Microbial contamination in next generation sequencing: implications for sequence-based analysis of clinical samples
The high level of accuracy and sensitivity of next generation sequencing for quantifying genetic material across organismal boundaries gives it tremendous potential for pathogen discovery and diagnosis in human disease. Despite this promise, substantial bacterial contamination is routinely found in...
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| Veröffentlicht in: | PLoS pathogens 2014-11, Vol.10 (11), p.e1004437-e1004437 |
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| creator | Strong, Michael J Xu, Guorong Morici, Lisa Splinter Bon-Durant, Sandra Baddoo, Melody Lin, Zhen Fewell, Claire Taylor, Christopher M Flemington, Erik K |
| description | The high level of accuracy and sensitivity of next generation sequencing for quantifying genetic material across organismal boundaries gives it tremendous potential for pathogen discovery and diagnosis in human disease. Despite this promise, substantial bacterial contamination is routinely found in existing human-derived RNA-seq datasets that likely arises from environmental sources. This raises the need for stringent sequencing and analysis protocols for studies investigating sequence-based microbial signatures in clinical samples. |
| doi_str_mv | 10.1371/journal.ppat.1004437 |
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Despite this promise, substantial bacterial contamination is routinely found in existing human-derived RNA-seq datasets that likely arises from environmental sources. 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This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited: Strong MJ, Xu G, Morici L, Splinter Bon-Durant S, Baddoo M, Lin Z, et al. (2014) Microbial Contamination in Next Generation Sequencing: Implications for Sequence-Based Analysis of Clinical Samples. 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Xu, Guorong ; Morici, Lisa ; Splinter Bon-Durant, Sandra ; Baddoo, Melody ; Lin, Zhen ; Fewell, Claire ; Taylor, Christopher M ; Flemington, Erik K</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c699t-58391fb56231f4406e377cc60f59b6328999bb484357ad04c8f7bc511afc7f103</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2014</creationdate><topic>Bioinformatics</topic><topic>Biology and Life Sciences</topic><topic>Cancer</topic><topic>Databases, Nucleic Acid</topic><topic>Datasets</topic><topic>DNA sequencing</topic><topic>Equipment Contamination</topic><topic>Genetic aspects</topic><topic>Genetic research</topic><topic>Genomes</topic><topic>Health aspects</topic><topic>High-Throughput Nucleotide Sequencing</topic><topic>Host-parasite relationships</topic><topic>Humans</topic><topic>Infections - diagnosis</topic><topic>Infections - genetics</topic><topic>Laboratories</topic><topic>Library collections</topic><topic>Medicine and Health Sciences</topic><topic>Microbial colonies</topic><topic>Microbiological research</topic><topic>Nucleotide sequencing</topic><topic>Opinion</topic><topic>Research and Analysis Methods</topic><topic>Studies</topic><topic>Viral infections</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Strong, Michael J</creatorcontrib><creatorcontrib>Xu, Guorong</creatorcontrib><creatorcontrib>Morici, Lisa</creatorcontrib><creatorcontrib>Splinter Bon-Durant, Sandra</creatorcontrib><creatorcontrib>Baddoo, Melody</creatorcontrib><creatorcontrib>Lin, Zhen</creatorcontrib><creatorcontrib>Fewell, Claire</creatorcontrib><creatorcontrib>Taylor, Christopher M</creatorcontrib><creatorcontrib>Flemington, Erik K</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>Gale In Context: Canada</collection><collection>Gale In Context: Science</collection><collection>MEDLINE - Academic</collection><collection>PubMed Central (Full Participant titles)</collection><collection>DOAJ Directory of Open Access Journals</collection><jtitle>PLoS pathogens</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Strong, Michael J</au><au>Xu, Guorong</au><au>Morici, Lisa</au><au>Splinter Bon-Durant, Sandra</au><au>Baddoo, Melody</au><au>Lin, Zhen</au><au>Fewell, Claire</au><au>Taylor, Christopher M</au><au>Flemington, Erik K</au><au>Rall, Glenn F.</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Microbial contamination in next generation sequencing: implications for sequence-based analysis of clinical samples</atitle><jtitle>PLoS pathogens</jtitle><addtitle>PLoS Pathog</addtitle><date>2014-11-01</date><risdate>2014</risdate><volume>10</volume><issue>11</issue><spage>e1004437</spage><epage>e1004437</epage><pages>e1004437-e1004437</pages><issn>1553-7374</issn><issn>1553-7366</issn><eissn>1553-7374</eissn><abstract>The high level of accuracy and sensitivity of next generation sequencing for quantifying genetic material across organismal boundaries gives it tremendous potential for pathogen discovery and diagnosis in human disease. 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| subjects | Bioinformatics Biology and Life Sciences Cancer Databases, Nucleic Acid Datasets DNA sequencing Equipment Contamination Genetic aspects Genetic research Genomes Health aspects High-Throughput Nucleotide Sequencing Host-parasite relationships Humans Infections - diagnosis Infections - genetics Laboratories Library collections Medicine and Health Sciences Microbial colonies Microbiological research Nucleotide sequencing Opinion Research and Analysis Methods Studies Viral infections |
| title | Microbial contamination in next generation sequencing: implications for sequence-based analysis of clinical samples |
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