New Physical Methodologies for Genomic Analysis

University Of Wisconsin-Madison, Madison WI

Investigators

Linked publications & trials

Abstract

DESCRIPTION (provided by applicant): The broad, long term objectives of this proposal are to develop a high-throughput platform for single molecule analysis capable of acquiring large datasets for human genomic analysis commensurate with next generation sequencing. The research proposed aims to integrate robust devices for genome analysis with equally robust biochemical and detection schemes. This high-throughput system, "Nanocoding," will feature disposable devices offering "effective" nanoscale geometries within disposable devices sufficiently small for the presentation of large elongated genomic DNA molecules, for the advancement of whole genome studies as a means for analysis of populations and cancer genomes. The research plan proposes to create disposable silastic devices with nanoconfinement capabilities that closely parallel those found in sub-100 nm devices requiring traditional lithographic approaches. A new single molecule labeling scheme has been shown to introduce fluorochome label at specific sites on genomic DNAs - and offers distinct advantages for robust detection and integration within a system for genome analysis. The aims focus on presentation, decoration and visualization of single genomic DNA molecules, and potentiate a nanoslit device based on physical modification of large single DNA molecules. The Research Plan describes new developments enabling the Nanocoding system to complete a high-resolution scan in 1-7 days (projected) allowing comprehensive discovery of structural variation within a human genome. This analysis capacity will be extended through software developments for melding and complementing the short comings of next generation sequencing platforms, thus allowing more comprehensive discernment of structural polymorphisms and aberrations. Integration of experimental studies with computational and simulation approaches as well as associated bioinformatic approaches lend promise to make Nanocoding robust and applicable to genome-wide analysis across human populations and cancer samples. PUBLIC HEALTH RELEVANCE: A new single molecule platform, Nanocoding, will be developed for cost-effective analysis of human populations for pinpointing genetic differences. Successful development and wide use of Nanocoding will identify a broad range of genetic differences that will span from entire chromosomes to regions smaller than a gene. These advances will foster large-scale human population studies that will power new drug discoveries, diagnostics, and perhaps, meaningful personal genomic profiles.