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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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Mestiri S, Boussetta S, Pakstis AJ, Elkamel S, Elgaaied ABA, Kidd KK, Cherni L. Genetic diversity of the North African population revealed by the typing of SNPs in the DRD2/ANKK1 genomic region. Gene 2021; 777:145466. [PMID: 33524518 DOI: 10.1016/j.gene.2021.145466] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2020] [Revised: 01/11/2021] [Accepted: 01/22/2021] [Indexed: 10/22/2022]
Abstract
The dopamine - related genes, like dopamine D2 receptor (DRD2) gene and ankyrin repeat and kinase domain containing 1 (ANKK1) gene are implicated in neurological functions. Some polymorphisms of the DRD2/ANKK1 locus (TaqIA, TaqIB, TaqID) have been used to study genetic diversity and the evolution of human populations. The present investigation aims to assess the genetic diversity in seven North African populations in order to explore their genetic structure and to compare them to others worldwide populations studied for the same locus. Nine single nucleotide polymorphisms (SNPs) from the DRD2/ANKK1 locus (rs1800497 TaqIA, rs2242592, rs1124492, rs6277, rs6275, rs1079727, rs2002453, rs2234690 and rs1079597 TaqIB) were typed in 366 individuals from seven North African populations: six from Tunisia (Sousse, Smar, Kesra, Kairouan, Mehdia and Kerkennah) and one from Libya. The allelic frequencies of rs2002453 and rs2234690 were higher in the Smar population than in the other North African populations. More, the Smar population showed the lowest average heterozygosity (0.313). The principal component analysis (PCA) showed that the Smar population was clearly separated from others. Furthermore, linkage disequilibrium analysis shown a high linkage disequilibrium in the North African population and essentially in Smar population. Comparison with other world populations has shown that the heterozygosity of North African population was very close to that of the African and European populations. The PCA and the haplotypic analysis suggested the presence of an important Eurasian genetic component for the North African population. These results suggested that the Smar population was isolated from the others North Africans ones by its peculiar genetic structure because of isolation, endogamy and genetic drift. On the other hand, the North African population is characterized by a multi ancestral gene pool from Eurasia and sub-Saharan Africa due to human migration since prehistoric times.
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Affiliation(s)
- Souhir Mestiri
- Laboratory of Genetics, Biodiversity and Bioresource Valorization (LR11ES41), University of Monastir, Monastir 5000, Tunisia; Higher Institute of Biotechnology of Monastir, Monastir University, 5000 Monastir, Tunisia.
| | - Sami Boussetta
- Laboratory of Genetics, Immunology and Human Pathologies, Faculty of Sciences of Tunis, University of Tunis El Manar, 2092 Tunis, Tunisia.
| | - Andrew J Pakstis
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06520, USA.
| | - Sarra Elkamel
- Laboratory of Genetics, Immunology and Human Pathologies, Faculty of Sciences of Tunis, University of Tunis El Manar, 2092 Tunis, Tunisia.
| | - Amel Ben Ammar Elgaaied
- Laboratory of Genetics, Immunology and Human Pathologies, Faculty of Sciences of Tunis, University of Tunis El Manar, 2092 Tunis, Tunisia
| | - Kenneth K Kidd
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06520, USA.
| | - Lotfi Cherni
- Higher Institute of Biotechnology of Monastir, Monastir University, 5000 Monastir, Tunisia; Laboratory of Genetics, Immunology and Human Pathologies, Faculty of Sciences of Tunis, University of Tunis El Manar, 2092 Tunis, Tunisia.
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Gareeva AE, Badretdinov UG, Akhmetova EA, Kinyasheva KO, Nasibullin TR, Samigullina LI, Timerbulatov IF, Timerbulatova MF, Asadullin AR. [The role of genetic factors in the development of suicidal behavior in individuals with dependence on synthetic cathinones]. Zh Nevrol Psikhiatr Im S S Korsakova 2020; 120:69-77. [PMID: 33244961 DOI: 10.17116/jnevro202012010169] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
OBJECTIVE To identify polymorphisms in the genes of dopaminergic and serotonergic systems associated with the risk of suicidal behavior in individuals with dependence on synthetic cathinones. MATERIAL AND METHODS One hundred and eighty-two men with the diagnosis of Substance dependence (ICD-10 F15) tested positive for metabolites of synthetic cathinones (a-PVP, MDPV) in the urine were studied. Genotyping was performed for rs1800497 DRD2, rs4646984 DRD4, VNTR 40 b.p. SLC6A3, rs27072 SLC6A3, rs6313 HTR2A and rs6296 HTR1B using PCR and RFLP technique. RESULTS AND CONCLUSION It was found that the genes of the serotonergic system HTR2A and HTR1B are predictors of the development of some endophenotypes of suicidal behavior in individuals with dependence on synthetic cathinones.
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Affiliation(s)
- A E Gareeva
- Bashkir State Medical University, Ufa, Russia.,Institute of Biochemistry and Genetics, the Russian Academy of Sciences, Ufa, Russia
| | | | | | - K O Kinyasheva
- Institute of Biochemistry and Genetics, the Russian Academy of Sciences, Ufa, Russia
| | - T R Nasibullin
- Institute of Biochemistry and Genetics, the Russian Academy of Sciences, Ufa, Russia
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Singh G, Sandhu HS, Srinivas Y, Matharoo K, Bhanwer AJS. Genetic portrait of North-West Indian population based on X chromosome Alu insertion markers. Int J Legal Med 2019; 134:1655-1657. [PMID: 31853675 DOI: 10.1007/s00414-019-02238-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Accepted: 12/11/2019] [Indexed: 11/25/2022]
Abstract
In the present study, allele frequencies and forensic parameters of four ethnic groups (Brahmin, Khatri, Jat Sikh, and Scheduled Caste) of Punjab, India, at 10 Alu insertions of X chromosome were calculated. Six Alu markers were observed to be highly polymorphic with no significant deviations from Hardy-Weinberg equilibrium and no linkage disequilibrium present in any marker. Multidimensional plot showed higher genetic affinity of studied populations with Asian populations. Overall, the tested markers were reliable and were found suitable in human forensics and population genetic studies.
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Affiliation(s)
- Gagandeep Singh
- Department of Anthropology, Panjab University, Chandigarh, India.
- Department of Human Genetics, Guru Nanak Dev University, Amritsar, Punjab, India.
| | - Harkirat Singh Sandhu
- Icahn School of Medicine at Mount Sinai, Tisch Cancer Institute, 1470 Madison Avenue, New York, NY, USA
| | | | - Kawaljit Matharoo
- Department of Human Genetics, Guru Nanak Dev University, Amritsar, Punjab, India
| | - A J S Bhanwer
- Department of Human Genetics, Guru Nanak Dev University, Amritsar, Punjab, India
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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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Kaur G, Singh Chavan B, Gupta D, Sinhmar V, Prasad R, Tripathi A, Garg PD, Gupta R, Khurana H, Gautam S, Margoob MA, Aneja J. An association study of dopaminergic (DRD2) and serotoninergic (5-HT2) gene polymorphism and schizophrenia in a North Indian population. Asian J Psychiatr 2019; 39:178-184. [PMID: 30389402 DOI: 10.1016/j.ajp.2018.10.022] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/18/2018] [Revised: 09/24/2018] [Accepted: 10/23/2018] [Indexed: 01/04/2023]
Abstract
The aim of this study was to investigate whether single nucleotide polymorphisms (SNPs) in DRD2 and 5-HT2 receptor genes are associated with schizophrenia in North Indian population. Four hundred forty-three patients who met ICD10-DCR criteria for schizophrenia were enrolled from six participating centers along with 443 genetically related healthy subjects and 150 genetically unrelated healthy participants. A total of 7 gene polymorphisms from DRD2 (rs1800497, rs1079597, rs1800498, rs1801028) and 5-HT2 A (rs6313, rs6311, rs6305) were genotyped for their association with schizophrenia. No significant difference was found in frequency of various genotypes and alleles of the studied markers for DRD2 and 5-HT2 A genes between the cases and their genetic controls. However, significant differences were noted for rs1079597 genotype (Taq1B; p = 0.039) and its allele frequencies (p = 0.029) in persons with schizophrenia and the unrelated healthy controls. The DRD2 (Taq1 A-B-D) and 5-HT2 A (rs6311-rs6313-rs6305) haplotype frequencies differed significantly for A2B1D2 [p = 0.038; OR = 0.685 (95%CI = 0.479-0.981)] and ACC [p = 0.001; OR = 0.621 (95%CI = 0.461-0.838)] for the cases vs genetically related healthy controls. Similarly, significant difference was observed for the frequencies of GCC [p = 0.006; OR = 0.692 (95%CI = 0.532-0.900)] and ACC [p < 0.001; OR = 3.622 (95%CI = 1.73-7.585)] in the cases and unrelated healthy controls. Unlike previous research from India as well as abroad, the predominance of B1 allele of rs1079597 in patients with schizophrenia and absence of Cys311 in all study participants is a salient difference. Concluding, the B2 allele of rs1079597 may increase the risk of schizophrenia while the A2B1D2 haplotype may be protective in North Indian population.
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Affiliation(s)
- Gurjit Kaur
- Department of Physiology, Government Medical College & Hospital, Sector 32, Chandigarh, India
| | - Bir Singh Chavan
- Department of Psychiatry, Government Medical College & Hospital, Sector 32, Chandigarh, India
| | - Deepti Gupta
- Genetic Centre, Government Medical College & Hospital, Sector 32, Chandigarh, India
| | - Vikas Sinhmar
- Genetic Centre, Government Medical College & Hospital, Sector 32, Chandigarh, India
| | - Rajendra Prasad
- Department of Biochemistry, Postgraduate Institute of Medical Education & Research, Sector 12, Chandigarh, India
| | - Adarsh Tripathi
- Department of Psychiatry, King George's Medical University, Lucknow, Uttar Pradesh, India
| | - P D Garg
- Department of Psychiatry, Government Medical College, Amritsar, Punjab, India
| | - Rajiv Gupta
- Department of Psychiatry, Postgraduate Institute of Medical Sciences, Rohtak, Haryana, India
| | - Hitesh Khurana
- Department of Psychiatry, Postgraduate Institute of Medical Sciences, Rohtak, Haryana, India
| | - Shiv Gautam
- Department of Psychiatry, SMS Medical College, Jaipur, Rajasthan, India
| | - Mushtaq Ahmed Margoob
- Department of Psychiatry, Government Medical College, Srinagar, Jammu & Kashmir, India
| | - Jitender Aneja
- Department of Psychiatry, All India Institute of Medical Sciences, Jodhpur, Rajasthan, India.
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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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Singh G, Talwar I, Sharma R, Matharoo K, Bhanwer AJS. Genetic differentiation and population structure of five ethnic groups of Punjab (North-West India). Mol Genet Genomics 2016; 291:2055-2063. [DOI: 10.1007/s00438-016-1239-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2016] [Accepted: 08/03/2016] [Indexed: 12/15/2022]
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