Individual
cancers harbor a set of genetic aberrations that can be informative for identifying rational
therapies currently available or in clinical trials. We implemented a pilot study to explore the practical challenges of applying high-throughput sequencing in clinical oncology. We enrolled patients with advanced or refractory
cancer who were eligible for clinical trials. For each patient, we performed whole-genome sequencing of the
tumor, targeted whole-exome sequencing of
tumor and normal
DNA, and transcriptome sequencing (
RNA-Seq) of the
tumor to identify potentially informative mutations in a clinically relevant time frame of 3 to 4 weeks. With this approach, we detected several classes of
cancer mutations including structural rearrangements, copy number alterations, point mutations, and gene expression alterations. A multidisciplinary Sequencing
Tumor Board (STB) deliberated on the clinical interpretation of the sequencing results obtained. We tested our sequencing strategy on human
prostate cancer xenografts. Next, we enrolled two patients into the clinical protocol and were able to review the results at our STB within 24 days of biopsy. The first patient had metastatic
colorectal cancer in which we identified somatic point mutations in NRAS, TP53,
AURKA, FAS, and MYH11, plus amplification and overexpression of
cyclin-dependent kinase 8 (CDK8). The second patient had
malignant melanoma, in which we identified a somatic point mutation in HRAS and a structural rearrangement affecting CDKN2C. The STB identified the CDK8 amplification and Ras mutation as providing a rationale for clinical trials with CDK inhibitors or
MEK (
mitogen-activated or extracellular signal-regulated
protein kinase kinase) and PI3K (phosphatidylinositol 3-kinase) inhibitors, respectively. Integrative high-throughput sequencing of patients with advanced
cancer generates a comprehensive, individual mutational landscape to facilitate
biomarker-driven clinical trials in oncology.