Scalable Cancer Genomics via Nanocoding and Sequencing

通过纳米编码和测序实现可扩展的癌症基因组学

• 批准号: 8851351
• 负责人: Jian Ma
• 金额: $ 37.25万
• 依托单位: UNIVERSITY OF WISCONSIN-MADISON
• 依托单位国家: 美国
• 财政年份: 2015
• 资助国家: 美国
• 起止时间: 2015-08-01 至 2018-07-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8851351
• 关键词: Address; Amaze; Beds; Bioinformatics; Biological Assay; Biomedical Research; Cataloging; Catalogs; Charge; Chemistry; Chromosomes; Complement; Computational algorithm; Computer Simulation; Cytogenetic Analysis; Cytogenetics; DNA; DNA Sequence Rearrangement; Data; Data Analyses; Data Set; Deposition; Development; Devices; Diagnosis; Diagnostic; Event; Fluorochrome; Future; Genetic Materials; Genome; Genomic DNA; Genomics; Glass; Goals; Graph; Hand; Human; Image; Individual; Investments; Label; Link; Malignant Neoplasms; Maps; Methods; Microfluidics; Modeling; Modification; Molecular Conformation; Multiple Myeloma; Nucleotides; Patient risk; Patients; Peripheral Blood Mononuclear Cell; Planets; Process; Protocols documentation; Reading; Research Infrastructure; Research Personnel; Resolution; Restriction Mapping; Risk; Sampling; Scheme; Site; Solutions; Speed; Stretching; Stromal Neoplasm; Structure; Surface; System; Techniques; Technology; Temperature; Testing; The Cancer Genome Atlas; Time; Translations; Variant; Vision; base; cancer genome; cancer genomics; candidate validation; computer framework; computer infrastructure; data acquisition; fluorescence microscope; genome analysis; high risk; human reference genome; image processing; neglect; new technology; next generation sequencing; novel; operation; programs; public health relevance; restriction enzyme; single molecule; tool; tumor

 DESCRIPTION (provided by applicant): Cancer genomes present amazing puzzles for genomicists to solve in terms of their structures. The size of the data "pieces" for attempting assembly into a complete view are both very large (cytogenetic) and very small (sequence data), often differing in scale by more than a thousand-fold. Add to this, genomic dispersity within a tumor and breakpoints within interspersed repeats, and the puzzle solution grows much more difficult. As such, the aims of this application are to effectively seamlessly scale data "piece" size by a hierarchical framework, through new algorithms and computational pipelines that will engage both long-range physical maps constructed by significant advancements to Nanocoding, and sequence data to create scalable views of cancer genomes that span from nucleotide-to-chromosome. This multipronged project will involve synergistic advancements to: DNA labeling, presentation of very large genomic DNA molecules, scanners for single molecule analytes, and machine vision-all system components that will be informed by advanced bioinformatic analysis techniques, developed for single molecule analysis, and cutting-edge computer simulations of DNA conformations within the devices that will be the foundry for large datasets. This highly integrated system will be aimed at the discovery of novel structural variants within four paired multiple myeloma / normal samples for tabulation of previously undetectable events as candidates for validation and further study. The resulting platform, comprising new single molecule technologies, melded with advanced bioinformatics techniques, portends scalable, comprehensive, fast genome analysis for navigating cancer genomes.

 描述(由申请人提供)：癌症基因组在其结构方面为基因学家提供了令人惊叹的谜题。试图组装成一个完整的视图的数据“片段”的大小既有非常大的(细胞遗传学的)，也有非常小的(序列数据)，通常在规模上相差一千倍以上。此外，基因组在肿瘤内的分散性和散布在重复序列中的断裂点，这个谜题的解决变得更加困难。因此，这一应用程序的目标是通过新的算法和计算管道，通过分层框架有效地无缝地扩展数据“块”的大小，这些新算法和计算管道将使用由纳米编码的重大进步构建的远程物理地图，以及用于创建从核苷酸到染色体的癌症基因组的可缩放视图的序列数据。这一多管齐下的项目将涉及以下方面的协同进展：DNA标记、非常大的基因组DNA分子的呈现、单分子分析器的扫描仪和机器视觉--所有系统组件都将得到为单分子分析开发的先进生物信息学分析技术的信息，以及将成为大型数据集铸造基础的设备内DNA构象的尖端计算机模拟。这一高度集成的系统将致力于在四个成对的多发性骨髓瘤/正常样本中发现新的结构变异，用于将以前无法检测到的事件制成表格，作为验证和进一步研究的候选。由此产生的平台，包括新的单分子技术，融合了先进的生物信息学技术，预示着可扩展的、全面的、快速的基因组分析，用于导航癌症基因组。