TCGA – The Cancer Genome Atlas Program

tcga

The Cancer Genome Atlas (TCGA) is a landmark cancer genomics program that molecularly characterized over 20,000 primary cancer and matched normal samples spanning 33 cancer types. The program is a joint effort between National Cancer Institute and the National Human Genome Research Institute first established in 2016.

Currently, two versions are hosted on the Data Ark: Version 31.0 and version 32.0. The gene model used as a reference across TCGA has been updated from GENCODE 22(GRC37/hg19)—version 31 to GENCODE 36 (GRCh38/hg38)–version 32. To learn more about the data sets from a different version, find the data release notes here.

All the TCGA data sets belong to the “open-access” category and were obtained from the Genomic Data Commons Data Portal. The TCGA folder on Minerva Supercomputer hosts all the biospecimen, clinical, RNA-seq counts, WXS -Mutation Annotation Format (MAF), and the TCGA data sets from cBioPortal.

 

TCGA Processed Data Sets

TCGA data set has been processed and uploaded to Data Ark by Dr.Deniz Demircioglu (deniz.demircioglu@mssm.edu), who combined data from the biospecimen and clinical folder and consolidated all the RNA-seq counts files (over 11,000 patients) into 33 different outcomes. See the table below. For more information about the TCGA Study Abbreviations, click here.

 Abbrev. Study Name  Abbrev. Study Name Abbrev. Study Name
 ACC Adrenocortical carcinoma BLCA Bladder Urothelial carcinoma BRCA Breast invasive carcinoma
CESC Cervical squamous cell carcinoma and endocervical adenocarcinoma CHOL Cholangiocarcinoma COAD Colon adenocarcinoma
DLBC Lymphoid Neoplasm Diffuse Large B-cell Lymphoma ESCA Esophageal carcinoma GBM Glioblastoma multiforme
HNSC Head and Neck squamous cell carcinoma KICH Kidney Chromophobe KIRC Kidney renal clear cell carcinoma
KIRP Kidney renal papillary cell carcinoma LAML Acute Myeloid Leukemia LGG Brain Lower Grade Glioma
LIHC Liver hepatocellular carcinoma LUAD Lung adenocarcinoma LUSC Lung squamous cell carcinoma
MESO Mesothelioma OV Ovarian serous cystadenocarcinoma PAAD Pancreatic adenocarcinoma
PCPG Pheochromocytoma and Paraganglioma PRAD Prostate adenocarcinoma READ Rectum adenocarcinoma
SARC Sarcoma SKCM Skin Cutaneous Melanoma STAD Stomach adenocarcinoma
TGCT Testicular Germ Cell Tumors THCA Thyroid carcinoma THYM Thymoma
UCEC Uterine Corpus Endometrial Carcinoma UCS Uterine Carcinosarcoma UVM Uveal Melanoma

 

Inside each outcome folder, you will see the following files:

aliquot.tsv count.tsv fpkm.tsv sample.tsv
analyte.tsv exposure.tsv fpkm_uq.tsv slide.tsv
clinical.tsv family_history.tsv portion.tsv  

 

TCGA Data Access

To use this data, NO DUA form is required, you can access the data at the following path on Minerva – /sc/arion/projects/data-ark/Public_Unrestricted/tcga $ module load dataark to see the path variables.

By using these data, you agree to acknowledge BiNGS–the Tisch Cancer Institute Bioinformatics Core for Next-Generation Sequencing and the Data Ark team for all oral and written presentations, grand submission, awards, and publications resulting from any analyses of the data sets.

Data Sets

Public Data Sets (unrestricted)

Public Data Sets (restricted)

Mount Sinai Generated Data (unrestricted)

Mount Sinai Generated Data (restricted)

Data Set Supplements (restricted)

Cloud-Hosted Data Sets (restricted)

School-Acquired Data Sets (restricted)

GooGhywoiu9839t543j0s7543uw1 - pls add laura.dent@mssm.edu to GA account UA-149832711-2 with 'Manage Users and Edit' permissions - date 12/2/22