Biodesix Presents Cell-free DNA Process Optimization for Liquid Biopsy Test

In two separate talks, Biodesix scientists presented information on further development and improvement of laboratory processes used for the GeneStrat^® test. GeneStrat is a genomic liquid biopsy test utilizing circulating tumor nucleic acids from plasma that is used by physicians to inform treatment of patients with non-small cell lung cancer (NSCLC). The talks described studies evaluating restriction enzymes for the analysis of cell-free DNA by droplet digital™ PCR (ddPCR™), and on the development of circulating RNA tests to identify fusion variants in NSCLC. The presentations were made at the Cancer Genomics Consortium Summer Meeting in Denver, Colorado.

Kristin Alexander, Biodesix Research Associate, provided an overview of the product development process prior to commercialization of the blood-based, which uses circulating RNA to test for tumor-derived transcripts resulting from the most common chromosomal rearrangements in NSCLC. Approved therapies are available to treat NSCLC patients who test positive for the ALK, ROS1 and RET targets.  An on-market study showed the GeneStrat RNA test result turnaround from sample receipt at Biodesix was less than 48 hours in 81% of cases, and less than 72 hours in 96% of cases (n = 3,518.)

Biodesix Research Associate Amanda Weaver presented findings regarding the existing DNA process used for GeneStrat. Restriction enzymes were initially used in the development of the test, as recommended by Bio-Rad, manufacturer of the ddPCR system. However, experiments showed that equivalent patient results were achieved without the use of restriction enzymes. Weaver hypothesized that, as the GeneStrat test uses highly fragmented cell-free DNA (cfDNA,) restriction enzymes were not necessary in the test workflow, because cfDNA is already small enough (~100-200bp) to obviate the need for further digestion by restriction enzymes. The benefits of restriction enzyme removal include reduction in potential sources of PCR contamination and exclusion of unnecessary steps that can increase potential for human error. In addition, eliminating the use of restriction enzymes makes the testing process more efficient, and saves time.

The GeneStrat^® Test                                             

A blood-based genomic test for patients with lung cancer that can inform the use of targeted therapies, the GeneStrat test provides results that are available within 72 hours. The liquid biopsy test delivers results for EGFR sensitizing; EGFR resistance (T790M), KRAS, and BRAF mutations; and EML4-ALK, ROS1 and RET fusion variants. The GeneStrat test measures circulating tumor DNA and RNA with a highly-sensitive droplet digital PCR platform.

The GeneStrat test is both widely reimbursed and supported by peer-reviewed scientific studies. The genes tested in GeneStrat are covered by Medicare and many private payers. The most recent publication supporting the clinical use of GeneStrat is The Journal of Molecular Diagnostics, “Development and Clinical Utility of a Blood-Based Test Service for the Rapid Identification of Actionable Mutations in Non–Small Cell Lung Carcinoma,” (Mellert, Hestia, et al. May 2017)

About Biodesix
Biodesix^® is a molecular diagnostics company advancing the development of innovative blood tests in oncology to enable precision medicine. Biodesix discovers, develops and commercializes multivariate protein and genomic diagnostic blood tests, including the GeneStrat^® and VeriStrat^® tests that deliver results within 72 hours. The company is changing the standard of care by providing physicians with diagnostic tests for better therapeutic guidance, more accurate prognosis and enhanced disease monitoring to improve patient outcomes. At the forefront of precision medicine, Biodesix is developing new blood tests to identify patients who may benefit from immunotherapies. In addition to developing novel diagnostics independently, the company partners with biotechnology and pharmaceutical companies to develop companion diagnostics for use with therapeutic agents.