All patients aged ≥ 18 years with t(9;22) (q34.1; q11.2)/BCR::ABL1 documented by karyotype or FISH and ≥ 20% blasts included in the DATAML registry between 2000 and 2021 were analyzed. The DATAML registry contains all patients with ≥ 20% blasts of myeloid lineage in the bone marrow or blood or with an AML diagnosis according to WHO classifications. De novo BCR::ABL1+ AML was defined as no previous history of CML, no previous treatment with TKI and ≥ 20% blasts in bone marrow. CML-BP was defined as the occurrence of ≥20% myeloid blasts in patients with previous diagnosis of CML in chronic phase. Patients with lymphoid CML-BP or with mixed-phenotype acute leukemia are not registered in DATAML. Additional data were retrospectively collected for this study including CML history (date of diagnosis, SOKAL and ELTS score, treatments), BCR-ABL1 isotype (P190, P210), ABL1 mutations, anthracycline dose and TKIs during intensive chemotherapy, measurable residual disease (MRD) evaluations following induction, first consolidation cycle, before allogeneic hematopoietic cell transplantation (alloHCT), end of treatment or 100 days post alloHCT. Response to treatment, relapse, relapse-free survival (RFS), event-free survival (EFS), and OS were defined according to the ELN criteria [11]. This study was performed in accordance with the Declaration of Helsinki. DATAML was approved by French authorities and informed consent was provided to all patients.

Conventional karyotyping was performed on the BM diagnostic aspirate after short-term culture (24–72 h). The chromosomes were analyzed after R and/or G-banding. All karyotypes were reported according to the the International System for Human Cytogenetic Nomenclature (ISCN 2020).

Multi-parameter flow cytometry (MFC) was performed on whole bone marrow (BM) or blood specimens using a standard stain-lyse-wash procedure with ammonium chloride lysis. 1 × 105 cells were stained per analysis tube, and data were acquired on at least 1 × 104 blasts when specimen quality permitted. Data on standardized 10-color staining combinations were acquired on Navios instruments analyzed using Kaluza (Beckman-Coulter). Several different tube configurations were used for leukemic bulk analysis, associated 20 different markers (CD3, CD7, CD11b, CD13, CD14, CD16, CD19, CD33, CD34, CD36, CD38, CD45, CD45RA, CD56, CD64, CD79a, CD117, CD133, HLA-DR, and MPO). A blast gate including CD45 dim mononuclear cells was analyzed according to cytomorphologic data. Leukemic hematopoietic stem and progenitor subpopulations were gated on CD34+ cells and selected according to their expression of CD38, CD45RA, CD135 and CD133. Flow cytometry-based immunophenotypic classification defining six stages of leukemia differentiation-arrest categories was based on CD34, CD117, CD13, CD33, MPO and HLA-DR expression [12]. For phenotypic comparisons, CML-BP (n = 9), BCR::ABL1+AML (n = 10) and non-BCR::ABL1+AML (n = 2455) were used.

Genomic DNA from bone marrow or blood samples was extracted by standard procedures and sequenced using an Illumina NextSeq550Dx (Bordeaux) or NextSeq500 (Toulouse) sequencers and Magnis SureSelect XT HS capture panel (Agilent, Santa Clara, CA, USA) covering the complete coding regions (and −2 to +2 splicing sites) of 49 genes recurrently mutated in myeloid neoplasms (ANKRD26, ASXL1, ASXL2,BCOR, BCORL1, CALR, CBL, CCND2, CEBPA, CSF3R, CUX1, DDX41, DHX15, DNMT3A, ETNK1, ETV6, EZH2, FLT3, GATA1, GATA2, GNAS, GNB1,IDH1, IDH2, IKZF1, JAK2, KDM6A, KIT, KRAS, MPL, MYC,NFE2, NPM1, NRAS, PHF6, PPM1D, PTEN, PTPN11, RAD21, RIT1, RUNX1, SAMD9, SAMD9L, SETBP1, SF3B1, SH2B3, SMC1A, SMC3, SRSF2, STAG2, TET2, TERC, TERT, TP53, U2AF1, UBA1, WT1 and ZRSR2). Raw NGS data were analyzed using different “variant callers”: Mutect2, Varscan2, Lofreq and Vardict (Bordeaux) or MuTect2, HaplotypeCaller (both from the GATK suite developed by the Broad Institute) and SureCall (Agilent) algorithms (Toulouse) for variant calling aggregated in the in-house remote pipeline for data visualization, elimination of sequencing/mapping errors and retention of variants with high quality metrics. Variant interpretation was performed considering minor allele frequencies (MAF) in the public GnomAD database of polymorphisms (variants with MAF > 0.02 in overall population/global ancestry or sub-continental ancestry are excluded), variant allele frequencies (VAF), prevalence and clinical interpretation (COSMIC, protein impact). All variants were checked manually on IGV and named according to the Human Genome Variation Society.

RNA was extracted from blood or bone marrow cells. Quantification of BCR::ABL1 transcript levels was performed after reverse transcription and quantitative real-time polymerase chain reaction (RT-qPCR) according to the Europe against cancer (EAC) protocol using ABL1 as control gene [13]. Results are expressed as a percentage of BCR::ABL1/ABL1.

Data analysis was performed using Stata software (Statistical Software: Release 18.0. Stata Corporation, College Station, Texas, USA). All reported P-values were two-sided and the significance threshold was set at <0.05. Comparisons of the patients’ characteristics between groups (de novo BCR::ABL1+AML vs CML-BP) were assessed using Student’s t test (or the Mann–Whitney test if necessary) for continuous variables, and the chi2-test (or Fisher’s exact test if necessary) for categorical variables (including response to induction). For survival endpoints (EFS, RFS and OS), Kaplan–Meier survival curves were drawn and described using median in months (with IQR) as well as survival rates at 2 and 5 years. Differences in survival functions were tested using the log-rank test. The median follow-up (and its interquartile range (IQR)) was described by the reverse Kaplan–Meier technique. In the flow cytometry analysis, comparisons were performed using a Mann–Whitney test for continuous variables and Fisher’s exact test for categorical variables with GraphPad Prism. Ward’s clustering and PCA were conducted with Tanagra statistical software. Statistical test results are graphically expressed: *p < 0.05, **p < 0.01, ***p < 0.001.