Characterizing false-positive fluorescence in situ hybridization results by mate-pair sequencing in a patient with chronic myeloid leukemia and progression to myeloid blast crisis

Cancer Genet. 2020 May;243:48-51. doi: 10.1016/j.cancergen.2020.02.008. Epub 2020 Mar 17.


Traditional cytogenetic testing methodologies, including conventional chromosome analysis and fluorescence in situ hybridization (FISH), are invaluable for the detection or recurrent genetic abnormalities in various hematologic malignancies. However, technological advances, including a novel next-generation sequencing technique termed mate-pair sequencing (MPseq), continue to revolutionize the field of cytogenetics by enabling the characterization of structural variants at a significantly higher resolution compared to traditional methodologies. To illustrate the power of MPseq, we present a 27-year-old male diagnosed with chronic myeloid leukemia in myeloid blast crisis with multiple chromosomal abnormalities observed in all 20 metaphases from a peripheral blood specimen, including t(9;22)(q34;q11.2) and t(4;11)(q12;p15). Suspicious of a novel NUP98/PDGFRA fusion [t(4;11)(q12;p15)], break-apart FISH probe sets for the PDGFRA (4q12) and NUP98 (11p15.4) gene regions were performed and were both positive in approximately 86% of 200 interphase nuclei. However, subsequent MPseq testing revealed breakpoints located within the NUP98 gene and within an intergenic region (4q12) located between the CHIC2 and PDGFRA genes, indicating this 4;11 translocation does not result in the predicted NUP98/PDGFRA gene fusion as inferred from FISH and conventional chromosome results. This case demonstrates the clinical utility of MPseq, particularly for characterizing novel gene fusion events which may ultimately identify a false-positive FISH result.

Keywords: Chronic myeloid leukemia (CML); Conventional chromosome analysis; Fluorescence in situ hybridization (FISH); Mate-pair sequencing (MPseq).

Publication types

  • Case Reports

MeSH terms

  • Adult
  • Blast Crisis / diagnosis
  • Blast Crisis / genetics*
  • Chromosome Aberrations
  • Chromosomes, Human, Pair 11 / genetics
  • Chromosomes, Human, Pair 22 / genetics
  • Chromosomes, Human, Pair 4 / genetics
  • Chromosomes, Human, Pair 9 / genetics
  • Cytogenetic Analysis
  • Disease Progression
  • False Positive Reactions
  • High-Throughput Nucleotide Sequencing*
  • Humans
  • In Situ Hybridization, Fluorescence*
  • Leukemia, Myelogenous, Chronic, BCR-ABL Positive / genetics*
  • Male
  • Nuclear Pore Complex Proteins / genetics
  • Oncogene Proteins, Fusion / genetics
  • Oncogene Proteins, Fusion / isolation & purification*
  • Receptor, Platelet-Derived Growth Factor alpha / genetics


  • Nuclear Pore Complex Proteins
  • Nup98 protein, human
  • Oncogene Proteins, Fusion
  • Receptor, Platelet-Derived Growth Factor alpha