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Tayyeh AM, Sequeira JJ, Kumar L, Babu I, van Driem G, Mustak MS. The maternal ancestry of the Kavaratti islanders and the last glacial maximum aftermath. Mol Genet Genomics 2023; 298:1467-1477. [PMID: 37823939 DOI: 10.1007/s00438-023-02072-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 09/23/2023] [Indexed: 10/13/2023]
Abstract
The prehistoric human settlement of the Lakshadweep islands remains a mystery for various reasons. Uncertainty about the existence of indigenous tribes in these islands and the lack of folklore records present major obstacles to the reconstruction of Lakshadweep ancestry. However, with extant population data, we seek to understand the maternal ancestry of the Kavaratti islanders. Mitochondrial control region variation analysis of 80 individuals from this island shows maternal links with the populations in the northwestern region of the South Asian mainland. The founder clade R30b2, observed in the Kavaratti islanders, is so far present only in the Scheduled Castes from the Punjab region, Jat Sikhs and Nairs. All other mainland populations carry basal R30 or R30a subclades. The presence of a specific Uralic U4 lineage in our samples, in addition to the Indo-European affinity observed in the phylogeny tree, substantiates a northwestern maternal ancestry of the Kavaratti islanders and implies an ancestral admixture with early humans in the Near East at the time of the last glacial maximum (LGM). Based on our Bayesian analysis, we furthermore propose that a group bearing mostly R30b2 during the LGM recovery, moved eastward and southward, where they received Indian-specific M haplogroups. Hence, the maternal ancestry of the Kavaratti islanders is evidently a consequence of the demographic changes in the northwestern region of the Indian subcontinent caused by the Last Glacial Maximum. The haplogroup distribution pattern and nucleotide sequence data produced in this study will enrich the forensic database of the Lakshadweep islands.
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Affiliation(s)
- Alnoman Mundher Tayyeh
- Department of Applied Zoology, Mangalore University, Mangalagangothri, 574199, India
- Department of Biosciences, Biotechnology Unit, Mangalore University, Mangalagangothri, 574199, India
| | | | - Lomous Kumar
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, Telangana, 500007, India
| | - Idrees Babu
- Department of Science and Technology, Lakshadweep Administration, Kavaratti, 682555, India
| | - George van Driem
- Institut für Sprachwissenschaft, Universität Bern, Länggassstrasse 49, 3012, Bern, Switzerland
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Beaumont R, Akam L, Singh P, Bhatti JS, Mastana S. Genomic diversity and differentiation of Alu insertion polymorphisms in a native British and four South Asian migrant populations. Ann Hum Biol 2023; 50:117-122. [PMID: 36786492 DOI: 10.1080/03014460.2023.2180091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/15/2023]
Abstract
BACKGROUND Alu insertions are bi-allelic and primate-specific, this makes them a useful marker for studying genetic variation, migration patterns, forensic analyses, paternity, and evolutionary heritage; however, specific population studies are limited. AIM The objective of this study is to document the level and extent of genetic variation at 39 different Alu loci in five populations (British, Indian Punjabi, Indian Gujarati, Pakistani, and Bangladeshi) from the East Midlands region of the UK. Genetic data on migrant populations is currently limited. SUBJECTS AND METHODS DNA samples (n = 543) were analysed for 39 Alu insertion polymorphisms using specific primers and standard protocols. Data were analysed for population and forensic genetic parameters. RESULTS All studied Alus were polymorphic in the British White population while South Asian migrant populations had a variable number of loci which were monomorphic. Highest heterozygosities and lowest match probabilities were observed in the British sample, while the Bangladeshi sample had the lowest heterozygosity and higher match probability. CONCLUSION The analysed Alus insertions (TPA25, Ya5NBC123, Ya5NBC182, Ya5NBC241, and Ya5NBC242) are highly polymorphic and variable among migrant populations. These loci could be useful for population genomic and differentiation studies.
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Affiliation(s)
- Rebekah Beaumont
- Human Genomics Lab, School of Sport, Exercise and Health Sciences, Loughborough University, Loughborough, UK
| | - Liz Akam
- Human Genomics Lab, School of Sport, Exercise and Health Sciences, Loughborough University, Loughborough, UK
| | - Puneetpal Singh
- Department of Human Genetics, Punjabi University, Patiala, India
| | - Jasvinder Singh Bhatti
- Department of Human Genetics and Molecular Medicine, School of Health Sciences, Central University of Punjab, Bathinda, India
| | - Sarabjit Mastana
- Human Genomics Lab, School of Sport, Exercise and Health Sciences, Loughborough University, Loughborough, UK
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Nadiger N, Anantharamu S, Priyanka CN, Vidal-Puig A, Mukhopadhyay A. Unique attributes of obesity in India: A narrative review. OBESITY MEDICINE 2022; 35:100454. [PMID: 38572212 PMCID: PMC7615800 DOI: 10.1016/j.obmed.2022.100454] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 04/05/2024]
Abstract
Obesity has become a burgeoning epidemic in India, even though the country is still dealing with undernutrition. As a significant determinant of the Metabolic Syndrome (MetS) and non-communicable diseases (NCDs) such as type 2 diabetes mellitus (T2DM) and cardiovascular disease (CVD), understanding the Indian context of the problem and learning how to deal with the obesity epidemic in this country has gained paramount importance. This narrative review points to the unique features of the obesity epidemic in India and its associated contributing factors, including the evolving nature of the Indian diet, the peculiarity of the increased adiposity at lower BMIs, unique obesity-associated genetic variants in Indians, the contribution of the gut microbiome, the impact of chronic inflammation and the role of ambient air pollution, and the contribution of decreased physical activity levels concerning the rapid urbanisation and the built environment. We believe that disseminating our insights into these unique features influencing the development of obesity in India will help increase global awareness and pave the way for better control and management of this obesity epidemic.
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Affiliation(s)
- Nikhil Nadiger
- Division of Nutrition, St. John's Research Institute, St. John's Medical College, Koramangala, Bangalore, India
| | - Sahana Anantharamu
- Division of Nutrition, St. John's Research Institute, St. John's Medical College, Koramangala, Bangalore, India
| | - CN Priyanka
- Division of Nutrition, St. John's Research Institute, St. John's Medical College, Koramangala, Bangalore, India
| | - Antonio Vidal-Puig
- University of Cambridge Metabolic Research Laboratories, Institute of Metabolic Science, MDU MRC, Addenbrooke's Hospital, Cambridge, UK
| | - Arpita Mukhopadhyay
- Division of Nutrition, St. John's Research Institute, St. John's Medical College, Koramangala, Bangalore, India
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Singh G, Yellapu S, Sandhu HS, Sharma I, Sharma V, Bhanwer AJS. Genetic characterisation of the North-West Indian populations: analysis of mitochondrial DNA control region variations. Ann Hum Biol 2021; 48:166-172. [PMID: 33494619 DOI: 10.1080/03014460.2021.1879933] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
BACKGROUND Human mitochondrial DNA presents several interesting characteristics, making it a favourable tool in the field of molecular anthropology, medical genetics, population history, and forensic science. AIM The present study investigated the mitochondrial DNA (mtDNA) control region variations in diverse ethnic groups of North-West India for which population data is insufficient. SUBJECTS AND METHODS The complete mtDNA control regions of 197 unrelated (for up to three generations) healthy individuals belonging to different ethnic groups of North-West India were sequenced. The haplotype frequencies, haplogroup distribution, and pairwise FST values between the studied and other worldwide populations were generated to study patterns of variation in human mtDNA. RESULTS The results ascertained high gene diversity (0.998) in the studied maternal lineages, identifying 166 distinct haplotypes, of which 158 were unique and characterised by 117 variable sites. Three haplogroups: M3, M30, and U7 were observed to be the most prevalent, and phylogeographically a total of 55.86% of sequences were characterised into South Asian, followed by West Eurasian (40.18%) and East Asian (3.96%), ancestry haplogroups. Pairwise genetic differentiation comparisons revealed maternal homogeneity in the studied groups. No population substructure was detected within the North-West Indian populations. CONCLUSION The results of this preliminary study will contribute to an existing database of mtDNA variations of the Indian population and facilitate prospective studies investigating population genetics and human diseases.
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Affiliation(s)
- Gagandeep Singh
- Department of Human Genetics, Guru Nanak Dev University, Amritsar, India.,Department of Anthropology, Panjab University, Chandigarh, India
| | | | | | - Indu Sharma
- Ancient DNA Laboratory, Birbal Sahni Institute of Palaeosciences, Lucknow, India
| | - Varun Sharma
- Ancient DNA Laboratory, Birbal Sahni Institute of Palaeosciences, Lucknow, India
| | - A J S Bhanwer
- Department of Human Genetics, Guru Nanak Dev University, Amritsar, India
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Chang S, Li J, Li Q, Yu CP, Xie LL, Wang S. Retrieving the deleterious mutations before extinction: genome-wide comparison of shared derived mutations in liver cancer and normal population. Postgrad Med J 2021; 98:584-590. [PMID: 33837126 DOI: 10.1136/postgradmedj-2021-139993] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2021] [Revised: 03/15/2021] [Accepted: 03/29/2021] [Indexed: 12/11/2022]
Abstract
STUDY PURPOSE Deleterious mutations would be rapidly purged from natural populations along with the extinction of their carriers. The currently observed mutations in existing species are mostly neutral. The inaccessibility of deleterious mutations impedes the functional studies on how these mutations affect the fitness at individual level. STUDY DESIGN The connection between the deleterious genotype and the non-adaptive phenotype could be bridged by sequencing the genome before extinction. Although this approach is no longer feasible for evolutionary biologists, it is feasible for cancer biologists by profiling the mutations in tumour samples which are so deleterious that the carriers hardly live. RESULTS By comparing the derived mutation profile between normal populations and patients with liver cancer, we found that the shared mutations, which are highly deleterious, are suppressed to low allele frequencies in normal populations and tissues, but show remarkably high frequency in tumours. The density of shared mutations is negatively correlated with gene conservation and expression levels. CONCLUSIONS Deleterious mutations are suppressed in functionally important genes as well as in normal populations. This work deepened our understanding on how natural selection act on deleterious mutations by analogising the cancer evolution to species evolution, which are essentially the same molecular process but at different time scales.
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Affiliation(s)
- Shuai Chang
- Department of Interventional Radiology, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Jian Li
- Department of Interventional Radiology, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Qun Li
- Department of Interventional Radiology, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Chun-Peng Yu
- Department of Interventional Radiology, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Ling-Ling Xie
- Department of Interventional Radiology, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Song Wang
- Department of Interventional Radiology, The Affiliated Hospital of Qingdao University, Qingdao, China
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Singh G, Sandhu HS, Sharma R, Srinivas Y, Matharoo K, Singh M, Bhanwer AJS. Genetic variation and population structure of five ethnic groups from Punjab, North-West India: Analysis of MHC class I polymorphic Alu insertions (POALINs). Gene 2019; 701:173-178. [PMID: 30935920 DOI: 10.1016/j.gene.2019.03.057] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Revised: 03/14/2019] [Accepted: 03/25/2019] [Indexed: 01/31/2023]
Abstract
Genetic variation and differentiation of five ethnic groups from Punjab, North-West India was characterized by analyzing data on polymorphic Alu insertions (POALINs) within the class I genomic region of major histocompatibility complex (MHC), which is completely non-existent in Indian population. The haplotype frequency, distribution and heterozygosity among these groups and their potential implications in molecular anthropology and evolutionary studies were also determined. A total of 479 unrelated healthy individuals representing five different ethnic groups: Banias, Brahmins, Khatri, Jat Sikhs and Scheduled Castes were genotyped for five MHC Alu elements (AluHG, AluMICB, AluHJ, AluTF and AluHF) using polymerase chain reaction (PCR). All the loci were found to be polymorphic among the studied populations. No significant deviation from Hardy-Weinberg equilibrium was observed, except for the AluHJ locus in Brahmins. The POALINs varied in allele frequency between 0.0260 and 0.4427. The average heterozygosity among the studied groups ranged from 0.1937 in Banias to 0.2666 in Jat Sikhs. The genetic differentiation among the studied groups was observed to be of the order of 0.01302. Single POALIN haplotypes were found to be more frequent than multiple POALIN haplotypes. The results of inter-population differentiations, haplotype frequencies, genetic distances, multidimensional scaling, phylogenetic and structure analyses indicated close genetic relationships between the five ethnic groups of Punjab, North-West India. Analyses of polymorphic Alu loci of MHC genomic region may represent reliable information about the ancestry, demographic history and geographic origins of the various human populations, facilitating better understanding of the evolutionary, forensic and epidemiological prospective.
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Affiliation(s)
- Gagandeep Singh
- Department of Anthropology, Panjab University, Chandigarh 160014, India; Department of Human Genetics, Guru Nanak Dev University, Amritsar, Punjab 143005, India.
| | - Harkirat Singh Sandhu
- Icahn School of Medicine at Mount Sinai, Tisch Cancer Institute, 1470 Madison Avenue, New York, NY 10029, USA
| | - Rubina Sharma
- Department of Surgery-Transplant, Regenerative Medicine, DRC-II, University of Nebraska Medical Center, Omaha, NE 68198-5965, USA
| | | | - Kawaljit Matharoo
- Department of Human Genetics, Guru Nanak Dev University, Amritsar, Punjab 143005, India
| | - Manroop Singh
- Department of Human Genetics, Guru Nanak Dev University, Amritsar, Punjab 143005, India
| | - A J S Bhanwer
- Department of Human Genetics, Guru Nanak Dev University, Amritsar, Punjab 143005, India.
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Aziz S, Nawaz M, Afridi SG, Khan A. Genetic structure of Kho population from north-western Pakistan based on mtDNA control region sequences. Genetica 2019; 147:177-183. [DOI: 10.1007/s10709-019-00060-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2018] [Accepted: 03/15/2019] [Indexed: 01/31/2023]
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Singh G, Bhanwer A. Distribution of angiotensin converting enzyme gene (insertion/deletion) polymorphism in Indian populations. GENE REPORTS 2019. [DOI: 10.1016/j.genrep.2018.12.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Screening of over 1000 Indian patients with breast and/or ovarian cancer with a multi-gene panel: prevalence of BRCA1/2 and non-BRCA mutations. Breast Cancer Res Treat 2018; 170:189-196. [PMID: 29470806 DOI: 10.1007/s10549-018-4726-x] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Accepted: 02/19/2018] [Indexed: 12/15/2022]
Abstract
PURPOSE Breast and/or ovarian cancers are among the most common cancers in women across the world. In the Indian population, the healthcare burden of breast and/or ovarian cancers has been steadily rising, thus stressing the need for early detection, surveillance, and disease management measures. However, the burden attributable to inherited mutations is not well characterized. METHODS We sequenced 1010 unrelated patients and families from across India with an indication of breast and/or ovarian cancers, using the TruSight Cancer panel which includes 14 genes, strongly associated with risk of hereditary breast and/or ovarian cancers. Genetic variations were identified using the StrandNGS software and interpreted using the StrandOmics platform. RESULTS We were able to detect mutations in 304 (30.1%) cases, of which, 56 mutations were novel. A majority (84.9%) of the mutations were detected in the BRCA1/2 genes as compared to non-BRCA genes (15.1%). When the cases were stratified on the basis of age at diagnosis and family history of cancer, the high rate of 75% of detection of hereditary variants was observed in patients whose age at diagnosis was below 40 years and had first-degree family member(s) affected by breast and/or ovarian cancers. Our findings indicate that in the Indian population, there is a high prevalence of mutations in the high-risk breast cancer genes: BRCA1, BRCA2, TP53, and PALB2. CONCLUSION In India, socioeconomic inequality limiting access to treatment is a major factor towards increased cancer burden; therefore, incorporation of a cost-effective and comprehensive multi-gene test will be helpful in ensuring widespread implementation of genetic screening in the clinical practice for hereditary breast and/or ovarian cancers.
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Singh G, Talwar I, Sandhu HS, Matharoo K, Bhanwer AJS. Genetic dissection of five ethnic groups from Punjab, North-West India-A study based on Autosomal Markers. Leg Med (Tokyo) 2017; 26:25-32. [PMID: 28549544 DOI: 10.1016/j.legalmed.2017.02.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Revised: 02/07/2017] [Accepted: 02/27/2017] [Indexed: 10/20/2022]
Abstract
The present study assessed the applicability of Alu insertion elements and Single Nucleotide Polymorphisms (SNPs) in forensic identification and estimated the extent of genetic variation in five major ethnic groups of Punjab, North-West India. A total of 1012 unrelated samples belonging to Banias, Brahmins, Jat Sikhs, Khatris and Scheduled Castes were genotyped for four Alu elements (ACE, APO, PLAT, D1) and six Single Nucleotide Polymorphisms [ESR (PvuII), LPL (PvuII), HTR2A (MspI), DRD2 Taq1A, Taq1B, Taq1D]. Allele frequencies observed heterozygosity and forensic efficacy parameters were determined. The data on the genetic affinity of the studied populations among themselves and with other populations of India was also analysed using a Neighbor-Joining tree and multidimensional scaling plot respectively. All the 10 loci were polymorphic and their average observed heterozygosity ranged from 0.3872 (Banias) to 0.4311 (Scheduled Castes). Allele frequency variation at the 9 out of 10 loci led to statistically significant pairwise differences among the five study population groups. The result from AMOVA, Structure analysis, and Phylogenetic tree suggests that these populations are homogenous. In the multidimensional scaling plot, the present study populations formed a compact cluster clearly separated from other populations, suggesting a unique genetic identity of the Punjab populations as a whole. All these observations suggest that either a recent common origin of these populations or extensive gene flow across the populations that dissolve the original genetic differences. The data generated in this study will be useful for forensic genetics, molecular anthropological and demographic studies.
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Affiliation(s)
- Gagandeep Singh
- Department of Anthropology, Panjab University, Chandigarh 160014, India; Department of Human Genetics, Guru Nanak Dev University, Amritsar, Punjab 143005, India.
| | - Indu Talwar
- Department of Anthropology, Panjab University, Chandigarh 160014, India.
| | - Harkirat Singh Sandhu
- Department of Human Genetics, Guru Nanak Dev University, Amritsar, Punjab 143005, India.
| | - Kawaljit Matharoo
- Department of Human Genetics, Guru Nanak Dev University, Amritsar, Punjab 143005, India.
| | - A J S Bhanwer
- Department of Human Genetics, Guru Nanak Dev University, Amritsar, Punjab 143005, India.
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