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Wednesday, August 2 • 10:00 - 11:00
Real-time nanopore sequencing and data analysis: in the field and by the patient

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In this talk I will examine the role of portable, real-time genome sequencing for the diagnosis and surveillance of infectious diseases. I will focus on the Oxford Nanopore MinION single molecule nanopore sequencing instrument for understanding the evolution and biology of pathogens. Since its release in mid-2014, this instrument has seen rapid platform improvements and is now capable of generating ~10 gigabases per run with a read error rate of ~10%. During the 2013-2016 Ebola epidemic we deployed nanopore sequencing to West Africa to track Ebola virus evolution. In 2016, in response to the Zika epidemic in the Americas we established a mobile sequencing laboratory that travelled through Brazil to understand the spread of Zika. Initially we have focused on virus applications but as the output of the nanopore sequencer has increased, bacterial whole genome assembly has become routine, even in field situations. Recently we were part of a group that sequenced a whole human genome on the MinION and developed a new protocol for generating up to 1 megabase single reads, significantly reducing complexity of de novo assembly. The nanopore platform permits detection of methylation and base modifications and can also sequence RNA directly, important in pathogen biology. I will discuss the bioinformatics challenges associated with working on this platform and the opportunities for near-patient ubiquitous genome sequencing on our ability to fight infectious diseases.

avatar for Nick Loman

Nick Loman

Ph.D., Independent Research Fellow, Institute of Microbiology and Infection, University of Birmingham

Wednesday August 2, 2017 10:00 - 11:00
Graduate School of Management Building, room 309 Volkhovskiy Pereulok, 3, St. Petersburg, Russia