A crowdsourcing database for the copy-number variation of the Spanish population
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 pathog...
| Autores: | , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , |
|---|---|
| Formato: | artículo |
| Fecha de publicación: | 2023 |
| País: | España |
| Recursos: | Servizo Galego de Saúde (SERGAS) |
| Repositorio: | RUNA. Repositorio da Consellería de Sanidade e Sergas |
| OAI Identifier: | oai:runa.sergas.gal:20.500.11940/20975 |
| Acesso em linha: | https://portalcientifico.sergas.gal//documentos/6420454be1b5e93884fa7937 http://hdl.handle.net/20.500.11940/20975 |
| Access Level: | acceso abierto |
| Palavra-chave: | DNA Copy Number Variations Crowdsourcing Genomics Phenotype Databases, Factual FPGMX AS Santiago |
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A crowdsourcing database for the copy-number variation of the Spanish populationLópez-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 Álvarez, ÁngelAmigo Lechuga, JorgeCastaño, 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.DNA Copy Number VariationsCrowdsourcingGenomicsPhenotypeDatabases, FactualFPGMXAS SantiagoFPGMXBackground: 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.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).2023info:eu-repo/semantics/articlehttps://portalcientifico.sergas.gal//documentos/6420454be1b5e93884fa7937http://hdl.handle.net/20.500.11940/20975reponame:RUNA. Repositorio da Consellería de Sanidade e Sergasinstname:Servizo Galego de Saúde (SERGAS)Ingléshttp://creativecommons.org/licenses/by/4.0/info:eu-repo/semantics/openAccessoai:runa.sergas.gal:20.500.11940/209752026-06-12T08:40:47Z |
| dc.title.none.fl_str_mv |
A crowdsourcing database for the copy-number variation of the Spanish population |
| title |
A crowdsourcing database for the copy-number variation of the Spanish population |
| spellingShingle |
A crowdsourcing database for the copy-number variation of the Spanish population López-López, D. DNA Copy Number Variations Crowdsourcing Genomics Phenotype Databases, Factual FPGMX AS Santiago FPGMX |
| title_short |
A crowdsourcing database for the copy-number variation of the Spanish population |
| title_full |
A crowdsourcing database for the copy-number variation of the Spanish population |
| title_fullStr |
A crowdsourcing database for the copy-number variation of the Spanish population |
| title_full_unstemmed |
A crowdsourcing database for the copy-number variation of the Spanish population |
| title_sort |
A crowdsourcing database for the copy-number variation of the Spanish population |
| dc.creator.none.fl_str_mv |
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 Álvarez, Ángel Amigo Lechuga, Jorge 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. |
| author |
López-López, D. |
| author_facet |
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 Álvarez, Ángel Amigo Lechuga, Jorge 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. |
| author_role |
author |
| author2 |
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 Álvarez, Ángel Amigo Lechuga, Jorge 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. |
| author2_role |
author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author |
| dc.subject.none.fl_str_mv |
DNA Copy Number Variations Crowdsourcing Genomics Phenotype Databases, Factual FPGMX AS Santiago FPGMX |
| topic |
DNA Copy Number Variations Crowdsourcing Genomics Phenotype Databases, Factual FPGMX AS Santiago FPGMX |
| description |
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. |
| publishDate |
2023 |
| dc.date.none.fl_str_mv |
2023 |
| dc.type.none.fl_str_mv |
info:eu-repo/semantics/article |
| format |
article |
| dc.identifier.none.fl_str_mv |
https://portalcientifico.sergas.gal//documentos/6420454be1b5e93884fa7937 http://hdl.handle.net/20.500.11940/20975 |
| url |
https://portalcientifico.sergas.gal//documentos/6420454be1b5e93884fa7937 http://hdl.handle.net/20.500.11940/20975 |
| dc.language.none.fl_str_mv |
Inglés |
| language_invalid_str_mv |
Inglés |
| dc.rights.none.fl_str_mv |
http://creativecommons.org/licenses/by/4.0/ info:eu-repo/semantics/openAccess |
| rights_invalid_str_mv |
http://creativecommons.org/licenses/by/4.0/ |
| eu_rights_str_mv |
openAccess |
| dc.source.none.fl_str_mv |
reponame:RUNA. Repositorio da Consellería de Sanidade e Sergas instname:Servizo Galego de Saúde (SERGAS) |
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Servizo Galego de Saúde (SERGAS) |
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RUNA. Repositorio da Consellería de Sanidade e Sergas |
| collection |
RUNA. Repositorio da Consellería de Sanidade e Sergas |
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| repository.mail.fl_str_mv |
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1869406214903824384 |
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15,812429 |