Direct circulating tumor DNA detection from unpurified plasma using a digital PCR platform

Abstract

Background: In standard pre-analytical conditions, an isolation step is required for circulating tumor DNA (ctDNA) analysis. The need for this step remains unclear with the development of ultrasensitive detection technologies such as digital PCR (dPCR). The aim of our study was to evaluate the ctDNA detection by dPCR platform either directly from plasma (plasma group, PG) or after an isolation step (isolation group, IG).

Methods: We included 17 patients corresponding to a selection of 43 blood samples in metastatic colorectal cancer patients. For each sample, ctDNA was analyzed with or without isolation step (IG and PG, respectively) using KRAS, NRAS and BRAF mutations identified from the tumor tissue. ctDNA detection was performed after a preamplication step using dPCR platform (QuantStudio™ 3D Digital PCR System). ctDNA detection rate and mutant allelic frequencies (MAF) were compared between IG and PG.

Results: Our results showed a detection rate at 93% in IG vs. 88% in PG. The concordance rate between the two groups was 91% (39/43) for ctDNA detection with the four discordant cases occurring in patients with low MAF (<0.5%). The mean value of MAF were 16.9±18.9 and 18.5±18.9 for IG and PG, respectively (p=0.24). The correlation coefficient r² for MAF was 0.82 between the two methods (p<0.0001).

Conclusion: In conclusion, our results show that direct detection of ctDNA from unpurified plasma is a feasible approach, particularly from sample with high MAF (>0.5%).

Keywords: Circulating tumor DNA; Digital PCR; Metastastic colorectal cancer; Unpurified plasma.