A crowdsourcing database for the copy-number variation of the Spanish population
Por:
López-López D., Roldán G., Fernández-Rueda J.L., Bostelmann G., Carmona R., Aquino V., Perez-Florido J., Ortuño F., Pita G., Núñez-Torres R., González-Neira A., Alonso A., Salgado-Garrido J., Pasalodos-Sanchez S., Ayuso C., Minguez P., Avila-Fernandez A., Corton M., Artuch R., Borrego S., Antiñolo G., Carracedo A., Amigo J., Castaño L.A., Tejada I., Delmiro A., Espinos C., Grinberg D., Guillén E., Lapunzina P., Lopez-Escámez J.A., Gallego-Martinez A., Martí R., Rovira E., Millán J.M., Moreno M.A., Morin M., Moreno-Galdó A., Fernández-Cancio M., Morte B., Mulero V., García D., Nunes V., Palau F., Perez B., Jurado L.P., Perona R., Pujol A., Ramos F., Lopez E., Ribes A., Rosell J., Surrallés J., Peña-Chilet M., Dopazo J.
Publicada:
1 ene 2023
Resumen:
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. © 2023, The Author(s).
Filiaciones:
López-López D.:
Computational Medicine Platform, Andalusian Public Foundation Progress and Health-FPS, Seville, 41013, Spain
Institute of Biomedicine of Seville, IBiS, University Hospital Virgen del Rocío/CSIC/University of Seville, Seville, Spain
Centro de Investigación Biomédica en Red en Enfermedades Raras (CIBERER), ISCIII, Madrid, Spain
Roldán G.:
Computational Medicine Platform, Andalusian Public Foundation Progress and Health-FPS, Seville, 41013, Spain
Fernández-Rueda J.L.:
Computational Medicine Platform, Andalusian Public Foundation Progress and Health-FPS, Seville, 41013, Spain
Bostelmann G.:
Computational Medicine Platform, Andalusian Public Foundation Progress and Health-FPS, Seville, 41013, Spain
Carmona R.:
Computational Medicine Platform, Andalusian Public Foundation Progress and Health-FPS, Seville, 41013, Spain
Centro de Investigación Biomédica en Red en Enfermedades Raras (CIBERER), ISCIII, Madrid, Spain
Aquino V.:
Computational Medicine Platform, Andalusian Public Foundation Progress and Health-FPS, Seville, 41013, Spain
Perez-Florido J.:
Computational Medicine Platform, Andalusian Public Foundation Progress and Health-FPS, Seville, 41013, Spain
Institute of Biomedicine of Seville, IBiS, University Hospital Virgen del Rocío/CSIC/University of Seville, Seville, Spain
Ortuño F.:
Computational Medicine Platform, Andalusian Public Foundation Progress and Health-FPS, Seville, 41013, Spain
Department of Computer Architecture and Computer Technology, University of Granada, Granada, 18071, Spain
Pita G.:
Human Genotyping Unit–CeGen, Spanish National Cancer Research Centre (CNIO), Madrid, 28029, Spain
Núñez-Torres R.:
Human Genotyping Unit–CeGen, Spanish National Cancer Research Centre (CNIO), Madrid, 28029, Spain
González-Neira A.:
Human Genotyping Unit–CeGen, Spanish National Cancer Research Centre (CNIO), Madrid, 28029, Spain
Alonso A.:
Navarrabiomed-IdiSNA, Complejo Hospitalario de Navarra, IdiSNA (Navarra Institute for Health Research), Universidad Pública de Navarra (UPNA), Navarre, Pamplona, Spain
Salgado-Garrido J.:
Navarrabiomed-IdiSNA, Complejo Hospitalario de Navarra, IdiSNA (Navarra Institute for Health Research), Universidad Pública de Navarra (UPNA), Navarre, Pamplona, Spain
Pasalodos-Sanchez S.:
Navarrabiomed-IdiSNA, Complejo Hospitalario de Navarra, IdiSNA (Navarra Institute for Health Research), Universidad Pública de Navarra (UPNA), Navarre, Pamplona, Spain
Ayuso C.:
Department of Genetics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
Minguez P.:
Department of Genetics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
Avila-Fernandez A.:
Department of Genetics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
Corton M.:
Department of Genetics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
Artuch R.:
Fundación Para la Investigación y Docencia Sant Joan de Deu, Barcelona, Spain
Borrego S.:
University Hospital Virgen del Rocío, Seville, Spain
Antiñolo G.:
University Hospital Virgen del Rocío, Seville, Spain
Carracedo A.:
Fundación Pública Galega de Medicina Xenómica, SERGAS, IDIS, Santiago de Compostela, Spain
Amigo J.:
Fundación Pública Galega de Medicina Xenómica, SERGAS, IDIS, Santiago de Compostela, Spain
Castaño L.A.:
Asociación Instituto de Investigación Sanitaria de Biocruces, Vizcaya, Spain
Tejada I.:
Asociación Instituto de Investigación Sanitaria de Biocruces, Vizcaya, Spain
Delmiro A.:
Hospital Univ. 12 de Octubre, Madrid, Spain
Espinos C.:
Centro de Investigación Príncipe Felipe, Valencia, Spain
Grinberg D.:
Universidad de Barcelona, Barcelona, Spain
Guillén E.:
Hospital Virgen de la Arrixaca, Murcia, Spain
Lapunzina P.:
Servicio Madrileño de Salud, Madrid, Spain
Lopez-Escámez J.A.:
Department of Genomic Medicine, Centre for Genomics and Oncological Research (GENYO), Pfizer University of Granada, Granada, Spain
Gallego-Martinez A.:
Department of Genomic Medicine, Centre for Genomics and Oncological Research (GENYO), Pfizer University of Granada, Granada, Spain
Martí R.:
Vall d’Hebron Institut de Recerca, Barcelona, Spain
Rovira E.:
Vall d’Hebron Institut de Recerca, Barcelona, Spain
Millán J.M.:
Fundación para la Investigación del Hospital la Fe, Valencia, Spain
Moreno M.A.:
Servicio de Genética, Ramón y Cajal Institute of Health Research (IRYCIS) and Biomedical Network Research Centre on Rare Diseases (CIBERER), Madrid, Spain
Morin M.:
Servicio de Genética, Ramón y Cajal Institute of Health Research (IRYCIS) and Biomedical Network Research Centre on Rare Diseases (CIBERER), Madrid, Spain
Moreno-Galdó A.:
Vall d’Hebron Institut de Recerca (VHIR), Hospital Universitari Vall d’Hebron, Barcelona, Spain
Fernández-Cancio M.:
Vall d’Hebron Institut de Recerca (VHIR), Hospital Universitari Vall d’Hebron, Barcelona, Spain
Morte B.:
Undiagnosed Rare Diseases Programme (ENoD), Center for Biomedical Research on Rare Diseases (CIBERER), ISCIII, Madrid, Spain
Mulero V.:
Universidad de Murcia, Murcia, Spain
García D.:
Universidad de Murcia, Murcia, Spain
Nunes V.:
Fundación IDIBELL, Barcelona, Spain
Palau F.:
Fundación Para la Investigación y Docencia Sant Joan de Deu, Barcelona, Spain
Perez B.:
Universidad Autónoma de Madrid, Madrid, Spain
Jurado L.P.:
Universidad Pompeu Fabra, Barcelona, Spain
Perona R.:
Agencia Estatal Consejo Superior de Investigaciones Científicas, Madrid, Spain
Pujol A.:
Fundación IDIBELL, Barcelona, Spain
Ramos F.:
Universidad de Zaragoza, Saragossa, Spain
Lopez E.:
Universidad de Zaragoza, Saragossa, Spain
Ribes A.:
Hospital Clínico y Provincial de Barcelona, Barcelona, Spain
Rosell J.:
Fundación Instituto de Investigación Sanitaria Illes Baleares (IdISBa), Palma, Spain
Surrallés J.:
Universidad Autónoma de Barcelona, Barcelona, Spain
Peña-Chilet M.:
Computational Medicine Platform, Andalusian Public Foundation Progress and Health-FPS, Seville, 41013, Spain
Institute of Biomedicine of Seville, IBiS, University Hospital Virgen del Rocío/CSIC/University of Seville, Seville, Spain
Centro de Investigación Biomédica en Red en Enfermedades Raras (CIBERER), ISCIII, Madrid, Spain
Dopazo J.:
Computational Medicine Platform, Andalusian Public Foundation Progress and Health-FPS, Seville, 41013, Spain
Institute of Biomedicine of Seville, IBiS, University Hospital Virgen del Rocío/CSIC/University of Seville, Seville, Spain
Centro de Investigación Biomédica en Red en Enfermedades Raras (CIBERER), ISCIII, Madrid, Spain
FPS/ELIXIR-ES, Andalusian Public Foundation Progress and Health-FPS, Seville, 41013, Spain
Green Published, gold, All Open Access, Gold, Green
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