title: Prevalence of RET/PTC rearrangements in thyroid papillary carcinomas: effects of the detection methods and genetic heterogeneity.
abstract: BACKGROUND
  RET/PTC rearrangements have been reported in papillary thyroid carcinomas with variable frequency in studies that used different detection methods.
  
  
  OBJECTIVE
  Our objective was to determine the role of different detection methods and tumor genetic heterogeneity on RET/PTC detection.
  
  
  METHODS
  Sixty-five papillary carcinomas were analyzed for RET/PTC1 and RET/PTC3 using five detection methods: standard-sensitivity RT-PCR, high-sensitivity RT-PCR, real-time LightCycler RT-PCR, Southern blot analysis, and fluorescence in situ hybridization.
  
  
  RESULTS
  RET/PTC rearrangements were detected by standard-sensitivity RT-PCR in 14 tumors. High-sensitivity RT-PCR detected RET/PTC in all of these and in 12 additional cases, where the levels of expression corresponded to one to five positive cells. Real-time LightCycler RT-PCR detected RET/PTC in 12 and Southern blot analysis in 11 tumors. By fluorescence in situ hybridization, 14 tumors were positive, including nine cases with 50-86% positive cells and five cases with 17-35% positive cells. Overall, nine (14%) tumors harbored clonal rearrangements, which were present in the majority of tumor cells and detected by all five methods. Five (8%) cases had subclonal rearrangements present in a smaller portion of tumor cells and detected by most methods. Twelve (18%) tumors had nonclonal RET/PTC that were detected only by high-sensitivity RT-PCR. No other mutations were found in tumors harboring clonal RET/PTC, whereas 60% of tumors with subclonal and 42% of tumors with nonclonal RET/PTC harbored additional mutations.
  
  
  CONCLUSIONS
  Our data suggest that broad variability in the reported prevalence of RET/PTC rearrangement is at least in part a result of the use of different detection methods and tumor genetic heterogeneity.
authors.affiliation: Department of Pathology, University of Cincinnati, 231 Albert Sabin Way, P.O. Box 670529, Cincinnati, Ohio 45267-0529, USA.
authors.forename: Zhaowen
authors.initials: Z
authors.lastname: Zhu
authors.forename: Raffaele
authors.initials: R
authors.lastname: Ciampi
authors.forename: Marina N
authors.initials: MN
authors.lastname: Nikiforova
authors.forename: Manoj
authors.initials: M
authors.lastname: Gandhi
authors.forename: Yuri E
authors.initials: YE
authors.lastname: Nikiforov
mesh_terms: D015139:Blotting, Southern; D002291:Carcinoma, Papillary / Q000235:genetics*; D015321:Gene Rearrangement; D011905:Genes, ras; D006801:Humans; D017404:In Situ Hybridization, Fluorescence; D015514:Oncogene Proteins, Fusion / Q000235:genetics*; D011505:Protein-Tyrosine Kinases / Q000235:genetics*; D048493:Proto-Oncogene Proteins B-raf / Q000235:genetics; D012334:RNA, Neoplasm / Q000235:genetics; D020133:Reverse Transcriptase Polymerase Chain Reaction; D013964:Thyroid Neoplasms / Q000235:genetics*
chemical_list: D015514:Oncogene Proteins, Fusion; D012334:RNA, Neoplasm; D011505:Protein-Tyrosine Kinases; C093573:ret-PTC fusion oncoproteins, human; C482119:BRAF protein, human; D048493:Proto-Oncogene Proteins B-raf