The DOI matches its Crossref record; 30 of the 30 references it cites were found in a registry or an index.
Readfish enables targeted nanopore sequencing of gigabase-sized genomes
Open accessAbstract
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 <15 h sequencing. These methods can be used to efficiently screen any target panel of genes without specialized sample preparation using any computer and a suitable GPU. Our toolkit, readfish, is available at https://www.github.com/looselab/readfish. A nanopore sequencer achieves selective sequencing of any region in the human genome.
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Cites
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Next-generation sequencing technologies: An overview
Hu, T., Chitnis, N., Monos, D., & Dinh, A. (2021) · Human Immunology · doi:10.1016/j.humimm.2021.02.012 · Cited by 949
Towards population-scale long-read sequencing
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Biases in bulk: DNA metabarcoding of marine communities and the methodology involved
van der Loos, L. M., & Nijland, R. (2021) · Molecular Ecology · doi:10.1111/mec.15592 · Cited by 268
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Metadata
- Authors
- Payne, A., Holmes, N., Clarke, T., Munro, R., Debebe, B. J., & Loose, M.
- Venue
- Nature Biotechnology
- Published
- 2020-11-30
- Volume
- 39
- Issue
- 4
- Pages
- 442-450
- ISSN
- 0733-222X (ISSN-L)
- 1087-0156
- 1546-1696
- OpenAlex
- W3107212993
- Cited by
- 408
- References
- 30
- FWCI
- 14.59
- Type
- journal article
- Language
- en
- Open access
- green
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- Payne, A., Holmes, N., Clarke, T., Munro, R., Debebe, B. J., & Loose, M. (2021). Readfish enables targeted nanopore sequencing of gigabase-sized genomes. Nature Biotechnology. https://doi.org/10.1038/s41587-020-00746-x
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