Abstract 2011: Feasibility of serum proteomic companion diagnostic (CDx) test development on the microflex LT platform
Authors: Nicholas Dupuis, Jamie Chang, Maximillian Steers, Zhigang Weng, Jeno Gyuris, Gary Pestano
Journal: Cancer Research (2015)

Abstract Clinical oncology assays using mass spectrometry have exclusively been run on instrument platforms designed for use in research laboratories. Here, we report on the use of a bench-top MALDI-TOF mass spectrometer (MS) to run a serum proteomic Laboratory Developed Test (LDT), VeriStrat®. A number of previous studies have shown that this assay measures a serum proteomic fingerprint using MALDI-TOF MS which, following spectral acquisition and data processing, classifies advanced non-small cell lung cancer (NSCLC) patients into treatment categories. An extension of VeriStrat, BDX004, is currently under development as part of a global, randomized, double-blind Phase 2 clinical study, FOCAL. BDX004 will be used prospectively to select previously untreated, EGFR mutation-positive patients with advanced NSCLC to receive one of two treatments: (1) the combination of ficlatuzumab (a humanized monoclonal antibody against hepatocyte growth factor) and an EGFR tyrosine kinase inhibitor (TKI), or (2) an EGFR TKI with placebo. For the development of BDX004 as a companion diagnostic (CDx), we have included the microflex™ LT (LT), a component of Bruker's MALDI Biotyper CA system, which was granted FDA clearance for the identification of Gram negative bacteria. In the present study, we evaluated the LT platform through comparative studies with other MALDI-TOF instruments (autoflex™ III and autoflex SPEED) utilizing samples from patients previously diagnosed with NSCLC. In summary, we found that under common laboratory procedures the LT produces results equivalent to research grade MALDI-TOF MS instrumentation. In initial studies, the microflex LT showed similar resolution (R &amp;gt; 600 at 6632.1 m/z) and sensitivity (S/N ≥ 50 with 500 fmoles BSA in 100 laser shots) performance parameters as the autoflex series research instruments (R &amp;gt; 800 at 6632.1 m/z and S/N ≥ 50 with 500 fmoles BSA in 250 laser shots). The LT was qualified with several independent sample sets [n = 4 (8 replicates; 2000 spectra/replicate); n = 67 (3 replicates; 2000 spectra/replicate) and n = 20 (3 replicates; 2000 spectra/replicate)]. In these studies, the LT achieved 100%, &amp;gt;97%, and 100% concordance with reference data sets previously acquired on the autoflex platforms. As expected, due to the lower laser repetition rate of the LT's nitrogen laser, the acquisition speed was slower on the LT as compared to the autoflex instruments by a factor of two. However, the slower acquisition speed is partially compensated for with increased sensitivity, which is particularly evident in the reference sample mass spectra which have signal-to-noise ratios ∼1.5 greater than those acquired on the autoflex platform. Based on these results, the microflex LT appears to be suitable for measurement of serum proteomic profiles in NSCLC and suggests that the inclusion of the microflex LT in CDx test development has the potential to expand the utility of MALDI-based testing in the clinic. Citation Format: Nicholas Dupuis, Jamie Chang, Maximillian Steers, Zhigang Weng, Jeno Gyuris, Gary Pestano. Feasibility of serum proteomic companion diagnostic (CDx) test development on the microflex LT platform. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 2011. doi:10.1158/1538-7445.AM2015-2011