title: FISH mapping of Philadelphia negative BCR/ABL1 positive CML.
abstract: BACKGROUND
  Chronic myeloid leukaemia (CML) is a haematopoietic stem cell disorder, almost always characterized by the presence of the Philadelphia chromosome (Ph), usually due to t(9;22)(q34;q11) or its variants. The Ph results in the formation of the BCR/ABL1 fusion gene, which is a constitutively activated tyrosine kinase. Around 1% of CML patients appear to have a Ph negative karyotype but carry a cryptic BCR/ABL1 fusion that can be located by fluorescence in situ hybridisation (FISH) at chromosome 22q11, 9q34 or a third chromosome. Here we present FISH mapping data of BCR and ABL1 flanking regions and associated chromosomal rearrangements in 9 Ph negative BCR/ABL1 positive CML patients plus the cell line CML-T1.
  
  
  RESULTS
  BCR/ABL1 was located at 9q34 in 3 patients, 22q11 in 5 patients and CML-T1 and 22p11 in 1 patient. In 3 of 6 cases with the fusion at 22q11 a distal breakpoint cluster was found within a 280 Kb region containing the RAPGEF1 gene, while in another patient and the CML-T1 the distal breakpoint fell within a single BAC clone containing the 3' RXRA gene. Two cases had a duplication of the masked Ph while genomic deletions of the flanking regions were identified in 3 cases. Even more complex rearrangements were found in 3 further cases.
  
  
  CONCLUSIONS
  BCR/ABL1 formation resulted from a direct insertion (one step mechanism) in 6 patients and CML-T1, while in 3 patients the fusion gene originated from a sequence of rearrangements (multiple steps). The presence of different rearrangements of both 9q34 and 22q11 regions highlights the genetic heterogeneity of this subgroup of CML. Future studies should be performed to confirm the presence of true breakpoint hot spots and assess their implications in Ph negative BCR/ABL1 positive CML.
authors.affiliation: Molecular Cytogenetics, Academic Haematology, Royal Free and UCL Medical School, Rowland Hill Street, London, NW3 2PF, UK. e.nacheva@ucl.ac.uk.
authors.forename: Anna
authors.initials: A
authors.lastname: Virgili
authors.forename: Diana
authors.initials: D
authors.lastname: Brazma
authors.forename: Alistair G
authors.initials: AG
authors.lastname: Reid
authors.forename: Julie
authors.initials: J
authors.lastname: Howard-Reeves
authors.forename: Mikel
authors.initials: M
authors.lastname: Valgañón
authors.forename: Anastasios
authors.initials: A
authors.lastname: Chanalaris
authors.forename: Valeria As
authors.initials: VA
authors.lastname: De Melo
authors.forename: David
authors.initials: D
authors.lastname: Marin
authors.forename: Jane F
authors.initials: JF
authors.lastname: Apperley
authors.forename: Colin
authors.initials: C
authors.lastname: Grace
authors.forename: Ellie P
authors.initials: EP
authors.lastname: Nacheva