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: 9552251
• 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 2021-07-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/9552251
• 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; Data Quality; 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; cost; cost effective; design; experimental study; field study; frontier; genetic analysis; genetic information; human genomics; indexing; individual patient; innovation; instrument; microbial; 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.

概括 该赠款续订提案旨在开发创新的新软件，以促进健康 研究人员利用 DNA 测序的新进展。 在过去的十年中，技术进步使 DNA 测序成为一种常规且成本低廉的方法。 生命科学研究许多领域的有效方法。当今的主导技术 生成数百万个短序列，由 75-300 个碱基对（组成字母的“字母”）组成 DNA 序列）。这些简短的“读物”必须以正确的顺序组合起来，才能使 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导者，并且获奖- 他们开发的获奖软件（在现有 NIH 拨款和其他资助的支持下） 资金）已用于各种 DNA 测序项目，包括癌症基因组 阿特拉斯项目。 更新的技术现在已经可用，可以生成更长时间的信息 输入 DNA 的延伸作为长读或链接读。长读平台可以测序 每次读取 100,000 个碱基对，但错误率非常高且吞吐量较低。链接阅读 平台可以将相似长度的多个读取关联起来，尽管数据包含许多 差距。尽管如此，如果与可以利用丰富信息的生物信息学工具相结合， 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 资助，以便他能够开发专门的软件 将快速、准确、高效地组装和分析长链序列读数。 这些工具将为一系列项目提供高级功能，例如跟踪 传染病爆发时，利用遗传信息选择最佳药物来治疗 个体患者的癌症以及其他应用。 新工具将免费在线提供给其他非营利研究人员在他们的研究中使用 自己的测序项目，使世界各地的团队能够在健康方面取得更快的进展 研究。