Correlation of Infinium HumanMethylation450K and MethylationEPIC BeadChip arrays in cartilage
DNA methylation of CpG sites is commonly measured using Illumina Infinium BeadChip platforms. The Infinium MethylationEPIC array has replaced the Infinium Methylation450K array. The two arrays use the same technology, with the EPIC array assaying almost double the number of sites than the 450K array...
| Main Authors: | , , , , |
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| Format: | Article |
| Language: | English |
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Taylor & Francis Group
2020-07-01
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| Series: | Epigenetics |
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| Online Access: | http://dx.doi.org/10.1080/15592294.2019.1700003 |
| _version_ | 1797678924106301440 |
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| author | Kathleen Cheung Marjolein J. Burgers David A. Young Simon Cockell Louise N. Reynard |
| author_facet | Kathleen Cheung Marjolein J. Burgers David A. Young Simon Cockell Louise N. Reynard |
| author_sort | Kathleen Cheung |
| collection | DOAJ |
| description | DNA methylation of CpG sites is commonly measured using Illumina Infinium BeadChip platforms. The Infinium MethylationEPIC array has replaced the Infinium Methylation450K array. The two arrays use the same technology, with the EPIC array assaying almost double the number of sites than the 450K array. In this study, we compare DNA methylation values of shared CpGs of the same human cartilage samples assayed using both platforms. DNA methylation was measured in 21 human cartilage samples using the both 450K and EPIC arrays. Additional matched 450K and EPIC data in whole tumour and whole blood were downloaded from GEO GSE92580 and GSE86833, respectively. Data were processed using the Bioconductor package Minfi. DNA methylation of six CpG sites was validated for the same 21 cartilage samples by pyrosequencing. In cartilage samples, overall sample correlations of methylation values between arrays were high (Pearson’s r > 0.96). However, 50.5% of CpG sites showed poor correlation (r < 0.2) between arrays. Sites with limited variance and with either very high or very low methylation levels in cartilage exhibited lower correlation values, corroborating prior studies in whole blood. Bisulphite pyrosequencing did not highlight one array as generating more accurate methylation values. For a specific CpG site, the array methylation correlation coefficient differed between cartilage, tumour, and whole blood, reflecting the difference in methylation variance between cell types. Researchers should be cautious when analysing methylation of CpG sites that show low methylation variance within the cell type of interest, regardless of the method used to assay methylation. |
| first_indexed | 2024-03-11T23:06:57Z |
| format | Article |
| id | doaj.art-df1f7d28e78143c3a7cc6a6f2d4c6408 |
| institution | Directory Open Access Journal |
| issn | 1559-2294 1559-2308 |
| language | English |
| last_indexed | 2024-03-11T23:06:57Z |
| publishDate | 2020-07-01 |
| publisher | Taylor & Francis Group |
| record_format | Article |
| series | Epigenetics |
| spelling | doaj.art-df1f7d28e78143c3a7cc6a6f2d4c64082023-09-21T13:09:23ZengTaylor & Francis GroupEpigenetics1559-22941559-23082020-07-01156-759460310.1080/15592294.2019.17000031700003Correlation of Infinium HumanMethylation450K and MethylationEPIC BeadChip arrays in cartilageKathleen Cheung0Marjolein J. Burgers1David A. Young2Simon Cockell3Louise N. Reynard4Newcastle University, Central ParkwayNewcastle University, Central ParkwayNewcastle University, Central ParkwayNewcastle UniversityNewcastle University, Central ParkwayDNA methylation of CpG sites is commonly measured using Illumina Infinium BeadChip platforms. The Infinium MethylationEPIC array has replaced the Infinium Methylation450K array. The two arrays use the same technology, with the EPIC array assaying almost double the number of sites than the 450K array. In this study, we compare DNA methylation values of shared CpGs of the same human cartilage samples assayed using both platforms. DNA methylation was measured in 21 human cartilage samples using the both 450K and EPIC arrays. Additional matched 450K and EPIC data in whole tumour and whole blood were downloaded from GEO GSE92580 and GSE86833, respectively. Data were processed using the Bioconductor package Minfi. DNA methylation of six CpG sites was validated for the same 21 cartilage samples by pyrosequencing. In cartilage samples, overall sample correlations of methylation values between arrays were high (Pearson’s r > 0.96). However, 50.5% of CpG sites showed poor correlation (r < 0.2) between arrays. Sites with limited variance and with either very high or very low methylation levels in cartilage exhibited lower correlation values, corroborating prior studies in whole blood. Bisulphite pyrosequencing did not highlight one array as generating more accurate methylation values. For a specific CpG site, the array methylation correlation coefficient differed between cartilage, tumour, and whole blood, reflecting the difference in methylation variance between cell types. Researchers should be cautious when analysing methylation of CpG sites that show low methylation variance within the cell type of interest, regardless of the method used to assay methylation.http://dx.doi.org/10.1080/15592294.2019.1700003dna methylation450k vs epiccartilage450kepic |
| spellingShingle | Kathleen Cheung Marjolein J. Burgers David A. Young Simon Cockell Louise N. Reynard Correlation of Infinium HumanMethylation450K and MethylationEPIC BeadChip arrays in cartilage Epigenetics dna methylation 450k vs epic cartilage 450k epic |
| title | Correlation of Infinium HumanMethylation450K and MethylationEPIC BeadChip arrays in cartilage |
| title_full | Correlation of Infinium HumanMethylation450K and MethylationEPIC BeadChip arrays in cartilage |
| title_fullStr | Correlation of Infinium HumanMethylation450K and MethylationEPIC BeadChip arrays in cartilage |
| title_full_unstemmed | Correlation of Infinium HumanMethylation450K and MethylationEPIC BeadChip arrays in cartilage |
| title_short | Correlation of Infinium HumanMethylation450K and MethylationEPIC BeadChip arrays in cartilage |
| title_sort | correlation of infinium humanmethylation450k and methylationepic beadchip arrays in cartilage |
| topic | dna methylation 450k vs epic cartilage 450k epic |
| url | http://dx.doi.org/10.1080/15592294.2019.1700003 |
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