CSBF Seminar: Integrated Genomic View of TCGA Lung Squamous Cell Carcinoma

Dec 12, 2012 (Wed) | 9:30 AM -10:30 AM
Munzer Auditorum-279 Campus Dr. West : Stanford, CA

In this presentation, we will use the data generated by The Cancer Genome Atlas (TCGA) project on approximately 300 lung squamous cell carcinoma samples to demonstrate how copy number, allelic changes, and gene expression data can interactively be explored using the Nexus Copy Number and Nexus Expression systems to gain knowledge about the underlying biology. In particular, we will show how SNP data from Affymetrix SNP 6 arrays have been processed to obtain copy number and LOH differences between samples and their matched normal. We will show how various population analyses can be performed quickly to identify regions that are different between subpopulations or to identify significant common aberrations in the sample. We will then show analysis of the associated expression data and identify differentially regulated genes and pathways. Finally, we will integrate the results between these analyses to identify possible driver events.

Department:  Beckman Center for Molecular and Genetic Medicine

Contact: Lee Kozar | 725-4483 |


  • SoheilShams PhD