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Influenza Neuraminidase Inhibitor IC 50 Data: Calculation, Interpretation and Statistical Analyses. Presentation Outline. Determining IC 50 values Curve-fitting methods Sources of variation Identifying IC 50 outliers Determining cut-offs/thresholds Outlier values versus resistant viruses

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  1. Influenza Neuraminidase Inhibitor IC50 Data:Calculation, Interpretation and Statistical Analyses

  2. Presentation Outline • Determining IC50 values • Curve-fitting methods • Sources of variation • Identifying IC50 outliers • Determining cut-offs/thresholds • Outlier values versus resistant viruses • Monitoring trends over time in IC50 data

  3. Abbreviations • NA: Neuraminidase • NI: Neuraminidase Inhibitor • RFU: Relative Fluorescence Units • RLU: Relative Luminescence Units • VC: Virus Control

  4. Determining NI IC50 Values • IC50: The concentration of NI which reduces NA activity by 50% of the virus-control, or upper asymptote • Estimated by: Measuring the NA activity (RFU or RLU) of an isolate against a range of dilutions of the drug, as well as without drug (virus-control)

  5. Determining IC50 Values: Calculation Options • Curve fitting-Statistical software • Graph Pad Prism (www.graphpad.com) • $595 • Grafit (www.erithacus.com/grafit/) • $400-500 • Jaspr (Developed by CDC) • Contact CDC for suitability and further details • Point-to-Point calculation • Excel templates (Created by Health Protection Agency, UK)

  6. IC50 Calculation: Curve-Fitting (Graph-pad) Upper Asymptote Non linear regression analysis Sigmoidal dose response curve

  7. IC50 Calculation: Curve-Fitting (Grafit)

  8. IC50 Calculation: Point to Point

  9. IC50 Calculation: Comparison of IC50 values from different calculation methods

  10. Determining IC50 Values: Sources of Variation • Method of calculation • Using point-to-point or curve fitting software • Choice of curve fitting software used • Intra-assay variation • Difference between 2 or more replicates • Inter-assay variation • Difference in calculated value for a given isolate in multiple assays

  11. IC50 Calculation: Comparison of Point to Point versus curve-fitting Curve Fitting WILL give an IC50 value by extrapolating the curve when drug dilutions do not reach a true end point: This does not necessarily give an accurate IC50 value

  12. IC50 Calculation: Troubleshooting • Important to examine curves carefully to ensure IC50 is valid Low VC: technical error Poor curve fit Drug titration error Poor curve fit

  13. Comments: Choice of IC50 Calculation Method • Choice of IC50 calculation method will make no more than about 5% difference to IC50 value, for most samples • Must be clear exactly how the curve fitting and calculation of IC50is working • Is IC50 based on 50% of RFU/RLU of VC or 50% of fitted upper asymptote. • Regardless of method used, careful examination of the curve produced is required to identify technical issues. • See presentation on validation and troubleshooting of IC50 testing methods

  14. Analysis of intra-assay variation

  15. Comments: Intra-assay Variation • Variation between replicates in the same assay can be 15%-20%. • This variation is greater than that seen with changes to curve-fitting method • Using replicates and taking the average reduces this effect. • A large difference between replicates (e.g. >30%) of a given virus indicates a technical issue • In these instances repeat testing should be performed

  16. Analysis of Inter-assay Variation Introduction of new drug batch

  17. Analysis of Inter-assay Variation

  18. Comments: Inter-assay Variation • Variation in IC50 values for a virus in multiple assays can be 50%. • Control viruses should be included in every assay to identify technical issues. • Control viruses should be validated, and have a defined range between which the IC50 is valid. • Assays in which the control virus IC50 falls outside the accepted range should be reaped in their entirety.

  19. Conclusions: Determining IC50 Values • Several methods for IC50 calculation available at a range of price and sophistication • Variation due to choice of IC50 calculation method is minimal (5-10%) in comparison with intra-assay (20%) and inter-assay (50%) variation. • Choice of curve-fitting method should be made based on individual laboratory circumstances • All variation can be minimised using appropriate assay controls (reference/control viruses, validation of curves generated) • Consistency in methodology used (statistical and laboratory) is important for long term analysis (time trends)

  20. Identifying IC50 outliers • Aim: identify isolates with higher (or lower) than expected IC50 values (outliers) • First determine the ‘normal range’ of IC50 values • Each • Various statistical methods may be used • Critical to ensure that any outliers do not unduly affect the cut-off/threshold • Outlier does not equal resistant • Identifies isolates that may be worth further investigation (retesting/sequencing)

  21. Identifying IC50 outliers: Commonly Used Statistical Methods • SMAD • Robust estimate of the standard deviation based on the median absolute deviation from the median • Box and Whisker plots • Graphical representation of the 5 number summary of the data (the sample minimum, the lower or first quartile, the median, the upper or third quartile, the sample maximum) • Both methods require a minimum dataset to perform robust analyses (>20) • Cut offs can be calculated mid-season, once a reasonable number of samples has been tested, to monitor outliers • At the end of the season, cut offs can be updated and a retrospective analysis of all season data performed.

  22. Using SMAD Analysis • Create a scatter plot of all data • Useful to see the spread and trend of the data • Log transform the data • Calculate a robust estimate of the standard deviation based on the median absolute deviation from the median using log10 data • Templates for this analyses are available from HPA, UK • Major outliers: all those with values more than 3SD above the median • Minor Outliers: all those more than 1.65SD above the median

  23. Using SMAD Analysis: Example Data

  24. Using Box and Whisker Analysis • This analysis can be performed in Graphpad Prism, with the box and whisker plots drawn automatically • Calculations can be done in excel, but drawing the box and whisker plots is more complicated • A template for plotting the graphs is available from Adam Meijer • Log transform the data • Calculate the median, upper quartile, lower quartile, interquartile range, upper minor and major fences, and lower major and minor fences • Mild outliers lie between the minor and major fences • Extreme outliers lie outside the major fence

  25. Box and Whisker Plots Principle Excel Formulae Upper quartile (Q3): (QUARTILE(B2:B150,3) Lower quartile )Q1): (QUARTILE(B2:B150,1) IQR: Q3-Q1 Mild outlier Extreme outlier Equivalent values in SMAD analysis

  26. Using Box and Whisker Analysis: Example Data Excel Output Graphpad Prism Output

  27. Do we need to log-transform? • Most results from dilution assays produce ‘geometric results’ so likely to be sensible • Sometimes data are skewed. (e.g. lower quartile much closer to median than upper quartile) • Important to log transform as robust methods assume data are normal once outliers are removed.

  28. Using Log10 versus non logged Data

  29. Impact of Excess Numbers of Outliers • If the data have a large number of outliers, both SMAD and B+W struggle to determine sensible cut offs. • As resistant virus is very clearly different, these values can be removed prior to analysis to allow sensible calculations of cut offs for the remaining data. • Below, data is shown for H1N1 in 2007/8, when sensitive and resistant virus co-circulated. • Cut offs calculated do not accurately apply to the sensitive IC50 data Sensitive and Resistant Isolates Resistant Isolates removed

  30. Conclusions: Identifying Outliers • Determining cut offs/thresholds identifies those isolates with IC50 values higher than the normal range • Cut offs/thresholds need to be subtype specific • Season specific cut offs are useful, if enough data is generated in one season, but data from multiple seasons can be merged to perform a more reliable analyses • Box and whisker plots and SMAD analyses generate slightly different cut offs • Q3+1.5xIQR (mild outlier cut off) is equivalent to 2.7SD from SMAD • Q3+3xICR is equivalent to 4.7SD from SMAD. • Cut offs calculated by box and whisker analyses are higher than those from SMAD analyses. • Choice depends on individual laboratory preference • Box and whisker plots present the data well • Both methods minimise the impact of outlier values on the analyses, but both will fail once too many outliers are present • Data begins to have two populations

  31. Monitoring Trends Over Time • The normal range of IC50 values for a particular subtype can change over time • This could be seen by an increase in the number of outliers, or by changes in the median • Simple to monitor, using the methods already described for identifying outliers • scatter plots/box-whisker • Other statistical methods can be used to further analyse data from several seasons

  32. Trends in IC50 Data: Scatter Plot

  33. Trends in IC50 Data: Box and Whisker

  34. Summary • Good use of statistical methods can help interpret the IC50 results and ensure assay results are reliable. • Analyses of data not only identifies individual outliers, but allows continuous monitoring of trends • Retrospective analyses of multiple seasons of data can identify changes in viral characteristics and susceptibilities • Do not use statistics without first looking at the data by scatter plot to find obvious deviations which require an adapted statistical approach • Challenge is to find explanations for trends

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