What is TCGA database?
The Cancer Genome Atlas (TCGA) is the world’s largest and richest collection of genomic data. It is a comprehensive and coordinated effort to accelerate our understanding of the molecular basis of cancer. There are around 200 types of cancer, each characterized by molecular changes of the genome.
What does TCGA stand for?
The Cancer Genome Atlas (TCGA), a landmark cancer genomics program, molecularly characterized over 20,000 primary cancer and matched normal samples spanning 33 cancer types.
What types of datasets are present in the TCGA database?
The Types of TCGA Data As the largest database of cancer gene information, TCGA dataset not only contains many cancer types, but also multi-omics data, involving gene expression data, miRNA expression data, copy number variation, DNA methylation, SNP, and Compared with the GEO database.
What is TCGA classification?
Abstract. In 2013, The Cancer Genome Atlas (TCGA) Research Network found four novel prognostic subgroups of endometrial carcinoma: POLE/ultramutated (POLE), microsatellite-instable/hypermutated (MSI), copy-number-low/TP53-wild-type (CNL), and copy-number-highTP53-mutant (CNH).
What is TCGA sample?
TCGA barcodes were used to tie together data that spans the TCGA network, since the IDs uniquely identify a set of results for a particular sample produced by a particular data-generating center (i.e. GCC, GSC or GDAC). The constitutive parts of this barcode provided metadata values for a sample.
How do I download Tcga Rnaseq data?
- go to cBioportal.
- click on the tumor type you want.
- on the right side click on “summary”
- on the top of the page you have “download data”
How do I submit dbGaP?
To fill out the study config, go to your study’s dbGaP Submission Portal (https://submit.ncbi.nlm.nih.gov/dbgap/). Click on “Create” if newly filling out the study config or click on “Edit” to modify an existing study config. Once done, press “Submit” and you will be taken back to the study’s Submission Portal page.
What is TCGA analysis?
TCGA applies high-throughput genome analysis techniques to improve the ability to diagnose, treat, and prevent cancer through a better understanding of the genetic basis of this disease.
What are pole mutations?
Mutations in the exonuclease domain of the DNA polymerase epsilon (POLE) gene define one such subtype, which causes an ultra-mutated tumour phenotype. These tumours may have an improved progression-free survival and may be receptive to specific therapies. However, the clinical phenotype of these tumours is unknown.
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.