The transcription factor Ikaros, encoded by the IKZF1 gene, has multiple functions in different steps of hematopoiesis. Loss of function mutations in IKZF1 are frequently associated with BCR-ABL1-positive ALL. IKZF1 deletions comprise whole gene deletions as well as smaller intragenic deletions. All IKZF1 aberrations are associated with a poor prognosis in terms of overall survival and frequency of relapse.

IKZF1 deletions were evaluated in a cohort of 180 adult BCR-ABL1-positive B-cell precursor ALL cases. MLPA analysis was used to assess both whole gene and intragenic deletions, whereas breakpoint-specific consensus multiplex PCR [Caye et al., Haematologica, 2013] and real-time quantitative (RQ)-PCR were used to specifically detect the recurrent intragenic deletions Δ2-7, Δ2-8, Δ4-7 and Δ4-8. Intragenic IKZF1 deletions were detected in 129 patients (71.7%). More than one intragenic deletion was detected in a subset of 44 patients. Unexpectedly, in the majority of these patients (41/180 patients; 22.8%), significant differences in relative frequencies of single intragenic deletions were detected by RQ-PCR analysis. Together with the finding of more than two distinct intragenic deletions in 19/44 patients this clearly indicates the presence of subclonal or oligoclonal intragenic IKZF1 deletions. In the remaining 3/44 patients, number and frequencies of detected intragenic deletions rather suggested the presence of bi-allelic deletions within the whole leukemic bulk. Specificity of individual (sub-) clonal deletions was validated by Sanger sequencing. These data indicate that IKZF1 deletions arise independently in different subclones more frequently than it was estimated in earlier reports.

The quantitative breakpoint-specific PCR approach was additionally used to correlate the detection of intragenic IKZF1 mutations with established Ig/TCR-based monitoring of minimal residual disease (MRD) during/after treatment in a subset of 17 patients. Comparative IKZF1- and Ig/TCR-based MRD monitoring was performed on a total of 207 samples of initial diagnosis and follow-up. Whereas good correlation of Ig/TCR-MRD results and detection of IKZF1 deletions was seen in 9 out of 17 patients, different kinetics of Ig/TCR-MRD results and IKZF1-based leukemia monitoring in the remaining 8 patients were additionally indicative for the existence of IKZF1 deletions in leukemic subclones besides the major leukemic clone with their own kinetics of clearance and persistence.

Illegitimate RAG-mediated recombination has been proposed as responsible mechanism for recurrent intragenic deletions in IKZF1. Our data suggest that these lesions occur repeatedly during leukemogenesis and support a model of multiclonal evolution in BCR-ABL1-positive B-cell precursor ALL.


No relevant conflicts of interest to declare.

Author notes


Asterisk with author names denotes non-ASH members.