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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Detalles Bibliográficos
Autores: Moreno-Cabrera, José M., Bigas Salvans, Anna, Lázaro, Conxi
Tipo de recurso: artículo
Estado:Versión publicada
Fecha de publicación:2024
País:España
Institución: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:10230/70158
Acceso en línea:http://hdl.handle.net/10230/70158
http://dx.doi.org/10.1093/database/baae055
Access Level:acceso abierto
Palabra clave:Gens del càncer
Càncer--Aspectes genètics
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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.Bigas Salvans, AnnaLázaro, ConxiGens del càncerCàncer--Aspectes genèticsAccurate 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/.Oxford University Press202520252024info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionapplication/pdfapplication/pdfhttp://hdl.handle.net/10230/70158http://dx.doi.org/10.1093/database/baae055http://hdl.handle.net/10230/70158reponame:Recercat. Dipósit de la Recerca de Catalunyainstname:Varias* (Consorci de Biblioteques Universitáries de Catalunya, Centre de Serveis Científics i Acadèmics de Catalunya)InglésDatabase (Oxford). 2024 Jul 4;2024:baae055© The Author(s) 2024. Published by Oxford University Press. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.http://creativecommons.org/licenses/by/4.0/info:eu-repo/semantics/openAccessoai:recercat.cat:10230/701582026-05-29T05:05:01Z
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.
Gens del càncer
Càncer--Aspectes genètics
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.
Bigas Salvans, Anna
Lázaro, Conxi
author Moreno-Cabrera, José M.
author_facet Moreno-Cabrera, José M.
Bigas Salvans, Anna
Lázaro, Conxi
author_role author
author2 Bigas Salvans, Anna
Lázaro, Conxi
author2_role author
author
dc.subject.none.fl_str_mv Gens del càncer
Càncer--Aspectes genètics
topic Gens del càncer
Càncer--Aspectes genètics
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/.
publishDate 2024
dc.date.none.fl_str_mv 2024
2025
2025
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 http://hdl.handle.net/10230/70158
http://dx.doi.org/10.1093/database/baae055
http://hdl.handle.net/10230/70158
url http://hdl.handle.net/10230/70158
http://dx.doi.org/10.1093/database/baae055
dc.language.none.fl_str_mv Inglés
language_invalid_str_mv Inglés
dc.relation.none.fl_str_mv Database (Oxford). 2024 Jul 4;2024:baae055
dc.rights.none.fl_str_mv http://creativecommons.org/licenses/by/4.0/
info:eu-repo/semantics/openAccess
rights_invalid_str_mv http://creativecommons.org/licenses/by/4.0/
eu_rights_str_mv openAccess
dc.format.none.fl_str_mv application/pdf
application/pdf
dc.publisher.none.fl_str_mv Oxford University Press
publisher.none.fl_str_mv Oxford University Press
dc.source.none.fl_str_mv 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
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