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)

基本信息

批准号：
9382151
负责人：
Inanc Birol
金额：
$ 6.83万
依托单位：
BRITISH COLUMBIA CANCER AGENCY
依托单位国家：
美国
项目类别：
财政年份：
2014
资助国家：
美国
起止时间：
2014-03-04 至 2018-03-31
项目状态：
已结题

来源：
https://reporter.nih.gov/project-details/9382151
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 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

项目摘要

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）必须以正确的顺序组装这些短“读段”。比罗尔博士和他的团队是基因组组装领域的世界领先者，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长读长或链接读长平台可以对输入 DNA 进行测序。每次读取 100,000 个碱基对，但错误率非常高且吞吐量较低。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，它们仍然存在差距。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，利用遗传信息选择治疗疾病的最佳药物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。