Issue 6, 2019

An ultrasensitive test for profiling circulating tumor DNA using integrated comprehensive droplet digital detection

Abstract

Current cancer detection systems lack the required sensitivity to reliably detect minimal residual disease (MRD) and recurrence at the earliest stages when treatment would be most effective. To address this issue, we present a novel liquid biopsy approach that utilizes an integrated comprehensive droplet digital detection (IC3D) digital PCR system which combines microfluidic droplet partitioning, fluorescent multiplex PCR chemistry, and our rapid 3D, large-volume droplet counting technology. The IC3D ddPCR assay can detect cancer-specific, ultra-rare genomic targets due to large sample input and high degree of partitioning. We first demonstrate our droplet digital PCR assay can robustly detect common cancer mutants including KRAS G12D spiked in wild-type genomic background or isolated from patient samples with 100% specificity. We then demonstrate that the IC3D ddPCR system can detect oncogenic KRAS G12D mutant alleles against a background of wild-type genomes at a sensitivity of 0.00125–0.005% with a false positive rate of 0% which is 50 to 1000× more sensitive than existing commercial liquid biopsy ddPCR and qPCR platforms, respectively. In addition, our technology can uniquely enable detection of circulating tumor cells using their genetic markers without a pre-enrichment step, and analysis of total tumor DNA isolated from blood samples, which will increase clinical sensitivity and specificity, and minimize inter-assay variability. Therefore, our technology holds the potential to provide clinicians with a powerful decision-making tool to monitor and treat MRD with unprecedented sensitivity for earlier stage intervention.

Graphical abstract: An ultrasensitive test for profiling circulating tumor DNA using integrated comprehensive droplet digital detection

Supplementary files

Article information

Article type
Paper
Submitted
22 Dec. 2018
Accepted
31 Janv. 2019
First published
04 Febr. 2019

Lab Chip, 2019,19, 993-1005

Author version available

An ultrasensitive test for profiling circulating tumor DNA using integrated comprehensive droplet digital detection

C. Ou, T. Vu, J. T. Grunwald, M. Toledano, J. Zimak, M. Toosky, B. Shen, J. A. Zell, E. Gratton, T. J. Abram and W. Zhao, Lab Chip, 2019, 19, 993 DOI: 10.1039/C8LC01399C

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