SpadaHC: a database to improve the classification of variants in hereditary cancer genes in the Spanish population

Moreno Cabrera, José M.; Feliubadaló, Lidia; Pineda, Marta; Prada Dacasa, Patricia; Ramos Muntada, Mireia; Valle, Jesús del; Brunet, Joan; Gel Moreno, Bernat; Currás Freixes, María; Calsina, Bruna; Salazar Hidalgo, Milton E.; Rodríguez Balada, Marta; Roig, Bàrbara; Fernández Castillejo, Sara; Durán Domínguez, Mercedes; Arranz Ledo, Mónica; Infante Sanz, Mar; Castillejo, Adela; Dámaso, Estela; Soto, José Luis; Miguel, Montserrat de; Hidalgo Calero, Beatriz; Sánchez Zapardiel, José M.; Ramon y Cajal, Teresa; Lasa, Adriana; Gisbert Beamud, Alexandra; López Novo, Anael; Ruiz Ponte, Clara; Potrony Mateu, Míriam; Álvarez Mora, María I.; Osorio, Ana; Lorda Sánchez, Isabel; Robledo, Mercedes; Cascón, Alberto; Ruiz, Anna; Spataro, Nino; Hernan, Imma; Borràs, Emma; Moles Fernández, Alejandro; Earl, Julie; Cadiñanos, Juan; Sánchez Heras, Ana B.; Bigas, Anna; Capellá, Gabriel; Lázaro, Conxi

SpadaHC: a database to improve the classification of variants in hereditary cancer genes in the Spanish population

Accurate classification of genetic variants is crucial for clinical decision-making in hereditary cancer. In Spain, genetic diagnostic laboratories have traditionally approached this task independently due to the lack of a dedicated resource. Here we present SpadaHC, a web-based database for sharing...

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Autores:	Moreno Cabrera, José M., Feliubadaló, Lidia, Pineda, Marta, Prada Dacasa, Patricia, Ramos Muntada, Mireia, Valle, Jesús del, Brunet, Joan, Gel Moreno, Bernat, Currás Freixes, María, Calsina, Bruna, Salazar Hidalgo, Milton E., Rodríguez Balada, Marta, Roig, Bàrbara, Fernández Castillejo, Sara, Durán Domínguez, Mercedes, Arranz Ledo, Mónica, Infante Sanz, Mar, Castillejo, Adela, Dámaso, Estela, Soto, José Luis, Miguel, Montserrat de, Hidalgo Calero, Beatriz, Sánchez Zapardiel, José M., Ramon y Cajal, Teresa, Lasa, Adriana, Gisbert Beamud, Alexandra, López Novo, Anael, Ruiz Ponte, Clara, Potrony Mateu, Míriam, Álvarez Mora, María I., Osorio, Ana, Lorda Sánchez, Isabel, Robledo, Mercedes, Cascón, Alberto, Ruiz, Anna, Spataro, Nino, Hernan, Imma, Borràs, Emma, Moles Fernández, Alejandro, Earl, Julie, Cadiñanos, Juan, Sánchez Heras, Ana B., Bigas, Anna, Capellá, Gabriel, Lázaro, Conxi
Formato:	artículo
Estado:	Versión publicada
Fecha de publicación:	2024
País:	España
Recursos:	Varias* (Consorci de Biblioteques Universitáries de Catalunya, Centre de Serveis Científics i Acadèmics de Catalunya)
Repositorio:	Recercat. Dipósit de la Recerca de Catalunya
OAI Identifier:	oai:recercat.cat:2445/214948
Acesso em linha:	https://hdl.handle.net/2445/214948
Access Level:	acceso abierto
Palavra-chave:	Càncer Genètica mèdica Cancer Medical genetics

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dc.title.none.fl_str_mv	SpadaHC: a database to improve the classification of variants in hereditary cancer genes in the Spanish population
title	SpadaHC: a database to improve the classification of variants in hereditary cancer genes in the Spanish population
spellingShingle	SpadaHC: a database to improve the classification of variants in hereditary cancer genes in the Spanish population Moreno Cabrera, José M. Càncer Genètica mèdica Cancer Medical genetics
title_short	SpadaHC: a database to improve the classification of variants in hereditary cancer genes in the Spanish population
title_full	SpadaHC: a database to improve the classification of variants in hereditary cancer genes in the Spanish population
title_fullStr	SpadaHC: a database to improve the classification of variants in hereditary cancer genes in the Spanish population
title_full_unstemmed	SpadaHC: a database to improve the classification of variants in hereditary cancer genes in the Spanish population
title_sort	SpadaHC: a database to improve the classification of variants in hereditary cancer genes in the Spanish population
dc.creator.none.fl_str_mv	Moreno Cabrera, José M. Feliubadaló, Lidia Pineda, Marta Prada Dacasa, Patricia Ramos Muntada, Mireia Valle, Jesús del Brunet, Joan Gel Moreno, Bernat Currás Freixes, María Calsina, Bruna Salazar Hidalgo, Milton E. Rodríguez Balada, Marta Roig, Bàrbara Fernández Castillejo, Sara Durán Domínguez, Mercedes Arranz Ledo, Mónica Infante Sanz, Mar Castillejo, Adela Dámaso, Estela Soto, José Luis Miguel, Montserrat de Hidalgo Calero, Beatriz Sánchez Zapardiel, José M. Ramon y Cajal, Teresa Lasa, Adriana Gisbert Beamud, Alexandra López Novo, Anael Ruiz Ponte, Clara Potrony Mateu, Míriam Álvarez Mora, María I. Osorio, Ana Lorda Sánchez, Isabel Robledo, Mercedes Cascón, Alberto Ruiz, Anna Spataro, Nino Hernan, Imma Borràs, Emma Moles Fernández, Alejandro Earl, Julie Cadiñanos, Juan Sánchez Heras, Ana B. Bigas, Anna Capellá, Gabriel Lázaro, Conxi
author	Moreno Cabrera, José M.
author_facet	Moreno Cabrera, José M. Feliubadaló, Lidia Pineda, Marta Prada Dacasa, Patricia Ramos Muntada, Mireia Valle, Jesús del Brunet, Joan Gel Moreno, Bernat Currás Freixes, María Calsina, Bruna Salazar Hidalgo, Milton E. Rodríguez Balada, Marta Roig, Bàrbara Fernández Castillejo, Sara Durán Domínguez, Mercedes Arranz Ledo, Mónica Infante Sanz, Mar Castillejo, Adela Dámaso, Estela Soto, José Luis Miguel, Montserrat de Hidalgo Calero, Beatriz Sánchez Zapardiel, José M. Ramon y Cajal, Teresa Lasa, Adriana Gisbert Beamud, Alexandra López Novo, Anael Ruiz Ponte, Clara Potrony Mateu, Míriam Álvarez Mora, María I. Osorio, Ana Lorda Sánchez, Isabel Robledo, Mercedes Cascón, Alberto Ruiz, Anna Spataro, Nino Hernan, Imma Borràs, Emma Moles Fernández, Alejandro Earl, Julie Cadiñanos, Juan Sánchez Heras, Ana B. Bigas, Anna Capellá, Gabriel Lázaro, Conxi
author_role	author
author2	Feliubadaló, Lidia Pineda, Marta Prada Dacasa, Patricia Ramos Muntada, Mireia Valle, Jesús del Brunet, Joan Gel Moreno, Bernat Currás Freixes, María Calsina, Bruna Salazar Hidalgo, Milton E. Rodríguez Balada, Marta Roig, Bàrbara Fernández Castillejo, Sara Durán Domínguez, Mercedes Arranz Ledo, Mónica Infante Sanz, Mar Castillejo, Adela Dámaso, Estela Soto, José Luis Miguel, Montserrat de Hidalgo Calero, Beatriz Sánchez Zapardiel, José M. Ramon y Cajal, Teresa Lasa, Adriana Gisbert Beamud, Alexandra López Novo, Anael Ruiz Ponte, Clara Potrony Mateu, Míriam Álvarez Mora, María I. Osorio, Ana Lorda Sánchez, Isabel Robledo, Mercedes Cascón, Alberto Ruiz, Anna Spataro, Nino Hernan, Imma Borràs, Emma Moles Fernández, Alejandro Earl, Julie Cadiñanos, Juan Sánchez Heras, Ana B. Bigas, Anna Capellá, Gabriel Lázaro, Conxi
author2_role	author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author
dc.subject.none.fl_str_mv	Càncer Genètica mèdica Cancer Medical genetics
topic	Càncer Genètica mèdica Cancer Medical genetics
description	Accurate classification of genetic variants is crucial for clinical decision-making in hereditary cancer. In Spain, genetic diagnostic laboratories have traditionally approached this task independently due to the lack of a dedicated resource. Here we present SpadaHC, a web-based database for sharing variants in hereditary cancer genes in the Spanish population. SpadaHC is implemented using a three-tier architecture consisting of a relational database, a web tool and a bioinformatics pipeline. Contributing laboratories can share variant classifications and variants from individuals in Variant Calling Format (VCF) format. The platform supports open and restricted access, flexible dataset submissions, automatic pseudo-anonymization, VCF quality control, variant normalization and liftover between genome builds. Users can flexibly explore and search data, receive automatic discrepancy notifications and access SpadaHC population frequencies based on many criteria. In February 2024, SpadaHC included 18 laboratory members, storing 1.17 million variants from 4306 patients and 16 343 laboratory classifications. In the first analysis of the shared data, we identified 84 genetic variants with clinically relevant discrepancies in their classifications and addressed them through a three-phase resolution strategy. This work highlights the importance of data sharing to promote consistency in variant classifications among laboratories, so patients and family members can benefit from more accurate clinical management.Database URL: https://spadahc.ciberisciii.es/ Overview of SpadaHC and its main views. (A) List of existing variants in SpadaHC (in the image, search for the ATM gene). The 'Expert Cl.' column shows the classification made by a group of experts; the 'Lab Cl.' column shows a summary of the classifications made by the laboratories. (B) Allele frequency of a variant in the SpadaHC population according to clinical suspicion and sex. (C) Classifications provided by the laboratories for a variant. (D) List of patients carrying a variant. (E) Histogram showing the coverage and frequency (allele balance) with which the variant was detected in carrier patients. Alt text: SpadaHC overview; laboratories can share datasets of variant classifications (Excel) and variants from individuals (VCFs + Excel). The datasets undergo quality control, bioinformatics pipeline annotation and database integration before being displayed in SpadaHC. The graphical abstract also shows five views of SpadaHC.
publishDate	2024
dc.date.none.fl_str_mv	2024 2024 2024 2024
dc.type.none.fl_str_mv	info:eu-repo/semantics/article info:eu-repo/semantics/publishedVersion
format	article
status_str	publishedVersion
dc.identifier.none.fl_str_mv	https://hdl.handle.net/2445/214948
url	https://hdl.handle.net/2445/214948
dc.language.none.fl_str_mv	Inglés
language_invalid_str_mv	Inglés
dc.relation.none.fl_str_mv	Reproducció del document publicat a: https://doi.org/10.1093/database/baae055 Database, 2024, vol. 2024 https://doi.org/10.1093/database/baae055
dc.rights.none.fl_str_mv	cc by (c) Moreno Cabrera, José M. et al, 2024 http://creativecommons.org/licenses/by/3.0/es/ info:eu-repo/semantics/openAccess
rights_invalid_str_mv	cc by (c) Moreno Cabrera, José M. et al, 2024 http://creativecommons.org/licenses/by/3.0/es/
eu_rights_str_mv	openAccess
dc.format.none.fl_str_mv	7 p. application/pdf
dc.publisher.none.fl_str_mv	Oxford University Press (OUP)
publisher.none.fl_str_mv	Oxford University Press (OUP)
dc.source.none.fl_str_mv	Articles publicats en revistes (Institut d'lnvestigació Biomèdica de Bellvitge (IDIBELL)) reponame:Recercat. Dipósit de la Recerca de Catalunya instname:Varias* (Consorci de Biblioteques Universitáries de Catalunya, Centre de Serveis Científics i Acadèmics de Catalunya)
instname_str	Varias* (Consorci de Biblioteques Universitáries de Catalunya, Centre de Serveis Científics i Acadèmics de Catalunya)
reponame_str	Recercat. Dipósit de la Recerca de Catalunya
collection	Recercat. Dipósit de la Recerca de Catalunya
repository.name.fl_str_mv
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spelling	SpadaHC: a database to improve the classification of variants in hereditary cancer genes in the Spanish populationMoreno Cabrera, José M.Feliubadaló, LidiaPineda, MartaPrada Dacasa, PatriciaRamos Muntada, MireiaValle, Jesús delBrunet, JoanGel Moreno, BernatCurrás Freixes, MaríaCalsina, BrunaSalazar Hidalgo, Milton E.Rodríguez Balada, MartaRoig, BàrbaraFernández Castillejo, SaraDurán Domínguez, MercedesArranz Ledo, MónicaInfante Sanz, MarCastillejo, AdelaDámaso, EstelaSoto, José LuisMiguel, Montserrat deHidalgo Calero, BeatrizSánchez Zapardiel, José M.Ramon y Cajal, TeresaLasa, AdrianaGisbert Beamud, AlexandraLópez Novo, AnaelRuiz Ponte, ClaraPotrony Mateu, MíriamÁlvarez Mora, María I.Osorio, AnaLorda Sánchez, IsabelRobledo, MercedesCascón, AlbertoRuiz, AnnaSpataro, NinoHernan, ImmaBorràs, EmmaMoles Fernández, AlejandroEarl, JulieCadiñanos, JuanSánchez Heras, Ana B.Bigas, AnnaCapellá, GabrielLázaro, ConxiCàncerGenètica mèdicaCancerMedical geneticsAccurate classification of genetic variants is crucial for clinical decision-making in hereditary cancer. In Spain, genetic diagnostic laboratories have traditionally approached this task independently due to the lack of a dedicated resource. Here we present SpadaHC, a web-based database for sharing variants in hereditary cancer genes in the Spanish population. SpadaHC is implemented using a three-tier architecture consisting of a relational database, a web tool and a bioinformatics pipeline. Contributing laboratories can share variant classifications and variants from individuals in Variant Calling Format (VCF) format. The platform supports open and restricted access, flexible dataset submissions, automatic pseudo-anonymization, VCF quality control, variant normalization and liftover between genome builds. Users can flexibly explore and search data, receive automatic discrepancy notifications and access SpadaHC population frequencies based on many criteria. In February 2024, SpadaHC included 18 laboratory members, storing 1.17 million variants from 4306 patients and 16 343 laboratory classifications. In the first analysis of the shared data, we identified 84 genetic variants with clinically relevant discrepancies in their classifications and addressed them through a three-phase resolution strategy. This work highlights the importance of data sharing to promote consistency in variant classifications among laboratories, so patients and family members can benefit from more accurate clinical management.Database URL: https://spadahc.ciberisciii.es/ Overview of SpadaHC and its main views. (A) List of existing variants in SpadaHC (in the image, search for the ATM gene). The 'Expert Cl.' column shows the classification made by a group of experts; the 'Lab Cl.' column shows a summary of the classifications made by the laboratories. (B) Allele frequency of a variant in the SpadaHC population according to clinical suspicion and sex. (C) Classifications provided by the laboratories for a variant. (D) List of patients carrying a variant. (E) Histogram showing the coverage and frequency (allele balance) with which the variant was detected in carrier patients. Alt text: SpadaHC overview; laboratories can share datasets of variant classifications (Excel) and variants from individuals (VCFs + Excel). The datasets undergo quality control, bioinformatics pipeline annotation and database integration before being displayed in SpadaHC. The graphical abstract also shows five views of SpadaHC.Oxford University Press (OUP)2024202420242024info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersion7 p.application/pdfhttps://hdl.handle.net/2445/214948Articles publicats en revistes (Institut d'lnvestigació Biomèdica de Bellvitge (IDIBELL))reponame:Recercat. Dipósit de la Recerca de Catalunyainstname:Varias* (Consorci de Biblioteques Universitáries de Catalunya, Centre de Serveis Científics i Acadèmics de Catalunya)InglésReproducció del document publicat a: https://doi.org/10.1093/database/baae055Database, 2024, vol. 2024https://doi.org/10.1093/database/baae055cc by (c) Moreno Cabrera, José M. et al, 2024http://creativecommons.org/licenses/by/3.0/es/info:eu-repo/semantics/openAccessoai:recercat.cat:2445/2149482026-05-29T05:05:01Z
score	15,811543

SpadaHC: a database to improve the classification of variants in hereditary cancer genes in the Spanish population

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