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High quality and quantity Genome-wide germline genotypes from FFPE normal tissue
Lisa A Cannon-Albright1, Kendal G Cooper, Ann Georgelas
1Genetic Epidemiology, Department of Internal Medicine, University of Utah School of Medicine, Salt Lake City, UT, USA. lisa.albright@utah.edu.
BMC Research Notes
|May 28, 2011
Summary
Genomic DNA can be reliably extracted from normal formalin-fixed paraffin-embedded (FFPE) tissues. This enables valuable genetic analysis from individuals unavailable for new DNA sampling.
Area of Science:
- Genomics
- Molecular Biology
- Biobanking
Background:
- Formalin-fixed paraffin-embedded (FFPE) tissue collections are vast but underutilized.
- Normal tissue within FFPE samples offers a unique source for genetic data.
- This is particularly important for individuals unable to provide new DNA samples.
Purpose of the Study:
- To assess the feasibility of extracting high-quality genome-wide genotype data from normal FFPE tissue.
- To evaluate the utility of FFPE-derived DNA for genetic analyses.
Main Methods:
- DNA extraction from normal tissue within FFPE prostate surgery blocks.
- Genome-wide genotyping using over 500,000 SNP markers.
- Comparison with DNA extracted from whole blood for select cases.
Main Results:
- Identifiable normal tissue was present in 4 out of 5 FFPE samples.
- Good quality genotype data (89-99% SNP coverage) was obtained from FFPE samples.
- High concordance (>99%) was observed between FFPE and whole blood DNA genotypes.
Conclusions:
- DNA from normal FFPE tissue yields excellent quality and quantity of genome-wide genotyping data.
- The data represents germline DNA suitable for linkage and association studies.
- This method facilitates genetic analysis in individuals no longer available for sampling.
