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Title: Small RNA profiling of low biomass samples: identification and removal of contaminants

Abstract

Here, 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, yet contamination with RNA is usually considered to be very 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 careful evaluation.

Authors:
 [1];  [2];  [3];  [4];  [3];  [5];  [3];  [5];  [6];  [4]; ORCiD logo [5]
  1. Univ. of Luxembourg, Esch-sur-Alzette (Luxembourg); German Centre for Integrative Biodiversity Research (iDiv) Leipzig-Halle-Jena, Leipzig (Germany); Helmholtz-Centre for Environmental Research GmbH (UFZ), Halle (Germany)
  2. Univ. of Luxembourg, Esch-sur-Alzette (Luxembourg); Univ. of Freiburg, Freiburg (Germany)
  3. Univ. of Luxembourg, Esch-sur-Alzette (Luxembourg); Centre Hospitalier de Luxembourg, Luxembourg (Luxembourg)
  4. Pacific Northwest Research Institute, Seattle, WA (United States)
  5. Univ. of Luxembourg, Esch-sur-Alzette (Luxembourg)
  6. Univ. of Luxembourg, Esch-sur-Alzette (Luxembourg); Massachusetts Inst. of Technology (MIT), Cambridge, MA (United States)
Publication Date:
Research Org.:
Pacific Northwest National Lab. (PNNL), Richland, WA (United States)
Sponsoring Org.:
USDOE
OSTI Identifier:
1441216
Grant/Contract Number:
AC05-76RL01830; ATTRACT/A09/03; CORE/15/BM/10404093; CORE/16/BM/11276306; PoC/13/02; 1180851; 5821107; CORE14/BM/8066232; 1U01HL126496; ImMicroDyn1
Resource Type:
Journal Article: Accepted Manuscript
Journal Name:
BMC Biology
Additional Journal Information:
Journal Volume: 16; Journal Issue: 1; Journal ID: ISSN 1741-7007
Publisher:
BioMed Central
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; RNA sequencing; Artefact removal; Exogenous RNA in human blood plasma; Contaminant RNA; Spin columns

Citation Formats

Heintz-Buschart, Anna, Yusuf, Dilmurat, Kaysen, Anne, Etheridge, Alton, Fritz, Joelle V., May, Patrick, de Beaufort, Carine, Upadhyaya, Bimal B., Ghosal, Anubrata, Galas, David J., and Wilmes, Paul. Small RNA profiling of low biomass samples: identification and removal of contaminants. United States: N. p., 2018. Web. doi:10.1186/s12915-018-0522-7.
Heintz-Buschart, Anna, Yusuf, Dilmurat, Kaysen, Anne, Etheridge, Alton, Fritz, Joelle V., May, Patrick, de Beaufort, Carine, Upadhyaya, Bimal B., Ghosal, Anubrata, Galas, David J., & Wilmes, Paul. Small RNA profiling of low biomass samples: identification and removal of contaminants. United States. doi:10.1186/s12915-018-0522-7.
Heintz-Buschart, Anna, Yusuf, Dilmurat, Kaysen, Anne, Etheridge, Alton, Fritz, Joelle V., May, Patrick, de Beaufort, Carine, Upadhyaya, Bimal B., Ghosal, Anubrata, Galas, David J., and Wilmes, Paul. Mon . "Small RNA profiling of low biomass samples: identification and removal of contaminants". United States. doi:10.1186/s12915-018-0522-7. https://www.osti.gov/servlets/purl/1441216.
@article{osti_1441216,
title = {Small RNA profiling of low biomass samples: identification and removal of contaminants},
author = {Heintz-Buschart, Anna and Yusuf, Dilmurat and Kaysen, Anne and Etheridge, Alton and Fritz, Joelle V. and May, Patrick and de Beaufort, Carine and Upadhyaya, Bimal B. and Ghosal, Anubrata and Galas, David J. and Wilmes, Paul},
abstractNote = {Here, 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, yet contamination with RNA is usually considered to be very 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 careful evaluation.},
doi = {10.1186/s12915-018-0522-7},
journal = {BMC Biology},
number = 1,
volume = 16,
place = {United States},
year = {Mon May 14 00:00:00 EDT 2018},
month = {Mon May 14 00:00:00 EDT 2018}
}

Journal Article:
Free Publicly Available Full Text
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