Poster Presentation GENEMAPPERS 2024

 Oxford Nanopore adaptive sampling aka real-time sequence enrichment/depletion: our exploration of sample, wet-lab and bioinformatic considerations to optimise success.  (#89)

Leticia Castro 1 , Jane Clapham 1 , Donia Macartney-Coxson 1
  1. Environmental Science and Research Ltd., PORIRUA, WELLINGTON, New Zealand

We have explored the use of Oxford Nanopore adaptive sampling in the context of a clinical genetics research project. Focussing in particular on developing an understanding of the approach in order to minimize the time and resources required to acquire sufficient long read genome sequencing data over genomic regions of interest (ROI).  We have utilised adaptive sampling in ‘enrichment mode'. This allows us to select for ROIs at the time of acquisition, via real time alignment to a given reference and selection against a .bed file defining these ROI.  By designing a bespoke gene panel of relevant genes and optimising various wet lab and in-silico parameters, we have successfully implemented this approach for DNA extracted from both saliva and blood samples. We now have an optimised approach which regularly yields a >12-fold enrichment in our ROI, yielding adequate coverage for SNP calling (>= 30x) with <10GB of sequencing data per patient. This demonstrates the feasible utilisation of this technology, showing its potential as an accessible and cost-effective approach for variant discovery.