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...
Autores principales: | , , , , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2018
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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. |
format | Online Article Text |
id | pubmed-6146123 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2018 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
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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