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Mission and Scope
The mission of the OMICs Interest Group (OMICs IG) is to provide a forum for discussion, and a means of raising awareness of the challenges and opportunities for OMICs in the environmental sciences and toxicology among stakeholders. OMICs IG
will also coordinate scientific efforts among diverse partners (e.g.,
Government, Academia, Industry, Consulting, etc.) and across regions, so
to explore and further develop OMICs technologies as an important
feature in regulations by connecting their molecular-based endpoints to
apical outcomes that are used for the protection of human and ecological
health throughout the globe.
is to improve the information used by decision makers, to provide
additional lines of evidence to conventional and novel methods, and to
facilitate the innovation of ethical and cost-effective testing
procedures. In the short and long terms, this IG will be a key player in
a global dialog, cementing a leading role for SETAC at fostering
ongoing discussions about how to proceed on a scientific level to
maximize gains for industry and policy makers around the world.
In this group, OMICs refers to technologies and approaches used to comprehensively and quantitatively measure differences and changes in genes, their molecular products and interactions to include genomics, transcriptomics, metabolomics, proteomics, lipidomics, metagenomics, etc.).
The SETAC interest groups follow the Society’s aim to improve Environmental Quality through Science. This requires the involvement of all stakeholders from Academia, Industry, Governments and Citizen Groups. The Global Interest Group on OMICs helps to fulfil SETAC’s aims to ensure highest quality science and communication among researchers across the relevant sectors, concerned with industrial needs and regulatory requirements.
Governments around the world are passing new legislation to regulate chemical substances based on their potential impacts on both human and environmental health. These are critical and complex rules, designed to better ensure public safety, a healthy environment and functioning ecosystems. However, there are huge scientific and logistical constraints in determining risks for an ever-increasing number and diversity of products introduced to markets. Standard operating procedures for toxicity testing are typically prescriptive and have not fundamentally changed in over thirty years. Meanwhile, there has been considerable and fundamental advancement in many of the OMICs sciences, including the standardization of experimental methods and data management. OMIC technologies have reached a required level of technical and analytical maturity to be applied towards prevention, detection, diagnosis and guidance of treatments in diverse human health problems. Yet, OMICs have not yet been adequately deployed to address environmental issues and there is a need to tie OMICs measurements to apical endpoints such as lethality, growth and/or reproductive impairments. OMICs have the potential to revolutionise “Knowledge Based Risk Assessment” of the possible health effects of compounds and other risk factors, on both humans and the environment, by discovering the molecular key events, or signatures, that are diagnostic of exposure, apical endpoints and predictive of adverse outcomes to plants and animals, their populations and communities, including humans.
To date, few OMICS data and methods have been integrated into a risk assessment framework, whole effluent or mixture testing, criteria development or monitoring. However, these methods and data may add rich mechanistic knowledge towards the creation of Adverse Outcome Pathways (OECD, 2012) and provide new lines of evidence for identifying and prioritizing environmental exposures. The hesitancies of both scientists and regulators stem, in part, from the fear that OMICs will increase costs while complicating the risk analysis and interpretation and a clear connection between OMIC endpoints and the guideline endpoints of lethality, growth and reproduction. Additional factors that have slowed the acceptance of OMICs technologies in risk assessment include over-promising outcomes, a general lack of standardized methods, unknowns regarding their applications and the fact that there are few examples demonstrating that they are reliable and efficient endpoints for characterizing risk or related to apical outcomes. Therefore, there is a particular need to improve our capacity to interpret OMICs data and to develop a strategy for its integration into risk-based decision-making, toxicity testing, monitoring and criteria development. At the same time, these processes must be economical and time efficient. Hence, coordinated, multi-disciplinary research and targeted application efforts are needed to optimize and achieve such integration.
Evolutionary and Multigenerational Effects of Chemicals (EVOGENERATE)
Workgroup Chairs: Elias Oziolor and Jana Asselman
2017 OMICS Global IG Annual Report
2016 OMICS Global IG Annual Report
Bruno Campos, Unilever, UK (co-chair, email@example.com)
Doris Vidal-Dorsch, Southern California Coastal Water Research Project, USA (co-chair, firstname.lastname@example.org)
Adam Biales, U.S. EPA, USA
Geoff Hodges, Unilever Research, UK
Natalia Garcia-Reyero, Mississippi State University, USA
Tarun Anumol, Agilent Technologies, USA
Ben Brown, University of California, USA
Sharon Hook, CSIRO, Australia
Jinhee Choi, University of Seoul, South Korea
Xiaowei Zhang, Nanjing University, China
Anze Zupanic, Swiss Federal Institute for Aquatic Research and Technology, Switzerland
Chris Martyniuk, University of Florida, USA
Pim Leonards, VU University, Amsterdam, Netherlands
Stefan Schade, University of Birmingham, UK
In the follow up of several discussions since the inception of the OMICS IG was identified the need for a list of seminal papers/resources which could be used both as an introduction to OMICS technologies and potential applications.
After a survey to the current members, some of the identified key reads are:
Ø A complete workflow for high-resolution spectral-stitching nanoelectrospray direct-infusion mass-spectrometry-based metabolomics and lipidomics (https://doi.org/10.1038/nprot.2016.156)
Ø A comprehensive assessment of RNA-seq accuracy, reproducibility and information content by the Sequencing Quality Control Consortium (https://doi.org/10.1038/nbt.2957)
Ø Differential gene transcription across the life cycle in Daphnia magna using a new all genome custom-made microarray (https://doi.org/10.1186/s12864-018-4725-7)
Ø Discovery of Metabolic Signatures for Predicting Whole Organism Toxicology (https://doi.org/10.1093/toxsci/kfq004)
Ø Environmental metabolomics: a critical review and future perspectives (https://doi.org/10.1007/s11306-008-0152-0)
Ø Environmental metabolomics: Databases and tools for data analysis (https://doi.org/10.1016/j.marchem.2015.06.012)
Ø Environmental toxicology and omics: A question of sex (https://doi.org/10.1016/j.jprot.2017.09.010)
Ø Evolutionary Conservation of Human Drug Targets in Organisms used for Environmental Risk Assessments (https://doi.org/10.1021/es8005173
Ø Gene Expression of Fathead Minnows (Pimephales promelas) Exposed to Two Types of Treated Municipal Wastewater Eﬄuents (dx.doi.org/10.1021/es401942n)
Ø How Omics Technologies can Enhance Chemical Safety Regulation: Perspectives from Academia, Government, and Industry (DOI: 10.1002/etc.4079)
Ø Identification of Metabolic Pathways in Daphnia magna Explaining Hormetic Effects of Selective Serotonin Reuptake Inhibitors and 4-Nonylphenol Using Transcriptomic and Phenotypic Responses (https://doi.org/10.1021/es4012299)
Ø Incorporating Transgenerational Epigenetic Inheritance into Ecological Risk Assessment Frameworks (https://doi.org/10.1021/acs.est.7b01094)
Ø Metabolic Profile Biomarkers of Metal Contamination in a Sentinel Terrestrial Species Are Applicable Across Multiple Sites (https://doi.org/10.1021/es0700303)
Ø Metabonomics in Toxicology: A Review (https://doi.org/10.1093/toxsci/kfi102)
Ø Molecular toxicity of cerium oxide nanoparticles to the freshwater alga Chlamydomonas reinhardtii is associated with supra-environmental exposure concentrations (https://doi.org/10.3109/17435390.2014.1002868)
Ø NMR-Based Metabolomics: A Powerful Approach for Characterizing the Effects of Environmental Stressors on Organism Health (https://doi.org/10.1021/es034281x)
Ø Omics Advances in Ecotoxicology (DOI:10.1021/acs.est.7b06494)
Ø Omics for aquatic ecotoxicology: Control of extraneous variability to enhance the analysis of environmental effects (https://doi.org/10.1002/etc.3002)
Ø The genomic landscape of rapid repeated evolutionary adaptation to toxic pollution in wild fish (DOI: 10.1126/science.aah4993)
Ø The Role of Epigenomics in Aquatic Toxicology (https://doi.org/10.1002/etc.3930)
Ø The transcriptome-wide effects of exposure to a pyrethroid pesticide on the Critically Endangered delta smelt Hypomesus transpacificus (DOI: https://doi.org/10.3354/esr00679)
Ø Transcriptome profiling of developmental and xenobiotic responses in a keystone soil animal, the oligochaete annelid Lumbricus rubellus (https://doi.org/10.1186/1471-2164-9-266)
Ø Transgenerational DNA Methylation Changes in Daphnia magna Exposed to Chronic γ Irradiation (https://doi.org/10.1021/acs.est.7b05695)
Ø Tryptophan hydroxylase (TRH) loss of function mutations induce growth and behavioral defects in Daphnia magna (https://doi.org/10.1038/s41598-018-19778-0)
Ø Understanding 'Global' Systems Biology: Metabonomics and the Continuum of Metabolism (https://doi.org/10.1038/nrd1157)
Ø Use of Metabolomics to Advance Research on Environmental Exposures and the Human Exposome (https://doi.org/10.17226/23414)
Ø Using Gene Expression to Assess the Status of Fish from Anthropogenically Influenced Estuarine Wetland (dx.doi.org/10.1021/es2011308)
This list does not intent, by any means, to be an endorsement, exhaustive, exclusive and/or permanent. Instead it should be seen as a community effort to educate the next generation of OMICs researchers. If you want to add/change this list, please email the IG Chairs who will be happy to edit this list!