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Ž. Antić et al.
Figure 4. Prevalence of relapse associated genomic alterations at diagnosis. Bar plot showing the percentage of relapses in cases with high-clonal (blue) or sub- clonal (yellow) mutations in seven relapse-associated genes, and in cases that were wild-type (black) for these genes. Only cases with high-clonal IKZF1 4-7 deletions showed a significantly higher percentage of relapse development compared to wild-type cases (Fisher exact test, P<0.01) (Online Supplementary Table S9).
Figure 5. Cumulative incidence of relapse for high-clonal and subclonal IKZF1 deletions. The cumulative incidence of relapse (CIR) was estimated using a compet- ing-risk model with death as a competing event. CIR plots are presented for the representative ALL9 (left) and ALL10 (right) cohorts. Lines represent the IKZF1 dele- tion status and include wild-type (black line), subclonal exon 4-7 deletion (yellow), other high-clonal deletion (purple), and high-clonal exon 4-7 deletion (blue). Straight lines depict relapses and dotted lines death. P-values shown are obtained by employing the Gray test to compare CIR curves. The 5-year CIR was higher in cases with high-clonal IKZF1 deletions, compared to wild-type cases in both representative cohorts.
(9/132) (Fisher exact test, P<0.01) (Figure 6, Online Supplementary Figure S3B, Online Supplementary Table S7). For IKZF1 exon 4-7 deletions, the difference was even more striking. Here, the presence of deletions was studied in 19 available relapse samples using breakpoint-spanning PCR, followed by Sanger sequencing to confirm that the breakpoint sequences were identical at diagnosis and relapse (Figure 6, Online Supplementary Figure S3B, Online Supplementary Tables S6 and S7). All major clone IKZF1 exon 4-7 deletions were found to be preserved in the major clone at the time of relapse (n=12), which is in agreement with earlier findings and illustrates their rele- vance to relapse development in these treatment proto- cols.12,24 In contrast, none of the subclonal exon 4-7 dele- tions in IKZF1 (n=13) was preserved in either the major or a minor clone at relapse. Collectively, the data from the
present study indicate that these deletions, when present at initial diagnosis at a subclonal level, do not drive relapse in pediatric ALL.
Discussion
ALL is a heterogeneous disease in which specific genomic alterations show strong associations with relapse risk and outcome. In this study, we assessed the clinical relevance and prognostic value of subclonal alterations in eight genes frequently mutated in relapsed B-cell precur- sor ALL in a cohort of 503 diagnostic samples. Our data demonstrate that subclonal alterations in these genes are very common at the time of diagnosis, but that these mutations do not provide a basis for risk stratification in
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haematologica | 2021; 106(12)