Terry Speed, University of California, Berkeley
Alternative Splicing in Tumors: Detection and Interpretation
In this talk I will discuss using the Affymetrix GeneChip Human Exon and Human Gene 1.0 ST arrays for the detection of genes spliced differently in some tumors in comparison with others. I plan to begin by introducing the arrays and the expression data they produce. Next I will outline the way in which we use such data in our attempts to identify exon-tumor combinations exhibiting splicing patterns different from the majority. This will be illustrated by examples from publicly available tissue and mixture data. Then I will briefly discuss some of the additional issues which arise when we seek to enumerate such alternative splicing patterns on a genome-wide scale. Finally, I will exhibit some of the results we have found applying these methods to glioblastoma tissue samples collected as part of The Cancer Genome Atlas (TCGA) project. (This is joint work with ELizabeth Purdom, Mark Robinson, Ken Simpson, and members of the Berkeley Cancer Genome Center.)