Digital PCR Applications: Liquid Biopsy

Identification and tracking of cancer-causing mutations via liquid biopsy are increasingly being used in research for measuring potential therapeutic response, quantifying residual tumor burden, and studying resistance to potential targeted therapies¹. However, detecting circulating tumor DNA is challenging because the targets of interest are only a small fraction of the total circulating cell-free nucleic acids collected in a serum sample.

Liquid biopsy analysis relies on highly sensitive assays to detect low-abundant quantities of tumor nucleic acids. Accurate quantification of single nucleotide polymorphisms that occur in low abundance amongst wild type background DNA requires an appropriate liquid biopsy assay with outstanding sensitivity and specificity. With its high precision and sensitivity, digital PCR (dPCR) is ideally suited for research applications such as liquid biopsy applications and rare mutation detection.

For research in liquid biopsy, dPCR assays are a simple, precise, and rapid method for tracking potential response and/or resistance to treatment by researching relevant cancer-driver and therapy-resistant mutations.

With the ability to quantify multiple cancer related mutations per reaction via multiplexing, dPCR is increasingly being used in the research of rare mutations and how their abundance relates to disease progression and resistance to therapy.

For accurate and precise ctDNA quantification, special care should be taken to ensure assays are highly specific and optimized for use with short fragment length DNA molecules. In the application notes below white paper, learn more about the use of digital PCR and optimized liquid biopsy dPCR assays as a sensitive methodology for the identification and quantification of cancer driver and resistance-related mutations.

1. What is dPCR and how is it used in liquid biopsy analysis?

Answer: Digital PCR (dPCR) is a method used to quantify nucleic acids in a sample with high precision and no need for a standard curve. In liquid biopsy analysis, precisely designed assays can be used with dPCR experiments to perform absolute quantification of tumor-derived mutations on circulating tumor DNA (ctDNA) present in a DNA sample collected from plasma. This can help in biomarker research  associated with early stage cancers, potential cancer progression, as well as to help in research exploring diagnosis and clinical management of disease.

2. What are the advantages of using dPCR for liquid biopsy analysis?

Answer: dPCR has several advantages over traditional PCR methods. It can detect extremely low levels of ctDNA even in samples with extremely low overall concentration. Because of efficient reagent digitization dPCR is also highly sensitive and precise, which makes it ideal for tracking small changes.

3. What are some of the challenges associated with using dPCR for liquid biopsy analysis?

Answer: One of the main challenges of using dPCR for liquid biopsy analysis is the need for specialized equipment and expertise. However, simpler, faster single instrument dPCR systems have been developed to reduce hands on time and user touchpoints in order to improve consistency and robustness of the dPCR workflows.

4. What are some of the potential future applications of dPCR in liquid biopsy analysis?

Answer: dPCR has the potential to help revolutionize liquid biopsy analysis in several ways. It may be used in biomarker research exploring earlier cancer diagnosis; in research following unique tumor-derived molecules to study disease progression and treatment response; for research in identifying and tracking residual circulating cancer biomarkers exploring minimally invasive monitoring of minimal residual disease (MRD).

1. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6023445/