COHCAP: City of Hope CpG Island Analysis Pipeline. COHCAP: City of Hope CpG Island Analysis Pipeline

COHCAP (City of Hope CpG Island Analysis Pipeline) is an algorithm to analyze single-nucleotide resolution DNA methylation data. It provides QC metrics, differential methylation for CpG Sites, differential methylation for CpG Islands, integration with gene expression data, and visualization of methylation values. COHCAP is currently the only DNA methylation package that can handle integration with gene expression data, and the results of this study show that COHCAP can identify regions of differential methylation with ~50% concordance with gene expression. COHCAP is scalable for analysis of both cell line data and heterogeneous patient data, and it can identify known cancer biomarkers as well as intriguing new roles of epigenetic regulation in cancer (such as methylation of estrogen receptor in breast cancer patients). This study also uses cell line data to show that COHCAP is capable of analyzing Illumina methylation array and targeted bisulfite sequencing data, with either 1-group or 2-group study designs. The accuracy of COHCAP is accessed using qPCR, EpiTect, and comparison of COHCAP regions of differential methylation with MIRA peaks. This software is freely available at https://sourceforge.net/projects/cohcap/. The following third-party datasets were utilized in the paper: BS-Seq data: GSE26826 Additional Microarray Data: GSE29290 This SuperSeries is composed of the SubSeries listed below. Overall design: Refer to individual Series.

COHCAP（希望之城CpG岛分析流程，City of Hope CpG Island Analysis Pipeline）是一款用于分析单核苷酸分辨率DNA甲基化数据的算法工具包。它可提供质量控制（Quality Control, QC）指标、CpG位点差异甲基化分析、CpG岛差异甲基化分析、基因表达数据整合分析，以及甲基化数值可视化功能。COHCAP是目前唯一可实现基因表达数据整合分析的DNA甲基化分析工具包，本研究结果表明，COHCAP能够识别出与基因表达具有约50%一致性的差异甲基化区域。COHCAP可适配细胞系数据与异质性患者样本的分析，不仅能够识别已知的癌症生物标志物，还能揭示癌症中表观遗传调控的新颖潜在机制（例如乳腺癌患者体内雌激素受体甲基化调控现象）。本研究还通过细胞系数据证实，COHCAP可分析Illumina甲基化芯片与靶向亚硫酸氢盐测序（Bisulfite Sequencing, BS-Seq）数据，支持单组或两组的研究设计方案。COHCAP的准确性通过定量聚合酶链反应(qPCR)、EpiTect技术，以及将COHCAP鉴定的差异甲基化区域与MIRA峰进行比对得以验证。该软件可在https://sourceforge.net/projects/cohcap/免费获取使用。本论文使用了以下第三方数据集：亚硫酸氢盐测序（BS-Seq）数据：GSE26826；附加微阵列数据：GSE29290。本超系列由下述子系列构成。整体设计详情参见各单个系列。