Reporting the limits of detection and quantification for environmental DNA assays

Environmental DNA

Chris C. Wilson¹  Caren C. Helbing²  Michael J. Allison²  Richard F. Lance³  Caren S. Goldberg⁴  Anna M. Mangan⁵  Antoinette J. Piaggio⁵  Emy M. Monroe⁶  Catherine A. Richter⁷  Katy E. Klymus⁷  Craig A. Jackson⁸  Christopher M. Merkes⁸  Joel P. Stokdyk⁹  Margaret E. Hunter^1,10 

[1] Aquatic Research and Monitoring Section Ontario Ministry of Natural Resources and Forestry Peterborough ON Canada;Department of Biochemistry and Microbiology University of Victoria Victoria BC Canada;Environmental Laboratory United States Army Engineer Research & Development Center Vicksburg MS USA;School of the Environment Washington State University Pullman WA USA;U.S. Department of Agriculture, Wildlife Genetics Lab, Animal and Plant Health Inspection Service, Wildlife Services National Wildlife Research Center Fort Collins CO USA;U.S. Fish and Wildlife Service, Whitney Genetics Laboratory Midwest Fisheries Center Onalaska WI USA;U.S. Geological Survey Columbia Environmental Research Center Columbia MO USA;U.S. Geological Survey Upper Midwest Environmental Sciences Center La Crosse WI USA;U.S. Geological Survey Upper Midwest Water Science Center Marshfield WI USA;U.S. Geological Survey Wetland and Aquatic Research Center Gainesville FL USA;

关键词: assay optimization;    eDNA;    qPCR;    standardization;   

DOI  :  10.1002/edn3.29

来源: DOAJ

【 摘 要 】

Abstract Background Environmental DNA (eDNA) analysis is increasingly being used to detect the presence and relative abundance of rare species, especially invasive or imperiled aquatic species. The rapid progress in the eDNA field has resulted in numerous studies impacting conservation and management actions. However, standardization of eDNA methods and reporting across the field is yet to be fully established, with one area being the calculation and interpretation of assay limit of detection (LOD) and limit of quantification (LOQ). Aims Here, we propose establishing consistent methods for determining and reporting of LOD and LOQ for single‐species quantitative PCR (qPCR) eDNA studies. Materials & Methods/ Results We utilize datasets from multiple cooperating laboratories to demonstrate both a discrete threshold approach and a curve‐fitting modeling approach for determining LODs and LOQs for eDNA qPCR assays. We also provide details of an R script developed and applied for the modeling method. Discussion/Conclusions Ultimately, standardization of how LOD and LOQ are determined, interpreted, and reported for eDNA assays will allow for more informed interpretation of assay results, more meaningful interlaboratory comparisons of experiments, and enhanced capacity for assessing the relative technical quality and performance of different eDNA qPCR assays.

【 授权许可】

Unknown