A crowdsourcing database for the copy-number variation of the Spanish population

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• dc.contributor.author López-López, Daniel
• dc.contributor.author Roldán, Gema
• dc.contributor.author Fernández-Rueda, Jose L.
• dc.contributor.author Bostelmann, Gerrit
• dc.contributor.author Carmona, Rosario
• dc.contributor.author Aquino, Virginia
• dc.contributor.author Perez-Florido, Javier
• dc.contributor.author Ortuño, Francisco José
• dc.contributor.author Pita, Guillermo
• dc.contributor.author Núñez-Torres, Rocío
• dc.contributor.author González Neira, Anna
• dc.contributor.author CSVS Crowdsourcing Group
• dc.contributor.author Peña-Chilet, María
• dc.contributor.author Dopazo, Joaquin
• dc.date.accessioned 2023-06-19T05:58:49Z
• dc.date.available 2023-06-19T05:58:49Z
• dc.date.issued 2023
• dc.description.abstract 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. 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/. 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.
• dc.description.sponsorship This work is supported by Grants PID2020-117979RB-I00 from the Spanish Ministry of Science and Innovation; by the Institute of Health Carlos III (project IMPaCT-Data, exp. IMP/00019, IMP/00009 and PI20/01305), co-funded by the European Union, European Regional Development Fund (ERDF, “A way to make Europe”).
• dc.format.mimetype application/pdf
• dc.identifier.citation López-López D, Roldán G, Fernández-Rueda JL, Bostelmann G, Carmona R, Aquino V, et al. A crowdsourcing database for the copy-number variation of the Spanish population. Hum Genomics. 2023 Mar 9;17(1):20. DOI: 10.1186/s40246-023-00466-8
• dc.identifier.doi http://dx.doi.org/10.1186/s40246-023-00466-8
• dc.identifier.issn 1479-7364
• dc.identifier.uri http://hdl.handle.net/10230/57215
• dc.language.iso eng
• dc.publisher Springer Nature
• dc.relation.ispartof Human Genomics. 2023 Mar 9;17(1):20
• dc.relation.projectID info:eu-repo/grantAgreement/ES/2PE/PID2020-117979RB-I00
• dc.rights This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unle
• dc.rights.accessRights info:eu-repo/semantics/openAccess
• dc.rights.uri http://creativecommons.org/publicdomain/zero/1.0/
• dc.subject.other Proveïment participatiu
• dc.subject.other Espanya -- Estadístiques
• dc.subject.other Espanya -- Població
• dc.title A crowdsourcing database for the copy-number variation of the Spanish population
• dc.type info:eu-repo/semantics/article
• dc.type.version info:eu-repo/semantics/publishedVersion