Research in the Loman group, which has developed new methods for rapidly and accurately generating whole-genome sequences of microbial genomes in austere, ‘field’ environments, has underpinned its impact throughout.
Rapid technical advances in ‘next-generation sequencing’ approaches have increased sequencing output whilst reducing the size of sequencing instruments. In the past 10 years this has increased access to genome sequencing for academic and clinical researchers. This has resulted in the development of the MinION sequencer by UK spin-out Oxford Nanopore Technologies Ltd. This “pocket sequencer” weighs <100 grams, costs $1000 and is powered by the USB port of a standard laptop. The MinION was released to the first early access users in May 2014.
Nick Loman (Independent Research Fellow 2014-2017 at University of Birmingham and subsequently Professor of Microbial Genomics and Bioinformatics) rapidly recognised the potential of this technology. However, when released, the technology was extremely hard to operate, documentation was limited and it had virtually no software support.
The Loman group were the first to generate and publish usable data of any type from this technology in June 2014 (demonstrating recognition of the serotype-determining region of Pseudomonas aeruginosa - also the first demonstration of the translational potential for this device, in June 2014). The group then tested the device on a large hospital outbreak of Salmonella enterica confirming its use to rapidly assign molecular types. Loman thus recognised that portable nanopore sequencing could have profound effects on wider access to genome sequencing technology and thus be vital for management of outbreaks of infectious diseases.
At release there were no bioinformatics approaches available for handling the long, “noisy” (error-prone) reads generated by this platform. To address this need, Loman developed (with Aaron Quinlan, University of Utah) a package for initial handling of nanopore data, an open-source software tool called Poretools (Loman and Quinlan 2014) which became heavily used.