Mah Clarence K, Mesirov Jill P, Chavez Lukas
Department of Medicine, University of California, San Diego, La Jolla, CA, 92093, USA.
Moores Cancer Center, University of California, San Diego, La Jolla, CA, 92093, USA.
F1000Res. 2018 Dec 5;7. doi: 10.12688/f1000research.16338.1. eCollection 2018.
Illumina Infinium DNA methylation arrays are a cost-effective technology to measure DNA methylation at CpG sites genome-wide and across cohorts of normal and cancer samples. While copy number alterations are commonly inferred from array-CGH, SNP arrays, or whole-genome DNA sequencing, Illumina Infinium DNA methylation arrays have been shown to detect copy number alterations at comparable sensitivity. Here we present an accessible, interactive GenePattern notebook for the analysis of copy number variation using Illumina Infinium DNA methylation arrays. The notebook provides a graphical user interface to a workflow using the R/Bioconductor packages and . The environment allows analysis to be performed without the installation of the R software environment, the packages and dependencies, and without the need to write or manipulate code.
Illumina Infinium DNA甲基化芯片是一种经济高效的技术，可在全基因组范围内以及在正常和癌症样本队列中测量CpG位点的DNA甲基化。虽然拷贝数改变通常可从阵列比较基因组杂交（array-CGH）、单核苷酸多态性（SNP）芯片或全基因组DNA测序中推断出来，但Illumina Infinium DNA甲基化芯片已被证明能以相当的灵敏度检测拷贝数改变。在此，我们展示了一个易于使用的交互式GenePattern笔记本，用于使用Illumina Infinium DNA甲基化芯片分析拷贝数变异。该笔记本为使用R/Bioconductor软件包和的工作流程提供了图形用户界面。该环境允许在不安装R软件环境、软件包及其依赖项的情况下进行分析，也无需编写或操作代码。
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