Comparison of the Precision and Sensitivity of
the Antivirogram and PhenoSense HIV Drug Susceptibility Assays

  1. vircoRAWdata_PI.txt / vircoRAWdata_RT.txt / virologicRAWdata_PI.txt / virologicRAWdata_RT.txt

    The files contain a list of mutations and a list of phenotype results for each isolate that was used on this study,
    Antivirogram(Virco) phenotype results on protease inhibitors, Antivirogram(Virco) phenotype results on RT inhibitors,
    PhenoSense(Virologic) phenotype results on protease inhibitors, PhenoSense(Virologic) phenotype results on RT inhibitors, respectively.

    1. IsolateID: a unique identifier for an isolate
    2. Category: 'WT' -- isolates lacking mutations at drug-resistance positions as defined in the methods.
      'Mut' -- isolates containing one or more drug-resistance mutations
    3. Pattern: a comma-delimited list of drug-resistance mutations
    4. a list of fold resistance (for PI, IDV, LPV, NFV, RTV, SQV, ATV and for RTI, DDI, DDC, 3TC, D4T, ABC, TDF, NVP, DLV, EFV)

  2. vircotable1PI.txt / virologictable1PI.txt / vircotable1RT.txt / virologictable1RT.txt

    The files contain the total number of phenotype results, mean, median, standard deviation, etc.,
    for each drug for the phenotypes that were done on wildtype isolates.

    1. Drug: name of drug
    2. Number: total number of phenotype results on wildtype isolates for the drug ('Drug')
    3. Fold: Level of fold resistance (an individual phenotype result)
    4. Log-Fold: Log(base 10) of the level of fold resistance.
    5. Mean (Log-Fold): Mean of all the phenotype results for the drug
    6. 10 ^ Mean (Log-Fold): Antilog of the mean ('Log-fold')
    7. SD (Log-Fold): Standard deviation of the Log-fold phenotype results
    8. 10 ^ SD (Log-Fold): Antilog of the standard deviation
    9. Median (Log-Fold): Median of the Log-Fold phenotype results
    10. 10 ^ Median (Log-Fold): Antilog of the median
    11. AbsDev(Log-Fold): Absolute value of ('Log-Fold' - 'Median') for the drug ('Drug')
    12. MAD (Log-Fold): Median of the absolute value of ('Log-Fold' - 'Median') for the drug ('Drug')

  3. vircotable2PI.txt / virologictable2PI.txt / vircotable2RT.txt / virologictable2RT.txt

    The files contain the total number of phenotype results, mean, median, standard deviation, etc.,
    for each drug for the phenotypes that were done on isolates containing the same drug resistance mutations.

    1. Drug: name of drug
    2. Number: total number of phenotype results on mutant isolates containing a drug resistance pattern for the drug ('Drug')
    3. Numpatterns: an unique identifier given for each pattern
    4. Mut_Patterns: a comma-delimited drug resistance mutations
    5. Numisolates: number of phenotype results on isolates containing the pattern in the column 'Mut_Patterns'
    6. Fold: Level of fold resistance (of an individual phenotype result)
    7. Log-Fold: Log(base 10) of the level of fold resistance (of an individual phenotype result)
    8. Pattern_mean(Log-Fold): mean of all the phenotype results('Log-Fold') on isolates containing the pattern in the column 'Mut_Patterns'
    9. 10 ^ Pattern_mean: Antilog of the Pattern_mean (Log-fold)
    10. Absvalue(Log_Fold-Pattern_mean): Absolute value of ('Log-Fold' - 'Pattern_mean')
    11. Pattern_SD (Log-Fold): Standard deviation of the Log-fold results on the same pattern
    12. Pattern_median (Log-Fold): Median of the Log-Fold results on the same pattern ('Mut_Patterns')
    13. 10 ^ Pattern_median (Log-Fold): Antilog of the Pattern_median
    14. AbsDev(Log-Fold): Absolute value of ('Log-Fold' - 'Pattern_median') for the drug ('Drug') for the pattern ('Mut_Patterns')
    15. MAD (Log-Fold): Median of AbsDev('Log-Fold' - 'Pattern_median') for the drug ('Drug') for the pattern ('Mut_Patterns')

  4. vircotable3data.txt / virologictable3data.txt

    The files contain the number of isolates containing a drug resistance mutation pattern that have phenotype results above a cut-off.

    1. Drug: name of drug
    2. Pattern: a comma-delimited drug resistance mutations
    3. NumofIsolates: total number of phenotype results of 'Drug' on isolates containing the drug resistance mutation pattern of 'Pattern'
    4. 10^(Mean+2*SD(Log-Fold)): a biological cut-offs that was defined as the mean plus 2 standard deviations calculated
      using the log-transformed levels of fold-resistance of 'Drug' on wild type isolates.
    5. Fold: level of fold resistance (of an individual phenotype result)
    6. NumofIsolates(Fold>cutoff): number of isolates of which fold resistance of 'Drug' is greater than the biological cut-offs('10^(Mean+2*SD(Log-Fold))')

  5. vircoROCdata.txt / virologicROCdata.txt

    The files contain the three different cut-offs and a list of numbers of isolates containing a drug resistance mutation pattern
    that have phenotype results above the each cut-off.

    1. Drug: name of drug
    2. Pattern: a comma-delimited drug resistance mutations
    3. NumofIsolates: total number of phenotype results of 'Drug' on isolates containing the drug resistance mutation pattern of 'Pattern'
    4. 10^(Mean+2*SD(Log-Fold)): cut-offs defined as the mean plus 2 standard deviations calculated
      using the log-transformed levels of fold-resistance of 'Drug' on wild type isolates.
    5. Published_cutoff: cut-offs from published reports
    6. The_98%ile_WT: cut-offs defined as 98th percentile fold-resistance changes on wild type isolates.
    7. Fold: level of fold resistance (of an individual phenotype result)
    8. NumofIsolates(Fold>cutoff): number of isolates of which fold resistance of 'Drug' is greater than the cut-offs('10^(Mean+2*SD(Log-Fold))')
    9. NumofIsolates(Fold>2nd_cutoff): number of isolates of which fold resistance of 'Drug' is greater than the cut-offs('Published_cutoff')
    10. NumofIsolates(Fold>3rd_cutoff): number of isolates of which fold resistance of 'Drug' is greater than the cut-offs('The_98%ile_WT')