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 b lots for gene rearrangement studies are not routinely performed on formalin -fixed, paraffin-embedded (FFPE) tissue samples. In this study, immunoglobu lin heavy-chain gene rearrangements by Southern blot using DNA extracted fr om FFPE tissue samples were studied. Methods and Results: Eleven paired freshly frozen and FFPE tissue samples w ere evaluated for immunoglobulin gene rearrangements by PCR and Southern bl ot analyses. An additional 14 selected samples sent to our laboratory to ru le out lymphoma, for which only FFPE tissue (no frozen tissue) was availabl e 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 fre sh or freshly frozen tissue and correlated well with the final diagnoses. T en interpretable Southern blots were generated in the 14 cases in which no frozen tissue was available. Four of these ten blots were interpreted as po sitive for an immunoglobulin gene rearrangement. Although the number of sam ples analyzed is small, success with Southern blotting correlated with incr eased 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, effici ent, and nontoxic techniques described in this report can be used in many c ases for Southern blotting for the detection of clonality by gene rearrange ment studies.