Somatic cancer mutation databases | Genome annotation
High-throughput DNA sequencing has revolutionized the study of cancer genomics with numerous discoveries that are relevant to cancer diagnosis and treatment. The latest sequencing and analysis methods have successfully identified somatic alterations, including single-nucleotide variants, insertions and deletions, copy-number aberrations, structural variants and gene fusions.
A comprehensive description of genomic, transcriptomic and epigenomic changes in 50 different tumor types and/or subtypes which are of clinical and societal importance across the globe. The ICGC facilitates communication among the members and provides a forum for coordination with the objective of maximizing efficiency among the scientists working to understand, treat, and prevent these diseases.
Provides a comprehensive resource of cancer evolutionary stage-specific events and their temporal orders. SEECancer is an online database containing over 1200 cancer evolutionary stage-specific somatic events. It supplies several features for browsing the query results: (1) users can filter entries by typing any term in the ‘Search’ field on the top right side above the table; (2) they can sort columns in an ascending fashion; (3) the table size per page can be selected by using the ‘Show entries’ pull-down menu.
Compiles information about mutational signatures in 73 TCGA/ICGC cancer projects. mSignatureDB is composed of four main panels: (i) the browse panel allows users to manipulate landscapes and contributions of mutational signatures according multiple views; (ii) the search panel authorizes to explore TCGA/ICGC cancer projects, individual sample or run cross-project comparisons; (iii) the analysis panel provides an interface for deconstructSigs and R-based WTSI Mutational Signature Framework software and; (iv) the download panel permits loading of mutational signature patterns of TCGA/ICGC tumors.
Facilitates feature retrieval and classification of very large single nucleotide variants (SNVs) datasets. SNVBox is a database of pre-computed predictive features that can be generally used to aid in the development of classification algorithms that predict the impact of either germline or somatic SNVs. The features have been precomputed for each codon in all protein-coding exons of annotated human mRNA transcripts.
Provides an interface for biologists and clinicians working on solid tumors and hematological malignancies. OncoPortal is a platform based on precision medicine intelligence with curated and reliable databases on gene biomarkers and clinical trials. It contains annotations of associations between human gene variants, disease causality, progression and drug efficacy and toxicity. It offers access to somatic classification, specific drug association with the disease and clinical evidence summaries.
Enables to explore the impact of somatic mutations in human cancer. COSMIC is a database system that collects these somatic mutation data from a variety of public sources into one standardized repository, and make it easily explorable in a variety of graphical, tabulated and downloadable ways. The database encompasses all forms of human cancer. COSMIC is built primarily via curation of published literature by expert scientists. The database is also available for download in multiple formats.
An online network for sharing somatic cancer genomic and clinical data from around the world, making the data accessible for research use in real time. CGTD provides a basic HTML interface and RESTful API to add, list and authenticate submissions as well as the peering relationship between stewards. Submissions consist of a JSON manifest with a list of fields and files. Fields typically include de-identified clinical data (i.e. tumor type). Files typically consist of somatic variant vcf files and gene expression tsv file. Manifest's and files are stored and referenced by the multihash of their content.