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News article30 January 2019

Digital PCR is a suitable reference measurement method for cancer genotyping

DNA strand and Cancer Cell Oncology Research Concept
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Eight laboratories, including the JRC, have demonstrated the applicability of digital Polymerase Chain Reaction (dPCR) as a primary (reference) method for cancer genotyping testing to support precision medicine. This joint effort was coordinated by LGC (UK).

Precision Medicine is an emerging approach for disease treatment and prevention that takes into account individual variability in genes, environment, and lifestyle for each person.

In cancer therapy the treatment decisions are increasingly made based on knowledge about the genetic variations (also called mutations) present in the tumour cells.

This genotyping can be done on tumour tissue samples; but also on plasma samples as the DNA that comes from cancer cells often circulates freely in the blood of patients.

Implementing tumour genotyping in clinical oncology remains challenging. Cancer mutations are multiple, often differing by only 1 base pair from the non-mutated DNA sequence (wild type) and only present at a very low concentration in the blood plasma of a patient.

Tumour genotyping is usually performed with molecular diagnostic methods that require calibration, such as real-time quantitative PCR.

Standardisation of these molecular diagnostic methods depends on the availability of primary reference materials which are intended to be used by reference laboratories and in vitro diagnostic (IVD) device manufacturers to calibrate the measurement procedure and to qualify their working calibrators. These working calibrators are used by clinical laboratories to quantify the analyte in patient samples. However, at this moment the limited number of reference materials available in molecular diagnostics do not provide traceable values due to the absence of a primary reference measurement procedure that can be used to assign values to the reference materials.

Digital polymerase chain reaction (dPCR) is a technique that counts individual DNA molecules without the need for a DNA calibrator.

It has therefore the potential to be used as primary reference measurement procedure. Now, scientists have shown that a colorectal cancer single-nucleotide variant, i.e. KRAS G12D can be quantify with dPCR over a wide range of copies per reaction with good repeatability, i.e. a low coefficient of variation(CV) of 2% - 8%) and interlaboratory reproducibility (CV of 5% - 10%), and validated the trueness of dPCR measurements by comparison with an orthogonal SI-traceable mass-spectrometry approach.

Those high-accuracy measurements using dPCR support the implementation and traceable standardization of molecular diagnostic procedures needed for advancements in precision medicine.

Read more in: Whale A. S. et al.: Assessment of Digital PCR as a Primary Reference Measurement Procedure to Support Advances in Precision Medicine. Clinical Chemistry (2018) 64:9, 1296-1307. doi:10.1373/clinchem.2017.285478

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Assessment of Digital PCR as a Primary Reference Measurement Procedure to Support Advances in Precision Medicine


Publication date
30 January 2019