Technical Evaluation of Commercial Mutation Analysis Platforms and Reference Materials for Liquid Biopsy Profiling

Sabrina Weber, Benjamin Spiegl, Samantha O Perakis, Christine M Ulz, Peter M Abuja, Karl Kashofer, Paul van der Leest, Maria Aguirre Azpurua, Menno Tamminga, Dan Brudzewsky, Dominic G Rothwell, Sumitra Mohan, Alexander Sartori, Rita Lampignano, Yves Konigshofer, Markus Sprenger-Haussels, Harriet Wikman, Inger R Bergheim, Vera Kloten, Ed SchuuringMichael R Speicher, Ellen Heitzer

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Molecular profiling from liquid biopsy, in particular cell-free DNA (cfDNA), represents an attractive alternative to tissue biopsies for the detection of actionable targets and tumor monitoring. In addition to PCR-based assays, Next Generation Sequencing (NGS)-based cfDNA assays are now commercially available and are being increasingly adopted in clinical practice. However, the validity of these products as well as the clinical utility of cfDNA in the management of patients with cancer has yet to be proven. Within framework of the Innovative Medicines Initiative (IMI) program CANCER-ID we evaluated the use of commercially available reference materials designed for ctDNA testing and cfDNA derived from Diagnostic Leukaphereses (DLA) for inter-and intra-assay as well as intra-and inter-laboratory comparisons. In three experimental setups, a broad range of assays including ddPCR, MassARRAY and various NGS-based assays were tested. We demonstrate that both reference materials with predetermined VAFs and DLA samples are extremely useful for the performance assessment of mutation analysis platforms. Moreover, our data indicate a substantial variability of NGS assays with respect to sensitivity and specificity.

Original languageEnglish
Article number1588
Pages (from-to)1-16
Number of pages16
Issue number6
Publication statusPublished - 16-Jun-2020

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