Next-generation sequencing platforms have fundamentally altered genetic diagnostics and genomic research by providing massive amounts of sequence data in a low-cost, high-throughput format. A major drawback of short sequence read platforms is their inability to resolve complex genomic regions. Long sequence read platforms can overcome this issue, but existing methods for sequence enrichment are unable to provide the large fragments required to analyze confounding sequence elements at important loci, such as determination of structural and copy number variation in complex genomic regions associated with human disease. The goal of this Phase I proposal is to demonstrate the feasibility of using Varigen's amplification-free ?DNATrap? method to isolate complex and problematic genomic regions of ~10-100 kb from human, rat and macaque genomes. This platform-independent, sequence-specific enrichment technology will provide full-length epigenetic sequence analysis of these regions, providing the basis to replace multiple molecular assays presently used for genetic testing. Development of the proposed technology will enable isolation and full-length sequencing of any genomic region, whether simple or complex, providing valuable long range haplotype-resolved information of disease genes for research or diagnostic applications. Long-term goals of this project in Phase II are to develop and validate diagnostic tests for the disease regions studied in Phase I.
Project Terms: accurate diagnosis; Achievement; Alleles; AT Rich Sequence; base; Biological Assay; Biological Sciences; Biotechnology; Cells; Clinical; clinical application; clinical sequencing; Clustered Regularly Interspaced Short Palindromic Repeats; Complex; Copy Number Polymorphism; cost; CYP2D6 gene; Data; Development; Diagnosis; Diagnostic; Diagnostic Procedure; Diagnostic tests; Disease; disease diagnosis; DNA; DNA sequencing; drug discovery; Elements; Enzymes; Epigenetic Process; Eukaryotic Cell; Excision; Fragile X Syndrome; Gene Targeting; gene therapy; Genes; Genetic; Genetic Diseases; Genetic screening method; Genome; Genomic DNA; Genomic Segment; genomic variation; Genomics; Goals; Haplotypes; Hour; Human; human disease; Human Genome; human tissue; improved; In Vitro; innovation; insertion/deletion mutation; Intellectual Property; interest; Interview; Legal patent; Length; Libraries; Macaca; medical schools; Medicine; member; Methods; microbial genome; Mitochondria; mitochondrial genome; Modeling; Modification; Molecular; Multigene Family; Mutation; next generation sequencing; novel; Patient-Focused Outcomes; Phase; platform-independent; Pseudogenes; rat genome; Rattus; Reagent; Research; Research Personnel; Sampling; Scientist; Sequence Analysis; Sequence Determination; sequencing platform; Services; Small Business Innovation Research Grant; Special Equipment; System; Technology; technology development; Testing; Time; tissue culture; Tissue Sample; tool; Universities; Variant; Viral Oncogene; Wisconsin;
