# Quality control checkpoints for high throughput DNA methylation measurement using the human MethylationEPICv1 array: application to formalin-fixed paraffin embedded prostate tissue

## TL;DR

This study evaluates the use of a third quality check for DNA methylation measurements in FFPE prostate tissue to improve data reliability.

## Contribution

The study introduces a third quality checkpoint for bisulfite conversion in FFPE-derived DNA methylation analysis.

## Key findings

- 99.6% of DNA samples produced high-quality methylation data when checkpoints 1 and 2 were passed.
- The third checkpoint showed limited value when DNA quantity and quality were already high.
- Controls and replicates demonstrated strong reproducibility with high correlation values.

## Abstract

The performance of FFPE tissue-derived DNA on the MethylationEpicV1.0 array can be unpredictable as the protocol only has two quality checks; checkpoint 1 for DNA quantity and checkpoint 2 for DNA quality assessment. We sought to incorporate a third, previously developed bisulfite conversion quality check prior to processing 255 FFPE tissue derived DNA samples.

FFPE tissue-derived DNAs were prepared for 255 prostate tumour specimens and four controls. Checkpoint 1 assessed all samples to have 500ng DNA available for analysis except for two samples that yielded 483 and 486ng. All DNA samples passed both the quality checkpoint 2 and the bisulfite conversion quality assessment checkpoint 3. Assessment of array performance showed one of the 259 (0.4%) DNA samples had less than 90% of probes detected at p = 0.05. Controls and replicate showed reliable reproducibility with correlations of 0.981 and 0.994. High quantity and quality measures of the FFPE tissue-derived DNAs (assessed by checkpoint 1 and 2) were likely responsible for 99.6% of DNAs producing high quality EPIC array data. This report suggests that checkpoint 3 has limited value in a setting where the FFPE tissue derived DNA has high quantity and quality measures.

The online version contains supplementary material available at 10.1186/s13104-025-07221-3.