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...

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Autores: 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.
Tipo de recurso: artículo
Estado:Versión publicada
Fecha de publicación:2023
País:España
Institución:Institut d’Investigació Biomèdica Sant Pau (IIB Sant Pau)
Repositorio:r-IIB SANT PAU. Repositorio Institucional de Producción Científica del Instituto de Investigación Biomédica Sant Pau
OAI Identifier:oai:iibsantpau.fundanetsuite.com:p16083
Acceso en línea:https://iibsantpau.fundanetsuite.com/Publicaciones/ProdCientif/PublicacionFrw.aspx?id=16083
Access Level:acceso abierto
Palabra clave:adult
anatomical concepts
Article
ataxia
bone dysplasia
brain disease
breast carcinoma
bronchiectasis
cardiomyopathy
colon cancer
congenital malformation
controlled study
copy number variation
crowdsourcing
data base
developmental delay
dystonia
genetic variability
human
hypertrophic cardiomyopathy
intellectual impairment
kidney cyst
kidney failure
learning disorder
leave one out cross validation
lung fibrosis
macrocephaly
microcephaly
muscle weakness
myopathy
neurofibroma
overlapping gene
parkinsonism
pathogenicity
perception deafness
peripheral neuropathy
pharmacogenetic testing
pharmacogenetic variant
phenotype
retinopathy
sensation
short stature
spastic paraplegia
stomach cancer
whole exome sequencing
whole genome sequencing
factual database
genetics
genomics
Crowdsourcing
Databases, Factual
DNA Copy Number Variations
Genomics
Phenotype
Descripción
Sumario: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).

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