The DOI matches its Crossref record; 34 of the 34 references it cites were found in a registry or an index.
Genome mapping on nanochannel arrays for structural variation analysis and sequence assembly
Open accessAbstract
We describe genome mapping on nanochannel arrays. In this approach, specific sequence motifs in single DNA molecules are fluorescently labeled, and the DNA molecules are uniformly stretched in thousands of silicon channels on a nanofluidic device. Fluorescence imaging allows the construction of maps of the physical distances between occurrences of the sequence motifs. We demonstrate the analysis, individually and as mixtures, of 95 bacterial artificial chromosome (BAC) clones that cover the 4.7-Mb human major histocompatibility complex region. We obtain accurate, haplotype-resolved, sequence motif maps hundreds of kilobases in length, resulting in a median coverage of 114× for the BACs. The final sequence motif map assembly contains three contigs. With an average distance of 9 kb between labels, we detect 22 haplotype differences. We also use the sequence motif maps to provide scaffolds for de novo assembly of sequencing data. Nanochannel genome mapping should facilitate de novo assembly of sequencing reads from complex regions in diploid organisms, haplotype and structural variation analysis and comparative genomics.
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Cites
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome.
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Cited by
Coming of age: ten years of next-generation sequencing technologies
Goodwin, S., McPherson, J. D., & McCombie, W. R. (2016) · Nature Reviews Genetics · doi:10.1038/nrg.2016.49 · Cited by 4,352
A chromosome conformation capture ordered sequence of the barley genome
Mascher, M., Gundlach, H., Himmelbach, A., Beier, S., Twardziok, S. O., Wicker, T., Radchuk, V., Dockter, C., Hedley, P. E., Russell, J., et al. (2017) · Nature · doi:10.1038/nature22043 · Cited by 1,450
Self-citationChromosome-scale scaffolding of de novo genome assemblies based on chromatin interactions
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The Third Revolution in Sequencing Technology
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The genome of Chenopodium quinoa
Jarvis, D. E., Ho, Y. S., Lightfoot, D. J., Schmöckel, S. M., Li, B., Borm, T. J. A., Ohyanagi, H., Mineta, K., Michell, C. T., Saber, N., et al. (2017) · Nature · doi:10.1038/nature21370 · Cited by 719
Metadata
- Authors
- Lam, E. T., Hastie, A., Lin, C., Ehrlich, D., Das, S. K., Austin, M. D., Deshpande, P., Cao, H., Nagarajan, N., Xiao, M., & Kwok, P.-Y.
- Venue
- Nature Biotechnology
- Published
- 2012-07-15
- Volume
- 30
- Issue
- 8
- Pages
- 771-776
- ISSN
- 0733-222X (ISSN-L)
- 1087-0156
- 1546-1696
- OpenAlex
- W2012012446
- Cited by
- 647
- References
- 34
- FWCI
- 13.01
- Type
- journal article
- Language
- en
- Open access
- bronze
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- Lam, E. T., Hastie, A., Lin, C., Ehrlich, D., Das, S. K., Austin, M. D., Deshpande, P., Cao, H., Nagarajan, N., Xiao, M., & Kwok, P.-Y. (2012). Genome mapping on nanochannel arrays for structural variation analysis and sequence assembly. Nature Biotechnology. https://doi.org/10.1038/nbt.2303
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