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Clin Chem. 2019 Oct 18. pii: clinchem.2019.306837. doi: 10.1373/clinchem.2019.306837. [Epub ahead of print]

Multicenter Evaluation of Circulating Cell-Free DNA Extraction and Downstream Analyses for the Development of Standardized (Pre)analytical Work Flows.

Author information

1
Bayer AG, Biomarker Research, Wuppertal, Germany.
2
Institute of Human Genetics, Diagnostic and Research Center for Molecular BioMedicine, Medical University of Graz, Graz, Austria.
3
Christian Doppler Laboratory for Liquid Biopsies for Early Detection of Cancer, Graz, Austria.
4
TATAA Biocenter Ab, Gothenburg, Sweden.
5
PreAnalytiX GmbH, Hombrechtikon, Switzerland.
6
University Medical Center Hamburg-Eppendorf, Hamburg, Germany.
7
University of Groningen, University Medical Center of Groningen, Groningen, the Netherlands.
8
QIAGEN GmbH, Hilden, Germany.
9
CR-UK Manchester Institute, University of Manchester, Manchester, UK.
10
Servier, Suresnes, France.
11
Department of Cancer Genetics, Institute of Cancer Research, Oslo University Hospital, Oslo, Norway.
12
Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Italy.
13
University of Trieste, DSM-Cattinara Hospital, Trieste, Italy.
14
Alacris Theranostics GmbH, Berlin, Germany.
15
Boehringer-Ingelheim, Ingelheim am Rhein, Germany.
16
University of Florence, Florence, Italy.
17
University of Athens, Athens, Greece.
18
Integrated BioBank of Luxembourg, Dudelange, Luxembourg.
19
Institute of Human Genetics, Diagnostic and Research Center for Molecular BioMedicine, Medical University of Graz, Graz, Austria; ellen.heitzer@medunigraz.at.

Abstract

BACKGROUND:

In cancer patients, circulating cell-free DNA (ccfDNA) can contain tumor-derived DNA (ctDNA), which enables noninvasive diagnosis, real-time monitoring, and treatment susceptibility testing. However, ctDNA fractions are highly variable, which challenges downstream applications. Therefore, established preanalytical work flows in combination with cost-efficient and reproducible reference materials for ccfDNA analyses are crucial for analytical validity and subsequently for clinical decision-making.

METHODS:

We describe the efforts of the Innovative Medicines Initiative consortium CANCER-ID (http://www.cancer-id.eu) for comparing different technologies for ccfDNA purification, quantification, and characterization in a multicenter setting. To this end, in-house generated mononucleosomal DNA (mnDNA) from lung cancer cell lines carrying known TP53 mutations was spiked in pools of plasma from healthy donors generated from 2 different blood collection tubes (BCTs). ccfDNA extraction was performed at 15 partner sites according to their respective routine practice. Downstream analysis of ccfDNA with respect to recovery, integrity, and mutation analysis was performed centralized at 4 different sites.

RESULTS:

We demonstrate suitability of mnDNA as a surrogate for ccfDNA as a process quality control from nucleic acid extraction to mutation detection. Although automated extraction protocols and quantitative PCR-based quantification methods yielded the most consistent and precise results, some kits preferentially recovered spiked mnDNA over endogenous ccfDNA. Mutated TP53 fragments derived from mnDNA were consistently detected using both next-generation sequencing-based deep sequencing and droplet digital PCR independently of BCT.

CONCLUSIONS:

This comprehensive multicenter comparison of ccfDNA preanalytical and analytical work flows is an important contribution to establishing evidence-based guidelines for clinically feasible (pre)analytical work flows.

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