DNA quality evaluation of formalin-fixed paraffin-embedded heart tissue for DNA methylation array analysis

Area of Science:

• Epigenetics
• Molecular Biology
• Biotechnology

Background:

• Archived formalin-fixed and paraffin-embedded (FFPE) heart tissue is crucial for studying DNA methylation in deceased individuals.
• DNA quality degradation in FFPE tissues can impact methylation analysis accuracy.
• Cost-effective DNA quality assessment methods are needed for FFPE samples.

Purpose of the Study:

• To evaluate the correlation between DNA quality assessment methods and usable DNA methylation data from FFPE heart tissues.
• To compare the performance of Illumina Infinium HD FFPE QC assay (Infinium QC) and Thermo Fisher's Quantifiler Trio DNA Quantification kit (QuantifilerTrio) in predicting DNA methylation data quality.
• To establish a predictive model for usable DNA methylation data based on DNA quality metrics.

Main Methods:

• Assessed DNA quality of FFPE heart tissues using Infinium QC and QuantifilerTrio.
• Measured usable DNA methylation data via probe detection rate (probe DR) using the Illumina Infinium MethylationEPIC array and SeSAMe analysis.
• Performed correlation analysis between DNA quality indices (QuantifilerTrio degradation index, DI) and probe DR.

Main Results:

• QuantifilerTrio DI showed a strong correlation (r² = 0.75, p < 10⁻¹¹) with usable DNA methylation data (SeSAMe probe DR).
• Infinium QC demonstrated a weaker correlation (r² = 0.17, p < 0.05) with SeSAMe probe DR.
• A linear model was proposed: SeSAMe probe DR = 0.80 - log₁₀(DI) × 0.25, predicting data usability.

Conclusions:

• QuantifilerTrio's degradation index (DI) is a reliable predictor of usable DNA methylation data from FFPE heart tissues analyzed with Illumina MethylationEPIC array and SeSAMe.
• Infinium QC assay is less effective in predicting DNA methylation data quality compared to QuantifilerTrio.
• QuantifilerTrio offers a valuable screening tool for assessing FFPE DNA quality for epigenomic studies.