Single Molecule Genome Analysis of Oligodendroglioma

描述(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构建全基因组图谱-这是一种实体肿瘤，混淆了传统的基因组分析方法，将杂合性缺失(LOH)与一组独特的基因联系起来(S)。这项研究反映了一项多学科的合作努力，即使用一个强大的单分子平台(光学映射)，从一组具有不同基因组群体的特征肿瘤中构建高分辨率限制图。在没有任何假设的情况下，除了1p/19q LOH和诊断目的之间已建立的联系之外，染色体异常将在全基因组的基础上进行评分和分类。肿瘤样本中的基因组异常-缺失、插入、易位、串联扩增和大体重排-将被精确定位和表征。20-50x的图谱复盖率将确保在50kb-500kb的基因组间隔内识别每个样本中不同的染色体异常群体。基于光学图谱数据，将开发新的算法，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，识别不同种类的异常基因组中的断点。我们将从统计学的角度对像差进行评估，以辨别携带特定基因组损伤的肿瘤细胞群体的百分比。为了协同这一点，将完善新一代微流控设备，在相同的一次性硅胶制造中整合细胞裂解和DNA负载。这些有史以来首次的少突胶质瘤肿瘤基因组全基因组图和全面的畸变率测定将作为额外的注释轨道输入到定制的Santa Cruz Genome浏览器中。这项技术提供了一个独特的平台，以高分辨率在全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.