Abstract 2929: High-Definition Digital PCR (HDPCR™) enables sensitive measurement of DNA and RNA variants in non-small cell lung cancer samples

Abstract

Digital PCR (dPCR) is an emerging platform for detecting genomic variants in cancer genomes due to its high sensitivity and fast time to result compared to massively parallel sequencing. However, translational oncology applications often require the measurement of more biomarkers than there are color channels available on dPCR platforms. One approach to address this is to split a sample across many wells and profile a subset of variants in each well. For input-limited samples, however, this results in fewer molecules being profiled in each well, resulting in a reduction in sensitivity and fewer samples processed per instrument run. ChromaCode has developed a research use only (RUO) high-definition digital PCR assay, for multiplexed detection of 14 DNA variants and 15 RNA fusion variants relevant in non-small cell lung cancer (NSCLC) samples. The assay is constructed using both amplitude modulation and multi-channel resilient signal encoding methods. Amplitude modulation enables different variants to generate a signal at different intensity levels in single color channel, allowing for greater than n targets in n color channels. In contrast, resilient encoding generates a signal in more than one color channel to create a form of error detecting code. DNA and RNA samples were obtained using a combination of synthetic templates, cell line nucleic acids, and commercially available reference materials. Samples were run with the HDPCR NSCLC RUO assay on the Thermo Fisher Absolute Q digital PCR system, and data analysis was performed with custom analysis algorithms. The HDPCR NSCLC RUO assay demonstrated a limit of detection as low as 10 variant copies in a 10,000 haploid human genome copy DNA background. By employing HDPCR technology on digital PCR systems, it is possible to build a comprehensive and sensitive research assay that quickly detects many genomic alterations relevant to NSCLC samples. Citation Format: Bryan Leatham, Katie McNall, Hari K. Subramanian, John Alvarado, Lucien Jacky, Mimi Wang, Aditya Rajagopal, Jerrod Schwartz. High-Definition Digital PCR (HDPCR™) enables sensitive measurement of DNA and RNA variants in non-small cell lung cancer samples [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 2929.