CSVS, a crowdsourcing database of the Spanish population genetic variability

descriptionPublicationkeyboard_double_arrow_right Article 29 Sep 2020 Spain, United Kingdom English Publisher:Oxford University Press (OUP)Journal:Nucleic Acids Research, volume 49, pages D1130-D1137 (issn: 0305-1048, eissn: 1362-4962,

Copyright policy )Funded by:EC | ELIXIR-EXCELERATE

Authors: María Peña-Chilet; Gema Roldán; Javier Perez-Florido; Francisco M. Ortuño; Rosario Carmona; Virginia Aquino; Daniel López-López; +53 Authors

doi: 10.1093/nar/gkaa794

pmid: 32990755

pmc: PMC7778906

handle: 10230/57224 , 20.500.12105/13340 , 10668/4371 , 10481/66652 , 20.500.12530/58857 , 2445/195162 , 10261/264616 , 20.500.11820/6d11e5e5-6da3-4443-8f9c-66bf91290697

CSVS, a crowdsourcing database of the Spanish population genetic variability

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Abstract

AbstractThe knowledge of the genetic variability of the local population is of utmost importance in personalized medicine and has been revealed as a critical factor for the discovery of new disease variants. Here, we present the Collaborative Spanish Variability Server (CSVS), which currently contains more than 2000 genomes and exomes of unrelated Spanish individuals. This database has been generated in a collaborative crowdsourcing effort collecting sequencing data produced by local genomic projects and for other purposes. Sequences have been grouped by ICD10 upper categories. A web interface allows querying the database removing one or more ICD10 categories. In this way, aggregated counts of allele frequencies of the pseudo-control Spanish population can be obtained for diseases belonging to the category removed. Interestingly, in addition to pseudo-control studies, some population studies can be made, as, for example, prevalence of pharmacogenomic variants, etc. In addition, this genomic data has been used to define the first Spanish Genome Reference Panel (SGRP1.0) for imputation. This is the first local repository of variability entirely produced by a crowdsourcing effort and constitutes an example for future initiatives to characterize local variability worldwide. CSVS is also part of the GA4GH Beacon network.CSVS can be accessed at: http://csvs.babelomics.org/.

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Spain, United Kingdom

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Keywords

Medical Subject Headings::Phenomena and Processes::Genetic Phenomena::Genetic Structures::Genome::Genome, Human, Població, Population, Proveïment participatiu, Genètica de poblacions humanes, Medical Subject Headings::Organisms::Eukaryota::Animals::Chordata::Vertebrates::Mammals::Primates::Haplorhini::Catarrhini::Hominidae::Humans, Bases de dades, Databases, Gene Frequency, Databases, Genetic, Database Issue, Humans, Exome, Espanya, Precision Medicine, Medical Subject Headings::Phenomena and Processes::Genetic Phenomena::Genetic Structures::Genome::Genome Components::Genes::Alleles, Alleles, Medical Subject Headings::Disciplines and Occupations::Natural Science Disciplines::Biological Science Disciplines::Biology::Genetics::Genomics, Internet, Genoma humà -- Espanya, Genome, Human, Medical Subject Headings::Disciplines and Occupations::Natural Science Disciplines::Biological Science Disciplines::Biology::Genetics::Genetics, Population, Medical Subject Headings::Information Science::Information Science::Information Storage and Retrieval::Databases as Topic::Databases, Factual::Databases, Genetic, Chromosome Mapping, Genetic Variation, Human population genetics, Medical Subject Headings::Analytical, Diagnostic and Therapeutic Techniques and Equipment::Investigative Techniques::Genetic Techniques::Chromosome Mapping::Physical Chromosome Mapping, Genomics, Medical Subject Headings::Geographical Locations::Geographic Locations::Europe::Spain, Medical Subject Headings::Phenomena and Processes::Genetic Phenomena::Gene Frequency, Medical Subject Headings::Phenomena and Processes::Genetic Phenomena::Genetic Structures::Genome::Exome, Genetics, Population, Spain, Crowdsourcing, Software, Medical Subject Headings::Phenomena and Processes::Genetic Phenomena::Genetic Variation, Medical Subject Headings::Information Science::Information Science::Data Collection::Crowdsourcing

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