What data is available in TCGA?
TCGA contains molecular data from multiple types of analysis:
- DNA sequencing. Whole genome sequences.
- RNA sequencing. miRNA sequences (calculated expression per miRNA and isoform)
- Copy number. Arrays (raw, unnormalized, normalized)
- Array-based expression. Gene expression (raw, normalized, calls)
- DNA methylation.
- Other.
What does TCGA stand for?
The Cancer Genome Atlas (TCGA) is a project, begun in 2005, to catalogue genetic mutations responsible for cancer, using genome sequencing and bioinformatics.
What is TCGA dataset?
The Cancer Genome Atlas (TCGA) is a comprehensive and coordinated effort to accelerate our understanding of the molecular basis of cancer through the application of genome analysis technologies, including large-scale genome sequencing.
Does TCGA have treatment data?
The Cancer Genome Atlas (TCGA) represents a valuable source of genomic and clinical data across different tumor types. In this work, TCGA treatment response information have been manually curated in order to be computationally exploited.
How do I get data from TCGA?
TCGA data is accessible via the NCI Genomic Data Commons (GDC) data portal, GDC Legacy Archive and the Broad Institute’s GDAC Firehose.
Does TCGA have normal samples?
Solid tissue normal samples from TCGA patients are typically limited in number but some cancer types may have enough for a robust statistical comparison. It is important to note that their proximity to tumor may introduce signals of tumor microenvironment in its transcriptome profile.
How do you cite TCGA data?
An example of a proper acknowledgement is: “The results here are in whole or part based upon data generated by the TCGA Research Network: https://www.cancer.gov/tcga.” Citation of original TCGA marker papers producing the data utilized is optional.
What is Pan oncology?
Pan is a Greek term for ‘all’, thus a pan tumor clinical trial enrolls patients across a variety of tumor types. A pan tumor clinical trial allows for multiple cancers to be treated within the same clinical trial. You may have heard of these trials referred to as multi-tumor or basket trials.
How do I get TCGA clinical data?
The TCGA clinical data were downloaded from the data portal of the Genomic Data Commons (GDC), where all TCGA molecular data are also available (https://gdc-portal.nci.nih.gov/legacy-archive/).
How many patients are in TCGA?
The Cancer Genome Atlas (TCGA) collected, characterized, and analyzed cancer samples from over 11,000 patients over a 12 year period. The process was complex and constantly evolving to accommodate new technologies, the nuances of different cancer types, and other changing factors.
What is UCSC Xena?
UCSC Xena (http://xena.ucsc.edu (link is external)) is a web-based, visual exploration tool for all modes of multi-omic data and associated annotations. UCSC Xena fully supports human cells, samples, cell lines, organoids, xenografts, etc, and also has basic support for mouse and other species.
What are the features of the TCGA dataset?
TCGA clinical data contain key features representing the democratized nature of the data collection process. To ensure proper use of this large clinical dataset associated with genomic features, we developed a standardized dataset named the TCGA Pan-Cancer Clinical Data Resource (TCGA-CDR), which includes four major clinical outcome endpoints.
What do you need to know about the TCGA?
Specifically, TCGA requires that samples contain at least 60% tumor nuclei and have less than 20% necrotic tissue. Once the sample passes the pathology review, nucleic acids are isolated and genotyping is performed so that each tumor sample is properly associated with the correct normal tissue.
Where can I find the NCI TCGA data?
As of June, 2016, primary TCGA data is available at NCI Genomic Data Commons. Some data files derived from TCGA controlled-access data that are not part of the official TCGA dataset may be hosted at dbGaP.
How does the Cancer Genome Atlas ( TCGA ) work?
An Integrated TCGA Pan-Cancer Clinical Data Resource to Drive High-Quality Survival Outcome Analytics For a decade, The Cancer Genome Atlas (TCGA) program collected clinicopathologic annotation data along with multi-platform molecular profiles of more than 11,000 human tumors across 33 different cancer types.