Sparse Representation for Prediction of HIV-1 Protease Drug Resistance

HIV rapidly evolves drug resistance in response to antiviral drugs used in AIDS therapy. Estimating the specific resistance of a given strain of HIV to individual drugs from sequence data has important benefits for both the therapy of individual patients and the development of novel drugs. We have d...

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Veröffentlicht in:Proceedings of the ... SIAM International Conference on Data Mining Jg. 2013; S. 342
Hauptverfasser: Yu, Xiaxia, Weber, Irene T, Harrison, Robert W
Format: Journal Article
Sprache:Englisch
Veröffentlicht: United States 2013
Schlagworte:
Drug resistance prediction
HIV protease
Sparse Representation
ISSN:2167-0102
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Zusammenfassung:HIV rapidly evolves drug resistance in response to antiviral drugs used in AIDS therapy. Estimating the specific resistance of a given strain of HIV to individual drugs from sequence data has important benefits for both the therapy of individual patients and the development of novel drugs. We have developed an accurate classification method based on the sparse representation theory, and demonstrate that this method is highly effective with HIV-1 protease. The protease structure is represented using our newly proposed encoding method based on Delaunay triangulation, and combined with the mutated amino acid sequences of known drug-resistant strains to train a machine-learning algorithm both for classification and regression of drug-resistant mutations. An overall cross-validated classification accuracy of 97% is obtained when trained on a publically available data base of approximately 1.5×10 known sequences (Stanford HIV database http://hivdb.stanford.edu/cgi-bin/GenoPhenoDS.cgi). Resistance to four FDA approved drugs is computed and comparisons with other algorithms demonstrate that our method shows significant improvements in classification accuracy.
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ISSN:2167-0102
DOI:10.1137/1.9781611972832.38