Please use this identifier to cite or link to this item:
https://hdl.handle.net/2440/137645
Citations | ||
Scopus | Web of Science® | Altmetric |
---|---|---|
?
|
?
|
Type: | Journal article |
Title: | DraculR: A Web-Based Application for In Silico Haemolysis Detection in High-Throughput microRNA Sequencing Data |
Author: | Smith, M.D. Leemaqz, S.Y. Jankovic-Karasoulos, T. McCullough, D. McAninch, D. Arthurs, A.L. Breen, J. Roberts, C.T. Pillman, K.A. |
Citation: | Genes, 2023; 14(2):1-10 |
Publisher: | MDPI AG |
Issue Date: | 2023 |
ISSN: | 2073-4425 2073-4425 |
Statement of Responsibility: | Melanie D. Smith, Shalem Y. Leemaqz, Tanja Jankovic-Karasoulos, Dylan McCullough, Dale McAninch, Anya L. Arthurs, James Breen, Claire T. Roberts, and Katherine A. Pillman |
Abstract: | The search for novel microRNA (miRNA) biomarkers in plasma is hampered by haemolysis, the lysis and subsequent release of red blood cell contents, including miRNAs, into surrounding fluid. The biomarker potential of miRNAs comes in part from their multicompartment origin and the longlived nature of miRNA transcripts in plasma, giving researchers a functional window for tissues that are otherwise difficult or disadvantageous to sample. The inclusion of red-blood-cell-derived miRNA transcripts in downstream analysis introduces a source of error that is difficult to identify posthoc and may lead to spurious results. Where access to a physical specimen is not possible, our tool will provide an in silico approach to haemolysis prediction. We present DraculR, an interactive Shiny/R application that enables a user to upload miRNA expression data from a short-read sequencing of human plasma as a raw read counts table and interactively calculate a metric that indicates the degree of haemolysis contamination. The code, DraculR web tool and its tutorial are freely available as detailed herein. |
Keywords: | haemolysis; microRNA; plasma; biomarker; prediction; bioinformatics |
Rights: | © 2023 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https:// creativecommons.org/licenses/by/ 4.0/). |
DOI: | 10.3390/genes14020448 |
Grant ID: | http://purl.org/au-research/grants/nhmrc/GNT1174971 |
Published version: | http://dx.doi.org/10.3390/genes14020448 |
Appears in Collections: | Medicine publications |
Files in This Item:
File | Description | Size | Format | |
---|---|---|---|---|
hdl_137645.pdf | Published version | 2.57 MB | Adobe PDF | View/Open |
Items in DSpace are protected by copyright, with all rights reserved, unless otherwise indicated.