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![Page 1: Evaluation of quantitative miRNA expression platforms in the microRNA quality control (miRQC) study nature methods | VOL.11 NO.8 | AUGUST 2014 doi:10.1038/nmeth.3014.](https://reader034.fdocuments.us/reader034/viewer/2022042821/56649d165503460f949ebfb4/html5/thumbnails/1.jpg)
Evaluation of quantitative miRNA expression platforms in the microRNA quality control
(miRQC) study
nature methods | VOL.11 NO.8 | AUGUST 2014 doi:10.1038/nmeth.3014
Kim Dong-in
Pieter Mestdagh1…and Jo Vandesompele1
![Page 2: Evaluation of quantitative miRNA expression platforms in the microRNA quality control (miRQC) study nature methods | VOL.11 NO.8 | AUGUST 2014 doi:10.1038/nmeth.3014.](https://reader034.fdocuments.us/reader034/viewer/2022042821/56649d165503460f949ebfb4/html5/thumbnails/2.jpg)
Abstract + Introduction
microRNA is… - negative regulator (protein coding gene)
- noninvasive biomarkers
- technologies – miRNA abundance sequencing(small RNA) RT-qPCR(reverse transcription-quantitative PCR) microarray(hybridization)
nature methods | VOL.11 NO.8 | AUGUST 2014 doi:10.1038/nmeth.3014
Pieter Mestdagh1…and Jo Vandesompele1
![Page 3: Evaluation of quantitative miRNA expression platforms in the microRNA quality control (miRQC) study nature methods | VOL.11 NO.8 | AUGUST 2014 doi:10.1038/nmeth.3014.](https://reader034.fdocuments.us/reader034/viewer/2022042821/56649d165503460f949ebfb4/html5/thumbnails/3.jpg)
Abstract + Introduction
Object - ill-defined quantifiable performance metrics(platforms) -> most appropriate method for particular study - comprehensively assess quantitative miRNA platform
miRQC(microRNA quality control) study involve 12 plaform of 9 vendors agree 16 (mandatory) and 4 (optional) samples
Developed performance metrics
nature methods | VOL.11 NO.8 | AUGUST 2014 doi:10.1038/nmeth.3014
Pieter Mestdagh1…and Jo Vandesompele1
![Page 4: Evaluation of quantitative miRNA expression platforms in the microRNA quality control (miRQC) study nature methods | VOL.11 NO.8 | AUGUST 2014 doi:10.1038/nmeth.3014.](https://reader034.fdocuments.us/reader034/viewer/2022042821/56649d165503460f949ebfb4/html5/thumbnails/4.jpg)
Result
miRQC study design
samples (16 mandatory, 4 optional) miRNA derived human serum(optional 4 samples) profiled(9 of 12 platforms) 196 microRNAs – 12 platforms
nature methods | VOL.11 NO.8 | AUGUST 2014 doi:10.1038/nmeth.3014
Pieter Mestdagh1…and Jo Vandesompele1
![Page 5: Evaluation of quantitative miRNA expression platforms in the microRNA quality control (miRQC) study nature methods | VOL.11 NO.8 | AUGUST 2014 doi:10.1038/nmeth.3014.](https://reader034.fdocuments.us/reader034/viewer/2022042821/56649d165503460f949ebfb4/html5/thumbnails/5.jpg)
Set of 196 miRNAs measured by all platforms.
nature methods | VOL.11 NO.8 | AUGUST 2014 doi:10.1038/nmeth.3014
Pieter Mestdagh1…and Jo Vandesompele1
![Page 6: Evaluation of quantitative miRNA expression platforms in the microRNA quality control (miRQC) study nature methods | VOL.11 NO.8 | AUGUST 2014 doi:10.1038/nmeth.3014.](https://reader034.fdocuments.us/reader034/viewer/2022042821/56649d165503460f949ebfb4/html5/thumbnails/6.jpg)
Figure 1.
nature methods | VOL.11 NO.8 | AUGUST 2014 doi:10.1038/nmeth.3014
Pieter Mestdagh1…and Jo Vandesompele1
UHmiRR Universal Human miRNA Reference RNA
HBR :human brain RNA
![Page 7: Evaluation of quantitative miRNA expression platforms in the microRNA quality control (miRQC) study nature methods | VOL.11 NO.8 | AUGUST 2014 doi:10.1038/nmeth.3014.](https://reader034.fdocuments.us/reader034/viewer/2022042821/56649d165503460f949ebfb4/html5/thumbnails/7.jpg)
Result
Titration response
nature methods | VOL.11 NO.8 | AUGUST 2014 doi:10.1038/nmeth.3014
Pieter Mestdagh1…and Jo Vandesompele1
100% Universal Human miRNA Reference RNA
100% human brain RNA
0.75A + 0.25B
0.25A + 0.75B
Determined titration response of each 196 microRNA sample / replicate 1
![Page 8: Evaluation of quantitative miRNA expression platforms in the microRNA quality control (miRQC) study nature methods | VOL.11 NO.8 | AUGUST 2014 doi:10.1038/nmeth.3014.](https://reader034.fdocuments.us/reader034/viewer/2022042821/56649d165503460f949ebfb4/html5/thumbnails/8.jpg)
Figure 2.
nature methods | VOL.11 NO.8 | AUGUST 2014 doi:10.1038/nmeth.3014
Pieter Mestdagh1…and Jo Vandesompele1
![Page 9: Evaluation of quantitative miRNA expression platforms in the microRNA quality control (miRQC) study nature methods | VOL.11 NO.8 | AUGUST 2014 doi:10.1038/nmeth.3014.](https://reader034.fdocuments.us/reader034/viewer/2022042821/56649d165503460f949ebfb4/html5/thumbnails/9.jpg)
Figure 2.
nature methods | VOL.11 NO.8 | AUGUST 2014 doi:10.1038/nmeth.3014
Pieter Mestdagh1…and Jo Vandesompele1
![Page 10: Evaluation of quantitative miRNA expression platforms in the microRNA quality control (miRQC) study nature methods | VOL.11 NO.8 | AUGUST 2014 doi:10.1038/nmeth.3014.](https://reader034.fdocuments.us/reader034/viewer/2022042821/56649d165503460f949ebfb4/html5/thumbnails/10.jpg)
Figure 3.
nature methods | VOL.11 NO.8 | AUGUST 2014 doi:10.1038/nmeth.3014
Pieter Mestdagh1…and Jo Vandesompele1
![Page 11: Evaluation of quantitative miRNA expression platforms in the microRNA quality control (miRQC) study nature methods | VOL.11 NO.8 | AUGUST 2014 doi:10.1038/nmeth.3014.](https://reader034.fdocuments.us/reader034/viewer/2022042821/56649d165503460f949ebfb4/html5/thumbnails/11.jpg)
Figure 4.
nature methods | VOL.11 NO.8 | AUGUST 2014 doi:10.1038/nmeth.3014
Pieter Mestdagh1…and Jo Vandesompele1
![Page 12: Evaluation of quantitative miRNA expression platforms in the microRNA quality control (miRQC) study nature methods | VOL.11 NO.8 | AUGUST 2014 doi:10.1038/nmeth.3014.](https://reader034.fdocuments.us/reader034/viewer/2022042821/56649d165503460f949ebfb4/html5/thumbnails/12.jpg)
Figure 5.
nature methods | VOL.11 NO.8 | AUGUST 2014 doi:10.1038/nmeth.3014
Pieter Mestdagh1…and Jo Vandesompele1
![Page 13: Evaluation of quantitative miRNA expression platforms in the microRNA quality control (miRQC) study nature methods | VOL.11 NO.8 | AUGUST 2014 doi:10.1038/nmeth.3014.](https://reader034.fdocuments.us/reader034/viewer/2022042821/56649d165503460f949ebfb4/html5/thumbnails/13.jpg)
Figure 6.
nature methods | VOL.11 NO.8 | AUGUST 2014 doi:10.1038/nmeth.3014
Pieter Mestdagh1…and Jo Vandesompele1
![Page 14: Evaluation of quantitative miRNA expression platforms in the microRNA quality control (miRQC) study nature methods | VOL.11 NO.8 | AUGUST 2014 doi:10.1038/nmeth.3014.](https://reader034.fdocuments.us/reader034/viewer/2022042821/56649d165503460f949ebfb4/html5/thumbnails/14.jpg)
Discussion
miRNA detection rate combination sensitivity, detection cutoff,platform content ( limited assays or probes) over-estimation difference for many platforms miRNA content
sensitivity, reproducibility, specificity, accuracy qPCR Guide platform choice
nature methods | VOL.11 NO.8 | AUGUST 2014 doi:10.1038/nmeth.3014
Pieter Mestdagh1…and Jo Vandesompele1
![Page 15: Evaluation of quantitative miRNA expression platforms in the microRNA quality control (miRQC) study nature methods | VOL.11 NO.8 | AUGUST 2014 doi:10.1038/nmeth.3014.](https://reader034.fdocuments.us/reader034/viewer/2022042821/56649d165503460f949ebfb4/html5/thumbnails/15.jpg)
Discussion
Each platform
specific strengths, weaknesses
Choose on the basis (experimental setting, specific research questions)
nature methods | VOL.11 NO.8 | AUGUST 2014 doi:10.1038/nmeth.3014
Pieter Mestdagh1…and Jo Vandesompele1