Genomic diversity and affinities in population groups of North West India: An analysis of Alu insertion and a single nucleotide polymorphism

Saini, Janmeet S.; Kumar, Ajay; Matharoo, Kawaljit; Sokhi, Jasmine; Badaruddoza,; Bhanwer, A.J.S.

doi:10.1016/j.gene.2012.08.034

Cited by 9 publications

(6 citation statements)

References 34 publications

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“…The clear functional picture of ESR1-XbaI polymorphism is still under exploration. The allele frequencies of ESRI-PvuII variants in the present study are in accordance with previous findings in population of Jammu [17] whereas these frequencies have been found to be higher when compared to adjoining North-west Indian populations [18]. The present study did not find any association of ESR1-(rs2234693) polymorphism with CAD in the studied population of Jammu region.…”

Section: Discussionsupporting

confidence: 91%

Association of ESR1 (rs2234693 and rs9340799), CETP (rs708272), MTHFR (rs1801133 and rs2274976) and MS (rs185087) polymorphisms with Coronary Artery Disease (CAD)

Raina

Sharma

Panjaliya

et al. 2020

BMC Cardiovasc Disord

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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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Section: Discussionsupporting

confidence: 91%

Association of ESR1 (rs2234693 and rs9340799), CETP (rs708272), MTHFR (rs1801133 and rs2274976) and MS (rs185087) polymorphisms with Coronary Artery Disease (CAD)

Raina

Sharma

Panjaliya

et al. 2020

BMC Cardiovasc Disord

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“…Overall results of well-studied Alu loci like ACE, TPA, APO and PV92 are comparable to many studies from Indian subcontinent (Majumder et al 1999;Veerraju et al 2008;Tripathi et al 2008;Kshatriya et al 2012;Saini et al 2012).…”

Section: Discussionsupporting

confidence: 87%

“…Unfortunately, there is paucity of data on new Alu polymorphisms to carry out comprehensive comparative analyses. Overall, the results of well-studied Alu loci like ACE, TPA, APO, and PV92 are comparable to many studies from Indian subcontinent (Kshatriya et al, 2011;Majumder et al, 1999;Saini et al, 2012;Tripathi et al, 2008;Veerraju et al, 2008).…”

Section: Discussionsupporting

confidence: 85%

“…While there are many reports on Alu polymorphisms in different populations of the world (Batzer et al, 1996), studies from the Indian subcontinent are limited to relatively small number of loci and populations (Kshatriya et al, 2011;Majumder et al, 1999;Saini et al, 2012;Tripathi et al, 2008). In order to extend and document genetic variation of Alu polymorphisms, we analyzed eight new Alu insertion polymorphisms together with four extensively studied Alus (ACE, TPA, APO, PV92) (Majumder et al, 1999;Mamedov et al, 2010) in three distinct populations from India (one caste population from Punjab (Lobana Sikhs) and two tribal populations (Chenchu and Koya) from Andhra Pradesh (now Telangana).…”

Section: Introductionmentioning

confidence: 99%

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Genetic analysis of novel Alu insertion polymorphisms in selected indian populations

Laybourn

Akam

Cox

et al. 2016

American J Hum Biol

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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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“…A very few number of genetic studies (Badaruddoza et al 2007(Badaruddoza et al , 2008Badaruddoza and Sudhir 2012;Saini et al 2012) have been carried out on Punjabi population. However, no STR marker based study on present study populations have been reported in the literature till date.…”

Section: Population Informationmentioning

confidence: 99%

Analysis of TNFRSF1A Gene R92Q Mutation in Familial Mediterranean Fever

Yuce

Bağcı

2014

IJHG

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Historically, Punjab has served a major passage way for human migration to Indian subcontinent and has influenced the genetic structure of extant populations in Punjab. Therefore, Punjabi population possesses an exclusive genetic profile primarily due to the many migratory events in this region which caused an extensive range of genetic diversity. Hence, the present study is an attempt to understand the effect of these influences on genetic differentiation, diversity a nd popula tion structure of Punjab. Genetic polymorphism at five highly polymorphic short tandem repeat loci (STR) is studied in four endogamous population groups of Punjab, India. The studied groups included Jat Sikh, Majbi Sikh, Brahmin and Ramdasia to evaluate their significance in human identification and genetic study. All selected groups practice endogamy and a total of 358 individuals belonging to these four endogamous groups were studied for five highly polymorphic with greater power of exclusion STR loci: THO1, TPOX, D7S820, CSF1PO and vWA. The highest observed heterozygosity was found in Ramdasia population for almost all the markers except vWA which had highest observed heterozygosity among Majbi Sikh population group. In this study, the average sub-ethnic differentiation (Fst) among the four populations of north-west Punjab was 0.0821. The marker with the highest contribution to interpopulation genetic difference was obser ved to be vWA.

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Genomic diversity and affinities in population groups of North West India: An analysis of Alu insertion and a single nucleotide polymorphism

Cited by 9 publications

References 34 publications

Association of ESR1 (rs2234693 and rs9340799), CETP (rs708272), MTHFR (rs1801133 and rs2274976) and MS (rs185087) polymorphisms with Coronary Artery Disease (CAD)

Association of ESR1 (rs2234693 and rs9340799), CETP (rs708272), MTHFR (rs1801133 and rs2274976) and MS (rs185087) polymorphisms with Coronary Artery Disease (CAD)

Genetic analysis of novel Alu insertion polymorphisms in selected indian populations

Analysis of TNFRSF1A Gene R92Q Mutation in Familial Mediterranean Fever

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