We present a case study on the discovery of clinically relevant domain knowledge in the field of HIV drug resistance. Novel mutations in the HIV genome associated with treatment failure were identified by mining a relational clinical database. Hierarchical cluster analysis suggests that two of these mutations form a novel mutational complex, while all others are involved in known resistance-conferring evolutionary pathways. The clustering is shown to be highly stable in a bootstrap procedure. Multidimensional scaling in mutation space indicates that certain mutations can occur within multiple pathways. Feature ranking based on support vector machines and matched genotype-phenotype pairs comprehensively reproduces current domain knowledge. Moreover, it indicates a prominent role of novel mutations in determining phenotypic resistance and in resensitization effects. These effects may be exploited deliberately to reopen lost treatment options. Together, these findings provide valuable insight into the interpretation of genotypic resistance tests.
Sing, T., Svicher, V., Beerenwinkel, N., CECCHERINI SILBERSTEIN, F., Daumer, M., Kaiser, R., et al. (2005). Characterization of novel HIV drug resistance mutations using clustering, multidimensional scaling and SVM-based feature ranking. In Knowledge discovery in databases: PKDD 2005: 9th European conference on principles and practice of knowledge discovery in databases: Porto, Portugal, October 3-7, 2005: proceedings (pp.285-296). Springer [10.1007/11564126_30].
Characterization of novel HIV drug resistance mutations using clustering, multidimensional scaling and SVM-based feature ranking
SVICHER, VALENTINA;CECCHERINI SILBERSTEIN, FRANCESCA;PERNO, CARLO FEDERICO;
2005-01-01
Abstract
We present a case study on the discovery of clinically relevant domain knowledge in the field of HIV drug resistance. Novel mutations in the HIV genome associated with treatment failure were identified by mining a relational clinical database. Hierarchical cluster analysis suggests that two of these mutations form a novel mutational complex, while all others are involved in known resistance-conferring evolutionary pathways. The clustering is shown to be highly stable in a bootstrap procedure. Multidimensional scaling in mutation space indicates that certain mutations can occur within multiple pathways. Feature ranking based on support vector machines and matched genotype-phenotype pairs comprehensively reproduces current domain knowledge. Moreover, it indicates a prominent role of novel mutations in determining phenotypic resistance and in resensitization effects. These effects may be exploited deliberately to reopen lost treatment options. Together, these findings provide valuable insight into the interpretation of genotypic resistance tests.Questo articolo è pubblicato sotto una Licenza Licenza Creative Commons