Gradients in Distribution of HLA – DRB1 Alleles in Castes and Tribes of South India

Balakrishnan, K.; Chinniah, Rathika; Raju, Kamaraj; Subashini, R.; Saravanan, M.; Asha, K.V.; Kananan, M.; Vinothkumar, R.; Kannan, Mani; Dhivakar, Mani; Vijayan, Murali

doi:10.1080/09723757.2012.11886162

Cited by 7 publications

(6 citation statements)

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“…Further, this study also documented a relatively high between-group differentiation among Indian tribal groups, probably attributable to geographic and reproductive isolation (‘taboo’ or ‘totem’) and subsequent drift [ 34 ]. Previously, the Kani tribes have documented with less number of HLA alleles (immune response genes) [ 35 ]. High level of homozygosity in a number of HLA loci could be the reason for the reduced polymorphism.…”

Section: Discussionmentioning

confidence: 99%

Polymorphic Alu Insertion/Deletion in Different Caste and Tribal Populations from South India

et al. 2016

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Seven human-specific Alu markers were studied in 574 unrelated individuals from 10 endogamous groups and 2 hill tribes of Tamil Nadu and Kerala states. DNA was isolated, amplified by PCR-SSP, and subjected to agarose gel electrophoresis, and genotypes were assigned for various Alu loci. Average heterozygosity among caste populations was in the range of 0.292–0.468. Among tribes, the average heterozygosity was higher for Paliyan (0.3759) than for Kani (0.2915). Frequency differences were prominent in all loci studied except Alu CD4. For Alu CD4, the frequency was 0.0363 in Yadavas, a traditional pastoral and herd maintaining population, and 0.2439 in Narikuravars, a nomadic gypsy population. The overall genetic difference (Gst) of 12 populations (castes and tribes) studied was 3.6%, which corresponds to the Gst values of 3.6% recorded earlier for Western Asian populations. Thus, our study confirms the genetic similarities between West Asian populations and South Indian castes and tribes and supported the large scale coastal migrations from Africa into India through West Asia. However, the average genetic difference (Gst) of Kani and Paliyan tribes with other South Indian tribes studied earlier was 8.3%. The average Gst of combined South and North Indian Tribes (CSNIT) was 9.5%. Neighbor joining tree constructed showed close proximity of Kani and Paliyan tribal groups to the other two South Indian tribes, Toda and Irula of Nilgiri hills studied earlier. Further, the analysis revealed the affinities among populations and confirmed the presence of North and South India specific lineages. Our findings have documented the highly diverse (micro differentiated) nature of South Indian tribes, predominantly due to isolation, than the endogamous population groups of South India. Thus, our study firmly established the genetic relationship of South Indian castes and tribes and supported the proposed large scale ancestral migrations from Africa, particularly into South India through West Asian corridor.

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Section: Discussionmentioning

confidence: 99%

Polymorphic Alu Insertion/Deletion in Different Caste and Tribal Populations from South India

et al. 2016

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“…One of the notable findings of the present study was the high frequency of HLA-DRB1*15 (41.14%) among the Kamis, which is the highest reported from North India till date. Previously, the high frequency of HLA-DRB1*15 was reported from South Indian populations such as the Kani tribe (45.91%) and Pallars (43%) [23]. Moreover, its high frequency was also observed among the Sri Lankan Sinhalese population [24].…”

Section: Discussion/conclusionmentioning

confidence: 96%

HLA Profile of Kami Population Refutes the Earlier Proposition of Exclusive Closer Genetic Affinity of All the Gorkhas to Mongoloids

2020

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Objective: Based on the HLA profile of Indian Gorkhas, Debnath and Chaudhuri (2006) proposed that Gorkhas are genetically closer to Mongoloids, and they may have originated from Mongolians or Tibetan stocks. However, the major limitation of the earlier study was that Gorkhas comprise 2 broad groups, i.e. Tibeto-Burmans and Indo-Aryans. Besides, Gorkhas have an assemblage of many sociocultural and linguistically distinct populations such as Rai, Magar, Limbu, Tamang, Newar, Bahun, Kami, and so on. Thus, the generalization of the findings on Gorkhas by considering them as a single homogenous population may not be free from biases. Therefore, the present study aims to understand the genetic affinity of a constituent population from the Gorkha community, i.e. Kami, based on HLA polymorphism. Methods: First field HLA typing was performed among 158 Kami individuals by PCR-SSP methods. Results: The most frequent genes observed were HLA-A*11, HLA-B*15, HLA-DRB1*15. The frequency of HLA-DRB1*15 reported here is the highest recorded among the North Indian population to date, which is a noteworthy finding of the study. The hierarchical cluster analysis and principal component analysis showed that the Kami population lies within the cluster of the Indian subcontinental population. Conclusion: The study refutes the earlier proposition of exclusive belongingness of all the Gorkhas to Mongoloids.

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“…This analyses revealed the most frequent alleles in South Indian population including HLA-A * 02 and A * 24; HLA-B * 40 and B * 35, and HLA-DRB1 * 15 and DRB1 * 04. Balakrishnan et al [20] have previously reported that HLA-DRB1 * 15 allele was the most frequent in Kani tribe (45.19%) and less frequent in Narikkuravars (1.02%) from Tamil Nadu and Kerela, respectively. Additionally, HLA-DRB1 * 10 and DRB1 * 07 were found to be most common alleles in South Indian populations, whereas Caucasians DRB1 * 01 allele was also reported in the Namboothiris of Kerala, Narikkuravars of Tamil Nadu and Maratha of Maharastra [14,20].…”

Section: Discussionmentioning

confidence: 99%

“…Balakrishnan et al [20] have previously reported that HLA-DRB1 * 15 allele was the most frequent in Kani tribe (45.19%) and less frequent in Narikkuravars (1.02%) from Tamil Nadu and Kerela, respectively. Additionally, HLA-DRB1 * 10 and DRB1 * 07 were found to be most common alleles in South Indian populations, whereas Caucasians DRB1 * 01 allele was also reported in the Namboothiris of Kerala, Narikkuravars of Tamil Nadu and Maratha of Maharastra [14,20]. Mehra et al [21] reported that HLA-A * 02 was the most frequently occuring HLA allele in North Indian populations.…”

Section: Discussionmentioning

confidence: 99%

Comparative Analyses of Low, Medium and High-Resolution HLA Typing Technologies for Human Populations

Gowda¹,

Ambardar²,

Dighe³

et al. 2016

J Clin Cell Immunol

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Human Leukocyte Antigen (HLA) encoding genes are part of the major histocompatibility complex (MHC) on human chromosome 6. This region is one of the most polymorphic regions in the human genome. Prior knowledge of HLA allelic polymorphisms is clinically important for matching donor and recipient during organ/tissue transplantation. HLA allelic information is also useful in predicting immune responses to various infectious diseases, genetic disorders and autoimmune conditions. India harbors over a billion people and its population is untapped for HLA allelic diversity. In this study, we explored and compared three HLA typing methods for South Indian population, using Sequence-Specific Primers (SSP), NGS (Roche/454) and single-molecule sequencing (PacBio RS II) platforms. Over 1020 DNA samples were typed at low resolution using SSP method to determine the major HLA alleles within the South Indian population. These studies were followed up with medium resolution HLA typing of 80 samples based on exonic sequences on the Roche/454 sequencing system and high-resolution (6-8 digit) typing of 8 samples for HLA alleles of class I genes (HLA-A, B and C) and class II genes (HLA-DRB1 and DQB1) using PacBio RS II platform. The long reads delivered by SMRT technology, covered the full-length class I and class II genes/alleles in contiguous reads including untranslated regions, exons and introns, which provided phased SNP information. We have identified three novel alleles from PacBio data that were verified by Roche 454 sequencing. This is the first case study of HLA typing using second and third generation NGS technologies for an Indian population. The PacBio platform is a promising platform for large-scale HLA typing for establishing an HLA database for the untapped ethnic populations of India.

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Gradients in Distribution of HLA – DRB1 Alleles in Castes and Tribes of South India

Cited by 7 publications

References 1 publication

Polymorphic Alu Insertion/Deletion in Different Caste and Tribal Populations from South India

Polymorphic Alu Insertion/Deletion in Different Caste and Tribal Populations from South India

HLA Profile of Kami Population Refutes the Earlier Proposition of Exclusive Closer Genetic Affinity of All the Gorkhas to Mongoloids

Comparative Analyses of Low, Medium and High-Resolution HLA Typing Technologies for Human Populations

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