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Contrasting maternal and paternal genetic histories among five ethnic groups from Khyber Pakhtunkhwa, Pakistan. Sci Rep 2022; 12:1027. [PMID: 35046511 PMCID: PMC8770644 DOI: 10.1038/s41598-022-05076-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 12/10/2021] [Indexed: 11/24/2022] Open
Abstract
Northwest Pakistan has served as a point of entry to South Asia for different populations since ancient times. However, relatively little is known about the population genetic history of the people residing within this region. To better understand human dispersal in the region within the broader history of the subcontinent, we analyzed mtDNA diversity in 659 and Y-chromosome diversity in 678 individuals, respectively, from five ethnic groups (Gujars, Jadoons, Syeds, Tanolis and Yousafzais), from Swabi and Buner Districts, Khyber Pakhtunkhwa Province, Pakistan. The mtDNAs of all individuals were subject to control region sequencing and SNP genotyping, while Y-chromosomes were analyzed using 54 SNPs and 19 STR loci. The majority of the mtDNAs belonged to West Eurasian haplogroups, with the rest belonging to either South or East Asian lineages. Four of the five Pakistani populations (Gujars, Jadoons, Syeds, Yousafzais) possessed strong maternal genetic affinities with other Pakistani and Central Asian populations, whereas one (Tanolis) did not. Four haplogroups (R1a, R1b, O3, L) among the 11 Y-chromosome lineages observed among these five ethnic groups contributed substantially to their paternal genetic makeup. Gujars, Syeds and Yousafzais showed strong paternal genetic affinities with other Pakistani and Central Asian populations, whereas Jadoons and Tanolis had close affinities with Turkmen populations from Central Asia and ethnic groups from northeast India. We evaluate these genetic data in the context of historical and archeological evidence to test different hypotheses concerning their origins and biological relationships.
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Raina JK, Sharma M, Panjaliya RK, Dogra V, Bakaya A, Kumar P. Association of ESR1 (rs2234693 and rs9340799), CETP (rs708272), MTHFR (rs1801133 and rs2274976) and MS (rs185087) polymorphisms with Coronary Artery Disease (CAD). BMC Cardiovasc Disord 2020; 20:340. [PMID: 32682401 PMCID: PMC7368753 DOI: 10.1186/s12872-020-01618-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Accepted: 07/09/2020] [Indexed: 12/29/2022] Open
Abstract
Background Coronary artery disease (CAD) is a complex disease resulting from the cumulative and interactive effects of large number of genes along with environmental exposure. Therefore, the present study was envisaged as an effort to study the association of candidate genes ESR1 (rs2234693 and rs9340799), CETP (rs708272), MTHFR (rs1801133 and rs2274976) and MS (rs185087) polymorphisms with the risk of CAD, targeting the populations of Jammu (JandK). Method A total of 400 confirmed CAD patients and 400 healthy controls were enrolled for the present study. Genotyping was done by polymerase chain reaction- restriction fragment length polymorphism (PCR-RFLP). Results ESR1 gene (rs9340799) polymorphism was found to be associated with CAD in all the genetic models. The haplotype analysis of ESR1 (rs2234693 and rs9340799) gene revealed that C-G haplotype was conferring approximately 5-fold risk and T-A haplotype was adding 1.4-fold risk towards the disease. ‘T’ allele of MTHFR rs1801133 SNP was observed to be responsible for development of CAD in our study population (p < 0.0001). In case of MTHFR (rs1801133 and rs2274976) gene, the haplotype T-G was observed to confer 4.7-fold risk towards CAD whereas haplotype C-G provided nearly a 1.7 fold protection towards development of CAD. For MS gene, rs185087 was also found to be associated with CAD in a co-dominant (p = 0.003 and p = 0.03), dominant (p = 0.001) and allelic models (p = 0.001). The gene-gene interaction revealed strong epistasis between single nucleotide polymorphisms (SNPs), ESR1 rs9340799 and MTHFR rs2274976. Furthermore, the dendrogram for gene-environment dataset indicated moderately synergistic interaction between CETP rs708272 and physical inactivity. Conclusion In the study under reference, a significant association of ESR1-XbaI (rs9340799), MTHFR C677T (rs1801133) and MS A2756G (rs185087) gene polymorphisms with the susceptibility of CAD in the population of Jammu region (JandK) has been observed.
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Affiliation(s)
- Jyotdeep Kour Raina
- Institute of Human Genetics, University of Jammu, Jammu, JandK, 180006, India
| | - Minakashee Sharma
- Institute of Human Genetics, University of Jammu, Jammu, JandK, 180006, India
| | | | - Vikas Dogra
- Department of Zoology, Government Degree College, Samba, JandK, India
| | - Ashok Bakaya
- Department of Cardiology, Acharaya Shri Chander College of Medical Sciences (ASCOMS) and Hospital, Sidhra, Jammu, JandK, India
| | - Parvinder Kumar
- Institute of Human Genetics, University of Jammu, Jammu, JandK, 180006, India.,Human Genetics Lab, Department of Zoology, University of Jammu, Jammu, JandK, India
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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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Kaur M, Badaruddoza M. Genetic Polymorphism of Five STR Markers among Four Groups of Punjabi Population in North-West Punjab, India. INT J HUM GENET 2017. [DOI: 10.1080/09723757.2014.11886220] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Manpreet Kaur
- Department of Human Genetics; Guru Nanak Dev University; Amritsar 143 005, Punjab, India
| | - Manpreet Badaruddoza
- Department of Human Genetics; Guru Nanak Dev University; Amritsar 143 005, Punjab, 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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Kaur M, Badaruddoza. Population genetic analysis of five northwest Punjabi endogamous groups using microsatellite markers. Meta Gene 2016. [DOI: 10.1016/j.mgene.2016.08.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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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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Laybourn S, Akam EC, Cox N, Singh P, Mastana SS. Genetic analysis of novel Alu insertion polymorphisms in selected indian populations. Am J Hum Biol 2016; 28:941-944. [PMID: 27292586 DOI: 10.1002/ajhb.22881] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2015] [Revised: 05/03/2016] [Accepted: 05/10/2016] [Indexed: 11/06/2022] Open
Abstract
OBJECTIVES Indian subpopulations (Chenchu, Koya, and Lobana Sikh) were analyzed at the genetic level for 12 Alu polymorphisms. These markers were then utilized to establish levels of genetic identity between the Indian populations and more widely between the Indian populations and a European population. METHODS Previously collected blood samples were extracted using the phenol-chloroform method. The samples were utilized as templates for PCR using Alu specific primers and then analyzed by agarose gel electrophoresis for the presence and absence of the approximately 300 bp insertions. Allele frequencies were calculated by the gene counting method and were tested for Hardy-Weinberg equilibrium, heterozygosities, inbreeding coefficient, and GST to assess the level of genetic differentiation. RESULTS All of the Alu loci were polymorphic in the three Indian populations studied and their average observed heterozygosity ranged from 0.294 (Lobana Sikh) to 0.357 (Koya). Allele and genotype frequency variation at the 2b, 9a, and ACE loci led to statistically significant pairwise differences among the three study populations. Overall population heterogeneity was observed for 7 out of 12 Alu polymorphisms. CONCLUSION The overall results show that these Indian samples, though displaying significant genetic variation and differences among themselves, form an Indian cluster, which as expected, is distinct from the European sample (Russian). As Alus are easily analyzed and quantified by standard and cost-effective methodologies, this finding further reinforces their utility as effective population genetic markers. Am. J. Hum. Biol., 2016. © 2016 Wiley Periodicals, Inc. Am. J. Hum. Biol. 28:941-944, 2016. © 2016Wiley Periodicals, Inc.
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Affiliation(s)
- Susie Laybourn
- Human Genomics Lab, School of Sport, Exercise and Heath Sciences, Loughborough University, Loughborough, Leicestershire, LE11 3TU, United Kingdom
| | - Elizabeth Claire Akam
- Human Genomics Lab, School of Sport, Exercise and Heath Sciences, Loughborough University, Loughborough, Leicestershire, LE11 3TU, United Kingdom
| | - Nick Cox
- Human Genomics Lab, School of Sport, Exercise and Heath Sciences, Loughborough University, Loughborough, Leicestershire, LE11 3TU, United Kingdom
| | - Puneetpal Singh
- Department of Human Genetics, Punjabi University, Patiala, Punjab, India
| | - Sarabjit S Mastana
- Human Genomics Lab, School of Sport, Exercise and Heath Sciences, Loughborough University, Loughborough, Leicestershire, LE11 3TU, United Kingdom
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