The DOI matches its Crossref record; 54 of the 54 references it cites were found in a registry or an index.
Mapping and phasing of structural variation in patient genomes using nanopore sequencing
Open accessAbstract
Despite improvements in genomics technology, the detection of structural variants (SVs) from short-read sequencing still poses challenges, particularly for complex variation. Here we analyse the genomes of two patients with congenital abnormalities using the MinION nanopore sequencer and a novel computational pipeline—NanoSV. We demonstrate that nanopore long reads are superior to short reads with regard to detection of de novo chromothripsis rearrangements. The long reads also enable efficient phasing of genetic variations, which we leveraged to determine the parental origin of all de novo chromothripsis breakpoints and to resolve the structure of these complex rearrangements. Additionally, genome-wide surveillance of inherited SVs reveals novel variants, missed in short-read data sets, a large proportion of which are retrotransposon insertions. We provide a first exploration of patient genome sequencing with a nanopore sequencer and demonstrate the value of long-read sequencing in mapping and phasing of SVs for both clinical and research applications.
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Cites
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Cited by
Opportunities and challenges in long-read sequencing data analysis
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Self-citationStructural variant calling: the long and the short of it
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Metadata
- Authors
- Cretu Stancu, M., van Roosmalen, M. J., Renkens, I., Nieboer, M. M., Middelkamp, S., de Ligt, J., Pregno, G., Giachino, D., Mandrile, G., Espejo Valle-Inclan, J., Korzelius, J., de Bruijn, E., Cuppen, E., Talkowski, M. E., Marschall, T., de Ridder, J., & Kloosterman, W. P.
- Venue
- Nature Communications
- Published
- 2017-11-06
- Volume
- 8
- Issue
- 1
- Pages
- 1326-1326
- ISSN
- 2041-1723 (ISSN-L)
- OpenAlex
- W2951149781
- Cited by
- 404
- References
- 54
- FWCI
- 22.59
- Type
- journal article
- Language
- en
- Open access
- gold
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- Cretu Stancu, M., van Roosmalen, M. J., Renkens, I., Nieboer, M. M., Middelkamp, S., de Ligt, J., Pregno, G., Giachino, D., Mandrile, G., Espejo Valle-Inclan, J., Korzelius, J., de Bruijn, E., Cuppen, E., Talkowski, M. E., Marschall, T., de Ridder, J., & Kloosterman, W. P. (2017). Mapping and phasing of structural variation in patient genomes using nanopore sequencing. Nature Communications. https://doi.org/10.1038/s41467-017-01343-4
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Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.
