Immunoglobulin heavy-chain gene rearrangement studies by Southern blot using DNA extracted from formalin-fixed, paraffin-embedded tissue.

Background: In most clinical molecular diagnostics laboratories, Southern blots for gene rearrangement studies are not routinely performed on formalin-fixed, paraffin-embedded (FFPE) tissue samples. In this study, immunoglobulin heavy-chain gene rearrangements by Southern blot using DNA extracted from FFPE tissue samples were studied.
Methods and Results: Eleven paired freshly frozen and FFPE tissue samples were evaluated for immunoglobulin gene rearrangements by PCR and Southern blot analyses. An additional 14 selected samples sent to our laboratory to rule out lymphoma, for which only FFPE tissue (no frozen tissue) was available and for which PCR was interpreted as negative, were evaluated by the same techniques. Southern blots generated from DNA extracted from FFPE tissues were qualitatively identical to those generated from DNA extracted from fresh or freshly frozen tissue and correlated well with the final diagnoses. Ten interpretable Southern blots were generated in the 14 cases in which no frozen tissue was available. Four of these ten blots were interpreted as positive for an immunoglobulin gene rearrangement. Although the number of samples analyzed is small, success with Southern blotting correlated with increased sample size and sample width (1.17 vs 0.49 cm(2); P <.024; 0.71 vs 0.43 cm; P <. 049, respectively).
Conclusion: DNA extracted from FFPE tissue samples using the simple, efficient, and nontoxic techniques described in this report can be used in many cases for Southern blotting for the detection of clonality by gene rearrangement studies.