Quality control checkpoints for high throughput DNA methylation measurement using the human MethylationEPICv1 array:...

Area of Science:

• Epigenetics
• Molecular Biology
• Genomics

Background:

• DNA methylation analysis using arrays like MethylationEpicV1.0 is crucial for research.
• Formalin-fixed paraffin-embedded (FFPE) tissues are a valuable source of DNA, but their quality can be variable.
• Existing quality control protocols for FFPE DNA on methylation arrays have limitations.

Purpose of the Study:

• To evaluate the utility of incorporating a third quality control checkpoint for bisulfite conversion efficiency.
• To assess the impact of this additional check on the performance of FFPE-derived DNA on the MethylationEpicV1.0 array.
• To analyze 255 FFPE prostate tumor DNA samples with an added quality control step.

Main Methods:

• DNA was extracted from 255 FFPE prostate tumor specimens and four controls.
• Quality control checkpoints assessed DNA quantity (checkpoint 1) and quality (checkpoint 2).
• A third checkpoint evaluated bisulfite conversion efficiency prior to array processing.

Main Results:

• All 259 DNA samples passed existing quality checks (quantity and quality).
• The bisulfite conversion quality check (checkpoint 3) also showed all samples passed.
• Array performance was high, with 99.6% of samples yielding good quality data, indicating the third checkpoint had limited added value.

Conclusions:

• The existing quality control measures for FFPE DNA quantity and quality are highly effective.
• An additional bisulfite conversion quality check may not be necessary when initial DNA quality is high.
• High-quality FFPE DNA ensures reliable performance on methylation arrays like MethylationEpicV1.0.