Technical and Regulatory Considerations for Taking Liquid Biopsy to the Clinic: Validation of the JAX PlasmaMonitor^TM Assay

Abstract

The standard of care in oncology has been genomic profiling of tumor tissue biopsies for the treatment and management of disease, which can prove to be quite challenging in terms of cost, invasiveness of procedure, and potential risk for the patient. As the number of available drugs in oncology continues to increase, so too does the demand for technologies and testing applications that can identify genomic alterations targetable by these new therapies. Liquid biopsies that use a blood draw from the diseased patient may offset the many disadvantages of the invasive procedure. However, as with any new technology or finding in the clinical field, the clinical utility of an analytical test such as that of the liquid biopsy has to be established. Here, we review the clinical testing space for liquid biopsy offerings and elucidate the technical and regulatory considerations to develop such an assay, using our recently validated PlasmaMonitorTM test.

Pre-analytical issues in liquid biopsy – where do we stand?

“…In recent years, several companies developed a range of DNA isolation kits of which only the "dedicated" kits were recommended for the extraction of cfDNA [192]. In several papers, a variety of different kits were compared [84,85,93,[193][194][195][196][197][198][199][200][201][202][203][204]. From these results, one can conclude that bead-based isolation methods worked somewhat better than membrane-based kits and that the former ones are especially useful for the isolation of low-molecularweight DNA.…”

Novel Epigenetic Biomarkers in Pregnancy-Related Disorders and Cancers

“…In contrast, an NGS assay allows for the assessment of a broader range of genomic alterations because sequencing can detect alterations anywhere within the captured regions (source: , visited 6 August 2019). Of note, liquid biopsy assays have already been utilized in clinical practice (e.g., Trovera™ EGFR urine-based liquid biopsy (three genes are covered: EGFR , KRAS , and BRAF ) and Cobas® EGFR mutation test v2 that covers the EGFR gene)) [8]. However, many issues related to the routinized use of liquid biopsy remain to be resolved, including pre-analytical sample handling, appropriate assays for cfDNA extraction, and optimal workflow for analyses [10].…”

“…For a successful clinical application of liquid biopsy, it is crucial to standardize analytical methods and pre-analytical procedures, including plasma separation and selection of the optimal isolation assay, that may yield a sufficient amount of high-quality DNA. Multiple studies confirmed that blood sampling and processing might significantly affect DNA yield and downstream analyses [8]. However, despite the substantial efforts to standardize and optimize the methodology, such as those of the European FP7 consortium SPIDIA4P (standardization and improvement of generic pre-analytical tools and procedures for in-vitro diagnostics, ) [9], no consensus has been reached on the pre-clinical preparations for liquid biopsy [10].…”

The Mutational Landscape of Pancreatic and Liver Cancers, as Represented by Circulating Tumor DNA

“…Other NGS assays using gene panels, currently in development for other cancer types, may also show promise for either pancreatic or liver cancer in the future. For example, the Cobas® EGFR Mutation Test v2 is used for non-small-cell lung carcinoma since EGFR, a KRAS-activating receptor, is often mutated in this particular cancer (65). Another NGS platform, the PlasmaSELECT-R64 assay, evaluates a panel of 64 genes and has been directly compared with the Guardant360 assay on samples from patients with metastatic prostate cancer.…”

“…Sensitivity and specificity are highly dependent on many pre-analytical parameters, e.g., plasma separation and method of ctDNA isolation, and optimization of the assay may require extra steps within the workflow (65). However, perfect sensitivity and specificity may not necessarily be required for therapy choices based on mutation status.…”