At gpcf microarray unit, we provide full service for the analysis of dna methylation on a genomewide level in human samples genomic dna derived from fresh frozen or ffpe material making use of the well established infinium technology of illumina. Dec 10, 2017 the illumina infinium beadchips are a powerful array based platform for genomewide dna methylation profiling at approximately 485,000 450k and 850,000 epic cpg sites across the genome. Differential methylation site identification software tools. The first four are available through bioconductor while rnbeads is a standalone rpackage. Analysis pipelines and packages for infinium humanmethylation450 beadchip 450k data.
This paper provides a bioconductor workflow using multiple packages for the analysis of methylation array data. Following this, additional steps in the 450k array analysis workflow include copy. Methylation arrays interrogate methylation sites across. Computational and statistical analysis of arraybased dna methylation data. Now, the epigenetic clock software allows one to select an advanced analysis for blood tissue measured on the illumina 450k array. The need for research investigating dna methylation dnam in clinical studies has.
The illumina infinium methylation arrays are by far the most common way to interrogate methylation across the human genome. Apr 30, 2012 methylation analysis using the 450k array. Accompanying this has been the necessary evolution of analysis pipelines to facilitate data processing. Aug 27, 20 historically, the 450k array has been the more popular platform for dna methylation analysis. Outline dna methylation illumina in nium 450k human methylation assay probes design statistical challenges jeanphilippe fortin illumina 450k. Establishing an analytic pipeline for genomewide dna methylation. The infinium humanmethylation450 beadchip array targets 450,000 methylation.
Review of processing and analysis methods for dna methylation. Software for all methods presented can be obtained through the free and. Dna methylation plays an important and dynamic role in regulating gene expression. The illumina infinium beadchips are a powerful array based platform for genomewide dna methylation profiling at approximately 485,000 450k and 850,000 epic cpg sites across the genome. Dna methylation analysis using the infinium humanmethylation450k beadchip illumina, inc. Here we introduce five comprehensive packages developed for 450k array data analysis. Mar 01, 2012 illumina methylation analyzer ima is a computational package designed to automate the pipeline for exploratory analysis and summarization of sitelevel and regionlevel methylation changes in epigenetic studies utilizing the 450k dna methylation microarray. I am planning to run differential methylation analysis for a dataset of which some samples are sequenced using illumina human methylation 450k array and some 27k array. It offers comprehensive, expertselected coverage, including 99% of refseq genes, 95% of cpg islands, high coverage of enhancer regions, and other content categories. The min package provides tools for analyzing illuminas methylation arrays, with a special focus on the new 450k array for humans.
Quantitative crossvalidation and content analysis of the. It features advanced visualization tools that enable researchers to view vast amounts of data in a single graph, such as heat maps, scatter plots, and line plots. A comprehensive overview of infinium humanmethylation450. We adapt our algorithm, functional normalization, to the illumina 450k methylation array and address the open problem of normalizing methylation data with global epigenetic changes, such as human cancers. All five packages allow the user to import raw idat files or tabular. Example data based on the illumina dna infinium platform. Comparison of preprocessing methodologies for illumina 450k. Illuminas software suite for analysis of this array is called genomestudio. Ffpe samples are already highly degraded, with a high level of crosslinking, so conversion does not occur effectively. We propose an extension to quantile normalization that removes unwanted technical variation using control probes. Cohcap 49 is a software package that takes methylation data 450k or. Jul 16, 2016 human methylome mapping in health and disease states has largely relied on illumina human methylation 450k array 450k array technology.
The humanmethylation450 beadchip was developed to assay more than 480,000 cpg sites selected cpg loci in parallel bibikova et al. Methylationepic data analysis is supported by the genomestudio methylation module. Estimating cell sybtype methylation from epic 450k array hi all, i am trying to estimate cell sub type methylation from epic array i have the normalized. Statistical and integrative systemlevel analysis of dna methylation data. The array density is much higher in the infinium humanmethylation450 beadchip. Comprehensive 450k analysis packages here we introduce. Methylation array data processing and analysis pipeline.
Powered by the industryleading infinium assay, the methylationepic beadchip is ideal for epigenome wide association studies ewas. A guide to illumina beadchip data analysis springer nature. In this section, we briefly introduce the 450k array as well as the terminology used. Dec 20, 2019 more recently, illumina has increased the genomic coverage of the platform to 850,000 sites with the release of their methylationepic 850k array. The tasks addressed in this package include preprocessing, qc assessments, identi cation of interesting methylation loci and plotting functionality.
Several approaches and pipelines have been developed. Methylation arrays interrogate methylation sites across the. This assay is used for methylation probes on the illumina infinium humanmethylation27 beadchip henceforth, 27k methylation array. Jun 22, 2016 illuminas humanmethylation450 arrays provide the most costeffective means of highthroughput dna methylation analysis. It features advanced visualization tools that enable researchers to view vast amounts of data in a single. Rrbs and 450k arrays face off over dna methylation analysis. All five packages allow the user to import raw idat files or tabular methylation values. Using data sets from the cancer genome atlas and a large casecontrol study. Genomestudio software enables researchers to effortlessly perform differential methylation analysis for smallscale studies. Can anyone suggest the best software to use for illumina methylome. Familiar array based protocols, simpler data analysis, and relatively lower costs as compared to sequencing, established the 450k arrays as a highly useful tool for analyzing differentially methylated regions dmrs, especially when studying known cpg. The infinium humanmethylation450 array makes it possible to assess the methylation status of 450 000 cpgs located throughout the genome. Infinium human methylation27 and the infinium hd 450k methylation array, which. Documentation, product files, faqs, and other support resources for the infinium human methylation 450k beadchip.
A guide to illumina beadchip data analysis springerlink. The methylation patterns allow distinctions according to cell types, age, or cancer vs. Tips from methylation array experts illumina 450k beadchip arrays. The platform is used in many largescale populationbased epigenetic studies of complex diseases, environmental exposures, or other experimental conditions. The goal of this tutorial is to present a standard analysis workflow of 450k data with the package minfi, incorporating the functions recently added to the package. An r package for comprehensive analysis of dna methylation data obtained with any experimental protocol that provides singlecpg resolution, including infinium 450k microarray and bisulfite sequencing protocols, but also medipseq and mbdseq. As with other types of microarray platforms, technical artifacts are a concern, including background fluorescence, dyebias from the use of two color channels, bias caused by type iii probe design, and batch effects. The min users guide analyzing illumina 450k methylation arrays. The recently released infinium humanmethylation450 is a preferred technology for studying the dna methylomes of various cell types in large. An evaluation of processing methods for humanmethylation450.
Dna methylation is involved in numerous physiological processes and also disease states, such as cancer. Table 1 major steps in the 450k array analysis pipeline. Human methylome mapping in health and disease states has largely relied on illumina human. May 24, 20 first, a report from the laboratory of rosanna weksberg and colleagues demonstrated that many of the probes in the illumina 450k array either crosshybridize to nontargeted genomic regions or target loci that contain known single nucleotide polymorphisms snps, both of which interfere with analysis of dna methylation levels. Methylation in the human genome is known to be associated with development and disease.
Here we introduce missmethyl, an r package with a suite of tools for performing normalization, removal of unwanted variation in differential methylation analysis, differential variability testing and gene set analysis for the 450k array. A crosspackage bioconductor workflow for analysing. Array overview and clinical utilization the 3rd epigenome informatics workshop bekim sadikovic, phd. At the moment illuminas 27k methylation arrays are not supported. Analysis pipelines and packages for infinium humanmethylation450. Illumina is phasing out 450k and introducing the new 850k as in the end of 2015. We invite you to read the software paper recently published martin j aryee et al. Methylation arrays interrogate methylation sites across the genome.
As methylation arrays are likely to remain popular for measuring methylation for the foreseeable future, it is necessary to provide robust workflows for methylation array analysis. Comparison of preprocessing methodologies for illumina 450k methylation array data in familial analyses emma cazaly1, russell thomson1,2, james r. Hear experts describe their approaches to methylation array data analysis at the second annual infinium humanmethylation450 array workshop. A guide to illumina beadchip data analysis request pdf. A datadriven approach to preprocessing illumina 450k methylation array data. With the methylationepic beadchip, researchers can interrogate over 850,000 methylation sites quantitatively across the genome at singlenucleotide resolution. Functional normalization of 450k methylation array data. Starting with raw data from the infinium methylationepic or infinium human methylation 450k beadchip array, you can use partek tools to perform every analysis step from differential methylation, to biological interpretation. Aug 27, 2012 450k array analysis of chronic lymphocytic leukemia cells reveals global dna methylation to be relatively stable over time and similar in resting and proliferative compartments. Introduction to methylation array analysis dna methylation plays an important and dynamic role in regulating gene expression. Here, we describe a new version of our rnbeads software an. Infinium methylationepic kit methylation profiling array. The majority of these pipelines, however, cater for experimental designs where matched controls or normal samples are available.
A new chip analysis methylation pipeline champ tiffany morris, ph. Dna differential methylation analysis for illumina human. The raw data format for the 450k array is known as idat. The illumina infinium beadchips are a powerful arraybased platform for genomewide dna methylation profiling at approximately 485,000 450k and 850,000 epic cpg sites across the genome. Its particularity lies in the use of two different types of chemical assays infinium i and infinium ii. Bioinformatics tools for dna methylation array analysis omicx. The major differences between ima and existing r packages for infinium methylation analysis e. There are a large number of cpgs for which multiple transcripts are listed and for which the cpg site can fall into different annotation categories. Gentleman rc, carey vj, bates dm et al 2004 bioconductor.
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