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More Information on Disease State and Trial Options for Patients with Advanced Non-Small Cell Lung Cancer; Evaluating Automated and Manual Workflows in cfDNA Extraction

Biodesix Presents Data from Two Studies at 2016 AMP Annual Meeting

Biodesix® is presenting two posters with results of separate genomics studies at the AMP 2016 Annual Meeting.  In the first study, analysis of blood test results from non-small cell (NSCLC) lung cancer patients who tested  EGFR wild-type, and have Poor prognosis as determined by the VeriStrat® test showed that targeted profiling using NGS on cfDNA from plasma can identify actionable mutations in samples from these patients.  The second study evaluated the optimization of the nucleic acid extraction step (manual versus automated) for the GeneStrat® test, a commercially-available diagnostic test for NSCLC.


Poster Title: “Analysis of the Presence of TP53 Mutations in Targeted NGS Profiles of EGFR wild-type, NSCLC patients with Poor Prognosis”

Poster #S58


Authors: Hestia Mellert, PhD, Leisa Jackson, Westen Hahn, Nicholas Dupuis, PhD, Amanda Weaver, Jakkie Greer, Gary A Pestano, PhD


The Study

Blood-based molecular tests can help target treatments for patients with advanced NSCLC. The VeriStrat® serum protein test measures acute phase reactant proteins in the blood known to be associated with aggressive disease, providing predictive and prognostic information by classifying patients as VeriStrat Good (VS-G) or VeriStrat Poor (VS-P). Patients with a VS-G classification have better clinical outcomes relative to those with VS-P status. VeriStrat is also predictive of response to EGFR-TKI therapies.[i] Treatment options for patients with NSCLC who are EGFR WT and VS-P are limited; thus, the use of more extensive genomic and proteomic testing may provide more comprehensive clinical information to support treatment planning and patient placement in clinical trials. For this study, we profiled circulating-free DNA (cfDNA) in matched plasma specimens determined to be EGFR WT (by droplet digital PCR) and VS-P (n=11) with a targeted next-generation sequencing (NGS) test of 15 genes to identify actionable somatic variant mutations. Six of the 11 plasma samples contained TP53 mutations, which included missense, splice-site, and frame-shifts. Drug development is underway for several TP53 targeted agents, with pre-clinical and clinical trials underway such as the TP53 re-activating agent APR-246 (a PRIMA-1 analogue). Targeted profiling using NGS on cfDNA from plasma can identify actionable mutations in patient samples with a poor prognosis as determined by the VeriStrat test. It is likely that additional profiling may uncover other targets associated with current therapy. Expanded profiling of EGFR WT/VS-P patients with a 15-gene NGS test that measures additional somatic variants, indels, and amplifications is underway. We expect that these studies will yield targets that could provide treatment options for VS-P patients with advanced stages of NSCLC.


Poster Title: “Equivalence Studies for Circulating Free DNA Extraction Methods Using a CLIA Laboratory Validated ddPCR Test Process”


Authors: Leisa Jackson, Alexander Wolf, Westen Hahn, Galen Roda, Hestia Mellert, PhD, Gary A Pestano, PhD.


The Study


Approximately 25% of patients with advanced non-small cell lung cancer (NSCLC) are not candidates for tissue biopsies, and in some patients, tissue obtained is not of sufficient quality or quantity for molecular testing. Thus, detecting circulating nucleic acids has become relevant in a clinical setting. This study, a collaboration with Qiagen, focused on the optimization of the nucleic acid extraction step (manual versus automated) for GeneStrat®, a commercially-available diagnostic test system for patients with NSCLC. GeneStrat® testing is available for 7 DNA variants of the KRAS, EGFR and BRAF genes.  Evaluation criteria included the yield of circulating free (cf) nucleic acids, droplet counts for somatic mutant variants as well as the counterpart wild-type, and percentage minor allelic frequency (%MVF) as measured with validated assays. The previously validated “manual” method developed was used as the reference method for evaluation of the automated Qiagen QIAsymphony ® SP. Performance was determined via detection of recovered DNA variants by droplet digital PCR (ddPCR). For reference and test arms, plasma from three donors with NSCLC as well as a spiked control DNA sample with known %MVF were extracted and tested by GeneStrat®.


The automated system yielded better results (as measured by copy counts) for the variant and wild-type analyses assessed using both clinical samples and analytic controls. The automated and manual methods of recovering circulating nucleic from plasma performed at least equivalently for the gene read-outs and test system evaluated here. The quality and yield of cfDNA from the automated process was sufficient to meet the previously established criteria for the manual performance of the assays. Evaluations are ongoing with the automated system for larger plasma volumes and increased numbers of samples that could be processed in parallel.



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.


[i] PROSE study

Topics: cfDNA from plasma, Press Releases, Qiagen, QIAsymphony, Non-Small Cell Lung Cancer