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

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cam.issuedOnline2018-08-28
dc.contributor.authorRisberg, Bente
dc.contributor.authorTsui, Dana WY
dc.contributor.authorBiggs, Heather
dc.contributor.authorRuiz-Valdepenas Martin de Almagro, Andrea
dc.contributor.authorDawson, Sarah-Jane
dc.contributor.authorHodgkin, Charlotte
dc.contributor.authorJones, Linda
dc.contributor.authorParkinson, Christine
dc.contributor.authorPiskorz, Anna
dc.contributor.authorMarass, Francesco
dc.contributor.authorChandrananda, Dineika
dc.contributor.authorMoore, Elizabeth
dc.contributor.authorMorris, James
dc.contributor.authorPlagnol, Vincent
dc.contributor.authorRosenfeld, Nitzan
dc.contributor.authorCaldas, Carlos
dc.contributor.authorBrenton, James D
dc.contributor.authorGale, Davina
dc.contributor.orcidHodgkin, Charlotte [0000-0002-2240-1740]
dc.contributor.orcidJones, Linda [0000-0001-9347-5715]
dc.contributor.orcidChandrananda, Sandunie [0000-0002-8834-9500]
dc.contributor.orcidRosenfeld, Nitzan [0000-0002-2825-4788]
dc.contributor.orcidCaldas, Carlos [0000-0003-3547-1489]
dc.contributor.orcidBrenton, James [0000-0002-5738-6683]
dc.contributor.orcidGale, Davina [0000-0002-4521-8199]
dc.date.accessioned2018-11-14T00:30:39Z
dc.date.available2018-11-14T00:30:39Z
dc.date.issued2018-11
dc.description.abstractCirculating 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 K3EDTA 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 K3EDTA tubes, but were stable in BCT tubes. K3EDTA 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 K3EDTA and BCT, or following shipment in BCT. This study provides insights into the effects of sample processing on ctDNA analysis.
dc.format.mediumPrint-Electronic
dc.identifier.doi10.17863/CAM.32396
dc.identifier.eissn1943-7811
dc.identifier.issn1525-1578
dc.identifier.urihttps://www.repository.cam.ac.uk/handle/1810/285026
dc.languageeng
dc.language.isoeng
dc.publisherElsevier BV
dc.publisher.urlhttp://dx.doi.org/10.1016/j.jmoldx.2018.07.005
dc.rightsAttribution 4.0 International
dc.rights.urihttps://creativecommons.org/licenses/by/4.0/
dc.subjectAlleles
dc.subjectCirculating Tumor DNA
dc.subjectDNA Copy Number Variations
dc.subjectHumans
dc.subjectMutation
dc.subjectNeoplasms
dc.subjectSpecimen Handling
dc.subjectTemperature
dc.subjectTransportation
dc.titleEffects of Collection and Processing Procedures on Plasma Circulating Cell-Free DNA from Cancer Patients.
dc.typeArticle
dcterms.dateAccepted2018-07-26
prism.endingPage892
prism.issueIdentifier6
prism.publicationDate2018
prism.publicationNameJ Mol Diagn
prism.startingPage883
prism.volume20
pubs.funder-project-idCancer Research UK (CB4150)
pubs.funder-project-idCancer Research UK (C14303/A17197)
pubs.funder-project-idCancer Research Uk (None)
pubs.funder-project-idCancer Research UK (unknown)
pubs.funder-project-idCancer Research UK (unknown)
pubs.funder-project-idCancer Research UK (unknown)
pubs.funder-project-idCancer Research UK (unknown)
pubs.funder-project-idCancer Research UK (unknown)
pubs.funder-project-idCancer Research Uk (None)
pubs.funder-project-idCancer Research UK (unknown)
pubs.funder-project-idEuropean Commission (260791)
pubs.funder-project-idCancer Research UK (60098573)
pubs.funder-project-idCancer Research UK (unknown)
pubs.funder-project-idCancer Research UK (CB4140)
pubs.funder-project-idCancer Research Uk (None)
pubs.funder-project-idCambridge University Hospitals NHS Foundation Trust (CUH) (RG51913)
pubs.funder-project-idCambridge University Hospitals NHS Foundation Trust (CUH) (unknown)
pubs.funder-project-idDepartment of Health (via National Institute for Health Research (NIHR)) (unknown)
pubs.funder-project-idEuropean Commission FP7 Network of Excellence (NoE) (260791)
pubs.funder-project-idDepartment of Health (via National Institute for Health Research (NIHR)) (NF-SI-0515-10090)
pubs.funder-project-idEuropean Research Council (337905)
pubs.funder-project-idCancer Research UK (16942)
pubs.funder-project-idCancer Research UK (20240)
rioxxterms.licenseref.startdate2018-11
rioxxterms.licenseref.urihttp://www.rioxx.net/licenses/all-rights-reserved
rioxxterms.typeJournal Article/Review
rioxxterms.versionVoR
rioxxterms.versionofrecord10.1016/j.jmoldx.2018.07.005

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