Technical Evaluation of Commercial Mutation Analysis Platforms and Reference Materials for Liquid Biopsy Profiling
Open Access
- 16 June 2020
- Vol. 12 (6), 1588
- https://doi.org/10.3390/cancers12061588
Abstract
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 highlighting the importance of extensive validation of the test performance before offering these tests in clinical routine practice.Keywords
Funding Information
- H2020 European Institute of Innovation and Technology (Cancer-ID IMI JU; #115749-1)
This publication has 36 references indexed in Scilit:
- Integration of next-generation sequencing in clinical diagnostic molecular pathology laboratories for analysis of solid tumours; an expert opinion on behalf of IQN Path ASBLVirchows Archiv, 2016
- Integrated digital error suppression for improved detection of circulating tumor DNANature Biotechnology, 2016
- Understanding next generation sequencing in oncology: A guide for oncologistsCritical Reviews in Oncology/Hematology, 2015
- Multifocal clonal evolution characterized using circulating tumour DNA in a case of metastatic breast cancerNature Communications, 2015
- Memorial Sloan Kettering-Integrated Mutation Profiling of Actionable Cancer Targets (MSK-IMPACT)The Journal of Molecular Diagnostics, 2015
- An ultrasensitive method for quantitating circulating tumor DNA with broad patient coverageNature Medicine, 2014
- Tumour heterogeneity in the clinicNature, 2013
- Intratumor Heterogeneity and Branched Evolution Revealed by Multiregion SequencingThe New England Journal of Medicine, 2012
- Improved Survival with Vemurafenib in Melanoma with BRAF V600E MutationThe New England Journal of Medicine, 2011
- KRAS Mutation Status Is Predictive of Response to Cetuximab Therapy in Colorectal CancerCancer Research, 2006