High resolution DNA copy/LOH measurements on WGG arrays

描述(申请人提供)：基因组异常，如先天性染色体失衡，可能从出生就存在，也可能在细胞分裂过程中出现，从而导致癌症的形成。可以通过监测基因组的变化来跟踪癌症的进展。例如，肿瘤抑制基因的等位基因缺失和癌基因的放大是癌症发生过程中众所周知的事件。该项目的主要目标是开发一种基于高分辨率阵列的方法来检测和监测肿瘤样本的变化。第二个目标是检测先天性染色体疾病中的微缺失和扩增。拟议的工作将集中于使用我们新的全基因组基因分型(WGG)平台开发DNA复制和杂合性丢失(LOH)测量。工作组的技术部分是通过第一阶段资金开发的。在第一阶段，我们开发了一种全基因组扩增方案和一种基于阵列的引物延伸分析，可以直接读出基因组--包括拷贝数和基因类型。这一发展消除了对原始提议的复杂性降低步骤(简化表示)的需要。可以从单个样本中读出的基因类型的数量仅受阵列上的探针数量的限制。这项拟议的工作将使用目前正在开发的WGG阵列来同时进行基因分型和拷贝数分析，整个基因组的平均分辨率约为30kb。这一革命性的检测系统将使基因组改变的区域得到精确、准确和强有力的定义，并有可能直接用于临床应用。一旦完全开发，该分析将被用于表征生物肿瘤/正常样本对以及先天性染色体失衡。

DESCRIPTION (provided by applicant): Anomalies of the genome, such as congenital chromosomal imbalances, can be present from birth or can arise during cell division and lead to formation of cancer. Progression of cancer can be followed by monitoring changes in the genome. For instance, allelic deletions of tumor suppressor genes and amplifications of oncogenes are well known events in carcinogenesis. The primary goal of this project is to develop a high resolution array-based approach to detecting and monitoring changes in tumor samples. A secondary goal is to detect microdeletions and amplifications in congenital chromosomal disorders. The proposed work will focus on developing DNA copy and loss of heterozygosity (LOH) measurements using our novel whole genome genotyping (WGG) platform. The WGG technology was developed, in part, through phase I funding. Under phase I, we developed a whole genome amplification protocol and an arraybased primer extension assay that enabled direct readout of the genome - both copy number and genotypes. This development obviates the need for the original proposed complexity reduction step (reduced representation). The number of genotypes that can be read out from a single sample is limited only by the number of probes on the array. The proposed work will use a WGG array that is currently under development to perform genotyping and copy number analysis at the same time, at an average resolution of approximately 30 kb across the genome. This revolutionary assay system will allow regions of genomic alteration to be precisely defined accurately and robustly, and has the potential to be used directly in clinical applications. Once fully developed, the assay will be employed to characterize biological tumor/normal sample pairs as well as congenital chromosomal imbalances.