title: Molecular diagnosis of Ewing's sarcoma/primitive neuroectodermal tumor in formalin-fixed paraffin-embedded tissues by RT-PCR and fluorescence in situ hybridization.
abstract: Recent studies have suggested that formalin-fixed paraffin-embedded (FFPE) tissues can be used for molecular analyses by fluorescence in situ hybridization (FISH) and RT-PCR. We analyzed 18 cases of ES/PNET for the t(11;22)(q24;q12) and t(21;22)(q22;q12) fusion transcripts by RT-PCR and analyzed for EWS translocation by interphase FISH with a dual color fusion probe to compare these two approaches directly. RT-PCR detected 13 (72%) EWS-FLI-1 fusions (type I=10, type II=3) and 2 (11%) EWS-ERG fusions. Three cases could not be evaluated because the housekeeping gene phosphoglycerate kinase (internal mRNA control) was not amplified. FISH was diagnostic in 15 of 18 cases (83%). There were three discordant cases between RT-PCR and FISH (concordance of 83%). Using a combination of RT-PCR and FISH, the results were complementary. One advantage of RT-PCR analysis was that subtypes of EWS translocation could be determined specifically (type I, type II and ERG). These findings indicate that because of the difficulties and limitations associated with the molecular analysis of FFPE tissues, a combination of RT-PCR and FISH may be a better approach to enhance the sensitivity and accuracy of detecting ES/PNET translocations in FFPE tissues with suboptimally preserved nucleic acids.
authors.affiliation: Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota 55905, USA.
authors.forename: Xiang
authors.initials: X
authors.lastname: Qian
authors.forename: Long
authors.initials: L
authors.lastname: Jin
authors.forename: Brandon M
authors.initials: BM
authors.lastname: Shearer
authors.forename: Rhett P
authors.initials: RP
authors.lastname: Ketterling
authors.forename: Syed M
authors.initials: SM
authors.lastname: Jalal
authors.forename: Ricardo V
authors.initials: RV
authors.lastname: Lloyd
mesh_terms: D001483:Base Sequence; D002880:Chromosomes, Human, Pair 11 / Q000235:genetics; D002891:Chromosomes, Human, Pair 21 / Q000235:genetics; D002892:Chromosomes, Human, Pair 22 / Q000235:genetics; D017931:DNA Primers / Q000235:genetics; D004273:DNA, Neoplasm / Q000235:genetics; D005557:Formaldehyde; D006801:Humans; D017404:In Situ Hybridization, Fluorescence / Q000379:methods* / Q000706:statistics & numerical data; D007399:Interphase; D018241:Neuroectodermal Tumors, Primitive, Peripheral / Q000175:diagnosis* / Q000235:genetics*; D015514:Oncogene Proteins, Fusion / Q000235:genetics; D016612:Paraffin Embedding; D051789:Proto-Oncogene Protein c-fli-1; D034802:RNA-Binding Protein EWS; D020133:Reverse Transcriptase Polymerase Chain Reaction / Q000379:methods* / Q000706:statistics & numerical data; D012512:Sarcoma, Ewing / Q000175:diagnosis* / Q000235:genetics*; D012680:Sensitivity and Specificity; D016707:Tissue Fixation; D014157:Transcription Factors / Q000235:genetics; D014178:Translocation, Genetic
chemical_list: D017931:DNA Primers; D004273:DNA, Neoplasm; C450460:EWS-ERG fusion protein, human; C106031:EWS-FLI fusion protein; D015514:Oncogene Proteins, Fusion; D051789:Proto-Oncogene Protein c-fli-1; D034802:RNA-Binding Protein EWS; D014157:Transcription Factors; D005557:Formaldehyde