Validation of DNA methylation profiling in formalin-fixed paraffin-embedded colon and breast tissue using the Infinium HumanMethylation450 Microarray

Abstract

DNA methylation is not only crucial for normal physiology but it is also involved in a myriad of diseases, which has raised wide interest in the development of methods for genome-wide DNA methylation profiling. Illumina’s Infinium 450K platform is regarded as the most attractive, powerful, and cost-effective technique currently available for generating quantitative DNA methylation profiles in clinical tissue samples. Formalinfixation and paraffin-embedding (FFPE) represents the standard method to preserve these clinical tissue samples. However, formalin-fixation introduces severe DNA damage, which restricts current DNA methylation analysis. The present study responds to this substantial limitation by examining the usability of Illumina’s DNA restoration protocol to allow for routinely analysis of formalin-fixed tissue specimens with the Infinium HumanMethylation450 technology. It is hypothesized that the HumanMethylation450 microarray in conjugation with Illumina’s Infinium HD FFPE DNA Restoration solution can be successfully employed as a discovery assay. To test this hypothesis, differentially methylated CpG sites between FFPE colon tissues and breast cancer specimens have been identified by 450K methylation microarray analysis, followed by validation with nested methylation specific PCR (MSP). This study also statistically assessed the performance of fresh frozen (FF), FFPE DNA-unrestored and FFPE DNA-restored colon tissue samples on the Infinium HumanMethylation450 microarray. The present study showed good correlation between matched FF and FFPE DNA-restored tissue specimens. The presence of a significant bias in methylation assignment introduced by formalin-fixation was excluded. MSP-based validation of the microarray’s discovery potential showed unexpected and rather questionable data. The current results suggest that – compared to the existing input titration standards – a considerable lower amount of input DNA may be successfully used on the Infinium platform. No significant correlation was detected between the length of FFPE storage and sample variability. It is concluded that the Infinium HumanMethylation450 microarray can be successfully used on FFPE sample material in conjugation with Illumina’s Infinium HD FFPE DNA restoration solution, while the microarray’s discovery potential remains to be elucidated.