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.
Current methods for diagnostic DNA sequencing are unable to resolve complex genomic loci, because they cannot target the large, complex fragments required to span confounding sequences, necessitating the use of multiple assays to accurately diagnose disease genes. We will fill this unmet need with the development of an innovative tool to rapidly and affordably capture and sequence full-length targeted segments up to 100 kb of human and microbial genomes associated with disease. This achievement will significantly improve the ability of researchers and clinicians to obtain complete and accurate characterization and diagnosis of complex genomic variations associated with human disease.
