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Rodríguez-Balada MAuthorRoig BAuthorFernández-Castillejo SAuthor
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SpadaHC: a database to improve the classification of variants in hereditary cancer genes in the Spanish population.

Publicated to:Database-The Journal Of Biological Databases And Curation. 2024 baae055- - 2024-07-04 2024(), DOI: 10.1093/database/baae055

Authors: 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

Affiliations

Biomedical Network Research Centre On Rare Diseases (CIBERER), Instituto de Salud Carlos III, Monforte de Lemos, 3-5, Madrid 28029, Spain. - Author
Cancer Genetic Counseling Unit, Medical Oncology Department, Elche General University Hospital, Almazara, 11, Elche 03203, Spain. - Author
Cancer Genetics Group, Unit of Excellence Institute of Biomedicine and Molecular Genetics, University of Valladolid-Spanish National Research Council (IBGM, UVa- CSIC), Sanz y Fores, 3, Valladolid 47003, Spain. - Author
Centro de Investigación Biomédica en Red Cáncer (CIBERONC), Instituto de Salud Carlos III, Monforte de Lemos, 3-5, Madrid, 28029, Spain. - Author
Department of Clinical and Molecular Genetics, Vall d'Hebron Barcelona Hospital Campus, Vall d'Hebron Hospital Universitari, Pg. de la Vall d'Hebron, 119, Barcelona 08035, Spain. - Author
Familial Cancer Clinic, Medical Oncology, Hospital de la Santa Creu i Sant Pau, Sant Quintí, 89, Barcelona 08041, Spain. - Author
Familial Cancer Clinical Unit, Human Cancer Genetics Program, Spanish National Cancer Research Centre (CNIO), Melchor Fernández Almagro, 3, Madrid 28029, Spain. - Author
Fundación Centro Médico de Asturias, José María Richard Grandío, s/n, Oviedo, Asturias 33193, Spain. - Author
Fundación Pública Galega de Medicina Xenómica (SERGAS), Instituto de Investigación Sanitaria de Santiago, Grupo de Medicina Xenómica-USC, Av. Barcelona, s/n, Santiago de Compostela 15706, Spain. - Author
Genetics Department, Hospital de la Santa Creu i Sant Pau, Sant Quintí, 89, Barcelona 08041, Spain. - Author
Genetics Laboratory, Center for Genomic Medicine, Parc Taulí Hospital Universitari, Institut d'Investigació i Innovació Parc Taulí (I3PT-CERCA), Universitat Autònoma de Barcelona, Plaça Torre de l'Aigua, s/n, Sabadell 08208, Spain. - Author
Hereditary Cancer Group, Program for Predictive and Personalized Medicine of Cancer, Germans Trias i Pujol Research Institute (PMPPC-IGTP), Campus Can Ruti, Ctra de Can Ruti, Camí de les Escoles, s/n, Badalona 08916, Spain. - Author
Hereditary Cancer Program, Catalan Institute of Oncology, Institut d'Investigació Biomèdica de Bellvitge-IDIBELL-ONCOBELL, L'Hospitalet de Llobregat, Barcelona 08908, Spain. - Author
Institut d'Oncologia de la Catalunya Sud (IOCS), Hospital Universitari Sant Joan de Reus (HUSJR), Institut d'Investigació Sanitària Pere Virgili (IISPV), Universitat Rovira i Virgili (URV), Dr. Josep Laporte, 2, Reus 43204, Spain. - Author
Institut de Recerca Sant Pau (IR Sant Pau), Sant Quintí, 77, Barcelona 08041, Spain. - Author
Laboratorio de cáncer hereditario, Servicio de Bioquímica clínica-Análisis clínicos, Hospital Universitario 12 de Octubre, Av. de Córdoba, s/n, Madrid 28041, Spain. - Author
Molecular Genetics Unit, Consorci Sanitari de Terrassa, Ctra. Torrebonica, S/N, Terrassa 08227, Spain. - Author
Unidad de Genética Molecular, Hospital General Universitario de Elche. Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunitat Valenciana (FISABIO), Av. de Catalunya, 21, Elche 03203, Spain. - Author
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Abstract

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/.

Keywords
Databases, geneticGenes, neoplasmGenetic predisposition to diseaseGenetic variationHumansNeoplasmsSpain

Quality index

Bibliometric impact. Analysis of the contribution and dissemination channel

The work has been published in the journal Database-The Journal Of Biological Databases And Curation due to its progression and the good impact it has achieved in recent years, according to the agency WoS (JCR), it has become a reference in its field. In the year of publication of the work, 2024 there are still no calculated indicators, but in 2023, it was in position 13/66, thus managing to position itself as a Q1 (Primer Cuartil), in the category Mathematical & Computational Biology.

Impact and social visibility

From the perspective of influence or social adoption, and based on metrics associated with mentions and interactions provided by agencies specializing in calculating the so-called "Alternative or Social Metrics," we can highlight as of 2025-05-11:

  • The use, from an academic perspective evidenced by the Altmetric agency indicator referring to aggregations made by the personal bibliographic manager Mendeley, gives us a total of: 13.
  • The use of this contribution in bookmarks, code forks, additions to favorite lists for recurrent reading, as well as general views, indicates that someone is using the publication as a basis for their current work. This may be a notable indicator of future more formal and academic citations. This claim is supported by the result of the "Capture" indicator, which yields a total of: 10 (PlumX).

With a more dissemination-oriented intent and targeting more general audiences, we can observe other more global scores such as:

  • The Total Score from Altmetric: 4.

It is essential to present evidence supporting full alignment with institutional principles and guidelines on Open Science and the Conservation and Dissemination of Intellectual Heritage. A clear example of this is:

  • The work has been submitted to a journal whose editorial policy allows open Open Access publication.