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

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

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

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

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

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

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

Figure 2.

nature methods | VOL.11 NO.8 | AUGUST 2014 doi:10.1038/nmeth.3014

Pieter Mestdagh1…and Jo Vandesompele1

Figure 2.

nature methods | VOL.11 NO.8 | AUGUST 2014 doi:10.1038/nmeth.3014

Pieter Mestdagh1…and Jo Vandesompele1

Figure 3.

nature methods | VOL.11 NO.8 | AUGUST 2014 doi:10.1038/nmeth.3014

Pieter Mestdagh1…and Jo Vandesompele1

Figure 4.

nature methods | VOL.11 NO.8 | AUGUST 2014 doi:10.1038/nmeth.3014

Pieter Mestdagh1…and Jo Vandesompele1

Figure 5.

nature methods | VOL.11 NO.8 | AUGUST 2014 doi:10.1038/nmeth.3014

Pieter Mestdagh1…and Jo Vandesompele1

Figure 6.

nature methods | VOL.11 NO.8 | AUGUST 2014 doi:10.1038/nmeth.3014

Pieter Mestdagh1…and Jo Vandesompele1

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

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