Toxicogenomics

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Toxicogenomics is a field of science that deals with the collection, interpretation, and storage of information about gene and protein activity within particular cell or tissue of an organism in response to toxic substances. Toxicogenomics combines toxicology with genomics or other high throughput molecular profiling technologies such as transcriptomics, proteomics and metabolomics[1][2]. Toxicogenomics endeavors to elucidate molecular mechanisms evolved in the expression of toxicity, and to derive molecular expression patterns (i.e., molecular biomarkers) that predict toxicity or the genetic susceptibility to it.

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 developed processes for of automated handling and storage. The analysis usually involves a wide array of bioinformatics and statistics.[4], regularly involving classification approaches[5].

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]

Public Toxicogenomics Projects

References

  1. The National Academies Press: Communicating Toxicogenomics Information to Nonexperts: A Workshop Summary (2005) [1]
  2. ed. by Hisham K. Hamadeh; Cynthia A. Afshari. (2004). Hamadeh HK, Afshari CA, ed. Toxicogenomics: Principles and Applications. Hoboken, NJ: Wiley-Liss. ISBN 0-471-43417-5. 
    Omenn GS (2004). "Book Review: Toxicogenomics: Principles and Applications". Environ Health Perspect. 112 (16): A962. PMC 1247673Freely accessible.  Unknown parameter |month= ignored (help)
  3. EPA Interim Genomics Policy
  4. Mattes WB, Pettit SD, Sansone SA, Bushel PR, Waters MD (2004). "Database development in toxicogenomics: issues and efforts". Environ. Health Perspect. 112 (4): 495–505. PMC 1241904Freely accessible. PMID 15033600.  Unknown parameter |month= ignored (help)
  5. Ellinger-Ziegelbauer H, Gmuender H, Bandenburg A, Ahr HJ (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. PMID 17689568. doi:10.1016/j.mrfmmm.2007.06.010.  Unknown parameter |month= ignored (help)
  6. Corvi R, Ahr HJ, Albertini S; et al. (2006). "Meeting report: Validation of toxicogenomics-based test systems: ECVAM-ICCVAM/NICEATM considerations for regulatory use". Environ Health Perspect. 114 (3): 420–9. PMC 1392237Freely accessible. PMID 16507466.  Unknown parameter |month= ignored (help)
  7. Collins BC, Clarke A, Kitteringham NR, Gallagher WM, Pennington SR (2007). "Use of proteomics for the discovery of early markers of drug toxicity". Expert Opin Drug Metab Toxicol. 3 (5): 689–704. PMID 17916055. doi:10.1517/17425225.3.5.689.  Unknown parameter |month= ignored (help)
  8. 8.0 8.1 Mattes WB (2008). "Public consortium efforts in toxicogenomics". Methods Mol Biol. 460: 221–38. PMID 18449490. doi:10.1007/978-1-60327-048-9_11. 
  9. Dix DJ, Houck KA, Martin MT, Richard AM, Setzer RW, Kavlock RJ (2007). "The ToxCast program for prioritizing toxicity testing of environmental chemicals". Toxicol. Sci. 95 (1): 5–12. PMID 16963515. doi:10.1093/toxsci/kfl103.  Unknown parameter |month= ignored (help)

See also

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Genomics topics
Genome project | Paleopolyploidy | Glycomics | Human Genome Project | Proteomics
Chemogenomics | Structural genomics | Pharmacogenetics | Pharmacogenomics | Toxicogenomics | Computational genomics
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