Critical evaluation of the Illumina MethylationEPIC BeadChip microarray for whole-genome DNA methylation profiling

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Abstract

Background

In recent years the Illumina HumanMethylation450 (HM450) BeadChip has provided a user-friendly platform to profile DNA methylation in human samples. However, HM450 lacked coverage of distal regulatory elements. Illumina have now released the MethylationEPIC (EPIC) BeadChip, with new content specifically designed to target these regions. We have used HM450 and whole-genome bisulphite sequencing (WGBS) to perform a critical evaluation of the new EPIC array platform.

Results

EPIC covers over 850,000 CpG sites, including >90 % of the CpGs from the HM450 and an additional 413,743 CpGs. Even though the additional probes improve the coverage of regulatory elements, including 58 % of FANTOM5 enhancers, only 7 % distal and 27 % proximal ENCODE regulatory elements are represented. Detailed comparisons of regulatory elements from EPIC and WGBS show that a single EPIC probe is not always informative for those distal regulatory elements showing variable methylation across the region. However, overall data from the EPIC array at single loci are highly reproducible across technical and biological replicates and demonstrate high correlation with HM450 and WGBS data. We show that the HM450 and EPIC arrays distinguish differentially methylated probes, but the absolute agreement depends on the threshold set for each platform. Finally, we provide an annotated list of probes whose signal could be affected by cross-hybridisation or underlying genetic variation.

Conclusion

The EPIC array is a significant improvement over the HM450 array, with increased genome coverage of regulatory regions and high reproducibility and reliability, providing a valuable tool for high-throughput human methylome analyses from diverse clinical samples.

Electronic supplementary material

The online version of this article (doi:10.1186/s13059-016-1066-1) contains supplementary material, which is available to authorized users.

Related collections

Most cited references 19

Record: found
Abstract: found
Article: not found

High density DNA methylation array with single CpG site resolution.

Marina Bibikova, Bret Barnes, Chan Tsan … (2011)

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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Record: found
Abstract: found
Article: not found

Genome-scale analysis of aberrant DNA methylation in colorectal cancer.

Toshinori Hinoue, Daniel Weisenberger, Christopher Lange … (2012)

Colorectal cancer (CRC) is a heterogeneous disease in which unique subtypes are characterized by distinct genetic and epigenetic alterations. Here we performed comprehensive genome-scale DNA methylation profiling of 125 colorectal tumors and 29 adjacent normal tissues. We identified four DNA methylation-based subgroups of CRC using model-based cluster analyses. Each subtype shows characteristic genetic and clinical features, indicating that they represent biologically distinct subgroups. A CIMP-high (CIMP-H) subgroup, which exhibits an exceptionally high frequency of cancer-specific DNA hypermethylation, is strongly associated with MLH1 DNA hypermethylation and the BRAF(V600E) mutation. A CIMP-low (CIMP-L) subgroup is enriched for KRAS mutations and characterized by DNA hypermethylation of a subset of CIMP-H-associated markers rather than a unique group of CpG islands. Non-CIMP tumors are separated into two distinct clusters. One non-CIMP subgroup is distinguished by a significantly higher frequency of TP53 mutations and frequent occurrence in the distal colon, while the tumors that belong to the fourth group exhibit a low frequency of both cancer-specific DNA hypermethylation and gene mutations and are significantly enriched for rectal tumors. Furthermore, we identified 112 genes that were down-regulated more than twofold in CIMP-H tumors together with promoter DNA hypermethylation. These represent ∼7% of genes that acquired promoter DNA methylation in CIMP-H tumors. Intriguingly, 48/112 genes were also transcriptionally down-regulated in non-CIMP subgroups, but this was not attributable to promoter DNA hypermethylation. Together, we identified four distinct DNA methylation subgroups of CRC and provided novel insight regarding the role of CIMP-specific DNA hypermethylation in gene silencing.

0 comments Cited 267 times – based on 0 reviews      Review now

Record: found
Abstract: found
Article: not found

Tobacco-smoking-related differential DNA methylation: 27K discovery and replication.

Lutz P. Breitling, Rongxi Yang, Bernhard Korn … (2011)

Tobacco smoking is responsible for substantial morbidity and mortality worldwide, in particular through cardiovascular, pulmonary, and malignant pathology. CpG methylation might plausibly play a role in a variety of smoking-related phenomena, as suggested by candidate gene promoter or global methylation studies. Arrays allowing hypothesis-free searches on a scale resembling genome-wide studies of SNPs have become available only very recently. Methylation extents in peripheral-blood DNA were assessed at 27,578 sites in more than 14,000 gene promoter regions in 177 current smokers, former smokers, and those who had never smoked, with the use of the Illumina HumanMethylation 27K BeadChip. This revealed a single locus, cg03636183, located in F2RL3, with genome-wide significance for lower methylation in smokers (p = 2.68 × 10(-31)). This was similarly significant in 316 independent replication samples analyzed by mass spectrometry and Sequenom EpiTyper (p = 6.33 × 10(-34)). Our results, which were based on a rigorous replication approach, show that the gene coding for a potential drug target of cardiovascular importance features altered methylation patterns in smokers. To date, this gene had not attracted attention in the literature on smoking. Copyright © 2011 The American Society of Human Genetics. Published by Elsevier Inc. All rights reserved.

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Author and article information

Contributors

Ruth Pidsley: r.pidsley@garvan.org.au

Elena Zotenko: e.zotenko@garvan.org.au

Timothy J. Peters: t.peters@garvan.org.au

Mitchell G. Lawrence: mitchell.lawrence@monash.edu

Gail P. Risbridger: gail.risbridger@monash.edu

Peter Molloy: peter.molloy@csiro.au

Susan Van Djik: susan.vandijk@csiro.au

Beverly Muhlhausler: beverly.muhlhausler@adelaide.edu.au

Clare Stirzaker: c.stirzaker@garvan.org.au

Susan J. Clark: 61-2-92958315 , s.clark@garvan.org.au

Journal

Journal ID (nlm-ta): Genome Biol

Journal ID (iso-abbrev): Genome Biol

Title: Genome Biology

Publisher: BioMed Central (London )

ISSN (Print): 1474-7596

ISSN (Electronic): 1474-760X

Publication date (Electronic): 7 October 2016

Publication date PMC-release: 7 October 2016

Publication date Collection: 2016

Volume: 17

Electronic Location Identifier: 208

Affiliations

[1 ]Epigenetics Research Laboratory, Genomics and Epigenetics Division, Garvan Institute of Medical Research, 384 Victoria St, Darlinghurst, Sydney, 2010 NSW Australia

[2 ]St Vincent’s Clinical School, University of NSW, Sydney, 2010 NSW Australia

[3 ]Prostate Research Group, Department of Anatomy and Developmental Biology, Biomedicine Discovery Institute, Monash Partners Comprehensive Cancer Consortium, Monash University, Clayton, Melbourne, VIC 3800 Australia

[4 ]CSIRO, Health and Biosecurity, PO Box 52, North Ryde, NSW 1670 Australia

[5 ]FOODplus Research Centre, Department of Food and Wine Science, School of Agriculture Food and Wine, Waite Campus, The University of Adelaide, Adelaide, SA Australia

[6 ]Child Nutrition Research Centre, South Australian Health and Medical Research Institute, Adelaide, SA Australia

Article

Publisher ID: 1066

DOI: 10.1186/s13059-016-1066-1

PMC ID: 5055731

PubMed ID: 27717381

SO-VID: 235a4167-051d-4a07-be6b-fadc525aab4e

License:

Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License ( http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver ( http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.

History

Date received : 21 July 2016

Date accepted : 19 September 2016

Funding

Funded by: FundRef http://dx.doi.org/10.13039/501100000925, National Health and Medical Research Council;

Award ID: 1035721

Award ID: 1102752

Award Recipient : Mitchell G. Lawrence Gail P. Risbridger

Funded by: FundRef http://dx.doi.org/10.13039/501100001111, Cancer Australia;

Award ID: 1044458

Award Recipient : Gail P. Risbridger

Funded by: Science and Industry Endowment Fund (AU)

Award ID: RP03-064

Award Recipient : Peter Molloy

Funded by: Cancer Institute of New South Wales

Award ID: 14/ECF/1-23

Award Recipient : Ruth Pidsley

Funded by: FundRef http://dx.doi.org/10.13039/501100000927, Prostate Cancer Foundation of Australia;

Award ID: YI0911

Award Recipient : Mitchell G. Lawrence

Custom metadata

ScienceOpen disciplines: Genetics

Keywords: epic,dna methylation,hm450,whole-genome bisulphite sequencing (wgbs),microarray,enhancers,validation

Data availability:

ScienceOpen disciplines: Genetics

Keywords: epic, dna methylation, hm450, whole-genome bisulphite sequencing (wgbs), microarray, enhancers, validation