“Like Sugar in Milk”: Reconstructing the genetic history of the Parsi population

Chaubey, Gyaneshwer; Ayub, Qasim; Rai, Niraj; Prakash, Satya; Mushrif-Tripathy, Veena; Mezzavilla, Massimo; Pathak, Ajai Kumar; Tamang, Rakesh; Firasat, Sadaf; Reidla, Maere; Karmin, Monika; Rani, Deepa Selvi; Reddy, Alla G.; Parik, Jüri; Metspalu, Ene; Rootsi, Siiri; Dalal, Kurush; Khaliq, Sagufta; Mehdi, S. Qasim; Singh, Lalji; Metspalu, Mait; Kivisild, Toomas; Tyler‐Smith, Chris; Villems, Richard; Thangaraj, Kumarasamy

doi:10.1101/128777

Cited by 4 publications

(6 citation statements)

References 37 publications

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“…In our search of the SNPs reported to be associated with high risk by Zeberg & Pääbo 6 , we found rs10490770 from genome-wide datasets 14,15,[18][19][20] . We applied the same tests done for the ACE2 SNPs (Fig.…”

Section: Resultsmentioning

confidence: 99%

“…Therefore, we searched the genotype datasets generated by this platform. The frequency data for both of the SNPs from various Indian populations were extracted by using Plink 1.9 11 , from 1000 genome project data phase 3 12 data published by the Estonian Biocentre [13][14][15][16] and our newly genotyped samples for various Indian states and Bangladesh (Supplementary Table 1). In addition to our previous study 10 , more samples were added for the SNP rs2285666.…”

Section: Methodsmentioning

confidence: 99%

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The Major Genetic Risk Factor for Severe COVID-19 Does Not Show Any Association Among Indian Populations

Singh

Shrivastava

Sultana

et al. 2021

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With the growing evidence on the variable human susceptibility against COVID-19, it is evident that some genetic loci modulate the severity of the infection. Recent studies have identified several loci associated with greater severity. More recently, a study has identified a 50kb segment introgressed from Neanderthal adding a risk for COVID-19, and this trait is present among 16% and 50% people of European and South Asian origin respectively. Contrary to this finding, our studies on ACE2 identified a haplotype present among 20% and 60% of European and South Asian populations respectively, which appears to be responsible for the low case fatality ratio among South Asian populations. This result was also consistent with the realtime infection rate and case fatality ratio among various states of India. We readdressed this issue using both of the contrasting datasets and compared them with the realtime infection rates and case fatality ratio in India. We found out that the polymorphism present in the 50kb introgressed segment (rs10490770) did not show any significant correlation with the realtime infection and case fatality ratio in India.

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Section: Resultsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

The Major Genetic Risk Factor for Severe COVID-19 Does Not Show Any Association Among Indian Populations

Singh

Shrivastava

Sultana

et al. 2021

Preprint

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“…South West coastal India is a region of high population diversity and with complex genetic history. Some earlier studies with groups like Jews (Behar, et al 2008; Behar, et al 2010; Chaubey, et al 2016), Parsees (Chaubey, et al 2017) and Roman catholic (Kumar, et al 2021) already pointed out the complex genetic history and multilayered genetic structure of populations in this region. Also, earlier studies (Moorjani, et al 2013; Narasimhan, et al 2019) indeed suggested about the multi layered admixture in the Indian subcontinent specially among caste groups.…”

Section: Discussionmentioning

confidence: 98%

“…Reason we proposed behind this was the complex nature of admixture history in the form of multiple layers of ancestries. More specifically in South West coast of India, studies with some unique population groups like Jews, Parsees and Roman Catholics have already pointed about the additional layers of admixture among them (Chaubey, et al 2016; Chaubey, et al 2017; Kumar, et al 2021). Previous genetic studies based on Y chromosomal microsatellite markers also found more west Eurasian or North West Indian genetic influence in gene pool of Nairs and Ezhava (Nair, et al 2011; Mahal and Matsoukas 2018).…”

Section: Introductionmentioning

confidence: 99%

Genetic affinities and adaptation of the South West coast populations of India

Kumar

Chowdhari

Sequeira

et al. 2022

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Evolutionary event has not only transformed the genetic structure of human populations but also associated with social and cultural transformation. South Asian populations were formed as a result of such evolutionary events of migration and admixture of genetically and culturally distinct groups. Most of the genetic studies pointed to large-scale admixture event between Ancestral North Indian (ANI) and Ancestral South Indian (ASI) groups, also additional layers of recent admixture. In the present study we have analyzed 213 individuals inhabited in South West coast India with traditional warriors and feudal lord status and historically associated with recent migrations events and possible admixture with Indo-Scythians, Saka, Huns and Kushans, whose genetic links are still missing. Analysis of autosomal SNP markers suggests that these groups possibly derived their ancestry from some groups of North West India having additional Middle Eastern genetic component and also their separation history suggests very early separation from North West Indian and Gangetic plain Indo-Europeans during late bronze or Iron age, most probably following central India and Godavari basin to South West coast. Higher distribution of west Eurasian mitochondrial haplogroups also points to admixture through maternal lineage. Selection screen using genome wide genealogy approach revealed genetic signatures related to their long-term coastal food habits. Thus, our study suggests that the South West coastal groups with traditional warriors and feudal lords status are of a distinct lineage compared to Dravidian and Gangetic plain Indo-Europeans and are remnants of very early migrations from North West India following Godavari basin to Karnataka and Kerala.

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“…We obtained a total of 5 SNPs (rs2070788, rs734056, rs12329760, rs2276205, and rs3787950) was observed in our data and studied subsequently in detail. Data from the Estonian Biocentre (42)(43)(44)(45), data from phase 3 of the 1,000 Genomes Project (46), and our new genotyped samples from several Indian states were used to calculate the frequency of each of these SNPs among various Indian populations using plink 1.9. State-wise frequency maps for rs2070788 and COVID-19 CFR among the Indian population were made by https://www.datawrapper.de/.…”

Section: Methodsmentioning

confidence: 99%

Genetic association of TMPRSS2 rs2070788 polymorphism with COVID-19 Case Fatality Rate among Indian populations

Pandey

Srivastava

Singh

et al. 2021

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SARS-CoV2, 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 difference in population disease susceptibility. The haplotype-based genetic sharing and structure of TMPRSS2 among global populations have not been studied so far. Therefore, in the present work, we used this approach with a focus on South Asia to study the haplotypes and their sharing among various populations worldwide. We have used next-generation sequencing data of 393 individuals and analysed the TMPRSS2 gene. Our analysis of genetic relatedness for this gene 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 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. We have also tested the SNPs frequencies of this gene among various Indian state populations with respect to the case fatality rate. Interestingly, we found a significant positive association between the rs2070788 SNP (G Allele) and the case fatality rate in India. It has been shown that the GG genotype of rs2070788 allele tends to have a higher expression of TMPRSS2 in the lung compared to the AG and AA genotypes, thus it might play a vital part in determining differential disease vulnerability. We trust that this information will be useful in underscoring the role of the TMPRSS2 variant in COVID-19 susceptibility and using it as a biomarker may help to predict populations at risk.

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“Like Sugar in Milk”: Reconstructing the genetic history of the Parsi population

Abstract: Background

Cited by 4 publications

References 37 publications

The Major Genetic Risk Factor for Severe COVID-19 Does Not Show Any Association Among Indian Populations

The Major Genetic Risk Factor for Severe COVID-19 Does Not Show Any Association Among Indian Populations

Genetic affinities and adaptation of the South West coast populations of India

Genetic association of TMPRSS2 rs2070788 polymorphism with COVID-19 Case Fatality Rate among Indian populations

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