You are here:
High-Throughput Chemical Safety Screening Using Targeted RNA-seq (ISMB 2021 Abstract)
Citation:
Everett, L., J. Harrill, D. Haggard, J. Bundy, B. Vallanat, I. Shah, AND R. Judson. High-Throughput Chemical Safety Screening Using Targeted RNA-seq (ISMB 2021 Abstract). Intelligent Systems for Molecular Biology (ISMB), Virtual, Virtual, July 25 - 30, 2021. https://doi.org/10.23645/epacomptox.15036114
Impact/Purpose:
This is an abstract to be submitted to the 29th conference on Intelligent Systems for Molecular Biology (ISMB), which is an international meeting covering bioinformatics and computational biology (July 2021, virtual). The abstract and subsequent poster or presentation will communicate our work on developing the bioinformatics infrastructure and methods critical to the analysis of high-throughput transcriptomics (HTTr) data generated by EPA/ORD.
Description:
Traditional toxicological testing is a costly and slow process and as a result thousands of chemicals lack sufficient safety data to protect human health and the environment. Transcriptomics has emerged as a cost-effective method for broadly assessing chemical toxicity across many target pathways and mechanisms of action in a single assay. US EPA has designed a rapid and automated in vitro screening platform using the TempO-seq targeted RNA-seq assay to profile chemical bioactivity across a range of concentrations and cell types. To date, this approach has been used to screen over 1,000 chemicals[EL1] in three biologically distinct cell lines, resulting in over 100,000 targeted RNA-seq profiles covering ~20,000 human protein-coding genes. The scale and complexity of this data has necessitated extensive development of novel bioinformatic methods, including: 1) an open-source pipeline optimized for rapid and robust processing of TempO-seq data; 2) novel QC procedures tailored to data generated in large-scale automated experiments; and 3) signature-level dose-response models to summarize results for each chemical and link the observed in vitro bioactivity to known targets, pathways, and hazards. This abstract does not necessarily reflect US EPA policy. Use of product or company names do not constitute endorsement by US EPA.
URLs/Downloads:
DOI: High-Throughput Chemical Safety Screening Using Targeted RNA-seq (ISMB 2021 Abstract)
EVERETT_ISMB_2021_HTTR_POSTER_V5.PDF (PDF, NA pp, 555.23 KB, about PDF)