID: 17558833 DOI: 10.1080/09273940601186727] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
PURPOSE To report the HLA profile of VKH patients from India. METHOD Forty-one patients and 50 controls were studied. Phenotyping using a lymphocytotoxicity assay was done for HLA-A and -B. DNA-based sequence-specific low resolution typing was done for HLA-DR and -DQ loci. RESULTS HLA-A9 was over-represented in the patient population (p = 0.01), whereas HLA-A11 (p = 0.03) and HLA-DRB1*13 (p = 0.007) were found to be underrepresented. The frequency of HLA-DRB1*04 was 14.6% and 10% in the patient population and controls, respectively. The HLA-DQ frequencies did not differ significantly between patients and controls. CONCLUSION Unlike that reported in most populations, we did not find a significant association between HLA-DRB1*04 and our patient population.
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Affiliation(s)
- Amod Gupta
- Department of Ophthalmology, Post Graduate Institute of Medical Education and Research, Chandigarh, India.
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Rani R, Marcos C, Lazaro AM, Zhang Y, Stastny P. Molecular diversity of HLA-A, -B and -C alleles in a North Indian population as determined by PCR-SSOP. Int J Immunogenet 2007; 34:201-8. [PMID: 17504510 DOI: 10.1111/j.1744-313x.2007.00677.x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We have used molecular methods to determine the frequencies of human leukocyte antigen (HLA)-A, -B and -C alleles in normal, healthy, unrelated individuals from North India using polymerase chain reaction and hybridization with sequence-specific oligonucleotide probes as there is no comprehensive report showing molecular diversity of all the class-I alleles present in North Indians. A*0101, A*0206, A*0301, A*1101, A*6801, A*2401 and A*3101 were the most prevalent alleles of the A locus with 91.11% of the samples showing heterozygosity. At the HLA-B locus a total of 47 B locus alleles were observed and the only allele found with an allele frequency of 15% was B*5801. Other frequent B-locus alleles observed were B*5101, B*3503 and B*4006 with relatively less frequent alleles like B*5201, B*3501, B*0702, B*4403, B*5701, B*1801 and B*5501. Of the samples studied 92.31% were heterozygous for B-locus alleles. Cw*0602 and Cw*0401 were the most frequent C-locus alleles. Other frequent C-locus alleles were Cw*0102, Cw*0302, Cw*0701, Cw*0702, Cw*1202, Cw*1203, Cw*1502 and Cw*1503. HLA alleles common in Africans like B*5801, A*68012, B*5301, B*44032, B*4006 and Cw*1701 were observed in the North Indians besides oriental alleles like B*1301, B*1502 and B*4001 confirming that the genetic make-up of North Indians is Caucasoid with elements of Mongoloid and Negrito races. Some new/rare alleles like B*1802, described as a new allele from Thailand and B*8101, described earlier in a Bubi population were also observed although with low frequencies, showing the diversity of HLA class-I alleles present in the North Indians.
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Affiliation(s)
- R Rani
- Neuroimmunology Laboratory, National Institute of Immunology, New Delhi, India.
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Kanga U, Panigrahi A, Kumar S, Mehra NK. Asian Indian donor marrow registry: All India Institute of Medical Sciences experience. Transplant Proc 2007; 39:719-20. [PMID: 17445580 DOI: 10.1016/j.transproceed.2007.01.057] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
A major limitation in hematopoietic stem cell transplantation (HSCT) is the availability of a genetically matched donor, particularly with respect to the human leukocyte antigens (HLA)-linked immune response genes located on chromosome 6 in humans. During the last 5 years, a total of 688 patients requiring HSCT underwent HLA testing in our department to identify a matched donor from their families. The sibship size ranged from 1 to > or =5 in all disease categories, except thalassemia major where the majority of patients had only 1 sibling. Family genotype analysis revealed that 39.3% of the total number of patients had an HLA-matched sibling and that families with sibship size of > or =4 had a higher probability (68.8%) compared with those with sibship size of < or =3 (29.7%). Because the Indian population is characterized by the presence of novel HLA alleles and unique haplotypes (HLA-A*0211, B*2707, A*26-B*08-DRB1*03), patients with rare HLA alleles have much less probability of finding an unrelated optimally matched donor than those with common HLA phenotypes. Smaller family size and unique HLA profile are limitations that can be overcome by developing unrelated volunteer marrow donor registries. The Asian Indian Donor Marrow Registry at our institute is regularly providing services to such patients.
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Affiliation(s)
- U Kanga
- Department of Transplant Immunology and Immunogenetics, All India Institute of Medical Sciences, Ansari Nagar, New Delhi, India.
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6
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Analysis of Distribution of HLA Class I Antigens in Population From Six North Indian States. APOLLO MEDICINE 2007. [DOI: 10.1016/s0976-0016(11)60431-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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7
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Vettriselvi V, Vijayalakshmi K, Suganya S, Krishnan M, Paul SFD, Jayanth V. Molecular diversity of HLA-A*19 group of alleles in south Indian population. Int J Immunogenet 2006; 33:69-72. [PMID: 16611249 DOI: 10.1111/j.1744-313x.2006.00570.x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
To determine the genetic diversity of the human leucocyte antigen (HLA)-A*19 group of alleles in the south Indian Tamil population, we studied 100 random healthy unrelated individuals. The frequency of HLA-A*19 was 37% with A*33 (45.9%), A*32 (29.7%), A*31 (16.2%), A*30 (5.4%), A*29 (2.7%) and A*74 (0%). The frequency distribution of the HLA-A*19 alleles was distinct and revealed marked similarities and variations with other populations.
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Affiliation(s)
- V Vettriselvi
- Dept. of Human Genetics, Sri Ramachandra Medical College and Research Institute, Chennai-600116, Tamil Nadu, India
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Farjadian S, Naruse T, Kawata H, Ghaderi A, Bahram S, Inoko H. Molecular analysis of HLA allele frequencies and haplotypes in Baloch of Iran compared with related populations of Pakistan. ACTA ACUST UNITED AC 2005; 64:581-7. [PMID: 15496201 DOI: 10.1111/j.1399-0039.2004.00302.x] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The extreme polymorphism in different loci of the human leukocyte antigen (HLA) system has been used as an invaluable tool for anthropological studies. Determination of HLA allele and haplotype frequencies in different ethnic groups is useful for population genetic analyses and the study of genetic relationships among them. In the present study, molecular analysis of HLA-A, -B, -C, -DQA1, -DQB1, and -DRB1 genes has been used to assign HLA allele and haplotype frequencies in 100 unrelated healthy individuals from the Baloch ethnic group of Iran. The results were compared with Baloch and other ethnic groups in the neighboring Pakistan. The results of this study showed that the most frequent HLA class I alleles were A*02011 (20.2%), B*4006 (11.1%), and C*04011 (28.6%). The most common HLA class II alleles were DQA1*0101/2 (42.5%), DQB1*0201 (32%), and DRB1*0301 (29%). Three-locus haplotype analysis revealed that A*11011-B*4006-C*15021 (5.8%) and DQA1*0501-DQB1*0201-DRB1*0301 (22.1%) were the most common HLA class I and II haplotypes, respectively, in this population. Neighbor-joining tree based on DA genetic distances and correspondence analysis according to HLA-A, -B, -DQB1, and -DRB1 allele frequencies showed that Baloch of Iran are genetically very close to Baloch and Brahui of Pakistan. This may reflect an admixture of Brahui and Baloch ethnic groups of Pakistan in the Balochistan province of Iran.
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Affiliation(s)
- S Farjadian
- Immunology Department, Shiraz University of Medical Sciences, Shiraz, Iran
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Shankarkumar U, Sridharan B, Pitchappan RM. HLA diversity among Nadars, a primitive Dravidian caste of South India. ACTA ACUST UNITED AC 2003; 62:542-7. [PMID: 14617038 DOI: 10.1046/j.1399-0039.2003.00118.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
South India is one of the oldest geophysical regions mainly occupied by Dravidian language-speaking people. Here a random panel of 61 unrelated Nadar healthy individual from Tamil Nadu State were analyzed and compared with other populations of India and the world. HLA-A, B and C alleles frequencies and their haplotype frequencies were determined by high-resolution typing of genomic DNA. The analysis revealed that the Nadar caste of South India have several characters shared with East Asian populations consistent with the demographic history of South India, as well as specific features including several unique alleles such as A*03011, A*31011, B*15011, B*3501, B*51011, Cw*02022. In addition, haplotypes such as A*31011-Cw*02022-B*3501, A*03011-Cw*04011-B*4406 and A*2402101-Cw*04011-B*51011 are of high frequency in both these populations but are rare or absent in other populations of India and the world. The study suggests that a comparatively lesser degree of genetic admixture occurred between the South Indian and North Indian racial groups than that between South Indian and East Asian groups.
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Affiliation(s)
- U Shankarkumar
- HLA Department, Institute of Immunohaematology (ICMR), K.E.M. Hospital, Parel, Mumbai, India.
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Saha A, Udhayasuriyan PT, Bhat KV, Bamezai R. Analysis of Indian Population Based on Y-STRs Reveals Existence of Male Gene Flow across Different Language Groups. DNA Cell Biol 2003; 22:707-19. [PMID: 14659043 DOI: 10.1089/104454903770946683] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
A study of three different Y-specific microsatellites (Y-STRs) in the populations from Uttar Pradesh (UP), Bihar (BI), Punjab (PUNJ), and Bengal (WB), speaking modern indic dialects with its roots in Indo-Aryan language, and from South of India (SI), speaking the South Indian languages with their root in Dravidian language, has shown that the predominant alleles observed represent the whole range of allelic variation reported in different population groups globally. These results indicate that the Indian population is most diverse. The similarity between the allelic variants between the populations studied by others in Africa and Asia and in this study between WB, PUNJ, UP, BI, and SI are of interest. It demonstrates that these population groups, housed in eight states of the country in different geographic locations, broadly correspond with Indo-Aryan and Dravidian language families. Further, our analyses based on haplotype frequency of different marker loci and gene diversity reveals that none of the population groups have remained isolated from others. High levels of haplotype diversity exist in all the clusters of population. Nonsignificant results based on Markov chain steps and Slatkin's linearized genetic distances indicate that there has been migration to and from in these population groups. However, some of the marginally significant interpopulation differences could be attributed to one or more of the castes with high diversity embedded within the population groups studied. Haplotype sharing between populations, F(ST) statistics, and phylogenetic analysis identifies genetic relatedness to be more between individuals belonging to two different states of India, WB and PUNJ, followed by UP and BI, whereas SI branched out separately.
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Affiliation(s)
- Anjana Saha
- National Centre of Applied Human Genetics, School of Life Sciences, Jawaharlal Nehru University, New Delhi-110067, India
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Sharma SK, Balamurugan A, Pandey RM, Saha PK, Mehra NK. Human leukocyte antigen-DR alleles influence the clinical course of pulmonary sarcoidosis in Asian Indians. Am J Respir Cell Mol Biol 2003; 29:225-31. [PMID: 12600814 DOI: 10.1165/rcmb.2003-0007oc] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Host genetic factors are known to contribute to disease susceptibility and course in sarcoidosis. They may also be important in defining the pattern of disease presentation and progression, as well as its overall prognosis. We have studied human leukocyte antigen (HLA) class I (n = 31) and class II alleles (n = 56) in a cohort of Indian patients with sarcoidosis and 275 healthy control subjects from north India. Although no specific HLA class I allele association was found among sarcoidosis, the functional classification of HLA-A, -B, and -Cw alleles into supertypes revealed an increased frequency of group 2 ligands (Cw2, Cw4, Cw5) for the Killer cell Ig-like receptors (KIR2DL1) in the patient group as compared with control subjects. Among class II alleles, positive association of DRB1*11, DRB1*14, DQA1*0101/4, and DQB1*0503 alleles with the disease was noticed. Clinical follow-up of the patient cohort up to a 5-yr period showed a predominant occurrence of DRB1*14 and its linked DQ alleles in patients with insidious onset, advanced disease on chest radiographs, and chronic course with frequent relapses on tapering off the prednisolone treatment. Further, multivariate logistic regression analysis revealed that the presence of DRB1*11(odds ratio [OR] 9) and DRB1*14 (OR 7), and absence of DRB1*07 (OR 63 and DQB1*0201(OR 3) alleles, were independent predictors of sarcoidosis. The present findings imply that HLA-associated genetic factors influence the risk for the development of sarcoidosis and disease progression.
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Affiliation(s)
- Surendra K Sharma
- Department of Medicine, All India Institute of Medical Sciences, New Delhi 110 029, India.
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Mohyuddin A, Williams F, Mansoor A, Mehdi SQ, Middleton D. Distribution of HLA-A alleles in eight ethnic groups from Pakistan. TISSUE ANTIGENS 2003; 61:286-91. [PMID: 12753666 DOI: 10.1034/j.1399-0039.2003.00049.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The extreme polymorphism found at some loci of the HLA system has made it an invaluable tool for population genetic analyses. In this study eight diverse ethnic groups from Pakistan were analyzed at the HLA-A locus using sequence specific primers for polymerase chain reaction (PCR-SSP) and then further typed to the allele level using a two-stage sequence specific oligonucleotide probe (SSOP) strategy. Four of these ethnic groups (Burusho, Hazara, Kalash, Pathan) were from the north and four (Baloch, Brahui, Sindhi and Parsi) were from the south of Pakistan. Nine alleles were identified as unique to a particular ethnic group within Pakistan. Maximum variation was seen in the HLA-A*02 allele family for which 11 alleles were detected in the eight Pakistani ethnic groups. The alleles that showed significant variation between the Pakistani ethnic groups include A*0101, A*0206, A*0209, A*0207, A*0217, A*1101, A*2402/09 N/11 N, A*2902, A*3301 and A*3001. A phylogenetic tree based on DA distances for HLA-A allele frequencies separated the Pakistani populations from other world populations and also separated the only Dravidian speaking population of Pakistan, the Brahui, from the remaining Indo-European speaking ethnic groups of Pakistan.
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Affiliation(s)
- A Mohyuddin
- Biomedical and Genetic Engineering Division, Dr A. Q. Khan Research Laboratories, Islamabad, Pakistan
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