Interphase fluorescence in situ hybridization assay for the detection of rearrangements of the EVI-1 locus in chromosome band 3q26 in myeloid malignancies.

Background and Objectives: Rearrangements of the EVI-1 locus in chromosome band 3q26 are associated with a poor prognosis in myeloid malignancies. To aid the diagnosis of such aberrations, and possibly disease monitoring, we established an interphase fluorescence in situ hybridization (FISH) assay for the affected breakpoint region.
Design and Methods: Several overlapping PAC (P1-derived artificial chromosome) clones centromeric to the EVI-1 gene were labeled with a red fluorescent dye, and PAC clones telomeric to EVI-1 with a green fluorochrome. This dual-color probe was hybridized to cytogenetic preparations of cell lines and patients' samples, which were also investigated for the presence of 3q26 rearrangements by chromosome banding analysis.
Results: In nuclei without 3q26 rearrangements, two pairs of co-localized red and green signals were observed, while separation of one red/green signal pair or splitting of one red or one green signal was found when 3q26 aberrations were present. The threshold value for true positivity, as determined on 20 samples from patients with myeloid malignancies without 3q26 rearrangements, was 10.2% for separation of one red/green signal pair, and 1% and 1.3% for splitting of one red or one green signal, respectively. In 17 samples from patients with a 3q26 aberration, the percentage of aberrant cells was significantly above these threshold levels.
Interpretation and Conclusions: We established an interphase FISH assay that efficiently identifies chromosome breakpoints affecting the EVI-1 locus in 3q26, and represents a useful complement to chromosome banding analysis for the detection of such aberrations.