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: 9791194
• 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/9791194
• 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; bioinformatics tool; 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 该赠款更新提案是关于开发创新的新软件，该软件将允许健康 研究人员利用DNA测序的新进展。 在过去的十年中，技术的进步使DNA测序了常规和成本 - 生命科学研究领域的有效方法。当今的主要技术 产生数百万个短序列，由75-300个基对组成（“字母”使得 向上DNA序列）。这些简短的“读取”必须按正确的顺序组装来制作 数据感。 Birol博士和他的团队是基因组议会的世界领导人，奖项 - 他们开发的赢得软件（在现有的NIH赠款和其他的支持下 资金）已用于潜水DNA测序项目，包括癌症基因组 Atlas项目。 现在，较新的技术已成为可以在更长的时间内生成信息 输入DNA的拉伸为长或链接的读数。长阅读平台可以顺序 每次读取100,000个碱基对，尽管错误率很高，吞吐量很低。链接阅读 平台可以将多个读取在相似的长度上关联，尽管数据包含许多 空白。不过，如果与生物信息学工具相结合，可以利用他们的丰富信息 提供这些新的测序平台将在健康研究中开放新的前沿。 Birol博士正在寻求续签他的NIH资金，以便他可以开发专业软件 将快速，准确，有效地组装和分析较长且链接的序列读取。 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，使用遗传信息选择最好的药物来治疗 个体患者的癌症和其他应用。 新工具将免费在线提供，以供其他非营利研究人员使用 自己的测序项目，使世界各地的团队能够更快地取得健康的进步 研究。