Channeling DNA for optical mapping

Abstract

volume 30 number 8 AuGuST 2012 nature biotechnology 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. e-mail: uv@post.tau.ac.il they require considerable expertise and have relatively low throughput. A key feature of the method reported by Lam et al.3 is the use of mass-produced arrays of silicon nanochannels read by a commercially available microscopy platform, which allows the data acquisition procedure to be standardized and made accessible to the wider biological community. To achieve high throughput, the authors linearize DNA molecules by squeezing them through the nanochannels using electrokinetic flow, followed by optical imaging of thousands of stretched molecules (Fig. 1). stretched and deposited on modified glass surfaces for imaging. Sequence information was labeled by hybridization of complementary probes or by creating sequence-specific gaps in the stretched DNA using restriction enzymes. These methods have been used to study genetic rearrangements, map genes for positional cloning and improve the assemblies of many largescale sequencing projects for both microbial and eukaryotic genomes. Despite impressive scientific results, the methods are not widely used and are practiced mainly by the laboratories that developed them, mostly because 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. The idea of stretching single genomic DNA molecules to a linear form for optical genetic readout has been around for nearly 20 years5,6. Traditionally, DNA molecules have been Channeling DNA for optical mapping

DOI: 10.1038/nbt.2324

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Cite this paper

@article{Michaeli2012ChannelingDF, title={Channeling DNA for optical mapping}, author={Yael Michaeli and Yuval Ebenstein}, journal={Nature Biotechnology}, year={2012}, volume={30}, pages={762-763} }