Highly Multiplexed FISH for In Situ Genomics

用于原位基因组学的高度多重 FISH

• 批准号: 9248273
• 负责人: Anthony John Iafrate
• 金额: $ 24.51万
• 依托单位: MASSACHUSETTS GENERAL HOSPITAL
• 依托单位国家: 美国
• 财政年份: 2015
• 资助国家: 美国
• 起止时间: 2015-05-08 至 2019-04-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/9248273
• 关键词: 3-Dimensional; Address; Algorithms; Amendment; Bar Codes; Biological Assay; Biopsy; Biopsy Specimen; Cancer Diagnostics; Cancer cell line; Cell Nucleus; Cells; Chromosome abnormality; Chromosomes; Clinic; Clinical; Clinical Data; Community Clinical Oncology Program; Computer software; Copy Number Polymorphism; Custom; Cytology; DNA; DNA Probes; DNA Sequence; Data; Detection; Development; Diagnostic; Diagnostic tests; ERBB2 gene; Epidermal Growth Factor Receptor; Evaluation; Event; Fluorescence Microscopy; Fluorescent in Situ Hybridization; Gene Amplification; Gene Deletion; Gene Dosage; Gene Library; Genes; Genetic Heterogeneity; Genomics; Genotype; Glioblastoma; Gold; Heterogeneity; Hybrids; Image; Image Analysis; In Situ; Informatics; Institution; Knowledge; Label; Laboratories; Libraries; Malignant Neoplasms; Methods; Microscope; Mutation; Neoplasm Circulating Cells; Noise; Normal tissue morphology; Operative Surgical Procedures; Optics; PTEN gene; Patients; Performance; Population Heterogeneity; Recurrence; Reproducibility; Resolution; Sampling; Signal Transduction; Slide; Software Tools; Specificity; Specimen; Spottings; Techniques; Technology; Testing; Therapeutic; Time; Tissues; Variant; cancer cell; cell preparation; cohort; combinatorial; comparative genomic hybridization; computerized data processing; deep sequencing; design; diagnostic assay; digital; digital imaging; experience; fluorophore; follow-up; genetic profiling; genome-wide; imaging system; improved; microscopic imaging; model development; neoplastic cell; next generation sequencing; predicting response; public health relevance; screening; sequencing platform; spectrograph; targeted treatment; technology development; therapeutic target; treatment response; tumor; tumor DNA; tumor heterogeneity

 DESCRIPTION (provided by applicant): The overall objective of this application is to design and develop a technology permitting highly- multiplexed fluorescence in situ hybridization using probes from a broad library of genes. We will focus on genes whose copy number variation represents possible actionable therapeutic targets. We will build, test and validate an optimal assay platform leveraging our long-standing experience implementing diagnostic tests for chromosomal abnormalities in cancer. This objective will be achieved in two aims: Aim I. Develop a robust, reproducible assay for constructing a library of at least 50 locus-specific DNA sequence probes. We will use a combinatorial labeling approach in which each probe is bar-coded with a combination of two or three fluorophores per probe, allowing for up to 120 DNA probes to be simultaneously hybridized. We will develop an imaging system to decode the combinatorial label, record, quantify and analyze the obtained data. Aim II. We will begin to test the clinical utility of the assay by screening for actionable gene copy number alterations in surgical biopsy specimens and in isolated circulating tumor cells (CTCs). The development of this technology will allow us to get closer to address the question of whether patient-specific dynamics of tumor heterogeneity underlie variation in response to treatment and whether the evaluation of CTCs copy number profile in the follow up of treatment can predict response to therapy. This project will serve as a model for development and clinical implementation of diagnostics for the benefit of patients, and will be used to disseminate knowledge and expertise to the clinical cancer diagnostic field in general.

 描述（由申请人提供）：本申请的总体目标是设计和开发一种允许使用来自广泛基因库的探针进行高度多重荧光原位杂交的技术。我们将重点关注拷贝数变异代表可能的可行治疗靶点的基因。我们将利用我们在癌症染色体异常诊断测试方面的长期经验，构建、测试和验证最佳检测平台。这一目标将通过两个目标来实现： 目标 I. 开发一种强大的、可重复的检测方法，用于构建至少 50 个位点特异性 DNA 序列探针的文库。我们将使用组合标记方法，其中每个探针都带有两个或三个荧光团组合的条形码，允许多达 120 个 DNA 探针同时杂交。我们将开发一种成像系统来解码组合标签，记录、量化和分析获得的数据。目标二。我们将通过筛选手术活检标本和分离的循环肿瘤细胞（CTC）中可操作的基因拷贝数变化来开始测试该测定的临床实用性。这项技术的发展将使我们能够更进一步地解决这样的问题：患者特异性的肿瘤异质性动态是否是治疗反应变化的基础，以及在治疗后续过程中对 CTC 拷贝数谱的评估是否可以预测对治疗的反应。该项目将作为诊断开发和临床实施的模型，造福于患者，并将用于向整个临床癌症诊断领域传播知识和专业知识。