A study recently published in the scientific journal Database: The Journal of Biological Database and Curation presents SpadaHC, a new tool that allows genetic diagnosis-registered Spanish centers share data among them. This collaboration aims to improve the classification of genetic variants that predispose to hereditary cancer. SpadaHC, whose name derives from “SPAnish DAtabase for Hereditary Cancer”, results from an effort promoted by the CIBER through its cancer area (CIBERONC), which includes researchers from the Bellvitge Biomedical Research Institute (IDIBELL) and the Catalan Institute of Oncology (ICO) and counted on the participation of the Spanish Society of Human Genetics (AEGH), the Spanish Society of Medical Oncology (SEOM) , and 20 Spanish research centers and hospitals.
Relevance of the genetic variants classification
The classification of genetic variants is essential for clinical decision-making in patients with suspected hereditary cancer, impacting both the patient and their relatives. Better cancer risk assessment, follow-up recommendations, reproductive counseling, and accurate treatments are possible through a correct classification of these variants. Classifying genetic variants is, however, a very complex task: it involves integrating information from different sources, from bioinformatics tools to genetic studies conducted on relatives.
In Spain, multiple genetic diagnostic laboratories that detect and classify these genetic variants did not have a tool to share these variants information until now. SpadaHC was born as a solution for them: this web platform allows Spanish genetic diagnosis laboratories to share data on variants in hereditary cancer genes, ensuring that the variants classification does not differ between laboratories.
Features of SpadaHC
SpadaHC allows laboratories to contribute both genetic variant classifications and individual variants in VCF (Variant Call Format), which is used to store detailed information about genetic variations observed in individuals. These variants are obtained using the advanced NGS (Next-Generation Sequencing) mass sequencing technique, which provides a detailed and efficient DNA reading, thus allowing a better understanding and management of the genetic predisposition to cancer.
José Marcos Moreno-Cabrera, first author of the study and responsible for the development of SpadaHC at IDIBELL, lists some of the most outstanding features of the tool. Among others, he highlights “the automatic notification system that warns when a variant of interest is classified by another laboratory. This helps to quickly identify potential discrepancies with other labs. In addition, SpadaHC has two levels of data access – open and restricted – to protect sensitive patient information, a flexible variant submission system to adapt to the specific format of each laboratory, multiple options to explore the data, and the calculation of the population frequencies of each variant in SpadaHC patients.”
Impact and scope of SpadaHC
Since its launch in May 2023, 20 laboratories belonging to 18 Spanish centers have joined SpadaHC, and 11 more are in the process of joining. As of July 2024, SpadaHC already stores 1.17 million variants from 4306 patients along with 16588 classifications submitted by laboratories. Anna Bigas, CIBERONC director, emphasizes that this effort already has an impact on the management of these patients and families.
A first example was the work that allowed the identification of 84 genetic variants whose classifications had clinically-relevant discrepancies between laboratories. These discrepancies were resolved using a three-phase resolution strategy explained in the aforementioned article. Conxi Lázaro and Gabriel Capellá, SpadaHC coordinators and CIBERONC research staff at IDIBELL and ICO, agree that “these results demonstrate the value of the platform to promote homogeneity in the classification of variants between laboratories.”
For more information about SpadaHC, you can visit the website spadahc.ciberisciii.es
The Bellvitge Biomedical Research Institute (IDIBELL) is a biomedical research center created in 2004. It is participated by the Bellvitge University Hospital and the Viladecans Hospital of the Catalan Institute of Health, the Catalan Institute of Oncology, the University of Barcelona and the City Council of L’Hospitalet de Llobregat.
IDIBELL is a member of the Campus of International Excellence of the University of Barcelona HUBc and is part of the CERCA institution of the Generalitat de Catalunya. In 2009 it became one of the first five Spanish research centers accredited as a health research institute by the Carlos III Health Institute. In addition, it is part of the “HR Excellence in Research” program of the European Union and is a member of EATRIS and REGIC. Since 2018, IDIBELL has been an Accredited Center of the AECC Scientific Foundation (FCAECC).