Dr. Alexandra Lespagnol, Technical Coordinator and Innovation Project Manager at Rennes University Hospital is actively involved in implementing and developing new technologies and biomarkers to assist with the diagnosis of solid tumours.
Digital PCR can be used for comprehensive mutation profiling, for example, in the case of ovarian cancer, where it profiles BRCA1 and BRCA2 through sequencing. In liquid biopsy for colorectal cancer if WIF1 and NPY are detected scientists know that they have tumour DNA and can continue analysis.
At her institute, she has recently produced a major advancement in the digital PCR world. Lespangol explained that her team opted for digital PCR over NGS. The workflow relies on automating the chip loading process, using the Nio+ system for managing PCR processes and developing a dashboard for result validation and interpretation.
The Nio+ system automates the partitioning, amplification, and reading of PCR without technician intervention, and includes two independent thermocyclers. Another key feature Lespagnol mentioned was that it enables 7-colour multiplexing for higher target throughput. Furthermore, it supports the continuous loading of plates.
By automating the system Lespagnol has reduced the turn-around time without needing a technician to intervene thus freeing up scientists’ time and this makes it user-friendly. An EGFR kit is a machine that is designed to identify all the mutations for lung cancer screening and adapt the therapy.
The EGFR kit was tested on FFPE samples with varying tumour content and DNA concentrations. For the positive and negative populations, it can be hard to distinguish between the two, but the digital PCR achieved 100% sensitivity and 98% specificity and detected one more mutation than NGS. Lespagnol stated that the correlation between the mutation alert frequency between digital PCR and NGS is concordant with a good score.
The second test evaluated was the ESR1 assay. This kit targets 10 ESR1 mutations, 1 AKT mutation, and a housekeeping gene. It leverages dual-colour detection per target to enhance multiplexing and reduce background noise. Fortunately, the kit achieved 100% sensitivity and specificity in a small cohort, with excellent repeatability.
A custom dashboard has also been developed for applying decision rules for each assay, integrating clinical context from LIMS, and validating run quality and sample integrity. In summary, this digital PCR workflow offers simplified, automated, and standardised processes.
