Determination of chemical-disease risk values to prioritize connections between environmental factors, genetic variants, and human diseases

Toxicol Appl Pharmacol. 2019 Sep 15;379:114674. doi: 10.1016/j.taap.2019.114674. Epub 2019 Jul 16.

Abstract

Traditional methods for chemical risk assessment are too time-consuming and resource-intensive to characterize either the diversity of chemicals to which humans are exposed or how that diversity may manifest in population susceptibility differences. The advent of novel toxicological data sources and their integration with bioinformatic databases affords opportunities for modern approaches that consider gene-environment (GxE) interactions in population risk assessment. Here, we present an approach that systematically links multiple data sources to relate chemical risk values to diseases and gene-disease variants. These data sources include high-throughput screening (HTS) results from Tox21/ToxCast, chemical-disease relationships from the Comparative Toxicogenomics Database (CTD), hazard data from resources like the Integrated Risk Information System, exposure data from the ExpoCast initiative, and gene-variant-disease information from the DisGeNET database. We use these integrated data to identify variants implicated in chemical-disease enrichments and develop a new value that estimates the risk of these associations toward differential population responses. Finally, we use this value to prioritize chemical-disease associations by exploring the genomic distribution of variants implicated in high-risk diseases. We offer this modular approach, termed DisQGOS (Disease Quotient Genetic Overview Score), for relating overall chemical-disease risk to potential for population variable responses, as a complement to methods aiming to modernize aspects of risk assessment.

Keywords: Data integration; Gene-environment interactions; New approach methodologies; Risk assessment.

Publication types

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

MeSH terms

  • Animals
  • Databases, Factual
  • Datasets as Topic
  • Environmental Exposure / adverse effects*
  • Environmental Exposure / statistics & numerical data
  • Gene-Environment Interaction*
  • Genetic Predisposition to Disease / etiology*
  • Genetic Predisposition to Disease / genetics
  • Genetic Variation*
  • High-Throughput Screening Assays
  • Humans
  • Information Storage and Retrieval
  • Risk Assessment* / methods
  • Toxicology / methods*