Added value of molecular karyotype in childhood acute lymphoblastic leukemia

Abstract

Background: Thanks to an improved therapeutic regimen in childhood B-cell precursor acute lymphoblastic leukemia (BCP-ALL), 5 year-overall survival now exceeds 90%. Unfortunately, the 25% of children who relapse have an initial poor prognosis, potentially driven by pre-existing or emerging molecular anomalies. The latter are initially and essentially identified by cytogenetics. However, some subtle alterations are not visible through karyotyping.

Methods: Single nucleotide polymorphisms (SNP) array is an alternative way of chromosomal analysis allowing for a more in-depth evaluation of chromosomal modifications such as the assessment of copy number alterations (CNA) and loss of heterozygosity (LOH). This method was applied here in retrospective diagnosis/relapse paired samples from seven children with BCP-ALL and in a prospective cohort of 38 newly diagnosed childhood cases.

Results: In the matched study, compared to the initial karyotype, SNP array analysis reclassified two patients as poor prognosis cases. Modulation during relapse was seen for 4 CNA and 0.9 LOH. In the prospective study, SNP reclassified the 10 patients with intermediate karyotype as 7 good prognosis and 3 poor prognosis. Ultimately, in all the children tested, SNP array allowed to identify additional anomalies compared to conventional karyotype, refine its prognostic value and identify some druggable anomalies that could be used for precision medicine. Overall, the anomalies detected could be segregated in four groups respectively involved in B-cell development, cell proliferation, transcription and molecular pathways.

Conclusion: SNP therefore appears to be a method of choice in the integrated diagnosis of BCP ALL, especially for patients initially classified as intermediate prognosis. This complementary method of both cytogenetics and high throughput sequencing allows to obtain further classified information and can be useful in case of failure of these techniques.

Keywords: BCP‐ALL; SNP array; karyotype; pediatric patients; prognosis.

Figure 1

Example of copy number alterations (CNA) modulation between diagnosis and relapse for one patient. with an IKZF1 deletion acquired at relapse. (a) CNA (deletions in red and gains in blue) for 1 patient with RUNX1 amplification at diagnosis (pink line) and relapse (green line). At relapse. Six additional CNAs were acquired (only deletions). (b) Zoom on the 7p12 locus showing an acquired deletion encompassing part of the IKZF1 gene at relapse.

Figure 2

Gene fusion between ZNF384 and CREBBP (translocation t[12;16]). (a) Copy number alterations (CNA) (deletion in red and gain in blue) for one patient from the prospective cohort with normal standard karyotype shows three CNA. especially a duplication in 12p13 associated with a deletion in 16p13. (b) In the 12p13 locus. there is a breakpoint in the ZNF384 gene with duplication from the proximal segment before this breakpoint. (c) In the 16p13 locus, there is a breakpoint in the CREBBP gene with a deletion from the proximal segment before this breakpoint. Duplication 12p13 with a breakpoint in the ZNF384 gene (b) and deletion 16p13 with a breakpoint in the CREBBP gene (c) could correspond to an unbalanced translocation t(12;16)(p13;13).