Personalized Oncology Through Integrative High-Throughput Sequencing: A Pilot Study

Abstract

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 (mitogenactivated 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.

Unsolicited findings of next-generation sequencing for tumor analysis within a Dutch consortium: clinical daily practice reconsidered

“…In other institutes, for example at the University of Michigan, all patients undergoing NGS procedure of their tumor had to meet with a genetic counselor before consenting to genomic analysis. 18 This may have been preferable in our second patient. She did not feel the necessity of further investigations or counseling concerning her unsolicited finding.…”

Novel agents in acute myeloid leukemia

“…Furthermore, those exact studies may also be able to pinpoint mechanisms of resistance to specific treatments, identify key molecular targets that predict response to certain drugs, and may be targets for future therapies [41]. This approach will depend on collaborative efforts between major academic centers to enroll patients based on detailed molecular characteristics Novel agents in acute myeloid leukemia 183 rather than diagnosis, and require the necessary infrastructure to analyze the high throughput sequencing data in a clinically actionable time frame [42]. Incorporation of genomics into clinical trials would only be the first step towards a more personalized therapy for AML in which each patient's therapy is tailored to their specific molecular abnormalities.…”

Melanoma genotypes and phenotypes get personal

“…21 The daunting fact of hundreds, if not thousands, of nonsynonymous somatic mutations in a given MM patient becomes even more of a stark reality as molecularly informed tumor boards are convened to deliver personalized treatment options based on whole-genome sequencing. 22 Where we once considered only a small number of so-called driver mutations of relevance to MM, the genomic landscape has rapidly expanded to include numerous driver mutations, passenger mutations, and even so-called back-seat mutations. 23,24 It will also be necessary to determine the relationship between numerous oncogenes associated with the melanoma cells (for example, Notch, RAC1, GRIN2a, ERBB4, loss of INK4a, and so on.)…”

“…83 Thus, sufficient progress has been made so that machine/technology-driven molecularly informed tumor boards, in conjunction with accurate interpretation by a highly trained dermatopathologist, might become the rule rather than the exception for MM patients in the not-so-distant future. 22 Cracking Signaling Codes for Therapeutic Benefits and Understanding Drug Resistance There are many therapeutic strategies emerging from the panoply of genetic alterations being detected by highthroughput sequencing technologies, facilitating development of precision medicine for MM patients. 27 One of the best therapeutic examples of exploiting the discovery of a BRAFV600E mutation identified in the majority of MM patients has been targeting signaling components linked to the Ras/Raf/MEK/ERK pathway.…”