About: Use of consensus sequences for the design of high density resequencing microarrays: the influenza virus paradigm

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About: Use of consensus sequences for the design of high density resequencing microarrays: the influenza virus paradigm Goto Sponge NotDistinct Permalink

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

Attributes	Values
type	Academic Article research paper schema:ScholarlyArticle
isDefinedBy	Covid-on-the-Web dataset
has title	Use of consensus sequences for the design of high density resequencing microarrays: the influenza virus paradigm
Creator	Manuguerra, Jean-Claude Batéjat, Christophe Berthet, Nicolas Dickinson, Philip Leclercq, India Kong, Katherine Rousseaux, Claudine Cole, Stewart Kennedy, Giulia Old, Iain
Source	Medline; PMC
abstract	BACKGROUND: A resequencing microarray called PathogenID v2.0 has been developed and used to explore various strategies of sequence selection for its design. The part dedicated to influenza viruses was based on consensus sequences specific for one gene generated from global alignments of a large number of influenza virus sequences available in databanks. RESULTS: For each HA (H1, H2, H3, H5, H7 and H9) and NA (N1, N2 and N7) molecular type chosen to be tested, 1 to 3 consensus sequences were computed and tiled on the microarray. A total of 12 influenza virus samples from different host origins (humans, pigs, horses and birds) and isolated over a period of about 50 years were used in this study. Influenza viruses were correctly identified, and in most cases with the accurate information of the time of their emergence. CONCLUSIONS: PathogenID v2.0 microarray demonstrated its ability to type and subtype influenza viruses, often to the level of viral variants, with a minimum number of tiled sequences. This validated the strategy of using consensus sequences, which do not exist in nature, for our microarray design. The versatility, rapidity and high discriminatory power of the PathogenID v2.0 microarray could prove critical to detect and identify viral genome reassortment events resulting in a novel virus with epidemic or pandemic potential and therefore assist health authorities to make efficient decisions about patient treatment and outbreak management.
has issue date	2010-10-20(xsd:dateTime)
bibo:doi	10.1186/1471-2164-11-586
bibo:pmid	20961419
has license	cc-by
sha1sum (hex)	f161447bea90a1e414e3cb22557efe9156bab8e2
schema:url	https://doi.org/10.1186/1471-2164-11-586
resource representing a document's title	Use of consensus sequences for the design of high density resequencing microarrays: the influenza virus paradigm
has PubMed Central identifier	PMC3091733
has PubMed identifier	20961419
schema:publication	BMC Genomics
resource representing a document's body	covid:f161447bea90a1e414e3cb22557efe9156bab8e2#body_text
is schema:about of	named entity 'USE OF' named entity 'consensus sequences' named entity 'selection' named entity 'RESEQUENCING' named entity 'PERIOD' named entity 'LARGE' named entity 'STUDY' named entity 'CONSENSUS' named entity 'HORSES' named entity 'GENERATED' named entity 'DESIGN' named entity 'RESULTS' named entity 'SEQUENCES' named entity 'THEIR' named entity 'BACKGROUND' named entity 'GLOBAL' covid:arg/f161447bea90a1e414e3cb22557efe9156bab8e2 named entity 'PIGS' named entity 'CHOSEN' named entity 'MICROARRAY' named entity 'DIFFERENT' named entity 'ACCURATE' named entity 'ITS' named entity 'GENE' named entity 'TESTED' named entity 'CONSENSUS' named entity 'SEQUENCES' named entity 'ABOUT' named entity 'USED' named entity 'PARADIGM' named entity 'INFORMATION' named entity 'STRATEGIES' named entity 'TYPE' named entity 'HOST' named entity 'SEQUENCE' named entity '1 TO 3' named entity 'DESIGN' named entity 'YEARS' named entity 'DATABANKS' named entity 'MOLECULAR' named entity 'SELECTION' named entity 'EMERGENCE' named entity 'SPECIFIC' named entity 'SAMPLES' named entity 'ORIGINS' named entity 'INFLUENZA VIRUSES' named entity 'COMPUTED' named entity 'BIRDS' named entity 'RESEQUENCING' named entity 'TOTAL' named entity 'INFLUENZA VIRUS' named entity 'TIME' named entity 'DEDICATED' named entity 'CASES' named entity 'BASED' named entity 'IDENTIFIED' named entity 'NUMBER OF' named entity 'MICROARRAYS' named entity 'INFLUENZA VIRUS' named entity 'VARIOUS' named entity 'HIGH DENSITY' named entity 'AVAILABLE' named entity 'ISOLATED' named entity 'microarray' named entity 'Influenza' named entity 'viruses' named entity 'For' named entity 'consensus sequences' named entity 'consensus sequences' named entity 'NS1' named entity 'microfluidic' named entity 'H7N7'

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