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: 9110904
• 负责人: Jian Ma
• 金额: $ 37.44万
• 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/9110904
• 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; Health; 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; 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; genomic aberrations; high risk; human reference genome; image processing; neglect; new technology; next generation sequencing; novel; operation; programs; reference genome; 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.