BAC-FISH Assays for Sensitive Karyotyping of Cancer Cells

描述（由申请人提供）：特别是对人类肿瘤和癌组织的详细细胞遗传学分析，揭示了大多数情况下存在结构性染色体异常。潜在的变化通常对肿瘤或癌症的类型和细胞改变的表型具有特异性。此外，研究人员可以证明染色体变化的类型或程度，疾病进展和结果之间的相关性。然而，目前的实验室技术的结构异常的筛选是非常有限的检测小，“神秘”易位。例如，中期染色体的Giemsa（G）-显带或基于荧光原位杂交（FISH）的全染色体涂染（WCP）技术和光谱核型分析（SKY）通常错过涉及小于10兆碱基对（Mbp）的区段的易位，即，大约是染色体带的大小。我们推测，小的隐性易位存在未被检测到的基因组中的一个正常的表型或疾病，如精神发育迟滞，生育能力受损，癌前病变，或早期肿瘤的个体。有关结构改变和染色体不平衡的知识可能有助于临床医生对疾病的发病和病程做出更准确的预测。这个R21项目将研究快速和廉价地筛选人类基因组中是否存在隐匿性隐性易位（OCT）的可行性。具体而言，我们将使用经验证的染色体特异性细菌人工染色体（BAC）的集合开发和测试FISH测定法，用于检测人类癌细胞中的OCT。BAC探针平均间隔0.9 Mbp，覆盖人类基因组的整个常染色质部分，我们希望我们的“BAC-FISH”检测与WCP或显带检测相比，灵敏度大大提高。我们的创新检测灵敏的全基因组筛查易位将开发与癌细胞系的结构异常的信息有限。在这个项目结束时，我们将有能力对正常人群和肿瘤细胞中OCT的频率进行更大规模的研究，并为研究和临床实验室提供BAC-FISH筛查服务和试剂进行合作研究。

DESCRIPTION (provided by applicant): The detailed cytogenetic analyses of human tumors and cancer tissues, in particular, have revealed the presence of structural chromosome abnormalities in most of cases. The underlying changes are often specific for the type of tumor or cancer and the cells' altered phenotype. Furthermore, investigators could demonstrate a correlation between the type or extent of chromosome changes, disease progression, and outcome. However, present laboratory techniques for the screening for structural abnormalities are very limited with respect to the detection of small, 'cryptic' translocations. For example, Giemsa (G)-banding of metaphase chromosomes or the fluorescence in situ hybridization (FISH)-based techniques of whole chromosome painting (WCP) and Spectral Karyotyping (SKY) analysis typically miss translocations that involve segments of less than 10 megabasepairs (Mbp), i.e., about the size of a chromosome band. We postulate that small cryptic translocations exist undetected in the genomes of individuals with a normal phenotype or diseases such as mental retardation, impaired fertility, precancerous lesions, or early stage tumors. Knowledge about structural alterations and chromosomal imbalances might help clinicians make more accurate predictions regarding the onset and course of a disease. This R21 project will investigate the feasibility to rapidly and inexpensively screen the human genome for the presence of occult cryptic translocations (OCTs). Specifically, we will develop and test FISH assays using collections of validated chromosome-specific bacterial artificial chromosomes (BACs) for the detection of OCTs in human cancer cells. With BAC probes spaced on average 0.9 Mbp apart and covering the entire euchromatic part of the human genome, we expect our 'BAC-FISH' assay to lead to greatly increased sensitivity compared to WCP or banding tests. Our innovative assay for sensitive genome-wide screening for translocations will be developed with cancer cell lines for which limited information about structural abnormalities is available. At the end of this project, we will be well positioned to conduct a larger study of the frequency of OCTs in the normal population as well as tumor cells and to offer BAC-FISH screening service and reagents to research and clinical laboratories for collaborative studies.