Abstract 5016: Building better contrived samples to properly evaluate Next-generation MRD and LBx assays
Authors: Paul Labrousse, Hugh Russell, David Shera, Daniel Stetson, Barrett Nuttall, Brian Dougherty, Darren Hodgson, James Hadfield
Journal: Cancer Research (2024)

Abstract Circulating tumor DNA (ctDNA) is a component of cell-free DNA (cfDNA) that originates from tumor tissue in the plasma of cancer patients. Although ctDNA is a broadly applicable tumor biomarker, the absolute amount of ctDNA varies across indication and stage, with the level of ctDNA present reflective of tumor volume. As novel methods for the characterization of ctDNA develop, there is need to evaluate these assays with appropriate samples. But current commercial reference standards, generated from modified cell lines or oligonucleotides lack important features such as DNA methylation, fragmentation pattern and nucleosome positioning, whilst clinical trial samples lack the required volume to perform multiple tests and often lack proper consent. We have created a framework for generating contrived samples containing the biological features of clinical samples and the attributes of a reference standard. The plasma-in-plasma contrived samples are generated from commercially purchased and fully consented matched tumor and plasma from cancer patients with age and gender matched healthy donor plasma. Samples are characterized by an internally validated 700 gene NGS panel to identify somatic variants and copy number alterations, which establishes ‘ground truth’. A contrived plasma dilution range based on the mean variant allele frequency (VAF) of the concordant somatic variants identified is generated. Using these methods, we have been able to generate sample sets for pan-cancer and disease specific evaluations. We have tested these samples through many novel high sensitivity assays that utilize both tumor-informed and tumor agnostic methods. We have confirmed that plasma-in-plasma contrived samples are amenable to all evaluated assays to date. The FFPE tumor tissue provide results matching clinical trial samples and the extraction yields of cfDNA are within the range of plasma samples from clinical trial data. Each dilution can be generated with replicates for reproducibility metrics. Current models of the sample dilutions have been generated to increase the number of replicates at relevant levels of tumor burden (i.e., 0.01% VAF). Negative samples consisting of the background plasma were also generated for each sample used. These plasma-in-plasma contrived samples have greater commutability to clinical samples than other commercial reference standards, however there are limitations. The complexity of generating these samples restrict the number of unique patients that can be utilized. Also, due to the volume of healthy plasma used as diluent, it is difficult to generate volumes greater than 4ml. To our knowledge, this is the first report examining the generation and usage of a contrived sample set that can be applied to evaluating novel high sensitivity MRD assays with clinical sample commutability. Citation Format: Paul Labrousse, Hugh Russell, David Shera, Daniel Stetson, Barrett Nuttall, Brian Dougherty, Darren Hodgson, James Hadfield. Building better contrived samples to properly evaluate Next-generation MRD and LBx assays [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 5016.