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...
| Authors: | , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , |
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| Format: | article |
| Status: | Published version |
| Publication Date: | 2024 |
| Country: | España |
| Institution: | Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunitat Valenciana (FISABIO) |
| Repository: | r-FISABIO. Repositorio Institucional de Producción Científica |
| OAI Identifier: | oai:fisabio.fundanetsuite.com:p17456 |
| Online Access: | https://fisabio.portalinvestigacion.com/publicaciones/17456 |
| Access Level: | Open access |
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SpadaHC: a database to improve the classification of variants in hereditary cancer genes in the Spanish populationMoreno-Cabrera JMFeliubadaló LPineda MPrada-Dacasa PRamos-Muntada MDel Valle JBrunet JGel BCurrás-Freixes MCalsina BSalazar-Hidalgo MERodríguez-Balada MRoig BFernández-Castillejo SDurán Domínguez MArranz Ledo MInfante Sanz MCastillejo ADámaso ESoto JLde Miguel MHidalgo Calero BSánchez-Zapardiel JMRamon Y Cajal TLasa AGisbert-Beamud ALópez-Novo ARuiz-Ponte CPotrony MÁlvarez-Mora MIOsorio ALorda-Sánchez IRobledo MCascón ARuiz ASpataro NHernan IBorràs EMoles-Fernández AEarl JCadiñanos JSánchez-Heras ABBigas ACapellá GLázaro CAccurate 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 UNIV PRESS2024info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionhttps://fisabio.portalinvestigacion.com/publicaciones/17456Database-The Journal of Biological Databases and CurationISSN: 17580463reponame:r-FISABIO. Repositorio Institucional de Producción Científicainstname:Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunitat Valenciana (FISABIO)Inglésinfo:eu-repo/semantics/openAccessoai:fisabio.fundanetsuite.com:p174562026-06-11T12:45:17Z |
| 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 JM |
| 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 JM Feliubadaló L Pineda M Prada-Dacasa P Ramos-Muntada M Del Valle J Brunet J Gel B Currás-Freixes M Calsina B Salazar-Hidalgo ME Rodríguez-Balada M Roig B Fernández-Castillejo S Durán Domínguez M Arranz Ledo M Infante Sanz M Castillejo A Dámaso E Soto JL de Miguel M Hidalgo Calero B Sánchez-Zapardiel JM Ramon Y Cajal T Lasa A Gisbert-Beamud A López-Novo A Ruiz-Ponte C Potrony M Álvarez-Mora MI Osorio A Lorda-Sánchez I Robledo M Cascón A Ruiz A Spataro N Hernan I Borràs E Moles-Fernández A Earl J Cadiñanos J Sánchez-Heras AB Bigas A Capellá G Lázaro C |
| author |
Moreno-Cabrera JM |
| author_facet |
Moreno-Cabrera JM Feliubadaló L Pineda M Prada-Dacasa P Ramos-Muntada M Del Valle J Brunet J Gel B Currás-Freixes M Calsina B Salazar-Hidalgo ME Rodríguez-Balada M Roig B Fernández-Castillejo S Durán Domínguez M Arranz Ledo M Infante Sanz M Castillejo A Dámaso E Soto JL de Miguel M Hidalgo Calero B Sánchez-Zapardiel JM Ramon Y Cajal T Lasa A Gisbert-Beamud A López-Novo A Ruiz-Ponte C Potrony M Álvarez-Mora MI Osorio A Lorda-Sánchez I Robledo M Cascón A Ruiz A Spataro N Hernan I Borràs E Moles-Fernández A Earl J Cadiñanos J Sánchez-Heras AB Bigas A Capellá G Lázaro C |
| author_role |
author |
| author2 |
Feliubadaló L Pineda M Prada-Dacasa P Ramos-Muntada M Del Valle J Brunet J Gel B Currás-Freixes M Calsina B Salazar-Hidalgo ME Rodríguez-Balada M Roig B Fernández-Castillejo S Durán Domínguez M Arranz Ledo M Infante Sanz M Castillejo A Dámaso E Soto JL de Miguel M Hidalgo Calero B Sánchez-Zapardiel JM Ramon Y Cajal T Lasa A Gisbert-Beamud A López-Novo A Ruiz-Ponte C Potrony M Álvarez-Mora MI Osorio A Lorda-Sánchez I Robledo M Cascón A Ruiz A Spataro N Hernan I Borràs E Moles-Fernández A Earl J Cadiñanos J Sánchez-Heras AB Bigas A Capellá G Lázaro C |
| 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 |
| 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 |
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2024 |
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info:eu-repo/semantics/article info:eu-repo/semantics/publishedVersion |
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article |
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publishedVersion |
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https://fisabio.portalinvestigacion.com/publicaciones/17456 |
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https://fisabio.portalinvestigacion.com/publicaciones/17456 |
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Inglés |
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Inglés |
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info:eu-repo/semantics/openAccess |
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openAccess |
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OXFORD UNIV PRESS |
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OXFORD UNIV PRESS |
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Database-The Journal of Biological Databases and Curation ISSN: 17580463 reponame:r-FISABIO. Repositorio Institucional de Producción Científica instname:Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunitat Valenciana (FISABIO) |
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Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunitat Valenciana (FISABIO) |
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r-FISABIO. Repositorio Institucional de Producción Científica |
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r-FISABIO. Repositorio Institucional de Producción Científica |
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