Comparison of Reproducibility, Accuracy, Sensitivity, and Specificity of miRNA Quantification Platforms

Paula M Godoy; Andrea J Barczak; Peter DeHoff; Srimeenakshi Srinivasan; Alton Etheridge; David Galas; Saumya Das; David J Erle; Louise C Laurent

doi:10.1016/j.celrep.2019.11.078

Comparison of Reproducibility, Accuracy, Sensitivity, and Specificity of miRNA Quantification Platforms

Cell Rep. 2019 Dec 17;29(12):4212-4222.e5. doi: 10.1016/j.celrep.2019.11.078.

Authors

Paula M Godoy¹, Andrea J Barczak², Peter DeHoff³, Srimeenakshi Srinivasan³, Alton Etheridge⁴, David Galas⁴, Saumya Das⁵, David J Erle⁶, Louise C Laurent⁷

Affiliations

¹ Division of Medical Oncology, Department of Medicine and Department of Developmental Biology, Washington University in Saint Louis, 4518 McKinley Ave., CB 8069, St. Louis, MO 63110, USA; Lung Biology Center, University of California, San Francisco, UCSF Box 2922, San Francisco, CA 94143, USA.
² Lung Biology Center, University of California, San Francisco, UCSF Box 2922, San Francisco, CA 94143, USA.
³ Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California, San Diego, 9500 Gilman Drive, Mail Code 0695, La Jolla, CA 92093-0695, USA; Sanford Consortium for Regenerative Medicine, 2880 Torrey Pines Scenic Drive, La Jolla, CA 92037, USA.
⁴ Pacific Northwest Research Institute, 720 Broadway, Seattle, WA 98122, USA.
⁵ Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA 02114, USA.
⁶ Lung Biology Center, University of California, San Francisco, UCSF Box 2922, San Francisco, CA 94143, USA; Cardiovascular Research Institute, University of California, San Francisco, UCSF Box 2922, San Francisco, CA 94143, USA.
⁷ Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California, San Diego, 9500 Gilman Drive, Mail Code 0695, La Jolla, CA 92093-0695, USA; Sanford Consortium for Regenerative Medicine, 2880 Torrey Pines Scenic Drive, La Jolla, CA 92037, USA. Electronic address: llaurent@ucsd.edu.

Abstract

Given the increasing interest in their use as disease biomarkers, the establishment of reproducible, accurate, sensitive, and specific platforms for microRNA (miRNA) quantification in biofluids is of high priority. We compare four platforms for these characteristics: small RNA sequencing (RNA-seq), FirePlex, EdgeSeq, and nCounter. For a pool of synthetic miRNAs, coefficients of variation for technical replicates are lower for EdgeSeq (6.9%) and RNA-seq (8.2%) than for FirePlex (22.4%); nCounter replicates are not performed. Receiver operating characteristic analysis for distinguishing present versus absent miRNAs shows small RNA-seq (area under curve 0.99) is superior to EdgeSeq (0.97), nCounter (0.94), and FirePlex (0.81). Expected differences in expression of placenta-associated miRNAs in plasma from pregnant and non-pregnant women are observed with RNA-seq and EdgeSeq, but not FirePlex or nCounter. These results indicate that differences in performance among miRNA profiling platforms impact ability to detect biological differences among samples and thus their relative utility for research and clinical use.

Keywords: Abcam FirePlex; HTG Molecular EdgeSeq; NanoString nCounter; extracellular RNA; miRNA quantification; small RNA-sequencing.

Publication types

Comparative Study
Research Support, N.I.H., Extramural

MeSH terms

Adult
Female
Gene Expression Profiling / methods*
High-Throughput Nucleotide Sequencing / methods*
Humans
Male
MicroRNAs / blood*
MicroRNAs / genetics*
Middle Aged
Placenta / metabolism*
Pregnancy
ROC Curve
Reproducibility of Results
Sequence Analysis, RNA / methods*
Young Adult

Substances

MicroRNAs

Abstract

Publication types

MeSH terms

Substances

Grants and funding