Single Molecule Genome Analysis of Oligodendroglioma

少突胶质细胞瘤的单分子基因组分析

• 批准号: 7118998
• 负责人: DAVID C. SCHWARTZ
• 金额: $ 44.84万
• 依托单位: UNIVERSITY OF WISCONSIN-MADISON
• 依托单位国家: 美国
• 财政年份: 2005
• 资助国家: 美国
• 起止时间: 2005-09-02 至 2008-08-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/7118998
• 关键词: chromosome aberrations; clinical research; functional /structural genomics; glioma; human genetic material tag; human tissue; loss of heterozygosity; microfluidics; molecular biology information system; molecular oncology; neoplasm /cancer genetics; nucleic acid sequence; restriction mapping

DESCRIPTION (provided by applicant): The proposed aims of this project center on constructing whole genome maps from 30 different oligodendroglioma tumor samples - a solid tumor that has confounded conventional genome analysis approaches to associate loss of heterozygosity (LOH) with a distinct set of gene(s). The research proposed reflects a multi-disciplinary collaborative effort to use a robust single molecule platform (Optical Mapping) to construct high-resolution restriction maps from a selected group of characterized tumors bearing a heterogeneous genome population. Chromosomal aberrations will be scored and classified on a whole genome basis in the absence of any hypothesis, outside of the established link between 1p/19q LOH and diagnostic purposes. Genomic aberrations in the tumor samples - deletions, insertions, translocations, tandem amplifications, and gross rearrangements - will be precisely located and characterized. Map coverage of 20-50x will ensure discernment of separate populations of chromosomal aberrations within each sample at 50 kb-500 kb genome intervals. New algorithms will be developed, based on Optical Mapping data, to identify breakpoints within a heterogeneous population of aberrant genomes based on the local alignment of single molecule barcodes, or Optical Maps, with the latest build of the human genome sequence. Aberrations will be statistically assessed to discern the percent of the tumor cell population bearing a given genomic lesion. To synergize this, a new generation of microfluidic device to incorporate cell lysis and DNA loading within the same disposable silicone fabrication will be perfected. These first-ever whole genome maps of oligodendroglioma tumor genomes and comprehensive determinations of aberrations will be entered into a customized Santa Cruz Genome Browser as additional annotation tracks. This technology provides a unique platform to decipher the complex molecular anatomy of cancer cells, on a whole genome basis, at high resolution.

描述（由申请人提供）：该项目的拟议目标集中在从 30 个不同的少突神经胶质瘤肿瘤样本构建全基因组图谱 - 一种实体瘤，它混淆了传统的基因组分析方法，将杂合性丢失 (LOH) 与一组不同的基因联系起来（s）。拟议的研究反映了多学科的合作努力，即使用强大的单分子平台（光学图谱）从一组具有异质基因组群的选定特征肿瘤中构建高分辨率限制性图谱。 在没有任何假设的情况下，除了 1p/19q LOH 与诊断目的之间已建立的联系之外，染色体畸变将在整个基因组的基础上进行评分和分类。肿瘤样本中的基因组畸变——缺失、插入、易位、串联扩增和总体重排——将被精确定位和表征。 20-50x 的图谱覆盖范围将确保以 50 kb-500 kb 基因组间隔辨别每个样本中染色体畸变的不同群体。 将开发基于光学图谱数据的新算法，以根据单分子条形码或光学图谱与最新构建的人类基因组序列的局部比对来识别异常基因组异质群体中的断点。 将统计评估畸变，以辨别携带给定基因组病变的肿瘤细胞群的百分比。 为了实现这一点的协同作用，将完善新一代微流体装置，将细胞裂解和 DNA 加载整合到同一一次性硅胶制造中。 这些首个少突胶质细胞瘤肿瘤基因组的全基因组图谱和畸变的综合测定将作为附加注释轨道输入定制的圣克鲁斯基因组浏览器中。 该技术提供了一个独特的平台，可以在全基因组的基础上以高分辨率破译癌细胞的复杂分子解剖结构。