Evaluation of quantitative miRNA expression platforms in the microRNA quality control (miRQC) study

Mestdagh, Pieter; Hartmann, Nicole; Baeriswyl, Lukas; Andreasen, Ditte; Bernard, Nathalie; Chen, Caifu; Cheo, David L.; D'Andrade, Petula; DeMayo, Mike; Dennis, Lucas; Derveaux, Stefaan; Feng, Yun; Fulmer-Smentek, Stephanie; Gerstmayer, Bernhard; Gouffon, Julia S.; Grimley, Chris; Lader, Eric; Lee, Kathy; Luo, Shujun; Mouritzen, Peter; Narayanan, Aishwarya; Patel, Sunali; Peiffer, Sabine; Rüberg, Silvia; Schroth, Gary P.; Schuster, Dave; Shaffer, James; Shelton, Elliot J; Silveria, Scott; Ulmanella, Umberto; Veeramachaneni, Vamsi; Staedtler, Frank; Peters, Thomas; Guettouche, Toumy; Wong, Linda; Vandesompele, Jo

doi:10.1038/nmeth.3014

Cited by 565 publications

(570 citation statements)

References 17 publications

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“…To characterize miRNA signatures in the plasma of AA, the Serum/Plasma Focus microRNA PCR Panel was used, as it is considered optimal in terms of reproducibility, sensitivity, accuracy, and specificity. 27 We found that circulating miRNAs were differentially expressed in AA and MDS vs. HC and in AA vs. MDS, which was validated in a larger separate cohort using a different normalization method. By multivariate analysis, we identified the 5 miRNAs (miR-150-5p, miR-146-5p, miR-1, miR-22-3p, and miR-424-5p) that were significantly associated with AA or MDS, and these miRNA expression patterns were similar between the 2 cohorts.…”

Section: Discussionmentioning

confidence: 60%

A plasma microRNA signature as a biomarker for acquired aplastic anemia

et al. 2016

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Section: Discussionmentioning

confidence: 60%

A plasma microRNA signature as a biomarker for acquired aplastic anemia

et al. 2016

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“…8,9,11 Moreover, PCR-based systems require great care with primer design due to their target-based amplification, and often introduce sequence bias. 9,12 Microarrays, however, allow large-scale parallel detection of miRNAs, but usually require relatively long assay times with complicated steps. 9,13 Therefore, there is a great demand for systems that provide high sensitivity and specificity without target-based amplification, a simple workflow, and the ability to multiplex small panels of miRNAs in a high throughput manner.…”

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confidence: 99%

Encoded Hydrogel Microparticles for Sensitive and Multiplex microRNA Detection Directly from Raw Cell Lysates

et al. 2016

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In recent years, microRNAs (miRNAs) have emerged as promising diagnostic markers because of their unique dysregulation patterns under various disease conditions and high stability in biological fluids. However, current methods of analyzing miRNA levels typically require RNA isolation, which is cumbersome and time-consuming. To achieve high-throughput and accurate miRNA profiling, this study eliminates the need for purification steps by detecting miRNA directly from raw cellular lysate using nonfouling polyethylene glycol microparticles. In contrast to recent studies on direct miRNA measurements from cell lysate, our hydrogel-based system provides high-confidence quantification with robust performance. The lysis buffer for the assay was optimized to maximize reaction and labeling efficiency, and this assay has a low limit of detection (<1000 cells) without target amplification. Additionally, the capability for multiplexing was demonstrated through analyzing the levels of three endogenous miRNAs in 3T3 cell lysate. This versatile platform holds great potential for rapid and reliable direct miRNA quantification in complex media, and can be further extended to single-cell analysis by exploiting the flexibility and scalability of our system.

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“…However, the NanoString platform uses a quantitative assay that has been validated in other studies. 31 We did not collect information on fathers and thus our study cannot address any effects of sperm or other paternal factors on cervical miRNA expression.…”

Section: Discussionmentioning

confidence: 99%

microRNA expression in the cervix during pregnancy is associated with length of gestation

et al. 2015

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(2015) microRNA expression in the cervix during pregnancy is associated with length of gestation , Epigenetics, 10:3, 221-228, DOI: 10.1080/15592294.2015 Preterm birth is a leading cause of infant mortality and can lead to poor life-long health and adverse neurodevelopmental outcomes. The pathophysiologic mechanisms that precede preterm labor remain elusive, and the role that epigenetic phenomena play is largely unstudied. The objective of this study was to assess the association between microRNA (miRNA) expression levels in cervical cells obtained from swabs collected during pregnancy and the length of gestation. We analyzed cervical samples obtained between 16 and 19 weeks of gestation from 53 women in a prospective cohort from Mexico City, and followed them until delivery. Cervical miRNA was extracted and expression was quantified using the NanoString nCounter Analysis System. Linear regression models were used to examine the association between miRNA expression levels and gestational age at delivery, adjusted for maternal age, education, parity, body mass index, smoke exposure, and inflammation assessed on a Papanicolaou smear. We identified 6 miRNAs that were significantly associated with gestational age at the time of delivery, including miR-21, 30e, 142, 148b, 29b, and 223. Notably, per each doubling in miR-21 expression, gestations were 0.9 (95% CI: 0.2-1.5) days shorter on average (P D 0.009). Per each doubling in miR-30e, 142, 148b, 29b, and 223 expression, gestations were shorter by 1.0 to 1.6 days. The predicted targets of the miRNAs were enriched for molecules involved in DNA replication and inflammatory processes. The levels of specific miRNAs in the human cervix during pregnancy are predictive of gestational age at delivery, and should be validated in future studies as potential biomarkers of preterm birth risk.

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Evaluation of quantitative miRNA expression platforms in the microRNA quality control (miRQC) study

Cited by 565 publications

References 17 publications

A plasma microRNA signature as a biomarker for acquired aplastic anemia

A plasma microRNA signature as a biomarker for acquired aplastic anemia

Encoded Hydrogel Microparticles for Sensitive and Multiplex microRNA Detection Directly from Raw Cell Lysates

microRNA expression in the cervix during pregnancy is associated with length of gestation

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