About: Phi29 polymerase based random amplification of viral RNA as an alternative to random RT-PCR

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About: Phi29 polymerase based random amplification of viral RNA as an alternative to random RT-PCR Goto Sponge NotDistinct Permalink

An Entity of Type : schema:ScholarlyArticle, within Data Space : covidontheweb.inria.fr associated with source document(s)

Attributes	Values
type	Academic Article research paper schema:ScholarlyArticle
isDefinedBy	Covid-on-the-Web dataset
has title	Phi29 polymerase based random amplification of viral RNA as an alternative to random RT-PCR
Creator	Manuguerra, Jean-Claude Batéjat, Christophe Berthet, Nicolas Bourhy, Hervé Dacheux, Laurent Dickinson, Philip Korfhage, Christian Leclercq, India Stamboliyska, Rayna Kong, Katherine Cole, Stewart Kennedy, Giulia Old, Iain Reinhardt, Anita Van Ooyen, Sven
Source	Medline; PMC
abstract	BACKGROUND: Phi29 polymerase based amplification methods provides amplified DNA with minimal changes in sequence and relative abundance for many biomedical applications. RNA virus detection using microarrays, however, can present a challenge because phi29 DNA polymerase cannot amplify RNA nor small cDNA fragments (<2000 bases) obtained by reverse transcription of certain viral RNA genomes. Therefore, ligation of cDNA fragments is necessary prior phi29 polymerase based amplification. We adapted the QuantiTect Whole Transcriptome Kit (Qiagen) to our purposes and designated the method as Whole Transcriptome Amplification (WTA). RESULTS: WTA successfully amplified cDNA from a panel of RNA viruses representing the diversity of ribovirus genome sizes. We amplified a range of genome copy numbers from 15 to 4 × 10(7 )using WTA, which yielded quantities of amplified DNA as high as 1.2 μg/μl or 10(10 )target copies. The amplification factor varied between 10(9 )and 10(6). We also demonstrated that co-amplification occurred when viral RNA was mixed with bacterial DNA. CONCLUSION: This is the first report in the scientific literature showing that a modified WGA (WTA) approach can be successfully applied to viral genomic RNA of all sizes. Amplifying viral RNA by WTA provides considerably better sensitivity and accuracy of detection compared to random RT-PCR.
has issue date	2008-09-04(xsd:dateTime)
bibo:doi	10.1186/1471-2199-9-77
bibo:pmid	18771595
has license	cc-by
sha1sum (hex)	155cca2a90a5430ac391b46983efa4c13f193289
schema:url	https://doi.org/10.1186/1471-2199-9-77
resource representing a document's title	Phi29 polymerase based random amplification of viral RNA as an alternative to random RT-PCR
has PubMed Central identifier	PMC2535778
has PubMed identifier	18771595
schema:publication	BMC Mol Biol
resource representing a document's body	covid:155cca2a90a5430ac391b46983efa4c13f193289#body_text
is schema:about of	named entity '2000' named entity 'amplification' named entity 'adapted' covid:arg/155cca2a90a5430ac391b46983efa4c13f193289 named entity 'GENOMES' named entity 'CERTAIN' named entity 'OBTAINED BY' named entity 'PRESENT' named entity 'BIOMEDICAL' named entity 'RNA' named entity 'WHOLE TRANSCRIPTOME' named entity 'VIRAL RNA' named entity 'PROVIDES' named entity 'RELATIVE ABUNDANCE' named entity 'VIRUS DETECTION' named entity 'DESIGNATED' named entity 'CDNA' named entity 'LIGATION' named entity 'RNA VIRUS' named entity 'SEQUENCE' named entity 'KIT' named entity 'PRIOR' named entity 'CHALLENGE' named entity 'METHOD' named entity 'BASES' named entity 'POLYMERASE' named entity 'BMC' named entity 'BACKGROUND' named entity 'MICROARRAYS' named entity 'NECESSARY' named entity 'BASED' named entity 'BASED' named entity 'MINIMAL' named entity 'VIRAL RNA' named entity 'RT-PCR' named entity 'MOLECULAR BIOLOGY' named entity 'POLYMERASE' named entity 'RANDOM' named entity 'ALTERNATIVE' named entity 'ADAPTED' named entity 'AMPLIFY' named entity 'CHANGES' named entity 'METHODS' named entity 'AMPLIFIED DNA' named entity 'OUR' named entity 'FRAGMENTS' named entity 'REVERSE TRANSCRIPTION' named entity 'AMPLIFICATION' named entity 'PURPOSES' named entity 'SMALL' named entity 'APPLICATIONS' named entity 'USING' named entity 'AMPLIFICATION' named entity 'DNA POLYMERASE' named entity 'bases' named entity 'cDNA' named entity 'based' named entity 'amplify' named entity 'ligation' named entity 'cDNA' named entity 'based' named entity 'minimal' named entity 'Kit' named entity 'WTA' named entity 'Transcriptome' named entity 'ligation' named entity 'WTA'

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