Efficient DNA extraction from 25-year-old paraffin-embedded tissues: study of 365 samples

Archival fixed paraffin-embedded tissue (PET) is a valuable source for population-based molecular genetic studies but the extraction of high quality DNA is still a problematic issue. The present study tested the grade of DNA fragmentation and the DNA adequacy for genetic investigations in a large series of tissue specimens that were formalin- or Bouin-fixed and paraffin-embedded between 1979 and 1983. Specific aims were to: (1) estimate the amount of archival tissue samples from which DNA is recoverable by conventional methods and the influence of variables (origin, fixative, section size) on DNA recovery; and (2) evaluate the feasibility of genetic investigations in large scale population studies.

DNA was extracted in 2005 from 365 PET samples from Italy and Spain and subjected to PCR analysis targeting fragments of 152, 268 and 676 bp of the beta-globin gene.

Amplification of a 152 bp fragment was obtained in 252/365 (69%) PET samples, a 268 bp fragment in 62/365 (17%), a 676 bp fragment in 19/365 (5%) and no amplification for any fragment was obtained in 113/365 (31%). A second processing of newly cut sections performed in a 25% simple random sample gave comparable results, with substantial concordance between the first and second tests (kappa value 0.62 [95% CI 0.59-0.64]).

The results of this study show that DNA can be efficiently extracted from PETs archived for more than 20 years, and that large scale population studies based on PCR amplification of short target sequences are feasible.