Integrated Assembly Software for Sanger and Next Generation Sequence Technologies

适用于 Sanger 和下一代序列技术的集成装配软件

• 批准号: 8011298
• 负责人: TIMOTHY J DURFEE
• 金额: $ 72.29万
• 依托单位: DNASTAR, INC.
• 依托单位国家: 美国
• 财政年份: 2007
• 资助国家: 美国
• 起止时间: 2007-09-01 至 2011-12-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8011298
• 关键词: Algorithms; Area; Bacterial Genome; Base Pairing; Binding; Bioinformatics; Biological Sciences; Biology; Characteristics; Chromosomes; Chromosomes, Human, Pair 21; Chromosomes, Human, Pair 8; Clinic; Computer software; Computers; DNA Resequencing; DNA Sequence; Data; Data Analyses; Data Set; Data Storage and Retrieval; Databases; Development; Diploidy; Evolution; Foundations; Funding; Future; Generations; Generic Drugs; Genes; Genetic Polymorphism; Genome; Goals; Healthcare; Hour; Human; Human Genome; Laboratory Research; Life; Link; Medicine; Memory; Methods; Mining; Online Systems; Paper; Performance; Phase; Price; Process; Reading; Relative (related person); Reporting; Research Personnel; Resources; Running; Single Nucleotide Polymorphism; Solutions; Sorting - Cell Movement; Stream; System; Technology; Time; Variant; base; computerized data processing; computing resources; cost; cost effective; data reduction; data structure; design; genome sequencing; genome-wide analysis; innovation; meetings; memory process; new technology; next generation; prototype; public health relevance; single molecule; tool; user-friendly

DESCRIPTION (provided by applicant): The advent of next-generation (Next-gen) sequencing technologies has begun a surge in whole genome sequencing and resequencing, exemplified spectacularly by four papers describing five complete human genomes in 2008 alone. One company, Knome, now even offers customers their entire genome sequence using Next-gen sequencing technology. These developments, together with targeted resequencing of genome, presage the day of the $1000 human genome. Broad-scale whole human genome resequencing (WHGR) will have enormous impact on the areas of personalized medicine, human evolution and human diversity. To fully realize that potential, however, software capabilities must be dramatically enhanced to meet the significant challenges posed by the sheer volume of data generated in these projects, the diversity of technology-specific data characteristics and simply analyzing the 6 billion base pair diploid human genome. Moreover, we see the day when technology improvements and cost reductions make WHGR as commonplace as bacterial genome sequencing has become today. For that to occur, assembly and analysis software must be accessible to a far broader and less computer savvy range of researchers than the highly specialized bioinformatics teams that decode the information now. Also, computer resources are far more limited even for a well funded research laboratory than available to a large sequencing center. Therefore, the overall goal of this proposal is to develop a Next-gen sequence assembly and analysis pipeline, DESKAPP, that will run on an affordable ($5000) high- end desktop computer and produce a human genome sequence in a reasonable timeframe (days, not weeks). WHGR by DESKAPP will involve a reference-guided main assembly as well as a de novo assembly branch to characterize unique regions of the new genome relative to the reference. Merging of the assemblies produces a complete sequence that can be evaluated for gene content, single nucleotide polymorphisms (SNPs) and structural variation (SV; indels, inversion, translocations) both by web-based searches of external databases to identify known allelic variation and by direct examination of the sequence to identify new polymorphisms. A Disk Sort Alignment algorithm allows the data sets which are far too large for in-memory processing to be evaluated and clustered for assembly by SeqMan N-Gen (SM N-Gen), our desktop assembly engine. Using a prototype DSA-SM N-Gen pipeline, we have processed the entire 7.4x 454 data set from the James Watson genome to a layout file in 31 hours using DSA and have assembled three chromosomes: 8; 21; and X; using SM N-Gen. Assembly times varied from 1 hour for Chromosome 21 to 10.6 hours for an average- sized chromosome, such as Chromosome 8. Together, these results demonstrate the feasibility of constructing a DESKAPP pipeline for WHGR. The Phase II Aims are designed to build upon this foundation and produce a seamless pipeline for the desktop assembly and analysis of a human genome in a matter of days. PUBLIC HEALTH RELEVANCE: Next-gen sequencing technologies have started a new revolution throughout biology by providing DNA sequence data in unprecedented quantities at continually decreasing costs. This data will be invaluable in the emerging era of personalized medicine and in exploring the immense diversity of life. The goal of this project is to develop desktop computer software that will enable research laboratories and clinics of any size to realize the promise of these new technologies.

描述（由申请人提供）：下一代（Next-gen）测序技术的出现已经开始了全基因组测序和重测序的热潮，仅2008年就有四篇论文描述了五个完整的人类基因组。Knome公司现在甚至向客户提供使用下一代测序技术的整个基因组序列。这些发展，加上有针对性的基因组重测序，预示着1000美元的人类基因组时代的到来。大规模人类全基因组重测序（WHGR）将对个性化医疗、人类进化和人类多样性等领域产生巨大影响。然而，为了充分实现这一潜力，必须大大增强软件功能，以应对这些项目中产生的庞大数据量、技术特定数据特征的多样性以及简单分析60亿个碱基对二倍体人类基因组所带来的重大挑战。此外，我们看到技术进步和成本降低使WHGR像今天的细菌基因组测序一样普遍的一天。为了实现这一目标，汇编和分析软件必须能够被更广泛的、不那么精通计算机的研究人员使用，而不是现在解码信息的高度专业化的生物信息学团队。此外，即使是资金充足的研究实验室，计算机资源也远比大型测序中心有限。因此，该提案的总体目标是开发下一代序列组装和分析管道，DESKAPP，它将在价格合理（5000美元）的高端台式计算机上运行，并在合理的时间范围内（几天，而不是几周）产生人类基因组序列。DESKAPP的WHGR将包括参考指导的主组装和从头组装分支，以表征相对于参考的新基因组的独特区域。这些片段的合并产生了一个完整的序列，可以通过基于网络的外部数据库搜索来确定已知的等位基因变异，也可以通过直接检查序列来确定新的多态性，从而评估基因含量、单核苷酸多态性（SNPs）和结构变异（SV；索引、倒置、易位）。磁盘排序对齐算法允许对内存中处理过于庞大的数据集进行评估，并通过我们的桌面组装引擎SeqMan N-Gen （SM N-Gen）进行聚类组装。使用原型DSA- sm N-Gen管道，我们使用DSA在31小时内将James Watson基因组的整个7.4x 454数据集处理为布局文件，并组装了三条染色体：8；21;和X;使用SM N-Gen。组装时间从21号染色体的1小时到8号染色体等平均大小的染色体的10.6小时不等。总之，这些结果证明了为WHGR构建DESKAPP管道的可行性。第二阶段的目标是建立在这个基础上，并在几天内为桌面组装和分析人类基因组提供一个无缝的管道。