Abstract B128: Comparative assessment of MALDI-TOF platforms for utility in CDx development of a proteomic signature for ficlatuzumab
Authors: Dupuis Nicholas F. , Steers Maximillian , Weaver Amanda , Weng Zhigang , Payumo Francis C. , Needle Michael N. , Pestano Gary A. 
Published: May 2016

Abstract
BDX004 is a multivariate serum proteomics companion diagnostic (CDx) test currently under development as part of a global, randomized, double-blind Phase 2 clinical study, FOCAL. The test will be used prospectively to select previously untreated, EGFR mut-positive patients with advanced NSCLC to receive one of two treatments: (1) the combination of ficlatuzumab (a humanized mAb against hepatocyte growth factor) and an EGFR tyrosine kinase inhibitor (TKI), or (2) an EGFR TKI with placebo. BDX004 measures the abundance of eight serum protein variants using MALDI-TOF mass spectrometry, the data from which is coupled with pre-processing steps and a k-nearest neighbors (kNN) algorithm to classify subjects into positive or negative groups. To date, clinical oncology assays using mass spectrometry, including those to measure serum proteomic profiles in NSCLC, have exclusively been run on instruments designed for use as research use only. Here, we describe a comparative assessment of three MALDI-TOF platforms (microflex™, autoflex™ and ultraflex™). The microflex LT we used is an RUO version of Bruker Daltonics' FDA cleared MALDI Biotyper CA system.
All three instrument platforms were qualified with at least two independent sample sets and achieved &gt;97% classification label concordance (Positive and Negative) with a gold standard data set. In summary, the microflex produced results equivalent to the other, higher performance MALDI-TOF MS instruments. In initial studies, the microflex showed similar resolution (R &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 and ultraflex instruments. The microflex was further evaluated with several additional 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)] and achieved 100%, &gt;97%, and 100% classification label concordance against reference data sets. At a quantitative level we also measured the feature value (protein peak) CVs that underlie the classification labels. These were found to be highly comparable across all three platforms at 5.7%, 6.4% and 4.8% for the microflex, autoflex and ultraflex, respectively. We conclude that all three of the platforms tested demonstrated equivalent performance, and the microflex LT is well suited for the development of novel MALDI-TOF CDx tests.
Citation Format: Nicholas F. Dupuis, Maximillian Steers, Amanda Weaver, Zhigang Weng, Francis C. Payumo, Michael N. Needle, Gary A. Pestano. Comparative assessment of MALDI-TOF platforms for utility in CDx development of a proteomic signature for ficlatuzumab. [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference: Molecular Targets and Cancer Therapeutics; 2015 Nov 5-9; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2015;14(12 Suppl 2):Abstract nr B128.