TY - JOUR
T1 - DraculR
T2 - A Web-Based Application for In Silico Haemolysis Detection in High-Throughput microRNA Sequencing Data
AU - Smith, Melanie D.
AU - Leemaqz, Shalem Y.
AU - Jankovic-Karasoulos, Tanja
AU - McCullough, Dylan
AU - McAninch, Dale
AU - Arthurs, Anya L.
AU - Breen, James
AU - Roberts, Claire T.
AU - Pillman, Katherine A.
PY - 2023/2
Y1 - 2023/2
N2 - 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 long-lived 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.
AB - 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 long-lived 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.
KW - bioinformatics
KW - biomarker
KW - haemolysis
KW - microRNA
KW - plasma
KW - prediction
UR - http://www.scopus.com/inward/record.url?scp=85148957438&partnerID=8YFLogxK
UR - http://purl.org/au-research/grants/NHMRC/1174971
U2 - 10.3390/genes14020448
DO - 10.3390/genes14020448
M3 - Article
C2 - 36833375
AN - SCOPUS:85148957438
SN - 2073-4425
VL - 14
JO - Genes
JF - Genes
IS - 2
M1 - 448
ER -