The Cancer Genome Atlas (TCGA)
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A The Cancer Genome Atlas (TCGA) is a cancer genomics knowledge base of genomic alterations associated with various types of human cancer.
- Context:
- It can be initiated by the National Cancer Institute (NCI) and the National Human Genome Research Institute (NHGRI) in 2006.
- It can have generated multi-dimensional genomic, epigenomic, transcriptomic, and proteomic data from over 11,000 patients across 33 cancer types.
- It can provide a valuable resource for researchers, clinicians, and patients in the field of cancer genomics and precision oncology.
- It can have Large-scale genomic data generation, including whole-genome sequencing, whole-exome sequencing, and targeted sequencing.
- It can have Multi-dimensional data integration, including gene expression, copy number variation, DNA methylation, and protein expression data.
- It can have standardized data processing and analysis pipelines for consistent and reproducible results.
- It can support Open-access data sharing to facilitate collaboration and discovery in the cancer research community.
- It can have:
- Example(s):
- ...
- Counter-Example(s):
- Gene Expression Omnibus (GEO): A public repository that archives and provides access to high-throughput gene expression data, including microarray and RNA-Seq data from various organisms and experimental conditions.
- ArrayExpress: A public database of functional genomics data, including gene expression data, that stores data from high-throughput functional genomics experiments in compliance with MIAME guidelines.
- OncoKB: A precision oncology knowledge base that provides information on the clinical implications of cancer-related genes and their mutations, as well as potential treatment options based on specific genomic alterations.
- ...
- See: Gene Expression Omnibus (GEO), ArrayExpress, OncoKB, Gene Expression KB, Genomic Record, Gene Expression Record.
References
2023
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- The Cancer Genome Atlas (TCGA) ... project that has been generating and releasing data since its inception in 2006. TCGA has produced a vast amount of multidimensional data, including genomic, transcriptomic, epigenomic, and proteomic information, for over 11,000 patients across 33 cancer types.
The TCGA project officially concluded in 2018. While the project is no longer actively generating new data, the data it produced remains a valuable resource for the scientific community. Researchers continue to analyze and build upon TCGA data, and the datasets are still available through various data portals, such as the National Cancer Institute's Genomic Data Commons (GDC) and the cBioPortal for Cancer Genomics.
- The Cancer Genome Atlas (TCGA) ... project that has been generating and releasing data since its inception in 2006. TCGA has produced a vast amount of multidimensional data, including genomic, transcriptomic, epigenomic, and proteomic information, for over 11,000 patients across 33 cancer types.
2015
- (Tomczak et al., 2015) ⇒ Katarzyna Tomczak, Patrycja Czerwińska, and Maciej Wiznerowicz. (2015). “Review The Cancer Genome Atlas (TCGA): An Immeasurable Source of Knowledge.” Contemporary Oncology / Współczesna Onkologia 2015, no. 1.
- ABSTRACT: The Cancer Genome Atlas (TCGA) is a public funded project that aims to catalogue and discover major cancer-causing genomic alterations to create a comprehensive “atlas” of cancer genomic profiles. So far, TCGA researchers have analysed large cohorts of over 30 human tumours through large-scale genome sequencing and integrated multi-dimensional analyses. Studies of individual cancer types, as well as comprehensive pan-cancer analyses have extended current knowledge of tumorigenesis. A major goal of the project was to provide publicly available datasets to help improve diagnostic methods, treatment standards, and finally to prevent cancer. This review discusses the current status of TCGA Research Network structure, purpose, and achievements.