Abstract
BackgroundAlthough collections of formalin fixed paraffin embedded (FFPE) samples exist, sometimes representing decades of stored samples, they have not typically been utilized to their full potential. Normal tissue from such samples would be extremely valuable for generation of genotype data for individuals who cannot otherwise provide a DNA sample.FindingsWe extracted DNA from normal tissue identified in FFPE tissue blocks from prostate surgery and obtained complete genome wide genotype data for over 500,000 SNP markers for these samples, and for DNA extracted from whole blood for 2 of the cases, for comparison.Four of the five FFPE samples of varying age and amount of tissue had identifiable normal tissue. We obtained good quality genotype data for between 89 and 99% of all SNP markers for the 4 samples from FFPE. Concordance rates of over 99% were observed for the 2 samples with DNA from both FFPE and from whole blood.ConclusionsDNA extracted from normal FFPE tissue provides excellent quality and quantity genome-wide genotyping data representing germline DNA, sufficient for both linkage and association analyses. This allows genetic analysis of informative individuals who are no longer available for sampling in genetic studies.
Highlights
Collections of formalin fixed paraffin embedded (FFPE) samples exist, sometimes representing decades of stored samples, they have not typically been utilized to their full potential
DNA extracted from normal FFPE tissue provides excellent quality and quantity genome-wide genotyping data representing germline DNA, sufficient for both linkage and association analyses
Recognizing that normal tissue is typically included in FFPE samples, we hypothesized that DNA could be extracted from normal tissue found in most FFPE samples, and that this would provide adequate genome-wide germline DNA for genotyping
Summary
Our attempt to generate genome-wide genotyping data for individuals not available for genotyping, has been both simple and revolutionary in several ways. We have shown that both high quality and high yield genome-wide genotyping data can be obtained from DNA extracted from normal FFPE tissue (even when samples are stored long term). Our innovative solution to procuring genome-wide genotyping data for informative individuals not otherwise available for sampling has provided a powerful way forward for a number of different genetic studies which require genome-wide genotyping data of good quality and quantity Those researchers and facilities with the foresight to store FFPE tissue have at their fingertips a vastly informative and valuable resource that we propose will allow many investigations not previously thought possible.
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