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A Pair Ranking (PRank) Method for Assessing Assay Transferability Among the Toxicogenomics Testing Systems

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Advances in Computational Toxicology

Part of the book series: Challenges and Advances in Computational Chemistry and Physics ((COCH,volume 30))

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Abstract

The use of animal models for risk assessment is not a reliable and satisfying paradigm. Accompanying the strategic planned shift by regulatory agencies , more and more advocating campaigns such as the 3Rs in Europe and Tox21 /ToxCast in the USA were proposed to develop in silico and in vitro approaches to eliminate animal use. To effectively implement non-animal models in risk assessment , novel approaches are urgently needed for investigating the concordance between testing systems to facilitate the selection of the fit-for-purpose assay . In this chapter, we introduce a Pair Ranking (PRank ) method for the quantitative evaluation of assay transferability among the different toxicogenomics (TGx) testing systems. First, we will summarize the critical issues of TGx related to its success in risk assessment . Second, we will elucidate the application of proposed PRank method for addressing key questions in TGx. Finally, we will suggest some potential use of the PRank method for advancing risk assessment .

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Abbreviations

3Rs:

Refine, Reduce and Replace

ALT:

Alanine Aminotransferase

AOPs:

Adverse Outcome Pathways

AST:

Aspartate Aminotransferase

ATC:

Anatomical Therapeutic Chemical

CTD:

Comparative Toxicogenomics Database

DILI:

Drug-Induced Liver Injury

ECFP:

Extended-Connectivity Fingerprints

EPA:

United States Environmental Protection Agency

GLP:

Good Laboratory Practice

hTERT:

Human Telomerase Reverse Transcriptase

ICH:

The International Conference on Harmonisation of Technical Requirements for Registration of Pharmaceuticals for Human Use

iPSC:

Induced Pluripotent Stem Cell

IVIVE:

In Vitro-to-In Vivo Extrapolation

LDH:

Lactate Dehydrogenase

LINCS:

The Library of Integrated Network-Based Cellular Signatures

MAQC:

Microarray Quality Control

OECD:

Organisation for Economic Co-operation and Development

POP:

Percentage of Overlapped Pathways

PRank:

Pair Ranking

REACH:

Registration, Evaluation, Authorisation and Restriction of Chemicals

ROC:

Receiver Operating Characteristic

SIDER:

Side Effect Resources

TG-GATEs:

Toxicogenomic Project—Genomics Assisted Toxicity Evaluation System

TGx:

Toxicogenomics

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This article reflects the views of the authors and should not be construed to represent FDA’s views or policies.

Author information

Authors and Affiliations

  1. Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, US Food and Drug Administration (FDA), Jefferson, AR, 72079, USA

    Zhichao Liu, Brian Delavan, Liyuan Zhu & Weida Tong

  2. Department of Biosciences, University of Little Rock, Little Rock, AR, USA

    Brian Delavan

  3. ApconiX, BioHub at Alderley Park, Alderley Edge, UK

    Ruth Robert

  4. Department of Biosciences, University of Birmingham, Birmingham, UK

    Ruth Robert

Authors
  1. Zhichao Liu
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  2. Brian Delavan
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  3. Liyuan Zhu
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  4. Ruth Robert
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  5. Weida Tong
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Corresponding author

Correspondence to Zhichao Liu .

Editor information

Editors and Affiliations

  1. National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR, USA

    Huixiao Hong

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Liu, Z., Delavan, B., Zhu, L., Robert, R., Tong, W. (2019). A Pair Ranking (PRank) Method for Assessing Assay Transferability Among the Toxicogenomics Testing Systems. In: Hong, H. (eds) Advances in Computational Toxicology. Challenges and Advances in Computational Chemistry and Physics, vol 30. Springer, Cham. https://doi.org/10.1007/978-3-030-16443-0_9

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