Third-Generation Sequencing in the Clinical Laboratory: Exploring the Advantages and Challenges of Nanopore Sequencing

ABSTRACT Metagenomic sequencing for infectious disease diagnostics is an important tool that holds promise for use in the clinical laboratory. Challenges for implementation so far include high cost, the length of time to results, and the need for technical and bioinformatics expertise. However, the recent technological innovation of nanopore sequencing from Oxford Nanopore Technologies (ONT) has the potential to address these challenges. ONT sequencing is an attractive platform for clinical laboratories to adopt due to its low cost, rapid turnaround time, and user-friendly bioinformatics pipelines. However, this method still faces the problem of base-calling accuracy compared to other platforms. This review highlights the general challenges of pathogen detection in clinical specimens by metagenomic sequencing, the advantages and disadvantages of the ONT platform, and how research to date supports the potential future use of nanopore sequencing in infectious disease diagnostics.

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A Rapid and Low-Cost PCR Thermal Cycler for Infectious Disease Diagnostics

PLoS ONE ◽

10.1371/journal.pone.0149150 ◽

2016 ◽

Vol 11 (2) ◽

pp. e0149150 ◽

Cited By ~ 23

Author(s):

Kamfai Chan ◽

Pui-Yan Wong ◽

Peter Yu ◽

Justin Hardick ◽

Kah-Yat Wong ◽

...

Keyword(s):

Infectious Disease ◽

Low Cost ◽

Disease Diagnostics ◽

Infectious Disease Diagnostics ◽

Thermal Cycler

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Nanopore Sequencing: The New Frontline of Infectious Disease Diagnostics

Clinical OMICs ◽

10.1089/clinomi.02.07.04 ◽

2015 ◽

Vol 2 (7) ◽

pp. 8-11

Author(s):

Jeff Buguliskis

Keyword(s):

Infectious Disease ◽

Nanopore Sequencing ◽

Disease Diagnostics ◽

Infectious Disease Diagnostics

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A highly multiplexed broad pathogen detection assay for infectious disease diagnostics

PLoS Neglected Tropical Diseases ◽

10.1371/journal.pntd.0006889 ◽

2018 ◽

Vol 12 (11) ◽

pp. e0006889 ◽

Cited By ~ 6

Author(s):

Jeffrey W. Koehler ◽

Christina E. Douglas ◽

Timothy D. Minogue

Keyword(s):

Infectious Disease ◽

Pathogen Detection ◽

Detection Assay ◽

Disease Diagnostics ◽

Infectious Disease Diagnostics

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Clinical laboratory applications of monoclonal antibodies.

Clinical Microbiology Reviews ◽

10.1128/cmr.1.3.313 ◽

1988 ◽

Vol 1 (3) ◽

pp. 313-329 ◽

Cited By ~ 32

Author(s):

W J Payne ◽

D L Marshall ◽

R K Shockley ◽

W J Martin

Keyword(s):

Infectious Disease ◽

Clinical Microbiology ◽

Clinical Laboratory ◽

Test System ◽

Significant Development ◽

Advantages And Disadvantages ◽

Antibody Assays ◽

Hybridoma Technology ◽

Immunological Assays ◽

The Impact

Monoclonal antibody (MAb) technology is well recognized as a significant development for producing specific serologic reagents to a wide variety of antigens in unlimited amounts. These reagents have provided the means for developing a number of highly specific and reproducible immunological assays for rapid and accurate diagnosis of an extensive list of diseases, including infectious diseases. The impact that MAbs have had in characterizing infectious disease pathogens, as well as their current and future applications for use in clinical microbiology laboratories, is reviewed. In addition, the advantages (and disadvantages) of the use of MAbs in a number of immunoassays, such as particle agglutination, radioimmunoassays, enzyme-linked immunosorbent assays, immunofluorescent-antibody assays, and immunohistology, are explored, including the use of these reagents in novel test system assays. Also, nucleic acid probe technology is compared with the use of MAbs from the perspective of their respective applications in the diagnosis of infectious disease agents. There is no question that hybridoma technology has the potential to alter significantly the methods currently used in most clinical microbiology laboratories.

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