Low-Cost Digital Gene Expression System

描述（由申请人提供）：癌症是美国第二常见的死亡原因，是由生物体基因组中的随机突变引起的。尽管对肿瘤组织中基因组序列的精确了解可以作为治疗的一个指标，例如乳腺癌的erbB-2受体基因（Her-2），但这种相关性很少，而且往往不能充分定义在治疗决策中重要的肿瘤亚型。这种无法识别可能对标准疗法无反应的肿瘤亚类可能会限制更有效治疗策略的发展。基因表达分析是通过分析调控途径间接测量肿瘤基因改变的一种方法。微阵列技术已被证明是强大的工具，并提供基于肿瘤表型的更好的临床决策的承诺。对白血病、淋巴瘤和实体瘤的初步研究表明，基因表达数据可以突出组织学上相同的疾病之间的差异。然而，基于微阵列的技术在分析低表达水平方面受到限制。我们使用独特的测序合成技术作为数字基因表达系统，以获得表达mRNA分子的精确计数。这可以提供比微阵列系统高一个数量级的灵敏度。在这个第二阶段的项目中，我们将建立在第一阶段开发的样品制备方案的基础上，并使用极低成本、专有的下一代测序系统，该系统可以执行基因表达研究所需的测序，价格约为100美元，约为最具竞争力的测序方法的1/20。

DESCRIPTION (provided by applicant): As the second most common cause of death in the US, cancer is caused by random mutations in an organism's genome. Although precise knowledge of the genomic sequence within neoplastic tissues can be an indicator for treatment, for example the erbB-2 receptor gene (Her-2) for breast cancer, such correlations are few and often do not adequately define tumor subtypes important in therapeutic decisions. Such inability to identify a subclass of tumors which may not respond to standard therapies can restrict the development of more efficacious treatment strategies. The analysis of gene expression represents an indirect measure of the genetic alterations in tumors through the analysis of regulatory pathways. Microarray technologies have proven to be powerful tools and offer the promise of better clinical decision-making based on tumor phenotypes. Highly promising preliminary studies of leukemia, lymphomas, and solid neoplasms demonstrate that gene expression data can highlight differences between otherwise histologically identical diseases. However, microarray-based technologies are limited in their ability to analyze low expression levels. We use of a unique sequencing by synthesis technology as a digital gene expression system to obtain precise counts of expressed mRNA molecules. This can provide an order of magnitude more sensitivity than microarray systems. In this Phase II project, we will build upon the sample preparation protocols developed in Phase I and use these with an extremely low-cost, proprietary, next-generation sequencing system that can perform the sequencing required for a gene expression study for about $100 or about 1/20th the price of the most competitive sequencing method. PUBLIC HEALTH RELEVANCE: Ultimately, the ability to produce very inexpensive gene expression and detailed DNA sequence information related to cancer will lead for a much wider use of expression and sequence analyses for research and treatment of this devastating disease. In addition, the ability to analyze complex organisms' genomes at a very low cost will both lead to accelerated discoveries throughout biology and provide the basis for Pharmacogenomics, a new paradigm in therapeutics wherein medicines are prescribed based on individual genotypes rather than just observed symptoms.