Logue Mark W, Smith Alicia K, Wolf Erika J, Maniates Hannah, Stone Annjanette, Schichman Steven A, McGlinchey Regina E, Milberg William, Miller Mark W
National Center for PTSD, VA Boston Healthcare System, USA.
Department of Psychiatry, Boston University School of Medicine, USA.
Epigenomics. 2017 Nov;9(11):1363-1371. doi: 10.2217/epi-2017-0078. Epub 2017 Aug 15.
We examined concordance of methylation levels across the Illumina Infinium HumanMethylation450 BeadChip and the Infinium MethylationEPIC BeadChip.
We computed the correlation for 145 whole blood DNA samples at each of the 422,524 CpG sites measured by both chips.
The correlation at some sites was high (up to r = 0.95), but many sites had low correlation (55% had r < 0.20). The low correspondence between 450K and EPIC measured methylation values at many loci was largely due to the low variability in methylation values for the majority of the CpG sites in blood.
Filtering out probes based on the observed correlation or low variability may increase reproducibility of BeadChip-based epidemiological studies.
我们检测了Illumina Infinium HumanMethylation450 BeadChip芯片和Infinium MethylationEPIC BeadChip芯片甲基化水平的一致性。
我们计算了通过两种芯片检测的422,524个CpG位点中每个位点的145份全血DNA样本的相关性。
某些位点的相关性较高（高达r = 0.95），但许多位点的相关性较低（55%的位点r < 0.20）。450K芯片和EPIC芯片在许多位点测得的甲基化值之间的低对应性主要是由于血液中大多数CpG位点甲基化值的低变异性。
基于观察到的相关性或低变异性筛选探针可能会提高基于BeadChip的流行病学研究的可重复性。
