Chapter 2.3.3 : Microarray-Based Environmental Diagnostics

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Before environmental microarrays can fulfill their diagnostic promise, it is necessary to define an environmental diagnostic. In this chapter, I propose a definition for an environmental diagnostic (EVD) that is consistent with the FDA's definition and meaning of an in vitro diagnostic (IVD), where the emphasis is on the use of the diagnostic to make a decision and take action relative to the effect of a particular condition on human health. In this context, the underlying microarray technologies, methods of manufacture, and intended use can significantly impact the quality and reliability of an environmental diagnosis. Current and future technology should therefore focus on reducing the variability of environmental microarrays during manufacture and use, so that repeatable results can be obtained independent of the user. Analytical process simplification, perhaps through amplification microarrays described in this chapter, may help achieve the objective of repeatability for independent users, but technology per se will not substitute for a clearly defined intended use, effective product design, and objective verification and validation data. At present, the absence of regulatory oversight for EVDs is both a blessing and a curse. It is therefore expected that future technical solutions for realizing microarray-based EVDs will only come with a consensus biological and regulatory opinion regarding the meaning of environmental nucleic acid signatures relative to the real or perceived risks associated with each intended use.

Citation: Chandler D. 2016. Microarray-Based Environmental Diagnostics, p 2.3.3-1-2.3.3-13. In Yates M, Nakatsu C, Miller R, Pillai S (ed), Manual of Environmental Microbiology, Fourth Edition. ASM Press, Washington, DC. doi: 10.1128/9781555818821.ch2.3.3
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Microarray workflow simplification through integrated biochemistry, resulting in an amplification microarray. Integrating nucleic acid sample preparation into a sample-to-answer, fully contained consumable is discussed in detail elsewhere (e.g., [ ], and chapter 2.3.4; Straub et al.), and is not considered here. Automated microarray image and data analysis methods likewise exist, and are expected to be a standard component of EVDs to minimize or eliminate user subjectivity in the process and diagnosis. doi: 10.1128/9781555818821.ch2.3.3.f1

Citation: Chandler D. 2016. Microarray-Based Environmental Diagnostics, p 2.3.3-1-2.3.3-13. In Yates M, Nakatsu C, Miller R, Pillai S (ed), Manual of Environmental Microbiology, Fourth Edition. ASM Press, Washington, DC. doi: 10.1128/9781555818821.ch2.3.3
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Common areas and sources of systematic variability associated with environmental microarrays

Citation: Chandler D. 2016. Microarray-Based Environmental Diagnostics, p 2.3.3-1-2.3.3-13. In Yates M, Nakatsu C, Miller R, Pillai S (ed), Manual of Environmental Microbiology, Fourth Edition. ASM Press, Washington, DC. doi: 10.1128/9781555818821.ch2.3.3

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