Oligonucleotide-Selective Sequencing for integrated and rapid cancer genome analy

描述（由申请人提供）：个性化癌症药物涉及在任何给定肿瘤中识别临床上可操作的癌症突变和基因组畸变。正如我们最近在2011年11月的Nature Biotechnology上发表的那样，寡核苷酸选择性测序（OS-Seq）是一种新的靶向重测序方法，从根本上提高了临床样本中癌症突变的检测。这项技术有可能使翻译研究和潜在的“个性化”癌症诊断能够快速，准确地检测癌症突变。OS-Seq提供了许多优势，使个性化癌症分析变得可访问，快速，稳健和准确。整个工作流程被简化，使得大多数制备步骤在标准流体设备上进行，并且实际的实验操作受到限制。与目前市售的靶向基因特异性癌症测序分析方法相比，性能得到了改善。基于我们的经验分析和随后在设计捕获探针方面的改进，我们证明了对基因组靶点的非常特异性的捕获，并且比其他方法具有更小的方差。我们在靶点上实现了高水平的测序覆盖率，从而可以灵敏和特异地检测癌症突变。随着测序技术速度的最新改进，OS-Seq可以在几天内分析大量癌症基因，这包括从活检中提取基因组DNA到完成靶向测序运行的时间。这使得从临床样本中快速识别癌症突变成为可能。我们的提案专注于开发OS-Seq技术，用于从临床肿瘤样本中识别癌症突变，重排，拷贝数改变和潜在的癌症相关感染因子。为了实现这一目标，我们将开发OS-Seq技术的关键方面，用于通过可靠、快速和高准确性的简单方案来综合检测癌症突变和基因组畸变。

DESCRIPTION (provided by applicant): Personalized cancer medicine involves identifying clinically actionable cancer mutations and genomic aberrations in any given tumor. As we recently published in the November 2011 issue of Nature Biotechnology, Oligonucleotide-Selective Sequencing (OS-Seq) is a novel targeted resequencing approach that fundamentally improves the detection of cancer mutations from clinical samples. This technology has the potential for enabling the rapid, accurate detection of cancer mutations for both translational research studies and potentially, "personalized" cancer diagnostics. OS-Seq provides a number of advantages to make personalized cancer analysis accessible, rapid, robust and accurate. The overall workflow is simplified such that the majority of preparative steps take place on a standard fluidics device and the actual experimental manipulation is limited. The performance is improved compared to the current commercially available methods for targeted, gene-specific cancer sequencing analysis. Based on our empirical analysis and subsequent refinements in designing capture probes, we demonstrate very specific capture of genomic targets with less variance than other methods. We achieve a high level of sequencing coverage on our targets that permit sensitive and specific detection of cancer mutations. With recent improvements in sequencing technology speed, OS-Seq can potentially be adapted to analyze large number of cancer genes in a matter of days which includes the time that genomic DNA is extracted from a biopsy to the completion of the targeted sequencing run. This holds the possibility of rapidly identifying cancer mutations from clinical samples. Our proposal is focused on development of the OS-Seq technology for identifying cancer mutations, rearrangements, copy number alterations and potential cancer-related infectious agents from clinical tumor samples. To achieve this goal, we will develop key aspects of OS-Seq technology for integrated detection of cancer mutations and genomic aberrations with simple protocols that are reliable, rapid and with high accuracy.