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Workflow for Defining Reference Chemicals for Assessing Performance of In Vitro Assays
Judson, R., R. Thomas, N. Baker, A. Simha, X. Howey, C. Marable, N. Kleinstreuer, AND K. Houck. Workflow for Defining Reference Chemicals for Assessing Performance of In Vitro Assays. ALTEX. Society ALTEX Edition, Kuesnacht, Switzerland, 36(2):261-276, (2019). https://doi.org/10.14573/altex.1809281
This manuscript describes a process for developing lists of reference chemicals for in vitro hazard assays. This is a necessary step in thevalidation of these assays for regulatory uses.
Instilling confidence in use of in vitro assays for predictive toxicology requires evaluation of assay performance. Performance is typically assessed using reference chemicals--compounds with defined activity or inactivity against the test system target. However, developing reference chemical lists has historically been very resource-intensive. We have developed a semi-automated process for selecting and annotating reference chemicals across many targets in a standardized format and we demonstrate the workflow here. A series of required fields defines the potential reference chemical: the in vitro molecular target, pathway, or phenotype affected; and the chemical’s mode (e.g. agonist, antagonist, inhibitor). Activity information was extracted into a database, using automated scripts, from multiple public sources including non-curated scientific literature and curated chemical-biological databases, resulting in the identification of chemical activity in 2995 molecular targets. The sample data from literature sources covering 54 molecular targets ranging from data-poor to data-rich was manually checked for accuracy. Precision rates were 82.7% from curated data sources and 39.5% from the automated literature extraction. We applied the final reference chemical lists to evaluating performance of EPA’s ToxCast program in vitro bioassays. The level of support, i.e. the number of independent reports in the database linking a chemical to a target, was found to strongly correlate with likelihood of positive results in the ToxCast assays, although individual assay performance had considerable variation. This overall approach allows rapid development of candidate reference chemical lists for a wide variety of targets that can facilitate performance evaluation of in vitro assays as a critical step in imparting confidence in alternative approaches.
Record Details:Record Type: DOCUMENT (JOURNAL/PEER REVIEWED JOURNAL)
Organization:U.S. ENVIRONMENTAL PROTECTION AGENCY
OFFICE OF RESEARCH AND DEVELOPMENT
NATIONAL CENTER FOR COMPUTATIONAL TOXICOLOGY