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（由应用程序提供）：本应用程序的总体目的是设计和开发一项技术，允许使用广泛基因库中的问题进行高度多重的荧光原位杂交。我们将专注于拷贝数变化代表可能可行的治疗靶标的基因。我们将建立，测试和验证一个最佳测定平台，以利用我们长期实施癌症异常诊断测试的经验。这一目标将在两个目标中实现：目标I。开发一种可重复的，可再现的测定法，以构建至少50个基因座特异性DNA序列问题的库。我们将使用一种组合标记方法，在该方法中，每个探针都用每个探针的两个或三个荧光团组合进行钢筋编码，从而使多达120个DNA问题简单地杂交。我们将开发一个成像系统来解码组合标签，记录，量化和分析所获得的数据。目标II。我们将开始通过筛选手术活检标本和分离的循环肿瘤细胞（CTC）中可起作的基因拷贝数改变来测试测定的临床实用性。这项技术的开发将使我们能够越来越近，以解决肿瘤异质性的特定特定动态的问题，这是对治疗的响应而变化的基础，以及对治疗后续的CTC拷贝数概况的评估是否可以预测治疗的反应。该项目将成为开发和临床实施诊断对患者益处的模型，并将用于将知识和专业知识传播到临床癌症诊断领域。