Accurate, long read length, whole human genome sequencing under $100

准确、长读长、全人类基因组测序不到 100 美元

• 批准号: 8728987
• 负责人: Theofilos Kotseroglou
• 金额: $ 24.32万
• 依托单位: EVE BIOMEDICAL, INC.
• 依托单位国家: 美国
• 财政年份: 2013
• 资助国家: 美国
• 起止时间: 2013-09-01 至 2015-07-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8728987
• 关键词: Address; Affect; Architecture; Benchmarking; Bioinformatics; Biological Assay; Biology; Cellular Phone; Clinical; Clinics and Hospitals; Color; Communities; DNA; DNA Sequence; DNA-Directed RNA Polymerase; Data; Detection; Development; Diagnostic; Enzymes; Fluorescence; Genetic Transcription; Genome; Genomics; Goals; Grant; Human; Human Genome; Image; Length; Licensing; Light; Maps; Measurement; Mechanics; Medicine; Methodology; Methods; Metric; Microscope; Modification; Molecular Motors; Motion; Mutation; Noise; Nucleotides; Optics; Performance; Phase; Plasmids; Preparation; Process; Property; Reading; Reagent; Research; Resistance; Reverse Transcription; Rotation; Sampling; Sequence Alignment; Signal Transduction; Software Tools; Staging; Surface; System; Technology; Testing; Time; Transducers; Universities; Work; base; commercialization; cost; design and construction; ds-DNA; genome sequencing; image processing; improved; microbial; mouse genome; nanoscale; novel; point-of-care diagnostics; public health relevance; single molecule; tool

DESCRIPTION (provided by applicant): The long-term goal of the proposed research is the design and construction of a DNA sequencing system that can sequence the whole human genome under $100 including sample preparation and with the cost of goods of the system well under $10,000. The system developed under the proposed research is at least an order of magnitude in cost better than the target of the solicitation while maintaining all performance metrics. In that respect it will break the barrier towards genomic medicine. The overall system is based on optically sequencing DNA on a consumer cell-phone camera chip by means of a transducer that relates the nanometer scale dynamics of single base of a DNA to a macro-motion that is easy to image without the use of fluorescence, but only with a single common white-light LED. Preliminary data shows that the proposed method can already achieve DNA readlength of 1,600 bases and accurate sequencing alignment of 100 base sections. While this is a great start, Phase I work will continue to investigate the accuracy and readlength and throughput limits of this approach. To achieve that, software tools such as image processing and bioinformatics need to be constructed at this first phase, while at same time we will need to improve the biology assays. If successful, the main goal is to completely sequence a microbial DNA (Ecoli) at the end of Phase I, and thus completely benchmark the proposed architecture. Beyond Phase I, a low cost benchtop system will be constructed using commercial cell-phone camera chips and will be used to perform sequencing of Whole Human Genome with the target cost defined as goal of this grant solicitation.

描述（由申请人提供）：拟议研究的长期目标是设计和构建一个 DNA 测序系统，该系统可以在 100 美元以下（包括样品制备）对整个人类基因组进行测序，并且系统的商品成本远低于 10,000 美元。根据拟议研究开发的系统在成本上至少比招标目标高一个数量级，同时保持所有性能指标。从这方面来说，它将打破基因组医学的障碍。整个系统基于消费手机相机芯片上的 DNA 光学测序，通过传感器将 DNA 单碱基的纳米级动力学与宏观运动联系起来，无需使用荧光即可轻松成像，但仅使用单个普通白光 LED。初步数据显示，该方法已经可以实现1600个碱基的DNA读长和100个碱基切片的精确测序比对。虽然这是一个很好的开始，但第一阶段的工作将继续研究这种方法的准确性、读取长度和吞吐量限制。为了实现这一目标，需要在第一阶段构建图像处理和生物信息学等软件工具，同时我们需要改进生物学检测。如果成功，主要目标是在第一阶段结束时对微生物 DNA（大肠杆菌）进行完整测序，从而对所提出的架构进行完全基准测试。在第一阶段之后，将使用商用手机摄像头芯片构建低成本台式系统，并将用于执行全人类基因组测序，目标成本定义为本次拨款募集的目标。