Center of Growth, Metabolism, and Aging, Key Laboratory of Bio-Resources and Eco-Environment, College of Life Sciences, Sichuan University, Chengdu, Sichuan, 610064, China.
Jiangsu Center for the Collaboration and Innovation of Cancer Biotherapy, Xuzhou, Jiangsu, 221002, China.
BMC Genomics. 2018 Feb 13;19(1):138. doi: 10.1186/s12864-018-4525-0.
The integration of DNA methylation and copy number alteration data promises to provide valuable insight into the underlying molecular mechanisms responsible for cancer initiation and progression. However, the generation and processing of these datasets are costly and time-consuming if carried out separately. The Illumina Infinium HumanMethylation450 BeadChip, initially designed for the evaluation of DNA methylation levels, allows copy number variant calling using bioinformatics tools.
A substantial amount of Infinium HumanMethylation450 data across various cancer types has been accumulated in recent years and is a valuable resource for large-scale data analysis. Here we present MethCNA, a comprehensive database for genomic and epigenomic data integration in human cancer. In the current release, MethCNA contains about 10,000 tumor samples representing 37 cancer types. All raw array data were collected from The Cancer Genome Atlas and NCBI Gene Expression Omnibus database and analyzed using a pipeline that integrated multiple computational resources and tools. The normalized copy number aberration data and DNA methylation alterations were obtained. We provide a user-friendly web-interface for data mining and visualization.
The Illumina Infinium HumanMethylation450 BeadChip enables the interrogation and integration of both genomic and epigenomic data from exactly the same DNA specimen, and thus can aid in distinguishing driver from passenger mutations in cancer. We expect MethCNA will enable researchers to explore DNA methylation and copy number alteration patterns, identify key oncogenic drivers in cancer, and assist in the development of targeted therapies. MethCNA is publicly available online at http://cgma.scu.edu.cn/MethCNA .
将 DNA 甲基化和拷贝数改变数据整合在一起，有望为癌症发生和发展的潜在分子机制提供有价值的见解。然而，如果单独进行，这些数据集的生成和处理既昂贵又耗时。最初设计用于评估 DNA 甲基化水平的 Illumina Infinium HumanMethylation450 BeadChip 可使用生物信息学工具进行拷贝数变异体调用。
近年来，已经积累了大量不同癌症类型的 Infinium HumanMethylation450 数据，这是进行大规模数据分析的宝贵资源。在这里，我们提出了 MethCNA，这是一个用于人类癌症中基因组和表观基因组数据整合的综合数据库。在当前版本中，MethCNA 包含约 10000 个肿瘤样本，代表 37 种癌症类型。所有原始阵列数据均来自癌症基因组图谱和 NCBI Gene Expression Omnibus 数据库，并使用集成了多个计算资源和工具的管道进行分析。获得了归一化的拷贝数异常数据和 DNA 甲基化改变。我们提供了一个用户友好的网络界面，用于数据挖掘和可视化。
Illumina Infinium HumanMethylation450 BeadChip 能够对来自同一 DNA 样本的基因组和表观基因组数据进行询问和整合，从而有助于区分癌症中的驱动突变和乘客突变。我们预计 MethCNA 将使研究人员能够探索 DNA 甲基化和拷贝数改变模式，识别癌症中的关键致癌驱动因子，并有助于开发靶向治疗。MethCNA 可在 http://cgma.scu.edu.cn/MethCNA 上在线公开获取。
