Feasibility of real time next generation sequencing of cancer genes linked to drug response: Results from a clinical trial

Abstract

The successes of targeted drugs with companion predictive biomarkers and the technological advances in gene sequencing have generated enthusiasm for evaluating personalized cancer medicine strategies using genomic profiling. We assessed the feasibility of incorporating real-time analysis of somatic mutations within exons of 19 genes into patient management. Blood, tumor biopsy and archived tumor samples were collected from 50 patients recruited from four cancer centers. Samples were analyzed using three technologies: targeted exon sequencing using Pacific Biosciences PacBio RS, multiplex somatic mutation genotyping using Sequenom MassARRAY and Sanger sequencing. An expert panel reviewed results prior to reporting to clinicians. A clinical laboratory verified actionable mutations. Fifty patients were recruited. Nineteen actionable mutations were identified in 16 (32%) patients. Across technologies, results were in agreement in 100% of biopsy specimens and 95% of archival specimens. Profiling results from paired archival/biopsy specimens were concordant in 30/34 (88%) patients. We demonstrated that the use of next generation sequencing for real-time genomic profiling in advanced cancer patients is feasible. Additionally, actionable mutations identified in this study were relatively stable between archival and biopsy samples, implying that cancer mutations that are good predictors of drug response may remain constant across clinical stages.International efforts to quantify and catalogue mutations, gene expression and epigenetic data for multiple forms of cancer, coupled with the successes of targeted agents in patients with molecularly defined tumors and improvements in genomic technology, have increased enthusiasm to adopt genomic profiling into clinical cancer practice. 1 As the numbers of clinically significant genetic variants have increased, clinical testing has evolved, moving from single mutations to multiplex hotspot evaluations in multiple cancer genes. Several pilot studies have demonstrated the feasibility and potential benefits of real-time multiplex hotspot evaluations in various cancer types. 2-8 However, as improvements in genomic technology overcome previous concerns of cost, complexity, time and tissue requirements, an increasing interest in adopting next generation sequencing (NGS) for genomic profiling in clinical cancer practice has developed. 6,9,10 Roychowdhury et al. recently reported the use of integrative sequencing in the clinic and demonstrated its potential to facilitate biomarker driven clinical trials. 11 However, it remains unclear whether the use of high-throughput, real-time NGS for genomic profiling is capable of generating results in a timeframe that allows for changes to patient management. Furthermore, the additional value of NGS over the multiplex hotspot genotyping approach is unclear, and

Testing personalized medicine: patient and physician expectations of next-generation genomic sequencing in late-stage cancer care

“…The tumor biopsy study evaluated whether high-throughput sequencing, accompanied by verification of results in a clinical laboratory, was feasible, could be used as a clinical tool to guide cancer therapy and would add value to the information generated by traditional genotyping methods. 37 With ethics approval from the Ontario Cancer Research Ethics Board, University of Toronto, and participating hospitals, as well as informed consent from participants, we conducted open-ended, semi-structured interviews from May 2011 to June 2012 with (i) adult patients with advanced solid malignancies enrolled in the tumor biopsy study; to enable face-to-face interviews, only patients from the three southern Ontario sites were eligible; and (ii) medical oncologist investigators involved in recruitment for the study at the three southern Ontario and two northern Ontario sites.…”

Noninvasive Diagnosis of Actionable Mutations by Deep Sequencing of Circulating Free DNA in Lung Cancer from Never-Smokers: A Proof-of-Concept Study from BioCAST/IFCT-1002

“…Several studies showed that these technologies can be applied to the detection of somatic mutation and suggested that they can be used in clinical settings (23).…”

Reflections on the Founding of the International Cancer Genome Consortium

“…The consortium's task is far from done. Although many members are engaged in exciting translational projects (21)(22)(23), the consortium needs to focus on achieving its primary goal of generating comprehensive descriptions of genomic, transcriptomic, and epigenomic changes in 50 different tumor types to provide the comprehensive perspective that motivated the consortium from the outset. Most projects under way have generated data for only a subset of planned samples and usually only 1 or 2 of the data types that are required.…”