CSVS, a crowdsourcing database of the Spanish population genetic variability
Por:
Pena-Chilet, M, Roldan, G, Perez-Florido, J, Ortuno, FM, Carmona, R, Aquino, V, Lopez-Lopez, D, Loucera, C, Fernandez-Rueda, JL, Gallego, A, Garcia-Garcia, F, Gonzalez-Neira, A, Pita, G, Nunez-Torres, R, Santoyo-Lopez, J, Ayuso, C, Minguez, P, Avila-Fernandez, A, Corton, M, Moreno-Pelayo, MA, Morin, M, Gallego-Martinez, A, Lopez-Escamez, JA, Borrego, S, Antinolo, G, Amigo, J, Salgado-Garrido, J, Pasalodos-Sanchez, S, Morte, B, Carracedo, A, Alonso, A, Dopazo, J, SURRALLES CALONGE, JORDI, Spanish Exome Crowdsourcing Consor
Publicada:
8 ene 2021
Resumen:
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.
Filiaciones:
Pena-Chilet, M:
Hosp Virgen del Rocio, Fdn Progreso & Salud FPS, Clin Bioinformat Area, Seville 41013, Spain
ISCIII, Ctr Biomed Network Res Rare Dis CIBERER, Bioinformat Rare Dis BiER, Seville 41013, Spain
Hosp Virgen del Rocio, Computat Syst Med Grp, Inst Biomed Seville IBIS, Seville 41013, Spain
Roldan, G:
Hosp Virgen del Rocio, Fdn Progreso & Salud FPS, Clin Bioinformat Area, Seville 41013, Spain
Perez-Florido, J:
Hosp Virgen del Rocio, Fdn Progreso & Salud FPS, Clin Bioinformat Area, Seville 41013, Spain
Hosp Virgen del Rocio, Computat Syst Med Grp, Inst Biomed Seville IBIS, Seville 41013, Spain
Hosp Virgen del Rocio, FPS ELIXIR ES, Funct Genom Node, Seville 41013, Spain
Ortuno, FM:
Hosp Virgen del Rocio, Fdn Progreso & Salud FPS, Clin Bioinformat Area, Seville 41013, Spain
Hosp Virgen del Rocio, Computat Syst Med Grp, Inst Biomed Seville IBIS, Seville 41013, Spain
Hosp Virgen del Rocio, FPS ELIXIR ES, Funct Genom Node, Seville 41013, Spain
Carmona, R:
Hosp Virgen del Rocio, Fdn Progreso & Salud FPS, Clin Bioinformat Area, Seville 41013, Spain
Aquino, V:
Hosp Virgen del Rocio, Fdn Progreso & Salud FPS, Clin Bioinformat Area, Seville 41013, Spain
Lopez-Lopez, D:
Hosp Virgen del Rocio, Fdn Progreso & Salud FPS, Clin Bioinformat Area, Seville 41013, Spain
Hosp Virgen del Rocio, Computat Syst Med Grp, Inst Biomed Seville IBIS, Seville 41013, Spain
Loucera, C:
Hosp Virgen del Rocio, Fdn Progreso & Salud FPS, Clin Bioinformat Area, Seville 41013, Spain
Hosp Virgen del Rocio, Computat Syst Med Grp, Inst Biomed Seville IBIS, Seville 41013, Spain
Fernandez-Rueda, JL:
Hosp Virgen del Rocio, Fdn Progreso & Salud FPS, Clin Bioinformat Area, Seville 41013, Spain
Gallego, A:
Sistemas Genom, Valencia 46980, Spain
Garcia-Garcia, F:
Ctr Invest Principe Felipe CIPF, Unidad Bioinformat & Bioestadist, Valencia 46012, Spain
Gonzalez-Neira, A:
Spanish Natl Canc Res Ctr CNIO, Human Genotyping Unit, Human Canc Genet Programme, Ctr Nacl Genotipado CEGEN, Madrid 28029, Spain
Pita, G:
Spanish Natl Canc Res Ctr CNIO, Human Genotyping Unit, Human Canc Genet Programme, Ctr Nacl Genotipado CEGEN, Madrid 28029, Spain
Nunez-Torres, R:
Spanish Natl Canc Res Ctr CNIO, Human Genotyping Unit, Human Canc Genet Programme, Ctr Nacl Genotipado CEGEN, Madrid 28029, Spain
Santoyo-Lopez, J:
Univ Edinburgh, Edinburgh Genom, Edinburgh EH9 3FL, Midlothian, Scotland
Ayuso, C:
Univ Autonoma Madrid IIS FJD, Inst Invest Sanitaria, Dept Genet, UAM,Fdn Jimenez Diaz Univ Hosp, Madrid 28040, Spain
Minguez, P:
Univ Autonoma Madrid IIS FJD, Inst Invest Sanitaria, Dept Genet, UAM,Fdn Jimenez Diaz Univ Hosp, Madrid 28040, Spain
ISCIII, Ctr Biomed Network Res Rare Dis CIBERER, Madrid 28040, Spain
Avila-Fernandez, A:
Univ Autonoma Madrid IIS FJD, Inst Invest Sanitaria, Dept Genet, UAM,Fdn Jimenez Diaz Univ Hosp, Madrid 28040, Spain
Corton, M:
Univ Autonoma Madrid IIS FJD, Inst Invest Sanitaria, Dept Genet, UAM,Fdn Jimenez Diaz Univ Hosp, Madrid 28040, Spain
Moreno-Pelayo, MA:
Ramon y Cajal Inst Hlth Res IRYCIS, Serv Genet, Madrid 28034, Spain
Biomed Network Res Ctr Rare Dis CIBERER, Madrid 28034, Spain
Morin, M:
Ramon y Cajal Inst Hlth Res IRYCIS, Serv Genet, Madrid 28034, Spain
Biomed Network Res Ctr Rare Dis CIBERER, Madrid 28034, Spain
Gallego-Martinez, A:
Pfizer Univ Granada, Ctr Genom & Oncol Res GENYO, Dept Genom Med, Otol & Neurotol Grp CTS 495, Granada 18016, Spain
Univ Granada, Hosp Univ Virgen de las Nieves, Inst Invest Biosanitaria, Dept Otolaryngol,IBS, Granada 18016, Spain
Lopez-Escamez, JA:
Pfizer Univ Granada, Ctr Genom & Oncol Res GENYO, Dept Genom Med, Otol & Neurotol Grp CTS 495, Granada 18016, Spain
Univ Granada, Hosp Univ Virgen de las Nieves, Inst Invest Biosanitaria, Dept Otolaryngol,IBS, Granada 18016, Spain
Borrego, S:
Univ Seville, Inst Biomed Seville IBIS, Dept Maternofetal Med Genet & Reprod, Univ Hosp Virgen del Rocio,CSIC, Seville 41013, Spain
Ctr Biomed Network Res Rare Dis CIBERER, Seville 41013, Spain
Antinolo, G:
Univ Seville, Inst Biomed Seville IBIS, Dept Maternofetal Med Genet & Reprod, Univ Hosp Virgen del Rocio,CSIC, Seville 41013, Spain
Ctr Biomed Network Res Rare Dis CIBERER, Seville 41013, Spain
Amigo, J:
IDIS, Fdn Publ Galega Med Xenom, SERGAS, Santiago De Compostela 15706, Spain
Salgado-Garrido, J:
Univ Publ Navarra UPNA, Complejo Hosp Navarra, IdiSNA Navarra Inst Hlth Res, Navarrabiomed IdiSNA, Navarra 31008, Spain
Pasalodos-Sanchez, S:
Univ Publ Navarra UPNA, Complejo Hosp Navarra, IdiSNA Navarra Inst Hlth Res, Navarrabiomed IdiSNA, Navarra 31008, Spain
Morte, B:
ISCIII, Undiagnosed Rare Dis Programme ENoD, Ctr Biomed Res Rare Dis CIBERER, Madrid 28029, Spain
Carracedo, A:
IDIS, Fdn Publ Galega Med Xenom, SERGAS, Santiago De Compostela 15706, Spain
Univ Santiago de Compostela, Ctr Invest Biomed Red Enfermedades Raras CIBERER, CIMUS, Grp Med Xenom, Santiago De Compostela, Spain
Alonso, A:
Univ Publ Navarra UPNA, Complejo Hosp Navarra, IdiSNA Navarra Inst Hlth Res, Navarrabiomed IdiSNA, Navarra 31008, Spain
Dopazo, J:
Hosp Virgen del Rocio, Fdn Progreso & Salud FPS, Clin Bioinformat Area, Seville 41013, Spain
ISCIII, Ctr Biomed Network Res Rare Dis CIBERER, Bioinformat Rare Dis BiER, Seville 41013, Spain
Hosp Virgen del Rocio, Computat Syst Med Grp, Inst Biomed Seville IBIS, Seville 41013, Spain
Hosp Virgen del Rocio, FPS ELIXIR ES, Funct Genom Node, Seville 41013, Spain
SURRALLES CALONGE, JORDI:
Institut d'Investigació Biomèdica Sant Pau (IIBSANTPAU)
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