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

Emma R Mcconnell,Lyle D Burgoon,Rong-Lin Wang,Edward J Perkins,Shannon M Bell,Ila Cote,Ping Gong,Natàlia Garcia-Reyero,Nancy Lan Guo

doi:10.1371/journal.pone.0110379

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.

Highlights

Government agencies and environmental consultants develop human health risk assessments to determine the potential exposure and toxicity risks of chemicals, a process which involves consideration of all of the available published scientific literature on that chemical
In acknowledgement of the complicated and varied procedures and analysis required to perform a microarray experiment, the gene expression microarray community created the ‘‘Minimum Information About a Microarray Experiment’’ (MIAME) [4] standard, along with data reporting requirements that have been adopted by several journals
The questions that pertained directly to microarray data came from MIAME [4], while general questions on information needed for repeating a toxicological study are drawn from the ToxRTool [3] and the Checklist [2]

Summary

Introduction

Government agencies and environmental consultants develop human health risk assessments to determine the potential exposure and toxicity risks of chemicals, a process which involves consideration of all of the available published scientific literature on that chemical. In acknowledgement of the complicated and varied procedures and analysis required to perform a microarray experiment, the gene expression microarray community created the ‘‘Minimum Information About a Microarray Experiment’’ (MIAME) [4] standard, along with data reporting requirements that have been adopted by several journals. Though this is a community standard for transcriptomic microarrays, it does not consider their application to toxicogenomic studies for the purpose of human health risk assessment

Methods

Results

Conclusion