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Channeling DNA for optical mapping

Nature Biotechnology volume 30, pages 762–763 (2012)Cite this article

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Stretching DNA molecules in nanochannels allows structural and copy-number variations to be visualized like beads on a string.

Next-generation sequencing technologies are considered the state of the art in DNA analysis as they provide single-base resolution on a whole-genome scale. But any sequencing approach that assembles a genome sequence from billions of short reads has certain inherent technical limitations. Repetitive genomic regions, which account for half of the human genome, cannot be directly mapped1, and technologies that rely on ensemble measurements are unable to detect rare genomic variations or small subpopulations, which are increasingly recognized as important for assessing disease states and progression2. In this issue, Lam et al.3 introduce a new method for high-throughput mapping of long, single DNA molecules that has the potential to address these issues and is amenable to routine whole-genome analysis and clinical applications. By fluorescently labeling DNA at specific sequences4, the authors create a distinctive optical pattern resembling a barcode that uniquely identifies the DNA fragment under observation. This pattern provides access to long-range sequence information, albeit at relatively low resolution, that depends on the density of labels and on the limits of optical resolution. The authors show that this resolution is sufficient to provide a scaffold for de novo assembly of sequencing data and to identify haplotype differences and structural variants, such as deletions and duplications, in the highly variable human major histocompatibility complex (MHC) region.

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Figure 1: Optical mapping with nanochannels.

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Affiliations

  1. Yael Michaeli & Yuval Ebenstein are in the School of Chemistry, The Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv, Israel.

    Yael Michaeli & Yuval Ebenstein

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  1. Yael Michaeli
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  2. Yuval Ebenstein
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Correspondence to Yael Michaeli.

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The authors declare no competing financial interests.

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Michaeli, Y., Ebenstein, Y. Channeling DNA for optical mapping. Nat Biotechnol 30, 762–763 (2012). https://doi.org/10.1038/nbt.2324

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