Genotypic Predictors of Human Immunodeficiency Virus Type 1 Drug Resistance

Data

1. Sets of mutations [Table 1]:
   • Complete
   • Expert panel
   • Non-polymorphic treatment-selected mutations (NP-TSM)
   • Common

2. Genotype-phenotype correlation data sets:
   • Protease inhibitors (PIs)
   • Nucleoside RT inhibitors (NRTIs)
   • Nonnucleoside RT inhibitors (NNRTIs)
   • Summary of isolates with genotype and phenotype correlations according to drug tested and level of resistance [Table 2]

3. Phenotype cut-offs between susceptible, low/intermediate resistance and high-level resistance for each drug

Results

1. Summary of 10 x 5 fold-cross validation results:
   • Complete
   • Expert panel: drug-specific mutations, complete set of mutations
   • NP-TSM, Complete set of TSM (including the polymorphic TSMs)
   • Common

1. Prediction accuracy [Table 3]
2. Number of highly discordant predictions according to mutation set and regression method [Table 4]
3. Highly Discordant Isolates: Predictions based on Least Angle Regression (LARS) Using Nonpolymorphic Treatment Selected Mutations [Table 5]
4. Correlation coefficients (r2) between actual and predicted result according to regression method and mutation dataset [Table 6]
5. Mean squared error between actual and predicted result according to regression method and mutation dataset [Table 7]
6. Regression coefficients for the PI treatment-selected mutations [Table 8], the NRTI treatment-selected mutations [Table 9] and the NNRTI treatment-selected mutations [Table 10] in the Least Squares Regression (LSR),Support Vector Regression (SVR), and Least Angle Regression (LARS) Models

1. Least-squares regression coefficients for protease inhibitor [figure 1A], nucleoside RT inhibitor [figure 1B] and non-nucleoside RT inhibitor [figure 1C] treatment-selected mutations
2. Distribution in the number of nonpolymorphic TSMs [figure 2A] and expert panel mutations [figure 2B] per isolate
3. Rate of learning using regression and nonpolymorphic treatment-selected mutations (TSMs) [figure 3]
4. Regression coefficients for each of the PI, NRTI and NNRTI TSMs determined by different regression methods [figure 4]

   [figure legends]