Uncertainty quantification reveals the importance of data variability and experimental design considerations for in silico proarrhythmia risk assessment
The Comprehensive in vitro Proarrhythmia Assay (CiPA) is a global initiative intended to improve drug proarrhythmia risk assessment using a new paradigm of mechanistic assays. Under the CiPA paradigm, the relative risk of drug-induced Torsade de Pointes (TdP) is assessed using an in silico model of...
| Main Authors: | , , , , , , , , , , |
|---|---|
| Format: | Article |
| Published: |
Frontiers Media
2017
|
| Subjects: | |
| Online Access: | https://eprints.nottingham.ac.uk/48312/ |
| _version_ | 1848797736694972416 |
|---|---|
| author | Chang, Kelly Dutta, Sara Mirams, Gary R. Beattie, Kylie Sheng, Jiansong Tran, Phu N. Wu, Min Wu, Wendy W. Colatsky, Thomas Strauss, David G. Li, Zhihua |
| author_facet | Chang, Kelly Dutta, Sara Mirams, Gary R. Beattie, Kylie Sheng, Jiansong Tran, Phu N. Wu, Min Wu, Wendy W. Colatsky, Thomas Strauss, David G. Li, Zhihua |
| author_sort | Chang, Kelly |
| building | Nottingham Research Data Repository |
| collection | Online Access |
| description | The Comprehensive in vitro Proarrhythmia Assay (CiPA) is a global initiative intended to improve drug proarrhythmia risk assessment using a new paradigm of mechanistic assays. Under the CiPA paradigm, the relative risk of drug-induced Torsade de Pointes (TdP) is assessed using an in silico model of the human ventricular action potential (AP) that integrates in vitro pharmacology data from multiple ion channels. Thus, modeling predictions of cardiac risk liability will depend critically on the variability in pharmacology data, and uncertainty quantification (UQ) must comprise an essential component of the in silico assay. This study explores UQ methods that may be incorporated into the CiPA framework. Recently, we proposed a promising in silico TdP risk metric (qNet), which is derived from AP simulations and allows separation of a set of CiPA training compounds into Low, Intermediate, and High TdP risk categories. The purpose of this study was to use UQ to evaluate the robustness of TdP risk separation by qNet. Uncertainty in the model parameters used to describe drug binding and ionic current block was estimated using the non-parametric bootstrap method and a Bayesian inference approach. Uncertainty was then propagated through AP simulations to quantify uncertainty in qNet for each drug. UQ revealed lower uncertainty and more accurate TdP risk stratification by qNet when simulations were run at concentrations below 5× the maximum therapeutic exposure (Cmax). However, when drug effects were extrapolated above 10× Cmax, UQ showed that qNet could no longer clearly separate drugs by TdP risk. This was because for most of the pharmacology data, the amount of current block measured was <60%, preventing reliable estimation of IC50-values. The results of this study demonstrate that the accuracy of TdP risk prediction depends both on the intrinsic variability in ion channel pharmacology data as well as on experimental design considerations that preclude an accurate determination of drug IC50-values in vitro. Thus, we demonstrate that UQ provides valuable information about in silico modeling predictions that can inform future proarrhythmic risk evaluation of drugs under the CiPA paradigm. |
| first_indexed | 2025-11-14T20:08:37Z |
| format | Article |
| id | nottingham-48312 |
| institution | University of Nottingham Malaysia Campus |
| institution_category | Local University |
| last_indexed | 2025-11-14T20:08:37Z |
| publishDate | 2017 |
| publisher | Frontiers Media |
| recordtype | eprints |
| repository_type | Digital Repository |
| spelling | nottingham-483122024-08-15T15:24:53Z https://eprints.nottingham.ac.uk/48312/ Uncertainty quantification reveals the importance of data variability and experimental design considerations for in silico proarrhythmia risk assessment Chang, Kelly Dutta, Sara Mirams, Gary R. Beattie, Kylie Sheng, Jiansong Tran, Phu N. Wu, Min Wu, Wendy W. Colatsky, Thomas Strauss, David G. Li, Zhihua The Comprehensive in vitro Proarrhythmia Assay (CiPA) is a global initiative intended to improve drug proarrhythmia risk assessment using a new paradigm of mechanistic assays. Under the CiPA paradigm, the relative risk of drug-induced Torsade de Pointes (TdP) is assessed using an in silico model of the human ventricular action potential (AP) that integrates in vitro pharmacology data from multiple ion channels. Thus, modeling predictions of cardiac risk liability will depend critically on the variability in pharmacology data, and uncertainty quantification (UQ) must comprise an essential component of the in silico assay. This study explores UQ methods that may be incorporated into the CiPA framework. Recently, we proposed a promising in silico TdP risk metric (qNet), which is derived from AP simulations and allows separation of a set of CiPA training compounds into Low, Intermediate, and High TdP risk categories. The purpose of this study was to use UQ to evaluate the robustness of TdP risk separation by qNet. Uncertainty in the model parameters used to describe drug binding and ionic current block was estimated using the non-parametric bootstrap method and a Bayesian inference approach. Uncertainty was then propagated through AP simulations to quantify uncertainty in qNet for each drug. UQ revealed lower uncertainty and more accurate TdP risk stratification by qNet when simulations were run at concentrations below 5× the maximum therapeutic exposure (Cmax). However, when drug effects were extrapolated above 10× Cmax, UQ showed that qNet could no longer clearly separate drugs by TdP risk. This was because for most of the pharmacology data, the amount of current block measured was <60%, preventing reliable estimation of IC50-values. The results of this study demonstrate that the accuracy of TdP risk prediction depends both on the intrinsic variability in ion channel pharmacology data as well as on experimental design considerations that preclude an accurate determination of drug IC50-values in vitro. Thus, we demonstrate that UQ provides valuable information about in silico modeling predictions that can inform future proarrhythmic risk evaluation of drugs under the CiPA paradigm. Frontiers Media 2017-11-21 Article PeerReviewed Chang, Kelly, Dutta, Sara, Mirams, Gary R., Beattie, Kylie, Sheng, Jiansong, Tran, Phu N., Wu, Min, Wu, Wendy W., Colatsky, Thomas, Strauss, David G. and Li, Zhihua (2017) Uncertainty quantification reveals the importance of data variability and experimental design considerations for in silico proarrhythmia risk assessment. Frontiers in Physiology, 8 . 917/1-917/12. ISSN 1664-042X Uncertainty quantification; Experimental variability; Cardiac electrophysiology; Action potential; Torsade de Pointes; Ion channel; Pharmacology; Computational modeling https://www.frontiersin.org/articles/10.3389/fphys.2017.00917/full doi:10.3389/fphys.2017.00917 doi:10.3389/fphys.2017.00917 |
| spellingShingle | Uncertainty quantification; Experimental variability; Cardiac electrophysiology; Action potential; Torsade de Pointes; Ion channel; Pharmacology; Computational modeling Chang, Kelly Dutta, Sara Mirams, Gary R. Beattie, Kylie Sheng, Jiansong Tran, Phu N. Wu, Min Wu, Wendy W. Colatsky, Thomas Strauss, David G. Li, Zhihua Uncertainty quantification reveals the importance of data variability and experimental design considerations for in silico proarrhythmia risk assessment |
| title | Uncertainty quantification reveals the importance of data variability and experimental design considerations for in silico proarrhythmia risk assessment |
| title_full | Uncertainty quantification reveals the importance of data variability and experimental design considerations for in silico proarrhythmia risk assessment |
| title_fullStr | Uncertainty quantification reveals the importance of data variability and experimental design considerations for in silico proarrhythmia risk assessment |
| title_full_unstemmed | Uncertainty quantification reveals the importance of data variability and experimental design considerations for in silico proarrhythmia risk assessment |
| title_short | Uncertainty quantification reveals the importance of data variability and experimental design considerations for in silico proarrhythmia risk assessment |
| title_sort | uncertainty quantification reveals the importance of data variability and experimental design considerations for in silico proarrhythmia risk assessment |
| topic | Uncertainty quantification; Experimental variability; Cardiac electrophysiology; Action potential; Torsade de Pointes; Ion channel; Pharmacology; Computational modeling |
| url | https://eprints.nottingham.ac.uk/48312/ https://eprints.nottingham.ac.uk/48312/ https://eprints.nottingham.ac.uk/48312/ |