Readfish enables targeted nanopore sequencing of gigabase-sized genomes

Payne, Alexander; Holmes, Nadine; Clarke, Thomas; Munro, Rory; Debebe, Bisrat; Loose, Matthew

Abstract

© 2020, The Author(s), under exclusive licence to Springer Nature America, Inc. Nanopore sequencers can be used to selectively sequence certain DNA molecules in a pool by reversing the voltage across individual nanopores to reject specific sequences, enabling enrichment and depletion to address biological questions. Previously, we achieved this using dynamic time warping to map the signal to a reference genome, but the method required substantial computational resources and did not scale to gigabase-sized references. Here we overcome this limitation by using graphical processing unit (GPU) base-calling. We show enrichment of specific chromosomes from the human genome and of low-abundance organisms in mixed populations without a priori knowledge of sample composition. Finally, we enrich targeted panels comprising 25,600 exons from 10,000 human genes and 717 genes implicated in cancer, identifying PML–RARA fusions in the NB4 cell line in

Citation

Payne, A., Holmes, N., Clarke, T., Munro, R., Debebe, B., & Loose, M. (2021). Readfish enables targeted nanopore sequencing of gigabase-sized genomes. Nature Biotechnology, 39, 442-450. https://doi.org/10.1038/s41587-020-00746-x

• Journal Article Type: Article
• Acceptance Date: Oct 21, 2020
• Online Publication Date: Nov 30, 2020
• Publication Date: 2021-04
• Deposit Date: Oct 28, 2020
• Publicly Available Date: May 31, 2021
• Journal: Nature Biotechnology
• Print ISSN: 1087-0156
• Electronic ISSN: 1546-1696
• Publisher: Nature Publishing Group
• Peer Reviewed: Peer Reviewed
• Volume: 39
• Pages: 442-450
• DOI: https://doi.org/10.1038/s41587-020-00746-x
• Public URL: https://nottingham-repository.worktribe.com/output/3918923
• Publisher URL: https://www.nature.com/articles/s41587-020-00746-x