Yan Pearlly S, Potter Dustin, Deatherage Daniel E, Huang Tim H-M, Lin Shili
Human Cancer Genetics Program, The Ohio State University Comprehensive Cancer Center, Columbus, OH, USA.
Methods Mol Biol. 2009;507:89-106. doi: 10.1007/978-1-59745-522-0_8.
Differential methylation hybridization (DMH) is a high-throughput DNA methylation screening tool that utilizes methylation-sensitive restriction enzymes to profile methylated fragments by hybridizing them to a CpG island microarray. This array contains probes spanning all the 27,800 islands annotated in the UCSC Genome Browser. Herein we describe a revised DMH protocol with clearly identified quality control points. In this manner, samples that are unlikely to provide good readouts for differential methylation profiles between the test and the control samples will be identified and repeated with appropriate modifications. In addition to the step-by-step laboratory DMH protocol, we also provide a detailed description regarding DMH data analysis. The suggested microarray platform contains 244,000 probes and it can be a daunting barrier for researchers with no prior experience in analyzing DNA methylation data. We have created a data analysis pipeline available in a user friendly, publicly available interface, the Broad Institute's GenePattern software, which can be accessed at http://bisr.osumc.edu :8080/gp. This permits scientists to use our existing data analysis modules on their own data. As we continue to update our analysis algorithm and approaches to integrate high-throughput methylation data with other large-scale data types, we will make these new computation protocols available through the GenePattern platform.
差异甲基化杂交（DMH）是一种高通量DNA甲基化筛选工具，它利用甲基化敏感的限制性内切酶，通过将甲基化片段与CpG岛微阵列杂交来分析甲基化片段。该阵列包含跨越UCSC基因组浏览器中注释的所有27,800个岛的探针。在此，我们描述了一种具有明确质量控制点的修订版DMH方案。通过这种方式，将识别出不太可能为测试样本和对照样本之间的差异甲基化谱提供良好读数的样本，并进行适当修改后重复实验。除了详细的实验室DMH方案步骤外，我们还提供了有关DMH数据分析的详细描述。建议的微阵列平台包含244,000个探针，这对于没有分析DNA甲基化数据经验的研究人员来说可能是一个令人生畏的障碍。我们创建了一个数据分析流程，可通过用户友好的公开可用界面——布罗德研究所的GenePattern软件访问，网址为http://bisr.osumc.edu :8080/gp。这使科学家能够在自己的数据上使用我们现有的数据分析模块。随着我们不断更新分析算法和方法，以将高通量甲基化数据与其他大规模数据类型整合，我们将通过GenePattern平台提供这些新的计算协议。
