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CHDbase: A Comprehensive Knowledgebase for Congenital Heart Disease-related Genes and Clinical Manifestations
Wei-Zhen Zhou1, Wenke Li1, Huayan Shen1
1State 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.
Insights
CHDbase is a new resource that consolidates information on congenital heart disease (CHD) genes and variations. This knowledgebase aids researchers and clinicians by organizing scattered findings on CHD etiology and genetic landscape.
Area of Science:
- Genetics
- Bioinformatics
- Medical Genetics
Background:
- Congenital heart disease (CHD) is a prevalent birth defect affecting 1% of newborns.
- Existing research on CHD etiology is fragmented, hindering clinical and research applications.
- A centralized, curated resource is needed to consolidate CHD genetic information.
Purpose of the Study:
- To develop CHDbase, an evidence-based knowledgebase for CHD-related genes and clinical manifestations.
- To manually curate data from extensive scientific literature on CHD.
- To provide a comprehensive and accessible resource for studying CHD genetics.
Main Methods:
- Manual curation of 1114 publications related to CHD.
- Integration of data on 1124 susceptibility genes, 3591 variations, and over 300 CHD types.
- Incorporation of functional annotations from approximately 50 databases and tools.
- Utilized a gene interaction network approach to identify a core CHD sub-network of 163 genes.
Main Results:
- CHDbase links 1124 genes and 3591 variations to over 300 CHD types and syndromes.
- Integrated metadata includes publication details, population/sample information, study strategies, and findings.
- Functional annotations facilitate the interpretation of gene and variation pathogenicity.
- A core CHD gene sub-network of 163 genes was identified, clarifying the genetic landscape.
Conclusions:
- CHDbase offers a comprehensive, freely available resource for CHD research.
- The knowledgebase supports phenotype classification based on shared genetic origins.
- Facilitates understanding of CHD susceptibilities for scientific and medical communities.
Abstract:
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.
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