2014-ASHG: Integrated Analysis of Transcriptomes and Exomes in Cancer Samples Improves Interpretation and Reveals Additional Therapeutic Insights

Next-generation sequencing is being increasingly applied as a method for cancer analysis in both research and clinical settings. Many basic research studies utilize gene panel, exome, genome, or transcriptome sequencing to assess the genetic basis of tumor progression. These analyses not only help to determine cancer progression, but can also guide therapeutic decision-making. While gene panel, exome, and whole genome sequencing of tumors are widely used for clinical guidance and translational research, transcriptome sequencing has yet to be widely adopted in the clinical environment. However, analyzing the transcriptome allows for observation of expression changes as well as direct detection of functional gene fusions, SNVs, and Indels. To assess these unique features of RNA, we performed whole transcriptome sequencing along with ACE exome sequencing of cancer samples. Our sample set included commonly used cell lines which contain known variants and gene fusions.