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DMRforPairs: identifying Differentially Methylated Regions between unique samples using array based methylation profiles

Martin A Rijlaarsdam, Yvonne G van der Zwan, Lambert CJ Dorssers and Leendert HJ Looijenga*

Author Affiliations

Department of Pathology, Laboratory for Experimental Patho-Oncology, Erasmus MC - University Medical Center Rotterdam, Be-432, P.O. Box 2040, Rotterdam 3000 CA, Netherlands

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BMC Bioinformatics 2014, 15:141  doi:10.1186/1471-2105-15-141

Published: 15 May 2014

Abstract

Background

Array based methylation profiling is a cost-effective solution to study the association between genome methylation and human disease & development. Available tools to analyze the Illumina Infinium HumanMethylation450 BeadChip focus on comparing methylation levels per locus. Other tools combine multiple probes into a range, identifying differential methylated regions (DMRs). These tools all require groups of samples to compare. However, comparison of unique, individual samples is essential in situations where larger sample sizes are not possible.

Results

DMRforPairs was designed to compare regional methylation status between unique samples. It identifies probe dense genomic regions and quantifies/tests their (difference in) methylation level between the samples. As a proof of concept, DMRforPairs is applied to public data from four human cell lines: two lymphoblastoid cell lines from healthy individuals and the cancer cell lines A431 and MCF7 (including 2 technical replicates each). DMRforPairs identified an increasing number of DMRs related to the sample phenotype when biological similarity of the samples decreased. DMRs identified by DMRforPairs were related to the biological origin of the cell lines.

Conclusion

To our knowledge, DMRforPairs is the first tool to identify and visualize relevant and significant differentially methylated regions between unique samples.

Keywords:
DMR; Methylation; Illumina Infinium HumanMethylation450 BeadChip; Unique samples; Array