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Intrachromosomal amplification of chromosome 21 (iAMP21) defines a rare subtype of pediatric acute lymphoblastic leukemia (pALL) occurring in approximately 2-3% of cases. The patients are older (median age is 9 years), usually have low white blood cell counts and show high relapse risk with standard therapy. Thus, it has been proposed to include ALL with iAMP21 as a distinct entity in the WHO classification of hematological malignancies.

To assess the frequency as well as the clinicopathological and genetic characteristics of ALL with iAMP21 in one of the three national diagnostic centers of pALL in Hungary. We sought to determine additional genetic aberrations associated with this rare entity.

Between 2008-2016, 175 samples of pALL patients were tested with FISH for BCR-ABL1, ETV6-RUNX1 and MLL translocations. When available, bone marrow karyotyping was used to verify the abnormal results. In one case with iAMP21, multiplex ligations-dependent probe amplification (MLPA) was used to verify the cytogenetic aberrations as well as to detect associated copy number alterations.

Among the 175 samples screened with FISH, three showed evidence of iAMP21 (1.7%). Case 1 was a 16-year-old male who presented with thrombocytopenia and hepatosplenomegaly. Flow cytometry (FCM) showed common ALL phenotype with the expression of CD13 and CD33. FISH showed >10 RUNX1 signals in clusters in leukemic blasts, while karyotyping demonstrated r(21) with 7q deletion and +X. The lesions were verified by MLPA, which additionally revealed biallelic CDKN2B and RB1 deletions. The patient was treated with ALL-IC BFM 2002 standard risk protocol. Following remission, isolated meningeal relapse occurred, for which he received radiotherapy. The patient died with recurrent meningeal disease without bone marrow involvement after 52 months. Case 2 was an 11-year-old girl, who presented with symptoms suggesting osteomyelitis of the tibia with unremarkable blood count. MRI showed multiple lesions in vertebrae as well as meningeal involvement of the spinal cord. Bone marrow biopsy and biopsy of the left tibia showed diffuse infiltration of lymphoblasts with only 5% leukemic cells in bone marrow aspirates. FISH detected 6-8 copies of RUNX1 in leukemic blasts, while karyotyping yielded only normal bone marrow cells. She was commenced on ALL-IC BFM 2002 standard risk and was later switched to high risk protocol. She is in complete remission after 14 months. Case 3 was an 11-year-old boy who presented with anemia and thrombocytopenia. FCM showed ALL with common phenotype with two populations; one being strong CD19+/CD66c+ and one with dim CD19+/CD66c-. FISH showed >10 RUNX1 signals in clusters in 95% of cells, while 52% showed BCR-ABL1 positivity. Bone marrow karyotyping yielded metaphases of poor quality.

ALL with iAMP21 is a rare subtype with distinct clinicopathological characteristics. Presenting with only mildly elevated WBC in older children is typical, relapses are frequent if standard risk chemotherapy is administered. Association with BCR-ABL1 translocation is rare, having been reported so far in only 4 cases. Observing BCR-ABL1 translocation in a subpopulation of leukemic cells is an intriguing phenomenon; it indicates that this translocation may occur as a secondary event even after leukemic transformation has commenced.