FUNCTIONAL ALLELOTYPING

描述(由申请人提供)：我们希望开发一种用于癌症基因组表征的技术，我们将其称为“功能性等位基因分型”，这是一种相对廉价的基于杂交的方法，用于检测基因的等位基因特异性表达(ASE)的定量差异，这些差异将用于区分肿瘤和匹配的正常组织。这种方法可以识别肿瘤抑制基因的一个等位基因的表达缺失(LOE)，以及肿瘤促进基因的正常沉默的等位基因的激活，如印迹丢失(LOI)，同时还可以检测表达基因的杂合性丢失(LOH)。我们的第一个目标是开发一种可扩展的基于杂交的功能等位基因分型方法，该方法基于肿瘤和匹配的正常样本之间的等位基因特异性表达的比较。我们的第二个目标是将功能等位基因分型扩展到人类基因集。我们的第三个目标是开发统计工具来区分LOH、LOE和LOI并对其进行评分。我们在这方面的努力受到初步数据的鼓舞，这些数据表明：在重组实验中检测ASE数量差异的能力；以及使用构成人类基因集10%的阵列准确识别一半等位基因不平衡的能力。一般来说，功能等位基因分型对癌症研究人员来说应该是有价值的，因为它的一些输出目前不能通过任何其他方式在基因组水平上获得，例如发现未知基因的LOI。然而，我们认为，它将特别有助于在TCGA下筛选样本进行进一步表征，作为一种通过优先考虑基因、单个肿瘤和用于进一步研究的分析类型来大幅降低项目成本的一种方式。对公众健康而言，拟议的工作将对公众健康产生重大影响，因为它使识别与人类癌症有关的高优先级基因成为可能，从而最有效地将时间和资源用于发现新的癌症基因。我们相信，这项工作将成为TCGA计划使用的工具的组成部分，并将对癌症研究人员发现新的肿瘤抑制基因和癌症中异常激活的基因具有独立价值。

DESCRIPTION (provided by applicant): We would like to develop a technology for cancer genomic characterization which we term "Functional Allelotyping," which is a relatively inexpensive hybridization-based approach to detect quantitative differences in allele-specific expression (ASE) of genes that will be used to distinguish tumors from matched normal tissue. This approach could identify loss of expression (LOE) of one allele of a tumor suppressor gene, as well as activation of the normally silent allele of a tumor promoting gene, such as loss of imprinting (LOI), while also detecting loss of heterozygosity (LOH) of expressed genes. Our first aim is to develop a scalable hybridization-based method for functional allelotyping, based on comparison of allele-specific expression between tumor and matched normal samples. Our second aim is to scale functional allelotyping to the human gene set. Our third aim is to develop statistical tools to distinguish and score LOH, LOE, and LOI. We are encouraged in this effort by our preliminary data that show: the ability to detect quantitative differences in ASE in reconstitution experiments; and the ability already to accurately identify half of allelic imbalances using an array constituting 10% of the human gene set. Functional allelotyping should be valuable to cancer researchers generally, as some of its output cannot currently be obtained any other way at a genome level, such as the discovery of LOI of unknown genes. However, we believe it will be particularly useful for screening samples for further characterization under TCGA, as a way of substantially reducing costs to the project by prioritizing genes, individual tumors, and types of analyses for further investigation. TO PUBLIC HEALTH The proposed work will have a substantial impact on public health, by making it possible to identify high priority genes involved in human cancer, thereby directing time and resources most efficiently in the discovery of new cancer genes. We believe that the work will be an integral part of the tools used by the TCGA program, and will also have independent value to cancer researchers in discovering new tumor suppressor genes and genes abnormally activated in cancer.