title: Detection of gene fusions in rhabdomyosarcoma by reverse transcriptase-polymerase chain reaction assay of archival samples.
abstract: Alveolar rhabdomyosarcoma is a pediatric soft-tissue tumor that is often difficult to distinguish from other small round-cell tumors. The PAX3-FKHR and PAX7-FKHR gene fusions that result from chromosomal translocations in this tumor provide potential molecular diagnostic markers. To apply these molecular markers to commonly available archival material, we used reverse transcriptase-polymerase chain reaction and oligonucleotide hybridization methodology to develop an assay capable of identifying PAX3-FKHR and PAX7-FKHR fusion transcripts in formalin-fixed, paraffin-embedded tissue. Use of a control assay for wild-type FKHR mRNA indicated that RNA was successfully isolated, reverse-transcribed, and amplified in 15 of 16 archival cases. Comparison of assay results for the PAX3-FKHR and PAX7-FKHR fusions with standard molecular assays of paired frozen material revealed that all eight cases of known fusion-positive rhabdomyosarcoma were correctly identified and distinguished as PAX3-FKHR or PAX7-FKHR. The seven cases of known fusion-negative rhabdomyosarcoma showed no evidence of either product. These results indicate that we have developed a molecular assay that accurately identifies the fusion transcripts characteristic of alveolar rhabdomyosarcoma in archival samples. This assay will be useful for diagnosis and for retrospective clinicopathologic correlative studies.
authors.affiliation: Department of Pathology and Laboratory Medicine, University of Pennsylvania School of Medicine, Philadelphia 19104-6082, USA.
authors.forename: R H
authors.initials: RH
authors.lastname: Edwards
authors.forename: J
authors.initials: J
authors.lastname: Chatten
authors.forename: Q B
authors.initials: QB
authors.lastname: Xiong
authors.forename: F G
authors.initials: FG
authors.lastname: Barr
mesh_terms: D001483:Base Sequence; D014408:Biomarkers, Tumor / Q000235:genetics; D002648:Child; D002675:Child, Preschool; D006801:Humans; D008969:Molecular Sequence Data; D019042:Muscle Neoplasms / Q000235:genetics*; D016133:Polymerase Chain Reaction; D012194:RNA-Directed DNA Polymerase; D012189:Retrospective Studies; D018232:Rhabdomyosarcoma, Alveolar / Q000235:genetics*; D016707:Tissue Fixation; D014178:Translocation, Genetic
chemical_list: D014408:Biomarkers, Tumor; D012194:RNA-Directed DNA Polymerase