HumMeth27QCReport: an R package for quality control and primary analysis of Illumina Infinium methylation data - PubMed (original) (raw)

HumMeth27QCReport: an R package for quality control and primary analysis of Illumina Infinium methylation data

Francesco M Mancuso et al. BMC Res Notes. 2011.

Abstract

Background: The study of the human DNA methylome has gained particular interest in the last few years. Researchers can nowadays investigate the potential role of DNA methylation in common disorders by taking advantage of new high-throughput technologies. Among these, Illumina Infinium assays can interrogate the methylation levels of hundreds of thousands of CpG sites, offering an ideal solution for genome-wide methylation profiling. However, like for other high-throughput technologies, the main bottleneck remains at the stage of data analysis rather than data production.

Findings: We have developed HumMeth27QCReport, an R package devoted to researchers wanting to quickly analyse their Illumina Infinium methylation arrays. This package automates quality control steps by generating a report including sample-independent and sample-dependent quality plots, and performs primary analysis of raw methylation calls by computing data normalization, statistics, and sample similarities. This package is available at CRAN repository, and can be integrated in any Galaxy instance through the implementation of ad-hoc scripts accessible at Galaxy Tool Shed.

Conclusions: Our package provides users of the Illumina Infinium Methylation assays with a simplified, automated, open-source quality control and primary analysis of their methylation data. Moreover, to enhance its use by experimental researchers, the tool is being distributed along with the scripts necessary for its implementation in the Galaxy workbench. Finally, although it was originally developed for HumanMethylation27, we proved its compatibility with data generated with the HumanMethylation450 Bead Chip.

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Figures

Figure 1

Figure 1

HumMeth27QCReport pipeline. Standard analysis workflow of Illumina Methylation Assay data. Steps facilitated by H_umMeth27QCReport_ are included in dark gray box.

Figure 2

Figure 2

Internal controls. Examples of sample-independent (A) and sample-dependent (B) plots generated by the HumMeth27QCReport package. a. Hybridization control, to check synthetic targets at low, medium, and high concentration level. Low percentage for each level is an indication of good performance; b. bisulfite control on green channel, to monitor the efficiency of genomic-DNA bisulfite conversion using the Infinium I assay design. Low percentage is an indication of good performance, whereas if the percentage is high we consider that the sample has lower performance. A detailed explanation of each plot is available at the HumMeth27QCReport homepage (

http://biocore.crg.es/wiki/HumMeth27QCReport

). JUR: Jurkat DNA; JUR MET: methylated Jurkat DNA; UNMET: unmethylated DNA; EZGOLD: EZ DNA Methylation-Gold Kit (Zymo Research, CA, USA); QIAGEN: EpiTect Bisulfite Kit (QiaGen); BIO1: biological replicate 1; BIO2: biological replicate 2; PD3 Amyg: example of sample of poor quality.

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