Single-Molecule Rapid Imaging of Linear Genomes in Nanochannel Array
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Single-Molecule Rapid Imaging of Linear Genomes in Nanochannel Array M. D. Austin, P. Deshpande, M. Requa, M. Kunkel, H. Sadowski, D. Bozinov, J. Sibert, S. Gallagher, W. Stedman, N. Fernandes, A. Thomas, S. Das, A. Hastie, J. Finklestein, A. Marlin, M. Xiao, H. Cao Bionanomatrix, Inc. 3701 Market St, 4th floor Philadelphia, PA 19104, U.S.A. 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. INTRODUCTION The Importance of Structural Variation in the Human Genome: Human genomic structural variation (SV) is a significant factor in genome complexity that has substantial implications to the cause, development and progression of disease. Studies designed to specifically detect genomic variability between individuals including copy number repeats, segmental duplications, deletions, inversions and balanced translocations are discovering increasing numbers of SVs [1]. These SVs, generally within the size range of 1kbp-1Mbp, have been found to be common in both normal and diseased genomes and are now estimated to contribute to the majority of the genome’s variation [2,3]. In concert with this, it is becoming increasingly clear that the etiology of numerous diseases, including multiple forms of cancer, autism, schizophrenia, Crohn’s disease, autoimmune and neuro-behavioral degenerative disorders, are intimately linked to structural genomic variability. [4,5] Current technologies for assessing SVs: Various strategies have been developed to address genomic SVs. Next generation sequencing technologies which typically have read lengths of tens to hundreds of bases, have employed paired-end strategies to bridge SVs [4]. The end reads are mapped to a reference
genome and the number of bases between the sequenced ends in the reference genome are compared
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