A tool for analysis of gene-specific DNA methylation in clinical samples

用于分析临床样本中基因特异性 DNA 甲基化的工具

• 批准号: 8074218
• 负责人: VICTOR V LEVENSON
• 金额: $ 23.82万
• 依托单位: RUSH UNIVERSITY MEDICAL CENTER
• 依托单位国家: 美国
• 财政年份: 2009
• 资助国家: 美国
• 起止时间: 2009-09-26 至 2011-08-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8074218
• 关键词: tool; analysis; gene; specific; DNA

DESCRIPTION (provided by applicant): In many cases, early detection of disease improves outcomes; as a result, search for molecular biomarkers became an important direction in biomedical research. Ideally, disease-specific biomarkers should be sensitive, specific, inexpensive, versatile, rapid, and observer-independent to allow objective screening of asymptomatic people. In addition, it would be advantageous to have a uniform platform for development of biomarkers for multiple diseases. Changes in DNA methylation are found in different diseases and can be detected in circulating cell-free DNA from blood; however, there is only a certain probability of methylation for each specific site. To solve this problem and increase the accuracy of detection, a composite biomarker with multiple informative elements can be used. While the multitude of methylation sites indicates that multiple potential components exit for each biomarker, selection of informative components is difficult and requires a platform for simultaneous measurements of methylation in multiple sites of each clinical sample. Such a tool will be developed in this project (Aim 1) and its performance will be tested by selecting informative elements for a breast cancer biomarker (Aim 2). The proposed tool consists of a customized array for methylation detection in promoters of genes that are known to be methylated in different diseases; a procedure for isolating cell-free DNA from small amounts of plasma; and a technique for methylation detection in this DNA. The approach was tested with a 56 gene prototype; accuracy of detection was 70-90% for different diseases. The proposed array will contain the majority of abnormally methylated genes that can be analyzed by this technique in order to select additional highly informative genes and increase the accuracy. To confirm the utility of the tool, biomarkers for detection of invasive breast cancer and ductal carcinoma in situ will be developed. As a result, biomarker components for one of the most frequent cancers in females will be identified as well. Once the problem of finding informative elements is solved, only they will be measured in a dedicated screening assay for breast cancer. It is likely that the tool will find application for biomarker research in different clinical areas - e.g. in oncology, psychiatry, prenatal diagnostics, and pharmacology - and in other areas of biology, e.g. in embryology and in stem cell research, where methylation is involved in imprinting and embryonic programming. Public Health Relevance Statement: In this project a platform for testing DNA methylation in multiple sites will be developed and validated with DNA from blood of healthy women and breast cancer patients. The developed platform will allow selection of blood-based biomarkers for different diseases, which will translate into a rapid, inexpensive, and very accurate test for their detection.

描述（由申请人提供）：在许多情况下，早期发现疾病可以改善结果；因此，寻找分子生物标志物成为生物医学研究的一个重要方向。理想情况下，疾病特异性生物标志物应该敏感、特异、廉价、通用、快速且独立于观察者，以便对无症状人群进行客观筛查。此外，拥有一个统一的平台来开发多种疾病的生物标志物将是有利的。 DNA 甲基化的变化存在于不同的疾病中，并且可以在血液中的循环游离 DNA 中检测到；然而，每个特定位点只有一定的甲基化概率。为了解决这个问题并提高检测的准确性，可以使用具有多种信息元素的复合生物标志物。虽然大量甲基化位点表明每个生物标志物存在多个潜在成分，但选择信息成分很困难，并且需要一个平台来同时测量每个临床样本的多个位点的甲基化。该项目将开发这样的工具（目标 1），并将通过选择乳腺癌生物标志物的信息元素来测试其性能（目标 2）。所提出的工具包括一个定制的阵列，用于检测已知在不同疾病中发生甲基化的基因启动子的甲基化；从少量血浆中分离游离 DNA 的程序；以及该 DNA 中甲基化检测的技术。该方法用 56 个基因原型进行了测试；对于不同疾病的检测准确率可达70-90%。所提出的阵列将包含大多数异常甲基化基因，可以通过该技术进行分析，以便选择额外的信息丰富的基因并提高准确性。为了证实该工具的实用性，将开发用于检测浸润性乳腺癌和导管原位癌的生物标志物。因此，女性最常见癌症之一的生物标志物成分也将被确定。一旦找到信息元素的问题得到解决，只有它们将在专门的乳腺癌筛查测定中进行测量。该工具很可能会在不同临床领域的生物标志物研究中得到应用——例如。在肿瘤学、精神病学、产前诊断和药理学以及其他生物学领域，例如在胚胎学和干细胞研究中，甲基化涉及印记和胚胎编程。 公共卫生相关性声明：在该项目中，将开发一个用于在多个位点测试 DNA 甲基化的平台，并使用健康女性和乳腺癌患者血液中的 DNA 进行验证。开发的平台将允许为不同疾病选择基于血液的生物标志物，这将转化为快速、廉价且非常准确的检测方法。