Performance comparison of commercial kits for isolating and detecting circulating tumor DNA

Circulating tumor DNA (ctDNA), a fraction of cell-free DNA (cfDNA) in the circulatory system, is released from tumor cells and thus carries tumor-specific genetic signatures. Using blood-derived ctDNA to detect somatic mutations has shown great value in guiding cancer targeted therapy. Isolation and detection efficiencies are the key factors affecting the performance of ctDNA detection. To optimize and standardize our clinical practice, in this study, we analyzed the isolation efficiency of four commercial cfDNA purification kits: QIAamp circulating nucleic acid kit, AmoyDx® Circulating DNA kits, Microdiag® circulating DNA isolation kit, and MagMAX cell-free DNA isolation kit; and the detection efficiency of two mainstream domestic EGFR gene mutation detection kits: MicroDiag EGFR gene mutation detection kit and Fluorometric real-time PCR Detection Kit for the analysis of EGFR gene mutations. Reference materials and plasma samples collected from lung cancer patients and healthy volunteers were used for the analysis. Our results showed that QIAamp circulating nucleic acid kit and Microdiag® circulating DNA kit had the highest recovery rate (up to 21.25 ng/mL) for short DNA fragments of about 173 bp which is the peak length of ctDNA. For ctDNA detection, the MicroDiag®EGFR gene mutation detection kit showed the highest detection rate and sensitivity for detecting EGFR mutations at a mutant frequency of 0.5%. This work provides a reliable choice of commercial kits for the clinical application of ctDNA.