Two approaches for estimating the lower limit of quantitation (LLOQ) of microRNA levels assayed as exploratory biomarkers by RT-qPCR

• Published in: BMC biotechnology Vol. 18; no. 1; p. 6
• Main Authors: Wolfinger, Russell D., Beedanagari, Sudheer, Boitier, Eric, Chen, Tao, Couttet, Philippe, Ellinger-Ziegelbauer, Heidrun, Guillemain, Gregory, Mariet, Claire, Mouritzen, Peter, O’Lone, Raegan, Pine, P. Scott, Sharapova, Tatiana, Yan, Jian, Yuen, Peter S., Thompson, Karol L.
• Format: Journal Article
• Language: English
• Published: England BioMed Central Ltd 02.02.2018; BioMed Central; BMC
• Subjects: Absolute quantitation; Animals; Biological markers; biomarkers; Calibration; data collection; drugs; Gene expression; Genetic Markers; guidelines; Limit of Detection; logit analysis; Lower limit of quantitation; Methodology; microRNA; MicroRNAs - genetics; Polymerase chain reaction; Quantitative genetics; Quantitative PCR; quantitative polymerase chain reaction; Rats; reverse transcriptase polymerase chain reaction; Reverse Transcriptase Polymerase Chain Reaction - methods; Reverse Transcriptase Polymerase Chain Reaction - statistics & numerical data; reverse transcription; Transcription (Genetics); uncertainty; Workflow; Lower limit of quantitation; Absolute quantitation; microRNA; Quantitative PCR
• ISSN: 1472-6750; 1472-6750
• DOI: 10.1186/s12896-018-0415-4

Circulating microRNAs are undergoing exploratory use as safety biomarkers in drug development. Reverse transcription quantitative polymerase chain reaction (RT-qPCR) is one common approach used to quantitate levels of microRNAs in samples that includes the use of a standard curve of calibrators fit to a regression model. Guidelines are needed for setting assay quantitation thresholds that are appropriate for this method and to biomarker pre-validation. In this report, we develop two workflows for determining a lower limit of quantitation (LLOQ) for RT-qPCR assays of microRNAs in exploratory studies. One workflow is based on an error threshold calculated by a logistic model of the calibration curve data. The second workflow is based on a threshold set by the sample blank, which is the no template control for RT-qPCR. The two workflows are used to set lower thresholds of reportable microRNA levels for an example dataset in which miR-208a levels in biofluids are quantitated in a cardiac injury model. LLOQ thresholds set by either workflow are effective in filtering out microRNA values with large uncertainty estimates. Two workflows for LLOQ determinations are presented in this report that provide methods that are easy to implement in investigational studies of microRNA safety biomarkers and offer choices in levels of conservatism in setting lower limits of acceptable values that facilitate interpretation of results.