title: A Data Analysis Pipeline Accounting for Artifacts in Tox21 Quantitative High-Throughput Screening Assays.
abstract: A main goal of the U.S. Tox21 program is to profile a 10K-compound library for activity against a panel of stress-related and nuclear receptor signaling pathway assays using a quantitative high-throughput screening (qHTS) approach. However, assay artifacts, including nonreproducible signals and assay interference (e.g., autofluorescence), complicate compound activity interpretation. To address these issues, we have developed a data analysis pipeline that includes an updated signal noise-filtering/curation protocol and an assay interference flagging system. To better characterize various types of signals, we adopted a weighted version of the area under the curve (wAUC) to quantify the amount of activity across the tested concentration range in combination with the assay-dependent point-of-departure (POD) concentration. Based on the 32 Tox21 qHTS assays analyzed, we demonstrate that signal profiling using wAUC affords the best reproducibility (Pearson's r = 0.91) in comparison with the POD (0.82) only or the AC(50) (i.e., half-maximal activity concentration, 0.81). Among the activity artifacts characterized, cytotoxicity is the major confounding factor; on average, about 8% of Tox21 compounds are affected, whereas autofluorescence affects less than 0.5%. To facilitate data evaluation, we implemented two graphical user interface applications, allowing users to rapidly evaluate the in vitro activity of Tox21 compounds.
authors.affiliation: Division of the National Toxicology Program, National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA jui-hua.hsieh@nih.gov.
authors.forename: Jui-Hua
authors.initials: JH
authors.lastname: Hsieh
authors.affiliation: MultiCASE Inc., Beachwood, OH, USA.
authors.forename: Alexander
authors.initials: A
authors.lastname: Sedykh
authors.affiliation: National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, USA.
authors.forename: Ruili
authors.initials: R
authors.lastname: Huang
authors.affiliation: National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, USA.
authors.forename: Menghang
authors.initials: M
authors.lastname: Xia
authors.affiliation: Division of the National Toxicology Program, National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA.
authors.forename: Raymond R
authors.initials: RR
authors.lastname: Tice
mesh_terms: D016477:Artifacts; D003627:Data Interpretation, Statistical; D055808:Drug Discovery / Q000379:methods* / Q000592:standards*; D057166:High-Throughput Screening Assays / Q000379:methods* / Q000592:standards*; D006801:Humans; D015203:Reproducibility of Results; D059629:Signal-To-Noise Ratio; D054852:Small Molecule Libraries; D014481:United States
chemical_list: D054852:Small Molecule Libraries
keywords: Tox21; concentration-response curve; in vitro activity profiling; qHTS data analysis