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.

摘要 这项拨款续期提案是关于开发创新的新软件，使健康 研究人员将利用DNA测序方面的新进展。 在过去的十年里，技术的进步使DNA测序成为例行公事和成本- 在生命科学研究的许多领域都是有效的方法。当今的主导技术 生成数百万个短序列，由75-300个碱基对(组成 向上的DNA序列)。这些简短的“阅读”必须按照正确的顺序组合起来才能完成 对数据的感觉。比罗尔博士和他的团队是基因组组装领域的世界领先者，该奖项- 他们开发的获奖软件(在他们现有的NIH拨款和其他支持下 资金)已被用于各种DNA测序项目，包括癌症基因组 阿特拉斯项目。 更新的技术现在正在变得可用，这些技术在更长的时间内产生信息 输入DNA的长度或链接的读数。长阅读平台可以按顺序排列 每次读取100,000个碱基对，但错误率非常高，吞吐量很低。链接读取 平台可以关联相似长度的多个读取，尽管数据包含多个 差距。尽管如此，如果与生物信息学工具相结合，可以利用它们丰富的信息 提供，这些新的测序平台将开辟健康研究的新领域。 比罗尔博士正在寻求更新他的NIH资金，这样他就可以开发专门的软件， 将快速、准确和高效地组合和分析长的和相连的序列读数。 这些工具将在一系列项目中提供高级功能，例如跟踪 传染病暴发，利用遗传信息选择最佳药物治疗 个别患者的癌症，以及其他应用。 这些新工具将在网上免费提供，供其他非营利性研究人员在他们的 自己的测序项目，使世界各地的团队在健康方面取得更快的进展 研究。