The long term objective of this proposal is to develop a fully integrated nanochannel chip and reader capable of single molecule mapping of linearized, long genomic material. The anticipated embodiment will permit direct visualization and analysis of megabase fragments of DNA extracted directly from a sample (possibly a single cell) with sub-kilobase resolution. Furthermore, the chip will accommodate massively parallel analyses of individual DNA molecules to permit standardized, high-throughput mapping of sequence motifs or polymorphic sites along the DNA. We propose a barcoding strategy (chip, reader and assay) for single DNA molecules. Our barcoding strategy is based on direct fluorescent imaging and localization of multiple sequence motifs or polymorphic sites along a linearized DNA molecule. Such capabilities will transform biological analyses, permitting highly sensitive detection of genetic loci for genome wide association studies, especially where haplotype information is required. In addition, mapping of pathogen genomes can also be performed. A critical consideration for the commercialization of this device is the consistent linearization and imaging of individual DNA molecules such that high resolution mapping of labeled sites can be performed. In light of this requirement, we propose a nanofluidic device in which individual DNA molecules are streamed and linearized in massively parallel nanoscale channels. The advantage of a nanochannel device is that DNA can be linearized in a standardized and repeatable manner due to the physical confinement of molecules within the channel. During linearization, the DNA is fluorescently imaged using a high resolution microscopy system thus permitting spatial mapping of site-specific fluorescent labels. Completion of this project will result in a chip, imaging system and assay for mapping sequence motifs and polymorphic sites along single molecules of DNA with 800 bp resolution. Such a device will transform and enhance our understanding of genetic diseases by providing crucial haplotype information. The device can be further extended to provide additional information regarding structural variations in the genome such as copy number variations and translocations.
Thesaurus Terms: Adenoviridae; Adenoviruses; Assay; Bioassay; Biologic Assays; Biological; Biological Assay; Cnp; Caliber; Cell Communication And Signaling; Cell Signaling; Cells; Complex; Copy Number Polymorphism; Dna; Dna Mapping; Data; Deoxyribonucleic Acid; Detection; Devices; Diagnostic; Diameter; Disease; Disease Model; Disorder; Environment; Exons; Gwas; Genes; Genetic; Genetic Condition; Genetic Diseases; Genome; Genomics; Goals; Haplotypes; Health Care Industry; Healthcare Industry; Hereditary Disease; Image; Imagery; Imaging Procedures; Imaging Techniques; Individual; Industry, Healthcare; Intervening Sequences; Intracellular Communication And Signaling; Introns; Label; Lead; Light; Maps; Methods; Microscopy; Molecular Disease; Pb Element; Phase; Photoradiation; Position; Positioning Attribute; Reader; Resolution; Sampling; Signal Transduction; Signal Transduction Systems; Signaling; Site; Solid; Stream; Stretching; Surface; System; System, Loinc Axis 4; Technics, Imaging; Testing; Variant; Variation; Visualization; Base; Biological Signal Transduction; Commercialization; Copy Number Variation; Design; Designing; Disease/Disorder; Disorder Model; Fluorophore; Genetic Disorder; Genome Wide Association Scan; Genome Wide Association Studies; Genome Wide Association Study; Genome-Wide Scan; Genomewide Association Scan; Genomewide Association Studies; Genomewide Association Study; Genomewide Scan; Heavy Metal Pb; Heavy Metal Lead; Hereditary Disorder; High Throughput Analysis; Imaging; Improved; Instrument; Nano Channel; Nano Fluidic; Nano Meter Scale; Nano Meter Sized; Nano Scale; Nanochannel; Nanofluidic; Nanometer Scale; Nanometer Sized; Nanoscale; Pathogen; Scale Up; Single Molecule; Whole Genome Association Studies; Whole Genome Association Study
