Show simple item record

dc.contributor.authorRisberg, Benteen
dc.contributor.authorTsui, Dana WYen
dc.contributor.authorBiggs, Heatheren
dc.contributor.authorRuiz-Valdepenas Martin de Almagro, Andreaen
dc.contributor.authorDawson, Sarah-Janeen
dc.contributor.authorHodgkin, Charlotteen
dc.contributor.authorJones, Lindaen
dc.contributor.authorParkinson, Christineen
dc.contributor.authorPiskorz, Annaen
dc.contributor.authorMarass, Francescoen
dc.contributor.authorChandrananda, Sandunieen
dc.contributor.authorMoore, Elizabethen
dc.contributor.authorMorris, Jamesen
dc.contributor.authorPlagnol, Vincenten
dc.contributor.authorRosenfeld, Nitzanen
dc.contributor.authorCaldas, Carlosen
dc.contributor.authorBrenton, Jamesen
dc.contributor.authorGale, Davinaen
dc.date.accessioned2018-11-14T00:30:39Z
dc.date.available2018-11-14T00:30:39Z
dc.date.issued2018-11en
dc.identifier.issn1525-1578
dc.identifier.urihttps://www.repository.cam.ac.uk/handle/1810/285026
dc.description.abstractCirculating tumour DNA (ctDNA) offers new opportunities for non-invasive cancer management. Detecting ctDNA in plasma is challenging since 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 (i) delay in processing (ii) storage temperatures, (iii) different blood collection tubes, (iv) centrifugation protocols and (v) sample shipment on cfDNA levels. Peripheral blood (n=231) from cancer patients (n=62) were collected into K3EDTA or Cell-free DNA BCT® (BCT) tubes and analysed by digital PCR (dPCR), targeted amplicon or shallow whole-genome (sWGS) sequencing. To assess pre-analytic effects, plasma was processed under different conditions after 0h, 6h, 24h, 48h, 96h and 1 week at room temperature (RT) or 4°C, or using different centrifugation protocols. dPCR 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 RT storage, but levels were elevated compared to BCT. A second centrifugation at 3000g gave similar cfDNA yields compared to 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-Electronicen
dc.languageengen
dc.publisherAmerican Society for Investigative Pathology
dc.rightsAttribution 4.0 International
dc.rights.urihttps://creativecommons.org/licenses/by/4.0/
dc.subjectHumansen
dc.subjectNeoplasmsen
dc.subjectSpecimen Handlingen
dc.subjectTemperatureen
dc.subjectMutationen
dc.subjectAllelesen
dc.subjectTransportationen
dc.subjectDNA Copy Number Variationsen
dc.subjectCirculating Tumor DNAen
dc.titleEffects of Collection and Processing Procedures on Plasma Circulating Cell-Free DNA from Cancer Patients.en
dc.typeArticle
prism.endingPage892
prism.issueIdentifier6en
prism.publicationDate2018en
prism.publicationNameThe Journal of molecular diagnostics : JMDen
prism.startingPage883
prism.volume20en
dc.identifier.doi10.17863/CAM.32396
dcterms.dateAccepted2018-07-26en
rioxxterms.versionofrecord10.1016/j.jmoldx.2018.07.005en
rioxxterms.licenseref.urihttp://www.rioxx.net/licenses/all-rights-reserveden
rioxxterms.licenseref.startdate2018-11en
dc.contributor.orcidDawson, Sarah-Jane [0000-0002-8276-0374]
dc.contributor.orcidHodgkin, Charlotte [0000-0002-2240-1740]
dc.contributor.orcidMarass, Francesco [0000-0002-8993-7320]
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.identifier.eissn1943-7811
rioxxterms.typeJournal Article/Reviewen
pubs.funder-project-idCancer Research UK (CB4150)
pubs.funder-project-idCancer Research UK (C14303_do not transfer)
pubs.funder-project-idCancer Research UK (A7325)
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 (A3086)
pubs.funder-project-idCancer Research UK (unknown)
pubs.funder-project-idEC FP7 NOE (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 (A15580)
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)


Files in this item

Thumbnail

This item appears in the following Collection(s)

Show simple item record

Attribution 4.0 International
Except where otherwise noted, this item's licence is described as Attribution 4.0 International