ArticleBMC research notes2025
Quality control checkpoints for high throughput DNA methylation measurement using the human MethylationEPICv1 array: application to formalin-fixed paraffin embedded prostate tissue.
Article in BMC research notes, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.
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Abstract
objectiveThe 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.
resultsFFPE 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.
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