Impact of Genomics Platform and Statistical Filtering on Transcriptional Benchmark Doses (BMD) and Multiple Approaches for Selection of Chemical Point of Departure (PoD)

PLoS One. 2015 Aug 27;10(8):e0136764. doi: 10.1371/journal.pone.0136764. eCollection 2015.


Many regulatory agencies are exploring ways to integrate toxicogenomic data into their chemical risk assessments. The major challenge lies in determining how to distill the complex data produced by high-content, multi-dose gene expression studies into quantitative information. It has been proposed that benchmark dose (BMD) values derived from toxicogenomics data be used as point of departure (PoD) values in chemical risk assessments. However, there is limited information regarding which genomics platforms are most suitable and how to select appropriate PoD values. In this study, we compared BMD values modeled from RNA sequencing-, microarray-, and qPCR-derived gene expression data from a single study, and explored multiple approaches for selecting a single PoD from these data. The strategies evaluated include several that do not require prior mechanistic knowledge of the compound for selection of the PoD, thus providing approaches for assessing data-poor chemicals. We used RNA extracted from the livers of female mice exposed to non-carcinogenic (0, 2 mg/kg/day, mkd) and carcinogenic (4, 8 mkd) doses of furan for 21 days. We show that transcriptional BMD values were consistent across technologies and highly predictive of the two-year cancer bioassay-based PoD. We also demonstrate that filtering data based on statistically significant changes in gene expression prior to BMD modeling creates more conservative BMD values. Taken together, this case study on mice exposed to furan demonstrates that high-content toxicogenomics studies produce robust data for BMD modelling that are minimally affected by inter-technology variability and highly predictive of cancer-based PoD doses.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Benchmarking
  • Carcinogens / administration & dosage
  • Carcinogens / toxicity
  • Dose-Response Relationship, Drug*
  • Female
  • Furans / administration & dosage
  • Furans / toxicity
  • Gene Expression Profiling / methods
  • Gene Expression Regulation / drug effects
  • Genomics / methods
  • Genomics / statistics & numerical data*
  • Liver / drug effects
  • Liver / physiology
  • Mice, Inbred Strains
  • Models, Theoretical
  • Oligonucleotide Array Sequence Analysis
  • Polymerase Chain Reaction
  • Risk Assessment / methods
  • Sequence Analysis, RNA / methods
  • Toxicogenetics / methods*


  • Carcinogens
  • Furans
  • furan

Associated data

  • GEO/GSE48644
  • GEO/GSE64371

Grants and funding

CLY’s research is funded by the Health Canada Genomics R&D Initiative. AFW was supported by the Natural Science and Engineering Research Council of Canada and the Ontario Graduate Scholarship. LR is an employee of ILS. ILS funded only the in-life portion: the exposure of mice to furan, collection of tissues, and RNA extractions for downstream molecular analysis. ILS laboratories are accredited by the Association for Assessment and Accreditation of Laboratory Animal Care (AALAC) and the animal use protocol for this study was reviewed and approved by the ILS Institutional Animal Care & Use Committee (IACUC). Funding for the conduct of the in-life portion of this study was derived from the ILS Research and Development budgets. ILS has no competing interest with respect to furan manufacture, sales or research. All molecular analysis of the RNA derived from animal tissues from this study were analyzed at Health Canada (Ottawa). ILS provided support in the form of salaries for LR, but did not have any additional role in the study design, data collection and analysis, decision to publish, or preparation of the manuscript. The specific roles of these authors are articulated in the ‘author contributions’ section.