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      Comprehensive Analysis of DNA Methylation Data with RnBeads

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          Abstract

          RnBeads is a software tool for large-scale analysis and interpretation of DNA methylation data, providing a user-friendly analysis workflow that yields detailed hypertext reports ( http://rnbeads.mpi-inf.mpg.de). Supported assays include whole genome bisulfite sequencing, reduced representation bisulfite sequencing, Infinium microarrays, and any other protocol that produces high-resolution DNA methylation data. Important applications of RnBeads include the analysis of epigenome-wide association studies and epigenetic biomarker discovery in cancer cohorts.

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          Most cited references41

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          High density DNA methylation array with single CpG site resolution.

          We have developed a new generation of genome-wide DNA methylation BeadChip which allows high-throughput methylation profiling of the human genome. The new high density BeadChip can assay over 480K CpG sites and analyze twelve samples in parallel. The innovative content includes coverage of 99% of RefSeq genes with multiple probes per gene, 96% of CpG islands from the UCSC database, CpG island shores and additional content selected from whole-genome bisulfite sequencing data and input from DNA methylation experts. The well-characterized Infinium® Assay is used for analysis of CpG methylation using bisulfite-converted genomic DNA. We applied this technology to analyze DNA methylation in normal and tumor DNA samples and compared results with whole-genome bisulfite sequencing (WGBS) data obtained for the same samples. Highly comparable DNA methylation profiles were generated by the array and sequencing methods (average R2 of 0.95). The ability to determine genome-wide methylation patterns will rapidly advance methylation research. Copyright © 2011 Elsevier Inc. All rights reserved.
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            Is Open Access

            The UCSC Genome Browser database: extensions and updates 2013

            The University of California Santa Cruz (UCSC) Genome Browser (http://genome.ucsc.edu) offers online public access to a growing database of genomic sequence and annotations for a wide variety of organisms. The Browser is an integrated tool set for visualizing, comparing, analysing and sharing both publicly available and user-generated genomic datasets. As of September 2012, genomic sequence and a basic set of annotation ‘tracks’ are provided for 63 organisms, including 26 mammals, 13 non-mammal vertebrates, 3 invertebrate deuterostomes, 13 insects, 6 worms, yeast and sea hare. In the past year 19 new genome assemblies have been added, and we anticipate releasing another 28 in early 2013. Further, a large number of annotation tracks have been either added, updated by contributors or remapped to the latest human reference genome. Among these are an updated UCSC Genes track for human and mouse assemblies. We have also introduced several features to improve usability, including new navigation menus. This article provides an update to the UCSC Genome Browser database, which has been previously featured in the Database issue of this journal.
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              Comparison of sequencing-based methods to profile DNA methylation and identification of monoallelic epigenetic modifications

              Sequencing-based DNA methylation profiling methods are comprehensive and, as accuracy and affordability improve, will increasingly supplant microarrays for genome-scale analyses. Here, four sequencing-based methodologies were applied to biological replicates of human embryonic stem cells to compare their CpG coverage genome-wide and in transposons, resolution, cost, concordance and its relationship with CpG density and genomic context. The two bisulfite methods reached concordance of 82% for CpG methylation levels and 99% for non-CpG cytosine methylation levels. Using binary methylation calls, two enrichment methods were 99% concordant, while regions assessed by all four methods were 97% concordant. To achieve comprehensive methylome coverage while reducing cost, an approach integrating two complementary methods was examined. The integrative methylome profile along with histone methylation, RNA, and SNP profiles derived from the sequence reads allowed genome-wide assessment of allele-specific epigenetic states, identifying most known imprinted regions and new loci with monoallelic epigenetic marks and monoallelic expression.
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                Author and article information

                Journal
                101215604
                32338
                Nat Methods
                Nat. Methods
                Nature methods
                1548-7091
                1548-7105
                11 September 2014
                28 September 2014
                November 2014
                01 May 2015
                : 11
                : 11
                : 1138-1140
                Affiliations
                [1 ]Max Planck Institute for Informatics, Saarbrücken, Germany
                [2 ]Department of Genetics/Epigenetics, Saarland University, Saarbrücken, Germany
                [3 ]CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
                [4 ]Department of Laboratory Medicine, Medical University of Vienna, Vienna, Austria
                Author notes
                Correspondence should be addressed to F.M. or C.B. ( rnbeads@ 123456mpi-inf.mpg.de )

                Author contributions Y.A., F.M. and P.L. developed and maintain RnBeads; J.W., T.L. and C.B. supervised the project; all authors contributed to the writing of the manuscript.

                [*]

                Present address: Division of Epigenomics and Cancer Risk Factors, German Cancer Research Center (DKFZ), Heidelberg, Germany Correspondence should be addressed to F.M. or C.B. ( rnbeads@ 123456mpi-inf.mpg.de )

                Article
                EMS60313
                10.1038/nmeth.3115
                4216143
                25262207
                fefb8dc1-5c20-4aca-b057-2ba741aa0dbb
                History
                Categories
                Article

                Life sciences
                dna methylation analysis,computational epigenetics,whole genome bisulfite sequencing,reduced representation bisulfite sequencing,epigenotyping microarrays,illumina infinium humanmethylation450 assay,bioinformatics software,epigenome-wide association studies,medical epigenomics

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