Systematic Omics Analysis Review (SOAR) tool to support risk assessment

PLoS One. 2014 Dec 22;9(12):e110379. doi: 10.1371/journal.pone.0110379. eCollection 2014.

Abstract

Environmental health risk assessors are challenged to understand and incorporate new data streams as the field of toxicology continues to adopt new molecular and systems biology technologies. Systematic screening reviews can help risk assessors and assessment teams determine which studies to consider for inclusion in a human health assessment. A tool for systematic reviews should be standardized and transparent in order to consistently determine which studies meet minimum quality criteria prior to performing in-depth analyses of the data. The Systematic Omics Analysis Review (SOAR) tool is focused on assisting risk assessment support teams in performing systematic reviews of transcriptomic studies. SOAR is a spreadsheet tool of 35 objective questions developed by domain experts, focused on transcriptomic microarray studies, and including four main topics: test system, test substance, experimental design, and microarray data. The tool will be used as a guide to identify studies that meet basic published quality criteria, such as those defined by the Minimum Information About a Microarray Experiment standard and the Toxicological Data Reliability Assessment Tool. Seven scientists were recruited to test the tool by using it to independently rate 15 published manuscripts that study chemical exposures with microarrays. Using their feedback, questions were weighted based on importance of the information and a suitability cutoff was set for each of the four topic sections. The final validation resulted in 100% agreement between the users on four separate manuscripts, showing that the SOAR tool may be used to facilitate the standardized and transparent screening of microarray literature for environmental human health risk assessment.

Publication types

  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Animals
  • Ecotoxicology / methods*
  • Ecotoxicology / standards
  • Gene Expression Profiling*
  • Humans
  • Oligonucleotide Array Sequence Analysis
  • Reference Standards
  • Review Literature as Topic*
  • Risk Assessment / methods*
  • Risk Assessment / standards
  • Surveys and Questionnaires
  • Toxicogenetics / methods*
  • Toxicogenetics / standards

Grants and funding

This work was funded by the US EPA's Human Health Risk Assessment Program. The funders had no role in study design, or data collection and analysis. EPA management cleared the manuscript for publication, which included helpful suggestions that improved the overall quality of the manuscript, consistent with the US EPA Scientific Integrity Policy. Co-author Ping Gong is employed by SpecPro, Inc. SpecPro, Inc provided support in the form of salary for author PG, 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 role of this author is articulated in the ‘author contributions’ section.