SpadaHC：一个用于改进西班牙人群遗传性癌症基因变异分类的数据库。
SpadaHC: a database to improve the classification of variants in hereditary cancer genes in the Spanish population.
发表日期：2024 Jul 04
作者：
José M Moreno-Cabrera, Lidia Feliubadaló, Marta Pineda, Patricia Prada-Dacasa, Mireia Ramos-Muntada, Jesús Del Valle, Joan Brunet, Bernat Gel, María Currás-Freixes, Bruna Calsina, Milton E Salazar-Hidalgo, Marta Rodríguez-Balada, Bàrbara Roig, Sara Fernández-Castillejo, Mercedes Durán Domínguez, Mónica Arranz Ledo, Mar Infante Sanz, Adela Castillejo, Estela Dámaso, José L Soto, Montserrat de Miguel, Beatriz Hidalgo Calero, José M Sánchez-Zapardiel, Teresa Ramon Y Cajal, Adriana Lasa, Alexandra Gisbert-Beamud, Anael López-Novo, Clara Ruiz-Ponte, Miriam Potrony, María I Álvarez-Mora, Ana Osorio, Isabel Lorda-Sánchez, Mercedes Robledo, Alberto Cascón, Anna Ruiz, Nino Spataro, Imma Hernan, Emma Borràs, Alejandro Moles-Fernández, Julie Earl, Juan Cadiñanos, Ana B Sánchez-Heras, Anna Bigas, Gabriel Capellá, Conxi Lázaro
来源：
BIOMEDICINE & PHARMACOTHERAPY
摘要：
遗传变异的准确分类对于遗传性癌症的临床决策至关重要。在西班牙，由于缺乏专用资源，遗传诊断实验室传统上独立完成这项任务。在这里，我们介绍 SpadaHC，一个基于网络的数据库，用于共享西班牙人群中遗传性癌症基因的变异。 SpadaHC 使用三层架构实现，包括关系数据库、Web 工具和生物信息学管道。贡献实验室可以以变体调用格式 (VCF) 格式共享变体分类和来自个体的变体。该平台支持开放和受限访问、灵活的数据集提交、自动伪匿名化、VCF 质量控制、变异标准化和基因组构建之间的提升。用户可以灵活地探索和搜索数据、接收自动差异通知并根据许多标准访问 SpadaHC 人口频率。 2024 年 2 月，SpadaHC 包括 18 个实验室成员，存储了来自 4306 名患者的 117 万个变异和 16 343 个实验室分类。在对共享数据的第一次分析中，我们确定了 84 个在分类上存在临床相关差异的遗传变异，并通过三阶段解决策略解决了这些问题。这项工作强调了数据共享对于促进实验室之间变异分类一致性的重要性，因此患者和家庭成员可以从更准确的临床管理中受益。数据库网址：https://spadahc.ciberisciii.es/。© 作者 2024。由牛津大学出版社出版。
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/.© The Author(s) 2024. Published by Oxford University Press.