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（下一代）测序技术的出现已经开始了整个基因组测序和重大方程的激增，仅在2008年仅描述了五个完整的人类基因组的四篇论文就示例了。一家公司Knome现在甚至使用下一代测序技术为客户提供整个基因组序列。这些事态发展及其基因组的有针对性的重新方程，预示着1000美元的人类基因组的当天。大规模的整个人类基因组重新配置（WHGR）将对个性化医学，人类进化和人类多样性的领域产生巨大影响。为了充分意识到，必须大大提高软件功能，以应对这些项目中产生的大量数据所带来的重大挑战，特定于技术的数据特征的多样性，并简单地分析了60亿个碱基对二倍体人类基因组。此外，我们看到了技术的改进和成本降低使WHGR与细菌基因组测序一样普遍的日子已经成为今天。为此，与现在解码信息的高度专业化的生物信息学团队相比，组装和分析软件的研究人员可以访问更广泛，精通计算机的研究人员。同样，即使对于资金良好的研究实验室，计算机资源也比大型测序中心可用的要受到限制。因此，该提案的总体目标是开发下一代序列组件和分析管道DeskApp，该管道将以负担得起的（5000美元）的高端桌面计算机运行，并在合理的时间范围内生成人类基因组序列（天数，而不是几周）。 DeskApp的WHGR将涉及参考引导的主组装以及从头组装分支，以表征相对于参考的新基因组的独特区域。组件的合并会产生一个完整的序列，可以通过基于Web的外部数据库搜索来识别已知的等位基因变异，并直接检查新的多聚甲形象来评估基因含量，单核苷酸多态性（SNP）和结构变化（SV； Indels，倒置，易位）。磁盘排序对齐算法允许数据集太大，无法进行内存处理，无法评估和聚集由Seqman N-Gen（SM N-Gen）（我们的桌面组装引擎）组装。使用原型DSA-SM N-gen管道，我们使用DSA在31小时内将整个7.4x 454数据集从James Watson基因组中处理为布局文件，并组装了三个染色体：8; 21;和x;使用sm n-gen。从21染色体染色体的1小时到平均尺寸的染色体（例如8号染色体）的组装时间不等。总之，这些结果证明了为WHGR构建DeskApp管道的可行性。 II期目标旨在建立在该基础上，并在几天之内为人类基因组的桌面组装和分析提供无缝的管道。 公共卫生相关性：下一代测序技术通过以前所未有的数量以不断降低的成本提供了DNA序列数据，从而开始了整个生物学的新革命。这些数据将在个性化医学的新兴时代和探索巨大的生活多样性时无价。该项目的目的是开发台式计算机软件，该软件将使研究实验室和任何规模的诊所能够实现这些新技术的希望。