A crowdsourcing database for the copy-number variation of the Spanish population.
Journal
Human genomics
ISSN: 1479-7364
Titre abrégé: Hum Genomics
Pays: England
ID NLM: 101202210
Informations de publication
Date de publication:
09 03 2023
09 03 2023
Historique:
received:
12
09
2022
accepted:
25
02
2023
entrez:
9
3
2023
pubmed:
10
3
2023
medline:
14
3
2023
Statut:
epublish
Résumé
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.
Sections du résumé
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.
Identifiants
pubmed: 36894999
doi: 10.1186/s40246-023-00466-8
pii: 10.1186/s40246-023-00466-8
pmc: PMC9997023
doi:
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
20Investigateurs
Angel Alonso
(A)
Josefa Salgado-Garrido
(J)
Sara Pasalodos-Sanchez
(S)
Carmen Ayuso
(C)
Pablo Minguez
(P)
Almudena Avila-Fernandez
(A)
Marta Corton
(M)
Rafael Artuch
(R)
Salud Borrego
(S)
Guillermo Antiñolo
(G)
Angel Carracedo
(A)
Jorge Amigo
(J)
Luis Antonio Castaño
(LA)
Isabel Tejada
(I)
Aitor Delmiro
(A)
Carmina Espinos
(C)
Daniel Grinberg
(D)
Encarnación Guillén
(E)
Pablo Lapunzina
(P)
Jose Antonio Lopez-Escámez
(JA)
Alvaro Gallego-Martinez
(A)
Ramón Martí
(R)
Eulalia Rovira
(E)
José Mª Millán
(JM)
Miguel Angel Moreno
(MA)
Matías Morin
(M)
Antonio Moreno-Galdó
(A)
Mónica Fernández-Cancio
(M)
Beatriz Morte
(B)
Victoriano Mulero
(V)
Diana García
(D)
Virginia Nunes
(V)
Francesc Palau
(F)
Belén Perez
(B)
Luis Pérez Jurado
(LP)
Rosario Perona
(R)
Aurora Pujol
(A)
Feliciano Ramos
(F)
Esther Lopez
(E)
Antonia Ribes
(A)
Jordi Rosell
(J)
Jordi Surrallés
(J)
Informations de copyright
© 2023. The Author(s).
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