Highly Multiplexed FISH for In Situ Genomics

用于原位基因组学的高度多重 FISH

基本信息

批准号：
9065528
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
项目类别：
财政年份：
2015
资助国家：
美国
起止时间：
2015-05-08 至 2018-04-30
项目状态：
已结题

来源：
https://reporter.nih.gov/project-details/9065528
关键词：
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 DNA DNA Probes DNA Sequence Data Detection Development Diagnostic Diagnostic tests Dimensions 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 Health Heterogeneity 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 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 screening sequencing platform spectrograph targeted treatment technology development therapeutic target treatment response tumor tumor DNA tumor heterogeneity

项目摘要

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，我们将重点关注其拷贝数变异代表可能可行的治疗的基因。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，以最佳方式构建、测试和验证一个检测平台。这一目标将通过两个目标来实现：目标 I. 开发一个强大的、可重复的方法。用于构建至少 50 个位点特异性 DNA 序列探针的文库的测定我们将使用组合标记方法，其中每个探针都用每个探针的两个或三个荧光团的组合进行条形码编码，从而允许最多 120 个 DNA 探针。我们将开发一个成像系统来解码组合标签，记录、量化和分析获得的数据，我们将通过筛选可操作的数据来测试该测定的临床实用性。手术活检标本和分离的循环肿瘤细胞（CTC）中的基因拷贝数变化这项技术的发展将使我们能够更进一步地解决以下问题：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。在治疗后续过程中对 CTC 拷贝数谱的评估可以预测对治疗的反应。该项目将作为诊断方法的开发和临床实施的模型，以造福于患者，并将用于向患者传播知识和专业知识。临床癌症诊断领域一般的。