Comparison of Illumina 450K and EPIC arrays in placental DNA methylation

Epigenetics. 2019 Dec;14(12):1177-1182. doi: 10.1080/15592294.2019.1634975. Epub 2019 Jun 28.

Abstract

Illumina HumanMethylation450 BeadChip (450K) has been commonly used to investigate DNA methylation in human tissues. Recently, it has been replaced by Illumina HumanMethylationEPIC BeadChip (EPIC) covering over 850,000 CpGs distributed genome-wide. Many consortia have now datasets coming from both arrays and aspire to analyze the two together. The placenta shows a high number of intermediate methylation levels and is often investigated for obstetric/birth outcomes, and potentially for long-term programming in offspring. We performed a systematic comparison between the two arrays using 108 duplicate placental samples from Gen3G birth cohort. We find that placenta shows a high per-sample correlation between the arrays, and higher median correlations at individual CpGs than those reported for blood. We identify 26,340 probes with absolute difference in per cent methylation >10%. We conclude that EPIC and 450K placental data can be combined, and we provide two lists of CpGs that should be excluded to avoid misleading results.

Keywords: DNA methylation; EPIC; Illumina 450K; placenta.

Publication types

  • Comparative Study
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Adult
  • CpG Islands
  • DNA Methylation*
  • Female
  • High-Throughput Nucleotide Sequencing / methods*
  • High-Throughput Nucleotide Sequencing / standards
  • Humans
  • Oligonucleotide Array Sequence Analysis / methods*
  • Oligonucleotide Array Sequence Analysis / standards
  • Placenta / metabolism*
  • Pregnancy
  • Reproducibility of Results
  • Sequence Analysis, DNA / methods*
  • Sequence Analysis, DNA / standards

Grants and funding

This work was supported by Fonds de recherche du Québec en santé #20697 (MFH); Canadian Institute of Health Research #MOP 115071 (MFH) and the American Diabetes Association accelerator award #1-15-ACE-26 (MFH). It was also partially funded by the Basque Department of Health (project 2018111086 to JRB) and ISCIII (PI18/01142 to NFJ - cofunded by ERDF, ‘A way to make Europe’).