Analysis pipelines and packages for Infinium HumanMethylation450 BeadChip (450k) data

Area of Science:

• Genomics and Bioinformatics
• Epigenetics and DNA Methylation Analysis

Background:

• The Illumina HumanMethylation450 BeadChip is a widely adopted platform for DNA methylation profiling.
• Its use has surged in large-scale projects like the International Cancer Genome Consortium (ICGC) and International Human Epigenome Consortium (IHEC).
• This has led to a substantial increase in 450k methylation data and the development of diverse analysis tools.

Purpose of the Study:

• To review and discuss the most popular analysis pipelines and standalone packages for Illumina HumanMethylation450 BeadChip data.
• To provide guidance for new users entering the field of 450k DNA methylation analysis.
• To facilitate efficient and effective utilization of the growing body of 450k epigenomic data.

Main Methods:

• Literature review and comparative analysis of existing software.
• Identification and discussion of currently popular integrated analysis pipelines.
• Evaluation of standalone packages commonly used for 450k data processing and interpretation.

Main Results:

• An overview of key pipelines and packages for handling Illumina HumanMethylation450 BeadChip data is presented.
• The review highlights tools suitable for various stages of epigenome-wide association studies (EWAS) and epigenomic resource projects.
• Popular options are discussed in terms of their features, usability, and suitability for new researchers.

Conclusions:

• Numerous analysis pipelines and packages are available to support the growing use of the HumanMethylation450 BeadChip.
• This review serves as a valuable resource for new users to navigate and select appropriate tools for their DNA methylation studies.
• Effective utilization of these tools is crucial for advancing research in epigenetics and related fields.