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. 2014 Jun;9(6):829-33.
doi: 10.4161/epi.28790. Epub 2014 Apr 14.

Validation of DNA methylation profiling in formalin-fixed paraffin-embedded samples using the Infinium HumanMethylation450 Microarray

Sebastián Moran  1 , Miguel Vizoso  1 , Anna Martinez-Cardús  1 , Antonio Gomez  1 , Xavier Matías-Guiu  2 , Sebastián M Chiavenna  3 , Andrés G Fernandez  3 , Manel Esteller  4
Affiliations

Validation of DNA methylation profiling in formalin-fixed paraffin-embedded samples using the Infinium HumanMethylation450 Microarray

Sebastián Moran et al. Epigenetics. 2014 Jun.

Abstract

A formalin-fixed paraffin-embedded (FFPE) sample usually yields highly degraded DNA, which limits the use of techniques requiring high-quality DNA, such as Infinium Methylation microarrays. To overcome this restriction, we have applied an FFPE restoration procedure consisting of DNA repair and ligation processes in a set of paired fresh-frozen (FF) and FFPE samples. We validated the FFPE results in comparison with matched FF samples, enabling us to use FFPE samples on the Infinium HumanMethylation450 Methylation array.

Keywords: 450K; DNA methylation; FFPE; epigenetics; infinium; methylation; microarray.

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Figures

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Figure 1. (A) Scatter plots of the first two principal components of variance, grouping samples on the basis of the DNA source (FFPE or FF), Array Position (Sentrix Position) and Array (SentrixID). (B) A representative example of the comparison of SNP values obtained from matched FF and FFPE samples, indicating correct matched FF-FFPE sample is being compared. (C) A comparison of the methylation values from paired FFPE and FF sample for tumor 17. (D) Percentage of CpG sites statistically significant among sample origin by ANOVA analysis.
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Figure 2. Unsupervised hierarchical clustering of a randomly selected 2% of CpGs from the array.
See this image and copyright information in PMC

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