Establishing detection thresholds for environmental DNA using receiver operator characteristic (ROC) curves

Serrao, Natasha R.; Reid, Scott M.; Wilson, Chris C.

doi:10.1007/s12686-017-0817-y

Cited by 26 publications

(30 citation statements)

References 45 publications

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“…Mismatches between eDNA and traditional sampling detections have similarly been reported elsewhere (Boothroyd, Mandrak, Fox, & Wilson, ; Serrao, ). This may be an example of a species occurrence that is below the limit of detection (Hunter et al, ; Serrao et al, in press), as only a single live mussel was found at the TTR site each of the three times it was sampled (2013; S. Reid, OMNRF, pers. comm.…”

Section: Discussionmentioning

confidence: 99%

“…Detection thresholds refer to the level of fluorescence above which the researcher is confident that the fluorescence is caused by target DNA presence rather than noise, and can be set at C q , an arbitrary value (e.g. > 1 copy), or using receiver operating characteristic (Nutz, Döll, & Karlovsky, ; Serrao, Wilson, & Reid, in press). For this study, LOD was approximated from validation assays, and detection thresholds were established by assessing false positive rates among negative controls.…”

Section: Methodsmentioning

confidence: 99%

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Validation of environmental DNA (eDNA) as a detection tool for at‐risk freshwater pearly mussel species (Bivalvia: Unionidae)

Currier

Morris

Wilson

et al. 2018

Aquatic Conservation

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1. Documenting the occurrence and habitat occupancy of rare aquatic species is an ongoing challenge for conservation. Characterization of environmental DNA (eDNA) from bulk water samples has emerged as a powerful tool to infer species presence or absence without the need to observe or handle organisms.2. Previous eDNA studies have yet to develop species-specific markers that target taxa with many potentially sympatric confamilials. Forty-one freshwater pearly mussel species (Unionidae) are found in southern Ontario, Canada, with many of these listed as threatened, endangered, or of conservation concern; however, locating populations for protection can be challenging owing to morphological crypsis and species scarcity.3. Species-specific eDNA markers were developed to target four unionid species. Following in silico and in vitro validation, markers were validated in the field by comparing eDNA results from water samples to detections based on quadrat sampling. 4. Target species were detected by eDNA sampling at all sites where they had previously been located by quadrat sampling. 5. The paired sampling design showed that species-specific markers can be designed even within speciose families, and that eDNA detection of mussels is at least as sensitive as quadrat sampling. Furthermore, detection probabilities were not affected by sampling depth, and eDNA concentrations were positively correlated with mussel densities. 6. These findings confirm that eDNA assays are a valuable complement to traditional methods for locating and managing imperilled unionid populations.

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Section: Discussionmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Validation of environmental DNA (eDNA) as a detection tool for at‐risk freshwater pearly mussel species (Bivalvia: Unionidae)

Currier

Morris

Wilson

et al. 2018

Aquatic Conservation

Self Cite

View full text Add to dashboard Cite

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“…The LOQ of the nPCR was lower than the detection limit of 1 9 10 -5 ng/lL reported by Clusa et al (2017), whereas Agersnap et al (2017) demonstrated a higher level of sensitivity (LOD and LOQ of one copy per lL of extracted sample) using qPCR than was recorded in this study. A LOD of less than one copy number per reaction has been reported in other studies using qPCR (Hunter et al 2017;Serrao et al 2017).…”

Section: Discussionmentioning

confidence: 54%

Is it absent or is it present? Detection of a non-native fish to inform management decisions using a new highly-sensitive eDNA protocol

et al. 2019

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Section: Discussionmentioning

confidence: 99%

“…ROC analysis is a standard approach to identify a detection cut-off for a disease biomarker ( 125 ). In ROC analysis, the AUC can be calculated to evaluate the power of an assay system to accurately distinguish between true and false results for diseases, especially cancer ( 125 , 126 ). As used by many researchers, the AUC scale was defined by Hosmer et al ( 127 ): if AUC=0.5, no discrimination; if 0.5<AUC<0.7, poor discrimination; if 0.7≤AUC<0.8, acceptable discrimination; if 0.8≤AUC<0.9, excellent discrimination; and if AUC≥0.9, discrimination is considered.…”

Section: Discussionmentioning

confidence: 99%

MicroRNA-196a-5p is a potential prognostic marker of delayed lymph node metastasis in early-stage tongue squamous cell carcinoma

et al. 2017

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MicroRNAs (miRs) are expected to serve as prognostic tools for cancer. However, many miRs have been reported as prognostic markers of recurrence or metastasis in oral squamous cell carcinoma patients. We aimed to determine the prognostic markers in early-stage tongue squamous cell carcinoma (TSCC). Based on previous studies, we hypothesized that miR-10a, 10b, 196a-5p, 196a-3p, and 196b were prognostic markers and we retrospectively performed miR expression analyses using formalin-fixed paraffin-embedded sections of surgical specimens. Total RNA was isolated from cancer tissues and adjacent normal tissue as control, and samples were collected by laser-capture microdissection. After cDNA synthesis, reverse transcription-quantitative polymerase chain reaction was performed. Statistical analyses for patient clinicopathological characteristics, recurrence/metastasis, and survival rates were performed to discern their relationships with miR expression levels, and the 2−ΔΔCq method was used. miR-196a-5p levels were significantly upregulated in early-stage TSCC, particularly in the lymph node metastasis (LNM) group. The LNM-free survival rate in the low miR-196a-5p ΔΔCq value regulation group was found to be lower than that in the high ΔΔCq value regulation group (P=0.0079). Receiver operating characteristic analysis of ΔΔCq values revealed that miR-196a-5p had a P-value=0.0025, area under the curve=0.740, and a cut-off value=−0.875 for distinguishing LNM. To our knowledge, this is the first study to examine LNM-related miRs in early-stage TSCC as well as miRs and ‘delayed LNM’ in head and neck cancer. miR-196a-5p upregulation may predict delayed LNM. Our data serve as a foundation for future studies to evaluate miR levels and facilitate the prediction of delayed LNM during early-stage TSCC, which prevent metastasis when combined with close follow-up and aggressive adjuvant therapy or elective neck dissection. Moreover, our data will serve as a foundation for future studies to evaluate whether miR-196a-5p can serve as a therapeutic marker for preventing metastasis.

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Establishing detection thresholds for environmental DNA using receiver operator characteristic (ROC) curves

Cited by 26 publications

References 45 publications

Validation of environmental DNA (eDNA) as a detection tool for at‐risk freshwater pearly mussel species (Bivalvia: Unionidae)

Validation of environmental DNA (eDNA) as a detection tool for at‐risk freshwater pearly mussel species (Bivalvia: Unionidae)

Is it absent or is it present? Detection of a non-native fish to inform management decisions using a new highly-sensitive eDNA protocol

MicroRNA-196a-5p is a potential prognostic marker of delayed lymph node metastasis in early-stage tongue squamous cell carcinoma

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