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

Michael J Strong1, Guorong Xu2, Lisa Morici3

  • 1Department of Pathology, Tulane University, New Orleans, Louisiana, United States of America; Tulane Cancer Center, Tulane University, New Orleans, Louisiana, United States of America.

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Next-generation sequencing offers high accuracy for pathogen discovery. However, bacterial contamination in human RNA-seq data necessitates strict protocols for reliable microbial signature analysis in clinical samples.

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Area of Science:

  • Genomics
  • Microbiology
  • Clinical Diagnostics

Background:

  • Next-generation sequencing (NGS) provides accurate quantification of genetic material.
  • NGS has significant potential for pathogen discovery and diagnosis in human diseases.
  • Existing human RNA-seq datasets often contain substantial bacterial contamination from environmental sources.

Purpose of the Study:

  • To highlight the potential of NGS for pathogen discovery.
  • To address the issue of bacterial contamination in human RNA-seq data.
  • To emphasize the need for stringent protocols in clinical sample analysis.

Main Methods:

  • Review of existing human-derived RNA-seq datasets.
  • Analysis of bacterial contamination sources.
  • Assessment of NGS accuracy and sensitivity.

Main Results:

  • NGS demonstrates high accuracy and sensitivity in quantifying genetic material.
  • Significant bacterial contamination is a common issue in human RNA-seq datasets.
  • Environmental sources are likely contributors to this contamination.

Conclusions:

  • Stringent sequencing and analysis protocols are crucial for studies involving clinical samples.
  • Addressing bacterial contamination is essential for accurate sequence-based microbial signature investigations.
  • The potential of NGS for pathogen discovery requires careful data handling to ensure reliability.