A confidence building exercise in data and identifiability: Modeling cancer chemotherapy as a case study

Marisa C. Eisenberg, Harsh V. Jain

Research output: Contribution to journalArticlepeer-review

16 Scopus citations

Abstract

Mathematical modeling has a long history in the field of cancer therapeutics, and there is increasing recognition that it can help uncover the mechanisms that underlie tumor response to treatment. However, making quantitative predictions with such models often requires parameter estimation from data, raising questions of parameter identifiability and estimability. Even in the case of structural (theoretical) identifiability, imperfect data and the resulting practical unidentifiability of model parameters can make it difficult to infer the desired information, and in some cases, to yield biologically correct inferences and predictions. Here, we examine parameter identifiability and estimability using a case study of two compartmental, ordinary differential equation models of cancer treatment with drugs that are cell cycle-specific (taxol) as well as non-specific (oxaliplatin). We proceed through model building, structural identifiability analysis, parameter estimation, practical identifiability analysis and its biological implications, as well as alternative data collection protocols and experimental designs that render the model identifiable. We use the differential algebra/input-output relationship approach for structural identifiability, and primarily the profile likelihood approach for practical identifiability. Despite the models being structurally identifiable, we show that without consideration of practical identifiability, incorrect cell cycle distributions can be inferred, that would result in suboptimal therapeutic choices. We illustrate the usefulness of estimating practically identifiable combinations (in addition to the more typically considered structurally identifiable combinations) in generating biologically meaningful insights. We also use simulated data to evaluate how the practical identifiability of the model would change under alternative experimental designs. These results highlight the importance of understanding the underlying mechanisms rather than purely using parsimony or information criteria/goodness-of-fit to decide model selection questions. The overall roadmap for identifiability testing laid out here can be used to help provide mechanistic insight into complex biological phenomena, reduce experimental costs, and optimize model-driven experimentation.

Original languageEnglish (US)
Pages (from-to)63-78
Number of pages16
JournalJournal of Theoretical Biology
Volume431
DOIs
StatePublished - Oct 27 2017
Externally publishedYes

Bibliographical note

Funding Information:
This work was supported by NIH grant U01CA182915 to MCE, and Simons Collaboration Grant for Mathematicians 280544 to HVJ. We also wish to thank our anonymous reviewers for their insights and comments in revising the manuscript.

Publisher Copyright:
© 2017

Keywords

  • Cancer
  • Chemotherapy model
  • Compartmental models
  • Identifiability
  • Parameter estimation

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