CSVS, a crowdsourcing database of the Spanish population genetic variability

María Peña-Chilet, Gema Roldán, Javier Perez-Florido, Francisco M Ortuño, Rosario Carmona, Virginia Aquino, Daniel Lopez-Lopez, Carlos Loucera, Jose L Fernandez-Rueda, Asunción Gallego, Francisco García-Garcia, Anna González-Neira, Guillermo Pita, Rocío Núñez-Torres, Javier Santoyo-López, Carmen Ayuso, Pablo Minguez, Almudena Avila-Fernandez, Marta Corton, Miguel Ángel Moreno-Pelayo, Matías Morin, Alvaro Gallego-Martinez, Jose A Lopez-Escamez, Salud Borrego, Guillermo Antiñolo, Jorge Amigo, Josefa Salgado-Garrido, Sara Pasalodos-Sanchez, Beatriz Morte, Spanish Exome Crowdsourcing Consortium, Ángel Carracedo, Ángel Alonso, Joaquín Dopazo, Fátima Al-Shahrour, Rafael Artuch, Javier Benitez, Luis Antonio Castaño, Ignacio Del Castillo, Aitor Delmiro, Carmina Espinos, Roser González, Daniel Grinberg, Encarnación Guillén, Pablo Lapunzina, Esther Lopez, Ramón Martí, Montserrat Milá, José Mª Millán, Virginia Nunes, Francesc Palau, Belen Perez, Luis Pérez Jurado, Rosario Perona, Aurora Pujol, Feliciano Ramos, Antonia Ribes, Jordi Rosell, Eulalia Rovira, Jordi Surrallés, Isabel Tejada, Magdalena Ugarte, María Peña-Chilet, Gema Roldán, Javier Perez-Florido, Francisco M Ortuño, Rosario Carmona, Virginia Aquino, Daniel Lopez-Lopez, Carlos Loucera, Jose L Fernandez-Rueda, Asunción Gallego, Francisco García-Garcia, Anna González-Neira, Guillermo Pita, Rocío Núñez-Torres, Javier Santoyo-López, Carmen Ayuso, Pablo Minguez, Almudena Avila-Fernandez, Marta Corton, Miguel Ángel Moreno-Pelayo, Matías Morin, Alvaro Gallego-Martinez, Jose A Lopez-Escamez, Salud Borrego, Guillermo Antiñolo, Jorge Amigo, Josefa Salgado-Garrido, Sara Pasalodos-Sanchez, Beatriz Morte, Spanish Exome Crowdsourcing Consortium, Ángel Carracedo, Ángel Alonso, Joaquín Dopazo, Fátima Al-Shahrour, Rafael Artuch, Javier Benitez, Luis Antonio Castaño, Ignacio Del Castillo, Aitor Delmiro, Carmina Espinos, Roser González, Daniel Grinberg, Encarnación Guillén, Pablo Lapunzina, Esther Lopez, Ramón Martí, Montserrat Milá, José Mª Millán, Virginia Nunes, Francesc Palau, Belen Perez, Luis Pérez Jurado, Rosario Perona, Aurora Pujol, Feliciano Ramos, Antonia Ribes, Jordi Rosell, Eulalia Rovira, Jordi Surrallés, Isabel Tejada, Magdalena Ugarte

Abstract

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/.

© The Author(s) 2020. Published by Oxford University Press on behalf of Nucleic Acids Research.

Figures

Figure 1.
Figure 1.
(A) data is contributed by different genomic projects and pass through different quality control steps including an artefact and kinship test (that detects upper outliers, with an unexpected high ratio of private variants, most likely errors, and lower outliers, that are duplicates or close kinship individuals) and locality test before being inserted in the database. (B) Initial CSVS page. (C) Query panel in the Search option. (D) List of variants found in the Spanish population within the selected region along with complementary information on impact, conservation, other's population frequencies and phenotype. (E) genomic browser that displays the selected variant in its genomic context. (F) Saturation plot. (G) Updated contents of the database.
Figure 2.
Figure 2.
Circos plot showing the different genes with high saturation (orange) and low saturation (green) along the chromosomes, which were significantly enriched in functional terms in Supplementary Figure S1.

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