Targeted resequencing of HIV variants by microarray thermodynamics.
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.
Flemish Institute for Technological Research, VITO, Boeretang 200, B-2400 Mol, Belgium, Institute for Theoretical Physics, KULeuven, Celestijnenlaan 200D, B-3001 Leuven, Belgium, Janssen Diagnostics bvba, Turnhoutseweg 30, B-2340 Beerse, Belgium and Theoretical Physics, Hasselt University, Campus Diepenbeek, Agoralaan - Building D, B-3590, Diepenbeek, Belgium.
Wahyu W
WW
Hadiwikarta
Bieke
B
Van Dorst
Karen
K
Hollanders
Lieven
L
Stuyver
Enrico
E
Carlon
Jef
J
Hooyberghs
D000465:Algorithms; D004252:DNA Mutational Analysis / Q000379:methods*; D054303:HIV Reverse Transcriptase / Q000235:genetics; D015497:HIV-1 / Q000235:genetics*; D009154:Mutation; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D013816:Thermodynamics
C514824:reverse transcriptase, Human immunodeficiency virus 1; D054303:HIV Reverse Transcriptase