title: Optimizing detection of RET and PPARg rearrangements in thyroid neoplastic cells using a home-brew tetracolor probe.
abstract: BACKGROUND
  Fluorescence in situ hybridization (FISH) to identify specific DNA target sequences in the nuclei of nondividing cells of numerous solid neoplasms has contributed to the introduction of molecular cytogenetics as a useful adjunct to cytology, leading recently to the "marriage" of the 2 disciplines. Numerous cancer molecular markers can now be investigated using different technical approaches, at both the gene and expression levels, in biopsies of various suspected cancers, including differentiated thyroid carcinoma. The limited amount of bioptic material is often insufficient to carry out multiple tests, and optimizing handling of the biopsy is desirable.
  
  
  METHODS
  We have developed a home-brew tetracolor break-apart probe able to simultaneously identify the 2 most common genetic alterations in differentiated thyroid carcinoma: RET/PTC variants in papillary thyroid carcinoma and PAX8/PPARg fusion and variants in follicular thyroid carcinoma.
  
  
  RESULTS
  The probe had 100% specificity, 99.5% sensitivity, and ≥ 3% cutoff. The probe was tested on RET/PTC and PAX8/PPARg RT-PCR positive controls, and feasibility was assessed in 368 thyroid nodule fine-needle aspirations (FNA). In the latter analysis, 24 FNAs had split RET signal, and 9 had split PPARg signal. FISH analysis of available surgically removed nodules confirmed the sensitivity of FISH in detecting abnormal clones and oligoclones.
  
  
  CONCLUSIONS
  The home-brew tetracolor probe showed high feasibility, optimizing the use of the biological material in relation to the available molecular tests and maximizing the FISH experimental and slide-scoring times. This probe may be considered an alternative to RT-PCR when recovery and quality of RNA amplification from FNA are insufficient.
authors: Department of Biomedical Sciences, University of Cagliari, Cagliari, Italy.
authors: Paola
authors: P
authors: Caria
authors: Daniela V
authors: DV
authors: Frau
authors: Tinuccia
authors: T
authors: Dettori
authors: Francesco
authors: F
authors: Boi
authors: Maria L
authors: ML
authors: Lai
authors: Stefano
authors: S
authors: Mariotti
authors: Roberta
authors: R
authors: Vanni
mesh_terms: D018263:Adenocarcinoma, Follicular / Q000235:genetics / Q000473:pathology; D044963:Biopsy, Fine-Needle; D002291:Carcinoma, Papillary / Q000235:genetics / Q000473:pathology; D005240:Feasibility Studies; D005456:Fluorescent Dyes; D005500:Follow-Up Studies; D015321:Gene Rearrangement; D006044:Goiter, Nodular / Q000235:genetics / Q000473:pathology; D006801:Humans; D017404:In Situ Hybridization, Fluorescence; D047495:PPAR gamma / Q000235:genetics*; D011379:Prognosis; D051096:Proto-Oncogene Proteins c-ret / Q000235:genetics*; D012333:RNA, Messenger / Q000235:genetics; D020133:Reverse Transcriptase Polymerase Chain Reaction; D012680:Sensitivity and Specificity; D013964:Thyroid Neoplasms / Q000235:genetics* / Q000473:pathology*
chemical_list: D005456:Fluorescent Dyes; D047495:PPAR gamma; D012333:RNA, Messenger; D051096:Proto-Oncogene Proteins c-ret; C099282:RET protein, human
keywords: FISH; FNA; PAX8/PPARg; RET/PTC; thyroid cancer