Hayato Hiraki, PhD, Assistant Professor, Division of Biomedical Research & Development , Iwate Medical University Institute for Biomedical Sciences
Hayato Hiraki, PhD is Assistant Professor in the Division of Biomedical Research & Development at Iwate Medical University Institute for Biomedical Sciences. He earned a PhD in Molecular Physiology from The United Graduate School of Agricultural Sciences, Iwate University. After graduation, Dr. Hiraki shifted focus to cancer research, developing optimized primer-probe libraries and new probe design methods for ctDNA monitoring using digital PCR.
Rethinking ctDNA monitoring for personalized cancer care
Effective cancer treatment increasingly relies on tracking how tumors change at the molecular level over time. Yet most clinical decisions still rely on single snapshots of tumor biology taken at diagnosis or early in treatment. While patient stratification has improved treatment selection, it often fails to capture how tumors evolve during therapy and does not support the repeated, highly sensitive measurements needed for truly personalized care.
Digital PCR (dPCR) is well suited for this task. Its high sensitivity and quantitative precision enable accurate detection of rare variants and support frequent monitoring of tumor-derived mutations during treatment.
However, personalized ctDNA monitoring introduces another challenge: Each patient-specific mutation requires a dedicated assay. To address this, the team is developing OTS-Probes (Quantdetect Inc.), a digital PCR primer-probe library designed to rapidly detect somatic mutations and support individualized ctDNA monitoring.
Removing bottlenecks in liquid biopsy monitoring
While sensitive detection technologies are essential, making ctDNA monitoring more practical for routine use also depends on improving laboratory efficiency.
In many labs, ccfDNA extraction from plasma remains a time-consuming and labor-intensive process. Traditional extraction methods often require constant manual attention, limiting sample throughput and introducing variability between samples.
To address these challenges, Dr. Hiraki and colleagues chose to automate their ccfDNA extractions using the EZ2 Connect system. With the automated platform, the researchers simply load plasma samples into the instrument before starting the run. The extraction then proceeds without manual intervention, allowing the lab to run other experiments in parallel.
Dr. Hiraki found that automating sample prep significantly reduced processing time: The total extraction time dropped from more than two hours to approximately 45 minutes.
Automation also reduced sample-to-sample variability by minimizing manual handling steps. Processing samples within a closed system further improved laboratory safety and reduced the risk of contamination.
Reliable and sensitive mutation detection with digital PCR
The researchers next evaluated how well ccfDNA extracted using EZ2 Connect performed in downstream dPCR analysis.
The team measured the VAF of selected genes using OTS-Probes on two dPCR platforms: QIAcuity and a conventional droplet digital PCR system. The results showed strong agreement between platforms, with a Pearson correlation coefficient of r = 0.949 (p < 0.0001).
These findings demonstrate that ccfDNA extracted with EZ2 Connect is fully compatible with sensitive mutation detection by digital PCR.
From plasma to mutation analysis within a single day
Dr. Hiraki noted that patient plasma samples typically arrive in his laboratory in the early afternoon. With previous methods, mutation analysis results were usually not available until the following day.
But with the team’s new approach of integrating automated ccfDNA extraction with digital PCR analysis, they can now move from plasma samples to mutation detection within the same day. This faster turnaround could be particularly valuable for future clinical applications where timely results are important.
