De Novo Assembly Tools: Research with Unbiased Engines - Renewal (DNA-TRUER)

从头组装工具：使用无偏差引擎进行研究 - 更新 (DNA-TRUER)

• 批准号: 9976547
• 负责人: Inanc Birol
• 金额: $ 24.29万
• 依托单位: PROVINCIAL HEALTH SERVICES AUTHORITY
• 依托单位国家: 美国
• 财政年份: 2014
• 资助国家: 美国
• 起止时间: 2014-03-04 至 2023-03-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/9976547
• 关键词: Algorithms; Award; Base Pairing; Bioinformatics; Biological Phenomena; Biological Sciences; Cancer Patient; Categories; Chromium; Cohort Studies; Collaborations; Communicable Diseases; Computer software; Consensus; Coupled; DNA; DNA Sequence; DNA Sequence Analysis; DNA sequencing; Data; Detection; Development; Disease; Disease Outbreaks; Disease Surveillance; Five-Year Plans; Funding; Genome; Genomics; Goals; Grant; Guidelines; Health; High-Throughput Nucleotide Sequencing; Length; Letters; Libraries; Link; Malignant Neoplasms; Methods; Modeling; Pharmaceutical Preparations; Process; Protein Isoforms; Protocols documentation; Publications; Quality Control; RNA; Reagent; Research; Research Personnel; Sequence Alignment; Software Tools; Stretching; System; Technology; The Cancer Genome Atlas; Transcript; United States National Institutes of Health; base; bioinformatics tool; cost; cost effective; design; experimental study; field study; frontier; genetic analysis; genetic information; human genomics; indexing; individual patient; innovation; instrument; microbial; microbial genomics; nanopore; new technology; personalized medicine; precision medicine; reconstruction; response; sequencing platform; symposium; tool; transcriptome sequencing; usability

SUMMARY This grant renewal proposal is about developing innovative new software that will allow health researchers to take advantage of new advances in DNA sequencing. Over the last decade, technology advances have made DNA sequencing a routine and cost- effective method in many fields of life sciences research. The dominant technology today generates millions of short sequences, consisting of 75-300 base pairs (the “letters” that make up the DNA sequence). These short “reads” have to be assembled in the right order to make sense of the data. Dr. Birol and his team are world leaders in genome assembly, and the award- winning software they have developed (with support from their existing NIH grant and other funding) has been used in diverse DNA sequencing projects, including The Cancer Genome Atlas project. Newer technologies are now becoming available that generate information on much longer stretches of the input DNA as long or linked reads. Long read platforms can sequence over 100,000 base pairs per read, though with a very high error rate and low throughput. Linked read platforms can associate multiple reads over similar lengths, although the data contains many gaps. Still, if coupled with bioinformatics tools that can leverage the rich information they provide, these new sequencing platforms will open new frontiers in health research. Dr. Birol is seeking to renew his NIH funding so that he can develop specialized software that will quickly, accurately, and efficiently assemble and analyse long and linked sequence reads. These tools would provide advanced capabilities in a range of projects, such as tracking infectious disease outbreaks, using genetic information to select the best drugs to treat an individual patient's cancer, and other applications. The new tools will be made available online free for other non-profit researchers to use in their own sequencing projects, allowing teams around the world to make faster progress in health research.

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