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

• Published in: Human genomics Vol. 17; no. 1; p. 20
• Main Authors: 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, Peña-Chilet, María, Dopazo, Joaquin
• Format: Journal Article
• Language: English
• Published: England BioMed Central 09-03-2023; BMC
• Subjects: Annotations; Collaboration; Copy number; Crowdsourcing; Databases, Factual; DNA Copy Number Variations - genetics; Genes; Genetic variability; Genomes; Genomics; Genotype & phenotype; Ontology; Pharmacogenomics; Phenotype; Phenotypes; Rare diseases
• ISSN: 1479-7364; 1473-9542; 1479-7364
• DOI: 10.1186/s40246-023-00466-8

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.