title: A comparative study of the quality of DNA obtained from fresh frozen and formalin-fixed decalcified paraffin-embedded bone marrow trephine biopsy specimens using two different methods.
abstract: BACKGROUND
  Given its prognostic value, there is renewed interest in molecular staging in non-Hodgkin's lymphoma (NHL) using immunoglobulin heavy and light chain (IgH, IgL) gene rearrangements.
  
  
  OBJECTIVE
  To compare the efficiency of DNA amplification from fresh frozen and formalin-fixed decalcified paraffin-embedded (FFDPE) bone marrow trephines for use in molecular staging using two methods.
  
  
  METHODS
  After manually extracting DNA from 13 FFDPE and 14 fresh frozen trephine biopsy specimens, two methods were used to test for amplifiability: use of the amplification control master mix supplied in the In Vivo Scribe immunoglobulin heavy chain (IgH) clonality kit, which creates 5 amplicons between 96-600 base pairs (bp); and real-time amplification of the beta-globin gene.
  
  
  RESULTS
  Using the first method, the mean maximum length of amplicons generated from FFDPE trephines was statistically lower at 300 bp compared to fresh frozen samples, all of which generated amplicons up to 600 bp in size (p<0.001). Real-time amplification of the beta-globin gene showed that the mean crossing threshold of fresh frozen samples was statistically lower than that of FFDPE samples (23.48 (95% CI 22.47 to 24.48) vs 33.64 (95% CI 32.15 to 35.12); p<0.001).
  
  
  CONCLUSIONS
  Although amplifiable DNA can be extracted from both fresh-frozen and FFDPE trephine samples for IgH/IgL analysis, freshly frozen specimens are superior as a source of template DNA, especially for higher base pair PCR products.
authors.affiliation: Department of Haematology, The Canberra Hospital, Garran, Australia. dipti.talaulikar@act.gov.au
authors.forename: D
authors.initials: D
authors.lastname: Talaulikar
authors.forename: J X
authors.initials: JX
authors.lastname: Gray
authors.forename: B
authors.initials: B
authors.lastname: Shadbolt
authors.forename: M
authors.initials: M
authors.lastname: McNiven
authors.forename: J E
authors.initials: JE
authors.lastname: Dahlstrom
mesh_terms: D001706:Biopsy; D001853:Bone Marrow / Q000473:pathology; D015925:Cryopreservation; D004273:DNA, Neoplasm / Q000032:analysis / Q000235:genetics*; D003648:Decalcification Technique; D004591:Electrophoresis, Polyacrylamide Gel / Q000379:methods; D005240:Feasibility Studies; D005404:Fixatives; D005557:Formaldehyde; D005803:Genes, Immunoglobulin; D005914:Globins / Q000235:genetics; D006801:Humans; D007143:Immunoglobulin Heavy Chains / Q000235:genetics; D007147:Immunoglobulin Light Chains / Q000235:genetics; D008228:Lymphoma, Non-Hodgkin / Q000235:genetics* / Q000473:pathology; D016612:Paraffin Embedding; D016133:Polymerase Chain Reaction / Q000379:methods; D014021:Tissue Preservation / Q000379:methods*
chemical_list: D004273:DNA, Neoplasm; D005404:Fixatives; D007143:Immunoglobulin Heavy Chains; D007147:Immunoglobulin Light Chains; D005557:Formaldehyde; D005914:Globins