Navigating the Rapids: The Development of Regulated Next-Generation Sequencing-Based Clinical Trial Assays and Companion Diagnostics

Abstract

Over the past decade, next-generation sequencing (NGS) technology has experienced meteoric growth in the aspects of platform, technology, and supporting bioinformatics development allowing its widespread and rapid uptake in research settings. More recently, NGS-based genomic data have been exploited to better understand disease development and patient characteristics that influence response to a given therapeutic intervention. Cancer, as a disease characterized by and driven by the tumor genetic landscape, is particularly amenable to NGS-based diagnostic (Dx) approaches. NGS-based technologies are particularly well suited to studying cancer disease development, progression and emergence of resistance, all key factors in the development of next-generation cancer Dxs. Yet, to achieve the promise of NGS-based patient treatment, drug developers will need to overcome a number of operational, technical, regulatory, and strategic challenges. Here, we provide a succinct overview of the state of the clinical NGS field in terms of the available clinically targeted platforms and sequencing technologies. We discuss the various operational and practical aspects of clinical NGS testing that will facilitate or limit the uptake of such assays in routine clinical care. We examine the current strategies for analytical validation and Food and Drug Administration (FDA)-approval of NGS-based assays and ongoing efforts to standardize clinical NGS and build quality control standards for the same. The rapidly evolving companion diagnostic (CDx) landscape for NGS-based assays will be reviewed, highlighting the key areas of concern and suggesting strategies to mitigate risk. The review will conclude with a series of strategic questions that face drug developers and a discussion of the likely future course of NGS-based CDx development efforts.

Genomic characterization of esophageal squamous cell carcinoma: Insights from next-generation sequencing

“…Depending on the purpose, NGS is applied in cancer genome studies, including whole genome, whole exome, targeted gene sequencing, RNA sequencing, and ChIP-Seq [11,12,[21][22][23] . For variant identification by resequencing target regions, whole genomes, or whole exons, it is key to sequence both the tumor and non-malignant tissues of an individual.…”

A Novel System Control for Quality Control of Diagnostic Tests Based on Next-Generation Sequencing

“…The current paradigm of "one-drug/one-gene Dx" appears increasingly unsustainable, due to its severe limitations in specimen amount and turnaround time and because more molecular information is needed with the advancement of precision medicine (10). While NGS will provide potential clinically important data for each patient at unprecedented throughput and speed, it is rather expensive and complicated.…”

“…A standard run starts with 1 pg of the SC-only sample and 7 FFPE-RM samples with 100 fg of spike-in SC. Sequencing results from the automated workflow showed that although the SC-only sample had a much lower DNA input, it can be recovered with similar percentage of total reads (e.g., 10.28% in Supplemental Table 1, which appears in the Data Supplement that accompanies the online version of this article at http://www.jalm.org/content/vol1/ issue1) to the other FFPE samples in the run, ranging from 7.31% to 15.50%. Notably, the equalization is only approximate with some coverage variation among samples.…”

Bringing Next-Generation Sequencing Oncology Tests into the Diagnostic Setting

“…Although the gradual permeation of NGS into the diagnostic setting has been envisaged, there have been many challenges particularly in the context of detecting somatic mutations in oncology [14][15][16][17]. The challenges range from assay design to sample preparation, data analysis, variant calling, and automation of the entire workflow from samples to results.…”