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Ranganathan S, Dee EC, Debnath N, Patel TA, Jain B, Murthy V. Access and barriers to genomic classifiers for breast cancer and prostate cancer in India. Int J Cancer 2024; 154:1335-1339. [PMID: 37962056 DOI: 10.1002/ijc.34784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 09/25/2023] [Accepted: 10/10/2023] [Indexed: 11/15/2023]
Abstract
The incidence of cancer in general, including breast and prostate cancer specifically, is increasing in India. Breast and prostate cancers have genomic classifiers developed to guide therapy decisions. However, these genomic classifiers are often inaccessible in India due to high cost. These classifiers may also be less suitable to the Indian population, as data primarily from patients in wealthy Western countries were used in developing these genomic classifiers. In addition to the limitations in using these existing genomic classifiers, developing and validating new genomic classifiers for breast and prostate cancer in India is challenging due to the heterogeneity in the Indian population. However, there are steps that can be taken to address the various barriers that currently exist for accurate, accessible genomic classifiers for cancer in India.
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Affiliation(s)
| | - Edward Christopher Dee
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Neha Debnath
- Department of Medicine, Icahn School of Medicine at Mount Sinai (Morningside/West), New York, New York, USA
| | - Tej A Patel
- Department of Healthcare Management & Policy, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Bhav Jain
- Department of Health Policy, Stanford University School of Medicine, Stanford, California, USA
| | - Vedang Murthy
- Department of Radiation Oncology, ACTREC, Tata Memorial Centre, Homi Bhabha National Institute, Mumbai, India
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Zhao W, Smith J, Wang Y, Chintalapati M, Ammous F, Yu M, Moorjani P, Ganna A, Gross A, Dey S, Benerjee J, Chatterjee P, Dey A, Lee J, Kardia S. Polygenic Risk Scores for Alzheimer's Disease and General Cognitive Function Are Associated With Measures of Cognition in Older South Asians. J Gerontol A Biol Sci Med Sci 2023; 78:743-752. [PMID: 36782352 PMCID: PMC10172981 DOI: 10.1093/gerona/glad057] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Indexed: 02/15/2023] Open
Abstract
Genome-wide association studies (GWAS) conducted in European ancestry (EA) have identified hundreds of single-nucleotide polymorphisms (SNPs) associated with general cognitive function and/or Alzheimer's disease (AD). The association between these SNPs and cognitive function has not been fully evaluated in populations with complex genetic substructure such as South Asians. This study investigated whether SNPs identified in EA GWAS, either individually or as polygenic risk scores (PRSs), were associated with general cognitive function and 5 broad cognitive domains in 932 South Asians from the Diagnostic Assessment of Dementia for the Longitudinal Aging Study in India (LASI-DAD). We found that SNPs identified from AD GWAS were more strongly associated with cognitive function in LASI-DAD than those from a GWAS of general cognitive function. PRSs for general cognitive function and AD explained up to 1.1% of the variability in LASI-DAD cognitive domain scores. Our study represents an important stepping stone toward better characterization of the genetic architecture of cognitive aging in the Indian/South Asian population and highlights the need for further research that may lead to the identification of new variants unique to this population.
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Affiliation(s)
- Wei Zhao
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, Michigan, USA
- Survey Research Center, Institute for Social Research, University of Michigan, Ann Arbor, Michigan, USA
| | - Jennifer A Smith
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, Michigan, USA
- Survey Research Center, Institute for Social Research, University of Michigan, Ann Arbor, Michigan, USA
| | - Yi Zhe Wang
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, Michigan, USA
| | - Manjusha Chintalapati
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California, USA
- Center for Computational Biology, University of California, Berkeley, Berkeley, California, USA
| | - Farah Ammous
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, Michigan, USA
| | - Miao Yu
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, Michigan, USA
| | - Priya Moorjani
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California, USA
- Center for Computational Biology, University of California, Berkeley, Berkeley, California, USA
| | - Andrea Ganna
- Institute for Molecular Medicine Finland, Helsinki, Finland
| | - Alden Gross
- Johns Hopkins Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland, USA
| | - Sharmistha Dey
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, India
| | - Joyita Benerjee
- Department of Geriatric Medicine, All India Institute of Medical Sciences, New Delhi, India
| | - Prasun Chatterjee
- Department of Geriatric Medicine, All India Institute of Medical Sciences, New Delhi, India
| | - Aparajit B Dey
- Department of Geriatric Medicine, All India Institute of Medical Sciences, New Delhi, India
| | - Jinkook Lee
- Department of Economics, University of Southern California, Los Angeles, California, USA
| | - Sharon L R Kardia
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, Michigan, USA
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Pojar T, Langstieh BT, Hemphill BE. An initial investigation of dental morphology variation among three southern Naga ethnic groups of Northeast India. AMERICAN JOURNAL OF BIOLOGICAL ANTHROPOLOGY 2022; 179:184-210. [PMID: 36790681 DOI: 10.1002/ajpa.24605] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2021] [Revised: 04/29/2022] [Accepted: 07/28/2022] [Indexed: 11/07/2022]
Abstract
OBJECTIVES This study examines dental morphology trait prevalence among three southern Naga groups and compares them to 10 ethnic groups from other regions of South Asia to accomplish two objectives: assess the biological relationship of these Tibeto-Burman-speakers to speakers of non-Tibeto-Burman languages in other South Asian regions, and determine which traits distinguish northeast Indians from other South Asians. METHODS Dental morphology traits were scored with the Arizona State University Dental Anthropology System. Tooth-trait combinations were evaluated for significant inter-trait correlation and intra-trait correspondence within dental fields. Comparisons were based on simple trait prevalence and with Smith's MMD. Affinities based on the former were accomplished with correspondence analysis and principal components analysis. Affinities based on the latter were undertaken with neighbor-joining cluster analysis and multidimensional scaling. RESULTS After elimination due to inter-trait correlations and uniform prevalence, biodistances based on the remaining 17 tooth-trait combinations identify significant differences between northeast Indians and other South Asian ethnic groups due to high frequencies of shoveling on the maxillary incisors and Cusp 6 on the mandibular molars coupled with low frequencies of Carabelli's trait and Cusp 5 on UM1 and UM2, respectively. CONCLUSIONS Patterns of biodistances obtained from dental morphology are consilient with those obtained from DNA indicating statistically significant differences between northeast Indians from members of ethnic groups of other regions of South Asia. Researchers should explore the sex-specific patterns. Biodistances should not be limited to "key" teeth within dental fields, for in almost every case traits present on mesial and distal teeth yield non-redundant information.
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Affiliation(s)
- Tsiapisa Pojar
- Department of Anthropology, North-Eastern Hill University, Shillong, India
| | | | - Brian E Hemphill
- Department of Anthropology, University of Alaska, Fairbanks, Fairbanks, Alaska, USA
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Phillips C, de la Puente M, Ruiz-Ramirez J, Staniewska A, Ambroa-Conde A, Freire-Aradas A, Mosquera-Miguel A, Rodriguez A, Lareu MV. Eurasiaplex-2: Shifting the focus to SNPs with high population specificity increases the power of forensic ancestry marker sets. Forensic Sci Int Genet 2022; 61:102780. [PMID: 36174251 DOI: 10.1016/j.fsigen.2022.102780] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Revised: 09/16/2022] [Accepted: 09/18/2022] [Indexed: 11/27/2022]
Abstract
To compile a new South Asian-informative panel of forensic ancestry SNPs, we changed the strategy for selecting the most powerful markers for this purpose by targeting polymorphisms with near absolute specificity - when the South Asian-informative allele identified is absent from all other populations or present at frequencies below 0.001 (one in a thousand). More than 120 candidate SNPs were identified from 1000 Genomes datasets satisfying an allele frequency screen of ≥ 0.1 (10 % or more) allele frequency in South Asians, and ≤ 0.001 (0.1 % or less) in African, East Asian, and European populations. From the candidate pool of markers, a final panel of 36 SNPs, widely distributed across most autosomes, were selected that had allele frequencies in the five 1000 Genomes South Asian populations ranging from 0.4 to 0.15. Slightly lower average allele frequencies, but consistent patterns of informativeness were observed in gnomAD South Asian datasets used to validate the 1000 Genomes variant annotations. We named the panel of 36 South Asian-specific SNPs Eurasiaplex-2, and the informativeness of the panel was evaluated by compiling worldwide population data from 4097 samples in four genome variation databases that largely complement the global sampling of 1000 Genomes. Consistent patterns of allele frequency distribution, which were specific to South Asia, were observed in all populations in, or closely sited to, the Indian sub-continent. Pakistani populations from the HGDP-CEPH panel had markedly lower allele frequencies, highlighting the need to develop a statistical system to evaluate the ancestry inference value of counting the number of population-specific alleles present in an individual.
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Affiliation(s)
- C Phillips
- Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, Spain; Institute of Anthropology and Ethnology, Adam Mickiewicz University in Poznań, Poland..
| | - M de la Puente
- Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, Spain
| | - J Ruiz-Ramirez
- Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, Spain
| | - A Staniewska
- Institute of Anthropology and Ethnology, Adam Mickiewicz University in Poznań, Poland
| | - A Ambroa-Conde
- Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, Spain
| | - A Freire-Aradas
- Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, Spain
| | - A Mosquera-Miguel
- Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, Spain
| | - A Rodriguez
- Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, Spain
| | - M V Lareu
- Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, Spain
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Ilori T, Watanabe A, Ng KH, Solarin A, Sinha A, Gbadegesin R. Genetics of Chronic Kidney Disease in Low-Resource Settings. Semin Nephrol 2022; 42:151314. [PMID: 36801667 PMCID: PMC10272019 DOI: 10.1016/j.semnephrol.2023.151314] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/19/2023]
Abstract
Advances in kidney genomics in the past 20 years has opened the door for more precise diagnosis of kidney disease and identification of new and specific therapeutic agents. Despite these advances, an imbalance exists between low-resource and affluent regions of the world. Individuals of European ancestry from the United States, United Kingdom, and Iceland account for 16% of the world's population, but represent more than 80% of all genome-wide association studies. South Asia, Southeast Asia, Latin America, and Africa together account for 57% of the world population but less than 5% of genome-wide association studies. Implications of this difference include limitations in new variant discovery, inaccurate interpretation of the effect of genetic variants in non-European populations, and unequal access to genomic testing and novel therapies in resource-poor regions. It also further introduces ethical, legal, and social pitfalls, and ultimately may propagate global health inequities. Ongoing efforts to reduce the imbalance in low-resource regions include funding and capacity building, population-based genome sequencing, population-based genome registries, and genetic research networks. More funding, training, and capacity building for infrastructure and expertise is needed in resource-poor regions. Focusing on this will ensure multiple-fold returns on investments in genomic research and technology.
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Affiliation(s)
- Titilayo Ilori
- Division of Nephrology, Boston University School of Medicine, Boston, MA
| | - Andreia Watanabe
- Division of Molecular Medicine, Department of Pediatrics, University of São Paulo School of Medicine, São Paulo, Brazil
| | - Kar-Hui Ng
- Department of Pediatrics, Yong Loo Lin School of Medicine, Singapore
| | - Adaobi Solarin
- Department of Pediatrics and Child Health, Lagos State University College of Medicine, Ikeja, Lagos, Nigeria
| | - Aditi Sinha
- Department of Pediatrics, All India Institute of Medical Sciences, New Delhi, India
| | - Rasheed Gbadegesin
- Division of Nephrology, Department of Pediatrics, Duke University School of Medicine, Durham, NC.
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Cross-continental admixture in the Kho population from northwest Pakistan. Eur J Hum Genet 2022; 30:740-746. [PMID: 35217804 DOI: 10.1038/s41431-022-01057-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2021] [Revised: 11/25/2021] [Accepted: 01/25/2022] [Indexed: 01/01/2023] Open
Abstract
Northern Pakistan is home to many diverse ethnicities and languages. The region acted as a prime corridor for ancient invasions and population migrations between Western Eurasia and South Asia. Kho, one of the major ethnic groups living in this region, resides in the remote and isolated mountainous region in the Chitral Valley of the Hindu Kush Mountain range. They are culturally and linguistically distinct from the rest of the Pakistani population groups and their genetic ancestry is still unknown. In this study, we generated genome-wide genotype data of ~1 M loci (Illumina WeGene array) for 116 unrelated Kho individuals and carried out comprehensive analyses in the context of worldwide extant and ancient anatomically modern human populations across Eurasia. The results inferred that the Kho can trace a large proportion of their ancestry to the population who migrated south from the Southern Siberian steppes during the second millennium BCE ~110 generations ago. An additional wave of gene flow from a population carrying East Asian ancestry was also identified in the Kho that occurred ~60 generations ago and may possibly be linked to the expansion of the Tibetan Empire during 7th to 9th centuries CE (current era) in the northwestern regions of the Indian sub-continent. We identified several candidate regions suggestive of positive selection in the Kho, that included genes mainly involved in pigmentation, immune responses, muscular development, DNA repair, and tumor suppression.
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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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The impact of prehistoric human dispersals on the presence of tobacco-related oral cancer in Northeast India. Gene 2021; 813:146098. [PMID: 34952175 DOI: 10.1016/j.gene.2021.146098] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 10/20/2021] [Accepted: 11/16/2021] [Indexed: 11/24/2022]
Abstract
BACKGROUND Northeast (NE) India is a subject of debate for predicting its involvement in prehistoric anatomically modern human (AMH) dispersal. The unique lifestyle and genetic characteristics of native ethnic groups in this region are believed to be responsible for their susceptibility to tobacco-related oral cancer (TrOC). The present study assessed mitochondrial macro-haplogroup (mHG) diversity and TrOC susceptibility autosomal loci to evaluate the impact of prehistoric AMH dispersal on the present day's high TrOC prevalence in major NE Indian ethnics. METHODS We considered 175 unrelated individuals from 35 ethnic groups and previously published 374 sequences for sequencing-based assessment of mtDNA-based marker by subsequent analyses like haplogroup diversity, phylogenetic, genetic structure by AMOVA, and MDS, descriptive statistics of demographic parameters, and migration analysis. Besides, we selected prolonged tobacco-chewing 124 case-control individuals from similar ethnic backgrounds for genotyping 115 autosomal loci in Sequenom iPLEX MassARRAY™ platform and mined 1000genome data (n = 398) for consequent global admixture and ancestry-specific allele frequencies-based analyses. RESULTS Our mtDNA-based findings suggested that NE populations were distinct from other Indian populations, owing to the first wave of migration from ancient southern China (∼54kya) and two successive spatial expansion events at ∼45kya and ∼43kya. Consequently, it probably acted as another source for prehistoric AMH dispersal in N/NE Asia. Besides, the second wave of back-migration from SE Asia (∼40kya) probably replaced the mitochondrial footprints of survivors from the first migrants and introduced the TrOC susceptibility traits in this region. Afterward, the autosomal marker-based observations on the transition of the disease-associated admixture component 'K6' from SE Asia reconfirmed these results. Moreover, we also observed that the mitochondrial mHG 'R' is significantly associated with the risk of TrOC (OR > 9.5) in NE India. Furthermore, the possible onset of the phenotypic expression of those traits was predicted at ∼4kya, thus, contributing to present-day's TrOC prevalence. CONCLUSIONS This study reflects its uniqueness by revealing an updated AMH dispersal route for the peopling in and out of NE India, which probably introduced the disease-causing traits in the ancestral NE Indian population. Those traits were then imprinted in their genome to get transferred through their respective generations, forming the present-day's TrOC-prevalent NE Indian population.
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Lv FH, Cao YH, Liu GJ, Luo LY, Lu R, Liu MJ, Li WR, Zhou P, Wang XH, Shen M, Gao L, Yang JQ, Yang H, Yang YL, Liu CB, Wan PC, Zhang YS, Pi WH, Ren YL, Shen ZQ, Wang F, Wang YT, Li JQ, Salehian-Dehkordi H, Hehua E, Liu YG, Chen JF, Wang JK, Deng XM, Esmailizadeh A, Dehghani-Qanatqestani M, Charati H, Nosrati M, Štěpánek O, Rushdi HE, Olsaker I, Curik I, Gorkhali NA, Paiva SR, Caetano AR, Ciani E, Amills M, Weimann C, Erhardt G, Amane A, Mwacharo JM, Han JL, Hanotte O, Periasamy K, Johansson AM, Hallsson JH, Kantanen J, Coltman DW, Bruford MW, Lenstra JA, Li MH. Whole-genome resequencing of worldwide wild and domestic sheep elucidates genetic diversity, introgression and agronomically important loci. Mol Biol Evol 2021; 39:6459180. [PMID: 34893856 PMCID: PMC8826587 DOI: 10.1093/molbev/msab353] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
Domestic sheep and their wild relatives harbor substantial genetic variants that can form the backbone of molecular breeding, but their genome landscapes remain understudied. Here, we present a comprehensive genome resource for wild ovine species, landraces and improved breeds of domestic sheep, comprising high-coverage (∼16.10×) whole genomes of 810 samples from 7 wild species and 158 diverse domestic populations. We detected, in total, ∼121.2 million single nucleotide polymorphisms, ∼61 million of which are novel. Some display significant (P < 0.001) differences in frequency between wild and domestic species, or are private to continent-wide or individual sheep populations. Retained or introgressed wild gene variants in domestic populations have contributed to local adaptation, such as the variation in the HBB associated with plateau adaptation. We identified novel and previously reported targets of selection on morphological and agronomic traits such as stature, horn, tail configuration, and wool fineness. We explored the genetic basis of wool fineness and unveiled a novel mutation (chr25: T7,068,586C) in the 3′-UTR of IRF2BP2 as plausible causal variant for fleece fiber diameter. We reconstructed prehistorical migrations from the Near Eastern domestication center to South-and-Southeast Asia and found two main waves of migrations across the Eurasian Steppe and the Iranian Plateau in the Early and Late Bronze Ages. Our findings refine our understanding of genome variation as shaped by continental migrations, introgression, adaptation, and selection of sheep.
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Affiliation(s)
- Feng-Hua Lv
- College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Yin-Hong Cao
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences (UCAS), Beijing, China
| | | | - Ling-Yun Luo
- College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Ran Lu
- College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Ming-Jun Liu
- Animal Biotechnological Research Center, Xinjiang Academy of Animal Science, Urumqi, China
| | - Wen-Rong Li
- Animal Biotechnological Research Center, Xinjiang Academy of Animal Science, Urumqi, China
| | - Ping Zhou
- Institute of Animal Husbandry and Veterinary Medicine, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, China
- State Key Laboratory of Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, China
| | - Xin-Hua Wang
- Institute of Animal Husbandry and Veterinary Medicine, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, China
- State Key Laboratory of Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, China
| | - Min Shen
- Institute of Animal Husbandry and Veterinary Medicine, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, China
- State Key Laboratory of Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, China
| | - Lei Gao
- Institute of Animal Husbandry and Veterinary Medicine, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, China
- State Key Laboratory of Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, China
| | - Jing-Quan Yang
- Institute of Animal Husbandry and Veterinary Medicine, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, China
- State Key Laboratory of Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, China
| | - Hua Yang
- Institute of Animal Husbandry and Veterinary Medicine, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, China
- State Key Laboratory of Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, China
| | - Yong-Lin Yang
- Institute of Animal Husbandry and Veterinary Medicine, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, China
- State Key Laboratory of Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, China
| | - Chang-Bin Liu
- Institute of Animal Husbandry and Veterinary Medicine, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, China
- State Key Laboratory of Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, China
| | - Peng-Cheng Wan
- Institute of Animal Husbandry and Veterinary Medicine, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, China
- State Key Laboratory of Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, China
| | - Yun-Sheng Zhang
- Institute of Animal Husbandry and Veterinary Medicine, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, China
- State Key Laboratory of Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, China
| | - Wen-Hui Pi
- Institute of Animal Husbandry and Veterinary Medicine, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, China
- State Key Laboratory of Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, China
| | - Yan-Ling Ren
- Shandong Binzhou Academy of Animal Science and Veterinary Medicine, Binzhou, China
| | - Zhi-Qiang Shen
- Shandong Binzhou Academy of Animal Science and Veterinary Medicine, Binzhou, China
| | - Feng Wang
- Institute of Sheep and Goat Science, Nanjing Agricultural University, Nanjing, China
| | - Yu-Tao Wang
- College of Life and Geographic Sciences, Kashi University, Kashi, China
| | - Jin-Quan Li
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China
| | - Hosein Salehian-Dehkordi
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences (UCAS), Beijing, China
| | - Eer Hehua
- Grass-Feeding Livestock Engineering Technology Research Center, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan, China
| | - Yong-Gang Liu
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming, China
| | - Jian-Fei Chen
- College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Jian-Kui Wang
- College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Xue-Mei Deng
- College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Ali Esmailizadeh
- Department of Animal Science, Faculty of Agriculture, Shahid Bahonar University of Kerman, Kerman, Iran
| | | | - Hadi Charati
- Department of Animal Science, Faculty of Agriculture, Shahid Bahonar University of Kerman, Kerman, Iran
| | - Maryam Nosrati
- Department of Agriculture, Payame Noor University, Tehran, Iran
| | - Ondřej Štěpánek
- Department of Virology, State Veterinary Institute Jihlava, Jihlava, Czech Republic
| | - Hossam E Rushdi
- Department of Animal Production, Faculty of Agriculture, Cairo University, 12613 Giza, Egypt
| | - Ingrid Olsaker
- Department of Preclinical Sciences and Pathology, Faculty of Veterinary Medicine, Norwegian University of Life Sciences, Ås, Norway
| | - Ino Curik
- Department of Animal Science, Faculty of Agriculture, University of Zagreb, Zagreb, Croatia
| | - Neena A Gorkhali
- Animal Breeding Division, National Animal Science Institute, Nepal Agriculture Research Council (NARC), Kathmandu, Nepal
| | - Samuel R Paiva
- Embrapa Recursos Genéticos e Biotecnologia, Parque Estação Biológica, PqEB, Brasília, DF, Brazil
| | - Alexandre R Caetano
- Embrapa Recursos Genéticos e Biotecnologia, Parque Estação Biológica, PqEB, Brasília, DF, Brazil
| | - Elena Ciani
- Dipartimento di Bioscienze, Biotecnologie e Biofarmaceutica, Università degli Studi di Bari Aldo 24 Moro, Bari, Italy
| | - Marcel Amills
- Department of Animal Genetics, Center for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus de la Universitat Autònoma de Barcelona, Bellaterra, Spain
- Department of Animal Sciences, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Christina Weimann
- Department of Animal Breeding and Genetics, Justus-Liebig-University Giessen, Giessen, Germany
| | - Georg Erhardt
- Department of Animal Breeding and Genetics, Justus-Liebig-University Giessen, Giessen, Germany
| | - Agraw Amane
- Department of Microbial, Cellular and Molecular Biology, Addis Ababa University, Addis Ababa, Ethiopia
- LiveGene Program, International Livestock Research Institute, Addis Ababa, Ethiopia
| | - Joram M Mwacharo
- Small Ruminant Genomics, International Centre for Agricultural Research in the Dry Areas (ICARDA), Addis Ababa, Ethiopia
- CTLGH and SRUC, The Roslin Institute Building, Easter Bush Campus, Edinburgh, Scotland
| | - Jian-Lin Han
- CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
- Livestock Genetics Program, International Livestock Research Institute (ILRI), Nairobi, Kenya
| | - Olivier Hanotte
- LiveGene Program, International Livestock Research Institute, Addis Ababa, Ethiopia
- School of Life Sciences, University of Nottingham, University Park, Nottingham, United Kingdom
| | - Kathiravan Periasamy
- Animal Production and Health Laboratory, Joint FAO/IAEA Division, International Atomic Energy Agency (IAEA), Vienna, Austria
| | - Anna M Johansson
- Department of Animal Breeding and Genetics, Faculty of Veterinary Medicine and Animal Science, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Jón H Hallsson
- Faculty of Natural Resources and Environmental Sciences, Agricultural University of Iceland, Borgarnes, Iceland
| | - Juha Kantanen
- Production Systems, Natural Resources Institute Finland (Luke), Jokioinen, Finland
| | - David W Coltman
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - Michael W Bruford
- School of Biosciences, Cardiff University, Cathays Park, Cardiff, Wales, United Kingdom
- Sustainable Places Research Institute, Cardiff University, Wales, United Kingdom
| | - Johannes A Lenstra
- Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands
| | - Meng-Hua Li
- College of Animal Science and Technology, China Agricultural University, Beijing, China
- Corresponding author: E-mail:
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10
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Bharti N, Banerjee R, Achalere A, Kasibhatla SM, Joshi R. Genetic diversity of 'Very Important Pharmacogenes' in two South-Asian populations. PeerJ 2021; 9:e12294. [PMID: 34824904 PMCID: PMC8590392 DOI: 10.7717/peerj.12294] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Accepted: 09/21/2021] [Indexed: 01/09/2023] Open
Abstract
Objectives Reliable identification of population-specific variants is important for building the single nucleotide polymorphism (SNP) profile. In this study, genomic variation using allele frequency differences of pharmacologically important genes for Gujarati Indians in Houston (GIH) and Indian Telugu in the U.K. (ITU) from the 1000 Genomes Project vis-à-vis global population data was studied to understand its role in drug response. Methods Joint genotyping approach was used to derive variants of GIH and ITU independently. SNPs of both these populations with significant allele frequency variation (minor allele frequency ≥ 0.05) with super-populations from the 1000 Genomes Project and gnomAD based on Chi-square distribution with p-value of ≤ 0.05 and Bonferroni’s multiple adjustment tests were identified. Population stratification and fixation index analysis was carried out to understand genetic differentiation. Functional annotation of variants was carried out using SnpEff, VEP and CADD score. Results Population stratification of VIP genes revealed four clusters viz., single cluster of GIH and ITU, one cluster each of East Asian, European, African populations and Admixed American was found to be admixed. A total of 13 SNPs belonging to ten pharmacogenes were identified to have significant allele frequency variation in both GIH and ITU populations as compared to one or more super-populations. These SNPs belong to VKORC1 (rs17708472, rs2359612, rs8050894) involved in Vitamin K cycle, cytochrome P450 isoforms CYP2C9 (rs1057910), CYP2B6 (rs3211371), CYP2A2 (rs4646425) and CYP2A4 (rs4646440); ATP-binding cassette (ABC) transporter ABCB1 (rs12720067), DPYD1 (rs12119882, rs56160474) involved in pyrimidine metabolism, methyltransferase COMT (rs9332377) and transcriptional factor NR1I2 (rs6785049). SNPs rs1544410 (VDR), rs2725264 (ABCG2), rs5215 and rs5219 (KCNJ11) share high fixation index (≥ 0.5) with either EAS/AFR populations. Missense variants rs1057910 (CYP2C9), rs1801028 (DRD2) and rs1138272 (GSTP1), rs116855232 (NUDT15); intronic variants rs1131341 (NQO1) and rs115349832 (DPYD) are identified to be ‘deleterious’. Conclusions Analysis of SNPs pertaining to pharmacogenes in GIH and ITU populations using population structure, fixation index and allele frequency variation provides a premise for understanding the role of genetic diversity in drug response in Asian Indians.
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Affiliation(s)
- Neeraj Bharti
- High Performance Computing: Medical & Bioinformatics Applications Group, Centre for Development of Advanced Computing, Pune, Maharashtra, India
| | - Ruma Banerjee
- High Performance Computing: Medical & Bioinformatics Applications Group, Centre for Development of Advanced Computing, Pune, Maharashtra, India
| | - Archana Achalere
- High Performance Computing: Medical & Bioinformatics Applications Group, Centre for Development of Advanced Computing, Pune, Maharashtra, India
| | - Sunitha Manjari Kasibhatla
- High Performance Computing: Medical & Bioinformatics Applications Group, Centre for Development of Advanced Computing, Pune, Maharashtra, India
| | - Rajendra Joshi
- High Performance Computing: Medical & Bioinformatics Applications Group, Centre for Development of Advanced Computing, Pune, Maharashtra, India
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11
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NyuWa Genome resource: A deep whole-genome sequencing-based variation profile and reference panel for the Chinese population. Cell Rep 2021; 37:110017. [PMID: 34788621 DOI: 10.1016/j.celrep.2021.110017] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 05/04/2021] [Accepted: 10/28/2021] [Indexed: 01/07/2023] Open
Abstract
The lack of haplotype reference panels and whole-genome sequencing resources specific to the Chinese population has greatly hindered genetic studies in the world's largest population. Here, we present the NyuWa genome resource, based on deep (26.2×) sequencing of 2,999 Chinese individuals, and construct a NyuWa reference panel of 5,804 haplotypes and 19.3 million variants, which is a high-quality publicly available Chinese population-specific reference panel with thousands of samples. Compared with other panels, the NyuWa reference panel reduces the Han Chinese imputation error rate by a margin ranging from 30% to 51%. Population structure and imputation simulation tests support the applicability of one integrated reference panel for northern and southern Chinese. In addition, a total of 22,504 loss-of-function variants in coding and noncoding genes are identified, including 11,493 novel variants. These results highlight the value of the NyuWa genome resource in facilitating genetic research in Chinese and Asian populations.
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12
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Bose A, Platt DE, Parida L, Drineas P, Paschou P. Integrating Linguistics, Social Structure, and Geography to Model Genetic Diversity within India. Mol Biol Evol 2021; 38:1809-1819. [PMID: 33481022 PMCID: PMC8097304 DOI: 10.1093/molbev/msaa321] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
India represents an intricate tapestry of population substructure shaped by geography, language, culture, and social stratification. Although geography closely correlates with genetic structure in other parts of the world, the strict endogamy imposed by the Indian caste system and the large number of spoken languages add further levels of complexity to understand Indian population structure. To date, no study has attempted to model and evaluate how these factors have interacted to shape the patterns of genetic diversity within India. We merged all publicly available data from the Indian subcontinent into a data set of 891 individuals from 90 well-defined groups. Bringing together geography, genetics, and demographic factors, we developed Correlation Optimization of Genetics and Geodemographics to build a model that explains the observed population genetic substructure. We show that shared language along with social structure have been the most powerful forces in creating paths of gene flow in the subcontinent. Furthermore, we discover the ethnic groups that best capture the diverse genetic substructure using a ridge leverage score statistic. Integrating data from India with a data set of additional 1,323 individuals from 50 Eurasian populations, we find that Indo-European and Dravidian speakers of India show shared genetic drift with Europeans, whereas the Tibeto-Burman speaking tribal groups have maximum shared genetic drift with East Asians.
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Affiliation(s)
- Aritra Bose
- Computational Genomics, IBM T.J. Watson Research Center, Yorktown Heights, NY, USA
| | - Daniel E Platt
- Computational Genomics, IBM T.J. Watson Research Center, Yorktown Heights, NY, USA
| | - Laxmi Parida
- Computational Genomics, IBM T.J. Watson Research Center, Yorktown Heights, NY, USA
| | - Petros Drineas
- Computer Science Department, Purdue University, West Lafayette, IN, USA
| | - Peristera Paschou
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
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13
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The forensic landscape and the population genetic analyses of Hainan Li based on massively parallel sequencing DNA profiling. Int J Legal Med 2021; 135:1295-1317. [PMID: 33847803 DOI: 10.1007/s00414-021-02590-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Accepted: 03/26/2021] [Indexed: 12/30/2022]
Abstract
Due to the formation of the Qiongzhou Strait by climate change and marine transition, Hainan island was isolated from the mainland southern China during the Last Glacial Maximum. Hainan island, located at the southernmost part of China and separated from the Leizhou Peninsula by the Qiongzhou Strait, laid on one of the modern human northward migration routes from Southeast Asia to East Asia. The Hlai language-speaking Li minority, the second largest population after Han Chinese in Hainan island, is the direct descendants of the initial migrants in Hainan island and has unique ethnic properties and derived characteristics; however, the forensic-associated studies on Hainan Li population are still insufficient. Hence, 136 Hainan Li individuals were genotyped in this study using the MPS-based ForenSeq™ DNA Signature Prep Kit (DNA Primer Set A, DPMA) to characterize the forensic genetic polymorphism landscape, and DNA profiles were obtained from 152 different molecular genetic markers (27 autosomal STRs, 24 Y-STRs, 7 X-STRs, and 94 iiSNPs). A total of 419 distinct length variants and 586 repeat sequence sub-variants, with 31 novel alleles (at 17 loci), were identified across the 58 STR loci from the DNA profiles of Hainan Li population. We evaluated the forensic characteristics and efficiencies of DPMA, demonstrating that the STRs and iiSNPs in DPMA were highly polymorphic in Hainan Li population and could be employed in forensic applications. In addition, we set up three datasets, which included the genetic data of (i) iiSNPs (27 populations, 2640 individuals), (ii) Y-STRs (42 populations, 8281 individuals), and (iii) Y haplogroups (123 populations, 4837 individuals) along with the population ancestries and language families, to perform population genetic analyses separately from different perspectives. In conclusion, the phylogenetic analyses indicated that Hainan Li, with a southern East Asia origin and Tai-Kadai language-speaking language, is an isolated population relatively. But the genetic pool of Hainan Li influenced by the limited gene flows from other Tai-Kadai populations and Hainan populations. Furthermore, the establishment of isolated population models will be beneficial to clarify the exquisite population structures and develop specific genetic markers for subpopulations in forensic genetic fields.
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14
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Tagore D, Aghakhanian F, Naidu R, Phipps ME, Basu A. Insights into the demographic history of Asia from common ancestry and admixture in the genomic landscape of present-day Austroasiatic speakers. BMC Biol 2021; 19:61. [PMID: 33781248 PMCID: PMC8008685 DOI: 10.1186/s12915-021-00981-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Accepted: 02/12/2021] [Indexed: 11/17/2022] Open
Abstract
BACKGROUND The demographic history of South and Southeast Asia (S&SEA) is complex and contentious, with multiple waves of human migration. Some of the earliest footfalls were of the ancestors of modern Austroasiatic (AA) language speakers. Understanding the history of the AA language family, comprising of over 150 languages and their speakers distributed across broad geographical region in isolated small populations of various sizes, can help shed light on the peopling of S&SEA. Here we investigated the genetic relatedness of two AA groups, their relationship with other ethno-linguistically distinct populations, and the relationship of these groups with ancient genomes of individuals living in S&SEA at different time periods, to infer about the demographic history of this region. RESULTS We analyzed 1451 extant genomes, 189 AAs from India and Malaysia, and 43 ancient genomes from S&SEA. Population structure analysis reveals neither language nor geography appropriately correlates with genetic diversity. The inconsistency between "language and genetics" or "geography and genetics" can largely be attributed to ancient admixture with East Asian populations. We estimated a pre-Neolithic origin of AA language speakers, with shared ancestry between Indian and Malaysian populations until about 470 generations ago, contesting the existing model of Neolithic expansion of the AA culture. We observed a spatio-temporal transition in the genetic ancestry of SEA with genetic contribution from East Asia significantly increasing in the post-Neolithic period. CONCLUSION Our study shows that contrary to assumptions in many previous studies and despite having linguistic commonality, Indian AAs have a distinct genomic structure compared to Malaysian AAs. This linguistic-genetic discordance is reflective of the complex history of population migration and admixture shaping the genomic landscape of S&SEA. We postulate that pre-Neolithic ancestors of today's AAs were widespread in S&SEA, and the fragmentation and dissipation of the population have largely been a resultant of multiple migrations of East Asian farmers during the Neolithic period. It also highlights the resilience of AAs in continuing to speak their language in spite of checkered population distribution and possible dominance from other linguistic groups.
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Affiliation(s)
- Debashree Tagore
- National Institute of Biomedical Genomics, Kalyani, 741251, India
| | - Farhang Aghakhanian
- Oklahoma Medical Research Foundation, Genes and Human Disease Program, 825 NE 13th Street, Oklahoma City, OK, 73104, USA
- Genomics Facility, School of Science, Monash University Malaysia, Jalan Lagoon Selatan, 47500, Bandar Sunway, Selangor, Malaysia
| | - Rakesh Naidu
- Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia, Jalan Lagoon Selatan, 47500, Bandar Sunway, Selangor Darul Ehsan, Malaysia
| | - Maude E Phipps
- Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia, Jalan Lagoon Selatan, 47500, Bandar Sunway, Selangor Darul Ehsan, Malaysia
| | - Analabha Basu
- National Institute of Biomedical Genomics, Kalyani, 741251, India.
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15
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Landini A, Yu S, Gnecchi‐Ruscone GA, Abondio P, Ojeda‐Granados C, Sarno S, De Fanti S, Gentilini D, Di Blasio AM, Jin H, Nguyen TT, Romeo G, Prata C, Bortolini E, Luiselli D, Pettener D, Sazzini M. Genomic adaptations to cereal-based diets contribute to mitigate metabolic risk in some human populations of East Asian ancestry. Evol Appl 2021; 14:297-313. [PMID: 33664777 PMCID: PMC7896717 DOI: 10.1111/eva.13090] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Revised: 07/20/2020] [Accepted: 08/04/2020] [Indexed: 12/21/2022] Open
Abstract
Adoption of diets based on some cereals, especially on rice, signified an iconic change in nutritional habits for many Asian populations and a relevant challenge for their capability to maintain glucose homeostasis. Indeed, rice shows the highest carbohydrates content and glycemic index among the domesticated cereals and its usual ingestion represents a potential risk factor for developing insulin resistance and related metabolic diseases. Nevertheless, type 2 diabetes and obesity epidemiological patterns differ among Asian populations that rely on rice as a staple food, with higher diabetes prevalence and increased levels of central adiposity observed in people of South Asian ancestry rather than in East Asians. This may be at least partly due to the fact that populations from East Asian regions where wild rice or other cereals such as millet have been already consumed before their cultivation and/or were early domesticated have relied on these nutritional resources for a period long enough to have possibly evolved biological adaptations that counteract their detrimental side effects. To test such a hypothesis, we compared adaptive evolution of these populations with that of control groups from regions where the adoption of cereal-based diets occurred many thousand years later and which were identified from a genome-wide dataset including 2,379 individuals from 124 East Asian and South Asian populations. This revealed selective sweeps and polygenic adaptive mechanisms affecting functional pathways involved in fatty acids metabolism, cholesterol/triglycerides biosynthesis from carbohydrates, regulation of glucose homeostasis, and production of retinoic acid in Chinese Han and Tujia ethnic groups, as well as in people of Korean and Japanese ancestry. Accordingly, long-standing rice- and/or millet-based diets have possibly contributed to trigger the evolution of such biological adaptations, which might represent one of the factors that play a role in mitigating the metabolic risk of these East Asian populations.
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Affiliation(s)
- Arianna Landini
- Laboratory of Molecular Anthropology & Centre for Genome BiologyDepartment of Biological, Geological and Environmental SciencesUniversity of BolognaBolognaItaly
- Centre for Global Health ResearchUsher Institute of Population Health Sciences and InformaticsUniversity of EdinburghEdinburghUK
| | - Shaobo Yu
- Laboratory of Molecular Anthropology & Centre for Genome BiologyDepartment of Biological, Geological and Environmental SciencesUniversity of BolognaBolognaItaly
| | | | - Paolo Abondio
- Laboratory of Molecular Anthropology & Centre for Genome BiologyDepartment of Biological, Geological and Environmental SciencesUniversity of BolognaBolognaItaly
| | - Claudia Ojeda‐Granados
- Laboratory of Molecular Anthropology & Centre for Genome BiologyDepartment of Biological, Geological and Environmental SciencesUniversity of BolognaBolognaItaly
- Department of Molecular Biology in MedicineCivil Hospital of Guadalajara “Fray Antonio Alcalde” and Health Sciences CenterUniversity of GuadalajaraGuadalajaraMexico
| | - Stefania Sarno
- Laboratory of Molecular Anthropology & Centre for Genome BiologyDepartment of Biological, Geological and Environmental SciencesUniversity of BolognaBolognaItaly
| | - Sara De Fanti
- Interdepartmental Centre Alma Mater Research Institute on Global Challenges and Climate ChangeUniversity of BolognaBolognaItaly
| | - Davide Gentilini
- Department of Brain and Behavioral SciencesUniversity of PaviaPaviaItaly
- Italian Auxologic Institute IRCCSCusano Milanino, MilanItaly
| | | | - Hanjun Jin
- Department of Biological SciencesCollege of Natural ScienceDankook UniversityCheonanSouth Korea
| | | | - Giovanni Romeo
- Medical Genetics UnitS. Orsola HospitalUniversity of BolognaBolognaItaly
- European School of Genetic MedicineItaly
| | - Cecilia Prata
- Department of Pharmacy and BiotechnologyUniversity of BolognaBolognaItaly
| | | | - Donata Luiselli
- Department of Cultural HeritageUniversity of BolognaRavennaItaly
| | - Davide Pettener
- Laboratory of Molecular Anthropology & Centre for Genome BiologyDepartment of Biological, Geological and Environmental SciencesUniversity of BolognaBolognaItaly
| | - Marco Sazzini
- Laboratory of Molecular Anthropology & Centre for Genome BiologyDepartment of Biological, Geological and Environmental SciencesUniversity of BolognaBolognaItaly
- Interdepartmental Centre Alma Mater Research Institute on Global Challenges and Climate ChangeUniversity of BolognaBolognaItaly
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16
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Chakravorty S, Nallamilli BRR, Khadilkar SV, Singla MB, Bhutada A, Dastur R, Gaitonde PS, Rufibach LE, Gloster L, Hegde M. Clinical and Genomic Evaluation of 207 Genetic Myopathies in the Indian Subcontinent. Front Neurol 2020; 11:559327. [PMID: 33250842 PMCID: PMC7674836 DOI: 10.3389/fneur.2020.559327] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Accepted: 09/23/2020] [Indexed: 12/13/2022] Open
Abstract
Objective: Inherited myopathies comprise more than 200 different individually rare disease-subtypes, but when combined together they have a high prevalence of 1 in 6,000 individuals across the world. Our goal was to determine for the first time the clinical- and gene-variant spectrum of genetic myopathies in a substantial cohort study of the Indian subcontinent. Methods: In this cohort study, we performed the first large clinical exome sequencing (ES) study with phenotype correlation on 207 clinically well-characterized inherited myopathy-suspected patients from the Indian subcontinent with diverse ethnicities. Results: Clinical-correlation driven definitive molecular diagnosis was established in 49% (101 cases; 95% CI, 42–56%) of patients with the major contributing pathogenicity in either of three genes, GNE (28%; GNE-myopathy), DYSF (25%; Dysferlinopathy), and CAPN3 (19%; Calpainopathy). We identified 65 variant alleles comprising 37 unique variants in these three major genes. Seventy-eight percent of the DYSF patients were homozygous for the detected pathogenic variant, suggesting the need for carrier-testing for autosomal-recessive disorders like Dysferlinopathy that are common in India. We describe the observed clinical spectrum of myopathies including uncommon and rare subtypes in India: Sarcoglycanopathies (SGCA/B/D/G), Collagenopathy (COL6A1/2/3), Anoctaminopathy (ANO5), telethoninopathy (TCAP), Pompe-disease (GAA), Myoadenylate-deaminase-deficiency-myopathy (AMPD1), myotilinopathy (MYOT), laminopathy (LMNA), HSP40-proteinopathy (DNAJB6), Emery-Dreifuss-muscular-dystrophy (EMD), Filaminopathy (FLNC), TRIM32-proteinopathy (TRIM32), POMT1-proteinopathy (POMT1), and Merosin-deficiency-congenital-muscular-dystrophy-type-1 (LAMA2). Thirteen patients harbored pathogenic variants in >1 gene and had unusual clinical features suggesting a possible role of synergistic-heterozygosity/digenic-contribution to disease presentation and progression. Conclusions: Application of clinically correlated ES to myopathy diagnosis has improved our understanding of the clinical and genetic spectrum of different subtypes and their overlaps in Indian patients. This, in turn, will enhance the global gene-variant-disease databases by including data from developing countries/continents for more efficient clinically driven molecular diagnostics.
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Affiliation(s)
- Samya Chakravorty
- Emory University Department of Pediatrics, Atlanta, GA, United States.,Emory University Department of Human Genetics, Atlanta, GA, United States.,Division of Neurosciences, Children's Healthcare of Atlanta, Atlanta, GA, United States.,School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, United States
| | | | - Satish Vasant Khadilkar
- Department of Neurology, Bombay Hospital, Mumbai, India.,Department of Neurology, Sir J J Group of Hospitals, Grant Medical College, Mumbai, India.,Bombay Hospital Institute of Medical Sciences, Mumbai, India
| | - Madhu Bala Singla
- Department of Neurology, Bombay Hospital, Mumbai, India.,Department of Neurology, Sir J J Group of Hospitals, Grant Medical College, Mumbai, India.,Bombay Hospital Institute of Medical Sciences, Mumbai, India
| | | | - Rashna Dastur
- Centre for Advanced Molecular Diagnostics in Neuromuscular Disorders (CAMDND), Mumbai, India
| | - Pradnya Satish Gaitonde
- Centre for Advanced Molecular Diagnostics in Neuromuscular Disorders (CAMDND), Mumbai, India
| | | | - Logan Gloster
- Emory University Department of Pediatrics, Atlanta, GA, United States.,School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, United States
| | - Madhuri Hegde
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, United States.,PerkinElmer Genomics, Global Laboratory Services, Waltham, MA, United States
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17
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Das R, Ivanisenko VA, Anashkina AA, Upadhyai P. The story of the lost twins: decoding the genetic identities of the Kumhar and Kurcha populations from the Indian subcontinent. BMC Genet 2020; 21:117. [PMID: 33092524 PMCID: PMC7583313 DOI: 10.1186/s12863-020-00919-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 05/28/2020] [Indexed: 11/10/2022] Open
Abstract
Background The population structure of the Indian subcontinent is a tapestry of extraordinary diversity characterized by the amalgamation of autochthonous and immigrant ancestries and rigid enforcement of sociocultural stratification. Here we investigated the genetic origin and population history of the Kumhars, a group of people who inhabit large parts of northern India. We compared 27 previously published Kumhar SNP genotype data sampled from Uttar Pradesh in north India to various modern day and ancient populations. Results Various approaches such as Principal Component Analysis (PCA), Admixture, TreeMix concurred that Kumhars have high ASI ancestry, minimal Steppe component and high genomic proximity to the Kurchas, a small and relatively little-known population found ~ 2500 km away in Kerala, south India. Given the same, biogeographical mapping using Geographic Population Structure (GPS) assigned most Kumhar samples in areas neighboring to those where Kurchas are found in south India. Conclusions We hypothesize that the significant genomic similarity between two apparently distinct modern-day Indian populations that inhabit well separated geographical areas with no known overlapping history or links, likely alludes to their common origin during or post the decline of the Indus Valley Civilization (estimated by ALDER). Thereafter, while they dispersed towards opposite ends of the Indian subcontinent, their genomic integrity and likeness remained preserved due to endogamous social practices. Our findings illuminate the genomic history of two Indian populations, allowing a glimpse into one or few of numerous of human migrations that likely occurred across the Indian subcontinent and contributed to shape its varied and vibrant evolutionary past.
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Affiliation(s)
- Ranajit Das
- Yenepoya Research Centre (YRC), Yenepoya (Deemed to be University), Mangalore, Karnataka, India.
| | - Vladimir A Ivanisenko
- Humanitarian Institute, Novosibirsk State University, 630090, Novosibirsk, Russia.,Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia
| | - Anastasia A Anashkina
- The Digital Health Institute, I.M. Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russia.,Engelhardt Institute of Molecular Biology RAS, Moscow, Russia
| | - Priyanka Upadhyai
- Department of Medical Genetics, Kasturba Medical College, Manipal Academy of Higher Education, Manipal, Karnataka, India
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18
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Li W, Wang X, Wang X, Wang F, Du Z, Fu F, Wu W, Wang S, Mu Z, Chen C, Hu X, Ding J, Meng Y, Qiu P, Fan H. Forensic characteristics and phylogenetic analyses of one branch of Tai-Kadai language-speaking Hainan Hlai (Ha Hlai) via 23 autosomal STRs included in the Huaxia ™ Platinum System. Mol Genet Genomic Med 2020; 8:e1462. [PMID: 32862500 PMCID: PMC7549582 DOI: 10.1002/mgg3.1462] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Revised: 07/20/2020] [Accepted: 08/04/2020] [Indexed: 01/10/2023] Open
Abstract
BACKGROUND Hainan Island, located in the South China Sea and separated from the Leizhou Peninsula by Qiongzhou Strait, is the second largest island after Taiwan in China. With the expansion of Han Chinese and the gradual formation of "South Hlai and North Han", nowadays, Hainan Hlai is the second largest population after Han Chinese in Hainan Island. Ha Hlai, distributed in southwest and southern Hainan Island, is the dominant branch of Hlai and speaks Ha localism. METHODS We utilized the Huaxia™ Platinum PCR Amplification System (including 23 autosomal STRs and 2 sex-linked markers) to obtain the first STR profiling batch of 657 Ha Hlai individuals (497 males and 160 females). In order to explore the genetic relationships between the studied Ha Hlai and other reference populations with different language families, population genetic analyses, including PCA, MDS, STRUCTURE, and phylogenetic analysis, were conducted based upon the raw data and allelic frequencies of the polymorphic autosomal STR markers. RESULTS In total, 271 distinct alleles were observed at the 23 STR loci. The number of diverse alleles ranged from 7 at TPOX locus to 23 at FGA locus, and the allelic frequencies varied from 0.0008 to 0.5533. In addition, the CPE and CPD were 1-7.39 × 10-10 and 1-3.13 × 10-28 , respectively. The phylogenetic analyses indicated that Ha Hlai is a Tai-Kadai language-speaking and relatively isolated population which has a close genetic and geographical relationship with Hainan Hlai, and M95 is the dominant haplogroup in Ha Hlai (56.18%). CONCLUSION The 23 autosomal STR genetic markers were highly polymorphic as well as potentially useful for forensic applications in Hainan Ha Hlai population. The phylogenetic analyses demonstrated that small geographic scale gene flows could not be ignored and the shaping of the unique gene pool for each population was the combination effects of geographic, language, and cultural isolations.
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Affiliation(s)
- Wenhui Li
- School of Basic Medicine and Life ScienceHainan Medical UniversityHaikouChina
- Forensic Science Center of Hainan Medical UniversityHainan Medical UniversityHaikouChina
| | - Xianwen Wang
- Criminal Technical DetachmentHaikou City Public Security BureauHaikouChina
| | - Xiehong Wang
- Criminal Technical DetachmentHaikou City Public Security BureauHaikouChina
| | - Fenfen Wang
- First Clinical Medical CollegeHainan Medical UniversityHaikouChina
| | - Zhengming Du
- First Clinical Medical CollegeHainan Medical UniversityHaikouChina
| | - Fangshu Fu
- School of Biomedical Information and EngineeringHainan Medical UniversityHaikouChina
| | - Wenlong Wu
- First Clinical Medical CollegeHainan Medical UniversityHaikouChina
| | - Shuya Wang
- School of Public HealthHainan Medical UniversityHaikouChina
| | - Ziqing Mu
- School of ManagementHainan Medical UniversityHaikouChina
| | - Chunwei Chen
- Public Security and Judicial Appraisal Center of Sanya CitySanyaChina
| | - Xiaomin Hu
- Hainan Zhujian Center for Molecular Cytogenetic Clinical TestingHaikouChina
| | - Jiuyang Ding
- School of Forensic MedicineGuizhou Medical UniversityGuiyangChina
| | - Yunle Meng
- School of Forensic MedicineSouthern Medical UniversityGuangzhouChina
| | - Pingming Qiu
- School of Forensic MedicineSouthern Medical UniversityGuangzhouChina
- Multi‐Omics Innovative Research Center of Forensic Identification, Department of Forensic Genetics, School of Forensic MedicineSouthern Medical UniversityGuangzhouChina
| | - Haoliang Fan
- School of Basic Medicine and Life ScienceHainan Medical UniversityHaikouChina
- Forensic Science Center of Hainan Medical UniversityHainan Medical UniversityHaikouChina
- School of Forensic MedicineSouthern Medical UniversityGuangzhouChina
- Multi‐Omics Innovative Research Center of Forensic Identification, Department of Forensic Genetics, School of Forensic MedicineSouthern Medical UniversityGuangzhouChina
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19
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Mahal DG. Y-DNA genetic evidence reveals several different ancient origins in the Brahmin population. Mol Genet Genomics 2020; 296:67-78. [PMID: 32978661 DOI: 10.1007/s00438-020-01725-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2020] [Accepted: 09/09/2020] [Indexed: 10/23/2022]
Abstract
The ancient geographical origins of Brahmins-a prominent ethnic group in the Indian subcontinent-have remained controversial for a long time. This study employed the AMOVA (analysis of molecular variance) test to evaluate genetic affinities of this group with thirty populations of Central Asia and Europe. A domestic comparison was performed with fifty non-Brahmin groups in India. The results showed that Brahmins had genetic affinities with several foreign populations and also shared their genetic heritage with several domestic non-Brahmin groups. The study identified the deep ancient origins of Brahmins by tracing their Y-chromosome haplogroups and genetic markers on the Y-DNA phylogenetic tree. It was confirmed that the progenitors of this group emerged from at least 12 different geographic regions of the world. The study concluded that about 83% of the Brahmins in the dataset belonged to four major haplogroups, of which two emerged from Central Asia, one from the Fertile Crescent, and one was of an indigenous Indian origin.
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Affiliation(s)
- David G Mahal
- DGM Associates, Pacific Palisades, CA, USA. .,Institut Avrio de Geneve, Geneva, Switzerland.
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20
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Zubair M, Hemphill BE, Schurr TG, Tariq M, Ilyas M, Ahmad H. Mitochondrial DNA diversity in the Khattak and Kheshgi of the Peshawar Valley, Pakistan. Genetica 2020; 148:195-206. [PMID: 32607672 DOI: 10.1007/s10709-020-00095-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2020] [Accepted: 05/12/2020] [Indexed: 11/29/2022]
Abstract
The strategic location of Pakistan and its presence at the crossroads of Asia has resulted in it playing a central role in both prehistoric and historic human migratory events, thereby linking and facilitating contacts between the inhabitants of the Middle East, Central Asia, China and South Asia. Despite the importance of this region and its inhabitants for our understanding of modern human origins and population dispersals, the nature of mitochondrial DNA (mtDNA) variation among members of the myriad populations of this area has largely been unexplored. Here, we report mtDNA control region sequences in 58 individuals from the Khattak and the Kheshgi, two major Pakhtun tribes residing within the Peshawar Valley of northwestern Pakistan. The results reveal that these ethnic groups are genetically heterogeneous, having 55.7% West Eurasian, 33.9% South Asian and 10.2% East Asian haplogroups. The genetic diversity observed for the Kheshgi was somewhat higher than that of the Khattak. A multidimensional scaling plot based on haplogroup frequencies for the Khattak, Kheshgi and neighboring populations indicates that the Khattak have close affinities with Baluch, Uzbek and Kazak populations but are only distantly related to the Kheshgi and other Pakistani populations. By contrast, the Kheshgi cluster closely with other Pakhtun or Pathan populations of Pakistan, suggesting a possible common maternal gene pool shared amongst them. These mtDNA data allow us to begin reconstructing the origins of the Khattak and Kheshgi and describe their complex interactions with populations from the surrounding regions.
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Affiliation(s)
- Muhammad Zubair
- Department of Zoology, Hazara University Mansehra, Mansehra, 21120, Pakistan.,Department of Genetics, Hazara University Mansehra, Mansehra, 21120, Pakistan
| | - Brian E Hemphill
- Department of Anthropology, University of Alaska, Fairbanks, AK, 99775, USA
| | - Theodore G Schurr
- Department of Anthropology, University of Pennsylvania, Philadelphia, 19104, USA
| | - Muhammad Tariq
- Centre for Omic Sciences, Islamia College Peshawar, Peshawar, 25120, Pakistan
| | - Muhammad Ilyas
- Centre for Omic Sciences, Islamia College Peshawar, Peshawar, 25120, Pakistan
| | - Habib Ahmad
- Department of Genetics, Hazara University Mansehra, Mansehra, 21120, Pakistan. .,Centre for Omic Sciences, Islamia College Peshawar, Peshawar, 25120, Pakistan.
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21
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Kumawat R, Shrivastava P, Shrivastava D, Mathur G. Molecular diversity of 23 Y-STR genetic markers in the population of Rajasthan, India. Meta Gene 2020. [DOI: 10.1016/j.mgene.2020.100694] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
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22
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Neogi A, Kumar J, Guan Y, Parani M. Genetic counseling education at the undergraduate level: An outreach initiative to promote professional recruitment and support workforce development. J Genet Couns 2020; 29:234-242. [PMID: 32227571 DOI: 10.1002/jgc4.1253] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2019] [Revised: 02/22/2020] [Accepted: 02/24/2020] [Indexed: 11/12/2022]
Abstract
As in many other countries, the field of genetic counseling is in its initial stages of development in India, where there are efforts to streamline the profession and to implement graduate-level training programs. We implemented an elective course on genetic counseling at the undergraduate level in a private university in India to assess students' interest, to provide early exposure for students interested in pursuing the career, and to aid recruitment. To assess satisfaction with the course and recruitment outcomes, we sent a course evaluation survey to 332 students and received 134 responses. Familiarity with genetic counseling topics increased significantly after completing the course. Of the 42 respondents who reported they were planning to pursue formal genetic counseling training, 21% (n = 9/42) became interested in the profession as a result of taking this course. Survey respondents who were prospective applicants to genetic counseling training programs referred mostly to the websites of the National Society of Genetic Counselors and the American Board of Genetic Counseling for information on genetic counseling and training. Barriers to entry into the field included lack of shadowing opportunities, inadequate coursework, and limited opportunities to interact with practicing genetic counselors. Respondents stated that additional case studies as well as observation of patient interactions would elucidate the role of a genetic counselor and help define the scope of the practice in India and other countries. Overall, genetic counseling education at the undergraduate level is a scalable way to improve understanding of genetic counseling topics, increase professional interest in the field, and support workforce development.
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Affiliation(s)
- Arpita Neogi
- Department of Genetic Engineering, SRM University, Chennai, India.,International Special Interest Group, National Society of Genetic Counselors, Chicago, IL, USA
| | - Jeevan Kumar
- Department of Genetic Engineering, SRM University, Chennai, India
| | - Yue Guan
- International Special Interest Group, National Society of Genetic Counselors, Chicago, IL, USA.,Behavioral Sciences and Health Education, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Madasamy Parani
- Department of Genetic Engineering, SRM University, Chennai, India
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23
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Srivastava A, Singh PP, Bandopadhyay A, Singh P, Das D, Tamang R, Chaubey AK, Shrivastava P, van Driem G, Chaubey G. Genetic and linguistic non-correspondence suggests evidence for collective social climbing in the Kol tribe of South Asia. Sci Rep 2020; 10:5593. [PMID: 32221319 PMCID: PMC7101412 DOI: 10.1038/s41598-020-61941-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Accepted: 03/02/2020] [Indexed: 11/24/2022] Open
Abstract
Both classical and recent genetic studies have unanimously concluded that the genetic landscape of South Asia is unique. At long distances the ‘isolation-by-distance’ model appears to correspond well with the genetic data, whereas at short distances several other factors, including the caste, have been shown to be strong determinant factors. In addition with these, tribal populations speaking various languages add yet another layer of genetic complexity. The Kol are the third most populous tribal population in India, comprising communities speaking Austroasiatic languages of the Northern Munda branch. Yet, the Kol have not hitherto undergone in-depth genetic analysis. In the present study, we have analysed two Kol groups of central and western India for hundreds thousands of autosomal and several mitochondrial DNA makers to infer their fine genetic structure and affinities to other Eurasian populations. In contrast, with their known linguistic affinity, the Kol share their more recent common ancestry with the Indo-European and Dravidian speaking populations. The geographic-genetic neighbour tests at both the temporal and spatial levels have suggested some degree of excess allele sharing of Kol1 with Kol2, thereby indicating their common stock. Our extensive analysis on the Kol ethnic group shows South Asia to be a living genetics lab, where real-time tests can be performed on existing hypotheses.
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Affiliation(s)
- Anshika Srivastava
- Cytogenetics Laboratory, Department of Zoology, Banaras Hindu University, Varanasi, 221005, India
| | - Prajjval Pratap Singh
- Cytogenetics Laboratory, Department of Zoology, Banaras Hindu University, Varanasi, 221005, India
| | - Audditiya Bandopadhyay
- Cytogenetics Laboratory, Department of Zoology, Banaras Hindu University, Varanasi, 221005, India
| | - Pooja Singh
- Cytogenetics Laboratory, Department of Zoology, Banaras Hindu University, Varanasi, 221005, India
| | - Debashruti Das
- Cytogenetics Laboratory, Department of Zoology, Banaras Hindu University, Varanasi, 221005, India
| | - Rakesh Tamang
- Department of Zoology, University of Calcutta, Kolkata, 700019, India
| | - Akhilesh Kumar Chaubey
- Krishi Vigyan Kendra, Singrauli, Jawaharlal Nehru Krishi Vishwavidyalay, Jabalpur, Madhya Pradesh, 462038, India
| | - Pankaj Shrivastava
- DNA Fingerprinting Unit, State Forensic Science Laboratory, Department of Home (Police), Government of MP, Sagar, 470001, India
| | - George van Driem
- Institut für Sprachwissenschaft, Universität Bern, 3012, Bern, Switzerland.,Sydney Social Sciences and Humanities Advanced Research Centre, University of Sydney, Sydney, Australia
| | - Gyaneshwer Chaubey
- Cytogenetics Laboratory, Department of Zoology, Banaras Hindu University, Varanasi, 221005, India. .,Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu, 51010, Estonia.
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24
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Singh M, Sarkar A, Kumar D, Nandineni MR. The genetic affinities of Gujjar and Ladakhi populations of India. Sci Rep 2020; 10:2055. [PMID: 32029844 PMCID: PMC7005309 DOI: 10.1038/s41598-020-59061-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Accepted: 01/22/2020] [Indexed: 11/27/2022] Open
Abstract
The Union Territories of Jammu and Kashmir (J&K) and Ladakh in North India owing to their unique geographic location offer a wide variety of landscape from plains to high altitudes and is a congruence of many languages and cultural practices. Here, we present the genetic diversity studies of Gujjars from Jammu region of J&K and Ladakhi population based on a battery of autosomal single nucleotide polymorphisms (SNPs) and short tandem repeats (STRs), Y-chromosomal STRs and the control region of the mitochondrial genome. These two populations were observed to be genetically distant to each other as well as to other populations from India. Interestingly, Y-STR analyses showed a closer affinity of Gujjars to other nomadic populations of Pashtuns from Baghlans and Kunduz provinces of Afghanistan and Pashtuns and Sindhis of Pakistan. Gujjars exhibited lesser genetic diversity as compared to Ladakhi population. M30f and M9 were the most abundant mitochondrial haplogroups observed among Gujjars and Ladakhis, respectively. A lower matrilineal to patrilineal diversity was observed for both these populations. The current study presents the first comprehensive analysis of Gujjars and Ladakhis and reveals their unique genetic affiliations with other populations of the world.
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Affiliation(s)
- Mugdha Singh
- Laboratory of Genomics and Profiling Applications, Centre for DNA Fingerprinting and Diagnostics, Uppal, Hyderabad, Telangana State, India
- Graduate studies, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Anujit Sarkar
- College of Public Health, University of South Florida, Tampa, FL, USA
| | - Devinder Kumar
- Central Forensic Science Laboratory, Kolkata, West Bengal, India
| | - Madhusudan R Nandineni
- Laboratory of Genomics and Profiling Applications, Centre for DNA Fingerprinting and Diagnostics, Uppal, Hyderabad, Telangana State, India.
- Laboratory of DNA Fingerprinting Services, Centre for DNA Fingerprinting and Diagnostics, Uppal, Hyderabad, Telangana State, India.
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25
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KULATILAKE SAMANTI. The Sarasins’ Collection of Historical Sri Lankan Crania. ANTHROPOL SCI 2020. [DOI: 10.1537/ase.200428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Affiliation(s)
- SAMANTI KULATILAKE
- Department of Sociology and Anthropology, Mount Royal University, Calgary
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26
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Syama A, Arun VS, ArunKumar G, Subhadeepta R, Friese K, Pitchappan R. Origin and identity of the Brokpa of Dah-Hanu, Himalayas – an NRY-HG L1a2 (M357) legacy. Ann Hum Biol 2019; 46:562-573. [DOI: 10.1080/03014460.2019.1694700] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Affiliation(s)
- Adikarla Syama
- The Genographic Laboratory, School of Biological Sciences, Madurai Kamaraj University, Madurai, India
- Department of Biotechnology, Faculty of Engineering and Technology, Manav Rachana, International University, Faridabad, India
| | | | - GaneshPrasad ArunKumar
- The Genographic Laboratory, School of Biological Sciences, Madurai Kamaraj University, Madurai, India
- Human Genomics Laboratory, Department of Bioinformatics, School of Chemical and Biotechnology, SASTRA Deemed University, Thirumalaisamudram, India
| | | | | | - Ramasamy Pitchappan
- The Genographic Laboratory, School of Biological Sciences, Madurai Kamaraj University, Madurai, India
- Nilgiri Adivasi Welfare Association, Kotagiri, India
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27
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Large-Scale Whole-Genome Sequencing of Three Diverse Asian Populations in Singapore. Cell 2019; 179:736-749.e15. [DOI: 10.1016/j.cell.2019.09.019] [Citation(s) in RCA: 76] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2019] [Revised: 06/24/2019] [Accepted: 09/19/2019] [Indexed: 12/19/2022]
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28
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Abstract
Rushton and Jensen argued that cognitive ability differs between human populations. But why are such differences expectable? Their answer: as modern humans spread out of Africa and into northern Eurasia, they entered colder and more seasonal climates that selected for the ability to plan ahead, in order to store food, make clothes, and build shelters for winter. This cold winter theory is supported by research on Paleolithic humans and recent hunter-gatherers. Tools become more diverse and complex as effective temperature decreases, apparently because food has to be obtained during limited periods and over large areas. There is also more storage of food and fuel and greater use of untended traps and snares. Finally, shelters have to be sturdier, and clothing more cold-resistant. The resulting cognitive demands are met primarily by women because the lack of opportunities for food gathering pushes them into more cognitively demanding tasks, like garment making, needlework, weaving, leatherworking, pottery, and kiln operation. The northern tier of Paleolithic Eurasia thus produced the “Original Industrial Revolution”—an explosion of creativity that preadapted its inhabitants for later developments, i.e., farming, more complex technology and social organization, and an increasingly future-oriented culture. Over time, these humans would spread south, replacing earlier populations that could less easily exploit the possibilities of the new cultural environment. As this environment developed further, it selected for further increases in cognitive ability. Indeed, mean intelligence seems to have risen during recorded history at temperate latitudes in Europe and East Asia. There is thus no unified theory for the evolution of human intelligence. A key stage was adaptation to cold winters during the Paleolithic, but much happened later.
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29
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A comprehensive portrait of Y-STR diversity of Indian populations and comparison with 129 worldwide populations. Sci Rep 2018; 8:15421. [PMID: 30337554 PMCID: PMC6194109 DOI: 10.1038/s41598-018-33714-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Accepted: 10/05/2018] [Indexed: 11/28/2022] Open
Abstract
India, known for its rich cultural, linguistic and ethnic diversity, has attracted the attention of population geneticists to understand its genetic diversity employing autosomal, Y-chromosomal and mitochondrial DNA markers. Y-chromosomal short tandem repeats (Y-STRs) are useful in understanding population substructures and reveal the patrilineal affinities among populations. Previous studies on Indian populations based on Y-STR markers were either limited to restricted number of markers or focused on few selected populations. In this study we genotyped 407 unrelated male individuals from 12 states in India employing the suite of Y-STRs present in PowerPlex Y23 (Promega, Madison, WI, USA). These populations clustered genetically close to each other irrespective of their geographic co-ordinates and were characterized primarily by R1a, H and L haplogroups. Interestingly, comparison with 129 worldwide populations showed genetic affinity of the Indian populations with few populations from Europe and Levantine. This study presents the first pan-Indian landscape of 23 Y-STRs and serves as a useful resource for construction of an Indian Y-STR database.
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30
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Sylvester C, Krishna MS, Rao JS, Chandrasekar A. Neolithic phylogenetic continuity inferred from complete mitochondrial DNA sequences in a tribal population of Southern India. Genetica 2018; 146:383-389. [PMID: 30032461 DOI: 10.1007/s10709-018-0030-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Accepted: 07/15/2018] [Indexed: 11/28/2022]
Abstract
The subsequent human migrations that dispersed out of Africa, both prehistoric and historic and colonization of India by modern humans is unanimous, and phylogeny of major mitochondrial DNA haplogroups have played a key role in assessing the genetic origin of people of India. To address more such events, complete mitogenomes of 113 Melakudiya tribe of Southern India were sequenced and 46 individuals showed the presence of west Eurasian autochthonous haplogroups HV14 and U7. Phylogenetic analysis revealed two novel subclades HV14a1b and HV14a1b1 and sequences representing haplogroup U7 were included under previously described subclade U7a3a1a2* specific to India. Moreover, the present analysis on complete mtDNA reveals addition information of the spread and distribution of west Eurasian haplogroups in southern India, in tracing an unexplored genetic link between Melakudiya tribe with the people of Iranian Plateau, South Caucasus, and Central Asia. Coalescence ages of HV14 and U7a3a1a2* trees in the present study dates ~ 16.1 ± 4.3 and ~ 13.4 ± 5.6 kya respectively.
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Affiliation(s)
- Charles Sylvester
- Department of Studies in Zoology, University of Mysore, Mysore, India.,Anthropological Survey of India, Southern Regional Center, Mysore, India
| | | | - Jaya Sankar Rao
- Anthropological Survey of India, Southern Regional Center, Mysore, India
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31
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Pigeyre M, Saqlain M, Turcotte M, Raja GK, Meyre D. Obesity genetics: insights from the Pakistani population. Obes Rev 2018; 19:364-380. [PMID: 29265593 DOI: 10.1111/obr.12644] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Revised: 10/10/2017] [Accepted: 10/15/2017] [Indexed: 01/26/2023]
Abstract
The Pakistani population is extensively diverse, indicating a genetic admixture of European and Central/West Asian migrants with indigenous South Asian gene pools. Pakistanis are organized in different ethnicities/castes based on cultural, linguistic and geographical origin. While Pakistan is facing a rapid nutritional transition, the rising prevalence of obesity is driving a growing burden of health complications and mortality. This represents a unique opportunity for the research community to study the interplay between obesogenic environmental changes and obesity predisposing genes in the time frame of one generation. This review recapitulates the ancestral origins of Pakistani population, the societal determinants of the rise in obesity and its governmental management. We describe the contribution of syndromic, monogenic non-syndromic and polygenic obesity genes identified in the Pakistani population. We then discuss the utility of gene identification approaches based on large consanguineous families and original gene × environment interaction study designs in discovering new obesity genes and causal pathways. Elucidation of the genetic basis of obesity in the Pakistani population may result in improved methods of obesity prevention and treatment globally.
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Affiliation(s)
- M Pigeyre
- Department of Health Research Methods, Evidence, and Impact, McMaster University, Hamilton, Canada.,Department of Nutrition, CHRU Lille, University of Lille, Lille, France
| | - M Saqlain
- Department of Biochemistry, PMAS-Arid Agriculture University Rawalpindi, Rawalpindi, Pakistan
| | - M Turcotte
- Department of Health Research Methods, Evidence, and Impact, McMaster University, Hamilton, Canada
| | - G K Raja
- Department of Biochemistry, PMAS-Arid Agriculture University Rawalpindi, Rawalpindi, Pakistan
| | - D Meyre
- Department of Health Research Methods, Evidence, and Impact, McMaster University, Hamilton, Canada.,Department of Pathology and Molecular Medicine, McMaster University, Hamilton, Canada
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32
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Pandey N, Pal S, Sharma LK, Guleria R, Mohan A, Srivastava T. SNP rs16969968 as a Strong Predictor of Nicotine Dependence and Lung Cancer Risk in a North Indian Population. ASIAN PACIFIC JOURNAL OF CANCER PREVENTION : APJCP 2017; 18:3073-3079. [PMID: 29172281 PMCID: PMC5773793 DOI: 10.22034/apjcp.2017.18.11.3073] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Background: The 15q24-25 loci contain genes (CHRNA5 and CHRNA3) encoding nicotinic acetylcholine receptor subunits. We here determined for the first time the association of genetic variants rs16969968 and rs3743074 in CHRNA5 and CHRNA3, respectively, on nicotine dependence and lung cancer risk in a North Indian population by a case-control approach. Methods: Venous blood samples were obtained from 324 participants (108 lung cancer patients and 216 healthy individuals). DNA was extracted and PCR amplified with primers flanking the SNPs rs16969968 and rs3743074. Amplicons were subjected to sequencing and logistic regression was used to analyze association between variables. Results: The risk variant SNP rs16969968 in both heterozygous and homozygous forms appeared to exert a significant effect on nicotine dependence [GA (OR=2.77) and AA (OR=2.53)]. As expected, smoking was strongly associated with lung cancer (OR= 2.62). Risk allele rs16969968 in CHRNA5 also showed a significant association with increased lung cancer risk in our cohort, alone (OR= 4.99) and with smoking as a co-variable (OR= 4.28). Comparison of our analysis with other populations suggested that individuals with rs16969968 risk allele in the Indian population are more susceptible to lung cancer. Conclusion: Overall, the results strongly indicated that, in our cohort North Indian population, the genetic variant rs16969968, but not rs3743074, is significantly associated with both nicotine dependence and increased risk of lung cancer. While the results are significant, there is further need to increase the sample size and improve precision of our risk prediction.
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Affiliation(s)
- Namita Pandey
- Department of Genetics, University of Delhi South Campus, New Delhi Delhi, India.
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33
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Pischedda S, Barral-Arca R, Gómez-Carballa A, Pardo-Seco J, Catelli ML, Álvarez-Iglesias V, Cárdenas JM, Nguyen ND, Ha HH, Le AT, Martinón-Torres F, Vullo C, Salas A. Phylogeographic and genome-wide investigations of Vietnam ethnic groups reveal signatures of complex historical demographic movements. Sci Rep 2017; 7:12630. [PMID: 28974757 PMCID: PMC5626762 DOI: 10.1038/s41598-017-12813-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Accepted: 09/14/2017] [Indexed: 01/21/2023] Open
Abstract
The territory of present-day Vietnam was the cradle of one of the world’s earliest civilizations, and one of the first world regions to develop agriculture. We analyzed the mitochondrial DNA (mtDNA) complete control region of six ethnic groups and the mitogenomes from Vietnamese in The 1000 Genomes Project (1000G). Genome-wide data from 1000G (~55k SNPs) were also investigated to explore different demographic scenarios. All Vietnamese carry South East Asian (SEA) haplotypes, which show a moderate geographic and ethnic stratification, with the Mong constituting the most distinctive group. Two new mtDNA clades (M7b1a1f1 and F1f1) point to historical gene flow between the Vietnamese and other neighboring countries. Bayesian-based inferences indicate a time-deep and continuous population growth of Vietnamese, although with some exceptions. The dramatic population decrease experienced by the Cham 700 years ago (ya) fits well with the Nam tiến (“southern expansion”) southwards from their original heartland in the Red River Delta. Autosomal SNPs consistently point to important historical gene flow within mainland SEA, and add support to a main admixture event occurring between Chinese and a southern Asian ancestral composite (mainly represented by the Malay). This admixture event occurred ~800 ya, again coinciding with the Nam tiến.
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Affiliation(s)
- S Pischedda
- Unidade de Xenética, Departamento de Anatomía Patolóxica e Ciencias Forenses, Instituto de Ciencias Forenses, Facultade de Medicina, Universidade de Santiago de Compostela, Galicia, Spain.,GenPoB Research Group, Instituto de Investigaciones Sanitarias (IDIS), Hospital Clínico Universitario de Santiago, Galicia, Spain.,Translational Pediatrics and Infectious Diseases, Hospital Clínico Universitario de Santiago, Santiago de Compostela, Spain.,GENVIP Research Group, Instituto de Investigación Sanitaria de Santiago, Galicia, Spain
| | - R Barral-Arca
- Unidade de Xenética, Departamento de Anatomía Patolóxica e Ciencias Forenses, Instituto de Ciencias Forenses, Facultade de Medicina, Universidade de Santiago de Compostela, Galicia, Spain.,GenPoB Research Group, Instituto de Investigaciones Sanitarias (IDIS), Hospital Clínico Universitario de Santiago, Galicia, Spain.,Translational Pediatrics and Infectious Diseases, Hospital Clínico Universitario de Santiago, Santiago de Compostela, Spain.,GENVIP Research Group, Instituto de Investigación Sanitaria de Santiago, Galicia, Spain
| | - A Gómez-Carballa
- Unidade de Xenética, Departamento de Anatomía Patolóxica e Ciencias Forenses, Instituto de Ciencias Forenses, Facultade de Medicina, Universidade de Santiago de Compostela, Galicia, Spain.,GenPoB Research Group, Instituto de Investigaciones Sanitarias (IDIS), Hospital Clínico Universitario de Santiago, Galicia, Spain.,Translational Pediatrics and Infectious Diseases, Hospital Clínico Universitario de Santiago, Santiago de Compostela, Spain.,GENVIP Research Group, Instituto de Investigación Sanitaria de Santiago, Galicia, Spain
| | - J Pardo-Seco
- Unidade de Xenética, Departamento de Anatomía Patolóxica e Ciencias Forenses, Instituto de Ciencias Forenses, Facultade de Medicina, Universidade de Santiago de Compostela, Galicia, Spain.,GenPoB Research Group, Instituto de Investigaciones Sanitarias (IDIS), Hospital Clínico Universitario de Santiago, Galicia, Spain.,Translational Pediatrics and Infectious Diseases, Hospital Clínico Universitario de Santiago, Santiago de Compostela, Spain.,GENVIP Research Group, Instituto de Investigación Sanitaria de Santiago, Galicia, Spain
| | - M L Catelli
- Equipo Argentino de Antropología Forense, Independencia, 644, Córdoba, Argentina
| | - V Álvarez-Iglesias
- Unidade de Xenética, Departamento de Anatomía Patolóxica e Ciencias Forenses, Instituto de Ciencias Forenses, Facultade de Medicina, Universidade de Santiago de Compostela, Galicia, Spain.,GenPoB Research Group, Instituto de Investigaciones Sanitarias (IDIS), Hospital Clínico Universitario de Santiago, Galicia, Spain
| | - J M Cárdenas
- Unidade de Xenética, Departamento de Anatomía Patolóxica e Ciencias Forenses, Instituto de Ciencias Forenses, Facultade de Medicina, Universidade de Santiago de Compostela, Galicia, Spain.,GenPoB Research Group, Instituto de Investigaciones Sanitarias (IDIS), Hospital Clínico Universitario de Santiago, Galicia, Spain.,Grupo de Investigación en Genética Forense - Instituto Nacional de Medicina Legal y Ciencias Forenses, Bogotá, Colombia
| | - N D Nguyen
- National Institute of Forensic Medicine, Ministry of Health, Ha Noi, Vietnam
| | - H H Ha
- National Institute of Forensic Medicine, Ministry of Health, Ha Noi, Vietnam
| | - A T Le
- National Institute of Forensic Medicine, Ministry of Health, Ha Noi, Vietnam
| | - F Martinón-Torres
- Translational Pediatrics and Infectious Diseases, Hospital Clínico Universitario de Santiago, Santiago de Compostela, Spain.,GENVIP Research Group, Instituto de Investigación Sanitaria de Santiago, Galicia, Spain
| | - C Vullo
- Equipo Argentino de Antropología Forense, Independencia, 644, Córdoba, Argentina
| | - A Salas
- Unidade de Xenética, Departamento de Anatomía Patolóxica e Ciencias Forenses, Instituto de Ciencias Forenses, Facultade de Medicina, Universidade de Santiago de Compostela, Galicia, Spain. .,GenPoB Research Group, Instituto de Investigaciones Sanitarias (IDIS), Hospital Clínico Universitario de Santiago, Galicia, Spain.
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Thakkar DN, Kodidela S, Sandhiya S, Dubashi B, Dkhar SA. A Polymorphism Located Near PMAIP1/Noxa Gene Influences Susceptibility to Hodgkin Lymphoma Development in South India. Asian Pac J Cancer Prev 2017; 18:2477-2483. [PMID: 28952280 PMCID: PMC5720654 DOI: 10.22034/apjcp.2017.18.9.2477] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Background: Single nucleotide polymorphisms (SNPs) in DNA repair and Toll-like receptor (TLR) genes have been reported to be associated with Hodgkin Lymphoma (HL) risk. Since such associations may be ethnicity dependent, polymorphisms in TLR4 rs1554973, Xeroderma pigmentosum C (XPC) rs2228000, rs2228001 and a variant near PMAIP1/Noxa gene rs8093763 were here investigated with regard to HL susceptibility in a south Indian population. Normative frequencies of SNPs were established and compared with data for 1000 genome populations. Methods: We conducted a case control study consisting of 200 healthy volunteers and 101 cases with HL. DNA samples were genotyped using real-time PCR. Linkage disequilibrium (LD) analysis between rs2228000 and rs2228001 was performed using HaploView (version 4.2). Results: Among the studied variants, we observed that a variant rs8093763 located near PMAIP1/Noxa gene was associated with HL risk (OR=1.72 and 95% CI=1.004-2.93). The major allele frequencies of XPC (rs2228000 and rs2228001), TLR4 (rs1554973) and PMAIP1/NOXA (rs8093763) variants were 79%, 66%, 67% and 59% respectively. The studied frequencies were significantly different from 1000 genome populations. Conclusion: The results suggest that a variant rs8093763 located near the PMAIP1/Noxa gene may modify risk of HL. We found variation in distribution of polymorphic frequencies between the study population and 1000 genome populations. The results may help identify individual risk of development of HL in our south Indian population.
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Affiliation(s)
- Dimpal N Thakkar
- Department of Pharmacology, Jawaharlal Institute of Postgraduate Medical Education and Research (JIPMER), Gorimedu, Puducherry, India.
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Inclusion of Population-specific Reference Panel from India to the 1000 Genomes Phase 3 Panel Improves Imputation Accuracy. Sci Rep 2017; 7:6733. [PMID: 28751670 PMCID: PMC5532257 DOI: 10.1038/s41598-017-06905-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2017] [Accepted: 06/20/2017] [Indexed: 12/23/2022] Open
Abstract
Imputation is a computational method based on the principle of haplotype sharing allowing enrichment of genome-wide association study datasets. It depends on the haplotype structure of the population and density of the genotype data. The 1000 Genomes Project led to the generation of imputation reference panels which have been used globally. However, recent studies have shown that population-specific panels provide better enrichment of genome-wide variants. We compared the imputation accuracy using 1000 Genomes phase 3 reference panel and a panel generated from genome-wide data on 407 individuals from Western India (WIP). The concordance of imputed variants was cross-checked with next-generation re-sequencing data on a subset of genomic regions. Further, using the genome-wide data from 1880 individuals, we demonstrate that WIP works better than the 1000 Genomes phase 3 panel and when merged with it, significantly improves the imputation accuracy throughout the minor allele frequency range. We also show that imputation using only South Asian component of the 1000 Genomes phase 3 panel works as good as the merged panel, making it computationally less intensive job. Thus, our study stresses that imputation accuracy using 1000 Genomes phase 3 panel can be further improved by including population-specific reference panels from South Asia.
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Silva M, Oliveira M, Vieira D, Brandão A, Rito T, Pereira JB, Fraser RM, Hudson B, Gandini F, Edwards C, Pala M, Koch J, Wilson JF, Pereira L, Richards MB, Soares P. A genetic chronology for the Indian Subcontinent points to heavily sex-biased dispersals. BMC Evol Biol 2017; 17:88. [PMID: 28335724 PMCID: PMC5364613 DOI: 10.1186/s12862-017-0936-9] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Accepted: 03/14/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND India is a patchwork of tribal and non-tribal populations that speak many different languages from various language families. Indo-European, spoken across northern and central India, and also in Pakistan and Bangladesh, has been frequently connected to the so-called "Indo-Aryan invasions" from Central Asia ~3.5 ka and the establishment of the caste system, but the extent of immigration at this time remains extremely controversial. South India, on the other hand, is dominated by Dravidian languages. India displays a high level of endogamy due to its strict social boundaries, and high genetic drift as a result of long-term isolation which, together with a very complex history, makes the genetic study of Indian populations challenging. RESULTS We have combined a detailed, high-resolution mitogenome analysis with summaries of autosomal data and Y-chromosome lineages to establish a settlement chronology for the Indian Subcontinent. Maternal lineages document the earliest settlement ~55-65 ka (thousand years ago), and major population shifts in the later Pleistocene that explain previous dating discrepancies and neutrality violation. Whilst current genome-wide analyses conflate all dispersals from Southwest and Central Asia, we were able to tease out from the mitogenome data distinct dispersal episodes dating from between the Last Glacial Maximum to the Bronze Age. Moreover, we found an extremely marked sex bias by comparing the different genetic systems. CONCLUSIONS Maternal lineages primarily reflect earlier, pre-Holocene processes, and paternal lineages predominantly episodes within the last 10 ka. In particular, genetic influx from Central Asia in the Bronze Age was strongly male-driven, consistent with the patriarchal, patrilocal and patrilineal social structure attributed to the inferred pastoralist early Indo-European society. This was part of a much wider process of Indo-European expansion, with an ultimate source in the Pontic-Caspian region, which carried closely related Y-chromosome lineages, a smaller fraction of autosomal genome-wide variation and an even smaller fraction of mitogenomes across a vast swathe of Eurasia between 5 and 3.5 ka.
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Affiliation(s)
- Marina Silva
- Department of Biological Sciences, School of Applied Sciences, University of Huddersfield, Queensgate, Huddersfield, HD1 3DH, UK
| | - Marisa Oliveira
- i3S (Instituto de Investigação e Inovação em Saúde, Universidade do Porto), R. Alfredo Allen 208, 4200-135, Porto, Portugal.,IPATIMUP (Instituto de Patologia e Imunologia Molecular da Universidade do Porto), Rua Júlio Amaral de Carvalho 45, 4200-135, Porto, Portugal
| | - Daniel Vieira
- Department of Informatics, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal.,CBMA (Centre of Molecular and Environmental Biology), Department of Biology, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
| | - Andreia Brandão
- i3S (Instituto de Investigação e Inovação em Saúde, Universidade do Porto), R. Alfredo Allen 208, 4200-135, Porto, Portugal.,IPATIMUP (Instituto de Patologia e Imunologia Molecular da Universidade do Porto), Rua Júlio Amaral de Carvalho 45, 4200-135, Porto, Portugal
| | - Teresa Rito
- i3S (Instituto de Investigação e Inovação em Saúde, Universidade do Porto), R. Alfredo Allen 208, 4200-135, Porto, Portugal.,Life and Health Sciences Research Institute (ICVS), School of Health Sciences, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal.,ICVS/3B's-PT Government Associate Laboratory, Braga/Guimarães, Portugal
| | - Joana B Pereira
- i3S (Instituto de Investigação e Inovação em Saúde, Universidade do Porto), R. Alfredo Allen 208, 4200-135, Porto, Portugal.,IPATIMUP (Instituto de Patologia e Imunologia Molecular da Universidade do Porto), Rua Júlio Amaral de Carvalho 45, 4200-135, Porto, Portugal
| | - Ross M Fraser
- Centre for Global Health Research, Usher Institute of Population Health Sciences and Informatics, University of Edinburgh, Teviot Place, Edinburgh, EH8 9AG, Scotland, UK.,Synpromics Ltd, Nine Edinburgh Bioquarter, Edinburgh, EH16 4UX, UK
| | - Bob Hudson
- Archaeology Department, University of Sydney, Sydney, NSW, 2006, Australia
| | - Francesca Gandini
- Department of Biological Sciences, School of Applied Sciences, University of Huddersfield, Queensgate, Huddersfield, HD1 3DH, UK
| | - Ceiridwen Edwards
- Department of Biological Sciences, School of Applied Sciences, University of Huddersfield, Queensgate, Huddersfield, HD1 3DH, UK
| | - Maria Pala
- Department of Biological Sciences, School of Applied Sciences, University of Huddersfield, Queensgate, Huddersfield, HD1 3DH, UK
| | - John Koch
- University of Wales Centre for Advanced Welsh and Celtic Studies, National Library of Wales, Aberystwyth, SY23 3HH, Wales, UK
| | - James F Wilson
- Centre for Global Health Research, Usher Institute of Population Health Sciences and Informatics, University of Edinburgh, Teviot Place, Edinburgh, EH8 9AG, Scotland, UK.,MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, EH4 2XU, Scotland, UK
| | - Luísa Pereira
- i3S (Instituto de Investigação e Inovação em Saúde, Universidade do Porto), R. Alfredo Allen 208, 4200-135, Porto, Portugal.,IPATIMUP (Instituto de Patologia e Imunologia Molecular da Universidade do Porto), Rua Júlio Amaral de Carvalho 45, 4200-135, Porto, Portugal
| | - Martin B Richards
- Department of Biological Sciences, School of Applied Sciences, University of Huddersfield, Queensgate, Huddersfield, HD1 3DH, UK.
| | - Pedro Soares
- IPATIMUP (Instituto de Patologia e Imunologia Molecular da Universidade do Porto), Rua Júlio Amaral de Carvalho 45, 4200-135, Porto, Portugal. .,CBMA (Centre of Molecular and Environmental Biology), Department of Biology, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal.
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Reconstructing the population history of the largest tribe of India: the Dravidian speaking Gond. Eur J Hum Genet 2017; 25:493-498. [PMID: 28145430 DOI: 10.1038/ejhg.2016.198] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2016] [Revised: 11/01/2016] [Accepted: 12/14/2016] [Indexed: 01/15/2023] Open
Abstract
The Gond comprise the largest tribal group of India with a population exceeding 12 million. Linguistically, the Gond belong to the Gondi-Manda subgroup of the South Central branch of the Dravidian language family. Ethnographers, anthropologists and linguists entertain mutually incompatible hypotheses on their origin. Genetic studies of these people have thus far suffered from the low resolution of the genetic data or the limited number of samples. Therefore, to gain a more comprehensive view on ancient ancestry and genetic affinities of the Gond with the neighbouring populations speaking Indo-European, Dravidian and Austroasiatic languages, we have studied four geographically distinct groups of Gond using high-resolution data. All the Gond groups share a common ancestry with a certain degree of isolation and differentiation. Our allele frequency and haplotype-based analyses reveal that the Gond share substantial genetic ancestry with the Indian Austroasiatic (ie, Munda) groups, rather than with the other Dravidian groups to whom they are most closely related linguistically.
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Kraker J, Viswanathan SK, Knöll R, Sadayappan S. Recent Advances in the Molecular Genetics of Familial Hypertrophic Cardiomyopathy in South Asian Descendants. Front Physiol 2016; 7:499. [PMID: 27840609 PMCID: PMC5083855 DOI: 10.3389/fphys.2016.00499] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Accepted: 10/12/2016] [Indexed: 12/14/2022] Open
Abstract
The South Asian population, numbered at 1.8 billion, is estimated to comprise around 20% of the global population and 1% of the American population, and has one of the highest rates of cardiovascular disease. While South Asians show increased classical risk factors for developing heart failure, the role of population-specific genetic risk factors has not yet been examined for this group. Hypertrophic cardiomyopathy (HCM) is one of the major cardiac genetic disorders among South Asians, leading to contractile dysfunction, heart failure, and sudden cardiac death. This disease displays autosomal dominant inheritance, and it is associated with a large number of variants in both sarcomeric and non-sarcomeric proteins. The South Asians, a population with large ethnic diversity, potentially carries region-specific polymorphisms. There is high variability in disease penetrance and phenotypic expression of variants associated with HCM. Thus, extensive studies are required to decipher pathogenicity and the physiological mechanisms of these variants, as well as the contribution of modifier genes and environmental factors to disease phenotypes. Conducting genotype-phenotype correlation studies will lead to improved understanding of HCM and, consequently, improved treatment options for this high-risk population. The objective of this review is to report the history of cardiovascular disease and HCM in South Asians, present previously published pathogenic variants, and introduce current efforts to study HCM using induced pluripotent stem cell-derived cardiomyocytes, next-generation sequencing, and gene editing technologies. The authors ultimately hope that this review will stimulate further research, drive novel discoveries, and contribute to the development of personalized medicine with the aim of expanding therapeutic strategies for HCM.
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Affiliation(s)
- Jessica Kraker
- Department of Internal Medicine, Heart, Lung and Vascular Institute, Division of Cardiovascular Health and Sciences, University of Cincinnati College of Medicine Cincinnati, OH, USA
| | - Shiv Kumar Viswanathan
- Department of Internal Medicine, Heart, Lung and Vascular Institute, Division of Cardiovascular Health and Sciences, University of Cincinnati College of Medicine Cincinnati, OH, USA
| | - Ralph Knöll
- AstraZeneca R&D Mölndal, Innovative Medicines and Early Development, Cardiovascular and Metabolic Diseases iMedMölndal, Sweden; Integrated Cardio Metabolic Centre, Karolinska Institutet, Myocardial Genetics, Karolinska University Hospital in HuddingeHuddinge, Sweden
| | - Sakthivel Sadayappan
- Department of Internal Medicine, Heart, Lung and Vascular Institute, Division of Cardiovascular Health and Sciences, University of Cincinnati College of Medicine Cincinnati, OH, USA
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Shrivastava P, Jain T, Trivedi VB. Structure and genetic relationship of five populations from central India based on 15 autosomal STR loci. Ann Hum Biol 2016; 44:74-86. [DOI: 10.3109/03014460.2016.1151932] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Affiliation(s)
- Pankaj Shrivastava
- DNA Fingerprinting Unit, State Forensic Science Laboratory, Department of Home (Police), Government of MP, Sagar-470001, India
| | - Toshi Jain
- DNA Fingerprinting Unit, State Forensic Science Laboratory, Department of Home (Police), Government of MP, Sagar-470001, India
| | - Veena Ben Trivedi
- DNA Fingerprinting Unit, State Forensic Science Laboratory, Department of Home (Police), Government of MP, Sagar-470001, India
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Hoffecker JF, Elias SA, O'Rourke DH, Scott GR, Bigelow NH. Beringia and the global dispersal of modern humans. Evol Anthropol 2016; 25:64-78. [DOI: 10.1002/evan.21478] [Citation(s) in RCA: 119] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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41
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42
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Syn NLX, Yong WP, Lee SC, Goh BC. Genetic factors affecting drug disposition in Asian cancer patients. Expert Opin Drug Metab Toxicol 2015; 11:1879-92. [PMID: 26548636 DOI: 10.1517/17425255.2015.1108964] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
INTRODUCTION In the era of genomic medicine, it is increasingly recognized that ethnogeographic differences in drug pharmacology exist between Asian and other populations. This is particularly pertinent to oncology, where drugs forming the backbone of chemotherapy often have narrow therapeutic windows and are frequently dosed close to maximally tolerable levels. AREAS COVERED At the population level, ancestry is important because historical-biogeographical confluences have shaped population genetics and pharmacoethnicity in the Asian race through allelic differentiation and interethnic differences in inheritance patterns of linkage disequilibrium. At the individual level, cis- and trans-acting germline polymorphisms and somatic mutations in genes encoding drug-metabolizing enzymes and transporters act in a multifactorial manner to determine drug disposition phenotype and clinical response in Asian cancer patients. A growing body of evidence also finds that complex genetic interactions and regulation, including a multiplicity of gene control mechanisms, are increasingly implicated in genotype-phenotype correlates than has hitherto been appreciated--potentially serving as the mechanistic links between hits in non-coding regions of genome-wide association studies and drug toxicity. Together, these genetic factors contribute to the clinical heterogeneity of drug disposition in Asian cancer patients. EXPERT OPINION This topic has broad relevance for the optimization and individualization of anticancer strategies in Asians.
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Affiliation(s)
- Nicholas Li-Xun Syn
- a Department of Haematology-Oncology , National University Cancer Institute , Singapore 119228
| | - Wei-Peng Yong
- a Department of Haematology-Oncology , National University Cancer Institute , Singapore 119228.,b Cancer Science Institute of Singapore , National University of Singapore, Centre for Translational Medicine , Singapore 117599
| | - Soo-Chin Lee
- a Department of Haematology-Oncology , National University Cancer Institute , Singapore 119228.,b Cancer Science Institute of Singapore , National University of Singapore, Centre for Translational Medicine , Singapore 117599
| | - Boon-Cher Goh
- a Department of Haematology-Oncology , National University Cancer Institute , Singapore 119228.,b Cancer Science Institute of Singapore , National University of Singapore, Centre for Translational Medicine , Singapore 117599.,c Department of Pharmacology, Yong Loo Lin School of Medicine , National University of Singapore , Singapore 119077
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Negi N, Tamang R, Pande V, Sharma A, Shah A, Reddy AG, Vishnupriya S, Singh L, Chaubey G, Thangaraj K. The paternal ancestry of Uttarakhand does not imitate the classical caste system of India. J Hum Genet 2015; 61:167-72. [PMID: 26511066 DOI: 10.1038/jhg.2015.121] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2015] [Revised: 08/03/2015] [Accepted: 09/11/2015] [Indexed: 01/17/2023]
Abstract
Although, there have been rigorous research on the Indian caste system by several disciplines, it is still one of the most controversial socioscientific topic. Previous genetic studies on the subcontinent have supported a classical hierarchal sharing of genetic component by various castes of India. In the present study, we have used high-resolution mtDNA and Y chromosomal markers to characterize the genetic structuring of the Uttarakhand populations in the context of neighboring regions. Furthermore, we have tested whether the genetic structuring of caste populations at different social levels of this region, follow the classical chaturvarna system. Interestingly, we found that this region showed a high level of variation for East Eurasian ancestry in both maternal and paternal lines of descent. Moreover, the intrapopulation comparison showed a high level of heterogeneity, likely because of different caste hierarchy, interpolated on asymmetric admixture of populations inhabiting on both sides of the Himalayas.
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Affiliation(s)
- Neetu Negi
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India.,Department of Biotechnology, Kumaun University, Nainital, Uttarakhand, India
| | - Rakesh Tamang
- Department of Evolutionary Biology, Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia.,Estonian Biocentre, Tartu, Estonia.,Department of Zoology, University of Calcutta, Kolkata, India.,Department of Genetics, Osmania University, Hyderabad, India
| | - Veena Pande
- Department of Biotechnology, Kumaun University, Nainital, Uttarakhand, India
| | - Amrita Sharma
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
| | - Anish Shah
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
| | - Alla G Reddy
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
| | | | - Lalji Singh
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India.,Genome Foundation, Hyderabad, India
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Vásquez-Loarte T, Trubnykova M, Guio H. Genetic association meta-analysis: a new classification to assess ethnicity using the association of MCP-1 -2518 polymorphism and tuberculosis susceptibility as a model. BMC Genet 2015; 16:128. [PMID: 26518714 PMCID: PMC4627623 DOI: 10.1186/s12863-015-0280-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2014] [Accepted: 10/12/2015] [Indexed: 12/15/2022] Open
Abstract
Background In meta-analyses of genetic association studies, ancestry and ethnicity are not accurately investigated. Ethnicity is usually classified using conventional race/ethnic categories or continental groupings even though they could introduce bias increasing heterogeneity between and within studies; thus decreasing the external validity of the results. In this study, we performed a meta-analysis using a novel ethnic classification system to test the association between MCP-1 -2518 polymorphism and pulmonary tuberculosis. Our new classification considers genetic distance, migration and linguistic origins, which will increase homogeneity within ethnic groups. Methods We included thirteen studies from three continents (Asia, Africa and Latin America) and considered seven ethnic groups (West Africa, South Africa, Saharan Africa, East Asia, South Asia, Persia and Latin America). Results The results were compared to the continental group classification. We found a significant association between MCP-1 -2518 polymorphism and TB susceptibility only in the East Asian and Latin American groups (OR 3.47, P = 0.08; OR 2.73, P = 0.02). This association is not observed in other ethnic groups that are usually considered in the Asian group, such as India and Persia, or in the African group. Conclusions There is an association between MCP-1 -2518 polymorphism and TB susceptibility only in the East Asian and Latin American groups. We suggest the use of our new ethnic classification in future meta-analysis of genetic association studies when ancestry markers are not available. This new classification increases homogeneity for certain ethnic groups compared to the continental classification. We recommend considering previous data about migration, linguistics and genetic distance when classifying ethnicity in further studies.
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Affiliation(s)
- Tania Vásquez-Loarte
- Laboratorio de Biotecnología y Biología Molecular, Instituto Nacional de Salud, Avenida Defensores del, Morro 2268, Lima 9, Peru.
| | - Milana Trubnykova
- Laboratorio de Biotecnología y Biología Molecular, Instituto Nacional de Salud, Avenida Defensores del, Morro 2268, Lima 9, Peru.
| | - Heinner Guio
- Laboratorio de Biotecnología y Biología Molecular, Instituto Nacional de Salud, Avenida Defensores del, Morro 2268, Lima 9, Peru.
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Aggarwal S, Phadke SR. Medical genetics and genomic medicine in India: current status and opportunities ahead. Mol Genet Genomic Med 2015; 3:160-71. [PMID: 26029702 PMCID: PMC4444157 DOI: 10.1002/mgg3.150] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Affiliation(s)
- Shagun Aggarwal
- Department of Medical Genetics, Nizam's Institute of Medical Sciences Hyderabad, India ; Diagnostics Division, Centre for DNA Fingerprinting and Diagnostics Hyderabad, India
| | - Shubha R Phadke
- Department of Medical Genetics, Sanjay Gandhi Postgraduate Institute of Medical Sciences Lucknow, India
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46
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ArunKumar G, Tatarinova TV, Duty J, Rollo D, Syama A, Arun VS, Kavitha VJ, Triska P, Greenspan B, Wells RS, Pitchappan R. Genome-wide signatures of male-mediated migration shaping the Indian gene pool. J Hum Genet 2015; 60:493-9. [DOI: 10.1038/jhg.2015.51] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Revised: 04/13/2015] [Accepted: 04/17/2015] [Indexed: 02/02/2023]
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47
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Mitra S, Khurana P, Panmei T, Kshatriya GK. Allele frequencies of PON1 Q192R polymorphism in four populations of India. ENVIRONMENTAL TOXICOLOGY AND PHARMACOLOGY 2015; 39:1051-1056. [PMID: 25867687 DOI: 10.1016/j.etap.2015.03.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2014] [Revised: 02/26/2015] [Accepted: 03/03/2015] [Indexed: 06/04/2023]
Abstract
The allelic distribution at Paraoxonase 1 (PON1) Q192R polymorphism determines differential sensitivity towards certain organophosphate pesticides. The alleles Q (Glutamine) and R (Arginine) at amino acid position 192 are responsible for the lower and higher activity of the enzyme towards paraoxon respectively, making knowledge of this distribution in different populations vital. This study reports the genotype and allele frequencies of the Gln192Arg polymorphism of PON1 in four populations of India, comprising two caste and two tribal groups hitherto unexamined for this polymorphism. The R allele frequencies in Jat, Meo, Santhal and Zeliangrong populations were found to be 0.47, 0.45, 0.54 and 0.51 respectively. The gene diversity analyses show a high genetic differentiation at this locus indicative of the role of populations' history and other evolutionary forces. A comparison with allele frequencies among 106 populations from different continents showed a concordance with their geographic distribution which will have repercussions in policies targeting pesticide usage.
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Affiliation(s)
- Siuli Mitra
- Department of Anthropology, University of Delhi, Delhi 110007, India
| | - Priyanka Khurana
- Department of Anthropology, School of Applied Sciences, Dr. Harisingh Gour University, Sagar, Madhya Pradesh, India
| | - Tabitha Panmei
- Department of Anthropology, University of Delhi, Delhi 110007, India
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Majumder PP, Basu A. A genomic view of the peopling and population structure of India. Cold Spring Harb Perspect Biol 2014; 7:a008540. [PMID: 25147176 DOI: 10.1101/cshperspect.a008540] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Recent advances in molecular and statistical genetics have enabled the reconstruction of human history by studying living humans. The ability to sequence and study DNA by calibrating the rate of accumulation of changes with evolutionary time has enabled robust inferences about how humans have evolved. These data indicate that modern humans evolved in Africa about 150,000 years ago and, consistent with paleontological evidence, migrated out of Africa. And through a series of settlements, demographic expansions, and further migrations, they populated the entire world. One of the first waves of migration from Africa was into India. Subsequent, more recent, waves of migration from other parts of the world have resulted in India being a genetic melting pot. Contemporary India has a rich tapestry of cultures and ecologies. There are about 400 tribal groups and more than 4000 groups of castes and subcastes, speaking dialects of 22 recognized languages belonging to four major language families. The contemporary social structure of Indian populations is characterized by endogamy with different degrees of porosity. The social structure, possibly coupled with large ecological heterogeneity, has resulted in considerable genetic diversity and local genetic differences within India. In this essay, we provide genetic evidence of how India may have been peopled, the nature and extent of its genetic diversity, and genetic structure among the extant populations of India.
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Affiliation(s)
| | - Analabha Basu
- National Institute of Biomedical Genomics, Kalyani 741251, India
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Glutathione-S-transferase polymorphism and acute lymphoblastic leukemia (ALL) in north Indian children: a case-control study and meta-analysis. J Hum Genet 2014; 59:529-35. [PMID: 25102096 DOI: 10.1038/jhg.2014.66] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2014] [Revised: 07/03/2014] [Accepted: 07/04/2014] [Indexed: 02/02/2023]
Abstract
Various studies on association of glutathione S-transferase (GST) polymorphisms and childhood acute lymphoblastic leukemia (ALL) have yielded conflicting results. We examined this association among north Indian children and conducted an updated meta-analysis to overcome sample size-related limitations. GSTM1, GSTP1 and GSTT1 genotypes in 100 children with ALL and 300 healthy controls were compared. GSTT1 null mutation (odds ratio (OR) 2.54, 95% confidence interval (CI) 1.50-4.32) and GSTP1 homozygous mutation (OR 3.13, 95%CI 1.48-6.59) were found to increase the risk of childhood ALL, while GSTM1 did not alter the risk. Meta-analysis included 22, 10 and 20 studies examining the association of childhood ALL with GSTM1, GSTP1 and GSTT1 genotypes, respectively. Only GSTM1 genotype (OR 1.29, 95%CI 1.10-1.62) was associated with increased risk in the overall analysis. However, both GSTM1 (OR 1.54, 95%CI 1.12-2.10) and GSTT1 (OR 1.63, 95%CI 1.32-1.99) null genotypes were associated with increased risk in Asian subjects. The risk of developing childhood ALL was not associated with GSTP1 genotype.
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Ali M, Liu X, Pillai EN, Chen P, Khor CC, Ong RTH, Teo YY. Characterizing the genetic differences between two distinct migrant groups from Indo-European and Dravidian speaking populations in India. BMC Genet 2014; 15:86. [PMID: 25053360 PMCID: PMC4120727 DOI: 10.1186/1471-2156-15-86] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2013] [Accepted: 07/11/2014] [Indexed: 12/15/2022] Open
Abstract
Background India is home to many ethnically and linguistically diverse populations. It is hypothesized that history of invasions by people from Persia and Central Asia, who are referred as Aryans in Hindu Holy Scriptures, had a defining role in shaping the Indian population canvas. A shift in spoken languages from Dravidian languages to Indo-European languages around 1500 B.C. is central to the Aryan Invasion Theory. Here we investigate the genetic differences between two sub-populations of India consisting of: (1) The Indo-European language speaking Gujarati Indians with genome-wide data from the International HapMap Project; and (2) the Dravidian language speaking Tamil Indians with genome-wide data from the Singapore Genome Variation Project. Results We implemented three population genetics measures to identify genomic regions that are significantly differentiated between the two Indian populations originating from the north and south of India. These measures singled out genomic regions with: (i) SNPs exhibiting significant variation in allele frequencies in the two Indian populations; and (ii) differential signals of positive natural selection as quantified by the integrated haplotype score (iHS) and cross-population extended haplotype homozygosity (XP-EHH). One of the regions that emerged spans the SLC24A5 gene that has been functionally shown to affect skin pigmentation, with a higher degree of genetic sharing between Gujarati Indians and Europeans. Conclusions Our finding points to a gene-flow from Europe to north India that provides an explanation for the lighter skin tones present in North Indians in comparison to South Indians.
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Affiliation(s)
| | | | | | | | | | | | - Yik-Ying Teo
- Life Sciences Institute, National University of Singapore, Singapore, Singapore.
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