Analysis of ex vivo drug response data of Plasmodium clinical isolates: the pros and cons of different computer programs and online platforms.
Wirjanata G., Handayuni I., Zaloumis SG., Chalfein F., Prayoga P., Kenangalem E., Poespoprodjo JR., Noviyanti R., Simpson JA., Price RN., Marfurt J.
BACKGROUND: In vitro drug susceptibility testing of malaria parasites remains an important component of surveillance for anti-malarial drug resistance. The half-maximal inhibition of growth (IC50) is the most commonly reported parameter expressing drug susceptibility, derived by a variety of statistical approaches, each with its own advantages and disadvantages. METHODS: In this study, licensed computer programs WinNonlin and GraphPad Prism 6.0, and the open access programs HN-NonLin, Antimalarial ICEstimator (ICE), and In Vitro Analysis and Reporting Tool (IVART) were tested for their ease of use and ability to estimate reliable IC50 values from raw drug response data from 31 Plasmodium falciparum and 29 P. vivax clinical isolates tested with five anti-malarial agents: chloroquine, amodiaquine, piperaquine, mefloquine, and artesunate. RESULTS: The IC50 and slope estimates were similar across all statistical packages for all drugs tested in both species. There was good correlation of results derived from alternative statistical programs and non-linear mixed-effects modelling (NONMEM) which models all isolate data simultaneously. The user-friendliness varied between packages. While HN-NonLin and IVART allow users to enter the data in 96-well format, IVART and GraphPad Prism 6.0 are capable to analyse multiple isolates and drugs in parallel. WinNonlin, GraphPad Prism 6.0, IVART, and ICE provide alerts for non-fitting data and incorrect data entry, facilitating data interpretation. Data analysis using WinNonlin or ICE took the longest computationally, whilst the offline ability of GraphPad Prism 6.0 to analyse multiple isolates and drugs simultaneously made it the fastest among the programs tested. CONCLUSION: IC50 estimates obtained from the programs tested were comparable. In view of processing time and ease of analysis, GraphPad Prism 6.0 or IVART are best suited for routine and large-scale drug susceptibility testing.