Intrachromosomal amplification of chromosome 21 (iAMP21) occurs in 2% of B-cell acute lymphoblastic leukemia (ALL) and is considered to confer a poor prognosis. Alterations related to chromosome 21, such as the constitutional r(21)c and rob(15;21)c, have been associated with a high hazard ratio for iAMP21-ALL. Here we describe the case of an adolescent with iAMP21-B-ALL presenting a non-Robertsonian somatic t(15;21)(q25.3;q22.1) with NTRK3 gene rearrangement, chromothripsis, and breakage-fusion-bridge of chromosome 21, besides a somatic homozygous deletion of the SH2B3 gene.

A 12-year-old girl was admitted to the Lagoa Federal Hospital, Rio de Janeiro, Brazil, with a 2-month history of fever, weight loss, arthritis, bone pain, and hepatomegaly. The bone marrow aspirate was hypercellular, with blasts cell suggestive of ALL phenotype. The Flow cytometry analysis confirmed a diagnosis compatible with pre-B-ALL phenotype. Due to the cytogenetics findings, the patient was treated under the high-risk ALL-BFM-2009 v.13 protocol. She achieved remission three months after the initial diagnosis. Currently, she is out of treatment and has been followed up on an outpatient basis. G-banding and FISH experiments were performed on bone marrow cells under standard protocols. Array-comparative genomic hybridization (aCGH) was performed according to standard procedures. Transcriptional expression of genes involved in the aberrations as revealed by aCGH analysis was determined by RT-qPCR. The copy number of SH2B3 was quantified by RT-qPCR in constitutive (epithelial) cells collected from mouth swabs.

Phytohemagglutinin-stimulated lymphocyte culture during follow-up, showed a normal karyotype 46,XX, eliminating the hypothesis of t(15;21) as a germline mutation. FISH analysis in bone marrow cells detected iAMP21, with aCGH analysis revealing further genomic imbalances. The RT-qPCR analysis detected elevated expression levels of the RUNX1 (68-fold) and reduced expression of the CDK6 (0.057-fold). Studies with constitutive cells collected from mouth swabs showed that SH2B3 biallelic deletion was a somatic alteration occurring during clonal evolution.

iAMP21 has been associated with type I and type II mutations as secondary aberrations. Besides, Harrison and co-workers have been describing a relation between chromosome 21 constitutional abnormalities and iAMP21 leukemogenesis. Thus, along with the standard clinical profile, a precise molecular characterization may help in iAMP21-ALL differential diagnosis. In our work, high-resolution cytogenetics combined with molecular approaches helped us characterize a non-Robertsonian somatic t(15;21)(q25.3;q22.1), with rearrangement of the putative leukemic gene NTRK3, ruling out the involvement of r(21)c and rob(15;21)c, both in constitutive and tumor cells.

The identification of novel secondary genetic changes was valuable to discuss sporadic iAMP21 leukemogenic mechanisms. For the first time, we show a non-Robertsonian translocation t(15;21)(q25.3;q22.1) with NTRK3 rearrangement in an adolescent with iAMP21-ALL with a favorable prognosis.