title: Detection of chromosomal translocations in formalin-fixed paraffin-embedded (FFPE) leukemic specimens by digital expression profiling.
abstract: BACKGROUND
  Detection of chromosomal translocations in formalin-fixed paraffin-embedded (FFPE) leukemic samples is important for confirmation of histopathological findings, classification, prognostication, and therapeutic decisions. Herein, we aim to determine whether digital expression profiling could detect chromosomal translocations in FFPE leukemic samples identified by RT-PCR, FISH, and/or karyotyping.
  
  
  METHODS
  RNA was extracted from 28 FFPE bone marrow specimens from 19 patients diagnosed with leukemia. Eight patients were translocation t(9;22) positive, three inv(16)/t(16/16) positive, five translocation t(15;17) positive, and one translocation t(8;21) positive. Two patients (four specimens) were normal. The extracted RNA was hybridized to DNA reporter probes overnight at 65 °C, followed by purification of the labeled translocations. Six hundred fields of view were counted to enumerate the number of translocations.
  
  
  RESULTS
  Digital expression profiling had 100% concordance with RT-PCR, FISH, or karyotyping analysis in the two normal individuals, eight translocation t(9;22) samples, five translocation t(15;17) samples, and one translocation t(8;21) sample. None of the inv(16) positive samples were detected. Digital expression profiling detected translocations with 0.014 p190 allelic burden.
  
  
  CONCLUSIONS
  Digital expression profiling can be used to measure translocation t(9;22), t(15;17), and t(8;21) in FFPE samples and is useful when a confirmatory test from a FFPE sample is necessary.
authors.affiliation: ARUP Institute for Clinical and Experimental Pathology, Salt Lake City, UT, USA.
authors.forename: M
authors.initials: M
authors.lastname: Liew
authors.affiliation: ARUP Institute for Clinical and Experimental Pathology, Salt Lake City, UT, USA.|Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT, USA.
authors.forename: R
authors.initials: R
authors.lastname: Mao
authors.affiliation: ARUP Institute for Clinical and Experimental Pathology, Salt Lake City, UT, USA.|Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT, USA.
authors.forename: C T
authors.initials: CT
authors.lastname: Wittwer
authors.affiliation: ARUP Institute for Clinical and Experimental Pathology, Salt Lake City, UT, USA.|Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT, USA.
authors.forename: M E
authors.initials: ME
authors.lastname: Salama
mesh_terms: D001853:Bone Marrow / Q000473:pathology; D020869:Gene Expression Profiling; D006801:Humans; D017404:In Situ Hybridization, Fluorescence; D059785:Karyotype; D007938:Leukemia / Q000175:diagnosis* / Q000235:genetics*; D016133:Polymerase Chain Reaction; D014178:Translocation, Genetic
keywords: nCounter analysis system