This broad definition is supported by the United States Environmental Protection Agency stating that "the term "genomics" encompasses a broader scope of scientific inquiry and associated technologies than when genomics was initially considered. A genome is the sum total of all an individual organism's genes. Thus, genomics is the study of all the genes of a cell, or tissue, at the DNA (genotype), mRNA (transcriptome), or protein (proteome) levels. Genomics methodologies are expected to provide valuable insights for evaluating how environmental stressors affect cellular/tissue function and how changes in gene expression may relate to adverse effects. However, the relationships between changes in gene expression and adverse effects are unclear at this time and may likely be difficult to elucidate."3
The nature and complexity of the data (in volume and variability) demands highly dvelopped processes for of automated handling and storage. The analysis usually involves a wide array of bioinformatics and statistics.4, regularly involving classification approaches5.
In pharmaceutical Drug discovery and development toxicogenomics is used to study adverse, i.e. toxic, effects, of pharmaceutical drugs in defined model systems in order to draw conclusions on the toxic risk to patients or the environment. Both the EPA and the U.S. Food and Drug Administration currently preclude basing regulatory decision making on genomics data alone. However, they do encourage the voluntary submission of well-documented, quality genomics data. Both agencies are considering the use of submitted data on a case-by-case basis for assessment purposes (e.g., to help elucidate mechanism of action or contribute to a weight-of-evidence approach) or for populating relevant comparative databases by encouraging parallel submissions of genomics data and traditional toxicologic test results.6
InnoMed PredTox assessing the value of combining results from omics technologies together with the results from more conventional toxicology methods in more informed decision making in preclinical safety evaluation.8
^ Ellinger-Ziegelbauer H, Gmuender H, Bandenburg A, Ahr HJ (Jan 2008). "Prediction of a carcinogenic potential of rat hepatocarcinogens using toxicogenomics analysis of short-term in vivo studies". Mutat. Res.637 (1-2): 23–39. doi:10.1016/j.mrfmmm.2007.06.010. PMID 17689568.
^ Collins BC, Clarke A, Kitteringham NR, Gallagher WM, Pennington SR (Oct 2007). "Use of proteomics for the discovery of early markers of drug toxicity". Expert Opin Drug Metab Toxicol3 (5): 689–704. doi:10.1517/17425225.3.5.689. PMID 17916055.
^ Dix DJ, Houck KA, Martin MT, Richard AM, Setzer RW, Kavlock RJ (Jan 2007). "The ToxCast program for prioritizing toxicity testing of environmental chemicals". Toxicol. Sci.95 (1): 5–12. doi:10.1093/toxsci/kfl103. PMID 16963515.
Comparative Toxicogenomics Database - a public database that integrates toxicogenomic data for chemicals, genes, and diseases from the scientific literature.
