CSVS, a crowdsourcing database of the Spanish population genetic variability.
Journal
Nucleic acids research
ISSN: 1362-4962
Titre abrégé: Nucleic Acids Res
Pays: England
ID NLM: 0411011
Informations de publication
Date de publication:
08 01 2021
08 01 2021
Historique:
accepted:
10
09
2020
revised:
08
09
2020
received:
13
08
2020
pubmed:
30
9
2020
medline:
29
1
2021
entrez:
29
9
2020
Statut:
ppublish
Résumé
The knowledge of the genetic variability of the local population is of utmost importance in personalized medicine and has been revealed as a critical factor for the discovery of new disease variants. Here, we present the Collaborative Spanish Variability Server (CSVS), which currently contains more than 2000 genomes and exomes of unrelated Spanish individuals. This database has been generated in a collaborative crowdsourcing effort collecting sequencing data produced by local genomic projects and for other purposes. Sequences have been grouped by ICD10 upper categories. A web interface allows querying the database removing one or more ICD10 categories. In this way, aggregated counts of allele frequencies of the pseudo-control Spanish population can be obtained for diseases belonging to the category removed. Interestingly, in addition to pseudo-control studies, some population studies can be made, as, for example, prevalence of pharmacogenomic variants, etc. In addition, this genomic data has been used to define the first Spanish Genome Reference Panel (SGRP1.0) for imputation. This is the first local repository of variability entirely produced by a crowdsourcing effort and constitutes an example for future initiatives to characterize local variability worldwide. CSVS is also part of the GA4GH Beacon network. CSVS can be accessed at: http://csvs.babelomics.org/.
Identifiants
pubmed: 32990755
pii: 5912819
doi: 10.1093/nar/gkaa794
pmc: PMC7778906
doi:
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
D1130-D1137Subventions
Organisme : NIMHD NIH HHS
ID : L60 MD003721
Pays : United States
Investigateurs
Fátima Al-Shahrour
(F)
Rafael Artuch
(R)
Javier Benitez
(J)
Luis Antonio Castaño
(LA)
Ignacio Del Castillo
(ID)
Aitor Delmiro
(A)
Carmina Espinos
(C)
Roser González
(R)
Daniel Grinberg
(D)
Encarnación Guillén
(E)
Pablo Lapunzina
(P)
Esther Lopez
(E)
Ramón Martí
(R)
Montserrat Milá
(M)
José Mª Millán
(JM)
Virginia Nunes
(V)
Francesc Palau
(F)
Belen Perez
(B)
Luis Pérez Jurado
(LP)
Rosario Perona
(R)
Aurora Pujol
(A)
Feliciano Ramos
(F)
Antonia Ribes
(A)
Jordi Rosell
(J)
Eulalia Rovira
(E)
Jordi Surrallés
(J)
Isabel Tejada
(I)
Magdalena Ugarte
(M)
Informations de copyright
© The Author(s) 2020. Published by Oxford University Press on behalf of Nucleic Acids Research.
Références
Nat Genet. 2014 Aug;46(8):818-25
pubmed: 24974849
PLoS Genet. 2013 May;9(5):e1003447
pubmed: 23717210
Hum Mutat. 2019 Nov;40(11):1968-1984
pubmed: 31343797
Nat Biotechnol. 2015 Sep;33(9):933-40
pubmed: 26258538
Nature. 2016 Aug 17;536(7616):285-91
pubmed: 27535533
Pharmacogenomics J. 2017 Dec;17(6):494-500
pubmed: 27503578
Orphanet J Rare Dis. 2013 Dec 02;8:187
pubmed: 24289864
Genet Med. 2013 Sep;15(9):733-47
pubmed: 23887774
Clin Pharmacol Ther. 2015 Mar;97(3):263-73
pubmed: 25669658
Nature. 2013 Jan 10;493(7431):216-20
pubmed: 23201682
Curr Protoc Hum Genet. 2013 Jan;Chapter 7:Unit7.20
pubmed: 23315928
Nature. 2011 Jul 13;475(7355):163-5
pubmed: 21753830
Nucleic Acids Res. 2012 Jul;40(Web Server issue):W609-14
pubmed: 22693220
Nucleic Acids Res. 2013 Jul;41(Web Server issue):W41-6
pubmed: 23748955
Nucleic Acids Res. 2019 Jan 8;47(D1):D941-D947
pubmed: 30371878
Brief Bioinform. 2016 Jan;17(1):23-32
pubmed: 25888696
Science. 2012 Jul 6;337(6090):100-4
pubmed: 22604722
Genet Med. 2017 Feb;19(2):209-214
pubmed: 27441994
Nature. 2012 Nov 1;491(7422):56-65
pubmed: 23128226
Nat Rev Genet. 2019 Nov;20(11):693-701
pubmed: 31455890
Nat Commun. 2015 Aug 21;6:8018
pubmed: 26292667
Nature. 2009 Sep 10;461(7261):272-6
pubmed: 19684571
Nucleic Acids Res. 2003 Jul 1;31(13):3812-4
pubmed: 12824425
Sci Transl Med. 2013 Apr 17;5(181):181re1
pubmed: 23596205
Nature. 2010 Oct 28;467(7319):1061-73
pubmed: 20981092
Genome Biol. 2011 Sep 14;12(9):R84
pubmed: 21917140
Nat Genet. 2013 May;45(5):468-9
pubmed: 23619782
PLoS Comput Biol. 2010 Dec 02;6(12):e1001025
pubmed: 21152010
Genome Biol. 2016 Jun 06;17(1):122
pubmed: 27268795
Nat Genet. 2015 May;47(5):435-44
pubmed: 25807286
Nat Genet. 2016 Oct;48(10):1284-1287
pubmed: 27571263
Hum Genomics. 2018 May 25;12(1):26
pubmed: 29793534
Cell. 2019 Mar 21;177(1):32-37
pubmed: 30901545
PLoS Genet. 2014 Jul 31;10(7):e1004494
pubmed: 25078778
Am J Hum Genet. 2011 Apr 8;88(4):440-9
pubmed: 21457909
Bioinformatics. 2017 Feb 15;33(4):471-474
pubmed: 27563026
Genome Biol. 2017 Mar 8;18(1):48
pubmed: 28274275
Hum Mutat. 2015 Oct;36(10):915-21
pubmed: 26295439
PLoS Genet. 2013 Nov;9(11):e1003925
pubmed: 24244192
Nat Genet. 2012 Feb 05;44(3):243-6
pubmed: 22306651
Nature. 2012 Sep 6;489(7414):57-74
pubmed: 22955616
Am J Hum Genet. 2017 May 4;100(5):695-705
pubmed: 28475856
Wiley Interdiscip Rev Syst Biol Med. 2018 Jul;10(4):e1417
pubmed: 29474005
Mol Biol Evol. 2016 May;33(5):1205-18
pubmed: 26764160
PLoS Genet. 2013;9(9):e1003815
pubmed: 24086152
Nat Protoc. 2017 Feb;12(2):213-218
pubmed: 28055035
Nat Genet. 2014 Mar;46(3):310-5
pubmed: 24487276
Am J Hum Genet. 2007 Apr;80(4):727-39
pubmed: 17357078
Database (Oxford). 2015 Apr 15;2015:bav028
pubmed: 25877637
Nat Biotechnol. 2019 Aug;37(8):848-850
pubmed: 31324891
Nucleic Acids Res. 2016 Jul 8;44(W1):W90-7
pubmed: 27141961
Nat Genet. 2010 Sep;42(9):790-3
pubmed: 20711175
Am J Hum Genet. 2013 Jan 10;92(1):52-66
pubmed: 23290073
Genome Res. 2009 Sep;19(9):1655-64
pubmed: 19648217
Hear Res. 2020 Nov;397:107872
pubmed: 31874721
Nat Genet. 2010 Jan;42(1):30-5
pubmed: 19915526
Nat Rev Genet. 2004 Sep;5(9):669-76
pubmed: 15372089
Nucleic Acids Res. 2018 Jan 4;46(D1):D1062-D1067
pubmed: 29165669
Nat Rev Genet. 2020 Aug;21(8):448
pubmed: 32488197
Nat Rev Genet. 2013 Oct;14(10):681-91
pubmed: 23999272