CB 399: Cancer Genomics - Principles and Applications Spring 2011

Intellectual Unit:

Cancer Genomics - Principles and Applications
Course Directors: Rameen Beroukhim, John Quackenbush, Levi Garraway, and Benjamin Ebert

Curriculum Fellow: Narveen Jandu, narveen_jandu@hms.harvard.edu

Cancer genomics is a rapidly growing field that applies genome-scale technologies to develop comprehensive descriptions of cancer cells.  A particular focus is the identification of genetic alterations that drive tumor growth and transcriptional, proteomic, and phenotypic correlates. An understanding of the biological impact of these alterations can potentially lead to the development cancer therapeutics. Currently many on-line tools are available that allow us to determine the impact of these alterations on tumor growth and development.  Some of these resources include: Tumorscape (Broad Institute), COSMIC (Catalogue of Somatic Mutations in Cancer, Sanger), Cancer Gene Census (Sanger), Gene Expression Omnibus (NCBI), Oncomine (NCBI), and Gene Pattern (Broad).  This nanocourse is designed to provide an introduction and an overview of the current on-line resources that are available on Cancer Genomics. The second session of this nanocourse will provide a hands-on approach to implementing these on-line resources in your research.



First Session: Friday, April 22, 2011, 12:30 – 4:30 PM
Location: TMEC Building, Rm. 250

Scroll down for DAY 1 - slides and video links

Second Session: Thursday, April 28, 2011, 2:30 – 5:30 PM
Location: Countway Library

 Scroll down for DAY 2 slides


Part I: Experimental Design

 All students are required to write and submit a (one page) description on how you could use one of the online Cancer Genomics tools that were presented on Day 1 of this nanocourse to address a specific biological question. This can be related to your research.

 Briefly introduce the question you are trying to answer.  Be sure to include a description of the tool that you plan to use, its benefits and pitfalls.  You can include general information on how this tool is routinely used to answer research questions and then how it specifically addresses your biological question. 

In addition, be sure to list and describe in detail the secondary assays (including controls) that you would perform to validate the results you obtained using one of the online genomics tool.  Finally, provide a concise conclusion addressing any future directions.

During this second session you will be able to use the online Cancer Genomics tools to answer your biological question. We would like to make this an interactive session – so please ask questions and provide feedback to your fellow students.


Part II: Computational Analysis

 Tutorial 1: NCBI Map Viewer and UCSC Genome Browser (provided and completed in-class on Day 2)

Tutorial 2: Gene Pattern (provided and completed in-class on Day 2)

Tutorial 3: TumorScape (provided and completed in-class on Day 2) 


Part III: Case-based Application (depending on time)


*copy and paste these links into your browser; you will need your eCommons login and password.

Lecture 1 (J. Quackenbush) and 2 (R. Beroukhim):


Lecture 3 (B. Ebert) and 4 (Levi Garraway):