Abstract
Multiple platforms are commercially available for the detection of circulating cell-free tumour DNA (ctDNA) from liquid biopsies. Since platforms have different input and output variables, deciding what platform to use for a given clinical or research question can be daunting. This study aimed to provide insight in platform selection criteria by comparing four commercial platforms that detect KRAS ctDNA hotspot mutations: Bio-Rad droplet digital PCR (ddPCR), BioCartis Idylla, Roche COBAS z480 and Sysmex BEAMing. Platform sensitivities were determined using plasma samples from metastatic colorectal cancer (mCRC) patients and synthetic reference samples, thereby eliminating variability in amount of plasma analysed and ctDNA isolation methods. The prevalence of KRAS nucleotide alterations was set against platform-specific breadth of target. Platform comparisons revealed that ddPCR and BEAMing detect more KRAS mutations amongst mCRC patients than Idylla and COBAS z480. Maximum sample throughput was highest for ddPCR and COBAS z480. Total annual costs were highest for BEAMing and lowest for Idylla and ddPCR. In conclusion, when selecting a platform for detection of ctDNA hotspot mutations the desired test sensitivity, breadth of target, maximum sample throughput, and total annual costs are critical factors that should be taken into consideration. Based on the results of this study, laboratories will be able to select the optimal platform for their needs.
Highlights
Patients with metastatic colorectal cancer may be treated with targeted therapies directed against epidermal growth factor receptor (EGFR)
Prospective Dutch Colorectal Cancer cohort (PLCRC) was approved by the Medical Ethical Committee (METC) of the University Medical Center Utrecht
The experimental set-up to determine the sensitivity of each platform is shown in Fig. 1, steps one to three. cell-free DNA (cfDNA) from six metastatic colorectal cancer (mCRC) patients was analysed following the manufacturer’s instructions as indicated in the first step of Fig. 1
Summary
Patients with metastatic colorectal cancer (mCRC) may be treated with targeted therapies directed against epidermal growth factor receptor (EGFR). Multiple commercial ctDNA detection platforms are available, ranging from PCR based hotspot analysis to broad targeted NGS applications These platforms show considerable differences in the amount of plasma required as input, the DNA isolation method, quantitative versus semi-quantitative results, the breadth of target and the total cost per sample analysed. Attempts to perform such comparisons have been made[6,7,8,9], but it cannot be excluded that the results were biased by using different amounts of plasma or cfDNA, different isolation methods[10] and/or the use of tissue biopsy results as the gold standard In addition these studies did not evaluate factors influencing the choice for a platform in daily practice such as the costs of analysis, the maximum annual throughput and the differences in the number of mutations targeted by a platform. The costs of analysis and the impact of the choice for a platform on detection of KRAS mutations in mCRC patients were investigated
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