TCGA Guide

Version 1.0

For questions, email Dr. Lasseigne at bnp0001@uab.edu

Introduction to TCGA

The Cancer Genome Atlas (TCGA) is a resource with omics data for over 20,000 cancer patient tissue profiles spanning 33 cancer types. It is a joint effort between the National Cancer Institute and the National Human Genome Research Institute and is publicly available. See the links below for more information:

• Click here for the NIH’s introduction to TCGA. You can also visit TCGA’s Wikipedia page here.
• This page describes cancers studied by the consortium.
• This is the NIH’s Genomic Data Commons data portal where you can access their data.
• Here is a list of the data types available in TCGA.

Literature

Below are some papers you can read for a better understanding of TCGA:

• TCGA Research Network Publications
  • a comprehensive list of publications by the TCGA program
• TCGA Pan-Cancer Analysis (2013)
  • a collection on the Pan-Cancer initiative’s effort to find similarities and differences among the genomic and cellular alterations found in the first dozen tumor types profiled by TCGA. For example:
    • The Cancer Genome Atlas Pan-Cancer analysis project
      • a commentary article providing further detail to the Pan-Cancer analysis project touched on in the collection summary
    • Pan-cancer patterns of somatic copy number alteration
      • a paper analyzing somatic copy number alterations’ roles in promoting cancer
    • Emerging landscape of oncogenic signatures across human cancers
      • a paper on classifying tumors hierarchically based on genetic and epigenetic alterations to show functional event patterns
• The Pan-Cancer Atlas Collection (2018)
  • a collection of papers aiming to reclassify human tumor types based on molecular similarity. For example:
    • The Cancer Genome Atlas Comprehensive Molecular Characterization of Renal Cell Carcinoma
      • a paper on finding genomic and phenotypic differences associated with different histologic subtypes in the interest of developing subtype-specific therapeutics
    • Perspective on Oncogenic Processes at the End of the Beginning of Cancer Genomics
      • a paper on the current state of findings on the molecular processes governing oncogenesis provided in the TCGA PanCancer Atlas
    • Genomic and Functional Approaches to Understanding Cancer Aneuploidy
      • a paper that defines genomic and phenotypic correlates of cancer aneuploidy and provides an experimental approach to study chromosome arm aneuploidy
    • An Integrated TCGA Pan-Cancer Clinical Data Resource to Drive High-Quality Survival Outcome Analytics
      • a paper detailing the TCGA Pan-Cancer Clinical Data Resource, a standardized dataset developed to ensure proper use of TCGA clinical data
• Pan-Cancer Analysis of Whole Genomes (2020)
  • a collection describing a PCAWG Project that performed whole-genome sequencing and integrative analysis on over 2,600 cancers and their matching tissues across 38 tumor types from Nature
• Multiomic Integration of Public Oncology Databases in Bioconductor
  • a paper on utilizing TCGA along with cBioPortal to create packages to aid in making fully integrated representations of multiomic pan-cancer databases

Data Analysis

See this page for a list of computational tools developed by researchers using TCGA data.

See this page for a user’s guide for accessing the GDC data portal.

TCGAbiolinks

TCGAbiolinks is an R package that can be used for integrative analysis with Genomic Data Commons data. This package facilitates data retrieval and analysis. You can learn more about its aim and install it here.

After installation, feel free to go through this webpage for a better understanding. There are case studies and workshops available through the page that might also be helpful.

This vignette is another walkthrough option for learning the TCGA Workflow.

You can also reference these YouTube videos from the creators of the package:

• TCGAbiolinks: data, analyses & applications by Antonio Colaprico
• TCGAbiolinks: data, analyses & applications (Network Stability) by Catharina Olsen

recount2

recount2 is a resource that allows access to thousands of RNA-seq samples from TCGA, GTEx, and the Sequence Read Archive. It can be accessed through the recount2 website and the recount Bioconductor package. See below for some helpful resources:

• Bioconductor page for recount r package
  • This includes a quick start guide to recount2 that can help you get a general idea of the package.
• recount workflow: accessing over 70,000 human RNA-seq samples with Bioconductor
  • This is a more in-depth workflow you can follow.
• recount2: a multi-experiment resource of analysis-ready RNA-seq gene and exon count datasets
  • This is a resource to download the recount2 datasets. It has a user friendly GUI to interact with these datasets, and allows you to choose from popular datasets, GTEx, TCGA, or all of the above.
• Reproducible RNA-seq analysis using recount2
  • This is a Nature Biotechnology paper detailing the development and utilization of recount2.

Version 1.1: Added Multiomic Integration paper