Oligonucleotide-Selective Sequencing for integrated and rapid cancer genome analy

描述(由申请人提供)：个性化癌症医学涉及识别临床上可操作的癌症突变和任何给定肿瘤的基因组异常。正如我们最近在2011年11月刊的《自然生物技术》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，它从根本上改进了从临床样本中检测癌症突变的方法。这项技术有可能为转化性研究和潜在的“个性化”癌症诊断提供快速、准确的癌症突变检测。OS-Seq提供了许多优势，使个性化癌症分析变得可访问、快速、健壮和准确。整个工作流程得到了简化，使得大多数制备步骤都在标准的流体设备上进行，并且实际的实验操作受到限制。与目前商业上可用的靶向、基因特异性癌症测序分析方法相比，该方法的性能得到了改进。基于我们的经验分析和随后在设计捕获探针时的改进，我们展示了与其他方法相比，非常特异的捕获基因组靶标的方法。我们在我们的目标上实现了高水平的测序覆盖率，从而允许对癌症突变进行敏感和特异的检测。随着最近测序技术速度的提高，OS-Seq有可能在几天内分析大量的癌症基因，包括从活检中提取基因组DNA到完成目标测序运行的时间。这为从临床样本中快速识别癌症突变提供了可能性。我们的建议集中在OS-Seq技术的开发上，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物。为了实现这一目标，我们将开发OS-Seq技术的关键方面，以可靠、快速和高精度的简单程序集成检测癌症突变和基因组异常。

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.