State Key Laboratory of Cardiovascular Disease, Beijing Key Laboratory for Molecular Diagnostics of Cardiovascular Diseases, Center of Laboratory Medicine, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100037, China.
International Joint Informatics Laboratory & Jiangsu Key Laboratory of Data Engineering and Knowledge Service, School of Information Management, Nanjing University, Nanjing 210023, China.
Genomics Proteomics Bioinformatics. 2023 Feb;21(1):216-227. doi: 10.1016/j.gpb.2022.08.001. Epub 2022 Aug 10.
Congenital heart disease (CHD) is one of themost common causes of major birth defects, with a prevalence of 1%. Although an increasing number of studies have reported the etiology of CHD, the findings scattered throughout the literature are difficult to retrieve and utilize in research and clinical practice. We therefore developed CHDbase, an evidence-based knowledgebase of CHD-related genes and clinical manifestations manually curated from 1114 publications, linking 1124susceptibility genes and 3591 variations to more than 300 CHD types and related syndromes. Metadata such as the information of each publication and the selected population and samples, the strategy of studies, and the major findings of studies were integrated with each item of the research record. We also integrated functional annotations through parsing ∼ 50 databases/tools to facilitate the interpretation of these genes and variations in disease pathogenicity. We further prioritized the significance of these CHD-related genes with a gene interaction network approach and extracted a core CHD sub-network with 163 genes. The clear genetic landscape of CHD enables the phenotype classification based on the shared genetic origin. Overall, CHDbase provides a comprehensive and freely available resource to study CHD susceptibilities, supporting a wide range of users in the scientific and medical communities. CHDbase is accessible at http://chddb.fwgenetics.org.
先天性心脏病（CHD）是最常见的重大出生缺陷之一，患病率为 1%。尽管越来越多的研究报告了 CHD 的病因，但文献中的发现难以检索和用于研究和临床实践。因此，我们开发了 CHDbase，这是一个从 1114 篇文献中手动整理的 CHD 相关基因和临床表现的循证知识库，将 1124 个易感基因和 3591 个变异与 300 多种 CHD 类型和相关综合征联系起来。每个项目都整合了元数据，如每个出版物的信息、选定的人群和样本、研究策略以及研究的主要发现。我们还通过解析 ∼ 50 个数据库/工具进行功能注释，以促进对这些基因和变异在疾病发病机制中的解释。我们还通过基因相互作用网络方法对这些 CHD 相关基因的重要性进行了优先级排序，并提取了一个包含 163 个基因的核心 CHD 子网络。CHD 的明确遗传图谱使得能够基于共享遗传起源进行表型分类。总的来说，CHDbase 提供了一个全面的、免费的资源，用于研究 CHD 的易感性，支持科学界和医学界的广泛用户。CHDbase 可在 http://chddb.fwgenetics.org 访问。
