PMID- 16607381
OWN - NLM
STAT- MEDLINE
DCOM- 20060725
LR  - 20230216
IS  - 0023-6837 (Print)
IS  - 0023-6837 (Linking)
VI  - 86
IP  - 6
DP  - 2006 Jun
TI  - Use of a novel FISH assay on paraffin-embedded tissues as an adjunct to diagnosis 
      of alveolar rhabdomyosarcoma.
PG  - 547-56
AB  - A valuable diagnostic adjunct and important prognostic parameter in alveolar 
      rhabdomyosarcoma (ARMS) is the identification of translocations t(2;13)(q35;q14) 
      and t(1;13)(p36;q14), and the associated PAX3-FKHR and PAX7-FKHR fusion 
      transcripts, respectively. Most RMS fusion gene type studies have been based on 
      reverse transcriptase-polymerase chain reaction (RT-PCR) detection of the fusion 
      transcript, a technique limited by RNA quality and failure of devised primer sets 
      to detect unusual variants. As an alternative approach, we developed a 
      fluorescence in situ hybridization (FISH) assay that can: (1) distinguish between 
      the two most common ARMS-associated fusion genes; (2) identify potential unusual 
      variant translocations; (3) assess histologic components in mixed 
      alveolar/embryonal RMS; and (4) be performed on paraffinized tissue. FISH 
      analyses of 75 specimens (40 ARMS, 16 ERMS, 8 mixed ARMS/ERMS, and 11 non-RMS 
      tumors) using selected cosmid clone, bacterial, P1-derived, and yeast artificial 
      chromosome probe sets were successful in all but two cases. Among specimens with 
      informative results for both FISH and RT-PCR or standard karyotyping, PAX/FKHR 
      classification results were concordant in 94.6% (53/56). The three discordant 
      cases included one exhibiting a t(2;13) by FISH that was subsequently confirmed 
      by repeat RT-PCR, a second showing a rearrangement of the PAX3 locus only 
      (consistent with the presence of a PAX3 variant translocation), and a third 
      revealing a t(2;13) by FISH that lacked this translocation cytogenetically. Both 
      alveolar and embryonal components of the mixed ARMS/ERMS subtype were negative 
      for PAX3, PAX7, and FKHR rearrangements, a surprising finding confirmed by RT-PCR 
      and/or conventional karyotyping. These data demonstrate that FISH with newly 
      designed probe sets is a reliable and highly specific method of detecting t(1;13) 
      and t(2;13) in routinely processed tissue and may be useful in differentiating 
      ARMS from other small round cell tumors. The findings also suggest that FISH may 
      be a more sensitive assay than RT-PCR in some settings, capable of revealing 
      variant translocations.
FAU - Nishio, Jun
AU  - Nishio J
AD  - Department of Pathology and Microbiology, University of Nebraska Medical Center, 
      983135 Nebraska Medical Center, Omaha, 68198-3135, USA.
FAU - Althof, Pamela A
AU  - Althof PA
FAU - Bailey, Jacqueline M
AU  - Bailey JM
FAU - Zhou, Ming
AU  - Zhou M
FAU - Neff, James R
AU  - Neff JR
FAU - Barr, Frederic G
AU  - Barr FG
FAU - Parham, David M
AU  - Parham DM
FAU - Teot, Lisa
AU  - Teot L
FAU - Qualman, Stephen J
AU  - Qualman SJ
FAU - Bridge, Julia A
AU  - Bridge JA
LA  - eng
GR  - CA36727/CA/NCI NIH HHS/United States
GR  - CA89461/CA/NCI NIH HHS/United States
GR  - CA98543/CA/NCI NIH HHS/United States
PT  - Comparative Study
PT  - Journal Article
PT  - Research Support, N.I.H., Extramural
PT  - Research Support, Non-U.S. Gov't
PL  - United States
TA  - Lab Invest
JT  - Laboratory investigation; a journal of technical methods and pathology
JID - 0376617
RN  - 0 (Oncogene Proteins, Fusion)
SB  - IM
MH  - Biological Assay
MH  - Chromosome Banding
MH  - Chromosomes, Human, Pair 13
MH  - Chromosomes, Human, Pair 2
MH  - Cytogenetic Analysis
MH  - Databases, Factual
MH  - Humans
MH  - *In Situ Hybridization, Fluorescence
MH  - Karyotyping
MH  - Oncogene Proteins, Fusion
MH  - Paraffin Embedding
MH  - Reverse Transcriptase Polymerase Chain Reaction
MH  - Rhabdomyosarcoma, Alveolar/*diagnosis/*genetics/pathology
MH  - Sensitivity and Specificity
MH  - Translocation, Genetic
EDAT- 2006/04/12 09:00
MHDA- 2006/07/26 09:00
CRDT- 2006/04/12 09:00
PHST- 2006/04/12 09:00 [pubmed]
PHST- 2006/07/26 09:00 [medline]
PHST- 2006/04/12 09:00 [entrez]
AID - S0023-6837(22)03269-X [pii]
AID - 10.1038/labinvest.3700416 [doi]
PST - ppublish
SO  - Lab Invest. 2006 Jun;86(6):547-56. doi: 10.1038/labinvest.3700416.