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CSVS, a crowdsourcing database of the Spanish population genetic variability

2020; Oxford University Press; Volume: 49; Issue: D1 Linguagem: Inglês

10.1093/nar/gkaa794

1362-4962

María Peña-Chilet, Gema Roldán, Javier Pérez-Florido, Francisco Ortuño, Rosario Carmona, Virginia Aquino, Daniel López-López, Carlos Loucera, Jose L. Fernández-Rueda, Asunción Gallego, Francisco García‐García, Anna González‐Neira, Guillermo Pita, Rocío Núñez‐Torres, Javier Santoyo‐López, Carmen Ayuso, Pablo Mínguez, Almudena Ávila‐Fernández, Marta Cortón, Miguel A. Moreno‐Pelayo, Matías Morín, Álvaro Gallego-Martinez, José A. López‐Escámez, Salud Borrego, Guillermo Antiñolo, Jorge Amigo, Josefa Salgado, Sara Pasalodos-Sánchez, Beatriz Morte, Fátima Al‐Shahrour, Rafael Artuch, Javier Benı́tez, Luís Castaño, Ignacio del Castillo, Aitor Delmiro, Carmen Espinós, R Estrada González, Daniel Grinberg, Encarna Guillén‐Navarro, Pablo Lapunzina, Esther López, Ramón Martí, Montserrat Milà, José M. Millán, Virginia Nunes, Francesc Palau, Belén Pérez, Luis Pérez Jurado, Rosario Perona, Aurora Pujol, Feliciano J. Ramos, Antònia Ribes, Jordi Rosell, Eulalia Rovira, Jordi Surrallés, Isabel Tejada, Magdalena Ugarte, Ángel Carracedo, Ángel Alonso, Joaquı́n Dopazo,

Single-cell and spatial transcriptomics

The 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/.