Course Details

  • Date: January 7th, 2016 - January 8th, 2016
  • Time: 9:30 am - 4:30 pm
  • Location: NIH Bldg 10 FAES Room 3 - B1C207 FAES
  • Presenter(s): Maxwell Lee (CCR, NCI), Parthav Jailwala (CCBR)


The Cancer Genome Atlas (TCGA) is a large-scale study that has cataloged genomic data accumulated for many different types of cancers, and includes mutations, copy number variation, mRNA and miRNA gene expression, and DNA methylation.  Being publicly distributed, it has become a major resource for cancer researchers in target discovery and in the biological interpretation and assessment of the clinical impact of genes of interest.  This 2-day workshop will familiarize the audience with the types of data available and analytical tools, including a number of software packages, that enable end-users to easily and effectively mine TCGA data.

PLEASE NOTE: This 2 day workshop is a BYOC (Bring your own laptop Computer) class. Government issued or personal computers are permitted. We will be able to supply a very limited set of computers, so if you want to take the class but cannot bring your own computer please indicate such in the Comment section on the registration form.

Direction to FAES Academic Center Classrooms – please go to this webpage:

Day 1 AM (Thu, Jan 7) – 9:30 am-12:30 pm  Introductory Lecture
(Maxwell Lee, PhD – CCR, NCI)

This session will include:

  • A brief history of TCGA
  • Overview of TCGA data portal
  • TCGA data access policy and download
  • Discussion of relevant TCGA publications

Day 1 PM (Thu, Jan 7) – 1:30 – 4:30 pm  Web-based exploration of TCGA data
(Parthav Jailwala, MS – CCBR, NCI)

  1. In this session, after an introductory overview of graphical tools and features in FireBrowse, we will carryout a brief hands-on exercise of running different queries using the online FireBrowse portal.

    • FireBrowse is a simple and elegant way to explore cancer data, backed by a powerful computational infrastructure, application programming interface (API), graphical tools and online reports.  Graphical tools like viewGene to explore expression levels, and iCoMut to explore the comprehensive analysis profile of each TCGA disease study within a single, interactive figure are novel features of this portal.

  2. In this session, after an introductory overview of NG-CHM user interface and features, we will carryout a brief hands-on exercise of generating different types of NG-CHMs on TCGA datasets.

    • Next-Generation (Clustered) Heat Maps (NG-CHMs) is another web-based tool for displaying clustered heat maps with links for statistical information, databases and other related analyses. These interactive heat maps enable the user to see an overview of the entire heatmap, and via interactive navigation controls, to zoom and pan across the heatmap to see details of the heatmap at many levels of resolution.


Day 2 AM (Fri, Jan 8) – 9:30 am -12:30 pm  BioDiscovery Nexus
(Andrea O’Hara, PhD – Field Application Scientist, BioDiscovery)

Nexus Copy Number is a platform independent copy number analysis software that includes co-visualization of sequence variants and gene expression data at both the individual and population wide levels. With an easy to use visual interface, the software allows for quick review and detailed analysis of population-wide copy number alterations across the entire genome.  NCI’s site license includes unlimited access to TCGA Premier, a database of re-processed, curated and reviewed TCGA samples.
In this workshop, you will learn how to use Nexus Copy Number software to mine TCGA copy number data. The Cancer Genome Atlas (TCGA) contains various types of genomic data from a wide variety of cancers, including several rare tumor types. The training session will focus on access of the TCGA data within the software and a detailed evaluation of one TCGA data set to identify statistically significant changes within the sample population.
Learning Objectives:

  • Access and integration of CNV, sequence variant and RNA-Seq expression TCGA data directly from Nexus.
  • Visualization and statistical approaches for discovery.
  • Sample stratification by clinical annotation factors or biomarkers.
  • Finding CNVs predictive of survival or other outcome data.
  • Generate publication-ready figures and charts during analysis.

Day 2 PM (Fri, Jan 8) – 1:30 – 4:30 pm  cBioPortal
(Nikolaus Schultz, PhD – Memorial Sloan-Kettering Cancer Center and Anand S. Merchant, MD, PhD. – CCBR, NCI)

This publicly accessible web-based resource provides visualization, analysis and download of large-scale cancer genomics data sets. As of early 2016 the portal contains multidimensional data from 105 cancer genomics studies. This session will include:

  • Introduction to cBioPortal – Niki Schultz
  • OncoQueryLanguage (OQL) – Key words and Codes
  • Features, Analytics, and Interpreting Results
  • Tutorials/Hands-on Exercises – Anand S. Merchant