High quality copy number and genotype data from FFPE samples using Molecular Inversion Probe (MIP) microarrays.

Area of Science:

• Genomics
• Molecular Biology
• Cancer Research

Background:

• Formalin-Fixed Paraffin Embedded (FFPE) samples are crucial for tumor studies but pose challenges for DNA analysis due to degradation.
• Existing DNA extraction methods often yield poor results from FFPE tissues, limiting copy number (CN) studies.
• Molecular Inversion Probe (MIP) technology, known for its success with fresh frozen DNA, was investigated for FFPE suitability.

Purpose of the Study:

• To evaluate the efficacy of MIP technology for assessing DNA copy number (CN) in Formalin-Fixed Paraffin Embedded (FFPE) tumor samples.
• To determine if MIP technology can overcome the limitations of DNA degradation in FFPE samples.
• To compare the performance of MIP technology on FFPE DNA versus fresh frozen DNA.

Main Methods:

• Utilized a Molecular Inversion Probe (MIP) panel with 50,000 markers.
• Assessed copy number (CN) in 93 diverse Formalin-Fixed Paraffin Embedded (FFPE) tumor samples.
• Compared results with matched fresh frozen tumor tissue for 38 samples.

Main Results:

• High-quality copy number (CN) data was generated using MIP technology in 88% of FFPE samples.
• Performance with FFPE DNA was comparable to fresh frozen DNA, achieving 99.9% genotype concordance.
• A modest decrease in performance was observed for FFPE samples compared to fresh frozen samples.

Conclusions:

• Molecular Inversion Probe (MIP) technology is effective for generating high-quality copy number (CN) and genotype data from FFPE samples.
• MIP technology provides a viable solution for genomic studies using valuable FFPE-preserved tumor tissues.
• This method enhances the utility of archived FFPE samples for comprehensive cancer research.