Droplet-based digital PCR and next generation sequencing for monitoring circulating tumor DNA: a cancer diagnostic perspective

ABSTRACT

Introduction: Early detection of cancers through the analysis of ctDNA could have a significant impact on morbidity and mortality of cancer patients. However, using ctDNA for early cancer diagnosis is challenging partly due to the low amount of tumor DNA released in the circulation and its dilution within DNA originating from non-tumor cells. Development of new technologies such as droplet-based digital PCR (ddPCR) or optimized next generation sequencing (NGS) has greatly improved the sensitivity, specificity and precision for the detection of rare sequences.

Areas covered: This paper will focus on the potential application of ddPCR and optimized NGS to detect ctDNA for detection of cancer recurrence and minimal residual disease as well as early diagnosis of cancer patients.

Expert commentary: Compared to tumor tissue biopsies, blood-based ctDNA analyses are minimally invasive and accessible for regular follow-up of cancer patients. They are also described as a better picture of patients’ pathology allowing to highlight both tumor heterogeneity and multiple tumor sites. After a brief introduction on the application of the follow-up of ctDNA using genetic or epigenetic biomarkers for prognosis and surveillance of cancer patients, potential perspectives of using ctDNA for early diagnosis of cancers will be presented.

KEYWORDS:

• Droplet-based digital PCR
• NGS
• circulating tumor DNA
• early cancer diagnosis
• mutation
• DNA methylation
• biomarker

Acknowledgments

The authors are grateful to Dr. Alexandre How-kit for his careful reading of the manuscript.

Declaration of Interest

V Taly discloses honoraries from RainDance Technologies and Boehringer Ingelheim. P Laurent-Puig discloses honoraries from Astra-Zeneca, Boehringer Ingelheim, Amgen, Integragen Roche, Sanofi. The authors have no other 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 apart from those disclosed.

Additional information

Funding

This work was supported by the Ministère de l’Enseignement Supérieur et de la Recherche, the Université Paris-Descartes, the Centre National de la Recherche Scientifique (CNRS), the Institut National de la Santé et de la Recherche Médicale (INSERM), the Institut National du Cancer (INCA, n°2009-1-RT-03-US-1 and 2009-RT-03-UP5-1), the Association pour la recherche contre le cancer (ARC, no. SL220100601375), the Agence Nationale de la Recherche (ANR Nanobiotechnologies; no.ANR-10-NANO-0002-09), the SIRIC CARPEM, the ligue nationale contre le cancer (LNCC, Program‘Equipe labelisée LIGUE’; no. EL2016.LNCC/VaT) and Advanced Merieux Research Grant (PLP and VT) and canceropole funding (no. 2011-1-LABEL-UP5-2) and SATT idF Innov (Grant no. 275). SF Wang-Renault receives salary from SATT idF Innov (Grant no.275).