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Microbial contamination in next generation sequencing: implications for sequence-based analysis of clinical samples.

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. 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.

SUBMITTER: Strong MJ

PROVIDER: S-EPMC4239086 | biostudies-literature | 2014 Nov

REPOSITORIES: biostudies-literature

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Microbial contamination in next generation sequencing: implications for sequence-based analysis of clinical samples.

Strong Michael J MJ Xu Guorong G Morici Lisa L Splinter Bon-Durant Sandra S Baddoo Melody M Lin Zhen Z Fewell Claire C Taylor Christopher M CM Flemington Erik K EK

PLoS pathogens 20141120 11

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 mic ...[more]

PMID: 25412476

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