Microfluidic sample preparation for genomic sequencing of clinical pathogen isolates

用于临床病原体分离株基因组测序的微流控样品制备

• 批准号: 9018768
• 负责人: Paul Clark Blainey
• 金额: $ 22.13万
• 依托单位: BROAD INSTITUTE, INC.
• 依托单位国家: 美国
• 财政年份: 2016
• 资助国家: 美国
• 起止时间: 2016-01-01 至 2017-12-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/9018768
• 关键词: Affect; Antibiotic Resistance; Bacteria; Bacterial Genome; Biomass; Capital; Cells; Clinical; Clinical Trials; Communicable Diseases; Consumption; Cultured Cells; DNA; DNA Microarray Chip; DNA Sequence; DNA purification; Data; Data Analyses; Data Collection; Data Quality; Data Set; Devices; Diagnosis; Disease; Elements; Epidemiology; Equipment; Genome; Genomic DNA; Genomics; Goals; Infection Control; Institutes; Laboratories; Laboratory culture; Learning; Libraries; Medical; Medical Device; Medicine; Microfluidics; National Institute of Allergy and Infectious Disease; Output; Patients; Performance; Population Dynamics; Preparation; Procedures; Process; Protocols documentation; Reading; Reagent; Research Design; Resistance; Risk Factors; Sampling; Scientist; Sequence Analysis; Specific qualifier value; Staphylococcus aureus; Surveys; System; Technology; Testing; Time; Validation; Walking; bacterial resistance; base; clinical decision-making; clinical sequencing; cost; design; expectation; genome analysis; genome sequencing; improved; instrument; methicillin resistant Staphylococcus aureus; micro-total analysis system; microbial; novel; pathogen; pathogen genome; prototype; public health relevance; resistance gene; transmission process; whole genome

 DESCRIPTION (provided by applicant): DNA sequencing has seen dramatic cost reductions in recent years, while sample preparation costs have been relatively flat. The result is a `sample preparation bottleneck' apparent today will affect essentially all sequencing studies within a few years. In addition, sample input quantity requirements for standard approaches exclude important low-yield clinical sample types. The goal of this R21 project is to validate and demonstrate a practical integrated microfluidic sample preparation technology for pathogen genome sequencing that enables a significant advance in sample preparation cost, turn-around-time, and low-input capability. Integration of the entire sample preparation process in a single micro device will reduce real-world cost for high-throughput sample preparation more than 10-fold by lowering reagent consumption, the need for other consumables, capital equipment costs, hands-on time, and procedural errors. We will validate this technology on S. Aureus samples from an ongoing clinical trial, Project CLEAR, and then go on to sequence a large number of additional Project CLEAR samples.