NatureMetrics team members Dr Kat Bruce and Dr Lynsey Harper are among the authors of a newly-published research paper titled ‘A validation scale to determine the readiness of environmental DNA assays for routine species monitoring’.
The paper appears in an issue of Environmental DNA. It outlines the five stages of validation for quantitative polymerase chain reaction (qPCR) assays to detect individual species from eDNA, ranging from computational development of assays though laboratory testing to ensure specificity (only returns positive results for the target species) and sensitivity (detects target species DNA even at low concentrations) and in-field trials to determine performance of the assay on water samples collected from natural environments where the target species is known to be present. To achieve the highest level of validation, testing needs to show how detection rates vary in different environments and at different times of year, since DNA shedding rates often vary between the different stages of a species’ life-history.
A key message of the paper is that assays at intermediate validation levels may still be highly effective and can be informative for applied monitoring. Crucially, the paper provides guidance on how to interpret positive and negative results from assays at each stage of the scale.
The paper was an output from a workshop led by NatureMetrics founder Kat Bruce as part of her role as leader of the Field and Lab Methods working group of the EU COST Action programme, DNAqua-net. Held at the University of Innsbruck in March 2018, the workshop brought together expert scientists from institutions across Europe to develop tools that could help environmental managers to understand whether a given qPCR assay (published in the scientific literature or developed by companies like NatureMetrics) is ready for application in a given monitoring context.
Dr Lynsey Harper said:
“hundreds of eDNA assays have been published, but they vary enormously in the extent to which they have been validated and their readiness for use in applied monitoring. This means it has been hard for potential users of eDNA to understand whether a given assay is fit for purpose. The scale we have published provides a consistent framework for scoring assays and for users to make informed decisions about when and how to apply them. At NatureMetrics, it also helps us communicate with our clients about which assays we offer, the extent to which they have been validated and how to robustly interpret results”.
In a further step towards operationalising the framework set out in the paper, NatureMetrics has been working with Natural England to develop an online tool for reporting and interpreting qPCR results. The Confidence Assessment Tool for eDNA qPCR Results (COASTER) takes into account the validation level of the assay itself, as well as the qPCR parameters under which it was applied in the laboratory. COASTER will soon be available to all users, and the published report is available here.
NatureMetrics has unrivalled global expertise in the practical application of DNA-based tools to environmental monitoring challenges. We now work with over three hundred clients globally, across eight major sectors.
Since eDNA is still a new technology, developing validation tools and standards is a huge step in maturing the field and mainstreaming its use around the globe. Our scientists play leading roles in international collaborations that are working to develop and operationalise these tools. Read the paper here.
Author: Ropafadzo Mugadza