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Single-Molecule Rapid Imaging of Linear Genomes in Nanochannel Array

  • M. D. Austin (a1), P. Deshpande (a1), M. Requa (a1), M. Kunkel (a1), H. Sadowski (a1), D. Bozinov (a1), J. Sibert (a1), S. Gallagher (a1), W. Stedman (a1), N. Fernandes (a1), A. Thomas (a1), S. Das (a1), A. Hastie (a1), J. Finklestein (a1), A. Marlin (a1), M. Xiao (a1) and H. Cao (a1)...

Abstract

Human genomic structural variation (SV) is significant factor in genome complexity, and thus has substantial implications to the cause, development and progression of genetic diseases. These SVs, ranging in size of 1kbp-1Mbp, are challenging to assess with current technologies. As such, we have developed a commercial system (nanoAnalyzer® 1000) for the rapid linear analysis of genomes at single-molecule level.

The core of our system is a nanofluidic chip consisting of an array of channels with a diameter less than 100 nm, nanofabricated on the surface of a silicon substrate. Thousands of unamplified genomic DNA molecules of 100’s kbps to several Mbps can be isolated and linearly streamed into the array for analysis in a parallel fashion. Fluorescently labeled sequence-specific signatures can then be identified and aligned to reference patterns at high resolution with custom software. This automated, multi-color imaging platform will enable a wide range of applications, such as accurate sequencing assembly, discovering genome structural variations, and uncovering epigenomic content. Nanochannel arrays promise to substantially lower the barriers of entry for single-molecule DNA analysis for scientists and clinicians, greatly impacting the advancement of molecular diagnostics, personalized medicine, and biomedical research.

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