SAGE: a comprehensive resource of genetic variants integrating South Asian whole genomes and exomes

South Asia is home to [Formula: see text] 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 availabi...

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Autores principales: Hariprakash, Judith Mary, Vellarikkal, Shamsudheen Karuthedath, Verma, Ankit, Ranawat, Anop Singh, Jayarajan, Rijith, Ravi, Rowmika, Kumar, Anoop, Dixit, Vishal, Sivadas, Ambily, Kashyap, Atul Kumar, Senthivel, Vigneshwar, Sehgal, Paras, Mahadevan, Vijayalakshmi, Scaria, Vinod, Sivasubbu, Sridhar
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2018
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6146123/
https://www.ncbi.nlm.nih.gov/pubmed/30184194
http://dx.doi.org/10.1093/database/bay080
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author Hariprakash, Judith Mary
Vellarikkal, Shamsudheen Karuthedath
Verma, Ankit
Ranawat, Anop Singh
Jayarajan, Rijith
Ravi, Rowmika
Kumar, Anoop
Dixit, Vishal
Sivadas, Ambily
Kashyap, Atul Kumar
Senthivel, Vigneshwar
Sehgal, Paras
Mahadevan, Vijayalakshmi
Scaria, Vinod
Sivasubbu, Sridhar
author_facet Hariprakash, Judith Mary
Vellarikkal, Shamsudheen Karuthedath
Verma, Ankit
Ranawat, Anop Singh
Jayarajan, Rijith
Ravi, Rowmika
Kumar, Anoop
Dixit, Vishal
Sivadas, Ambily
Kashyap, Atul Kumar
Senthivel, Vigneshwar
Sehgal, Paras
Mahadevan, Vijayalakshmi
Scaria, Vinod
Sivasubbu, Sridhar
author_sort Hariprakash, Judith Mary
collection PubMed
description South Asia is home to [Formula: see text] 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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spelling pubmed-61461232018-09-25 SAGE: a comprehensive resource of genetic variants integrating South Asian whole genomes and exomes Hariprakash, Judith Mary Vellarikkal, Shamsudheen Karuthedath Verma, Ankit Ranawat, Anop Singh Jayarajan, Rijith Ravi, Rowmika Kumar, Anoop Dixit, Vishal Sivadas, Ambily Kashyap, Atul Kumar Senthivel, Vigneshwar Sehgal, Paras Mahadevan, Vijayalakshmi Scaria, Vinod Sivasubbu, Sridhar Database (Oxford) Database Tool South Asia is home to [Formula: see text] 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. Oxford University Press 2018-09-13 /pmc/articles/PMC6146123/ /pubmed/30184194 http://dx.doi.org/10.1093/database/bay080 Text en © The Author(s) 2018. Published by Oxford University Press. http://creativecommons.org/licenses/by/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Database Tool
Hariprakash, Judith Mary
Vellarikkal, Shamsudheen Karuthedath
Verma, Ankit
Ranawat, Anop Singh
Jayarajan, Rijith
Ravi, Rowmika
Kumar, Anoop
Dixit, Vishal
Sivadas, Ambily
Kashyap, Atul Kumar
Senthivel, Vigneshwar
Sehgal, Paras
Mahadevan, Vijayalakshmi
Scaria, Vinod
Sivasubbu, Sridhar
SAGE: a comprehensive resource of genetic variants integrating South Asian whole genomes and exomes
title SAGE: a comprehensive resource of genetic variants integrating South Asian whole genomes and exomes
title_full SAGE: a comprehensive resource of genetic variants integrating South Asian whole genomes and exomes
title_fullStr SAGE: a comprehensive resource of genetic variants integrating South Asian whole genomes and exomes
title_full_unstemmed SAGE: a comprehensive resource of genetic variants integrating South Asian whole genomes and exomes
title_short SAGE: a comprehensive resource of genetic variants integrating South Asian whole genomes and exomes
title_sort sage: a comprehensive resource of genetic variants integrating south asian whole genomes and exomes
topic Database Tool
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6146123/
https://www.ncbi.nlm.nih.gov/pubmed/30184194
http://dx.doi.org/10.1093/database/bay080
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