Abstract
The Cancer Genome Atlas (TCGA) is a large-scale collaborative effort to systematically characterize the genomic changes of over 10000 human cancers, using multiple data platforms including: whole exome sequencing, DNA copy by SNP array, RNA-seq, microRNA-seq, DNA methylation array, and Reverse Phase Protein Array (RPPA). With the conclusion of the data generation phase of TCGA, there is ample opportunity for “second-wave” studies to address questions not covered in the initial TCGA-sponsored marker studies that were first published for each tumor type. In my talk, I will cover examples of analyses we have contributed to TCGA marker papers studying ovarian, breast, and kidney cancers. A common theme in our work is that domain-specific knowledge of cancer-relevant pathways can often provide the necessary context for meaningfully interpreting genomic results. In the future, TCGA data can serve as an important resource for molecular biology studies, e.g. in helping to establish correlative relationships in the setting of human disease, where corresponding functional studies would establish cause-and-effect relationships in the experimental model setting.