A Canadian Guideline on the Use of Next-Generation Sequencing in Oncology

Abstract

Rapid advancements in next-generation sequencing (ngs) technology have created an unprecedented opportunity to decipher the molecular profile of tumours to more effectively prevent, diagnose, and treat cancer. Oncologists now have the option to order molecular tests that can guide treatment decisions. However, to date, most oncologists have received limited training in genomics, and they are now faced with the challenge of understanding how such tests and their interpretation align with patient management. Guidance on how to effectively use ngs technology is therefore needed to aid oncologists in applying the results of genomic tests. The Canadian guideline presented here describes best practices and unmet needs related to ngs-based testing for somatic variants in oncology, including clinical application, assay and sample selection, bioinformatics and interpretation of reports performed by laboratories, patient communication, and clinical trials.

Feasibility of next-generation sequencing in clinical practice: results of a pilot study in the Department of Precision Medicine at the University of Campania ‘Luigi Vanvitelli’

“…This technique is able to sequence long sequences of DNA in a short time. 5 In fact, differently from other cheaper techniques, NGS covers a huge number of base pairs with a good sensitivity, less than digital pathological complete response (PCR) but more than Sanger sequencing. There are three main types of NGS sequencing: wholegenome sequencing (WGS), whole-exome sequencing (WES) and targeted sequencing (TS).…”

Molecular profiling for precision cancer therapies

“…To date, WES and WGS have been largely confined to the research space, with the goal of collecting large amounts of genomic information for translational research applications that can improve knowledge in cancer biology over time. Targeted gene panels have been used preferably in the clinical setting because they provide greater depth of coverage in selected areas of interest (e.g., hotspot regions with known actionable mutations), faster turnaround, and more clinically relevant data when compared to broader genomic profiling by WES or WGS approaches [22]. The number of genes included in these panels can vary, ranging from 20-30 to over 400-500 genes.…”

A highly sensitive and specific real-time quantitative PCR for BRAF V600E/K mutation screening

“…The current practice before treatment involves screening a number of drugable mutations; hence, high-throughput techniques, such as next-generation sequencing, have been taken as an ultimate solution to the screening requirement. However, these high-throughput techniques are either technically more challenging or have not been widely applied and validated, greater caution is thus needed for establishing detailed consensus in experimental procedures and data processing 30 – 32 . The turnaround time and total cost of these high-throughput assays in each run could become satisfactory only when the sample volume and number of targets exceed certain threshold values.…”