Author:
López-López Daniel,Roldán Gema,Fernández-Rueda Jose L.,Bostelmann Gerrit,Carmona Rosario,Aquino Virginia,Perez-Florido Javier,Ortuño Francisco,Pita Guillermo,Núñez-Torres Rocío,González-Neira Anna,Alonso Angel,Salgado-Garrido Josefa,Pasalodos-Sanchez Sara,Ayuso Carmen,Minguez Pablo,Avila-Fernandez Almudena,Corton Marta,Artuch Rafael,Borrego Salud,Antiñolo Guillermo,Carracedo Angel,Amigo Jorge,Castaño Luis Antonio,Tejada Isabel,Delmiro Aitor,Espinos Carmina,Grinberg Daniel,Guillén Encarnación,Lapunzina Pablo,Lopez-Escámez Jose Antonio,Gallego-Martinez Alvaro,Martí Ramón,Rovira Eulalia,Millán José Mª,Moreno Miguel Angel,Morin Matías,Moreno-Galdó Antonio,Fernández-Cancio Mónica,Morte Beatriz,Mulero Victoriano,García Diana,Nunes Virginia,Palau Francesc,Perez Belén,Jurado Luis Pérez,Perona Rosario,Pujol Aurora,Ramos Feliciano,Lopez Esther,Ribes Antonia,Rosell Jordi,Surrallés Jordi,Peña-Chilet María,Dopazo Joaquin,
Abstract
Abstract
Background
Despite being a very common type of genetic variation, the distribution of copy-number variations (CNVs) in the population is still poorly understood. The knowledge of the genetic variability, especially at the level of the local population, is a critical factor for distinguishing pathogenic from non-pathogenic variation in the discovery of new disease variants.
Results
Here, we present the SPAnish Copy Number Alterations Collaborative Server (SPACNACS), which currently contains copy number variation profiles obtained from more than 400 genomes and exomes of unrelated Spanish individuals. By means of a collaborative crowdsourcing effort whole genome and whole exome sequencing data, produced by local genomic projects and for other purposes, is continuously collected. Once checked both, the Spanish ancestry and the lack of kinship with other individuals in the SPACNACS, the CNVs are inferred for these sequences and they are used to populate the database. A web interface allows querying the database with different filters that include ICD10 upper categories. This allows discarding samples from the disease under study and obtaining pseudo-control CNV profiles from the local population. We also show here additional studies on the local impact of CNVs in some phenotypes and on pharmacogenomic variants. SPACNACS can be accessed at: http://csvs.clinbioinfosspa.es/spacnacs/.
Conclusion
SPACNACS facilitates disease gene discovery by providing detailed information of the local variability of the population and exemplifies how to reuse genomic data produced for other purposes to build a local reference database.
Funder
Instituto de Salud Carlos III
Ministerio de Ciencia e Innovación
Publisher
Springer Science and Business Media LLC
Subject
Drug Discovery,Genetics,Molecular Biology,Molecular Medicine