Comparison of Illumina 450K and EPIC arrays in placental DNA methylation.
Nora Fernandez-JimenezCatherine AllardLuigi BouchardPatrice PerronMariona BustamanteJose Ramon BilbaoMarie-France HivertPublished in: Epigenetics (2019)
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 Recently, it has been replaced by Illumina HumanMethylationEPIC BeadChip (EPIC) covering over 850,000 CpGs distributed genome-wide.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.
Keyphrases
- dna methylation
- genome wide
- gene expression
- high density
- copy number
- endothelial cells
- high throughput sequencing
- small molecule
- pregnant women
- high fat diet
- type diabetes
- big data
- atomic force microscopy
- single molecule
- photodynamic therapy
- insulin resistance
- adipose tissue
- metabolic syndrome
- living cells
- high resolution
- skeletal muscle
- induced pluripotent stem cells
- machine learning
- pregnancy outcomes
- mass spectrometry
- artificial intelligence
- preterm birth
- fluorescent probe