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Open Access Data Note

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

Francesco M Mancuso1*, Magda Montfort2, Anna Carreras3, Andreu Alibés1 and Guglielmo Roma1*

Author Affiliations

1 Bioinformatics Unit, Centre for Genomic Regulation (CRG) and UPF, Dr. Aiguader 88, 08003 Barcelona, Spain

2 Genotyping Unit-Centro Nacional de Genotipado (CeGen), Centre for Genomic Regulation (CRG) and UPF, Dr. Aiguader 88, 08003 Barcelona, Spain

3 Genes and Disease Programme, Centre for Genomic Regulation (CRG) and UPF, Dr. Aiguader 88, 08003 Barcelona, Spain

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BMC Research Notes 2011, 4:546  doi:10.1186/1756-0500-4-546

Published: 19 December 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.