Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2017 Sep;23(9):1441-1445.
doi: 10.3201/eid2309.170416.

Bioinformatic Analyses of Whole-Genome Sequence Data in a Public Health Laboratory

Kelly F Oakeson, Jennifer Marie Wagner, Michelle Mendenhall, Andreas Rohrwasser, Robyn Atkinson-Dunn

Bioinformatic Analyses of Whole-Genome Sequence Data in a Public Health Laboratory

Kelly F Oakeson et al. Emerg Infect Dis. 2017 Sep.

Abstract

The ability to generate high-quality sequence data in a public health laboratory enables the identification of pathogenic strains, the determination of relatedness among outbreak strains, and the analysis of genetic information regarding virulence and antimicrobial-resistance genes. However, the analysis of whole-genome sequence data depends on bioinformatic analysis tools and processes. Many public health laboratories do not have the bioinformatic capabilities to analyze the data generated from sequencing and therefore are unable to take full advantage of the power of whole-genome sequencing. The goal of this perspective is to provide a guide for laboratories to understand the bioinformatic analyses that are needed to interpret whole-genome sequence data and how these in silico analyses can be implemented in a public health laboratory setting easily, affordably, and, in some cases, without the need for intensive computing resources and infrastructure.

Keywords: Utah; antimicrobial resistance; bioinformatics; genes; genome; genomics; infectious diseases; next-generation sequencing; public health laboratory; whole-genome sequencing.

PubMed Disclaimer

Figures

Figure
Figure
Steps in the bioinformatics pipeline implemented at Utah Public Health Laboratory.
See this image and copyright information in PMC

References

    1. Koboldt DC, Steinberg KM, Larson DE, Wilson RK, Mardis ER. The next-generation sequencing revolution and its impact on genomics. Cell. 2013;155:27–38. 10.1016/j.cell.2013.09.006 - DOI - PMC - PubMed
    1. Bahassi M, Stambrook PJ. Next-generation sequencing technologies: breaking the sound barrier of human genetics. Mutagenesis. 2014;29:303–10. 10.1093/mutage/geu031 - DOI - PMC - PubMed
    1. Scharff RL, Besser J, Sharp DJ, Jones TF, Peter G-S, Hedberg CW. An economic evaluation of PulseNet: a network for foodborne disease surveillance. Am J Prev Med. 2016;50(Suppl 1):S66–73. 10.1016/j.amepre.2015.09.018 - DOI - PubMed
    1. Swaminathan B, Barrett TJ, Hunter SB, Tauxe RV; CDC PulseNet Task Force. PulseNet: the molecular subtyping network for foodborne bacterial disease surveillance, United States. Emerg Infect Dis. 2001;7:382–9. 10.3201/eid0703.017303 - DOI - PMC - PubMed
    1. Afgan E, Baker D, van den Beek M, Blankenberg D, Bouvier D, Čech M, et al. The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update. Nucleic Acids Res. 2016;44(W1):W3–10. 10.1093/nar/gkw343 - DOI - PMC - PubMed

MeSH terms

LinkOut - more resources