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Kumar S, Singh PP, Pasupuleti N, Tripathy VM, Chauley MK, Chaubey G, Rai N. The genetic admixture and assimilation of Ahom: a historic migrant from Thailand to India. Hum Mol Genet 2024; 33:1015-1019. [PMID: 38538568 DOI: 10.1093/hmg/ddae054] [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] [Received: 11/14/2023] [Revised: 03/02/2024] [Accepted: 03/14/2024] [Indexed: 04/23/2024] Open
Abstract
The Northeastern region of India is considered a gateway for modern humans' dispersal throughout Asia. This region is a mixture of various ethnic and indigenous populations amalgamating multiple ancestries. One reason for such amalgamation is that, South Asia experienced multiple historic migrations from various parts of the world. A few examples explored genetically are Jews, Parsis and Siddis. Ahom is a dynasty that historically migrated to India during the 12th century. However, this putative migration has not been studied genetically at high resolution. Therefore, to validate this historical evidence, we genotyped autosomal data of the Modern Ahom population residing in seven sister states of India. Principal Component and Admixture analyses haave suggested a substantial admixture of the Ahom population with the local Tibeto-Burman populations. Moreover, the haplotype-based analysis has linked these Ahom individuals mainly with the Kusunda (a language isolated from Nepal) and Khasi (an Austroasiatic population of Meghalaya). Such unexpected presence of widespread population affinities suggests that Ahom mixed and assimilated a wide variety of Trans-Himalayan populations inhabiting this region after the migration. In summary, we observed a significant deviation of Ahom from their ancestral homeland (Thailand) and extensive admixture and assimilation with the local South Asian populations.
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Affiliation(s)
- Sachin Kumar
- Ancient DNA Lab, Birbal Sahni Institute of Palaeosciences, 53 University Road, Lucknow 226607, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Prajjval Pratap Singh
- Cytogenetics Laboratory, Department of Zoology, Banaras Hindu University, Varanasi 221005, India
| | | | - Veena Mushrif Tripathy
- Department of Archaeology, Deccan College Post-Graduate and Research Institute, Pune, Maharashtra 411006, India
| | - Milan Kumar Chauley
- Archaeological Survey of India, Nagpur Circle, Seminary Hills, Nagpur, Maharashtra 440001, India
| | - Gyaneshwer Chaubey
- Cytogenetics Laboratory, Department of Zoology, Banaras Hindu University, Varanasi 221005, India
| | - Niraj Rai
- Ancient DNA Lab, Birbal Sahni Institute of Palaeosciences, 53 University Road, Lucknow 226607, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
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2
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Stoneman HR, Price A, Trout NS, Lamont R, Tifour S, Pozdeyev N, Crooks K, Lin M, Rafaels N, Gignoux CR, Marker KM, Hendricks AE. Characterizing substructure via mixture modeling in large-scale genetic summary statistics. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.29.577805. [PMID: 38766180 PMCID: PMC11100604 DOI: 10.1101/2024.01.29.577805] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
Genetic summary data are broadly accessible and highly useful including for risk prediction, causal inference, fine mapping, and incorporation of external controls. However, collapsing individual-level data into groups masks intra- and inter-sample heterogeneity, leading to confounding, reduced power, and bias. Ultimately, unaccounted substructure limits summary data usability, especially for understudied or admixed populations. Here, we present Summix2, a comprehensive set of methods and software based on a computationally efficient mixture model to estimate and adjust for substructure in genetic summary data. In extensive simulations and application to public data, Summix2 characterizes finer-scale population structure, identifies ascertainment bias, and identifies potential regions of selection due to local substructure deviation. Summix2 increases the robust use of diverse publicly available summary data resulting in improved and more equitable research.
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Affiliation(s)
- Hayley R Stoneman
- Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
- Human Medical Genetics and Genomics Program, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Adelle Price
- Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
- Mathematical and Statistical Sciences, University of Colorado Denver, Denver, CO 80204, USA
| | - Nikole Scribner Trout
- Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
- Mathematical and Statistical Sciences, University of Colorado Denver, Denver, CO 80204, USA
| | - Riley Lamont
- Mathematical and Statistical Sciences, University of Colorado Denver, Denver, CO 80204, USA
| | - Souha Tifour
- Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
- Mathematical and Statistical Sciences, University of Colorado Denver, Denver, CO 80204, USA
| | - Nikita Pozdeyev
- Colorado Center for Personalized Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
- Division of Endocrinology, Diabetes and Metabolism, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Kristy Crooks
- Colorado Center for Personalized Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
- Department of Pathology, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Meng Lin
- Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
- Colorado Center for Personalized Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Nicholas Rafaels
- Colorado Center for Personalized Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Christopher R Gignoux
- Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
- Human Medical Genetics and Genomics Program, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
- Colorado Center for Personalized Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Katie M Marker
- Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
- Human Medical Genetics and Genomics Program, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
- Colorado Center for Personalized Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Audrey E Hendricks
- Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
- Human Medical Genetics and Genomics Program, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
- Colorado Center for Personalized Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
- Mathematical and Statistical Sciences, University of Colorado Denver, Denver, CO 80204, USA
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3
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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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4
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Schilling J, Shokouhi S, Montgomery A, Nadkarni GN, Charney AW, Shanker A, Singh R, Jhaveri K, Singh KS, Khadke P, Jain P. Development of a decentralized cohort for studying post-acute sequelae of COVID-19 in India in the Data4life Study. COMMUNICATIONS MEDICINE 2023; 3:117. [PMID: 37626117 PMCID: PMC10457339 DOI: 10.1038/s43856-023-00349-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Accepted: 08/15/2023] [Indexed: 08/27/2023] Open
Abstract
BACKGROUND Decentralized, digital health studies can provide real-world evidence of the lasting effects of COVID-19 on physical, socioeconomic, psychological, and social determinant factors of health in India. Existing research cohorts, however, are small and were not designed for longitudinal collection of comprehensive data from India's diverse population. Data4Life is a nationwide, digitally enabled, health research initiative to examine the post-acute sequelae of COVID-19 across individuals, communities, and regions. Data4Life seeks to build an ethnically and geographically diverse population of at least 100,000 participants in India. METHODS Here we discuss the feasibility of developing a completely decentralized COVID-19 cohort in India through qualitative analysis of data collection procedures, participant characteristics, participant perspectives on recruitment and reported study motivation. RESULTS As of June 13th, 2022, more than 6,000 participants from 17 Indian states completed baseline surveys. Friend and family referral were identified as the most common recruitment method (64.8%) across all demographic groups. Helping family and friends was the primary reason reported for joining the study (61.5%). CONCLUSIONS Preliminary findings support the use of digital technology for rapid enrollment and data collection to develop large health research cohorts in India. This demonstrates the potential for expansion of digitally enabled health research in India. These findings also outline the value of person-to-person recruitment strategies when conducting digital health research in modern-day India. Qualitative analysis reveals opportunities to increase diversity and retention in real time. It also informs strategies for improving participant experiences in the current Data4Life initiative and future studies.
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Affiliation(s)
- Josh Schilling
- Vibrent Health, 4114 Legato Rd #900, Fairfax, VA, 22033, USA
| | | | | | - Girish N Nadkarni
- Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Pl, New York, NY, 10029, USA
| | - Alexander W Charney
- Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Pl, New York, NY, 10029, USA
| | - Anil Shanker
- Meharry Medical College, 1005 Dr DB Todd Jr Blvd, Nashville, TN, 37208, USA
| | - Rajbir Singh
- Meharry Medical College, 1005 Dr DB Todd Jr Blvd, Nashville, TN, 37208, USA
| | - Kenar Jhaveri
- Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, 500 Hofstra Blvd, Hempstead, NY, 11549, USA
| | - Karandeep S Singh
- Learning Health Sciences, University of Michigan, 1111 E Catherine St, Ann Arbor, MI, 48109, USA
| | - Prashant Khadke
- Pensieve Health, 3A, 3rd Floor, Vascon Wekfield Chambers, Satpal Malhotra Marg, Nagar Road, Pune, Maharashtra, 411014, India
| | - Praduman Jain
- Vibrent Health, 4114 Legato Rd #900, Fairfax, VA, 22033, USA
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5
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Prajapati PJ, Bhavsar V, Bhatt D, Konat A, Shah S, Zapadia V, Nanavati D, Shroff S, Vora N, Sharma K. Prevalence of Traditional Risk Factors in First-Degree Relatives of Patients With Established Cardiovascular Disease. Cureus 2023; 15:e39061. [PMID: 37323318 PMCID: PMC10267422 DOI: 10.7759/cureus.39061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/15/2023] [Indexed: 06/17/2023] Open
Abstract
INTRODUCTION World Health Organization (WHO)/International Society of Hypertension (ISH) risk prediction charts are useful for predicting 10-year combined myocardial infarction and stroke risk (fatal and non-fatal). Hence the current study was conducted to assess the 10-year risk of cardiovascular disease among adults in Ahmedabad, India. AIMS The primary aim of the study was to assess the cardiovascular risk among first-degree relatives of patients attending the outpatient clinic. Also, to create awareness regarding assessment of cardiovascular risk among the studied group. METHODS AND MATERIALS A cross-sectional study was carried out among 372 first-degree relatives of patients at an out-patient cardiology clinic present in Vadaj, Ahmedabad. The WHO/ISH risk prediction chart for South-East Asia Region D (SEAR D) was used for calculating the 10-year cardiovascular risk. RESULTS A maximum (80.10%) of the study participants were in the low-risk (<10%) category followed by 8.33% for moderate-risk (10-20%), 7.25% for moderately high-risk (20-30%), 2.42% for high-risk (30-40%) and 1.88% for very high-risk (>40%). CONCLUSION WHO/ISH risk prediction charts provide a quick and effective way to assess and categorize the population in a low-resource setting which in turn helps in delivering focused intervention to the high-risk groups.
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Affiliation(s)
| | - Vatsa Bhavsar
- Internal Medicine, B. J. Medical College, Ahmedabad, IND
| | - Dakshey Bhatt
- Internal Medicine, GMERS (Gujarat Medical Education and Research Society), Himmatnagar, IND
| | - Ashwati Konat
- Department of Zoology, Biomedical Technology and Human Genetics, Gujarat University, Ahmedabad, IND
| | - Saujas Shah
- Internal Medicine, Gujarat Cancer Society (GCS) Medical College, Ahmedabad, IND
| | - Vatsal Zapadia
- Internal Medicine, B. J. Medical College, Ahmedabad, IND
| | - Dhruvam Nanavati
- Internal Medicine, Gujarat Cancer Society (GCS) Medical College, Ahmedabad, IND
| | - Shailee Shroff
- Internal Medicine, GMERS (Gujarat Medical Education and Research Society), Himmatnagar, IND
| | - Neel Vora
- Internal Medicine, B. J. Medical College, Ahmedabad, IND
| | - Kamal Sharma
- Cardiology, Dr. Kamal Sharma Cardiology Clinic, Ahmedabad, IND
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6
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Mendes M, Jonnalagadda M, Ozarkar S, Lima Torres FC, Borda Pua V, Kendall C, Tarazona-Santos E, Parra EJ. Identifying signatures of natural selection in Indian populations. PLoS One 2022; 17:e0271767. [PMID: 35925921 PMCID: PMC9352006 DOI: 10.1371/journal.pone.0271767] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 07/06/2022] [Indexed: 11/18/2022] Open
Abstract
In this study, we present the results of a genome-wide scan for signatures of positive selection using data from four tribal groups (Kokana, Warli, Bhil, and Pawara) and two caste groups (Deshastha Brahmin and Kunbi Maratha) from West of the Maharashtra State In India, as well as two samples of South Asian ancestry from the 1KG project (Gujarati Indian from Houston, Texas and Indian Telugu from UK). We used an outlier approach based on different statistics, including PBS, xpEHH, iHS, CLR, Tajima’s D, as well as two recently developed methods: Graph-aware Retrieval of Selective Sweeps (GRoSS) and Ascertained Sequentially Markovian Coalescent (ASMC). In order to minimize the risk of false positives, we selected regions that are outliers in all the samples included in the study using more than one method. We identified putative selection signals in 107 regions encompassing 434 genes. Many of the regions overlap with only one gene. The signals observed using microarray-based data are very consistent with our analyses using high-coverage sequencing data, as well as those identified with a novel coalescence-based method (ASMC). Importantly, at least 24 of these genomic regions have been identified in previous selection scans in South Asian populations or in other population groups. Our study highlights genomic regions that may have played a role in the adaptation of anatomically modern humans to novel environmental conditions after the out of Africa migration.
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Affiliation(s)
- Marla Mendes
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
- Department of Anthropology, University of Toronto—Mississauga Campus, Mississauga, ON, Canada
| | - Manjari Jonnalagadda
- Symbiosis School for Liberal Arts (SSLA), Symbiosis International University (SIU), Pune, India
| | - Shantanu Ozarkar
- Department of Anthropology, Savitribai Phule Pune University, Pune, India
| | - Flávia Carolina Lima Torres
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | - Victor Borda Pua
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, United States of America
| | - Christopher Kendall
- Department of Anthropology, University of Toronto—Mississauga Campus, Mississauga, ON, Canada
| | - Eduardo Tarazona-Santos
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | - Esteban J. Parra
- Department of Anthropology, University of Toronto—Mississauga Campus, Mississauga, ON, Canada
- * E-mail:
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7
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Extending precision medicine tools to populations at high risk of type 2 diabetes. PLoS Med 2022; 19:e1003989. [PMID: 35588405 PMCID: PMC9119471 DOI: 10.1371/journal.pmed.1003989] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
In this Perspective, Shivani Misra and Jose C Florez discuss the application of precision medicine tools in under-represented populations.
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8
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Prakrithi P, Singhal K, Sharma D, Jain A, Bhoyar RC, Imran M, Senthilvel V, Divakar MK, Mishra A, Scaria V, Sivasubbu S, Mukerji M. An Alu insertion map of the Indian population: identification and analysis in 1021 genomes of the IndiGen project. NAR Genom Bioinform 2022; 4:lqac009. [PMID: 35178516 PMCID: PMC8846365 DOI: 10.1093/nargab/lqac009] [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: 04/15/2021] [Revised: 12/21/2021] [Accepted: 01/25/2022] [Indexed: 11/14/2022] Open
Abstract
Abstract
Actively retrotransposing primate-specific Alu repeats display insertion-deletion (InDel) polymorphism through their insertion at new loci. In the global datasets, Indian populations remain under-represented and so do their Alu InDels. Here, we report the genomic landscape of Alu InDels from the recently released 1021 Indian Genomes (IndiGen) (available at https://clingen.igib.res.in/indigen). We identified 9239 polymorphic Alu insertions that include private (3831), rare (3974) and common (1434) insertions with an average of 770 insertions per individual. We achieved an 89% PCR validation of the predicted genotypes in 94 samples tested. About 60% of identified InDels are unique to IndiGen when compared to other global datasets; 23% of sites were shared with both SGDP and HGSVC; among these, 58% (1289 sites) were common polymorphisms in IndiGen. The insertions not only show a bias for genic regions, with a preference for introns but also for the associated genes showing enrichment for processes like cell morphogenesis and neurogenesis (P-value < 0.05). Approximately, 60% of InDels mapped to genes present in the OMIM database. Finally, we show that 558 InDels can serve as ancestry informative markers to segregate global populations. This study provides a valuable resource for baseline Alu InDels that would be useful in population genomics.
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Affiliation(s)
- P Prakrithi
- CSIR Institute of Genomics and Integrative Biology, Mathura Road, New Delhi 110025, India
| | - Khushboo Singhal
- CSIR Institute of Genomics and Integrative Biology, Mathura Road, New Delhi 110025, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, Uttar Pradesh, India
| | - Disha Sharma
- CSIR Institute of Genomics and Integrative Biology, Mathura Road, New Delhi 110025, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, Uttar Pradesh, India
| | - Abhinav Jain
- CSIR Institute of Genomics and Integrative Biology, Mathura Road, New Delhi 110025, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, Uttar Pradesh, India
| | - Rahul C Bhoyar
- CSIR Institute of Genomics and Integrative Biology, Mathura Road, New Delhi 110025, India
| | - Mohamed Imran
- CSIR Institute of Genomics and Integrative Biology, Mathura Road, New Delhi 110025, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, Uttar Pradesh, India
| | - Vigneshwar Senthilvel
- CSIR Institute of Genomics and Integrative Biology, Mathura Road, New Delhi 110025, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, Uttar Pradesh, India
| | - Mohit Kumar Divakar
- CSIR Institute of Genomics and Integrative Biology, Mathura Road, New Delhi 110025, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, Uttar Pradesh, India
| | - Anushree Mishra
- CSIR Institute of Genomics and Integrative Biology, Mathura Road, New Delhi 110025, India
| | - Vinod Scaria
- CSIR Institute of Genomics and Integrative Biology, Mathura Road, New Delhi 110025, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, Uttar Pradesh, India
| | - Sridhar Sivasubbu
- CSIR Institute of Genomics and Integrative Biology, Mathura Road, New Delhi 110025, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, Uttar Pradesh, India
| | - Mitali Mukerji
- CSIR Institute of Genomics and Integrative Biology, Mathura Road, New Delhi 110025, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, Uttar Pradesh, India
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9
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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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10
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Singh PP, Suravajhala P, Basu Mallick C, Tamang R, Rai AK, Machha P, Singh R, Pathak A, Mishra VN, Shrivastava P, Singh KK, Thangaraj K, Chaubey G. COVID-19: Impact on linguistic and genetic isolates of India. Genes Immun 2022; 23:47-50. [PMID: 34635809 PMCID: PMC8504558 DOI: 10.1038/s41435-021-00150-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 09/21/2021] [Accepted: 09/28/2021] [Indexed: 11/24/2022]
Abstract
The rapid expansion of coronavirus SARS-CoV-2 has impacted various ethnic groups all over the world. The burden of infectious diseases including COVID-19 are generally reported to be higher for the Indigenous people. The historical knowledge have also suggested that the indigenous populations suffer more than the general populations in the pandemic. Recently, it has been reported that the indigenous groups of Brazil have been massively affected by COVID-19. Series of studies have shown that many of the indigenous communities reached at the verge of extinction due to this pandemic. Importantly, South Asia also has several indigenous and smaller communities, that are living in isolation. Till date, despite the two consecutive waves in India, there is no report on the impact of COVID-19 for indigenous tribes. Since smaller populations experiencing drift may have greater risk of such pandemic, we have analysed Runs of Homozygosity (ROH) among South Asian populations and identified several populations with longer homozygous segments. The longer runs of homozygosity at certain genomic regions may increases the susceptibility for COVID-19. Thus, we suggest extreme careful management of this pandemic among isolated populations of South Asia.
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Affiliation(s)
- Prajjval Pratap Singh
- grid.411507.60000 0001 2287 8816Cytogenetics Laboratory, Department of Zoology, Banaras Hindu University, Varanasi, 221005 India
| | - Prashanth Suravajhala
- grid.469354.90000 0004 0610 6228Department of Biotechnology and Bioinformatics, Birla Institute of Scientific Research Statue Circle, Jaipur, Rajasthan India ,grid.411370.00000 0000 9081 2061Amrita School of Biotechnology, Amrita University Kerala India, Vallikavu, 690525 India
| | - Chandana Basu Mallick
- grid.411507.60000 0001 2287 8816Centre for Genetic Disorders, Institute of Science, Banaras Hindu University, Varanasi, 221005 India
| | - Rakesh Tamang
- grid.59056.3f0000 0001 0664 9773Department of Zoology, University of Calcutta, Kolkata, 700019 India
| | - Ashutosh Kumar Rai
- grid.411975.f0000 0004 0607 035XDepartment of Biochemistry, College of Medicine, Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
| | - Pratheusa Machha
- grid.417634.30000 0004 0496 8123CSIR-Centre for Cellular and Molecular Biology, Hyderabad, 500007 India ,grid.469887.c0000 0004 7744 2771Academy of Scientific and Innovative Research, (AcSIR), Ghaziabad, 201002 India
| | - Royana Singh
- grid.411507.60000 0001 2287 8816Department of Anatomy, Institute of Medical Sciences, Banaras Hindu University, Varanasi, 221005 India
| | - Abhishek Pathak
- grid.411507.60000 0001 2287 8816Department of Neurology, Institute of Medical Sciences, Banaras Hindu University, Varanasi, 221005 India
| | - Vijay Nath Mishra
- grid.411507.60000 0001 2287 8816Department of Neurology, Institute of Medical Sciences, Banaras Hindu University, Varanasi, 221005 India
| | - Pankaj Shrivastava
- Department of Home (Police), DNA Fingerprinting Unit, State Forensic Science Laboratory, Government of MP, Sagar, India
| | - Keshav K. Singh
- grid.265892.20000000106344187Department of Genetics, School of Medicine, University of Alabama at Birmingham, Kaul Genetics Building, Birmingham, AL USA
| | - Kumarasamy Thangaraj
- grid.417634.30000 0004 0496 8123CSIR-Centre for Cellular and Molecular Biology, Hyderabad, 500007 India ,grid.145749.a0000 0004 1767 2735Centre for DNA Fingerprinting and Diagnostics (CDFD), Hyderabad, 500039 India
| | - Gyaneshwer Chaubey
- grid.411507.60000 0001 2287 8816Cytogenetics Laboratory, Department of Zoology, Banaras Hindu University, Varanasi, 221005 India
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11
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Banerjee J, Gupta A, Agnihotri V, Pradhan R, Kandel R, Upadhyay AD, Dwivedi S, Kumar L, Dey S, Dey AB. Lung cancer in the older population:Interactive effects of angiotensin converting enzyme gene polymorphism (rs 4340 ID) and tobacco addiction in risk assessment. Indian J Cancer 2021; 0:318894. [PMID: 34380830 DOI: 10.4103/ijc.ijc_1082_19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
BACKGROUND rs4340ID polymorphism of angiotensin-converting enzyme (ACE) correlates with serum ACE levels in many known cancers. This study analyzed ACE rs4340 ID polymorphism in lung cancer (LC) in older patients of North India and correlated it with addiction status. METHODS The study enrolled all subjects aged 60 years and above with 154 LC and 205 healthy controls. Genotyping was done by polymerase chain reaction (PCR) and validated by sequencing of 10% of the sample. Statistical analysis was done by SPSS Statistics 21. RESULTS Genotype II was observed to have a significant 2.21-fold increased risk of LC as compared to the DD genotype and 3.43-folds enhanced risk with interaction of I allele with tobacco consumption habits as compared to D allele in LC was seen. CONCLUSION The risk of LC was higher with II genotype as compared to DD genotype. Interactive effect showed that I allele with tobacco habits may increase the risk of LC.
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Affiliation(s)
- Joyita Banerjee
- Department of Geriatric Medicine, All India Institute of Medical Sciences, New Delhi, India
| | - Abhishek Gupta
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, India
| | - Vertica Agnihotri
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, India
| | - Rashmita Pradhan
- Department of Geriatric Medicine, All India Institute of Medical Sciences, New Delhi, India
| | - Ramesh Kandel
- Department of Geriatric Medicine, All India Institute of Medical Sciences, New Delhi, India
| | - Ashish D Upadhyay
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, India
| | - Sadanand Dwivedi
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, India
| | - Lalit Kumar
- Department of Medical Oncology, All India Institute of Medical Sciences, New Delhi, India
| | - Sharmistha Dey
- Department of Biophysics, 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
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12
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Disease characteristics and clinical outcomes of adults and children with anti-MDA-5 antibody-associated myositis: a prospective observational bicentric study. Rheumatol Int 2021; 42:1155-1165. [PMID: 34050793 DOI: 10.1007/s00296-021-04897-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2021] [Accepted: 05/15/2021] [Indexed: 12/14/2022]
Abstract
To study the demographic, clinical and serologic characteristics of anti-MDA5-positive DM from two geographically and ethnically disparate inception cohorts in India. To identify the clinical and serological parameters at inception that could predict mortality among these individuals. Individuals with anti-MDA5 antibody-positive DM diagnosed between 2017 and 2020 from two centres in India were prospectively followed up. The clinical and serological characteristics at baseline and the treatment outcome at follow-up were assessed for this study. Anti-MDA5 antibody was positive in 25 (7.5%) out of the 330 individuals with myositis. These 25 (21 adults, 4 juvenile) patients were followed up for a median duration of 14 months. Among adults, a majority had cutaneous manifestations 21 (84%) followed by, arthritis 17 (80%), and interstitial lung disease 12 (ILD, 57.1%). Four (19%) had rapidly progressive ILD (RP-ILD). Eight (38%) presented as clinically amyopathic DM. Among cutaneous manifestations, majority (62%) had classic features (gottron's papules/sign, heliotrope rash) while 8 (38%) had cutaneous ulceration and 2 each had periorbital edema and tendon rupture. Eight (38%) were positive for anti-Ro-52 antibody. Out of 21 adults, 8 (38%) succumbed to the diseases. RP-ILD (n = 4; 19%), ulcerative gottron's (n = 5) and anti-Ro-52 (n = 8) were significantly associated with mortality (p < 0.05). Upon binary logistic regression, positive anti-Ro-52 antibody predicted mortality [HR 17.3 (95%CI 1.4-210, p = 0.025)]. All juvenile anti-MDA5-positive DMs had classic cutaneous features with 2 of them having ulcerative gottron's. None of the juvenile patients had ILD and everyone survived till the last follow-up. Indian adults with anti-MDA5 DM have high mortality. Rarer atypical features like tendon rupture or periorbital edema could assist in diagnosis. Ulcerative gottron's, positive anti-Ro 52 antibodies, and RP-ILD are valuable clinical-serological markers that portend poor prognosis.
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13
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Kausthubham N, Shukla A, Gupta N, Bhavani GS, Kulshrestha S, Das Bhowmik A, Moirangthem A, Bijarnia-Mahay S, Kabra M, Puri RD, Mandal K, Verma IC, Bielas SL, Phadke SR, Dalal A, Girisha KM. A data set of variants derived from 1455 clinical and research exomes is efficient in variant prioritization for early-onset monogenic disorders in Indians. Hum Mutat 2021; 42:e15-e61. [PMID: 33502066 PMCID: PMC10052794 DOI: 10.1002/humu.24172] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 01/05/2021] [Accepted: 01/24/2021] [Indexed: 12/16/2022]
Abstract
Given the genomic uniqueness, a local data set is most desired for Indians, who are underrepresented in existing public databases. We hypothesize patients with rare monogenic disorders and their family members can provide a reliable source of common variants in the population. Exome sequencing (ES) data from families with rare Mendelian disorders was aggregated from five centers in India. The dataset was refined by excluding related individuals and removing the disease-causing variants (refined cohort). The efficiency of these data sets was assessed in a new set of 50 exomes against gnomAD and GenomeAsia. Our original cohort comprised 1455 individuals from 1203 families. The refined cohort had 836 unrelated individuals that retained 1,251,064 variants with 181,125 population-specific and 489,618 common variants. The allele frequencies from our cohort helped to define 97,609 rare variants in gnomAD and 44,520 rare variants in GenomeAsia as common variants in our population. Our variant dataset provided an additional 1.7% and 0.1% efficiency for prioritizing heterozygous and homozygous variants respectively for rare monogenic disorders. We observed additional 19 genes/human knockouts. We list carrier frequency for 142 recessive disorders. This is a large and useful resource of exonic variants for Indians. Despite limitations, datasets from patients are efficient tools for variant prioritization in a resource-limited setting.
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Affiliation(s)
- Neethukrishna Kausthubham
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Anju Shukla
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Neerja Gupta
- Division of Genetics, Department of Pediatrics, All India Institute of Medical Sciences, New Delhi, India
| | - Gandham S Bhavani
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Samarth Kulshrestha
- Institute of Medical Genetics and Genomics, Sir Ganga Ram Hospital, New Delhi, India
| | - Aneek Das Bhowmik
- Division of Diagnostics, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India.,ASPIRE (Diagnostics Facility), CSIR-Centre for Cellular & Molecular Biology, CCMB Annexe II, Hyderabad, India
| | - Amita Moirangthem
- Department of Medical Genetics, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow, India
| | - Sunita Bijarnia-Mahay
- Institute of Medical Genetics and Genomics, Sir Ganga Ram Hospital, New Delhi, India
| | - Madhulika Kabra
- Division of Genetics, Department of Pediatrics, All India Institute of Medical Sciences, New Delhi, India
| | - Ratna D Puri
- Institute of Medical Genetics and Genomics, Sir Ganga Ram Hospital, New Delhi, India
| | - Kausik Mandal
- Department of Medical Genetics, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow, India
| | - Ishwar C Verma
- Institute of Medical Genetics and Genomics, Sir Ganga Ram Hospital, New Delhi, India
| | - Stephanie L Bielas
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Shubha R Phadke
- Department of Medical Genetics, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow, India
| | - Ashwin Dalal
- Division of Diagnostics, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India
| | - Katta M Girisha
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
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14
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Srivastava A, Pandey RK, Singh PP, Kumar P, Rasalkar AA, Tamang R, van Driem G, Shrivastava P, Chaubey G. Most frequent South Asian haplotypes of ACE2 share identity by descent with East Eurasian populations. PLoS One 2020; 15:e0238255. [PMID: 32936832 PMCID: PMC7494073 DOI: 10.1371/journal.pone.0238255] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Accepted: 08/12/2020] [Indexed: 12/31/2022] Open
Abstract
It was shown that the human Angiotensin-converting enzyme 2 (ACE2) is the receptor of recent coronavirus SARS-CoV-2, and variation in this gene may affect the susceptibility of a population. Therefore, we have analysed the sequence data of ACE2 among 393 samples worldwide, focusing on South Asia. Genetically, South Asians are more related to West Eurasian populations rather than to East Eurasians. In the present analyses of ACE2, we observed that the majority of South Asian haplotypes are closer to East Eurasians rather than to West Eurasians. The phylogenetic analysis suggested that the South Asian haplotypes shared with East Eurasians involved two unique event polymorphisms (rs4646120 and rs2285666). In contrast with the European/American populations, both of the SNPs have largely similar frequencies for East Eurasians and South Asians, Therefore, it is likely that among the South Asians, host susceptibility to the novel coronavirus SARS-CoV-2 will be more similar to that of East Eurasians rather than to that of Europeans.
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Affiliation(s)
- Anshika Srivastava
- Department of Zoology, Cytogenetics Laboratory, Banaras Hindu University, Varanasi, India
| | - Rudra Kumar Pandey
- Department of Zoology, Cytogenetics Laboratory, Banaras Hindu University, Varanasi, India
| | - Prajjval Pratap Singh
- Department of Zoology, Cytogenetics Laboratory, Banaras Hindu University, Varanasi, India
| | - Pramod Kumar
- National Centre for Disease Control, Delhi, India
| | | | - Rakesh Tamang
- Department of Zoology, University of Calcutta, Kolkata, India
| | - George van Driem
- Institut für Sprachwissenschaft, Universität Bern, Bern, Switzerland
| | - Pankaj Shrivastava
- Department of Home (Police), DNA Fingerprinting Unit, State Forensic Science Laboratory, Government of MP, Sagar, India
| | - Gyaneshwer Chaubey
- Department of Zoology, Cytogenetics Laboratory, Banaras Hindu University, Varanasi, India
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15
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Tätte K, Pagani L, Pathak AK, Kõks S, Ho Duy B, Ho XD, Sultana GNN, Sharif MI, Asaduzzaman M, Behar DM, Hadid Y, Villems R, Chaubey G, Kivisild T, Metspalu M. The genetic legacy of continental scale admixture in Indian Austroasiatic speakers. Sci Rep 2019; 9:3818. [PMID: 30846778 PMCID: PMC6405872 DOI: 10.1038/s41598-019-40399-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Accepted: 02/13/2019] [Indexed: 11/21/2022] Open
Abstract
Surrounded by speakers of Indo-European, Dravidian and Tibeto-Burman languages, around 11 million Munda (a branch of Austroasiatic language family) speakers live in the densely populated and genetically diverse South Asia. Their genetic makeup holds components characteristic of South Asians as well as Southeast Asians. The admixture time between these components has been previously estimated on the basis of archaeology, linguistics and uniparental markers. Using genome-wide genotype data of 102 Munda speakers and contextual data from South and Southeast Asia, we retrieved admixture dates between 2000–3800 years ago for different populations of Munda. The best modern proxies for the source populations for the admixture with proportions 0.29/0.71 are Lao people from Laos and Dravidian speakers from Kerala in India. The South Asian population(s), with whom the incoming Southeast Asians intermixed, had a smaller proportion of West Eurasian genetic component than contemporary proxies. Somewhat surprisingly Malaysian Peninsular tribes rather than the geographically closer Austroasiatic languages speakers like Vietnamese and Cambodians show highest sharing of IBD segments with the Munda. In addition, we affirmed that the grouping of the Munda speakers into North and South Munda based on linguistics is in concordance with genome-wide data.
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Affiliation(s)
- Kai Tätte
- Department of Evolutionary Biology, Institute of Cell and Molecular Biology, University of Tartu, Tartu, 51010, Estonia. .,Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu, 51010, Estonia.
| | - Luca Pagani
- Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu, 51010, Estonia.,APE Lab, Department of Biology, University of Padova, Padova, 35121, Italy
| | - Ajai K Pathak
- Department of Evolutionary Biology, Institute of Cell and Molecular Biology, University of Tartu, Tartu, 51010, Estonia.,Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu, 51010, Estonia
| | - Sulev Kõks
- Centre for Comparative Genomics, Murdoch University, Murdoch, 6150, Australia.,The Perron Institute for Neurological and Translational Science, Sarich Neuroscience Research Institute, Nedlands, 6009, Australia
| | - Binh Ho Duy
- Department of Orthopedic and Traumatology, Hue University of Medicine and Pharmacy, Hue University, 06 Ngo Quyen street, Vinh Ninh ward, Hue, Vietnam
| | - Xuan Dung Ho
- Department of Oncology, Hue University of Medicine and Pharmacy, Hue University, 06 Ngo Quyen street, Vinh Ninh ward, Hue, Vietnam
| | - Gazi Nurun Nahar Sultana
- Centre for Advanced Research in Sciences (CARS), DNA Sequencing Research Laboratory, University of Dhaka, Dhaka, 1000, Bangladesh
| | - Mohd Istiaq Sharif
- Centre for Advanced Research in Sciences (CARS), DNA Sequencing Research Laboratory, University of Dhaka, Dhaka, 1000, Bangladesh
| | - Md Asaduzzaman
- Centre for Advanced Research in Sciences (CARS), DNA Sequencing Research Laboratory, University of Dhaka, Dhaka, 1000, Bangladesh
| | - Doron M Behar
- Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu, 51010, Estonia
| | - Yarin Hadid
- The Genomic Laboratory, The Simon Winter Institute for Human Genetics, The Bnai-Zion Medical Center, 7 Golomb St., Haifa, 31048, Israel
| | - Richard Villems
- Department of Evolutionary Biology, Institute of Cell and Molecular Biology, University of Tartu, Tartu, 51010, Estonia.,Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu, 51010, Estonia
| | - Gyaneshwer Chaubey
- Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu, 51010, Estonia.,Cytogenetics laboratory, Department of Zoology, Banaras Hindu University, Varanasi, 221005, India
| | - Toomas Kivisild
- Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu, 51010, Estonia.,Department of Human Genetics, Katholieke Universiteit Leuven, Leuven, 3000, Belgium
| | - Mait Metspalu
- Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu, 51010, Estonia.
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16
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Kumari S, Sharma N, Mishra J, Saraswathy KN, Sagar SK, Mondal PR. General obesity and Cardiovascular diseases among Gaur Brahmin population of NCR/Delhi. Diabetes Metab Syndr 2019; 13:1335-1339. [PMID: 31336488 DOI: 10.1016/j.dsx.2019.02.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Accepted: 02/04/2019] [Indexed: 10/27/2022]
Abstract
AIMS Cardiovascular diseases are one of the leading causes of mortality and morbidity among human beings. The presence of endemic Cardiovascular diseases and their risk factors differ from population to population. The Cardiovascular diseases associated risk factors are sub-categorised into two forms, one is traditional and the other is non-traditional risk factors. The present study shows the prevalence of both risk factors and its association with Cardiovascular diseases, especially with reference to general obesity. MATERIALS AND METHODS The present study includes a total of 506 Gaur Brahmins residing in Delhi and National Capital Region India. Household survey was conducted and data were collected by using pre-tested interview schedule. Somatometric measurements were taken following the international standard techniques. Approx 5 ml blood was collected from each individual unrelated up to the first cousion. The serum was used to analyse the lipid profiles and fasting glucose level. All necessary statistical analyses were performed using the Statistical Package for Social Sciences (SPSS) and MS Excel. The ethical clearance was obtained from the Ethical Committee of the Department of Anthropology, University of Delhi, Delhi. RESULTS AND CONCLUSION The mean value of Somatometric variables such as Body Mass Index, Waist circumference and Waist-hip ratio and physiological variables DBP and SBP (diastolic blood pressure and systolic blood pressure) were found to be higher than their respective ranges in the studied population. General obesity, though found to be less common in this population as compared to abdominal obesity, but it is found to be contributing to dyslipidemia.
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Affiliation(s)
- Shobha Kumari
- Laboratory of Biochemical and Molecular Anthropology, Department of Anthropology, University of Delhi, Delhi, India
| | - Nidhi Sharma
- Laboratory of Biochemical and Molecular Anthropology, Department of Anthropology, University of Delhi, Delhi, India
| | - Jyoti Mishra
- Laboratory of Biochemical and Molecular Anthropology, Department of Anthropology, University of Delhi, Delhi, India
| | - K N Saraswathy
- Laboratory of Biochemical and Molecular Anthropology, Department of Anthropology, University of Delhi, Delhi, India
| | - S K Sagar
- Laboratory of Biochemical and Molecular Anthropology, Department of Anthropology, University of Delhi, Delhi, India
| | - P R Mondal
- Laboratory of Biochemical and Molecular Anthropology, Department of Anthropology, University of Delhi, Delhi, India.
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17
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Mylavarapu S, Kumar H, Kumari S, Sravanthi LS, Jain M, Basu A, Biswas M, Mylavarapu SVS, Das A, Roy M. Activation of Epithelial-Mesenchymal Transition and Altered β-Catenin Signaling in a Novel Indian Colorectal Carcinoma Cell Line. Front Oncol 2019; 9:54. [PMID: 30828563 PMCID: PMC6385509 DOI: 10.3389/fonc.2019.00054] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Accepted: 01/18/2019] [Indexed: 12/18/2022] Open
Abstract
Colorectal cancer is the third major cause of cancer-related mortality worldwide. The upward trend in incidence and mortality rates, poor sensitivity to conventional therapies and a dearth of early diagnostic parameters pose a huge challenge in the management of colorectal cancer in India. Due to the high level of genetic diversity present in the Indian population, unraveling the genetic contributions toward pathogenesis is key for understanding the etiology of colorectal cancer and in reversing this trend. We have established a novel cell line, MBC02, from an Indian colorectal cancer patient and have carried out extensive molecular characterization to unravel the pathological alterations in this cell line. In-depth molecular analysis of MBC02 revealed suppression of E-cadherin expression, concomitant with overexpression of EMT related molecules, which manifested in the form of highly migratory and invasive cells. Loss of membrane-tethered E-cadherin released β-catenin from the adherens junction resulting in its cytoplasmic and nuclear accumulation and consequently, upregulation of c-Myc. MBC02 also showed dramatic transcriptional upregulation of β-catenin. Remarkably, we observed significantly elevated proteasome activity that perhaps co-evolved to compensate for the unnaturally high mRNA level of β-catenin to regulate the increased protein load. In addition, there was substantial misregulation of other clinically relevant signaling pathways that have clinical relevance in the pathogenesis of colorectal cancer. Our findings pave the way toward understanding the molecular differences that could define pathogenesis in cancers originating in the Indian population.
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Affiliation(s)
- Sanghamitra Mylavarapu
- Invictus Oncology Pvt. Ltd., New Delhi, India.,Department of Biotechnology, Delhi Technological University, New Delhi, India
| | - Harsh Kumar
- Regional Centre for Biotechnology, Faridabad, India.,School of Life Sciences, Manipal Academy of Higher Education, Manipal, India
| | | | | | - Misti Jain
- Division of Cancer Biology, MITRARxDx India Pvt. Ltd., Bangalore, India
| | - Aninda Basu
- Division of Cancer Biology, MITRARxDx India Pvt. Ltd., Bangalore, India
| | - Manjusha Biswas
- Department of Molecular Pathology, MITRARxDx India Pvt. Ltd., Bangalore, India
| | - Sivaram V S Mylavarapu
- Regional Centre for Biotechnology, Faridabad, India.,School of Life Sciences, Manipal Academy of Higher Education, Manipal, India
| | - Asmita Das
- Department of Biotechnology, Delhi Technological University, New Delhi, India
| | - Monideepa Roy
- Invictus Oncology Pvt. Ltd., New Delhi, India.,India Innovation Research Center, New Delhi, India
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18
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Pathak AK, Kadian A, Kushniarevich A, Montinaro F, Mondal M, Ongaro L, Singh M, Kumar P, Rai N, Parik J, Metspalu E, Rootsi S, Pagani L, Kivisild T, Metspalu M, Chaubey G, Villems R. The Genetic Ancestry of Modern Indus Valley Populations from Northwest India. Am J Hum Genet 2018; 103:918-929. [PMID: 30526867 DOI: 10.1016/j.ajhg.2018.10.022] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Accepted: 10/25/2018] [Indexed: 11/26/2022] Open
Abstract
The Indus Valley has been the backdrop for several historic and prehistoric population movements between South Asia and West Eurasia. However, the genetic structure of present-day populations from Northwest India is poorly characterized. Here we report new genome-wide genotype data for 45 modern individuals from four Northwest Indian populations, including the Ror, whose long-term occupation of the region can be traced back to the early Vedic scriptures. Our results suggest that although the genetic architecture of most Northwest Indian populations fits well on the broader North-South Indian genetic cline, culturally distinct groups such as the Ror stand out by being genetically more akin to populations living west of India; such populations include prehistorical and early historical ancient individuals from the Swat Valley near the Indus Valley. We argue that this affinity is more likely a result of genetic continuity since the Bronze Age migrations from the Steppe Belt than a result of recent admixture. The observed patterns of genetic relationships both with modern and ancient West Eurasians suggest that the Ror can be used as a proxy for a population descended from the Ancestral North Indian (ANI) population. Collectively, our results show that the Indus Valley populations are characterized by considerable genetic heterogeneity that has persisted over thousands of years.
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19
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Metspalu M, Mondal M, Chaubey G. The genetic makings of South Asia. Curr Opin Genet Dev 2018; 53:128-133. [PMID: 30286387 DOI: 10.1016/j.gde.2018.09.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Accepted: 09/13/2018] [Indexed: 11/17/2022]
Abstract
South Asia is home for more than a billion people culturally structured into innumerable groups practicing different levels of endogamy. Linguistically South Asia is broadly characterized by four major language families which has served as access way for disentangling the genetic makings of South Asia. In this review we shall give brief account on the recent developments in the field. Advances are made in two fronts simultaneously. Whole genome characterisation of many extant South Asians paint the picture of the genetic diversity and its implications to health-care. On the other hand ancient DNA studies, which are finally reaching South Asia, provide new incites to the demographic history of the subcontinent. Before the spread of agriculture, South Asia was likely inhabited by hunter-gatherer groups deriving much of their ancestry from a population that split from the rest of humanity soon after expanding from Africa. Early Iranian agriculturalists mixing with these local hunter-gatherers probably formed the population that flourished during the blossoming of the Indus Valley Civilisation. Further admixture with the still persisting HG groups and population(s) from the Eurasian Steppe, formed the two ancestral populations (ANI and ASI), the north-south mixing pattern of whom is known today as the 'Indian Cline'. Studies on natural selection in South Asia have so far revealed strong signals of sweeps that are shared with West Eurasians. Future studies will have to fully unlock the aDNA promise for South Asia.
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Affiliation(s)
- Mait Metspalu
- Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Mayukh Mondal
- Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Gyaneshwer Chaubey
- Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu, Estonia; Cytogenetics Laboratory, Department of Zoology, Banaras Hindu University, Varanasi, India
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20
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Cabrera VM, Marrero P, Abu-Amero KK, Larruga JM. Carriers of mitochondrial DNA macrohaplogroup L3 basal lineages migrated back to Africa from Asia around 70,000 years ago. BMC Evol Biol 2018; 18:98. [PMID: 29921229 PMCID: PMC6009813 DOI: 10.1186/s12862-018-1211-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Accepted: 06/05/2018] [Indexed: 11/15/2022] Open
Abstract
Background The main unequivocal conclusion after three decades of phylogeographic mtDNA studies is the African origin of all extant modern humans. In addition, a southern coastal route has been argued for to explain the Eurasian colonization of these African pioneers. Based on the age of macrohaplogroup L3, from which all maternal Eurasian and the majority of African lineages originated, the out-of-Africa event has been dated around 60-70 kya. On the opposite side, we have proposed a northern route through Central Asia across the Levant for that expansion and, consistent with the fossil record, we have dated it around 125 kya. To help bridge differences between the molecular and fossil record ages, in this article we assess the possibility that mtDNA macrohaplogroup L3 matured in Eurasia and returned to Africa as basal L3 lineages around 70 kya. Results The coalescence ages of all Eurasian (M,N) and African (L3 ) lineages, both around 71 kya, are not significantly different. The oldest M and N Eurasian clades are found in southeastern Asia instead near of Africa as expected by the southern route hypothesis. The split of the Y-chromosome composite DE haplogroup is very similar to the age of mtDNA L3. An Eurasian origin and back migration to Africa has been proposed for the African Y-chromosome haplogroup E. Inside Africa, frequency distributions of maternal L3 and paternal E lineages are positively correlated. This correlation is not fully explained by geographic or ethnic affinities. This correlation rather seems to be the result of a joint and global replacement of the old autochthonous male and female African lineages by the new Eurasian incomers. Conclusions These results are congruent with a model proposing an out-of-Africa migration into Asia, following a northern route, of early anatomically modern humans carrying pre-L3 mtDNA lineages around 125 kya, subsequent diversification of pre-L3 into the basal lineages of L3, a return to Africa of Eurasian fully modern humans around 70 kya carrying the basal L3 lineages and the subsequent diversification of Eurasian-remaining L3 lineages into the M and N lineages in the outside-of-Africa context, and a second Eurasian global expansion by 60 kya, most probably, out of southeast Asia. Climatic conditions and the presence of Neanderthals and other hominins might have played significant roles in these human movements. Moreover, recent studies based on ancient DNA and whole-genome sequencing are also compatible with this hypothesis. Electronic supplementary material The online version of this article (10.1186/s12862-018-1211-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Vicente M Cabrera
- Departamento de Genética, Facultad de Biología, Universidad de La Laguna, E-38271 La Laguna, Tenerife, Spain.
| | - Patricia Marrero
- Research Support General Service, E-38271, La Laguna, Tenerife, Spain
| | - Khaled K Abu-Amero
- Glaucoma Research Chair, Department of Ophthalmology, College of Medicine, King Saud University, Riyadh, Saudi Arabia.,Department of Ophthalmology and Visual Sciences, University of Illinois at Chicago, Chicago, IL, USA
| | - Jose M Larruga
- Departamento de Genética, Facultad de Biología, Universidad de La Laguna, E-38271 La Laguna, Tenerife, Spain
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21
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Mahal DG, Matsoukas IG. The Geographic Origins of Ethnic Groups in the Indian Subcontinent: Exploring Ancient Footprints with Y-DNA Haplogroups. Front Genet 2018; 9:4. [PMID: 29410676 PMCID: PMC5787057 DOI: 10.3389/fgene.2018.00004] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Accepted: 01/04/2018] [Indexed: 02/05/2023] Open
Abstract
Several studies have evaluated the movements of large populations to the Indian subcontinent; however, the ancient geographic origins of smaller ethnic communities are not clear. Although historians have attempted to identify the origins of some ethnic groups, the evidence is typically anecdotal and based upon what others have written before. In this study, recent developments in DNA science were assessed to provide a contemporary perspective by analyzing the Y chromosome haplogroups of some key ethnic groups and tracing their ancient geographical origins from genetic markers on the Y-DNA haplogroup tree. A total of 2,504 Y-DNA haplotypes, representing 50 different ethnic groups in the Indian subcontinent, were analyzed. The results identified 14 different haplogroups with 14 geographic origins for these people. Moreover, every ethnic group had representation in more than one haplogroup, indicating multiple geographic origins for these communities. The results also showed that despite their varied languages and cultural differences, most ethnic groups shared some common ancestors because of admixture in the past. These findings provide new insights into the ancient geographic origins of ethnic groups in the Indian subcontinent. With about 2,000 other ethnic groups and tribes in the region, it is expected that more scientific discoveries will follow, providing insights into how, from where, and when the ancestors of these people arrived in the subcontinent to create so many different communities.
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Affiliation(s)
- David G Mahal
- School of Sport and Biomedical Sciences, University of Bolton, Bolton, United Kingdom.,Extension Division, University of California, Los Angeles, Los Angeles, CA, United States
| | - Ianis G Matsoukas
- School of Sport and Biomedical Sciences, University of Bolton, Bolton, United Kingdom
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22
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Hariprakash JM, Vellarikkal SK, Verma A, Ranawat AS, Jayarajan R, Ravi R, Kumar A, Dixit V, Sivadas A, Kashyap AK, Senthivel V, Sehgal P, Mahadevan V, Scaria V, Sivasubbu S. SAGE: a comprehensive resource of genetic variants integrating South Asian whole genomes and exomes. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2018; 2018:1-10. [PMID: 30184194 PMCID: PMC6146123 DOI: 10.1093/database/bay080] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/05/2018] [Accepted: 07/03/2018] [Indexed: 11/20/2022]
Abstract
South Asia is home to \documentclass[12pt]{minimal}
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}{}$\sim $\end{document}20% of the world population and characterized by distinct ethnic, linguistic, cultural and genetic lineages. Only limited representative samples from the region have found its place in large population-scale international genome projects. The recent availability of genome scale data from multiple populations and datasets from South Asian countries in public domain motivated us to integrate the data into a comprehensive resource. In the present study, we have integrated a total of six datasets encompassing 1213 human exomes and genomes to create a compendium of 154 814 557 genetic variants and adding a total of 69 059 255 novel variants. The variants were systematically annotated using public resources and along with the allele frequencies are available as a browsable-online resource South Asian genomes and exomes. As a proof of principle application of the data and resource for genetic epidemiology, we have analyzed the pathogenic genetic variants causing retinitis pigmentosa. Our analysis reveals the genetic landscape of the disease and suggests subset of genetic variants to be highly prevalent in South Asia.
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Affiliation(s)
- Judith Mary Hariprakash
- GN Ramachandran Knowledge Center for Genome Informatics, Council of Scientific and Industrial Research (CSIR) Institute of Genomics & Integrative Biology, Mathura Road, Delhi 110025, India
| | - Shamsudheen Karuthedath Vellarikkal
- Genomics & Molecular Medicine, Council of Scientific and Industrial Research (CSIR) Institute of Genomics & Integrative Biology, Mathura Road, Delhi 110025, India
| | - Ankit Verma
- Genomics & Molecular Medicine, Council of Scientific and Industrial Research (CSIR) Institute of Genomics & Integrative Biology, Mathura Road, Delhi 110025, India
| | - Anop Singh Ranawat
- GN Ramachandran Knowledge Center for Genome Informatics, Council of Scientific and Industrial Research (CSIR) Institute of Genomics & Integrative Biology, Mathura Road, Delhi 110025, India
| | - Rijith Jayarajan
- Genomics & Molecular Medicine, Council of Scientific and Industrial Research (CSIR) Institute of Genomics & Integrative Biology, Mathura Road, Delhi 110025, India
| | - Rowmika Ravi
- Genomics & Molecular Medicine, Council of Scientific and Industrial Research (CSIR) Institute of Genomics & Integrative Biology, Mathura Road, Delhi 110025, India
| | - Anoop Kumar
- Genomics & Molecular Medicine, Council of Scientific and Industrial Research (CSIR) Institute of Genomics & Integrative Biology, Mathura Road, Delhi 110025, India
| | - Vishal Dixit
- Genomics & Molecular Medicine, Council of Scientific and Industrial Research (CSIR) Institute of Genomics & Integrative Biology, Mathura Road, Delhi 110025, India
| | - Ambily Sivadas
- GN Ramachandran Knowledge Center for Genome Informatics, Council of Scientific and Industrial Research (CSIR) Institute of Genomics & Integrative Biology, Mathura Road, Delhi 110025, India
| | - Atul Kumar Kashyap
- Genomics & Molecular Medicine, Council of Scientific and Industrial Research (CSIR) Institute of Genomics & Integrative Biology, Mathura Road, Delhi 110025, India
| | - Vigneshwar Senthivel
- Genomics & Molecular Medicine, Council of Scientific and Industrial Research (CSIR) Institute of Genomics & Integrative Biology, Mathura Road, Delhi 110025, India
| | - Paras Sehgal
- Genomics & Molecular Medicine, Council of Scientific and Industrial Research (CSIR) Institute of Genomics & Integrative Biology, Mathura Road, Delhi 110025, India
| | - Vijayalakshmi Mahadevan
- School of Chemical & Biotechnology, Shanmugha Arts, Science, Technology and Research Academy (SASTRA) University, Thanjavur, Tamil Nadu 613402, India
| | - Vinod Scaria
- GN Ramachandran Knowledge Center for Genome Informatics, Council of Scientific and Industrial Research (CSIR) Institute of Genomics & Integrative Biology, Mathura Road, Delhi 110025, India
| | - Sridhar Sivasubbu
- Genomics & Molecular Medicine, Council of Scientific and Industrial Research (CSIR) Institute of Genomics & Integrative Biology, Mathura Road, Delhi 110025, India
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23
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Reyes-Centeno H, Rathmann H, Hanihara T, Harvati K. Testing Modern Human Out-of-Africa Dispersal Models Using Dental Nonmetric Data. CURRENT ANTHROPOLOGY 2017. [DOI: 10.1086/694423] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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24
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Carbonell-Caballero J, Amadoz A, Alonso R, Hidalgo MR, Çubuk C, Conesa D, López-Quílez A, Dopazo J. Reference genome assessment from a population scale perspective: an accurate profile of variability and noise. Bioinformatics 2017; 33:3511-3517. [PMID: 28961772 PMCID: PMC5870781 DOI: 10.1093/bioinformatics/btx482] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Revised: 07/10/2017] [Accepted: 07/28/2017] [Indexed: 11/14/2022] Open
Abstract
MOTIVATION Current plant and animal genomic studies are often based on newly assembled genomes that have not been properly consolidated. In this scenario, misassembled regions can easily lead to false-positive findings. Despite quality control scores are included within genotyping protocols, they are usually employed to evaluate individual sample quality rather than reference sequence reliability. We propose a statistical model that combines quality control scores across samples in order to detect incongruent patterns at every genomic region. Our model is inherently robust since common artifact signals are expected to be shared between independent samples over misassembled regions of the genome. RESULTS The reliability of our protocol has been extensively tested through different experiments and organisms with accurate results, improving state-of-the-art methods. Our analysis demonstrates synergistic relations between quality control scores and allelic variability estimators, that improve the detection of misassembled regions, and is able to find strong artifact signals even within the human reference assembly. Furthermore, we demonstrated how our model can be trained to properly rank the confidence of a set of candidate variants obtained from new independent samples. AVAILABILITY AND IMPLEMENTATION This tool is freely available at http://gitlab.com/carbonell/ces. CONTACT jcarbonell.cipf@gmail.com or joaquin.dopazo@juntadeandalucia.es. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
| | - Alicia Amadoz
- Computational Genomics, Principe Felipe Research Centre, Valencia
| | - Roberto Alonso
- Computational Genomics, Principe Felipe Research Centre, Valencia
| | - Marta R Hidalgo
- Computational Genomics, Principe Felipe Research Centre, Valencia
| | - Cankut Çubuk
- Computational Genomics, Principe Felipe Research Centre, Valencia
| | - David Conesa
- Estadística e investigación Operativa, Universitat de València, Burjassot
| | | | - Joaquín Dopazo
- Computational Genomics, Principe Felipe Research Centre, Valencia
- Clinical Bioinformatics Area, Fundación Progreso y Salud, Hospital Virgen del Rocio, Sevilla
- Functional Genomics Node (INB), Fundación Progreso y Salud, Hospital Virgen del Rocio, Sevilla
- Bioinformatics in Rare Diseases (BiER), Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Fundación Progreso y Salud, Hospital Virgen del Rocio, Sevilla, Spain
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25
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Mahal DG, Matsoukas IG. Y-STR Haplogroup Diversity in the Jat Population Reveals Several Different Ancient Origins. Front Genet 2017; 8:121. [PMID: 28979290 PMCID: PMC5611447 DOI: 10.3389/fgene.2017.00121] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Accepted: 08/30/2017] [Indexed: 11/19/2022] Open
Abstract
The Jats represent a large ethnic community that has inhabited the northwest region of India and Pakistan for several thousand years. It is estimated the community has a population of over 123 million people. Many historians and academics have asserted that the Jats are descendants of Aryans, Scythians, or other ancient people that arrived and lived in northern India at one time. Essentially, the specific origin of these people has remained a matter of contention for a long time. This study demonstrated that the origins of Jats can be clarified by identifying their Y-chromosome haplogroups and tracing their genetic markers on the Y-DNA haplogroup tree. A sample of 302 Y-chromosome haplotypes of Jats in India and Pakistan was analyzed. The results showed that the sample population had several different lines of ancestry and emerged from at least nine different geographical regions of the world. It also became evident that the Jats did not have a unique set of genes, but shared an underlying genetic unity with several other ethnic communities in the Indian subcontinent. A startling new assessment of the genetic ancient origins of these people was revealed with DNA science.
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Affiliation(s)
- David G Mahal
- School of Sport and Biomedical Sciences, University of BoltonBolton, United Kingdom.,Extension Division, University of California, Los AngelesLos Angeles, CA, United States
| | - Ianis G Matsoukas
- School of Sport and Biomedical Sciences, University of BoltonBolton, United Kingdom
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26
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Vyas DN, Al‐Meeri A, Mulligan CJ. Testing support for the northern and southern dispersal routes out of Africa: an analysis of Levantine and southern Arabian populations. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2017; 164:736-749. [DOI: 10.1002/ajpa.23312] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Revised: 08/28/2017] [Accepted: 08/29/2017] [Indexed: 11/10/2022]
Affiliation(s)
- Deven N. Vyas
- Department of AnthropologyUniversity of Florida, 1112 Turlington Hall, PO Box 117305Gainesville Florida 32611‐7305
- Genetics InstituteUniversity of Florida, Cancer & Genetics Research Complex, PO Box 103610Gainesville Florida 32610‐3610
| | - Ali Al‐Meeri
- Department of Clinical Biochemistry, Faculty of Medicine and Health SciencesUniversity of Sana'aSana'a Yemen
| | - Connie J. Mulligan
- Department of AnthropologyUniversity of Florida, 1112 Turlington Hall, PO Box 117305Gainesville Florida 32611‐7305
- Genetics InstituteUniversity of Florida, Cancer & Genetics Research Complex, PO Box 103610Gainesville Florida 32610‐3610
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27
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Larruga JM, Marrero P, Abu-Amero KK, Golubenko MV, Cabrera VM. Carriers of mitochondrial DNA macrohaplogroup R colonized Eurasia and Australasia from a southeast Asia core area. BMC Evol Biol 2017; 17:115. [PMID: 28535779 PMCID: PMC5442693 DOI: 10.1186/s12862-017-0964-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2017] [Accepted: 05/11/2017] [Indexed: 11/21/2022] Open
Abstract
BACKGROUND The colonization of Eurasia and Australasia by African modern humans has been explained, nearly unanimously, as the result of a quick southern coastal dispersal route through the Arabian Peninsula, the Indian subcontinent, and the Indochinese Peninsula, to reach Australia around 50 kya. The phylogeny and phylogeography of the major mitochondrial DNA Eurasian haplogroups M and N have played the main role in giving molecular genetics support to that scenario. However, using the same molecular tools, a northern route across central Asia has been invoked as an alternative that is more conciliatory with the fossil record of East Asia. Here, we assess as the Eurasian macrohaplogroup R fits in the northern path. RESULTS Haplogroup U, with a founder age around 50 kya, is one of the oldest clades of macrohaplogroup R in western Asia. The main branches of U expanded in successive waves across West, Central and South Asia before the Last Glacial Maximum. All these dispersions had rather overlapping ranges. Some of them, as those of U6 and U3, reached North Africa. At the other end of Asia, in Wallacea, another branch of macrohaplogroup R, haplogroup P, also independently expanded in the area around 52 kya, in this case as isolated bursts geographically well structured, with autochthonous branches in Australia, New Guinea, and the Philippines. CONCLUSIONS Coeval independently dispersals around 50 kya of the West Asia haplogroup U and the Wallacea haplogroup P, points to a halfway core area in southeast Asia as the most probable centre of expansion of macrohaplogroup R, what fits in the phylogeographic pattern of its ancestor, macrohaplogroup N, for which a northern route and a southeast Asian origin has been already proposed.
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Affiliation(s)
- Jose M Larruga
- Departamento de Genética, Facultad de Biología, Universidad de La Laguna, E-38271 La Laguna, Tenerife, Spain
| | - Patricia Marrero
- Research Support General Service, Universidad de La Laguna, E-38271 La Laguna, Tenerife, Spain
| | - Khaled K Abu-Amero
- Glaucoma Research Chair, Department of Ophthalmology, College of Medicine, King Saud University, Riyadh, Saudi Arabia
| | | | - Vicente M Cabrera
- Departamento de Genética, Facultad de Biología, Universidad de La Laguna, E-38271 La Laguna, Tenerife, Spain.
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28
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Rustagi N, Zhou A, Watkins WS, Gedvilaite E, Wang S, Ramesh N, Muzny D, Gibbs RA, Jorde LB, Yu F, Xing J. Extremely low-coverage whole genome sequencing in South Asians captures population genomics information. BMC Genomics 2017; 18:396. [PMID: 28532386 PMCID: PMC5440948 DOI: 10.1186/s12864-017-3767-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2016] [Accepted: 05/07/2017] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND The cost of Whole Genome Sequencing (WGS) has decreased tremendously in recent years due to advances in next-generation sequencing technologies. Nevertheless, the cost of carrying out large-scale cohort studies using WGS is still daunting. Past simulation studies with coverage at ~2x have shown promise for using low coverage WGS in studies focused on variant discovery, association study replications, and population genomics characterization. However, the performance of low coverage WGS in populations with a complex history and no reference panel remains to be determined. RESULTS South Indian populations are known to have a complex population structure and are an example of a major population group that lacks adequate reference panels. To test the performance of extremely low-coverage WGS (EXL-WGS) in populations with a complex history and to provide a reference resource for South Indian populations, we performed EXL-WGS on 185 South Indian individuals from eight populations to ~1.6x coverage. Using two variant discovery pipelines, SNPTools and GATK, we generated a consensus call set that has ~90% sensitivity for identifying common variants (minor allele frequency ≥ 10%). Imputation further improves the sensitivity of our call set. In addition, we obtained high-coverage for the whole mitochondrial genome to infer the maternal lineage evolutionary history of the Indian samples. CONCLUSIONS Overall, we demonstrate that EXL-WGS with imputation can be a valuable study design for variant discovery with a dramatically lower cost than standard WGS, even in populations with a complex history and without available reference data. In addition, the South Indian EXL-WGS data generated in this study will provide a valuable resource for future Indian genomic studies.
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Affiliation(s)
- Navin Rustagi
- Department of Molecular and Human Genetics, Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030 USA
| | - Anbo Zhou
- Department of Genetics, Human Genetics Institute of New Jersey, Rutgers, The State University of New Jersey, Piscataway, NJ 08854 USA
| | - W. Scott Watkins
- Department of Human Genetics, Eccles Institute of Human Genetics, University of Utah, Salt Lake City, UT 84112 USA
| | - Erika Gedvilaite
- Department of Genetics, Human Genetics Institute of New Jersey, Rutgers, The State University of New Jersey, Piscataway, NJ 08854 USA
| | - Shuoguo Wang
- Department of Genetics, Human Genetics Institute of New Jersey, Rutgers, The State University of New Jersey, Piscataway, NJ 08854 USA
| | - Naveen Ramesh
- Department of Molecular and Human Genetics, Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030 USA
| | - Donna Muzny
- Department of Molecular and Human Genetics, Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030 USA
| | - Richard A. Gibbs
- Department of Molecular and Human Genetics, Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030 USA
| | - Lynn B. Jorde
- Department of Human Genetics, Eccles Institute of Human Genetics, University of Utah, Salt Lake City, UT 84112 USA
| | - Fuli Yu
- Department of Molecular and Human Genetics, Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030 USA
| | - Jinchuan Xing
- Department of Genetics, Human Genetics Institute of New Jersey, Rutgers, The State University of New Jersey, Piscataway, NJ 08854 USA
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29
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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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30
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Chronic pancreatitis in Eastern India: Experience from a tertiary care center. Indian J Gastroenterol 2017; 36:131-136. [PMID: 28271470 DOI: 10.1007/s12664-017-0733-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/24/2016] [Accepted: 02/02/2017] [Indexed: 02/04/2023]
Abstract
There is a wide variation in the clinical presentation of chronic pancreatitis (CP) in the different parts of India. Data regarding the clinical profile of CP from eastern India are scarce. We describe the clinical and demographic profiles of patients with CP in eastern India. Consecutive patients were evaluated for the clinical presentation, etiology and complication of CP. One hundred and thirty-nine patients with CP (mean age 39.57±14.88 years; M/F 3.48:1) were included. Idiopathic CP (50.35%) was the most common etiology followed by alcohol (33.81%); 68.34% had calcific CP and 31.65% had noncalcific CP. The median duration of symptoms was 24 (1-240) months. Pain was the most common symptom, being present in 93.52% of the patients. Diabetes, steatorrhea and pseudocyst were present in 45.32%, 14.38% and 7.19% of the cases, respectively. Moderate to severe anemia was revealed in 16.53% of the patients. Benign biliary stricture was diagnosed in 19.42% of the cases (symptomatic in 6.47%). The common radiological findings were the following: pancreatic calculi (68.34%), dilated pancreatic duct (PD) (58.99%), parenchymal atrophy (25.89%) and PD stricture (23.74%). In our center, idiopathic CP followed by alcoholic CP was the most frequent form of CP. Tropical CP was distinctly uncommon.
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Liu X, Lu D, Saw WY, Shaw PJ, Wangkumhang P, Ngamphiw C, Fucharoen S, Lert-Itthiporn W, Chin-Inmanu K, Chau TNB, Anders K, Kasturiratne A, de Silva HJ, Katsuya T, Kimura R, Nabika T, Ohkubo T, Tabara Y, Takeuchi F, Yamamoto K, Yokota M, Mamatyusupu D, Yang W, Chung YJ, Jin L, Hoh BP, Wickremasinghe AR, Ong RH, Khor CC, Dunstan SJ, Simmons C, Tongsima S, Suriyaphol P, Kato N, Xu S, Teo YY. Characterising private and shared signatures of positive selection in 37 Asian populations. Eur J Hum Genet 2017; 25:499-508. [PMID: 28098149 DOI: 10.1038/ejhg.2016.181] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Revised: 10/22/2016] [Accepted: 11/01/2016] [Indexed: 11/09/2022] Open
Abstract
The Asian Diversity Project (ADP) assembled 37 cosmopolitan and ethnic minority populations in Asia that have been densely genotyped across over half a million markers to study patterns of genetic diversity and positive natural selection. We performed population structure analyses of the ADP populations and divided these populations into four major groups based on their genographic information. By applying a highly sensitive algorithm haploPS to locate genomic signatures of positive selection, 140 distinct genomic regions exhibiting evidence of positive selection in at least one population were identified. We examined the extent of signal sharing for regions that were selected in multiple populations and observed that populations clustered in a similar fashion to that of how the ancestry clades were phylogenetically defined. In particular, populations predominantly located in South Asia underwent considerably different adaptation as compared with populations from the other geographical regions. Signatures of positive selection present in multiple geographical regions were predicted to be older and have emerged prior to the separation of the populations in the different regions. In contrast, selection signals present in a single population group tended to be of lower frequencies and thus can be attributed to recent evolutionary events.
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Affiliation(s)
- Xuanyao Liu
- NUS Graduate School for Integrative Science and Engineering, National University of Singapore, Singapore, Singapore.,Saw Swee Hock School of Public Health, National University of Singapore, Singapore, Singapore
| | - Dongsheng Lu
- Max Planck Independent Research Group on Population Genomics, Chinese Academy of Sciences and Max Planck Society Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Woei-Yuh Saw
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore, Singapore.,Life Sciences Institute, National University of Singapore, Singapore, Singapore
| | - Philip J Shaw
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathum Thani, Thailand
| | - Pongsakorn Wangkumhang
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathum Thani, Thailand
| | - Chumpol Ngamphiw
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathum Thani, Thailand
| | - Suthat Fucharoen
- Institute of Molecular Biosciences, Mahidol University, Nakhon Pathom, Thailand
| | - Worachart Lert-Itthiporn
- Faculty of Science, Molecular Medicine Graduate Programme, Mahidol University, Bangkok, Thailand.,Division of Bioinformatics and Data Management for Research, Department of Research and Development, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Kwanrutai Chin-Inmanu
- Division of Bioinformatics and Data Management for Research, Department of Research and Development, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Tran Nguyen Bich Chau
- Oxford University Clinical Research Unit, Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam
| | - Katie Anders
- Oxford University Clinical Research Unit, Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam.,Nuffield Department of Clinical Medicine, Centre for Tropical Medicine, University of Oxford, Oxford, UK
| | | | - H Janaka de Silva
- Department of Medicine, Faculty of Medicine, University of Kelaniya, Ragama, Sri Lanka
| | - Tomohiro Katsuya
- Department of Clinical Gene Therapy, Osaka University Graduate School of Medicine, Suita, Japan
| | - Ryosuke Kimura
- Department of Human Biology and Anatomy, Graduate School of Medicine, University of the Ryukyus, Nishihara-cho, Japan
| | - Toru Nabika
- Department of Functional Pathology, Shimane University School of Medicine, Izumo, Japan
| | - Takayoshi Ohkubo
- Department of Hygiene and Public Health, Teikyo University School of Medicine, Tokyo, Japan
| | - Yasuharu Tabara
- Center for Genomic Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Fumihiko Takeuchi
- Department of Gene Diagnostics and Therapeutics, National Center for Global Health and Medicine, Tokyo, Japan
| | - Ken Yamamoto
- Department of Medical Chemistry, Kurume University School of Medicine, Kurume, Japan
| | - Mitsuhiro Yokota
- Department of Genome Science, School of Dentistry, Aichi Gakuin University, Nagoya, Japan
| | - Dolikun Mamatyusupu
- College of the Life Sciences and Technology, Xinjiang University, Urumqi, China
| | - Wenjun Yang
- Key Laboratory of Reproduction and Heredity of Ningxia Region, Ningxia Medical University, YinchuanChina
| | - Yeun-Jun Chung
- Department of Microbiology, Integrated Research Center for Genome Polymorphism, The Catholic University Medical College, Seoul, Korea
| | - Li Jin
- State Key Laboratory of Genetic Engineering and Ministry of Education (MOE), Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, China
| | - Boon-Peng Hoh
- Faculty of Medicine and Health Sciences, UCSI University, Kuala Lumpur, Malaysia
| | | | - RickTwee-Hee Ong
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore, Singapore
| | - Chiea-Chuen Khor
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, Singapore
| | - Sarah J Dunstan
- Oxford University Clinical Research Unit, Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam.,Nuffield Department of Clinical Medicine, Centre for Tropical Medicine, University of Oxford, Oxford, UK.,The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria, Australia
| | - Cameron Simmons
- Oxford University Clinical Research Unit, Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam.,Nuffield Department of Clinical Medicine, Centre for Tropical Medicine, University of Oxford, Oxford, UK.,Department of Microbiology and Immunology, The University of Melbourne, Melbourne, Victoria, Australia
| | - Sissades Tongsima
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathum Thani, Thailand
| | - Prapat Suriyaphol
- Division of Bioinformatics and Data Management for Research, Department of Research and Development, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand.,Institute of Personalized Genomics and Gene Therapy (IPGG), Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Norihiro Kato
- Department of Gene Diagnostics and Therapeutics, National Center for Global Health and Medicine, Tokyo, Japan
| | - Shuhua Xu
- Max Planck Independent Research Group on Population Genomics, Chinese Academy of Sciences and Max Planck Society Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China.,School of Life Sciences and Technology, ShanghaiTech University, Shanghai, China.,Collaborative Innovation Center of Genetics and Development, Shanghai, China
| | - Yik-Ying Teo
- NUS Graduate School for Integrative Science and Engineering, National University of Singapore, Singapore, Singapore.,Saw Swee Hock School of Public Health, National University of Singapore, Singapore, Singapore.,Life Sciences Institute, National University of Singapore, Singapore, Singapore.,Department of Gene Diagnostics and Therapeutics, National Center for Global Health and Medicine, Tokyo, Japan.,Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, Singapore.,Department of Statistics and Applied Probability, National University of Singapore, Singapore, Singapore
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Bhute S, Pande P, Shetty SA, Shelar R, Mane S, Kumbhare SV, Gawali A, Makhani H, Navandar M, Dhotre D, Lubree H, Agarwal D, Patil R, Ozarkar S, Ghaskadbi S, Yajnik C, Juvekar S, Makharia GK, Shouche YS. Molecular Characterization and Meta-Analysis of Gut Microbial Communities Illustrate Enrichment of Prevotella and Megasphaera in Indian Subjects. Front Microbiol 2016; 7:660. [PMID: 27242691 PMCID: PMC4860526 DOI: 10.3389/fmicb.2016.00660] [Citation(s) in RCA: 82] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2015] [Accepted: 04/21/2016] [Indexed: 12/30/2022] Open
Abstract
The gut microbiome has varied impact on the wellbeing of humans. It is influenced by different factors such as age, dietary habits, socio-economic status, geographic location, and genetic makeup of individuals. For devising microbiome-based therapies, it is crucial to identify population specific features of the gut microbiome. Indian population is one of the most ethnically, culturally, and geographically diverse, but the gut microbiome features remain largely unknown. The present study describes gut microbial communities of healthy Indian subjects and compares it with the microbiota from other populations. Based on large differences in alpha diversity indices, abundance of 11 bacterial phyla and individual specific OTUs, we report inter-individual variations in gut microbial communities of these subjects. While the gut microbiome of Indians is different from that of Americans, it shared high similarity to individuals from the Indian subcontinent i.e., Bangladeshi. Distinctive feature of Indian gut microbiota is the predominance of genus Prevotella and Megasphaera. Further, when compared with other non-human primates, it appears that Indians share more OTUs with omnivorous mammals. Our metagenomic imputation indicates higher potential for glycan biosynthesis and xenobiotic metabolism in these subjects. Our study indicates urgent need of identification of population specific microbiome biomarkers of Indian subpopulations to have more holistic view of the Indian gut microbiome and its health implications.
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Affiliation(s)
- Shrikant Bhute
- Department of Zoology, Savitribai Phule Pune University Pune, India
| | - Pranav Pande
- Microbial Culture Collection, National Centre for Cell Sciences, Savitribai Phule Pune University campus Pune, India
| | - Sudarshan A Shetty
- Microbial Culture Collection, National Centre for Cell Sciences, Savitribai Phule Pune University campus Pune, India
| | - Rahul Shelar
- Microbial Culture Collection, National Centre for Cell Sciences, Savitribai Phule Pune University campus Pune, India
| | - Sachin Mane
- Microbial Culture Collection, National Centre for Cell Sciences, Savitribai Phule Pune University campus Pune, India
| | - Shreyas V Kumbhare
- Microbial Culture Collection, National Centre for Cell Sciences, Savitribai Phule Pune University campus Pune, India
| | - Ashwini Gawali
- Microbial Culture Collection, National Centre for Cell Sciences, Savitribai Phule Pune University campus Pune, India
| | - Hemal Makhani
- Microbial Culture Collection, National Centre for Cell Sciences, Savitribai Phule Pune University campus Pune, India
| | - Mohit Navandar
- Microbial Culture Collection, National Centre for Cell Sciences, Savitribai Phule Pune University campus Pune, India
| | - Dhiraj Dhotre
- Microbial Culture Collection, National Centre for Cell Sciences, Savitribai Phule Pune University campus Pune, India
| | | | - Dhiraj Agarwal
- Vadu Rural Health Program, KEM Hospital Research Centre Pune, India
| | - Rutuja Patil
- Vadu Rural Health Program, KEM Hospital Research Centre Pune, India
| | - Shantanu Ozarkar
- Department of Anthropology, Savitribai Phule Pune University Pune, India
| | - Saroj Ghaskadbi
- Department of Zoology, Savitribai Phule Pune University Pune, India
| | | | - Sanjay Juvekar
- Vadu Rural Health Program, KEM Hospital Research Centre Pune, India
| | - Govind K Makharia
- Department of Gastroenterology and Human Nutrition, All India Institute of Medical Sciences New Delhi, India
| | - Yogesh S Shouche
- Microbial Culture Collection, National Centre for Cell Sciences, Savitribai Phule Pune University campus Pune, India
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Maddaloni E, D'Onofrio L, Pozzilli P. Frailty and geography: should these two factors be added to the ABCDE contemporary guide to diabetes therapy? Diabetes Metab Res Rev 2016; 32:169-75. [PMID: 26484614 DOI: 10.1002/dmrr.2762] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/14/2015] [Revised: 09/13/2015] [Accepted: 10/09/2015] [Indexed: 12/19/2022]
Abstract
On the road towards personalized treatments for type 2 diabetes, we suggest here that two parameters could be added to the ABCDE algorithm, 'F' for frailty and 'G' for geography. Indeed, the progressive ageing of population is causing a simultaneous increase of frailty worldwide. The identification of the optimal therapeutic approach is often difficult in frail subjects because of the complexity of 'frailty syndrome'. Nevertheless, given the relevance of diabetes in the development and progression of frailty, a safe and effective cure of diabetes is extremely important to guarantee a good medical outcome. There are few data about diabetes treatment in this delicate category of patients, and the choice of the appropriate therapy mostly remains a challenge. Moreover, type 2 diabetes affects more than 382 million people of different countries, races and ethnicities. To face the lack of solid evidence-based medicine for the treatment of diabetes in different ethnic groups, it is extremely important to increase knowledge about the different pathophysiology of diabetes according to ethnicity. In this way, a tailored approach to treatment of various ethnic groups living in the same or different regions can eventually be developed. Copyright © 2016 John Wiley & Sons, Ltd.
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Affiliation(s)
- Ernesto Maddaloni
- Unit of Endocrinology and Diabetes, Department of Medicine, Università Campus Bio-Medico di Roma, Italy
| | - Luca D'Onofrio
- Unit of Endocrinology and Diabetes, Department of Medicine, Università Campus Bio-Medico di Roma, Italy
| | - Paolo Pozzilli
- Unit of Endocrinology and Diabetes, Department of Medicine, Università Campus Bio-Medico di Roma, Italy
- Centre of Immunobiology, The Blizard Institute, Barts and The London School of Medicine, Queen Mary University of London, London, UK
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34
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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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35
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Reyes-Centeno H, Hubbe M, Hanihara T, Stringer C, Harvati K. Testing modern human out-of-Africa dispersal models and implications for modern human origins. J Hum Evol 2015; 87:95-106. [DOI: 10.1016/j.jhevol.2015.06.008] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2014] [Revised: 03/02/2015] [Accepted: 06/14/2015] [Indexed: 11/26/2022]
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36
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Raghu A, Praveen D, Peiris D, Tarassenko L, Clifford G. Implications of Cardiovascular Disease Risk Assessment Using the WHO/ISH Risk Prediction Charts in Rural India. PLoS One 2015; 10:e0133618. [PMID: 26287807 PMCID: PMC4545825 DOI: 10.1371/journal.pone.0133618] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2015] [Accepted: 06/30/2015] [Indexed: 11/26/2022] Open
Abstract
Cardiovascular disease (CVD) risk in India is currently assessed using the World Health Organization/International Society for Hypertension (WHO/ISH) risk prediction charts since no population-specific models exist. The WHO/ISH risk prediction charts have two versions-one with total cholesterol as a predictor (the high information (HI) model) and the other without (the low information (LI) model). However, information on the WHO/ISH risk prediction charts including guidance on which version to use and when, as well as relative performance of the LI and HI models, is limited. This article aims to, firstly, quantify the relative performance of the LI and HI WHO/ISH risk prediction (for WHO-South East Asian Region D) using data from rural India. Secondly, we propose a pre-screening (simplified) point-of-care (POC) test to identify patients who are likely to benefit from a total cholesterol (TC) test, and subsequently when the LI model is preferential to HI model. Analysis was performed using cross-sectional data from rural Andhra Pradesh collected in 2005 with recorded blood cholesterol measurements (N = 1066). CVD risk was computed using both LI and HI models, and high risk individuals who needed treatment(THR) were subsequently identified based on clinical guidelines. Model development for the POC assessment of a TC test was performed through three machine learning techniques: Support Vector Machine (SVM), Regularised Logistic Regression (RLR), and Random Forests (RF) along with a feature selection process. Disagreement in CVD risk predicted by LI and HI WHO/ISH models was 14.5% (n = 155; p<0.01) overall and comprised 36 clinically relevant THR patients (31% of patients identified as THR by using either model). Using two patient-specific parameters (age, systolic blood pressure), our POC assessment can pre-determine the benefit of TC testing and choose the appropriate risk model (out-of-sample AUCs:RF-0.85,SVM-0.84,RLR:0.82 and maximum sensitivity-98%). The identification of patients benefitting from a TC test for CVD risk stratification can aid planning for resource-allocation and save costs for large-scale screening programmes.
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Affiliation(s)
- Arvind Raghu
- Institute of Biomedical Engineering, Department of Engineering Science, University of Oxford, Oxford, United Kingdom
| | - Devarsetty Praveen
- The George Institute of Global Health, Hyderabad, India
- University of Sydney, Sydney, NSW, Australia
| | - David Peiris
- The George Institute of Global Health, Sydney, Australia
| | - Lionel Tarassenko
- Institute of Biomedical Engineering, Department of Engineering Science, University of Oxford, Oxford, United Kingdom
| | - Gari Clifford
- Emory University, Atlanta, United States of America
- Georgia Institute of Technology, Atlanta, United States of America
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37
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Chaubey G, Kadian A, Bala S, Rao VR. Genetic Affinity of the Bhil, Kol and Gond Mentioned in Epic Ramayana. PLoS One 2015; 10:e0127655. [PMID: 26061398 PMCID: PMC4465503 DOI: 10.1371/journal.pone.0127655] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2014] [Accepted: 04/17/2015] [Indexed: 01/24/2023] Open
Abstract
Kol, Bhil and Gond are some of the ancient tribal populations known from the Ramayana, one of the Great epics of India. Though there have been studies about their affinity based on classical and haploid genetic markers, the molecular insights of their relationship with other tribal and caste populations of extant India is expected to give more clarity about the the question of continuity vs. discontinuity. In this study, we scanned >97,000 of single nucleotide polymorphisms among three major ancient tribes mentioned in Ramayana, namely Bhil, Kol and Gond. The results obtained were then compared at inter and intra population levels with neighboring and other world populations. Using various statistical methods, our analysis suggested that the genetic architecture of these tribes (Kol and Gond) was largely similar to their surrounding tribal and caste populations, while Bhil showed closer affinity with Dravidian and Austroasiatic (Munda) speaking tribes. The haplotype based analysis revealed a massive amount of genome sharing among Bhil, Kol, Gond and with other ethnic groups of South Asian descent. On the basis of genetic component sharing among different populations, we anticipate their primary founding over the indigenous Ancestral South Indian (ASI) component has prevailed in the genepool over the last several thousand years.
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Affiliation(s)
| | - Anurag Kadian
- 5 Ror Colony, Behind Sector 7, Karnal, Haryana132001, India
| | - Saroj Bala
- Institute of Scientific Research on Vedas, I-SERVE Delhi Chapter, C-6 / 302, Clarion the Legend, Gurgaon 122011, India
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38
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Subramanian S, Mohandesan E, Millar CD, Lambert DM. Distance-dependent patterns of molecular divergences in Tuatara mitogenomes. Sci Rep 2015; 5:8703. [PMID: 25731894 PMCID: PMC4346810 DOI: 10.1038/srep08703] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2014] [Accepted: 02/02/2015] [Indexed: 01/21/2023] Open
Abstract
Population genetic models predict that populations that are geographically close to each other are expected to be genetically more similar to each other compared to those that are widely separate. However the patterns of relationships between geographic distance and molecular divergences at neutral and constrained regions of the genome are unclear. We attempted to clarify this relationship by sequencing complete mitochondrial genomes of the relic species Tuatara (Sphenodon punctatus) from ten offshore islands of New Zealand. We observed a positive relationship that showed a proportional increase in the neutral diversity at synonymous sites (dS), with increasing geographical distance. In contrast we showed that diversity at evolutionarily constrained sites (dC) was elevated in the case of comparisons involving closely located populations. Conversely diversity was reduced in the case of comparisons between distantly located populations. These patterns were confirmed by a significant negative relationship between the ratio of dC/dS and geographic distance. The observed high dC/dS could be explained by the abundance of deleterious mutations in comparisons involving closely located populations, due to the recent population divergence times. Since distantly related populations were separated over long periods of time, deleterious mutations might have been removed by purifying selection.
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Affiliation(s)
- Sankar Subramanian
- Enviromental Futures Research Institute, Griffith University, Nathan 4111, Australia
| | - Elmira Mohandesan
- Allan Wilson Centre for Molecular Ecology and Evolution, Massey University, New Zealand
| | - Craig D Millar
- Allan Wilson Centre for Molecular Ecology and Evolution, School of Biological Sciences, University of Auckland, Private 92019, Auckland, New Zealand
| | - David M Lambert
- Enviromental Futures Research Institute, Griffith University, Nathan 4111, Australia
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Robinson JD, Coffman AJ, Hickerson MJ, Gutenkunst RN. Sampling strategies for frequency spectrum-based population genomic inference. BMC Evol Biol 2014; 14:254. [PMID: 25471595 PMCID: PMC4269862 DOI: 10.1186/s12862-014-0254-4] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2014] [Accepted: 11/24/2014] [Indexed: 01/25/2023] Open
Abstract
Background The allele frequency spectrum (AFS) consists of counts of the number of single nucleotide polymorphism (SNP) loci with derived variants present at each given frequency in a sample. Multiple approaches have recently been developed for parameter estimation and calculation of model likelihoods based on the joint AFS from two or more populations. We conducted a simulation study of one of these approaches, implemented in the Python module δaδi, to compare parameter estimation and model selection accuracy given different sample sizes under one- and two-population models. Results Our simulations included a variety of demographic models and two parameterizations that differed in the timing of events (divergence or size change). Using a number of SNPs reasonably obtained through next-generation sequencing approaches (10,000 - 50,000), accurate parameter estimates and model selection were possible for models with more ancient demographic events, even given relatively small numbers of sampled individuals. However, for recent events, larger numbers of individuals were required to achieve accuracy and precision in parameter estimates similar to that seen for models with older divergence or population size changes. We quantify i) the uncertainty in model selection, using tools from information theory, and ii) the accuracy and precision of parameter estimates, using the root mean squared error, as a function of the timing of demographic events, sample sizes used in the analysis, and complexity of the simulated models. Conclusions Here, we illustrate the utility of the genome-wide AFS for estimating demographic history and provide recommendations to guide sampling in population genomics studies that seek to draw inference from the AFS. Our results indicate that larger samples of individuals (and thus larger AFS) provide greater power for model selection and parameter estimation for more recent demographic events. Electronic supplementary material The online version of this article (doi:10.1186/s12862-014-0254-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- John D Robinson
- Department of Biology, City College of New York, New York, NY, 10031, USA. .,Current Address: South Carolina Department of Natural Resources, Marine Resources Research Institute, Charleston, SC, 29412, USA.
| | - Alec J Coffman
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, AZ, 85721, USA.
| | - Michael J Hickerson
- Department of Biology, City College of New York, New York, NY, 10031, USA. .,Subprogram in Ecology, Evolution and Behavior, the Graduate Center of the City University of New York, New York, NY, 10016, USA. .,Division of Invertebrate Zoology, American Museum of Natural History, New York, NY, 10024, USA.
| | - Ryan N Gutenkunst
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, AZ, 85721, USA.
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40
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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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41
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Juyal G, Mondal M, Luisi P, Laayouni H, Sood A, Midha V, Heutink P, Bertranpetit J, Thelma BK, Casals F. Population and genomic lessons from genetic analysis of two Indian populations. Hum Genet 2014; 133:1273-87. [PMID: 24980708 DOI: 10.1007/s00439-014-1462-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2014] [Accepted: 06/05/2014] [Indexed: 12/25/2022]
Abstract
Indian demographic history includes special features such as founder effects, interpopulation segregation, complex social structure with a caste system and elevated frequency of consanguineous marriages. It also presents a higher frequency for some rare mendelian disorders and in the last two decades increased prevalence of some complex disorders. Despite the fact that India represents about one-sixth of the human population, deep genetic studies from this terrain have been scarce. In this study, we analyzed high-density genotyping and whole-exome sequencing data of a North and a South Indian population. Indian populations show higher differentiation levels than those reported between populations of other continents. In this work, we have analyzed its consequences, by specifically assessing the transferability of genetic markers from or to Indian populations. We show that there is limited genetic marker portability from available genetic resources such as HapMap or the 1,000 Genomes Project to Indian populations, which also present an excess of private rare variants. Conversely, tagSNPs show a high level of portability between the two Indian populations, in contrast to the common belief that North and South Indian populations are genetically very different. By estimating kinship from mates and consanguinity in our data from trios, we also describe different patterns of assortative mating and inbreeding in the two populations, in agreement with distinct mating preferences and social structures. In addition, this analysis has allowed us to describe genomic regions under recent adaptive selection, indicating differential adaptive histories for North and South Indian populations. Our findings highlight the importance of considering demography for design and analysis of genetic studies, as well as the need for extending human genetic variation catalogs to new populations and particularly to those with particular demographic histories.
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Affiliation(s)
- Garima Juyal
- Department of Genetics, University of Delhi South Campus, New Delhi, 110 021, India
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Roy Moulik N, Parveen F, Kumar A, Awasthi S, Agrawal S. MTHFR gene polymorphism in acute lymphoblastic leukemia among North Indian children: a case-control study and meta-analysis updated from 2011. J Hum Genet 2014; 59:397-404. [PMID: 24919644 DOI: 10.1038/jhg.2014.44] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2013] [Revised: 03/13/2014] [Accepted: 04/27/2014] [Indexed: 11/09/2022]
Abstract
Studies on the association of methylenetetrahydrofolate reductase (MTHFR) genotype in childhood acute lymphoblastic leukemia (ALL) have yielded conflicting results. The present study examines this association in north Indian children with ALL and includes an updated meta-analysis. MTHFR (677 and 1298) genotype of children with ALL and healthy adult controls were done by the PCR-restriction fragment length polymorphism (PCR-RFLP) method and were compared using various models of inheritance. A total of 150 patients and 300 controls were included. The 677T allele was found protective (odds ratio (OR) 0.21, 95% confidence interval (CI) 0.04-0.94), whereas 1298C allele led to an increase in risk (OR 4.44, 95% CI 2.19-8.99) of childhood ALL. Meta-analysis included 31 and 27 studies examining the association of 677 and 1298 genotypes, respectively. The 677 C -> T polymorphism was protective (OR 0.90, 95% CI 0.82-0.99). Protection was more pronounced in folate-sufficient populations as compared with those not covered by folate fortification guidelines. The 1298A->C polymorphism was associated with a marginal increase in risk (OR 1.19, 95% CI 1.01-1.40).
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Affiliation(s)
- Nirmalya Roy Moulik
- Division of Pediatric Hematology-Oncology, Department of Pediatrics, King George's Medical University, Lucknow, India
| | - Farah Parveen
- Department of Medical Genetics, Sanjay Gandhi Post Graduate Institute of Medical Sciences, Lucknow, India
| | - Archana Kumar
- Division of Pediatric Hematology-Oncology, Department of Pediatrics, King George's Medical University, Lucknow, India
| | - Shally Awasthi
- Department of Pediatrics, King George's Medical University, Lucknow, India
| | - Suraksha Agrawal
- Department of Medical Genetics, Sanjay Gandhi Post Graduate Institute of Medical Sciences, Lucknow, India
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Jin HJ, Kim KC, Yoon CE, Kim W. Forensic and population genetic analyses of eighteen non-CODIS miniSTR loci in the Korean population. J Forensic Leg Med 2013; 20:1093-7. [PMID: 24237828 DOI: 10.1016/j.jflm.2013.09.027] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2013] [Revised: 09/23/2013] [Accepted: 09/28/2013] [Indexed: 10/26/2022]
Abstract
We analyzed the variation of eighteen miniSTR loci in 411 randomly chosen individuals from Korea to increase the probability that a degraded sample can be typed, as well as to provide an expanded and reliable population database. Six multiplex PCR systems were developed (multiplex I: D1S1677, D2S441 and D4S2364; multiplex II: D10S1248, D14S1434 and D22S1045; multiplex III: D12S391, D16S3253 and D20S161; multiplex IV: D3S4529, D8S1115 and D18S853; multiplex V: D6S1017, D11S4463 and D17S1301; multiplex VI: D5S2500, D9S1122 and D21S1437). Allele frequencies and forensic parameters were calculated to evaluate the suitability and robustness of these non-CODIS miniSTR systems. No significant deviation from Hardy-Weinberg equilibrium expectations were observed, except for D4S2364, D5S2500 and D20S161 loci. A multidimensional scaling plot based on allele frequencies of the six miniSTR loci (D1S1677, D2S441, D4S2364, D10S1248, D14S1434 and D22S1045) showed that Koreans appeared to have most genetic affinity with Chinese and Japanese than to other Eurasian populations compared here. The combined probability of match calculated from the 18 miniSTR loci was 2.902 × 10(-17), indicating a high degree of polymorphism. Thus, the 18 miniSTR loci can be suitable for recovering useful information for analyzing degraded forensic casework samples and for adding supplementary genetic information for a variety of analyses involving closely related individuals where there is a need for additional genetic information.
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Affiliation(s)
- Han Jun Jin
- Department of Nanobiomedical Science, Dankook University, Cheonan 330-714, Republic of Korea
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Khan N, Pande V, Das A. NAT2 sequence polymorphisms and acetylation profiles in Indians. Pharmacogenomics 2013; 14:289-303. [PMID: 23394391 DOI: 10.2217/pgs.13.2] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND NAT2, a broad-spectrum drug-metabolizing gene, is of high pharmacogenetic interest. Based on seven different mutations in the NAT2 gene, an individual can either be categorized as a slow or fast acetylator. MATERIALS & METHODS In order to characterize acetylation profiles of Indians, where data are poorly available, we sequenced the 873 bp NAT2 coding region in 250 Indians, covering the whole of India including three tribes. RESULTS Altogether, 35 NAT2 alleles forming two acetylator phenotypes (distributed almost in equal proportion in India) were found; while the alleles determining slow acetylators were highly differentiated, the fast acetylator alleles were less in number but highly frequent. CONCLUSION Interestingly, distribution of two different acetylation phenotypes correlated well with historical dietary pattern in India. The neighbor-joining phylogenetic tree based on NAT2 gene polymorphisms in worldwide humans revealed genetic affinities among populations with similar acetylation phenotypes, which also placed Indians and Africans together in a single cluster.
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Affiliation(s)
- Naazneen Khan
- Evolutionary Genomics & Bioinformatics Laboratory, Division of Genomics & Bioinformatics, National Institute of Malaria Research, New Delhi, India
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Affiliation(s)
- Elizabeth G Holliday
- Centre for Clinical Epidemiology and Biostatistics, Hunter Medical Research Institute and School of Medicine and Public Health, University of Newcastle, Newcastle, Australia.
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Magalhães TR, Casey JP, Conroy J, Regan R, Fitzpatrick DJ, Shah N, Sobral J, Ennis S. HGDP and HapMap analysis by Ancestry Mapper reveals local and global population relationships. PLoS One 2012; 7:e49438. [PMID: 23189146 PMCID: PMC3506643 DOI: 10.1371/journal.pone.0049438] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2012] [Accepted: 10/09/2012] [Indexed: 11/18/2022] Open
Abstract
Knowledge of human origins, migrations, and expansions is greatly enhanced by the availability of large datasets of genetic information from different populations and by the development of bioinformatic tools used to analyze the data. We present Ancestry Mapper, which we believe improves on existing methods, for the assignment of genetic ancestry to an individual and to study the relationships between local and global populations. The principle function of the method, named Ancestry Mapper, is to give each individual analyzed a genetic identifier, made up of just 51 genetic coordinates, that corresponds to its relationship to the HGDP reference population. As a consequence, the Ancestry Mapper Id (AMid) has intrinsic biological meaning and provides a tool to measure similarity between world populations. We applied Ancestry Mapper to a dataset comprised of the HGDP and HapMap data. The results show distinctions at the continental level, while simultaneously giving details at the population level. We clustered AMids of HGDP/HapMap and observe a recapitulation of human migrations: for a small number of clusters, individuals are grouped according to continental origins; for a larger number of clusters, regional and population distinctions are evident. Calculating distances between AMids allows us to infer ancestry. The number of coordinates is expandable, increasing the power of Ancestry Mapper. An R package called Ancestry Mapper is available to apply this method to any high density genomic data set.
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Affiliation(s)
- Tiago R. Magalhães
- School of Medicine and Medical Science, University College Dublin, Dublin, Ireland
| | - Jillian P. Casey
- School of Medicine and Medical Science, University College Dublin, Dublin, Ireland
- National Children’s Research Centre, Our Lady’s Childrens Hospital Crumlin, Dublin, Ireland
| | - Judith Conroy
- School of Medicine and Medical Science, University College Dublin, Dublin, Ireland
| | - Regina Regan
- School of Medicine and Medical Science, University College Dublin, Dublin, Ireland
- National Children’s Research Centre, Our Lady’s Childrens Hospital Crumlin, Dublin, Ireland
| | - Darren J. Fitzpatrick
- School of Medicine and Medical Science, University College Dublin, Dublin, Ireland
- Clique Research Cluster, School of Computer Science and Informatics, University College Dublin, Dublin, Ireland
| | - Naisha Shah
- School of Medicine and Medical Science, University College Dublin, Dublin, Ireland
- Complex and Adaptive Systems Laboratory, and Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin, Ireland
| | - João Sobral
- Instituto Gulbenkian de Ciência, Oeiras, Portugal
| | - Sean Ennis
- School of Medicine and Medical Science, University College Dublin, Dublin, Ireland
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Chakrabarti B, Kumar S, Singh R, Dimitrova N. Genetic diversity and admixture patterns in Indian populations. Gene 2012; 508:250-5. [PMID: 22892377 DOI: 10.1016/j.gene.2012.07.047] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2012] [Revised: 06/21/2012] [Accepted: 07/30/2012] [Indexed: 01/05/2023]
Abstract
India is a diverse land whose population holds the history of waves of human dispersal. Recent studies suggest two major ancestral contributions to most of the Indian sub-populations. However, present day Indians are thought to contain huge genetic diversity derived consequent to multiple cultural, linguistic and geographical variations. Genome-wide survey of individuals from current North (N-In) and South (S-In) India along with populations from HapMap Phase III and Indian sub-populations from HUGO Pan-Asian SNP Consortium is performed. Multivariate analysis (MDS and PCA) was carried out after merging data from the current study and other consortia. Indian sub-populations clustered separately from populations of major global geographical regions in MDS and PCA in a loose agglomeration except for two Indian subpopulations clustering near far eastern populations. F(st) values indicated diversity among Indian sub-populations which was substantiated by STRUCTURE analysis suggesting the possibility of additional admixture events.
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Affiliation(s)
- Biswaroop Chakrabarti
- Philips Research Asia, Bangalore, Philips Innovation Campus, Manyata Tech Park, Nagavara, Bangalore, 560045, India
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Demographic inference using spectral methods on SNP data, with an analysis of the human out-of-Africa expansion. Genetics 2012; 192:619-39. [PMID: 22865734 PMCID: PMC3454885 DOI: 10.1534/genetics.112.141846] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
We present an implementation of a recently introduced method for estimating the allele-frequency spectrum under the diffusion approximation. For single-nucleotide polymorphism (SNP) frequency data from multiple populations, the method computes numerical solutions to the allele-frequency spectrum (AFS) under a complex model that includes population splitting events, migration, population expansion, and admixture. The solution to the diffusion partial differential equation (PDE) that mimics the evolutionary process is found by means of truncated polynomial expansions. In the absence of gene flow, our computation of frequency spectra yields exact results. The results are compared to those that use a finite-difference method and to forward diffusion simulations. In general, all the methods yield comparable results, although the polynomial-based approach is the most accurate in the weak-migration limit. Also, the economical use of memory attained by the polynomial expansions makes the study of models with four populations possible for the first time. The method was applied to a four-population model of the human expansion out of Africa and the peopling of the Americas, using the Environmental Genome Project (EGP) SNP database. Although our confidence intervals largely overlapped previous analyses of these data, some were significantly different. In particular, estimates of migration among African, European, and Asian populations were considerably lower than those in a previous study and the estimated time of migration out of Africa was earlier. The estimated time of founding of a human population outside of Africa was 52,000 years (95% confidence interval: 36,000–80,800 years).
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Metspalu M, Romero I, Yunusbayev B, Chaubey G, Mallick C, Hudjashov G, Nelis M, Mägi R, Metspalu E, Remm M, Pitchappan R, Singh L, Thangaraj K, Villems R, Kivisild T. Shared and unique components of human population structure and genome-wide signals of positive selection in South Asia. Am J Hum Genet 2011; 89:731-44. [PMID: 22152676 DOI: 10.1016/j.ajhg.2011.11.010] [Citation(s) in RCA: 106] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2011] [Revised: 09/06/2011] [Accepted: 11/12/2011] [Indexed: 02/06/2023] Open
Abstract
South Asia harbors one of the highest levels genetic diversity in Eurasia, which could be interpreted as a result of its long-term large effective population size and of admixture during its complex demographic history. In contrast to Pakistani populations, populations of Indian origin have been underrepresented in previous genomic scans of positive selection and population structure. Here we report data for more than 600,000 SNP markers genotyped in 142 samples from 30 ethnic groups in India. Combining our results with other available genome-wide data, we show that Indian populations are characterized by two major ancestry components, one of which is spread at comparable frequency and haplotype diversity in populations of South and West Asia and the Caucasus. The second component is more restricted to South Asia and accounts for more than 50% of the ancestry in Indian populations. Haplotype diversity associated with these South Asian ancestry components is significantly higher than that of the components dominating the West Eurasian ancestry palette. Modeling of the observed haplotype diversities suggests that both Indian ancestry components are older than the purported Indo-Aryan invasion 3,500 YBP. Consistent with the results of pairwise genetic distances among world regions, Indians share more ancestry signals with West than with East Eurasians. However, compared to Pakistani populations, a higher proportion of their genes show regionally specific signals of high haplotype homozygosity. Among such candidates of positive selection in India are MSTN and DOK5, both of which have potential implications in lipid metabolism and the etiology of type 2 diabetes.
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