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Project

LeapSEQ: Lean data processing solutions for adaptive and portable genome sequencing, applied to infectious disease monitoring.

Infectious diseases are becoming an increasing challenge to public health worldwide with urbanization, increased travel, climate change, habitat destruction, and deforestation fuelling local outbreaks and global spread. Metagenomic sequencing provides an attractive solution to identify all genomic material present in a patient sample without prior knowledge of the target. While metagenomic sequencing thus far relied on large, expensive and operationally demanding DNA-sequencers reserved for expert labs, the recent introduction of USB-stick sized nanopore sequencing devices offers an attractive portable and affordable solution for metagenomic sequencing in low-cost settings around the world. However for the context of pathogen detection, this technology still suffers from major data roadblocks in terms of data interpretation. In this strategic basic research project, we aim to remove significant roadblocks that stand between nanopore sequencing and its implementation for portable pathogen detection, characterisation and monitoring. These roadblocks include: (1) the reliance on expert bioinformatics skills to convert the sequencer data into interpretable results; (2) the lack of realtime interaction with the ongoing sequencing process; and (3) the selectivity challenge of detection low abundant pathogens within highly abundant host DNA. We will tackle these problems by implementing a Lean and Adaptive bioinformatics solution for Portable Sequencing ("LeapSEQ") based on in house developed data processing techniques. We will optimise and validate this tool with highly relevant infectious disease use cases together with strategic partners of ITM and UA and explore its valorisation potential in the context of global pathogen identification.
Date:1 Oct 2021 →  30 Sep 2023
Keywords:NANOPORE SEQUENCING, MACHINE LEARNING, DIAGNOSTICS, VIROLOGY
Disciplines:Analysis of next-generation sequence data, Development of bioinformatics software, tools and databases, Medical biotechnology diagnostics, Medical metagenomics