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000140475 0247_ $$2doi$$a10.1038/s41598-019-38733-1
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000140475 037__ $$aDZNE-2020-06797
000140475 041__ $$aEnglish
000140475 082__ $$a600
000140475 1001_ $$aWally, N.$$b0
000140475 245__ $$aPlasmid DNA contaminant in molecular reagents.
000140475 260__ $$a[London]$$bMacmillan Publishers Limited, part of Springer Nature$$c2019
000140475 264_1 $$2Crossref$$3online$$bSociety for Mining, Metallurgy and Exploration Inc.$$c2019-02-07
000140475 264_1 $$2Crossref$$3print$$bSociety for Mining, Metallurgy and Exploration Inc.$$c2019-12-01
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000140475 520__ $$aBackground noise in metagenomic studies is often of high importance and its removal requires extensive post-analytic, bioinformatics filtering. This is relevant as significant signals may be lost due to a low signal-to-noise ratio. The presence of plasmid residues, that are frequently present in reagents as contaminants, has not been investigated so far, but may pose a substantial bias. Here we show that plasmid sequences from different sources are omnipresent in molecular biology reagents. Using a metagenomic approach, we identified the presence of the (pol) of equine infectious anemia virus in human samples and traced it back to the expression plasmid used for generation of a commercial reverse transcriptase. We found fragments of multiple other expression plasmids in human samples as well as commercial polymerase preparations. Plasmid contamination sources included production chain of molecular biology reagents as well as contamination of reagents from environment or human handling of samples and reagents. Retrospective analyses of published metagenomic studies revealed an inaccurate signal-to-noise differentiation. Hence, the plasmid sequences that seem to be omnipresent in molecular biology reagents may misguide conclusions derived from genomic/metagenomics datasets and thus also clinical interpretations. Critical appraisal of metagenomic data sets for the possibility of plasmid background noise is required to identify reliable and significant signals.
000140475 536__ $$0G:(DE-HGF)POF3-342$$a342 - Disease Mechanisms and Model Systems (POF3-342)$$cPOF3-342$$fPOF III$$x0
000140475 542__ $$2Crossref$$i2019-02-07$$uhttps://creativecommons.org/licenses/by/4.0
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000140475 650_2 $$2MeSH$$aComputational Biology
000140475 650_2 $$2MeSH$$aDNA Contamination
000140475 650_2 $$2MeSH$$aDNA, Viral: analysis
000140475 650_2 $$2MeSH$$aDNA, Viral: genetics
000140475 650_2 $$2MeSH$$aDiagnostic Errors: prevention & control
000140475 650_2 $$2MeSH$$aGenes, pol: genetics
000140475 650_2 $$2MeSH$$aHigh-Throughput Nucleotide Sequencing
000140475 650_2 $$2MeSH$$aHumans
000140475 650_2 $$2MeSH$$aIndicators and Reagents: analysis
000140475 650_2 $$2MeSH$$aInfectious Anemia Virus, Equine: genetics
000140475 650_2 $$2MeSH$$aMetagenomics
000140475 650_2 $$2MeSH$$aPlasmids: analysis
000140475 650_2 $$2MeSH$$aPlasmids: genetics
000140475 650_2 $$2MeSH$$aRetrospective Studies
000140475 650_2 $$2MeSH$$aSequence Analysis, DNA: methods
000140475 7001_ $$aSchneider, M.$$b1
000140475 7001_ $$aThannesberger, J.$$b2
000140475 7001_ $$aKastner, M. T.$$b3
000140475 7001_ $$aBakonyi, T.$$b4
000140475 7001_ $$aIndik, S.$$b5
000140475 7001_ $$aRattei, T.$$b6
000140475 7001_ $$0P:(DE-2719)2811747$$aBedarf, J.$$b7$$udzne
000140475 7001_ $$aHildebrand, F.$$b8
000140475 7001_ $$aLaw, J.$$b9
000140475 7001_ $$aJovel, J.$$b10
000140475 7001_ $$0P:(DE-HGF)0$$aSteininger, C.$$b11$$eCorresponding author
000140475 77318 $$2Crossref$$3journal-article$$a10.1038/s41598-019-38733-1$$b : Society for Mining, Metallurgy and Exploration Inc., 2019-02-07$$n1$$p1652$$tScientific Reports$$v9$$x2045-2322$$y2019
000140475 773__ $$0PERI:(DE-600)2615211-3$$a10.1038/s41598-019-38733-1$$gVol. 9, no. 1, p. 1652$$n1$$p1652$$q9:1<1652$$tScientific reports$$v9$$x2045-2322$$y2019
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