CGH arrays compared for DNA isolated from formalin-fixed, paraffin-embedded material

Area of Science:

• Genomics
• Cancer Research
• Molecular Biology

Background:

• Formalin-fixed, paraffin-embedded (FFPE) archival tissue is a valuable source for DNA extraction.
• Array comparative genomic hybridization (aCGH) is a key technique for identifying copy number aberrations in tumorigenesis.
• Copy number analysis from FFPE-derived DNA presents unique challenges but yields reproducible results.

Purpose of the Study:

• To compare commercially available aCGH platforms for high-resolution copy number analysis using FFPE-derived DNA.
• Evaluate platform performance based on median absolute deviation (MAD), deflection, signal-to-noise ratio, and DNA input requirements.
• Assess the feasibility and reproducibility of copy number analysis from FFPE samples across different platforms.

Main Methods:

• Evaluation of two dual-channel aCGH platforms (Agilent, NimbleGen) and one single-channel SNP-based platform (Affymetrix).
• Analysis of seven FFPE colon cancer samples.
• Quality assessment using median absolute deviation (MAD), deflection, signal-to-noise ratio, and DNA input needs.

Main Results:

• Agilent and NimbleGen demonstrated superior Median Absolute Deviation (MAD) values (0.13) compared to Affymetrix (0.22).
• Affymetrix exhibited a better deflection (0.94) than Agilent (0.71) and NimbleGen (0.51).
• All platforms achieved comparable signal-to-noise ratios, and high-quality profiles were obtained even with DNA input below recommended levels.

Conclusions:

• Copy number analysis from FFPE archival material is feasible using Agilent, NimbleGen, and Affymetrix platforms.
• Reproducible results can be achieved across these platforms, irrespective of DNA input amounts.
• FFPE-derived DNA is a viable source for high-resolution copy number analysis in cancer research.