Reference : Small RNA profiling of low biomass samples: identification and removal of contaminants
Scientific journals : Article
Life sciences : Biochemistry, biophysics & molecular biology
Life sciences : Environmental sciences & ecology
Life sciences : Microbiology
Systems Biomedicine
http://hdl.handle.net/10993/35695
Small RNA profiling of low biomass samples: identification and removal of contaminants
English
Heintz-Buschart, Anna []
Yusuf, Dilmurat []
Kaysen, Anne mailto [University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB) > >]
Etheridge, Alton []
Fritz, Joëlle mailto [University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB) > >]
May, Patrick mailto [University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB) > >]
de Beaufort, Carine []
Upadhyaya, Bimal Babu []
Ghosal, Anubrata []
Galas, David J []
Wilmes, Paul mailto [University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB) > >]
14-May-2018
BMC Biology
BioMed Central
16
52
Yes (verified by ORBilu)
International
1741-7007
[en] small RNAs ; contamination ; gene expression
[en] Background: Sequencing-based analyses of low-biomass samples are known to be prone to misinterpretation due to the potential presence of contaminating molecules derived from laboratory reagents and environments. DNA contamination has been previously reported, however contamination with RNA is usually considered to be unlikely due to its inherent instability. Small RNAs (sRNAs) identified in tissues and bodily fluids such as blood plasma, have implications for physiology and pathology, and therefore the potential to act as disease biomarkers. Thus, the possibility for RNA contaminants demands a careful evaluation.
Results: Here we report the presence of small RNA contaminants in widely used microRNA extraction kits and propose an approach for their depletion. We sequenced sRNAs extracted from human plasma samples and detected important levels of non-human (exogenous) sequences whose source could be traced to the microRNA extraction columns through a careful qPCR-based analysis of several laboratory reagents. Furthermore, we also detected the presence of artefactual sequences related to these contaminants in a range of published datasets, arguing for a re-evaluation of reports suggesting the presence of exogenous RNAs of microbial and dietary origins in blood plasma. To avoid artefacts in future experiments, we also devise several protocols of contaminant RNAs, define minimal amounts of starting material for artefact-free analyses, and confirm the reduction of contaminant levels for identification of bona fide sequences using ‘ultra-clean’ extraction kits.
Conclusion: This is the first report of the presence of RNA molecules as contaminants in RNA extraction kits. The described protocols should be applied in the future to avoid confounding sRNA studies.
Luxembourg Centre for Systems Biomedicine (LCSB): Eco-Systems Biology (Wilmes Group) ; Luxembourg Centre for Systems Biomedicine (LCSB): Bioinformatics Core (R. Schneider Group) ; University of Luxembourg: High Performance Computing - ULHPC
Fonds National de la Recherche - FnR
Researchers
http://hdl.handle.net/10993/35695
10.1186/s12915-018-0522-7
https://bmcbiol.biomedcentral.com/articles/10.1186/s12915-018-0522-7
FnR ; FNR10404093 > Paul Wilmes > microCancer > Non-invasive microbiome-derived multi-omic biomarkers for early-stage colorectal cancer detection > 01/05/2016 > 30/04/2019 > 2015

File(s) associated to this reference

Fulltext file(s):

FileCommentaryVersionSizeAccess
Limited access
HeintzBuschart.BMCBiology2018.pdfPublisher postprint1.61 MBRequest a copy

Bookmark and Share SFX Query

All documents in ORBilu are protected by a user license.