Cancer Genomics Technology Development

微阵列技术的最新进展与高分辨率微阵列的发展有关，它可以以极高的分辨率定位DNA拷贝数的基因组变化和组成变异。我们已经以这种方式将高分辨率阵列应用于几个系统，并将这项技术应用于DNase I超敏感部位的测绘。最近，我们证明了它们可以用来绘制复制的DNA起始点。我们还努力通过将样本类型扩展到福尔马林固定、石蜡包埋样本和流动分选原代细胞来提高检测极限。我们已经确定，有用的核酸制剂可以从固定的组织中获得，并正在继续扩大对这种材料的分析，用于更广泛的基因组技术。目前的努力主要是针对下一代测序技术的实施。这些方法主要依赖于产生一系列DNA分子，这些分子在测序反应期间被顺序成像。我们正在研究使用这些方法对大小RNA进行基因表达谱分析，检测基因组重排、突变，并测量染色质修饰、DNA酶I超敏感部位和转录因子的定位。这项工作的一个主要部分是开发一个强大的计算环境，可以用来分析由这项工作产生的大量序列数据。虽然这是一个具有挑战性的过程，但它最终将产生一个简化的分析流水线，其中基于多个序列的分析将很容易集成，并且没有阵列平台特定的人工产物。我们计算工作的具体目标包括优化管道，以处理染色质分析、染色体重排、基因表达和突变检测的序列数据。我们目前正在寻求新的方法来针对由基因组成的一小部分基因组进行定向测序工作，以便能够在单个样本中以互补的方式对数千个基因进行排序，并在数百个样本中对几个关键基因进行排序。这些目标是在数千种合成寡核苷酸的帮助下实现的，这些寡核苷酸被用于靶向基因组所需的部分。

Recent progress in microarray technology has been related to the development of high resolution microarrays which can map genomic alterations and constitutional variants in DNA copy number at an extremely high resolution. We have applied high resolution arrays in this fashion to several systems and have also adapted this technology to the mapping of DNase I hypersensitive sites. Recently, we have demonstrated that they can be used to map DNA origins of replication. We have also worked to push the limits of detection by extending sample types to formalin fixed, paraffin embedded samples and flow sorted primary cells. We have established that useful nucleic acid preparations can be obtained from fixed tissues and are continuing to extend the analysis of this material for a wider range of genomic technologies. Current efforts have been directed primarily at the implementation of next generation sequencing technologies. These methods primarily depend on producing an array of DNA molecules which are sequentially imaged during the sequencing reaction. We are investigating the use of these methods for gene expression profiling for large and small RNAs, for the detection of genome rearrangements, mutations, and for the measurement of chromatin modifications, DNase I hypersensitive sites, and transcription factor localization. A major part of this effort is the development of a powerful computational environment which can be used to analyze the massive amount of sequence data which is generated by this work. Although this is a challenging process, it ultimately will yield a streamlined analysis pipeline in which multiple sequence based assays will be easy to integrate and free of array platform specific artifacts. Specific goals of our computational efforts include the optimization of pipelines to process sequence data for chromatin analysis, chromosome rearrangements, gene expression, and mutation detection. We are currently engaged in pursuing new approaches to target sequencing efforts to the small proportion of the genome composed of genes in order to be able to sequence thousands of genes in individual samples and in a complementary fashion, to sequence a few key genes in hundreds of samples. These are goals are being accomplished with the aid of thousands of synthetic oligonucleotides which are used to target the desired portion of the genome.