Dataset Information

A comparison of the whole genome approach of MeDIP-seq to the targeted approach of the Infinium HumanMethylation450 BeadChip(®) for methylome profiling.

ABSTRACT: DNA methylation is one of the most studied epigenetic marks in the human genome, with the result that the desire to map the human methylome has driven the development of several methods to map DNA methylation on a genomic scale. Our study presents the first comparison of two of these techniques - the targeted approach of the Infinium HumanMethylation450 BeadChip® with the immunoprecipitation and sequencing-based method, MeDIP-seq. Both methods were initially validated with respect to bisulfite sequencing as the gold standard and then assessed in terms of coverage, resolution and accuracy. The regions of the methylome that can be assayed by both methods and those that can only be assayed by one method were determined and the discovery of differentially methylated regions (DMRs) by both techniques was examined. Our results show that the Infinium HumanMethylation450 BeadChip® and MeDIP-seq show a good positive correlation (Spearman correlation of 0.68) on a genome-wide scale and can both be used successfully to determine differentially methylated loci in RefSeq genes, CpG islands, shores and shelves. MeDIP-seq however, allows a wider interrogation of methylated regions of the human genome, including thousands of non-RefSeq genes and repetitive elements, all of which may be of importance in disease. In our study MeDIP-seq allowed the detection of 15,709 differentially methylated regions, nearly twice as many as the array-based method (8070), which may result in a more comprehensive study of the methylome.

SUBMITTER: Clark C

PROVIDER: S-EPMC3510246 | biostudies-literature | 2012

REPOSITORIES: biostudies-literature

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A comparison of the whole genome approach of MeDIP-seq to the targeted approach of the Infinium HumanMethylation450 BeadChip(®) for methylome profiling.

Clark Christine C Palta Priit P Joyce Christopher J CJ Scott Carol C Grundberg Elin E Deloukas Panos P Palotie Aarno A Coffey Alison J AJ

PloS one 20121129 11

DNA methylation is one of the most studied epigenetic marks in the human genome, with the result that the desire to map the human methylome has driven the development of several methods to map DNA methylation on a genomic scale. Our study presents the first comparison of two of these techniques - the targeted approach of the Infinium HumanMethylation450 BeadChip® with the immunoprecipitation and sequencing-based method, MeDIP-seq. Both methods were initially validated with respect to bisulfite s ...[more]

PMID: 23209683

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Project description:Understanding the role of DNA methylation often requires accurate assessment and comparison of these modifications in a genome-wide fashion. Sequencing-based DNA methylation profiling provides an unprecedented opportunity to map and compare complete DNA CpG methylomes. These include whole genome bisulfite sequencing (WGBS), Reduced-Representation Bisulfite-Sequencing (RRBS), and enrichment-based methods such as MeDIP-seq, MBD-seq, and MRE-seq. An investigator needs a method that is flexible with the quantity of input DNA, provides the appropriate balance among genomic CpG coverage, resolution, quantitative accuracy, and cost, and comes with robust bioinformatics software for analyzing the data. In this chapter, we describe four protocols that combine state-of-the-art experimental strategies with state-of-the-art computational algorithms to achieve this goal. We first introduce two experimental methods that are complementary to each other. MeDIP-seq, or methylation-dependent immunoprecipitation followed by sequencing, uses an anti-methylcytidine antibody to enrich for methylated DNA fragments, and uses massively parallel sequencing to reveal identity of enriched DNA. MRE-seq, or methylation-sensitive restriction enzyme digestion followed by sequencing, relies on a collection of restriction enzymes that recognize CpG containing sequence motifs, but only cut when the CpG is unmethylated. Digested DNA fragments enrich for unmethylated CpGs at their ends, and these CpGs are revealed by massively parallel sequencing. The two computational methods both implement advanced statistical algorithms that integrate MeDIP-seq and MRE-seq data. M&M is a statistical framework to detect differentially methylated regions between two samples. methylCRF is a machine learning framework that predicts CpG methylation levels at single CpG resolution, thus raising the resolution and coverage of MeDIP-seq and MRE-seq to a comparable level of WGBS, but only incurring a cost of less than 5% of WGBS. Together these methods form an effective, robust, and affordable platform for the investigation of genome-wide DNA methylation.

Project description:BACKGROUND: Measurement of genome-wide DNA methylation (DNAm) has become an important avenue for investigating potential physiologically-relevant epigenetic changes. Illumina Infinium (Illumina, San Diego, CA, USA) is a commercially available microarray suite used to measure DNAm at many sites throughout the genome. However, it has been suggested that a subset of array probes may give misleading results due to issues related to probe design. To facilitate biologically significant data interpretation, we set out to enhance probe annotation of the newest Infinium array, the HumanMethylation450 BeadChip (450 k), with >485,000 probes covering 99% of Reference Sequence (RefSeq) genes (National Center for Biotechnology Information (NCBI), Bethesda, MD, USA). Annotation that was added or expanded on includes: 1) documented SNPs in the probe target, 2) probe binding specificity, 3) CpG classification of target sites and 4) gene feature classification of target sites. RESULTS: Probes with documented SNPs at the target CpG (4.3% of probes) were associated with increased within-tissue variation in DNAm. An example of a probe with a SNP at the target CpG demonstrated how sample genotype can confound the measurement of DNAm. Additionally, 8.6% of probes mapped to multiple locations in silico. Measurements from these non-specific probes likely represent a combination of DNAm from multiple genomic sites. The expanded biological annotation demonstrated that based on DNAm, grouping probes by an alternative high-density and intermediate-density CpG island classification provided a distinctive pattern of DNAm. Finally, variable enrichment for differentially methylated probes was noted across CpG classes and gene feature groups, dependant on the tissues that were compared. CONCLUSION: DNAm arrays offer a high-throughput approach for which careful consideration of probe content should be utilized to better understand the biological processes affected. Probes containing SNPs and non-specific probes may affect the assessment of DNAm using the 450 k array. Additionally, probe classification by CpG enrichment classes and to a lesser extent gene feature groups resulted in distinct patterns of DNAm. Thus, we recommend that compromised probes be removed from analyses and that the genomic context of DNAm is considered in studies deciphering the biological meaning of Illumina 450 k array data.

Project description:BackgroundDNA methylation is indispensible for normal human genome function. Currently there is an increasingly large number of DNA methylomic data being released in the public domain allowing for an opportunity to investigate the relationships between the DNA methylome, genome function, and human phenotypes. The Illumina450K is one of the most popular platforms for assessing DNA methylation with over 10,000 samples available in the public domain. However, accessing all this data requires downloading each individual experiment and due to inconsistent annotation, accessing the right data can be a challenge.DescriptionHere we introduce 'Marmal-aid', the first standardised database for DNA methylation (freely available at http://marmal-aid.org). In Marmal-aid, the majority of publicly available Illumina HumanMethylation450 data is incorporated into a single repository allowing for re-processing of data including normalisation and imputation of missing values. The database is accessible in two ways: (1) Using an R package to allow for incorporation into existing analysis pipelines which can then be easily queried to gain insight into the functionality of certain CpG sites. This is aimed at a bioinformatician with experience in R. (2) Using a graphical interface allowing general biologists to query a pre-defined set of tissues (currently 15) providing a reference database of the methylation state in these tissues for the 450,000 CpG sites profiled by the Illumina HumanMethylation450.ConclusionMarmal-aid is the largest publicly available Illumina HumanMethylation450 methylation database combining Illumina HumanMethylation450 data from a number of sources into a single location with a single common annotation format. This allows for automated extraction using the R package and inclusion into existing analysis pipelines. Marmal-aid also provides a easy to use GUI to visualise methylation data in user defined genomic regions for various reference tissues.

Dataset Information

A comparison of the whole genome approach of MeDIP-seq to the targeted approach of the Infinium HumanMethylation450 BeadChip(®) for methylome profiling.

Publications

A comparison of the whole genome approach of MeDIP-seq to the targeted approach of the Infinium HumanMethylation450 BeadChip(®) for methylome profiling.

Similar Datasets

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