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Nanopore Sequencing in a Clinical Routine Laboratory: Challenges and Opportunities by Jonas Schmidt, Frithjof Blessing, Lea Fimpler, Folker Wenzel

Background: About forty-five years ago the advent of Sanger sequencing (Sanger and Coulson 1975) was revolutionary as it allowed deciphering of complete genome sequences. A second revolution came when next-generation sequencing (NGS) technologies accelerated and cheapened genome sequencing. Recently, third generation/longread sequencing methods have appeared, which can directly detect epigenetic modifications on native DNA and allow whole-transcript sequencing without the need for assembly. Nanopore sequencing is one of these third-generation approaches, enabling a single molecule of DNA or RNA to be sequenced in real-time without the need for PCR amplification or chemical labelling of the sample. It works by monitoring changes to an electrical current as nucleic acids are passed through protein or synthetic nanopores.
Methods: A literature search was performed in order to collect and summarize current information about the methodological aspects of nanopore sequencing as well as some application examples.
Results: The review describes concisely and comprehensibly the technical aspects of nanopore sequencing and stresses the advantages and disadvantages of this technique thereby also giving examples of their potential applications in the clinical routine laboratory as are rapid identification of viral pathogens, monitoring Ebola, environmental and food safety monitoring, human and plant genome sequencing, monitoring of antibiotic resistance, and other applications.
Conclusions: It is a useful incitation for such ones being permanently in search of upgrading their laboratory.

DOI: 10.7754/Clin.Lab.2019.191114