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| Status |
Public on Jan 20, 2022 |
| Title |
A MicroRNA Next-Generation-Sequencing Discovery Assay (miND) For Genome-Scale and Absolute Quantitation of Circulating MicroRNA Biomarkers |
| Organisms |
Homo sapiens; synthetic construct |
| Experiment type |
Non-coding RNA profiling by high throughput sequencing
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| Summary |
The plasma levels of tissue-specific microRNAs can be used as prognostic and diagnostic biomarkers for chronic and acute diseases. Thereby, the combination of diverse miRNAs into biomarker signatures using multivariate statistics seems especially powerful in view to tissue and condition specific miRNA shedding into the plasma. Although Next-Generation Sequencing (NGS) technology enables to analyse circulating microRNAs on a genome-scale level, it suffers from potential biases (e.g. adapter ligation bias) and lacks absolute transcript quantitation. In order to develop a robust NGS discovery assay for genome-scale quantitation of circulating microRNAs we first evaluated the sensitivity, repeatability and ligation bias of four commercially available small RNA library preparation protocols. The protocol from RealSeq Biosciences was selected based on its performance and usability, and coupled with a novel panel of exogenous small RNA spike-in controls to enable absolute quantitation and ensure comparability of data across independent NGS experiments. The established MicroRNA Next-Generation-Sequencing Discovery Assay (miND) was validated for its relative accuracy, precision, analytical measurement range and sequencing bias and was considered fit-for-purpose for microRNA biomarker discovery. Summarized, all these criteria were met and thus our analytical platform is considered fit-for-purpose for microRNA biomarker discovery from plasma, serum, cerebrospinal fluid (CSF), synovial fluid (SF), or extracellular vesicles (EV) extracted from cell culture medium in the setting of any diagnostic, prognostic or patient stratification need.
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| Overall design |
A comprehensive comparison of four commersially available small RNA sequencing protocols followed by the assay development and validation for the MicroRNA Next-Generation Discovery Assay (miND)
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| Contributor(s) |
Khamina K, Diendorfer AB, Skalicky S, Weigl M, Pultar M, Krammer T, Fournier CA, Schofield AL, Otto C, Smith AT, Buchtele N, Schoergenhofer C, Jilma B, Frank BJ, Hofstaetter JG, Grillari R, Grillari J, Ruprecht K, Goldring CE, Rehrauer H, Glaab WE, Hackl M |
| Citation(s) |
35163149 |
| Submission date |
Dec 01, 2021 |
| Last update date |
Mar 31, 2022 |
| Contact name |
Andreas B Diendorfer |
| E-mail(s) |
service@tamirna.com
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| Organization name |
TAmiRNA GmbH
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| Street address |
Leberstraße 20
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| City |
Wien |
| ZIP/Postal code |
1110 |
| Country |
Austria |
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| Platforms (2) |
| GPL16791 |
Illumina HiSeq 2500 (Homo sapiens) |
| GPL19604 |
Illumina HiSeq 2500 (synthetic construct) |
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| Samples (81)
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| Relations |
| BioProject |
PRJNA785168 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE189930_RAW.tar |
1.4 Mb |
(http)(custom) |
TAR (of CSV) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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