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Please use this identifier to cite or link to this item: http://hdl.handle.net/1942/15993

Title: Targeted resequencing of HIV variants by microarray thermodynamics
Authors: Hadiwikarta, Wahyu W.
Van Dorst, Bieke
Hollanders, Karen
Stuyver, Lieven
Carlon, Enrico
Issue Date: 2013
Citation: NUCLEIC ACIDS RESEARCH, 41 (18), (ART N° e173)
Abstract: Within a single infected individual, a virus population can have a high genomic variability. In the case of HIV, several mutations can be present even in a small genomic window of 20-30 nucleotides. For diagnostics purposes, it is often needed to resequence genomic subsets where crucial mutations are known to occur. In this article, we address this issue using DNA microarrays and inputs from hybridization thermodynamics. Hybridization signals from multiple probes are analysed, including strong signals from perfectly matching (PM) probes and a large amount of weaker cross-hybridization signals from mismatching (MM) probes. The latter are crucial in the data analysis. Seven coded clinical samples (HIV-1) are analyzed, and the microarray results are in full concordance with Sanger sequencing data. Moreover, the thermodynamic analysis of microarray signals resolves inherent ambiguities in Sanger data of mixed samples and provides additional clinically relevant information. These results show the reliability and added value of DNA microarrays for point-of-care diagnostic purposes.
Notes: Hooyberghs, J (reprint author), VITO, Flemish Inst Technol Res, Boeretang 200, B-2400 Mol, Belgium. jef.hooyberghs@vito.be
URI: http://hdl.handle.net/1942/15993
DOI: 10.1093/nar/gkt682
ISI #: 000325776600004
ISSN: 0305-1048
Category: A1
Type: Journal Contribution
Validation: ecoom, 2014
Appears in Collections: Research publications

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