Bioinformatics for Portable Sequencing Technologies

Third-generation sequencing technologies –including Oxford Nanopore’s MinION and SmidgION– are revolutionizing again biomedical sciences by combining large throughput with miniaturization and portability. A sequencer now fits the palm of a hand and plugs directly into a smartphone, ready for on-site, real-time genomic applications. Proof-of-concept studies showed how they can be used with rapid turnaround time (<40 minutes) to screen for Escherichia coli, Salmonella, and many other organisms.

Portability is necessary in many circumstances that require on-site, real-time examination of environmental samples. One such need is identification of pathogen and antimicrobial resistance (AMR) in hospitals and healthcare facilities, especially in rural settings, when even a turnaround of a few hours can make the difference (e.g. if a p

atient goes to sepsis or in case of life-threatening food intoxication). AMR is  an  increasingly  serious  threat  to  global  public  health since  it  causes  standard  treatments  (e.g.  antibiotics)  to  be  ineffective,  and  outbreaks  become more  frequent,  wide-spread,  and  severe.

However, while a nanopore sequencer now connects to a smartphone, data analysis is not available on the device and needs both high-speed wireless communication to transfer data and a dedicated cloud computing service for analyses. Therefore, real-time on-site analytics is not feasible yet. The goal of this project is to create mobile bioinformatics methods  for on-site, real-time detection of pathogens and AMR using nanopore technology. Currently there is no software for portable devices running independently from the cloud: as a result, there are no applications that fit the smart-connected-health (SCH) paradigm: NanoSMART aims to bridge such technology gap. Major challenges include the size of the sequencing data (20+GB) and the physical stress that a smartphone/tablet is subject to during intensive usage (e.g. overheating, battery life).

This proposal further brings advancement in colored succinct de Bruijn graphs for more efficient metagenomics assembly and indexing of genetic signatures, as well as user-centered design of interfaces. Therefore, the specific objectives are to: (1) Create methods  to  identify and quantify  bacteria  in  a  sample by (1.1) developing a real-time portable nanopore bacterial 16S gene mapper and (1.2) testing on recently generated data from outbreaks; (2) Create methods for AMR characterization (including new AMR signature discovery); (3) Incorporate  user-centered  design  principles to  develop  and  evaluate  a  graphical  user  interface  for NanoSMART.

The investigative team greatly appreciates the funding they receive for this project from NSF SCH.

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