Single Molecule Genome Analysis of Oligodendroglioma

描述（由申请人提供）：该项目的拟议目标是从30个不同的少突胶质细胞瘤肿瘤样本中构建全基因组图谱，少突胶质细胞瘤是一种实体瘤，其混淆了将杂合性缺失（洛）与一组不同基因相关联的常规基因组分析方法。这项研究反映了多学科的合作努力，使用一个强大的单分子平台（光学作图），从一组选定的具有异质性基因组群体的特征肿瘤中构建高分辨率限制性图谱。 在不存在任何假设的情况下，在1 p/19 q洛与诊断目的之间的既定联系之外，将在全基因组基础上对染色体畸变进行评分和分类。肿瘤样本中的基因组畸变-缺失、插入、易位、串联扩增和总重排-将被精确定位和表征。 20- 50倍的图谱覆盖率将确保在50 kb-500 kb基因组间隔下辨别每个样品内的染色体畸变的单独群体。 将基于光学图谱数据开发新算法，以基于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的异质群体内的断点。 将对畸变进行统计学评估，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，将完善新一代微流体装置，以将细胞裂解和DNA加载纳入同一一次性硅胶制造中。 这些有史以来第一次全基因组图谱的少突胶质细胞瘤肿瘤基因组和全面的测定畸变将进入一个定制的圣克鲁斯基因组浏览器作为额外的注释轨道。 这项技术提供了一个独特的平台，以高分辨率在整个基因组的基础上破译癌细胞的复杂分子解剖结构。

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.