The advent of next-generation sequencing (NGS) technologies has allowed researchers to make unprecedented progress in the analysis of genomes, the results of which have profound implications in the realms of human health, agricultural productivity, and (natural history). The ability to fully characterize genomes remains unrealized however due in large part to our inability to reconcile sequence information over long distances. Short fragmented DNA libraries and their subsequent alignment to reference genomes, while highly useful in identifying single nucleotide variants (SNV), make de novo genome assembly and genomic structural analysis difficult. Long template NGS sequencing offers a potential solution but suffers from complex and expensive library preparation strategies. Such strategies frequently require significant amounts of input DNA due to complicated and inefficient manipulation steps. We have proposed an approach for creating long template libraries that addresses these issues with a simple, efficient, and relatively inexpensive method involving the innovative pairing of long dumbbell templates with solid-phase rolling circle replication. The successful development of this technology would greatly enhance the research community's ability to interrogate genomes, particularly those with large structural variation which likely plays a significant role in oncogenesis and tumor progression.
Public Health Relevance Statement: Public Health Relevance: The study and sequencing of human DNA has lead to amazing discoveries in forensics, history, and medicine. As of 2013, the methods associated with preparing a DNA sample for sequencing are prone to inefficiency, waste, and error, all of which increase the cost of the process. The research proposed here is oriented toward significantly improving the methods of sample preparation, which will lead to improved efficiency, accuracy, and reduced costs to sequence DNA, thereby making the technology more accessible to more people.
Project Terms: Address; Agriculture; Amaze; Area; Biological Sciences; Chemistry; Clinical; Communities; comparative genomics; Complex; cost; Couples; Custom; Data; density; design; Development; Diagnostic; Disadvantaged; Disease; DNA; DNA Library; DNA Sequence; Enzymes; Forensic Medicine; Foundations; Generations; Genome; genome analysis; genome-wide; Genomic DNA; Genomic medicine; Genomics; Glean; Health; History of Medicine; Human; human DNA sequencing; human genomics; Hybridization Array; improved; innovation; innovative technologies; Investigation; Lead; Length; Libraries; method development; Methodology; Methods; Microfluidics; Natural History; New England; next generation sequencing; Nucleic Acids; Nucleotides; Phase; Play; Population Dynamics; Preparation; Process; Productivity; Protein Array; Protein Hybridization; public health relevance; rapid detection; Reading; Reagent; reference genome; Replicon; Research; Research Personnel; RNA; RNA-Protein Interaction; Role; Running; Sampling; screening; sequencing platform; small molecule; Solid; Solutions; structural genomics; Structure; Surface; Systems Biology; Technology; technology development; tool; tumor progression; tumorigenesis; Variant; wasting
