Abstract A20: Validation of the QuantStudio5 instrument for use in Biocept’s TargetSelectorTM ctDNA lung cancer assays
Authors: Wu Shan Fu , Poole Jason C. , Lu Tim T. , Arnold Lyle J. , Chen Jeffrey , Pham Anh , Singh Veena M. 
Published: February 2019

Abstract
Background: Liquid biopsies represent a noninvasive alternative to traditional tissue biopsies, enabling the detection and tracking of cancer driver mutations from a simple blood draw. Biocept’s Target SelectorTM test platform offers the unique ability to analyze biomarkers from both circulating tumor cells (CTCs) and circulating tumor DNA (ctDNA). Here we performed a clinical concordance study, comparing the ABI 7900 to the newer ABI QuantStudio 5 (QS5) for integration of the QS5 into Biocept’s CAP/CLIA certified laboratory. TargetSelectorTM ctDNA mutation tests were validated for five targets, including EGFR (Del19, L858R, or T790M), BRAF, and KRAS, all markers integral to devising personalized therapies for non-small cell lung cancer (NSCLC) patients.
Methods: Prior to assessing clinical samples, extensive analytical validation was performed with DNA extracted from cancer cell lines containing the relevant EGFR, BRAF or KRAS mutations. TargetSelectorTM ctDNA mutant assays procedurally incorporate real-time PCR and DNA sequencing. The analytical validation was conducted to compare the performance of the ABI 7900 vs QS5 instruments within Biocept’s ctDNA testing platform. Evaluation of 3000 samples across the five TargetSelectorTM assays demonstrated single mutant copy detection sensitivity on the QS5 platform, with &gt;99% sensitivity and &gt;99% specificity for each of the ctDNA mutant assays. Following analytical evaluation, synchronized aliquots of 13 patient ctDNA samples, extracted from whole blood collected in Biocept CEE-SureTM Blood Collection tubes, were used to test the performance of both the ABI 7900 and QS5 instruments in the TargetSelectorTM ctDNA assays.
Results: EGFR, BRAF and KRAS TargetSelectorTM assays that incorporate the ABI QS5 vs the ABI 7900 enable more sensitive ctDNA testing, as demonstrated by analytical validation and subsequent analyses of clinical samples. In patient samples, TargetSelectorTM tests using the QS5 identified all of the mutations detected by same assays on the ABI 7900 platform. Utilization of the QS5 instrument within the TargetSelectorTM also enabled identification of additional mutations not detected in the assays where the ABI 7900 was used.
Conclusions: Implementation of the QuantStudio 5 real-time PCR instrument into Biocept’s TargetSelectorTM ctDNA assays has improved performance over the older TargetSelectorTM platform that utilized the ABI 7900. The more sensitive QS5-based TargetSelectorTM assays increase the likelihood of identifying molecular drivers linked to a patient’s cancer. Liquid biopsy detection of EGFR, BRAF and KRAS mutant ctDNA provides a minimally invasive means to gain valuable information towards developing personalized treatment strategies, monitoring therapeutic response, and identifying potential resistance mechanisms, all of which are vital for disease management and NSCLC patient care.
Citation Format: Shan Fu Wu, Jason C. Poole, Tim T. Lu, Lyle J. Arnold, Jeffrey Chen, Anh Pham, Veena M. Singh. Validation of the QuantStudio5 instrument for use in Biocept’s TargetSelectorTM ctDNA lung cancer assays [abstract]. In: Proceedings of the Fifth AACR-IASLC International Joint Conference: Lung Cancer Translational Science from the Bench to the Clinic; Jan 8-11, 2018; San Diego, CA. Philadelphia (PA): AACR; Clin Cancer Res 2018;24(17_Suppl):Abstract nr A20.