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PLoS Pathog. 2014 Nov 20;10(11):e1004437. doi: 10.1371/journal.ppat.1004437. eCollection 2014 Nov.

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

Author information

1
Department of Pathology, Tulane University, New Orleans, Louisiana, United States of America; Tulane Cancer Center, Tulane University, New Orleans, Louisiana, United States of America.
2
Department of Genomic Medicine, University of California, San Diego, California, United States of America.
3
Department of Microbiology and Immunology, Tulane University, New Orleans, Louisiana, United States of America.
4
University of Wisconsin Biotechnology Center, University of Wisconsin, Madison, Wisconsin, United States of America.
5
Department of Microbiology, Immunology & Parasitology, Louisiana State University School of Medicine, New Orleans, Louisiana, United States of America; Research Institute for Children, Children's Hospital of New Orleans, New Orleans, Louisiana, United States of America.

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.

PMID:
25412476
PMCID:
PMC4239086
DOI:
10.1371/journal.ppat.1004437
[Indexed for MEDLINE]
Free PMC Article

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