Single Molecule Genome Analysis of Oligodendroglioma

描述（由申请人提供）：本项目拟建立30个不同的少突胶质细胞瘤肿瘤样本的全基因组图谱，这是一种实体肿瘤，传统的基因组分析方法无法将杂合性缺失（LOH）与一组不同的基因联系起来。提出的研究反映了多学科合作的努力，使用强大的单分子平台（光学测绘）从一组具有异质基因组群体的特征肿瘤中构建高分辨率限制图。除了1p/19q LOH与诊断目的之间的既定联系外，染色体畸变将在没有任何假设的情况下以全基因组为基础进行评分和分类。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的地图覆盖率将确保在50 kb-500 kb基因组间隔内识别每个样本中单独的染色体畸变群体。基于光学图谱数据的新算法将被开发出来，以基于单分子条形码的局部比对，或光学图谱，与最新构建的人类基因组序列，来识别异质异常基因组群体中的断点。畸变将被统计评估，以辨别肿瘤细胞群的百分比承载一个给定的基因组病变。为了协同这一点，新一代的微流体装置，结合细胞裂解和DNA装载在同一个一次性硅胶制造将会完善。这些少突胶质细胞瘤肿瘤基因组的首次全基因组图谱和畸变的综合测定将作为额外的注释轨道进入定制的Santa Cruz基因组浏览器。这项技术提供了一个独特的平台，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。

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.