Effects of Collection and Processing Procedures on Plasma Circulating Cell-Free DNA from Cancer Patients.

Autor:	Risberg B; Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Robinson Way, University of Cambridge, Cambridge, United Kingdom; Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital, Norway; Department of Pathology, Oslo University Hospital, Oslo, Norway., Tsui DWY; Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Robinson Way, University of Cambridge, Cambridge, United Kingdom; Cancer Research UK Major Centre, Cambridge, United Kingdom. Electronic address: tsuiw@mskcc.org., Biggs H; Cambridge Breast Unit, Cambridge University Hospitals NHS Foundation Trust, Addenbrooke's Hospital, Cambridge, United Kingdom., Ruiz-Valdepenas Martin de Almagro A; Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Robinson Way, University of Cambridge, Cambridge, United Kingdom; Cancer Research UK Major Centre, Cambridge, United Kingdom., Dawson SJ; Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Robinson Way, University of Cambridge, Cambridge, United Kingdom; Cambridge Breast Unit, Cambridge University Hospitals NHS Foundation Trust, Addenbrooke's Hospital, Cambridge, United Kingdom; Department of Oncology, Cambridge University Hospitals NHS Foundation Trust, Addenbrooke's Hospital, Cambridge, United Kingdom., Hodgkin C; Department of Oncology, Cambridge University Hospitals NHS Foundation Trust, Addenbrooke's Hospital, Cambridge, United Kingdom., Jones L; Cambridge Breast Unit, Cambridge University Hospitals NHS Foundation Trust, Addenbrooke's Hospital, Cambridge, United Kingdom., Parkinson C; Department of Oncology, Cambridge University Hospitals NHS Foundation Trust, Addenbrooke's Hospital, Cambridge, United Kingdom., Piskorz A; Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Robinson Way, University of Cambridge, Cambridge, United Kingdom; Cancer Research UK Major Centre, Cambridge, United Kingdom., Marass F; Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Robinson Way, University of Cambridge, Cambridge, United Kingdom; Cancer Research UK Major Centre, Cambridge, United Kingdom., Chandrananda D; Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Robinson Way, University of Cambridge, Cambridge, United Kingdom; Cancer Research UK Major Centre, Cambridge, United Kingdom., Moore E; Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Robinson Way, University of Cambridge, Cambridge, United Kingdom; Cancer Research UK Major Centre, Cambridge, United Kingdom., Morris J; Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Robinson Way, University of Cambridge, Cambridge, United Kingdom; Cancer Research UK Major Centre, Cambridge, United Kingdom., Plagnol V; UCL Genetics Institute, University College London, London, United Kingdom., Rosenfeld N; Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Robinson Way, University of Cambridge, Cambridge, United Kingdom; Cancer Research UK Major Centre, Cambridge, United Kingdom., Caldas C; Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Robinson Way, University of Cambridge, Cambridge, United Kingdom; Cancer Research UK Major Centre, Cambridge, United Kingdom; Cambridge Breast Unit, Cambridge University Hospitals NHS Foundation Trust, Addenbrooke's Hospital, Cambridge, United Kingdom; Department of Oncology, Cambridge University Hospitals NHS Foundation Trust, Addenbrooke's Hospital, Cambridge, United Kingdom., Brenton JD; Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Robinson Way, University of Cambridge, Cambridge, United Kingdom; Cancer Research UK Major Centre, Cambridge, United Kingdom; Department of Oncology, Cambridge University Hospitals NHS Foundation Trust, Addenbrooke's Hospital, Cambridge, United Kingdom., Gale D; Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Robinson Way, University of Cambridge, Cambridge, United Kingdom; Cancer Research UK Major Centre, Cambridge, United Kingdom. Electronic address: davina.gale@cruk.cam.ac.uk.
Jazyk:	angličtina
Zdroj:	The Journal of molecular diagnostics : JMD [J Mol Diagn] 2018 Nov; Vol. 20 (6), pp. 883-892. Date of Electronic Publication: 2018 Aug 28.
DOI:	10.1016/j.jmoldx.2018.07.005
Abstrakt:	Circulating tumor DNA (ctDNA) offers new opportunities for noninvasive cancer management. Detecting ctDNA in plasma is challenging because it constitutes only a minor fraction of the total cell-free DNA (cfDNA). Pre-analytical factors affect cfDNA levels contributed from leukocyte lysis, hence the ability to detect low-frequency mutant alleles. This study investigates the effects of the delay in processing, storage temperatures, different blood collection tubes, centrifugation protocols, and sample shipment on cfDNA levels. Peripheral blood (n = 231) from cancer patients (n = 62) were collected into K 3 EDTA or Cell-free DNA BCT tubes and analyzed by digital PCR, targeted amplicon, or shallow whole-genome sequencing. To assess pre-analytic effects, plasma was processed under different conditions after 0, 6, 24, 48, 96 hours, and 1 week at room temperature or 4°C, or using different centrifugation protocols. Digital PCR showed that cfDNA levels increased gradually with time in K 3 EDTA tubes, but were stable in BCT tubes. K 3 EDTA samples stored at 4°C showed less variation than room temperature storage, but levels were elevated compared with BCT. A second centrifugation at 3000 × g gave similar cfDNA yields compared with higher-speed centrifugation. Next-generation sequencing showed negligible differences in background error or copy number changes between K 3 EDTA and BCT, or following shipment in BCT. This study provides insights into the effects of sample processing on ctDNA analysis. (Copyright © 2018 American Society for Investigative Pathology and the Association for Molecular Pathology. Published by Elsevier Inc. All rights reserved.)
Databáze:	MEDLINE
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