RESUMEN
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/.
Asunto(s)
Bases de Datos Genéticas , Humanos , España , Variación Genética , Neoplasias/genética , Genes Relacionados con las Neoplasias , Predisposición Genética a la EnfermedadRESUMEN
Este documento de posicionamiento, auspiciado por la Asociación Española de Gastroenterología, la Sociedad Española de Oncología Médica, la Asociación Española de Genética Humana y el consorcio IMPaCT-Genómica, tiene como objetivo realizar recomendaciones para el uso de paneles de genes en la evaluación de individuos con alto riesgo de cáncer digestivo hereditario. Para medir la calidad de la evidencia y los niveles de recomendación se ha utilizado la metodología basada en el sistema Grading of Recommendations Assessment, Development and Evaluation (GRADE). Se obtuvo el consenso entre expertos mediante un método Delphi. El documento incluye recomendaciones sobre escenarios clínicos en los que se recomienda el uso de paneles de genes en cáncer colorrectal, síndromes polipósicos, cáncer gástrico y pancreático, así como los genes de los paneles a ser considerados en cada una de estas situaciones clínicas. También se establecen recomendaciones sobre la evaluación de mosaicismos, las estrategias de asesoramiento ante la ausencia de sujeto índice y, finalmente, el análisis constitucional tras identificación de variantes patogénicas tumorales. (AU)
This position statement, sponsored by the Asociación Española de Gastroenterología, the Sociedad Española de Oncología Médica, the Asociación Española de Genética Humana and the IMPaCT-Genómica Consortium aims to establish recommendations for use of multi-gene panel testing in patients at high risk of hereditary gastrointestinal and pancreatic cancer. To rate the quality of the evidence and the levels of recommendation, we used the methodology based on the GRADE system (Grading of Recommendations Assessment, Development and Evaluation). We reached a consensus among experts using a Delphi method. The document includes recommendations on clinical scenarios where multi-gene panel testing is recommended in colorectal cancer, polyposis syndromes, gastric and pancreatic cancer, as well as the genes to be considered in each clinical scenario. Recommendations on the evaluation of mosaicisms, counseling strategies in the absence of an index subject and, finally, constitutional analysis after identification of pathogenic tumor variants are also made. (AU)