Browsing by Author "Chaubey G."
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Item Correction to: Genetic evidence for a single founding population of the Lakshadweep Islands (Molecular Genetics and Genomics, (2024), 299, 1, (8), 10.1007/s00438-024-02110-z)(Springer Science and Business Media Deutschland GmbH, 2024) Kumar S.; Singh P.P.; Pasupuleti N.; Shendre S.S.; Sequeira J.J.; Babu I.; Mustak M.S.; Rai N.; Chaubey G.In this article the author name Mohammed S. Mustak was incorrectly written as Mohammed S. Mutak. The original article has been corrected. � The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature 2024.Item Correction to: Novel genetic association of the Furin gene polymorphism rs1981458 with COVID-19 severity among Indian populations (Scientific Reports, (2024), 14, 1, (7822), 10.1038/s41598-024-54607-7)(Nature Research, 2024) Pandey R.K.; Srivastava A.; Mishra R.K.; Singh P.P.; Chaubey G.Correction to: Scientific Reportshttps://doi.org/10.1038/s41598-024-54607-7, published online 03 April 2024 The original version of this Article contained errors in the Material and Methods section and in the legend of Figure�3 (A, B, C). In the Material and Methods section, under the subheading �Insilco analysis�, �To analyse the TMPRSS2 expression in various human tissues, the GTEx portal database (http://www.gtexportal.org/home/) was used.� now reads: �To analyse the FURIN expression in various human tissues, the GTEx portal database (http://www.gtexportal.org/home/) was used.� In the legend of Figure�3, �(A) and (B) display the allele frequency distribution of rs2070788 across Indian populations in a frequency map and the corresponding COVID-19 Case Fatality Rate (CFR) as of August 30th, 2021.� now reads: �(A) and (B) display the allele frequency distribution of rs1981458 across Indian populations in a frequency map and the corresponding COVID-19 Case Fatality Rate (CFR) as of August 30th, 2021.� �The linear regression graph depicts the association between the rs1981458 allele frequency of the TMPRSS2 gene with COVID-19 CFR.� now reads: �The linear regression graph depicts the association between the rs1981458 allele frequency of the FURIN gene with COVID-19 CFR.� The original Article has been corrected. � The Author(s) 2024.Item Exploring the genetic implications of demographic dynamics in Jammu and Kashmir using autosomal STRs(Springer Science and Business Media Deutschland GmbH, 2024) Mubarik N.; Ganei M.A.; Dixit S.; Kumawat R.K.; Sequeira J.J.; Ahangar N.A.; Kanth S.A.; Dar I.A.; Mushtaq I.; Mohsin M.; Mustak M.S.; Chaubey G.; Hamid S.; Shrivastava P.The Union Territory of Jammu and Kashmir has always been a point of contention among India, Pakistan, and China for various reasons. This region has great significance historically due to its geography and ethnic diversity. However, a comprehensive genetic study providing the genetic landscape of Jammu and Kashmir was lacking until now. In this study, we analysed 21 hyper-variable autosomal STR loci of 694 individuals from Jammu and Kashmir and compared them with neighbouring populations to explore the genetic implications of demographic dynamics that have taken place in this region. Our findings suggest that the population of Jammu and Kashmir is a genetic mixture of two major clines, northern and southern, that correspond with the variation in geography, linguistics, and demography of the region. Broadly, the gene flow into the southern cline appears to be in historical times perhaps as a result of the spread of Gurjars, Dogri language and invasions of Mongols. However, the arrival of ancient nomadic tribes into this region may belong to the time depth of the arrival of pastoralist communities in this region. As a future perspective, a comprehensive study including samples from individual tribes will provide fine-scale structure of the gene pool of Jammu and Kashmir. � The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature 2024.Item Forensic Characterization, Genomic Variability and Ancestry Analysis of Six Populations from Odisha Using mtDNA SNPs and Autosomal STRs(Springer, 2024) Sequeira J.J.; Panda M.; Dixit S.; Kumawat R.; Mustak M.S.; Sharma A.N.; Chaubey G.; Shrivastava P.Located on India's eastern coast, Odisha is known for its diverse tribes and castes. In the early days of genome sequencing technology, researchers primarily studied the Austroasiatic communities inhabiting this region to reconstruct the ancient origins and dispersal of this broad linguistic group. However, current research has shifted towards identifying population and individual-specific genome variation for forensic applications. This study aims to analyze the forensic efficiency and ancestry of six populations from Odisha. We assessed the SF mtDNA-SNP60� PCR Amplification Kit by comparing it with PowerPlex� Fusion 6C System, a widely used autosomal STR (aSTR) kit, in an Indian cohort. Although the mtDNA SNP kit showed low discriminating power for individuals of a diverse population, it could identify deep lineage divergence. Also, we utilized mitochondrial and autosomal variation information to analyze the ancestry of six endogamous ethnic groups in Odisha. We observe two extremities�populations with higher West Asian affinity and those with East Asian affinity. This observation is in congruence with the existing information of their tribal and non-tribal affiliation. When compared with neighbouring populations from Central and Eastern India, multivariate analysis showed that the Brahmins clustered separately or with the Gopala, Kaibarta appeared as an intermediate, Pana and Kandha clustered with the Gonds, and Savara with the Munda tribes. Our findings indicate significant deep lineage stratification in the ethnic populations of Odisha and a gene flow from West and East Asia. The artefacts of unique deep lineage in such a diverse population will help in improving forensic identification. In addition, we conclude that the SF mtDNA-SNP60 PCR Amplification Kit may be used only as a supplementary tool for forensic analysis. � The Author(s), under exclusive licence to Springer Science+Business Media, LLC, part of Springer Nature 2024.Item Genetic evidence for a single founding population of the Lakshadweep Islands(Springer Science and Business Media Deutschland GmbH, 2024) Kumar S.; Singh P.P.; Pasupuleti N.; Shendre S.S.; Sequeira J.J.; Babu I.; Mutak M.S.; Rai N.; Chaubey G.Lakshadweep is an archipelago of 36 islands located in the Southeastern Arabian Sea. In the absence of a detailed archaeological record, the human settlement timing of this island is vague. Previous genetic studies on haploid DNA makers suggested sex-biased ancestry linked to North and South Indian populations. Maternal ancestry suggested a closer link with the Southern Indian, while paternal ancestry advocated the Northern Indian genetic�affinity. Since the haploid markers are more sensitive to genetic drift, which is evident for the Island populations, we have used the biparental high-resolution single-nucleotide polymorphic markers to reconstruct the population history of Lakshadweep Islands. Using the fine-scaled analyses, we specifically focused on (A) the ancestry components of Lakshadweep Islands populations; (B) their relation with East, West Eurasia and South Asia; (C) the number of founding lineages and (D) the putative migration from Northern India as the paternal ancestry was closer to the North Indian populations. Our analysis of ancestry components confirmed relatively higher North Indian ancestry among the Lakshadweep population. These populations are closely related to the South Asian populations. We identified mainly�a single founding population for these Islands, geographically divided into two sub-clusters. By examining the population�s genetic composition and analysing the gene flow from different source populations, this study contributes to our understanding of Lakshadweep Island�s evolutionary history and population dynamics. These findings shed light on the complex interactions between ethnic groups and their genetic contributions in making the Lakshadweep population. � The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature 2024.Item Identification of significant differentially expressed miRNA and their targets common in idiopathic Parkinson's diseaseand Parkinson plus syndrome(Elsevier B.V., 2024) Srivastava N.; Rana N.K.; Chaubey G.; Kumar B.; Pathak A.; Mishra V.N.Idiopathic Parkinson's disease is the most prevalent type of Parkinsonism. Its pathogenesis involves oxidative stress, glutamate excitotoxicity, protein aggregation, and neurodegeneration. Parkinson's plus syndrome presents additional progressing symptoms and shows temporary or no evident responses to dopaminergic therapy, whereas idiopathic Parkinson's responds effectively. Currently, there are no widely accepted biomarkers for both types of Parkinsonism. This study aims to identify differentially expressed (DE) miRNAs that target genes associated with neurodegeneration in idiopathic Parkinson's disease and Parkinson's plus syndrome by using micro RNA expression profiling and bioinformatics tools. Combined study results through miRNA expression analysis and network analysis revealed five significant miRNAs (hsa-miR-34, hsa-miR-29, hsa-miR-128, hsa-miR-3175, and hsa-miR-6809) that were found to be common in both conditions. Their selected target genes (SNCA, PAK1, and PRKN) play crucial roles in the Parkinson's disease pathway and neurodegeneration. Thus, this research sheds light on potential therapeutic targets and a common pathway between idiopathic Parkinson's disease and Parkinson's plus syndrome. � 2023Item Novel genetic association of the Furin gene polymorphism rs1981458 with COVID-19 severity among Indian populations(Nature Research, 2024) Pandey R.K.; Srivastava A.; Mishra R.K.; Singh P.P.; Chaubey G.SARS CoV-2, the causative agent for the ongoing COVID-19 pandemic, it enters the host cell by activating the ACE2 receptor with the help of two proteasesi.e., Furin and TMPRSS2. Therefore, variations in these genes may account for differential susceptibility and severity between populations. Previous studies have shown that the role of ACE2 and TMPRSS2 gene variants in understanding COVID-19 susceptibility among Indian populations. Nevertheless, a knowledge gap exists concerning the COVID-19 susceptibility of Furin gene variants among diverse South Asian ethnic groups. Investigating the role of Furin gene variants and their global phylogeographic structure is essential to comprehensively understanding COVID-19 susceptibility in these populations. We have used 450 samples from diverse Indian states and performed linear regression to analyse the Furin gene variant's with COVID-19 Case Fatality Rate (CFR) that could be epidemiologically associated with disease severity outcomes. Associated genetic variants were further evaluated for their expression and regulatory potential through various Insilco analyses. Additionally, we examined the Furin gene using next-generation sequencing (NGS) data from 393 diverse global samples, with a particular emphasis on South Asia, to investigate its Phylogeographic structure among�diverse world populations. We found a significant positive association for the SNP rs1981458 with COVID-19 CFR (p < 0.05) among diverse Indian populations at different timelines of the first and second waves. Further, QTL and other regulatory analyses showed various significant associations for positive regulatory roles of rs1981458 and Furin gene, mainly in Immune cells and virus infection process, highlighting their role in host immunity and viral assembly and processing. The Furin protein�protein interaction suggested that COVID-19 may contribute to Pulmonary arterial hypertension via a typical inflammation mechanism. The phylogeographic architecture of the Furin gene demonstrated a closer genetic affinity of South Asia with West Eurasian populations. Therefore, it is worth proposing that for the Furin gene, the COVID-19 susceptibility of South Asians will be more similar to the West Eurasian population. Our previous studies on the ACE2 and TMPRSS2 genes showed genetic affinity of South Asian with East Eurasians and West Eurasians, respectively. Therefore, with the collective information from these three important genes (ACE2, TMPRSS2 and Furin) we modelled COVID-19 susceptibilityof South Asia in between these two major ancestries with an inclination towards West Eurasia. In conclusion, this study, for the first time, concluded the role of rs1981458 in COVID-19 severity among the Indian population and outlined its regulatory potential.This study also highlights that the genetic structure for COVID-19 susceptibilityof South Asia is distinct, however, inclined to the West Eurasian population. We believe this insight may be utilised as a genetic biomarker to identify vulnerable populations, which might be directly relevant for developing policies and allocating resources more effectively during an epidemic. � The Author(s) 2024.Item Reconstructing the population history of the�Nicobarese(Springer Nature, 2024) Mishra R.K.; Singh P.P.; Rai N.; Desai S.; Pandey P.; Tiwary S.K.; Tamang R.; Suravajhala P.; Shrivastava P.; Thangaraj K.; van Driem G.; Chaubey G.The Nicobarese are the major tribal groups in the Nicobar district, situated south of the Andaman group of Islands. Linguistic phylogeny suggests that the linguistic ancestors of the Nicobarese settled the Nicobar archipelago in the early Holocene. So far, genetic research on them is low-resolution and restricted to the haploid DNA markers. Therefore, in the present analysis, we have used the high-resolution biparental (1554 published and 5 newly genotyped Nicobarese individuals) and uniparental genetic markers and looked at the genetic association of Nicobarese with the South and Southeast Asian populations. We report a common ancestral component shared among the Austroasiatic of South and Southeast Asia. Our analyses have suggested that the Nicobarese peoples retain this ancestral Austroasiatic predominant component in their genomes in the highest proportion. On the Southeast Asian mainland, the Htin Mal, who speak an Austroasiatic language of the Khmuic branch, represent a population that has preserved their ethnic distinctness from other groups over time and consequently shown the highest drift with the Nicobarese. The analysis based on haplotypes indicated a significant level of genomic segment sharing across linguistic groups, indicating an ancient broader distribution of Austroasiatic populations in Southeast Asia. Based on the temporal analyses of haploid DNA, it is suggested that the forebears of the Nicobarese people may have arrived on the Nicobar Islands in the last 5000 YBP. Therefore, among the modern populations, the Nicobarese peoples and the Htin Mal language community represent good genetic proxies for ancient Austroasiatics. � The Author(s), under exclusive licence to European Society of Human Genetics 2024.Item The genetic admixture and assimilation of Ahom: a historic migrant from Thailand to India(Oxford University Press, 2024) Kumar S.; Singh P.P.; Pasupuleti N.; Tripathy V.M.; Chauley M.K.; Chaubey G.; Rai N.The Northeastern region of India is considered a gateway for modern humans' dispersal throughout Asia. This region is a mixture of various ethnic and indigenous populations amalgamating multiple ancestries. One reason for such amalgamation is that, South Asia experienced multiple historic migrations from various parts of the world. A few examples explored genetically are Jews, Parsis and Siddis. Ahom is a dynasty that historically migrated to India during the 12th century. However, this putative migration has not been studied genetically at high resolution. Therefore, to validate this historical evidence, we genotyped autosomal data of the Modern Ahom population residing in seven sister states of India. Principal Component and Admixture analyses haave suggested a substantial admixture of the Ahom population with the local Tibeto-Burman populations. Moreover, the haplotype-based analysis has linked these Ahom individuals mainly with the Kusunda (a language isolated from Nepal) and Khasi (an Austroasiatic population of Meghalaya). Such unexpected presence of widespread population affinities suggests that Ahom mixed and assimilated a wide variety of Trans-Himalayan populations inhabiting this region after the migration. In summary, we observed a significant deviation of Ahom from their ancestral homeland (Thailand) and extensive admixture and assimilation with the local South Asian populations. � 2024 The Author(s). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.Item The genetic identity of the Vedda: A language isolate of South Asia(Elsevier B.V., 2024) Welikala A.; Desai S.; Pratap Singh P.; Fernando A.; Thangaraj K.; van Driem G.; Adikari G.; Tennekoon K.; Chaubey G.; Ranasinghe R.Linguistic data from South Asia identified several language isolates in the subcontinent. The Vedda, an indigenous population of Sri Lanka, are the least studied amongst them. Therefore, to understand the initial peopling of Sri Lanka and the genetic affinity of the Vedda with other populations in Eurasia, we extensively studied the high-resolution autosomal and mitogenomes from the Vedda population of Sri Lanka. Our autosomal analyses suggest a close genetic link of Vedda with the tribal populations of India despite no evidence of close linguistic affinity, thus suggesting a deep genetic link of the Vedda with these populations. The mitogenomic analysis supports this association by pointing to an ancient link with Indian populations. We suggest that the Vedda population is a genetically drifted group with limited gene flow from neighbouring Sinhalese and Sri Lankan Tamil populations. Interestingly, the genetic ancestry sharing of Vedda neglects the isolation-by-distance model. Collectively, the demography of Sri Lanka is unique, where Sinhalese and Sri Lankan Tamil populations excessively admixed, whilst Vedda largely preserved their isolation and deep genetic association with India. � 2024 Elsevier B.V. and Mitochondria Research SocietyItem The maternal genetic history of tribal populations of Chhattisgarh, India(Elsevier B.V., 2024) Dixit S.; Shrivastava P.; Jeevan Sequeira J.; Mustak M.S.; Rana M.; Kushwaha P.; Shrivastava D.; Kumawat R.K.; Pratap Singh P.; Tiwary S.K.; Chauhan N.K.; Chaubey G.The central region of India boasts a rich tribal heritage and the highest number of tribal populations in the country. Analysing the genetic history of this population can offer valuable insights into various demographic processes that shaped the gene pool of present-day settlers of this region. In this study, we utilize a recently validated Next-generation sequencing (NGS) technique to sequence 24 tribal mitogenomes from the Chhattisgarh population for genetic ancestry and forensic analysis. The identified ancient haplogroups in this population can be traced back to the pre-Last Glacial Maximum (LGM) period. Our Bayesian analysis provides evidence for maternal ancestral expansion following the earliest Out-of-Africa migration, followed by a prolonged steady phase. We identified three basal founding haplogroups, M2, R5, and U2 in the Chhattisgarh region that diversified during the Neolithic period. Indistinct distribution pattern of these haplogroups among tribes and castes suggests that the maternal ancestry of Chhattisgarh population predates any kind of social stratification that exists today in the Indian subcontinent. Furthermore, our analysis suggests that this region remained unaffected by the Last Glacial Maximum. The forensic analysis of the mitogenomes demonstrates a high power of discrimination (0.9256) within the Chhattisgarh population, thus supporting the applicability of mitogenome NGS technology in forensic contexts. � 2024 Elsevier B.V. and Mitochondria Research Society
