Please use this identifier to cite or link to this item: http://hdl.handle.net/1942/41798
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dc.contributor.authorGleerup, David-
dc.contributor.authorChen, Yao-
dc.contributor.authorVan Snippenberg, Willem-
dc.contributor.authorValcke, Cedric-
dc.contributor.authorTHAS, Olivier-
dc.contributor.authorTrypsteen, Wim-
dc.contributor.authorDe Spiegelaere, Ward-
dc.date.accessioned2023-11-15T09:11:02Z-
dc.date.available2023-11-15T09:11:02Z-
dc.date.issued2023-
dc.date.submitted2023-11-15T09:06:28Z-
dc.identifier.citationAnalytica Chimica Acta, 1279 (Art N° 341822)-
dc.identifier.urihttp://hdl.handle.net/1942/41798-
dc.description.abstractBackground: Accurate methods to assess DNA integrity are needed for many biomolecular methods. A multiplex digital PCR (dPCR) method designed for interspaced target sequences can be used to assess sequence integrity of large DNA strands. The ratio of single positive partitions versus double positive partitions is then used to calculate the sheared DNA strands. However, this simple calculation is only valid with low DNA concentration. We here describe a method based on probability calculations which enables DNA quality analysis in a large dynamic range of DNA concentrations. Results: Known DNA integrity percentages were mimicked using artificial double stranded DNA in low, inter-mediate and high DNA concentration scenarios, respectively 600, 12500 and 30000 copies of DNA per reaction. At low concentrations both methods were similar. However, at the intermediate concentration (12500 copies per reaction) the ratio based method started producing a larger error than the proposed probability calculation method with a mean relative error of 20.7 and 16.7 for the Bruner and the proposed method respectively. At the high concentration (30000 copies per reaction) only the proposed method provided accurate measurements with a mean relative error of 60.9 and 9.3 for the ratio based and the proposed method respectively. Furthermore, while both methods have a bias, it is constant for the proposed method, while it decreases with the integrity of the DNA for the ratio based method. The probability calculation equation was extended to 4 dimensions and a proof of concept experiment was performed, the data suggested that the 4 dimensional equation is valid.Significance and novelty: We here validate a method of estimating DNA integrity with dPCR using multiple probe combinations, allowing fast and flexible DNA integrity analysis. Additionally, we extend the method from 2 to 4 plex for more accurate DNA integrity measurements.-
dc.description.sponsorshipThis work was financially supported by an interdisciplinary grant of the special research fund of Ghent University (01IO0420).-
dc.language.isoen-
dc.publisherELSEVIER-
dc.rights2023 Elsevier B.V. All rights reserved.-
dc.subject.otherdPCR-
dc.subject.otherHIV-
dc.subject.otherDNA integrity-
dc.subject.otherDigital PCR-
dc.titleMeasuring DNA quality by digital PCR using probability calculations-
dc.typeJournal Contribution-
dc.identifier.volume1279-
local.format.pages7-
local.bibliographicCitation.jcatA1-
dc.description.notesDe Spiegelaere, W (corresponding author), Univ Ghent, Fac Vet Med, Campus Merelbeke,Salisburylaan 133, B-9820 Merelbeke, Belgium.-
dc.description.notesDavidgrandjean.gleerup@ugent.be; yao.chen@ugent.be;-
dc.description.noteswillem.vansnippenberg@ugent.be; Cedric.Valcke@gmail.com;-
dc.description.notesolivier.thas@ugent.be; wim.trypsteen@ugent.be;-
dc.description.notesWard.DeSpiegelaere@ugent.be-
local.publisher.placeRADARWEG 29, 1043 NX AMSTERDAM, NETHERLANDS-
local.type.refereedRefereed-
local.type.specifiedArticle-
local.bibliographicCitation.artnr341822-
dc.identifier.doi10.1016/j.aca.2023.341822-
dc.identifier.pmid37827643-
dc.identifier.isi001089049400001-
dc.contributor.orcidValcke, Cedric/0009-0006-1795-5120; van Snippenberg,-
dc.contributor.orcidWillem/0000-0001-8903-3631-
local.provider.typewosris-
local.description.affiliation[Gleerup, David; De Spiegelaere, Ward] Univ Ghent, Lab Vet Morphol, Ghent, Belgium.-
local.description.affiliation[Gleerup, David; Chen, Yao; Thas, Olivier; Trypsteen, Wim; De Spiegelaere, Ward] Univ Ghent, Digital PCR Consortium, Ghent, Belgium.-
local.description.affiliation[Chen, Yao; Thas, Olivier] Univ Ghent, Dept Appl Math Comp Sci & Stat, Ghent, Belgium.-
local.description.affiliation[Van Snippenberg, Willem; Trypsteen, Wim] Univ Ghent, HIV Cure Res Ctr, Dept Internal Med & Pediat, Ghent, Belgium.-
local.description.affiliation[Van Snippenberg, Willem; Trypsteen, Wim] Ghent Univ Hosp, Ghent, Belgium.-
local.description.affiliation[Thas, Olivier] Univ Wollongong, Natl Inst Appl Stat Res Australia NIASRA, Wollongong, Australia.-
local.description.affiliation[Thas, Olivier] Hasselt Univ, Data Sci Inst, I BioStat, Hasselt, Belgium.-
local.description.affiliation[Valcke, Cedric] HOGENT Univ Appl Sci & Arts, Dept Healthcare, Ghent, Belgium.-
local.description.affiliation[De Spiegelaere, Ward] Univ Ghent, Fac Vet Med, Campus Merelbeke,Salisburylaan 133, B-9820 Merelbeke, Belgium.-
local.uhasselt.internationalyes-
item.fulltextWith Fulltext-
item.fullcitationGleerup, David; Chen, Yao; Van Snippenberg, Willem; Valcke, Cedric; THAS, Olivier; Trypsteen, Wim & De Spiegelaere, Ward (2023) Measuring DNA quality by digital PCR using probability calculations. In: Analytica Chimica Acta, 1279 (Art N° 341822).-
item.accessRightsRestricted Access-
item.contributorGleerup, David-
item.contributorChen, Yao-
item.contributorVan Snippenberg, Willem-
item.contributorValcke, Cedric-
item.contributorTHAS, Olivier-
item.contributorTrypsteen, Wim-
item.contributorDe Spiegelaere, Ward-
crisitem.journal.issn0003-2670-
crisitem.journal.eissn1873-4324-
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