Uncertainty quantification in ToxCast high throughput screening

• Published in: PloS one Vol. 13; no. 7; p. e0196963
• Main Authors: Watt, Eric D., Judson, Richard S.
• Format: Journal Article
• Language: English
• Published: United States Public Library of Science 25.07.2018; Public Library of Science (PLoS)
• Subjects: Analysis; BASIC BIOLOGICAL SCIENCES; Biocompatibility; Biological activity; Biology and Life Sciences; Chemicals; colorimetric assays; Computation; Computer applications; curve fitting; Data analysis; Dosimetry; Environmental protection; Environmental toxicology; estrogen; Estrogens; High-throughput screening; Inspection; Internet; kidneys; Laws, regulations and rules; Medical screening; Medicine and Health Sciences; Normal distribution; Organic chemistry; Parameter estimation; Physical Sciences; predictive toxicology; Regression analysis; Resampling; Research and Analysis Methods; Risk assessment; Statistical methods; Stem cells; Toxicity; Toxicology; United States; North Carolina; New York; United States > US
• DOI: 10.1371/journal.pone.0196963
• ISSN: 1932-6203

High throughput screening (HTS) projects like the U.S. Environmental Protection Agency's ToxCast program are required to address the large and rapidly increasing number of chemicals for which we have little to no toxicity measurements. Concentration-response parameters such as potency and efficacy are extracted from HTS data using nonlinear regression, and models and analyses built from these parameters are used to predict in vivo and in vitro toxicity of thousands of chemicals. How these predictions are impacted by uncertainties that stem from parameter estimation and propagated through the models and analyses has not been well explored. While data size and complexity makes uncertainty quantification computationally expensive for HTS datasets, continued advancements in computational resources have allowed these computational challenges to be met. This study uses nonparametric bootstrap resampling to calculate uncertainties in concentration-response parameters from a variety of HTS assays. Using the ToxCast estrogen receptor model for bioactivity as a case study, we highlight how these uncertainties can be propagated through models to quantify the uncertainty in model outputs. Uncertainty quantification in model outputs is used to identify potential false positives and false negatives and to determine the distribution of model values around semi-arbitrary activity cutoffs, increasing confidence in model predictions. At the individual chemical-assay level, curves with high variability are flagged for manual inspection or retesting, focusing subject-matter-expert time on results that need further input. This work improves the confidence of predictions made using HTS data, increasing the ability to use this data in risk assessment.