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1
Coronavirus (SARS-CoV-2) and Mortality Rate in India: The Winning Edge
Dergi Makalesi

Dergi Makalesi
Open Access
Kaynak :
Directory of Open Access Journals (DOAJ)
Dergi:
Frontiers in Public Health
Yazar(lar) :
Gyaneshwer Chaubey
Yıl :
2020
Gyaneshwer Chaubey
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DOI : 10.3389/fpubh.2020.00397
Anahtar Kelimeler : COVID-19, India, endogamy, disease susceptibility, herd immunity
ISSN: 2296-2565
Cilt: 8
Sınıflandırma :
2
Language isolates and their genetic identity: a commentary on mitochondrial DNA history of Sri Lankan ethnic people: their relations within the island and with the Indian subcontinental populations
Dergi Makalesi

Dergi Makalesi
Open Access
Kaynak :
Springer Nature
Dergi:
Journal of Human Genetics
Yayıncı:
Springer Nature
Yazar(lar) :
Gyaneshwer Chaubey
Konu :
Mitochondrial genome, Population genetics
Yıl :
2013
Gyaneshwer Chaubey
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DOI : 10.1038/jhg.2013.122
ISSN: 1435-232X
Cilt: 59
Sayı: 2
Sayfa: 61-63
Sınıflandırma :
3
The genetic makings of South Asia
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Dergi Makalesi
Kaynak 1:
Science Direct
Kaynak 2:
PubMed
Dergi:
Current Opinion in Genetics & Development
Yayıncı:
Elsevier
Yazar(lar) :
Mait Metspalu , Mayukh Mondal , Gyaneshwer Chaubey
Yıl :
2018
Gyaneshwer Chaubey
Tam Metin
Kaydet Alıntıla
South Asia is home for more than a billion people culturally structured into innumerable groups practicing different levels of endogamy. Linguistically South Asia is broadly characterized by four major language families which has served as access way for disentangling the genetic makings of South Asia. In this review we shall give brief account on the recent developments in the field. Advances are made in two fronts simultaneously. Whole genome characterisation of many extant South Asians paint the picture of the genetic diversity and its implications to health-care. On the other hand ancient DNA studies, which are finally reaching South Asia, provide new incites to the demographic history of the subcontinent. Before the spread of agriculture, South Asia was likely inhabited by hunter-gatherer groups deriving much of their ancestry from a population that split from the rest of humanity soon after expanding from Africa. Early Iranian agriculturalists mixing with these local hunter-gatherers probably formed the population that flourished during the blossoming of the Indus Valley Civilisation. Further admixture with the still persisting HG groups and population(s) from the Eurasian Steppe, formed the two ancestral populations (ANI and ASI), the north-south mixing pattern of whom is known today as the ‘Indian Cline’. Studies on natural selection in South Asia have so far revealed strong signals of sweeps that are shared with West Eurasians. Future studies will have to fully unlock the aDNA promise for South Asia.
DOI : 10.1016/j.gde.2018.09.003
ISSN: 0959-437X
Cilt: 53
Sayfa: 128-133
4
A case of “false tri-allelic pattern” on D7S820, caused by invasion of a short SE33 allele into the bins of D7S820
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Dergi Makalesi
Kaynak :
Springer Link
Dergi:
International Journal of Legal Medicine
Yazar(lar) :
Kamlesh Kaitholia , Pankaj Shrivastava , Gyaneshwer Chaubey
Konu :
Pathology and Forensic Medicine
Yıl :
2021
Gyaneshwer Chaubey
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Autosomal short tandem repeats (asSTR) serve as genetic markers for discriminating individuals and have been extensively used for criminal investigations as well as the establishment of genetic relationships. Tri-allelic pattern usually occurs due to chromosomal duplication, trisomy, and chimerism during mitotic division, but a false tri-allelic pattern at the D7S820 locus was encountered in our laboratory during the analysis of a case exhibit. DNA isolation from exhibit for profiling was done as per manufacturer’s protocol. This is the first report which observed false tri-allelic pattern (10, 11, 14.1 allele) on D7S820 locus by analysis with GlobalFiler™ PCR Amplification Kit in Indian population. Findings were re-confirmed using other available asSTR kits in the laboratory, viz., AmpFLSTR™ Identifiler™ Plus PCR Amplification Kit and PowerPlex® Fusion 6C System. Two alleles (10, 11) found at D7S820, apart from SE33 marker, showed homozygous condition, but one Off Marker (OMR) peak was observed before start of SE33 marker region with the analysis using PowerPlex® Fusion 6C System. As it has been confirmed that the OMR allele belongs to the SE33 locus, this could be possible because of the adjacent locations of the D7S820 and the SE33 in the GlobalFiler® PCR amplification kit. 14.1 allele appeared within the allelic window of D7S820. The false tri-allelic pattern was due to the overlapping of SE33 marker allele (1.2 repeat) with bin window of D7S820 Marker. This finding might create confusion for the establishment of genetic relationships. We, therefore, conclude that such uncommon observations with rare events should be carefully investigated and interpreted.
DOI : 10.1007/s00414-020-02484-w
Anahtar Kelimeler : Allele, D7S820, SE33
ISSN: 0937-9827 1437-1596
Sayı: 2
Cilt: 135
Sayfa: 427-430
Sınıflandırma :
5
The demographic history of India: A perspective based on genetic evidence
Tez

Tez
Open Access
Kaynak 1:
The Dart-Europe
Kaynak 2:
The Dart-Europe
Dergi:
Tartu University
Yazar(lar) :
Gyaneshwer Chaubey
Yıl :
2010
Gyaneshwer Chaubey
Kaydet Alıntıla
Sınıflandırma :
6
Peopling of South Asia: investigating the caste–tribe continuum in India
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Dergi Makalesi
Kaynak :
Wiley Online Library
Dergi:
BioEssays
Yazar(lar) :
Gyaneshwer Chaubey , Mait Metspalu , Toomas Kivisild , Richard Villems
Yıl :
2006
Gyaneshwer Chaubey
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In recent years, mtDNA and Y chromosome studies involving human populations from South Asia and the rest of the world have revealed new insights about the peopling of the world by anatomically modern humans during the late Pleistocene, some 40,000–60,000 years ago, over the southern coastal route from Africa. Molecular studies and archaeological record are both largely consistent with autochthonous differentiation of the genetic structure of the caste and tribal populations in South Asia. High level of endogamy created by numerous social boundaries within and between castes and tribes, along with the influence of several evolutionary forces such as genetic drift, fragmentation and long‐term isolation, has kept the Indian populations diverse and distant from each other as well as from other continental populations. This review attempts to summarize recent genetic studies on Indian caste and tribal populations with the focus on the information embedded in the socially defined structure of Indian populations. BioEssays 29: 91–100, 2007. © 2006 Wiley Periodicals, Inc.
DOI : 10.1002/bies.20525
ISSN: 0265-9247
Sayı: 1
Cilt: 29
Sayfa: 91-100
Sınıflandırma :
7
Population History of the Gond: The Largest Tribal Population of South Asia
Referans Girişi

Referans Girişi
Kaynak :
Wiley Online Library
Yazar(lar) :
Gyaneshwer Chaubey , Rakesh K Upadhyay , George van Driem
Yıl :
2018
Gyaneshwer Chaubey
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DOI : 10.1002/9780470015902.a0027474
ISBN:9780470016176
Sayfa: 1-8
8
Genetic Affinity of the Bhil, Kol and Gond Mentioned in Epic Ramayana.
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Dergi Makalesi
Open Access
Kaynak :
Directory of Open Access Journals (DOAJ)
Dergi:
PLoS ONE
Yazar(lar) :
Gyaneshwer Chaubey , Anurag Kadian , Saroj Bala , Vadlamudi Raghavendra Rao
Yıl :
2015
Gyaneshwer Chaubey
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Kol, Bhil and Gond are some of the ancient tribal populations known from the Ramayana, one of the Great epics of India. Though there have been studies about their affinity based on classical and haploid genetic markers, the molecular insights of their relationship with other tribal and caste populations of extant India is expected to give more clarity about the the question of continuity vs. discontinuity. In this study, we scanned >97,000 of single nucleotide polymorphisms among three major ancient tribes mentioned in Ramayana, namely Bhil, Kol and Gond. The results obtained were then compared at inter and intra population levels with neighboring and other world populations. Using various statistical methods, our analysis suggested that the genetic architecture of these tribes (Kol and Gond) was largely similar to their surrounding tribal and caste populations, while Bhil showed closer affinity with Dravidian and Austroasiatic (Munda) speaking tribes. The haplotype based analysis revealed a massive amount of genome sharing among Bhil, Kol, Gond and with other ethnic groups of South Asian descent. On the basis of genetic component sharing among different populations, we anticipate their primary founding over the indigenous Ancestral South Indian (ASI) component has prevailed in the genepool over the last several thousand years.
DOI : 10.1371/journal.pone.0127655
ISSN: 1932-6203
Cilt: 10
Sayı: 6
Sayfa: e0127655
Sınıflandırma :
9
Reply to Winters
Dergi Makalesi

Dergi Makalesi
Kaynak :
Wiley Online Library
Dergi:
BioEssays
Yazar(lar) :
Gyaneshwer Chaubey , Mait Metspalu , Richard Villems , Toomas Kivisild
Konu :
General Biochemistry, Genetics and Molecular Biology
Yıl :
2007
Gyaneshwer Chaubey
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DOI : 10.1002/bies.20574
ISSN: 0265-9247
Sayı: 5
Cilt: 29
Sayfa: 499-499
10
Genomic diversity at 22 STR loci (extended CODIS STR) in the population of Rajasthan, India
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Dergi Makalesi
Kaynak :
Science Direct
Dergi:
Gene Reports
Yayıncı:
Elsevier BV
Yazar(lar) :
Anand Kumar , Rajesh Kumar , R.K. Kumawat , Pankaj Shrivastava , Gyaneshwer Chaubey
Yıl :
2021
Gyaneshwer Chaubey
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This study presents genetic diversity at 22 autosomal STR loci (extended CODIS STR) in the population of Rajasthan. It provides an allelic database of this population for the purpose of forensic inference. 595 unrelated healthy individuals residing in the state were randomly selected from the routine casework of the laboratory. Compliance of ethical standards was ensured during the collection of blood samples. The allele 15 of locus D22S1045 was found to be the most frequent allele among all the studied genetic markers. The matching probability was found to be 1.80 × 10−26 at all the studied markers. The loci Penta E and TPOX were found to be highest and least forensic importance respectively, among all the studied loci. The heterozygosity ranged from 0.711 for locus TPOX to 0.926 for the locus Penta E. The discrimination and exclusion power were found as 1 and 0.999999998292 respectively at all the studied loci. Overall, the highest polymorphism was observed 0.907 for locus Penta E among the studied markers in the population of Rajasthan. In population differentiation test, the population of Rajasthan showed a greater genetic affinity with north-western and central Indian populations than southern and eastern Indian, as well as East Asian populations.
DOI : 10.1016/j.genrep.2021.101150
Anahtar Kelimeler : STR Short Tendem Repeat, Short Tendem Repeat, CODIS Combined DNA Index System, Combined DNA Index System, coPD Combined Power of Discrimination, Combined Power of Discrimination, coPE Combined Power of Exclusion, Combined Power of Exclusion, PIC Polymorphic Information Content, Polymorphic Information Content, PM Probability of a Match, Probability of a Match, HIPS Human Identification Professional Services, Human Identification Professional Services, ILS Internal Lane Standard, Internal Lane Standard, Hi Di Formamide Highly Deionized Formamide, Highly Deionized Formamide, CODIS STR, Polymorphism, Genetic database, Paternity index, Rajasthan
ISSN: 2452-0144
Cilt: 23
Sayfa: 101150
11
mtDNA from the early Bronze Age to the Roman period suggests a genetic link between the Indian subcontinent and Mesopotamian cradle of civilization.
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Dergi Makalesi
Open Access
Kaynak 1:
Directory of Open Access Journals (DOAJ)
Kaynak 2:
PLOS - Public Library of Science
Dergi:
PLoS ONE
Yazar(lar) :
Henryk W Witas , Jacek Tomczyk , Krystyna Jędrychowska-Dańska , Gyaneshwer Chaubey , Tomasz Płoszaj
Yıl :
2013
Gyaneshwer Chaubey
Piri Tam Metin Bulucu
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Ancient DNA methodology was applied to analyse sequences extracted from freshly unearthed remains (teeth) of 4 individuals deeply deposited in slightly alkaline soil of the Tell Ashara (ancient Terqa) and Tell Masaikh (ancient Kar-Assurnasirpal) Syrian archaeological sites, both in the middle Euphrates valley. Dated to the period between 2.5 Kyrs BC and 0.5 Kyrs AD the studied individuals carried mtDNA haplotypes corresponding to the M4b1, M49 and/or M61 haplogroups, which are believed to have arisen in the area of the Indian subcontinent during the Upper Paleolithic and are absent in people living today in Syria. However, they are present in people inhabiting today's Tibet, Himalayas, India and Pakistan. We anticipate that the analysed remains from Mesopotamia belonged to people with genetic affinity to the Indian subcontinent since the distribution of identified ancient haplotypes indicates solid link with populations from the region of South Asia-Tibet (Trans-Himalaya). They may have been descendants of migrants from much earlier times, spreading the clades of the macrohaplogroup M throughout Eurasia and founding regional Mesopotamian groups like that of Terqa or just merchants moving along trade routes passing near or through the region. None of the successfully identified nuclear alleles turned out to be ΔF508 CFTR, LCT-13910T or Δ32 CCR5.
DOI : 10.1371/journal.pone.0073682
ISSN: 1932-6203
Cilt: 8
Sayı: 9
Sayfa: e73682
Sınıflandırma :
12
Genetic association of TMPRSS2 rs2070788 polymorphism with COVID-19 case fatality rate among Indian populations
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Dergi Makalesi
Kaynak :
Science Direct
Dergi:
Infection, Genetics and Evolution
Yayıncı:
Elsevier BV
Yazar(lar) :
Rudra Kumar Pandey , Anshika Srivastava , Prajjval Pratap Singh , Gyaneshwer Chaubey
Yıl :
2022
Gyaneshwer Chaubey
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SARS-CoV-2, the causative agent for COVID-19, an ongoing pandemic, engages the ACE2 receptor to enter the host cell through S protein priming by a serine protease, TMPRSS2. Variation in the TMPRSS2 gene may account for the disparity in disease susceptibility between populations. Therefore, in the present study, we have used next-generation sequencing (NGS) data of world populations from 393 individuals and analyzed the TMPRSS2 gene using a haplotype-based approach with a major focus on South Asia to study its phylogenetic structure and their haplotype sharing among various populations worldwide. Our analysis of phylogenetic relatedness showed a closer affinity of South Asians with the West Eurasian populations therefore, host disease susceptibility and severity particularly in the context of TMPRSS2 will be more akin to West Eurasian instead of East Eurasian. This is in contrast to our prior study on the ACE2 gene which shows South Asian haplotypes have a strong affinity towards West Eurasians. Thus ACE2 and TMPRSS2 have an antagonistic genetic relatedness among South Asians. Considering the significance of the TMPRSS2 gene in the SARS-CoV-2 pathogenicity, COVID-19 infection and intensity trends could be directly associated with increased expression therefore, we have also tested the SNPs frequencies of this gene among various Indian state populations with respect to the case fatality rate (CFR). Interestingly, we found a significant positive association between the rs2070788 SNP (G Allele) and the CFR among Indian populations. Further our cis eQTL analysis of rs2070788 shows that the GG genotype of the rs2070788 tends to have a significantly higher expression of TMPRSS2 gene in the lung compared to the AG and AA genotypes thus validating the previous observation and therefore it might play a vital part in determining differential disease vulnerability. We trust that this information will be useful in understanding the role of the TMPRSS2 variant in COVID-19 susceptibility and using it as a biomarker may help to predict populations at risk.
DOI : 10.1016/j.meegid.2022.105206
Anahtar Kelimeler : COVID-19, TMPRSS2, India, rs2070788, Haplotype, Linkage disequilibrium
ISSN: 1567-1348
Cilt: 98
Sayfa: 105206
13
Evaluating the genetic impact of South and Southeast Asia on the peopling of Bangladesh
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Dergi Makalesi
Kaynak :
Science Direct
Dergi:
Legal Medicine
Yayıncı:
Elsevier
Yazar(lar) :
Gazi Nurun Nahar Sultana , Mohd Istiaq Sharif , Md Asaduzzaman , Gyaneshwer Chaubey
Yıl :
2015
Gyaneshwer Chaubey
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Despite rapidly growing understandings and dependency on single nucleotide polymorphisms (SNPs), highly variable autosomal short tandem repeats (STRs) are still regarded as the most established method to differentiate individuals at forensic level. Here with large number of various ethnic groups we undertook this study to reveal the genetic structure of the most densely populated part of South Asia i.e. the Bangladesh. The purpose of this work was to estimate population parameters based on the allele frequencies obtained for 15 polymorphic autosomal STR loci investigated in caste and tribal populations from Bangladesh (n = 706). We compared the results in a broader context by merging 24 different populations of Asia to pertain their affinity. Various statistical analyses suggested a clear cut demarcation of tribal and non-tribal in Bangladesh. Moreover, beside the phylogenetic structure of the studied populations, it is found that the mean heterozygosity value was highest among the populations of Bangladesh, likely because of gene flow from different directions. However, Tonchangya, Adi and Khumi showed sign of genetic isolation and reduced diversity, possibly as a result of genetic drift and/or strong founder effects working on small endogamous populations.
DOI : 10.1016/j.legalmed.2015.09.004
Anahtar Kelimeler : Caste, Tribe, Bangladesh, Autosomal STR, South Asia
ISSN: 1344-6223
Sayı: 6
Cilt: 17
Sayfa: 446-450
Sınıflandırma :
14
Polymorphic variants near 1p22 and 20q11.2 loci and the risk of non-syndromic cleft lip and palate in South Indian population
Dergi Makalesi

Dergi Makalesi
Kaynak :
Science Direct
Dergi:
International Journal of Pediatric Otorhinolaryngology
Yayıncı:
Elsevier
Yazar(lar) :
Venkatesh Babu Gurramkonda , Altaf Hussain Syed , Jyotsna Murthy , Gyaneshwer Chaubey , V.K.S. Bhaskar Lakkakula
Yıl :
2015
Gyaneshwer Chaubey
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Background Recent genome-wide association studies (GWAS) have reported multiple genetic risk loci for non-syndromic orofacial clefts (NSOFCs) in many populations. However, the contribution of these loci to NSOFC in India, which comprises one-fifth of the global population, is completely lacking. Our aim was to replicate the association of the SNPs located on 1p22 chromosomal loci (rs540026, rs481931) and 20q11.2 (rs13041247, rs11696257) in the aetiology of NSOFCs, in South Indian populations. Methods The SNPs were genotyped by using KBiosciences KASPar SNP genotyping chemistry in 173 cases and 176 controls for NSOFCs in South India. To estimate the association between these SNPs and NSOFCs, chi-square test was adopted. Odds ratios (OR) with 95% confidence intervals (CI) were also calculated in order to assess the risk. Results Single nucleotide polymorphisms located at chromosomal region 1p22 are not found to be associated with cleft lip with or without non-syndromic cleft palate (NSCL/P) and non-syndromic cleft palate only (NSCPO) at either the genotype or allele levels. Further, there is no LD observed between these variants. The polymorphic variants near 20q11.2 (rs13041247, rs11696257) are in complete linkage disequilibrium (LD) and are significantly associated with only NSCL/P in genotypic (p = 0.013) and allelic models (p = 0.029). In the genotypic model significance persisted even after Bonferroni correction (p < 0.016). Conclusion These results suggest that 20q11.2 SNPs could play a contributory role in the pathophysiology and risk of NSCL/P, while the variations in 1p22 do not underlie the pathophysiology of NSOFCs in South Indian populations.
DOI : 10.1016/j.ijporl.2015.10.055
Anahtar Kelimeler : 1p22 and 20q11.2 chromosomal loci, SNP, NSOFCs, NSCL/P, NSCPO, India
ISSN: 0165-5876
Sayı: 12
Cilt: 79
Sayfa: 2389-2393
Sınıflandırma :
15
NAT2 genetic variations among South Indian populations
Dergi Makalesi

Dergi Makalesi
Open Access
Kaynak :
Springer Nature
Dergi:
Human Genome Variation
Yayıncı:
Springer Nature
Yazar(lar) :
Saikrishna Lakkakula , Ram Mohan Pathapati , Gyaneshwer Chaubey , Arasambattu Kannan Munirajan , Bhaskar VKS Lakkakula , Rajasekhar Maram
Konu :
Evolutionary biology
Yıl :
2014
Gyaneshwer Chaubey
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Kaydet Alıntıla
The N-acetyltransferases (NATs) are xenobiotic-metabolizing enzymes involved in the metabolism of drugs, environmental toxins and the aromatic amine carcinogens present in cigarette smoke. Genetic variations in NAT2 have long been recognized as the cause of variable enzymatic activity or stability, leading to slow or rapid acetylation. In the present study, we genotyped three single-nucleotide polymorphisms (SNPs) from the NAT2 gene (rs1799929, rs1799930 and rs1799931), using TaqMan allelic discrimination, among 212 individuals from six major South Indian populations and compared the results with other available Indian and worldwide data. All three of the markers followed Hardy–Weinberg equilibrium and were highly polymorphic in the studied populations. The constructed haplotypes showed a high level of heterozygosity. All of the populations in the present study commonly shared only four haplotypes out of the eight possible three-site haplotypes. The haplotypes exhibited fairly high frequencies across multiple populations, where three haplotypes were shared by all six populations with a cumulative frequency ranging from 88.2% (Madiga) to 97.0% (Balija). We also observed a tribal-specific haplotype. A strong linkage disequilibrium (LD) between rs1799929 and rs1799930 was consistent in all of the studied populations, with the exception of the Madiga. A comparison of the genomic regions 20-kb up- and downstream of rs1799930 in a large number of worldwide samples showed a strong LD of this SNP with another NAT2 SNP, rs1112005, among the majority of the populations. Moreover, our lifestyle test (hunter–gatherer versus agriculturist) in comparison with the NAT2 variant suggested that two of the studied populations (Balija and Madiga) have likely shifted their diet more recently. Patterns of genetic variation show that some Indian populations shifted from hunting and gathering to farming more recently than others. The enzyme N-acetyltransferase 2 (NAT2) metabolizes various drugs and environmental toxins via acetylation, replacing a hydrogen atom with an acetyl group. The slow acetylator type of NAT2 is more common in agrarian populations and the fast acetylator type more common in hunter-gatherer populations. Rajasekhar Maram of Sri Venkateswara University in India and co-workers in India and Estonia examined genetic variation in the NAT2 gene in 212 individuals from six major south Indian populations. The populations contained a high diversity of NAT2 types. Four of the populations contained several slow-acetylator types but two of the populations showed a higher frequency of a fast-acetylator type, indicating a more recent transition to farming.
DOI : 10.1038/hgv.2014.14
ISSN: 2054-345X
Cilt: 1
Sayı: 1
Sayfa: 1-7
Sınıflandırma :
16
Peopling of Rajasthan, India: Evaluating the gene flow from east and west
Dergi Makalesi

Dergi Makalesi
Kaynak :
Science Direct
Dergi:
Gene Reports
Yayıncı:
Elsevier BV
Yazar(lar) :
R.K. Kumawat , Pankaj Shrivastava , Divya Shrivastava , G.K. Mathur , Hirak Ranjan Dash , Gyaneshwer Chaubey
Yıl :
2021
Gyaneshwer Chaubey
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Kaydet Alıntıla
Rajasthan is a state located in the north-western part of India and it has been cited as a major route of human migration since ancient times. The present study was conducted to find out the genetic affinity of Rajasthani population with the population living in its east as well as the west. In particular, we compared them with the population of Pakistan which shares the common geographical boundary with the Rajasthan while also having a look at their inter and intra population affinities with the population belonging to other Indian states. We investigated the genetic structure and population parameters of Rajasthani populations obtained for twenty polymorphic autosomal STR loci from 669 unrelated individuals belonging to its three population groups including Mina, Gujjar and the admixed population of Rajasthan. The studied populations showed a wide range of genetic diversity and besides the genetic structure of the studied populations, it was found that the average heterozygosity value was highest among the populations of Rajasthan, possibly, because of gene flow from different directions. Various statistical analyses suggested that the Rajasthani populations had a higher affinity with the North Indian populations rather than with the Pakistani population.
DOI : 10.1016/j.genrep.2020.100990
Anahtar Kelimeler : STR Short Tandem Repeat, Short Tandem Repeat, RFU Relative Fluorescence Unit, Relative Fluorescence Unit, Hobs Observed Heterozygosity, Observed Heterozygosity, Hexp Expected Heterozygosity, Expected Heterozygosity, POP Performance Optimized Polymer, Performance Optimized Polymer, HWE Hardyu2013Weinberg equilibrium, Hardyu2013Weinberg equilibrium, NJ Neighbour Joining, Neighbour Joining, PCA Principal Component Analysis, Principal Component Analysis, AMOVA Analysis of Molecular Variance, Analysis of Molecular Variance, Genetic affinity, STR, Rajasthan, Heterozygosity, Polymorphic
ISSN: 2452-0144
Cilt: 22
Sayfa: 100990
17
Relic excavated in western India is probably of Georgian Queen Ketevan
Dergi Makalesi

Dergi Makalesi
Kaynak :
Science Direct
Dergi:
Mitochondrion
Yayıncı:
Elsevier
Yazar(lar) :
Niraj Rai , Nizamuddin Taher , Manvendra Singh , Gyaneshwer Chaubey , Aditya Nath Jha , Lalji Singh , Kumarasamy Thangaraj
Yıl :
2014
Gyaneshwer Chaubey
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History has well documented the execution of Queen Ketevan of Georgia by the Persian Emperor of modern day Iran. Based on historical records, in 1624 two Augustinian friars unearthed the queen's remains and one of them brought the relic to the St. Augustine convent in Goa, India. We carried out ancient DNA analysis on the human bone remains excavated from the St. Augustine convent by sequencing and genotyping of the mitochondrial DNA. The investigations of the remains revealed a unique mtDNA haplogroup U1b, which is absent in India, but present in Georgia and surrounding regions. Since our genetic analysis corroborates archaeological and literary evidence, it is likely that the excavated bone belongs to Queen Ketevan of Georgia.
DOI : 10.1016/j.mito.2013.12.002
Anahtar Kelimeler : Ancient DNA, Ancestry, Queen Ketevan, Relic
ISSN: 1567-7249
Cilt: 14
Sayfa: 1-6
Sınıflandırma :
18
Sequence variations, flanking region mutations, and allele frequency at 31 autosomal STRs in the central Indian population by next generation sequencing (NGS)
Dergi Makalesi

Dergi Makalesi
Kaynak :
Springer Nature
Dergi:
Scientific Reports
Yayıncı:
Springer Science and Business Media LLC
Yazar(lar) :
Hirak Ranjan Dash , Kamlesh Kaitholia , R. K. Kumawat , Anil Kumar Singh , Pankaj Shrivastava , Gyaneshwer Chaubey , Surajit Das
Yıl :
2021
Gyaneshwer Chaubey
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AbstractCapillary electrophoresis-based analysis does not reflect the exact allele number variation at the STR loci due to the non-availability of the data on sequence variation in the repeat region and the SNPs in flanking regions. Herein, this study reports the length-based and sequence-based allelic data of 138 central Indian individuals at 31 autosomal STR loci by NGS. The sequence data at each allele was compared to the reference hg19 sequence. The length-based allelic results were found in concordance with the CE-based results. 20 out of 31 autosomal STR loci showed an increase in the number of alleles by the presence of sequence variation and/or SNPs in the flanking regions. The highest gain in the heterozygosity and allele numbers was observed in D5S2800, D1S1656, D16S539, D5S818, and vWA. rs25768 (A/G) at D5S818 was found to be the most frequent SNP in the studied population. Allele no. 15 of D3S1358, allele no. 19 of D2S1338, and allele no. 22 of D12S391 showed 5 isoalleles each with the same size and with different intervening sequences. Length-based determination of the alleles showed Penta E to be the most useful marker in the central Indian population among 31 STRs studied; however, sequence-based analysis advocated D2S1338 to be the most useful marker in terms of various forensic parameters. Population genetics analysis showed a shared genetic ancestry of the studied population with other Indian populations. This first-ever study to the best of our knowledge on sequence-based STR analysis in the central Indian population is expected to prove the use of NGS in forensic case-work and in forensic DNA laboratories.
DOI : 10.1038/s41598-021-02690-5
ISSN: 2045-2322
Sayı: 1
Cilt: 11
19
Molecular characterization and forensic relevance of the autosomal STRs for the population of North Indian geographical province Himachal Pradesh, India
Dergi Makalesi

Dergi Makalesi
Kaynak :
Science Direct
Dergi:
Legal Medicine
Yayıncı:
Elsevier BV
Yazar(lar) :
Arun Sharma , Naresh Kumar , Ashwani Bhardwaj , Vivek Sahajpal , R.K. Kumawat , Shivani Dixit , Gyaneshwer Chaubey , Pankaj Shrivastava
Yıl :
2021
Gyaneshwer Chaubey
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Keeping in view the diverse demography of India, present study was undertaken to explore the molecular characterization and forensic relevance of 20 autosomal STRs for the highly diverse population of north Indian state Himachal Pradesh. 724 unrelated individuals from the admixed population of Himachal Pradesh were undertaken for present study and 20 autosomal STRs used to explore genomic diversity of studied population. A total of 270 different alleles along with 13.5 alleles per locus were observed. The allele 8 of the locus TPOX was observed as the most frequent allele. Observed heterozygosity ranged from 0.677 to 0.898, which supported wide range of selection of the unrelated individuals for this study. Combined power of discrimination, power of exclusion, matching probability and paternity index were observed as 1, 0.9999999958, 3.9 × 10−26 and 2.3 × 108 respectively, across the studied loci. In the population differentiation test, studied population showed genetic relatedness with Indian population rather than the populations of West, North and North east countries. Present study deciphered the novel autosomal STR data, which could be useful for the forensic application and population genetic studies.
DOI : 10.1016/j.legalmed.2021.101958
Anahtar Kelimeler : Molecular characterization, STRs, Himachal Pradesh, Population genetic, Forensic DNA
ISSN: 1344-6223
Cilt: 53
Sayfa: 101958
20
A genomic exploration of 15 autosomal STR loci for establishment of a DNA profile database of the population of Himachal Pradesh
Dergi Makalesi

Dergi Makalesi
Kaynak :
Science Direct
Dergi:
Legal Medicine
Yayıncı:
Elsevier
Yazar(lar) :
B.K. Mohapatra , Kamal Chauhan , Pankaj Shrivastava , Shivani Dixit , R.K. Kumawat , Anchal Sharma , Seema Dagar , Gyaneshwer Chaubey
Yıl :
2020
Gyaneshwer Chaubey
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In order to create an autosomal STR loci population database for Himachal Pradesh, 259 blood samples were taken from people residing in various regions of the state and AmpFlSTR® Identifiler® Plus PCR amplification kit was used for evaluation of 15 autosomal STR markers. A total of 149 alleles were investigated in this study with a mean allele number of 9.933 per locus. The locus D2S1338 was most informative in our data, as it had the highest discrimination power (PD-0.967) and the highest polymorphic information content (PIC-0.86). The matching probability and typical paternity index for all the studied loci were observed as 2.9x10-18 and 4.7x105, respectively. Discrimination power (CPD) and exclusion power (CPE) for all the studied loci were observed as 1 and 0.999998.
DOI : 10.1016/j.legalmed.2020.101719
Anahtar Kelimeler : Autosomal STRs, Forensic DNA typing, Population database, Himachal Pradesh, India
ISSN: 1344-6223
Cilt: 46
Sayfa: 101719
Sınıflandırma :
21
Allelic frequency database of 15 polymorphic autosomal STRs in the Malayalam-speaking population of Kerala, India
Dergi Makalesi

Dergi Makalesi
Kaynak :
Springer Link
Dergi:
International Journal of Legal Medicine
Yazar(lar) :
R. Sreekumar , Ajeesh Thekkatavan , Pankaj Shrivastava , R. K. Kumawat , Shivani Dixit , Gyaneshwer Chaubey
Konu :
Pathology and Forensic Medicine
Yıl :
2020
Gyaneshwer Chaubey
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In this study, we assessed and established an allelic frequency database of Malayalam-speaking population of south western Indian state Kerala, using 15 polymorphic short tandem repeats (STRs) genetic markers. For this study, 464 unrelated healthy individuals were randomly selected following the ethical standards. The most polymorphic and most discriminating locus was D2S1338, with a value of 0.860 and 0.968, respectively. The range of heterozygosity extended from a minimum of 0.668 (TH01) to a maximum of 0.847 (D2S1338). The combined discrimination power (CPD) and combined exclusion power (CPE) were 1 and 0.999997861, respectively, for all 15 autosomal STR loci under study. The combined probability of match (CPM) and combined paternity index (CPI) for all 15 autosomal STR loci were found to be 9.85 × 10−19 and 4.18 × 105, respectively.
DOI : 10.1007/s00414-020-02286-0
Anahtar Kelimeler : Polymorphism, STRs, Genetic diversity, Malayalam-speaking population, Kerala
ISSN: 0937-9827 1437-1596
Sayı: 5
Cilt: 134
Sayfa: 1679-1681
22
Genetic variation (population database) at 20 autosomal STR loci in the population of Rajasthan (north-western India)
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Dergi Makalesi
Kaynak :
Springer Link
Dergi:
International Journal of Legal Medicine
Yazar(lar) :
Anand Kumar , Rajesh Kumar , R. K. Kumawat , Ajay Tilawat , Pankaj Shrivastava , Gyaneshwer Chaubey
Konu :
Pathology and Forensic Medicine
Yıl :
2020
Gyaneshwer Chaubey
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To explore the genetic diversity and establish the allelic database of the population of Rajasthan, we assessed 571 randomly selected unrelated healthy individuals residing in the state. Blood samples of the selected individuals were collected with the compliance of ethical standards. Locus Penta E was observed to be the most polymorphic (0.908), whereas locus TPOX was observed to be the least polymorphic (0.639). The observed heterozygosity ranged from a minimum of 0.667 (TPOX) to a maximum of 0.925 (Penta E). The combined value of the power of discrimination (PD) and power of exclusion (PE) for all the studied 20 short tandem repeat (STR) loci were observed to be 1 and 0.999999997560235 respectively. The combined values of matching probability (PM) and paternity index (PI) for all the studied 20 STR loci were 7 × 10−26 and 4 × 108 respectively. The obtained genetic data are useful for forensic DNA applications and expected to enrich the genetic database of Indian populations.
DOI : 10.1007/s00414-020-02280-6
Anahtar Kelimeler : Genetic database, Autosomal STRs, Polymorphism, Paternity index, Rajasthan
ISSN: 0937-9827 1437-1596
Sayı: 5
Cilt: 134
Sayfa: 1667-1669
23
Genomic diversity of the Muslim population from Telangana (India) inferred from 23 autosomal STRs
Dergi Makalesi

Dergi Makalesi
Kaynak :
Taylor and Francis
Dergi:
Annals of Human Biology
Yayıncı:
Informa UK Limited
Yazar(lar) :
Varsha Srivastava , Hanumanth Surekha Rani , Ramkishan Kumawat , Gyaneshwer Chaubey , Pankaj Shrivastava
Konu :
Public Health, Environmental and Occupational Health, Genetics, Ageing, Epidemiology, Physiology
Yıl :
2020
Gyaneshwer Chaubey
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Aim This study aimed to investigate the genomic diversity and population structure in the Muslim community of Telangana, India, using 23 autosomal microsatellite genetic markers. We also examined genetic relatedness between Muslim and non-Muslim populations of India. Subjects and methods A sample of 184 randomly selected unrelated healthy Muslim individuals from the Telangana state were included in this study. The genotyping of 23 autosomal STR markers included in PowerPlex® Fusion 6 C multiplex system (Promega)was done. Results A total of 273 alleles were observed in the studied population, and locus SE33 showed 37 observed alleles, which is the highest number of observed alleles among all the studied loci. Among all the studied loci the most polymorphic and discriminatory locus was SE33, with the values of polymorphic information content (PIC) = 9.411E–01 and power of discrimination (PD) = 9.865E–01. Observed heterozygosity ranged from 6.630E–01 (D22S1045) to 9.239E–01 (SE33). Discrimination power, exclusion power, matching probability and paternity index for all the studied loci were 1.00E + 00, 1.00E + 00, 2.01E–28, and 5.68E + 09, respectively. The studied Muslim population showed genetic relatedness with non-Muslim populations i.e. populations of central India, Jharkhand, and Uttar Pradesh, suggesting the conversion of Hindus during the Muslim invasion. Conclusion Neighbor-joining (NJ) tree and principal component analysis (PCA) revealed that the studied population showed genetic affinity with communities of Jharkhand, Madhya Pradesh and Uttar Pradesh states. The genetic data of this study may be useful for forensic, medical, and anthropological studies.
DOI : 10.1080/03014460.2020.1822915
Anahtar Kelimeler : Polymorphism, STRs, genetic diversity, Telangana, PowerPlex® Fusion 6C multiplex system
ISSN: 0301-4460
Sayı: 7-8
Cilt: 47
Sayfa: 652-658
24
Forensic characterization and genetic evaluation in the Central Indian population using 27 Y-STRs
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Dergi Makalesi
Kaynak :
Springer Link
Dergi:
International Journal of Legal Medicine
Yazar(lar) :
Kamlesh Kaitholia , Hirak Ranjan Dash , Pankaj Shrivastava , R. K. Kumawat , Shivani Dixit , Gyaneshwer Chaubey
Konu :
Pathology and Forensic Medicine
Yıl :
2021
Gyaneshwer Chaubey
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Forensic characterization and genetic evaluation study in the 539 randomly selected unrelated adult healthy individuals belonging to the Central Indian population was undertaken. The study was performed using a multiplex of 27 Y-STRs incoporated in Yfiler™ Plus multiplex kit. Out of 539 samples, 6 samples were observed for large deletion and tri-allelic patterns, which were removed from the analysis, and out of 533 samples, a total of 507 haplotypes were found, and out of these haplotypes, 482 unique haplotypes were found in this piece of work. The forensically important parameters, i.e., gene diversity (GD) and discrimination capacity (DC), were found to be 0.669 and 0.951, respectively, for the tested Y STR loci. The genetic data of this study will enrich the Y STR data bank and being used as a potential tool for forensic DNA and various genetic studies.
DOI : 10.1007/s00414-020-02486-8
Anahtar Kelimeler : Forensic, Y-STR, Madhya Pradesh, India, Population data, Haplotype
ISSN: 0937-9827 1437-1596
Sayı: 3
Cilt: 135
Sayfa: 791-792
25
Genetic Profile of Nine Autosomal STR Loci Among Halakki and Kunabhi Populations of Karnataka, India
Dergi Makalesi

Dergi Makalesi
Kaynak :
Wiley Online Library
Dergi:
Journal of Forensic Sciences
Yazar(lar) :
Kumarasamy Thangaraj , Gyaneshwer Chaubey , Vijay Kumar Singh , Alla G. Reddy , P. P. Pavate , Lalji Singh
Konu :
Pathology and Forensic Medicine, Genetics
Yıl :
2006
Gyaneshwer Chaubey
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POPULATION: Blood samples were collected from a total of 84 healthy and unrelated Halakki (44) and Kunabhi (40) populations, with their informed written consent. The geographic location of the sampled area is shown in Fig. 1. Both the populations are endogamous, and they belong to Dravidian linguistic family. Halakki is a tribal group having a population size of approximately 3383. They claim that they originally belong to Gujarat and Rajasthan, and migrated through Andhra Pradesh to Karnataka. Kunabhi is also a tribal population, who are approximately 35,214 in number. The male Kunabhi can be identified by their tattoo marks. A necklace is the symbol of married women. They were hunters and gatherers, but at present they practice agriculture.
DOI : 10.1111/j.1556-4029.2005.00038.x
ISSN: 0022-1198
Sayı: 1
Cilt: 51
Sayfa: 190-192
26
Genomic polymorphism in tribal population of Tripura: Signifying their closer affinity with the Nepalese and Tibetan populations
Dergi Makalesi

Dergi Makalesi
Kaynak :
Taylor and Francis
Dergi:
Annals of Human Biology
Yayıncı:
Informa UK Limited
Yazar(lar) :
Subhankar Nath , Pankaj Shrivastava , R. K. Kumawat , Shivani Dixit , Gyaneshwer Chaubey
Yıl :
2021
Gyaneshwer Chaubey
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Background India is the second most populous country in the world, which is aligned into various community segments. Aim To evaluate the genetic diversity of the tribal population of Tripura, we carried out this study. Subjects and methods 15 autosomal STR markers were used for investigation of genomic diversity, inter- and intra- population relationships among the studied population, and other reported neighbouring tribal and caste populations. Results Results indicated that the tribals of Tripura share their closer genetic affinity with the Trans-Himalayan (Nepalese, Bhutanese and Tibetan) populations. Locus D18S51 was found as the most discriminatory among all the studied loci with uppermost discrimination power (PD = 0.964) and lowest matching probability (Pm = 0.036) in the study. All the evaluated loci herein are useful, having the maximum value of combined power of discrimination (CPD = 1), combined power of exclusion (CPE = 0.99999746), combined paternity index (CPI = 3 × 105) and combined matching probability (CPm = 2.12 × 1 0 −7). Conclusion Population genetic analysis showed that the studied population has genetic relatedness with the compared Nepalese and Tibetan populations i.e., Kathmandu, Tibet, Newar, and Gorkhas, followed by eastern and central Indian populations.
DOI : 10.1080/03014460.2021.1957148
Anahtar Kelimeler : STR Tribal population, allele frequency, genetic profile ancestry
ISSN: 0301-4460
Sayı: 4
Cilt: 48
Sayfa: 360-368
27
Historic migration to South Asia in the last two millennia: A case of Jewish and Parsi populations
Dergi Makalesi

Dergi Makalesi
Kaynak :
Springer Link
Dergi:
Journal of Biosciences
Yazar(lar) :
Ajai K Pathak , Anshika Srivastava , Prajjval Pratap Singh , Debashruti Das , Audditiya Bandopadhyay , Pooja Singh , Gyaneshwer Chaubey
Konu :
General Agricultural and Biological Sciences, General Biochemistry, Genetics and Molecular Biology, General Medicine
Yıl :
2019
Gyaneshwer Chaubey
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The South Asian populations have a mosaic of ancestries likely due to the interactions of long-term populations of the landmass and those of East and West Eurasia. Apart from prehistoric dispersals, there are some known population movements to India. In this study, we focussed on the migration of Jewish and Parsi populations on temporal and spatial scales. The existence of Jewish and Parsi communities in India are recorded since ancient times. However, due to the lack of high-resolution genetic data, their origin and affiliation with other Indian and non-Indian populations remains shrouded in legends. Earlier genetic studies on populations of Indian Jews have found evidence for a minor shared ancestry of Indian Jews with Middle Eastern (Jews) populations, whereas for Parsis, the Iranian link was proposed. Recently, in our high-resolution study, we were able to quantify the admixture dynamics of these groups, which has suggested a male-biased admixture. Here, we added the newly available ancient samples and revisited the interplay of genes and cultures. Thus, in this study we reconstructed a broad genetic profile of Indian Jews and Parsis to paint a fine-grained picture of these ethnic groups.
DOI : 10.1007/s12038-019-9873-7
Anahtar Kelimeler : Autosomes, cultural assimilation, Kerala Jews, Mumbai Jews, Parsi, Zoroastrian
ISSN: 0250-5991 0973-7138
Sayı: 3
Cilt: 44

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