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

Ruth Pidsley, Elena Zotenko, Timothy J. Peters, Mitchell G. Lawrence, Gail P. Risbridger, Peter Molloy, Susan Van Djik, Beverly Muhlhausler, Clare Stirzaker, Susan J. Clark

Research output: Contribution to journalArticleResearchpeer-review

161 Citations (Scopus)

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.

Original languageEnglish
Article number208
Number of pages17
JournalGenome Biology
Volume17
Issue number1
DOIs
Publication statusPublished - 7 Oct 2016

Keywords

  • DNA methylation
  • Enhancers
  • EPIC
  • HM450
  • Microarray
  • Validation
  • Whole-genome bisulphite sequencing (WGBS)

Cite this

Pidsley, Ruth ; Zotenko, Elena ; Peters, Timothy J. ; Lawrence, Mitchell G. ; Risbridger, Gail P. ; Molloy, Peter ; Van Djik, Susan ; Muhlhausler, Beverly ; Stirzaker, Clare ; Clark, Susan J. / Critical evaluation of the Illumina MethylationEPIC BeadChip microarray for whole-genome DNA methylation profiling. In: Genome Biology. 2016 ; Vol. 17, No. 1.
@article{9d338a087afd4b00bd09fede6a580dcd,
title = "Critical evaluation of the Illumina MethylationEPIC BeadChip microarray for whole-genome DNA methylation profiling",
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.",
keywords = "DNA methylation, Enhancers, EPIC, HM450, Microarray, Validation, Whole-genome bisulphite sequencing (WGBS)",
author = "Ruth Pidsley and Elena Zotenko and Peters, {Timothy J.} and Lawrence, {Mitchell G.} and Risbridger, {Gail P.} and Peter Molloy and {Van Djik}, Susan and Beverly Muhlhausler and Clare Stirzaker and Clark, {Susan J.}",
year = "2016",
month = "10",
day = "7",
doi = "10.1186/s13059-016-1066-1",
language = "English",
volume = "17",
journal = "Genome Biology",
issn = "1474-760X",
publisher = "BioMed Central",
number = "1",

}

Pidsley, R, Zotenko, E, Peters, TJ, Lawrence, MG, Risbridger, GP, Molloy, P, Van Djik, S, Muhlhausler, B, Stirzaker, C & Clark, SJ 2016, 'Critical evaluation of the Illumina MethylationEPIC BeadChip microarray for whole-genome DNA methylation profiling', Genome Biology, vol. 17, no. 1, 208. https://doi.org/10.1186/s13059-016-1066-1

Critical evaluation of the Illumina MethylationEPIC BeadChip microarray for whole-genome DNA methylation profiling. / Pidsley, Ruth; Zotenko, Elena; Peters, Timothy J.; Lawrence, Mitchell G.; Risbridger, Gail P.; Molloy, Peter; Van Djik, Susan; Muhlhausler, Beverly; Stirzaker, Clare; Clark, Susan J.

In: Genome Biology, Vol. 17, No. 1, 208, 07.10.2016.

Research output: Contribution to journalArticleResearchpeer-review

TY - JOUR

T1 - Critical evaluation of the Illumina MethylationEPIC BeadChip microarray for whole-genome DNA methylation profiling

AU - Pidsley, Ruth

AU - Zotenko, Elena

AU - Peters, Timothy J.

AU - Lawrence, Mitchell G.

AU - Risbridger, Gail P.

AU - Molloy, Peter

AU - Van Djik, Susan

AU - Muhlhausler, Beverly

AU - Stirzaker, Clare

AU - Clark, Susan J.

PY - 2016/10/7

Y1 - 2016/10/7

N2 - 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.

AB - 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.

KW - DNA methylation

KW - Enhancers

KW - EPIC

KW - HM450

KW - Microarray

KW - Validation

KW - Whole-genome bisulphite sequencing (WGBS)

UR - http://www.scopus.com/inward/record.url?scp=84990856282&partnerID=8YFLogxK

UR - https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5055731/

U2 - 10.1186/s13059-016-1066-1

DO - 10.1186/s13059-016-1066-1

M3 - Article

VL - 17

JO - Genome Biology

JF - Genome Biology

SN - 1474-760X

IS - 1

M1 - 208

ER -