Array-based methylation analysis using anti-5mC antibody

使用抗 5mC 抗体进行基于阵列的甲基化分析

• 批准号: 7267930
• 负责人: FUMIICHIRO YAMAMOTO
• 金额: $ 17.62万
• 依托单位: SANFORD BURNHAM PREBYS MEDICAL DISCOVERY INSTITUTE
• 依托单位国家: 美国
• 财政年份: 2006
• 资助国家: 美国
• 起止时间: 2006-07-01 至 2009-06-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/7267930
• 关键词: Antibodies; Applications Grants; Breast; Condition; DNA; DNA Methylation; DNA Microarray Chip; DNA Microarray format; Dependence; Detection; Development; Embryonic Development; Fluorescence; Genome; Global Change; Label; Malignant neoplasm of prostate; Methods; Methylation; Mind; Mus; Nature; Oligonucleotide Microarrays; Pilot Projects; Population; Reproducibility; Research Project Grants; Role; Sensitivity and Specificity; Techniques; Testing; Work; base; cancer diagnosis; cancer type; clinical application; concept; interest; magnetic beads; novel; research study; restriction enzyme

DESCRIPTION (provided by applicant): An alteration in DNA methylation is one of the most prominent changes associated with early embryo development, cellular differentiation, and progression of many types of cancers, including breast and prostate cancers. In the past several years we have been developing techniques to detect alterations in DNA methylation, targeting potential clinical applications for cancer diagnosis. The DNA Microarray MS- AFLP method that we developed has been proven to be useful in detecting DNA methylation alterations at the Notl landmarks in the genome. However, the utility has been limited due to the absence of commercial interest in producing the DNA microarrays based on the technique. The dependence on Notl restriction enzymes to identify the methylated regions has also restricted the scope of interrogation of the genome. Keeping this in mind, we propose, in this Exploratory/Developmental R21 Research Grant application, to perform several pilot experiments to test the feasibility of a conceptually novel method for the detection of alterations in DNA methylation that can utilize the DNA microarrays that are currently available. As with any pilot study, this project is risky in nature because we have not experimentally tested the concept yet. However, if proven feasible, the new method may achieve a revolutionary role in analyzing the genome- wide detection of global changes in DNA methylation. In this application, we propose the following two specific aims. 1. To examine the utility of anti-5-methylcytosine (anti-5mC) antibodies toward the magnetic bead-based separation of methylated and unmethylated DNA fragment populations. We will establish the experimental conditions under which 2 different fractions rich in methylated and unmethylated DNA fragments may be separated, using anti-5mC. 2. To examine the utility of methylated and unmethylated DNA fragment populations separated above toward the array-based detection of differences in DNA methylation. We will fluorescently label DNA from those 2 fractions and perform DNA microarray hybridization experiments. We will evaluate the sensitivity, specificity, and reproducibility of the method, using BAG clone microarrays, DNA fragment microarrays, and oligonucleotide microarrays.

描述（由申请人提供）：DNA甲基化的改变是与早期胚胎发育、细胞分化和许多类型癌症（包括乳腺癌和前列腺癌）进展相关的最显著变化之一。在过去的几年里，我们一直在开发检测DNA甲基化改变的技术，目标是癌症诊断的潜在临床应用。我们开发的DNA微阵列MS-AFLP方法已被证明可用于检测基因组中Notl标志点的DNA甲基化改变。然而，由于在基于该技术生产DNA微阵列方面缺乏商业兴趣，该实用性受到限制。依赖于NotI限制酶来鉴定甲基化区域也限制了基因组的询问范围。考虑到这一点，我们建议，在这个探索性/发展性R21研究资助申请，进行几个试点实验，以测试一个概念上的新方法的可行性，用于检测DNA甲基化的改变，可以利用目前可用的DNA微阵列。与任何试点研究一样，这个项目本质上是有风险的，因为我们还没有对这个概念进行实验测试。但是，如果被证明是可行的，新方法可能会在分析DNA甲基化全局变化的全基因组检测方面实现革命性的作用。在本申请中，我们提出以下两个具体目标。1.检测抗5-甲基胞嘧啶（抗5 mC）抗体对基于磁珠的甲基化和非甲基化DNA片段群体分离的效用。我们将建立实验条件，在此条件下，可以使用抗5 mC分离富含甲基化和未甲基化DNA片段的2种不同组分。2.为了检查上述分离的甲基化和未甲基化DNA片段群体对基于阵列的DNA甲基化差异检测的效用。我们将荧光标记DNA从这2个部分，并进行DNA微阵列杂交实验。我们将使用BAG克隆微阵列、DNA片段微阵列和寡核苷酸微阵列评估该方法的灵敏度、特异性和重复性。