Abstract
Summary Measuring differential methylation of the DNA is the nowadays most common approach to linking epigenetic modifications to diseases (called epigenome-wide association studies, EWAS). For its low cost, its efficiency and easy handling, the Illumina HumanMethylation450 BeadChip and its successor, the Infinium MethylationEPIC BeadChip, is the by far most popular techniques for conduction EWAS in large patient cohorts. Despite the popularity of this chip technology, raw data processing and statistical analysis of the array data remains far from trivial and still lacks dedicated software libraries enabling high quality and statistically sound downstream analyses. As of yet, only R-based solutions are freely available for low-level processing of the Illumina chip data. However, the lack of alternative libraries poses a hurdle for the development of new bioinformatic tools, in particular when it comes to web services or applications where run time and memory consumption matter, or EWAS data analysis is an integrative part of a bigger framework or data analysis pipeline. We have therefore developed and implemented Jllumina, an open-source Java library for raw data manipulation of Illumina Infinium HumanMethylation450 and Infinium MethylationEPIC BeadChip data, supporting the developer with Java functions covering reading and preprocessing the raw data, down to statistical assessment, permutation tests, and identification of differentially methylated loci. Jllumina is fully parallelizable and publicly available at http://dimmer.compbio.sdu.dk/download.html
Highlights
DNA methylation is an epigenetic process associated to genomic imprinting, inactivation of the X chromosome in females, and cellular specialization [1]
The lack of alternative libraries poses a hurdle for the development of new bioinformatic tools, in particular when it comes to web services or applications where run time and memory consumption matter, or EWAS data analysis is an integrative part of a bigger framework or data analysis pipeline
Methylated DNA loci can be identified by using DNA bisulftite treatment and quantified by microarray technologies such as the Illumina Infinium HumanMethylation450 and Infinium MethylationEPIC BeadChip, which cover around 450,000 and 850,000 CpG sites respectively along the human genome [3, 4]
Summary
DNA methylation is an epigenetic process associated to genomic imprinting, inactivation of the X chromosome in females, and cellular specialization [1]. Methylated DNA loci can be identified by using DNA bisulftite treatment and quantified by microarray technologies such as the Illumina Infinium HumanMethylation450 and Infinium MethylationEPIC BeadChip, which cover around 450,000 and 850,000 CpG sites respectively along the human genome [3, 4]. In order to provide the community with a wider basis for future software implementations, we have developed Jllumina, a Java library for the handling and processing of Illumina raw data files. It is the backbone of the recently published DiMmer tool [8]. Jllumina 14 secs Minfi 68 secs 66 secs 194 secs 21 secs 32 secs 89 secs 126 secs
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