Course Details

  • Date: October 27th, 2014 - October 28th, 2014
  • Time: 9:30 am - 4:30 pm
  • Location: Bldg 10 - FAES Classroom 1 (B1C204)
  • Presenter(s): Andrea O'Hara (BioDiscovery Nexus), Mary Goldman (UC Santa Cruz), Maxwell Lee (CCR, NCI)

PLEASE NOTE: This 2 day workshop is  a BYOC (Bring your own Laptop Computer) class. In order to provide more flexibility with room scheduling we are experimenting with a new format that involves students brining their own laptop computers to the class. This has the advantage that you can continue exactly where you left-off following the 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 of FAES Classrooms (B1C204, B1C205) can be found here http://www.faes.org/announcements/directions_faes_classrooms_nih_campus


This class is now full – you may still register, but will be place on a waiting list for potential openings

 Click Here to Register 

Day 1 AM (Oct 27) – 9:30-12:30  Introductory Lecture
(Maxwell Lee, PhD – CCR, NCI)

  1. Introduction

    • A brief history
    • Overview of TCGA data
    • TCGA data access policy and download
  2. Discussion of TCGA papers

    • Identification of a CpG island methylator phenotype that defines a distinct subgroup of glioma.
      Cancer Cell. 2010 May 18;17(5):510-22.
       
    • Comprehensive molecular portraits of human breast tumours.
      Nature. 2012 Oct 4;490(7418):61-70.
       
    • Discovery and saturation analysis of cancer genes across 21 tumour types.
      Nature. 2014 Jan 23;505(7484):495-501.
       
    • Multiplatform analysis of 12 cancer types reveals molecular classification within and across tissues of origin.
      Cell. 2014 Aug 14;158(4):929-44. 

Day 1 PM (Oct 27) – 1:30-4:30  UCSC Cancer Browser
(Mary Goldman, PhD – U.C. Santa Cruz)

This workshop will teach users how to use the UCSC Cancer Browser, https://genome-cancer.ucsc.edu/, a web-based tool that integrates relevant data, analysis and visualization, allowing users to easily discover and share their research observations. Users will learn how to explore the relationship between genomic alterations and phenotypes by visualizing various -omic data alongside clinical and phenotypic features, such as age, subtype classifications and genomic biomarkers.

Users will download and upload clinical data, generate Kaplan-Meier plots dynamically as well as generate URL bookmarks of specific views of the data to share with others. The Cancer Genomics Browser currently hosts 575 datasets from genome-wide analyses of over 227,000 samples, including datasets from TCGA, CCLE, Connectivity Map and TARGET.


Day 2 AM (Oct 28) – 9:30-12:30  BioDiscovery Nexus
(Andrea O’Hara, PhD – Field Appliction Sceintist, BioDiscovery)

Nexus Copy Number is a platform independent copy number analysis and visualization tool that includes co-visualization of sequence variants. With an easy to use visual interface, Nexus Copy Number allows for quick review and detailed analysis of population-wide copy number alterations across the entire genome.  NCI¹s 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 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:

  • How to access of CNV TCGA data directly from Nexus.
  • Visualization and statistical approaches for CNV 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.
  • Query and integration of TCGA CNV tumor profiles with existing copy number data.

Day 2 PM (Oct 28) – 1:30-4:30  CBioPortal
(Nikolaus Schultz, PhD – Memorial Sloan-Kettering Cancer Center and Anand Merchant, MD, PhD. – CCR, NCI)

This publicly accessible web-based resource provides visualization, analysis and download of large-scale cancer genomics data sets.
As of early 2014 the Portal contains data for 15506 tumor samples from 56 cancer studies. This presentation will include:

  • Introduction to the web application – mission and evolving goals – What is the purpose?
  • Website walk-through – Where is the information and how to query it?
  • Review of the Cancer and Data Types available in the underlying cBio database
  • Advantages and Limitations
  • OncoQueryLanguage (OQL) – Key words and Codes
  • Features and Analytics
  • Viewing and Interpretation of results
  • Example Case  with TCGA dataset (Breast Cancer – 2012 Nature publication)
  • References/Tutorials/FAQ/Pre-set queries
  • Q&A