dPCR application in liquid biopsies: divide and conquer

ABSTRACT

Introduction: Precision medicine is already a reality in oncology, since biomarker-driven therapies have clearly improved patient survival. Furthermore, a new, minimally invasive strategy termed ‘liquid biopsy’ (LB) has revolutionized the field by allowing comprehensive cancer genomic profiling through the analysis of circulating tumor DNA (ctDNA). However, its detection requires extremely sensitive and efficient technologies. A powerful molecular tool based on the principle of ‘divide and conquer’ has emerged to solve this problem. Thus, digital PCR (dPCR) allows absolute and accurate quantification of target molecules.

Areas covered: In this review we will discuss the fundamentals of dPCR and the most common approaches used for partition of samples and quantification. The advantages and limitations of dPCR will be mentioned in the context of LB in oncology.

Expert opinion: In our opinion, dPCR has proven to be one of the most sensitive methods available for LB analysis, albeit some aspects such as its capacity of multiplexing and protocol standardization still require further improvements. Furthermore, the increasing sensitivities and lower costs of next generation sequencing (NGS) methods position dPCR as a confirmatory and complementary technique for NGS results which will likely prove to be very useful for treatment monitoring and assessing minimal residual disease.

KEYWORDS:

• Digital PCR
• liquid biopsy
• cfDNA
• biomarker
• ctDNA
• precision medicine
• oncology.

Article highlights

• Digital PCR (dPCR) is a powerful technology which enables the minimally-invasive detection of molecular alterations in cancer, based on sample partition to achieve absolute quantification with a high sensitivity and reproducibility.

• Liquid biopsy (LB) testing is a validated alternative for tissue testing because its concordance with tissue biopsy and dPCR is high, thus making the latter one of the most useful tools for LB analysis.

• dPCR is mainly used to detect previously known molecular alterations and lacks versatility for the discovery of new biomarkers.

• dPCR is based on sample partition to achieve absolute quantification with a high sensitivity and reproducibility, performing accurate analysis of liquid biopsy samples.

Declaration of interest

The authors have no relevant affiliations or financial involvement with any organization or entity with a financial interest in or financial conflict with the subject matter or materials discussed in the manuscript. This includes employment, consultancies, honoraria, stock ownership or options, expert testimony, grants or patents received or pending, or royalties.

Reviewer Disclosures

Peer reviewers on this manuscript have no relevant financial or other relationships to disclose.

Additional information

Funding

This work was supported by the Spanish Health Institute Carlos III (ISCII, Fondo de Investigación Sanitaria: CB16/12/00350 and PI18/00266). A. Moreno-Manuel has a predoctoral fellowship from the Scientific Foundation of the Asociación Española Contra el Cáncer, Valencia (AECC Valencia).