Digital PCR Outperforms Conventional Methods for ctDNA-Based MRD Tracking in Colorectal Liver Metastases
A pilot study of 10 colorectal cancer patients with liver metastases compared four PCR methods for longitudinal ctDNA monitoring after tissue NGS-guided mutation identification. Digital PCR platforms (dPCR and ddPCR) achieved 100% qualitative concordance and detected ultra-low variant allele frequencies that correlated with clinical progression, while HRM-PCR lacked sufficient sensitivity in plasma. Personalised ctDNA tracking via digital PCR provided superior prognostic value for recurrence monitoring.
The original study
Multistep ctDNA Monitoring of Minimal Residual Disease in Colorectal Cancer Liver Metastases: From Tissue NGS to Highly Sensitive Digital PCR Platforms.
- Authors
- Górzyńska I, Konieczka A, Gaj P, Świerniak M, Stokłosa T, Grąt M, et al.
- Journal
- Diagnostics (Basel, Switzerland)
- PMID
- 41827921
Original abstract
Background/Objectives: Colorectal cancer (CRC) liver metastases present a significant clinical challenge due to high recurrence risks post-resection. Traditional diagnostics often fail to detect early-stage minimal residual disease (MRD). This preliminary pilot study evaluated ctDNA dynamics in 10 patients with liver metastases using a personalized multistep approach. Methods: Following primary tumor Next-Generation Sequencing (NGS) to identify somatic mutations in KRAS, NRAS, TP53, RET, APC, and WRN, custom TaqMan assays were designed for longitudinal plasma analysis. Four methodologies were compared: HRM-PCR, PNA-enhanced qPCR, and two digital platforms (dPCR and ddPCR). Results: While HRM-PCR sensitivity was limited in plasma, digital platforms demonstrated 100% qualitative concordance. MRD-negative status (VAF 0.00%) was identified in 70% of cases (P01, P03, P06, P07, P08, P09, P10), while detectable ctDNA in patients P02, P04, and P05 strongly correlated with aggressive progression. Digital PCR enabled the ultra-low detection of Variant Allele Frequencies (VAFs), identifying high molecular burdens (e.g., P05, VAF 49%) correlating with rapid decline, and capturing early molecular residue in P04 (VAF 0.62%). Conclusions: Our preliminary findings confirm that personalized longitudinal VAF tracking via digital PCR provides superior prognostic value, serving as a robust tool for recurrence monitoring in personalized CRC therapy.