Wu Michael C, Kuan Pei-Fen
Public Health Sciences Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, M3-C102, Seattle, WA, 98109, USA.
Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, NY, USA.
Methods Mol Biol. 2018;1708:303-330. doi: 10.1007/978-1-4939-7481-8_16.
The Illumina Infinium BeadChips are a powerful array-based platform for genome-wide DNA methylation profiling at approximately 485,000 (450K) and 850,000 (EPIC) CpG sites across the genome. The platform is used in many large-scale population-based epigenetic studies of complex diseases, environmental exposures, or other experimental conditions. This chapter provides an overview of the key steps in analyzing Illumina BeadChip data. We describe key preprocessing steps including data extraction and quality control as well as normalization strategies. We further present principles and guidelines for conducting association analysis at the individual CpG level as well as more sophisticated pathway-based association tests.
Illumina Infinium 芯片是一个强大的基于阵列的平台，可在全基因组范围内约485,000个（450K）和850,000个（EPIC）CpG位点进行DNA甲基化分析。该平台用于许多基于大规模人群的复杂疾病、环境暴露或其他实验条件的表观遗传学研究。本章概述了分析Illumina芯片数据的关键步骤。我们描述了关键的预处理步骤，包括数据提取和质量控制以及标准化策略。我们还介绍了在单个CpG水平进行关联分析以及更复杂的基于通路的关联测试的原则和指南。
