2-AIN-506 a 2-AIN-252: Seminár z bioinformatiky (2) a (4)
Leto 2021

Alexander Payne, Nadine Holmes, Thomas Clarke, Rory Munro, Bisrat Debebe, Matthew Loose. Nanopore adaptive sequencing for mixed samples, whole exome capture and targeted panels. Technical Report bioRxiv, 10.1101/2020.02.03.926956,

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Nanopore sequencers enable selective sequencing of single molecules in 
real time by individually reversing the voltage across specific nanopores. 
Thus DNA molecules can be rejected and replaced with new molecules 
enabling targeted sequencing to enrich, deplete or achieve specific 
coverage in a set of reads to address a biological question. We previously 
demonstrated this method worked using dynamic time warping mapping signal 
to reference, but required significant compute and did not scale to 
gigabase references. Using direct base calling with GPU we can now scale 
to gigabase references. We enrich for specific chromosomes mapping against 
the human genome and we develop pipelines enriching low abundance 
organisms from mixed populations without prior knowledge of sample 
composition. Finally, we enrich panels including 25,600 exon targets from 
10,000 human genes and 717 genes implicated in cancer. Using this approach 
we identify PML-RARA fusions in the NB4 cell line in under 15 hours 
sequencing. These methods can be used to efficiently screen any target 
panel of genes without specialised sample preparation using a single 
computer and suitably powerful GPU.