Liquid biopsies are now becoming a frequently used tool for various cancers. Fragments of DNA called as Cell free DNA (cfDNA) are shed into blood regularly. In the case of cancer, such fragments contain circulating tumor DNA (ctDNA) that are shed  via tumor cell necrosis, apoptosis and active release of DNA that can be analysed to determine specific DNA aberrations. Recent advances in blood based minimally invasive liquid biopsies is revolutionizing the process of early detection of cancer, cancer recurrence and screening. Liquid biopsies offer several advantages over tissue biopsies such as but not limited to (i) collection of peripheral blood instead of surgical tissue removal and (ii) Ease of access to monitor the genetic and epigenetic aberrational status during therapy or post-surgery. In addition, monitoring of cfDNA may enable detection of tumor during early stages or recurrence wherein the imaging results are indeterminate. 

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The three important factors for clinical translation of liquid biopsies and DNA testing include (i) Technology platform, (ii) Cost and (iii) Turn-Around-Time. A useful technology that is expensive for translation to clinics is of limited clinical utility. Also, any diagnosis that takes multiple weeks for generating results is detrimental towards the cause.

 

Next Generation Sequencing (NGS) is a state-of-the-art technology. However, use of NGS in clinical settings is highly limited due to the extensive time, usually 3-4 weeks, for generating results and the cost of NGS analysis which is significantly high. In addition, 2 separate analyses would have to be carried out for identification of epigenetic aberrations and genetic aberrations increasing the cost, time, and the amount of cfDNA required (usually low abundance in plasma).

 

On the other hand, droplet digital PCR (ddPCR) is an established tool for amplicon-based sequencing. Unlike NGS, Detection of genetic and epigenetic aberrations can be carried out simultaneously in the case of ddPCR. The time from collection of blood to analysis takes less than 48 hours for ddPCR and does not require any sample preparation steps such as library build, a crucial step in the case of NGS. Any errors in library builds can cause erratic results leading to loss of time and in some cases, exhaustion of patient samples. Unlike NGS wherein multiple samples have to be analyzed together to reduce analysis cost, ddPCR can be used for analysis with even a single sample for almost the same cost as that of multiple samples. 

 

The most important advantage of ddPCR is the determination of absolute copy number of mutant alleles or aberrant genes that would allow to set personalized baselines before and after procedures. In the view of these advantages, clinical utility of ddPCR for multimode analysis of samples is highly relevant.