Genomic Analysis of Gene Copy Number in Thyroid Cancer

描述(申请人提供)：特定基因拷贝数的变化有助于人类肿瘤的发展。比较基因组与cDNA微阵列杂交(ARRAY-CGH)是一种新兴的检测这些遗传变化的功能基因组技术。使用ARRAY-CGH，我们已经获得了在切尔诺贝利事故中暴露于电离辐射的儿童的甲状腺上皮癌中存在的多个聚集性基因座广泛存在的初步证据，但在没有已知辐射暴露的美国儿童的可比甲状腺上皮癌中则没有。我们假设基因组中存在一个通过低水平的基因扩增对辐射做出反应的位置池。为了扩展我们最初的发现，并检验我们的假设，我们将收集和分析同一人群中的新甲状腺癌病例。这一新材料将使我们能够获得有关甲状腺中辐射相关基因拷贝数变化的肿瘤特异性、暴露年龄、肿瘤潜伏期和估计辐射剂量对基因拷贝数变化的关系的数据。利用人类基因组序列，我们将在基因组中绘制这些明显辐射效应的相对敏感度。此外，我们将尝试通过利用在肿瘤相关扩增中存在长回文的报道来增强阵列CGH技术。在阵列分析中，用于长回文的丰富的探针将与传统的DNA片段进行比较。一种新的人类BAC阵列将被选择性地用于补充从cDNA阵列获得的数据，以便在需要的地方更好地定义扩增产物。最后，通过这些新获得的患者样本，我们将利用微阵列技术的力量来探索基因复制变化与基因表达水平的关系，并寻找在这些甲状腺癌中持续过度表达的候选癌基因。该项目的完成将增强阵列CGH作为一种在全基因组范围内检测和定位基因拷贝数变化的技术，并为辐射诱发甲状腺肿瘤的潜在机制提供更完整的描述。

DESCRIPTION (provided by applicant): Changes in copy-number of specific genes contributes to the development of human neoplasia. Comparative genomic hybridization to cDNA microarrays (array-CGH) is an emerging functional genomic technique for detecting these genetic changes. Using array-CGH we have obtained preliminary evidence of widespread gene amplification in multiple, clustered loci present in thyroid epithelial cancers from children who were exposed to ionizing radiation from the Chernobyl accident, but not in comparable thyroid epithelial cancers from US children lacking known radiation exposure. We hypothesize the existence of a pool of sites in the genome which respond to radiation by low level gene amplification. To extend our initial findings, and test our hypothesis, we will collect and analyze new thyroid cancer cases from the same population. This fresh material will allow us to obtain data regarding the tumor-specificity of radiation-associated gene copy number change in the thyroid, the relationship of age at exposure, tumor latency and estimated radiation dose on gene copy number change. Taking advantage of the human genome sequence, we will map relative sensitivity of these apparent radiation effects within the genome. Additionally we will attempt to enhance the array CGH techniques by exploiting the reported presence of long palindromes in tumor-associated amplicons. Probes enriched for long palindromes will be compared with conventional DNA fragments in array analysis. A new human BAC array will be used selectively to supplement data obtained from cDNA arrays to better define amplicons where needed. Finally, by means of these newly acquired patient samples, we will exploit the power of microarray technology to explore the relationship of gene copy change to gene expression levels, and to seek candidate oncogenes consistently over expressed in these thyroid cancers. Completion of this project will enhance array CGH as a technique for detecting and mapping changes in gene copy-number on a genome-wide scale, and provide a more complete description of mechanisms underlying radiation-induce thyroid neoplasia.