A novel tricolor, dual-fusion fluorescence in situ hybridization method to detect BCR/ABL fusion in cells with t(9;22)(q34;q11.2) associated with deletion of DNA on the derivative chromosome 9 in chronic myelocytic leukemia

Dual-color, dual-fusion fluorescence in situ hybridization (D-FISH) can accurately detect and quantify cells with BCR/ABL fusion in <1% of 500 nuclei in 80% of patients with chronic myelocytic leukemia (CML) and t(9;22)(q34;q11.2). The remaining patients have one of three forms of atypical D-FISH patterns; these patterns have different sensitivities to detect disease. Neoplastic cells with one ABL, one BCR, and one BCR/ABL fusion are particularly problematic, because normal cells with coincidental overlap have the same pattern. For these patients, the normal cutoff for D-FISH is >23%. We tested a new method that incorporates an aqua-labeled probe for the argininosuccinate synthetase (ASS) gene into the conventional BCR/ABL D-FISH probe set. This tricolor D-FISH (TD-FISH) method takes advantage of the aqua-labeled ASS probe to distinguish between neoplastic and normal cells. We used TD-FISH to study 20 normal specimens and 35 specimens from 20 patients with known loss of both BCR and ABL from the derivative chromosome 9. The results show that TD-FISH effectively discriminates between cells with overlapping BCR and ABL signals from cells with true BCR/ABL fusion and improves the ability to quantify minimal residual disease from >23% to >1% of 500 interphase nuclei.     

Interpretation of submicroscopic deletions of the BCR or ABL gene should not depend on extra signal-FISH: problems in interpretation of submicroscopic deletion of the BCR or ABL gene with extra signal-FISH

Several groups have demonstrated that a submicroscopic gene deletion in Ph+ chronic myelogenous leukemia (CML) is associated with a poor prognosis and reduced response to treatment. To assess the variation between detection methods in the interpretation of a submicroscopic gene deletion, we performed an extra signal (ES)-FISH BCR/ABL and double-FISH (D-FISH) BCR/ABL on frozen bone marrow cells from 79 patients with CML (63 in the chronic phase, 6 in the accelerated phase, and 10 in blast crisis) and 30 patients with a BCR/ABL-negative myeloproliferative disorder as determined by RT-PCR. The normal cutoff values were 0.22% for ES-FISH and 0.25% for D-FISH. The cutoff values for false-positive signals from a juxtaposition of the BCR and ABL gene were 11% in ES-FISH and 13% in D-FISH. Of the 14 patients who showed an ABL gene deletion by ES-FISH, 5 had an ABL deletion only, 5 had both a BCR and an ABL deletion, but 4 proved to have a classic BCR/ABL rearrangement without a submicroscopic deletion, as determined by D-FISH. Discrepant results between ES- and D-FISH were observed in 12 of the 79 patients (15.8%), and the main causes of a discrepancy were a false-positive ABL deletion (4 of 12, 33%), a variant Philadelphia chromosome (3 of 12, 25%), an inversion of derivative chromosome 9 at the very breakpoint of the ABL gene (9q32) (1 of 12, 8.3%), a cryptic variant Ph chromosome (1 of 12, 8.3%), and a marker chromosome (1 of 12, 8.3%). Although there was no significant difference in the sensitivity for the detection of the fusion signal between ES- and D-FISH, ES-FISH showed a high percentage of cells with false-positive fusion signals (1 orange, 1 green, 1 yellow), which makes it difficult to interpret the submicroscopic ABL deletion. In conclusion, an interpretation of the submicroscopic deletions of the BCR or ABL gene should not depend on ES-FISH.     

Emergence of chronic myelogenous leukemia in a patient with primary thrombocythemia and absence of BCR/ABL rearrangement

A 65-year-old woman presented with clinical features of primary thrombocythemia (PT), and absence of the BCR/ABL fusion gene. She responded to hydroxyurea treatment, although after 1 year she required progressive increases in the dose. Six years later, she maintained a high platelet count despite hydroxyurea at 2 g/day and treatment was changed to anagrelide. After 3 weeks, both platelet and leukocyte counts increased. A karyotype study detected the Philadelphia chromosome in all of the 24 metaphases studied. Fluorescent in situ hybridization (FISH) analysis revealed the BCR/ABL rearrangement. The patient was treated with imatinib mesylate and achieved a normal platelet and leukocyte count in 3 weeks. Patients presenting clinical features of PT expressing the Ph chromosome or the BCR/ABL fusion gene have been well documented but, to our knowledge, this is the first report of evolution from typical PT to chronic myeloid leukemia.     

Integration of amplified BCR/ABL fusion genes into the short arm of chromosome 17 as a novel mechanism of disease progression in chronic myeloid leukemia

We describe the cases of two patients with Philadelphia chromosome-positive chronic myeloid leukemia (CML), in whom the extramedullary blastic phase developed during disease progression. The similar clinical presentations of these patients was accompanied by gain of identical secondary chromosome abnormalities, that is, monosomies 9, 14, and 22, and by a clustered amplification of the BCR/ABL fusion gene. The additional copies of the BCR/ABL fusion gene were integrated into the short arm of structurally abnormal chromosomes 17 in both patients. The conformity of these genetic features in two patients with a rare disease manifestation leads us to the assumption that either the clustered amplification of the BCR/ABL fusion gene or the integration of this cluster into the short arm of chromosome 17 or both are associated with extramedullar disease progression in CML. Furthermore, the insertion of amplified BCR/ABL fusion genes into structurally abnormal chromosomes provides a novel mechanism of disease progression in BCR/ABL-positive CML.     

A FISH study of variant Philadelphia rearrangements

A total of 39 variant Philadelphia (Ph) translocations were studied by fluorescence in situ hybridization (FISH) using MBCR/ABL, mBCR/ABL, or DBCR/ABL probes. Seven cases did not have a BCR/ABL fusion signal. Of a total of 32 fusion-positive cases, 5 were simple variants involving chromosome 22 and another chromosome apart from chromosome 9; 23 were complex variants involving chromosomes 22, 9, and a third chromosome (18 cases), or 22, 9, and two other chromosomes (4 cases). Masked Ph rearrangements were detected in 4 cases. One case was a Ph chromosome mimic. Fluorescence in situ hybridization has become a widely used method for studying Ph rearrangements. The latest probe that is being used is the DBCR/ABL (double reciprocal BCR/ABL signals). The expected pattern for this probe is one green ABL signal (1G) on the normal 9, one red BCR signal (1R) on the normal 22, and two fusion signals, BCR/ABL and ABL/BCR (2F), on a derivative 22 and a derivative 9, respectively. Deviant patterns from 1G1R2F, and sometimes 1G1R2F, were indicative of a variant, as long as there was a fusion signal. However, in interphase analysis, it is not possible to visualize a variant rearrangement, and when a deviant pattern involving at least one fusion signal is observed, the following possibilities should be contemplated. The different patterns observed in fifteen Ph variants are described. The patterns observed in variants studied with the DBCR/ABL probe were 2G2R1F (40%), 1G1R2F (20%), 1G1R1F (20%), 1G2R1F (13.3%), and 2G1R1F (6.66%). A single mechanism is involved in the formation of each of these patterns. A 2G2R1F, FISH pattern in 6 cases appears to involve a single concerted event of simultaneous breaks on the participating chromosomes followed by mismatched joining. The three cases with 1G1R2F most probably arose by two sequential rearrangements. The 1G1R1F pattern suggests that either the BCR and ABL breakpoints are different, or there are deletions at the breakpoints, because residual signals are not observed. Two independent events appear to be involved in 1G2R1F with a reverse cryptic 9,22 rearrangement as the first event. In one case of 2G1R1F, the plausible explanation is an insertion of ABL next to BCR and either a simultaneous or a sequential translocation with another chromosome.     

Amplification of the BCR/ABL fusion gene clustered on a masked Philadelphia chromosome in a patient with myeloblastic crisis of chronic myelocytic leukemia

Although the chronic phase of chronic myelocytic leukemia (CML) is characterized by the Philadelphia (Ph) chromosome creating a hybrid BCR/ABL gene, additional genetic changes involved in blast crisis are poorly understood. We report a 4-8-fold amplification by tandem duplication of the BCR/ABL fusion gene clustered on a masked Ph chromosome in a 61-year-old male patient with CML in myeloblastic crisis. Our finding suggests that the BCR/ABL amplification may play a role as a novel mechanism in the progression to an aggressive blast transformation in some cases of Ph-positive CML.     

两种BCR/ABL探针在Ph阳性白血病荧光原位杂交检测中的不同信号模式及其意义

目的 比较BCR/ABL双色额外信号探针(dual color extra-signal BCR/ABL probe,ESFISH探针)及BCR/ABL双色双融合探针(dual color dual fusion BCR/ABL probe,D-FISH探针)在Ph阳性白血病荧光原位杂交(fluorescence in situ hybridization,FISH)检测中信号模式的差异,探讨它们的诊断价值.方法 分别采用D-FISH和ES-FISH探针对74例伴有单纯t(9;22)(q34;q11)及37例伴有变异Ph易位或复杂核型异常的Ph阳性白血病患者骨髓细胞进行间期FISH检测.结果 所有单纯t(9;22)(q34;q11)易位的白血病患者应用两种探针均检测到BCR/ABL阳性信号,ES-FISH探针显示2个橙色信号、1个绿色信号和1个黄色信号模式,而D-FISH探针显示1个橙色信号、1个绿色信号和2个黄色信号模式.ES-FISH探针在9例(12.2%)Ph阳性白血病患者中识别次要BCR断裂位点(1个橙色信号、1个绿色信号和2个黄色信号),而D-FISH探针不能识别主要BCR和次要BCR断裂位点;D-FISH探针在8例(10.8%)Ph阳性白血病中区分ABL基因单独缺失(1个橙色信号、2个绿色信号、1个黄色信号)和ABL、BCR基因共同缺失(1个橙色信号、1个绿色信号和1个黄色信号),ES-FISH则不能区分之.检测变异Ph易位和含Ph易位的复杂核型异常时,两种探针的信号模式分别有4种和6种之多,且以不典型者居多,对于它们的精确解释必须依赖常规染色体分析和中期FISH结果 .结论 ES-FISH及D-FISH探针由于BCR探针大小及覆盖区域不同,在Ph阳性白血病的FISH检测中显示不同信号模式,可分别作为Ph+急性淋巴细胞白血病和慢性髓系白血病患者FISH检测的首选.若采用伊马替尼治疗,主要BCR断裂点和次要BCR断裂点、伴或不伴有衍生9号染色体部分序列缺失均不影响预后,但鉴于ES-FISH探针性价比优于D-FISH探针,推荐其作为Ph阳性白血病FISH检测的首选.     

两种BCR/ABL探针在Ph阳性白血病荧光原位杂交检测中的不同信号模式及其意义

目的 比较BCR/ABL双色额外信号探针(dual color extra-signal BCR/ABL probe,ESFISH探针)及BCR/ABL双色双融合探针(dual color dual fusion BCR/ABL probe,D-FISH探针)在Ph阳性白血病荧光原位杂交(fluorescence in situ hybridization,FISH)检测中信号模式的差异,探讨它们的诊断价值.方法 分别采用D-FISH和ES-FISH探针对74例伴有单纯t(9;22)(q34;q11)及37例伴有变异Ph易位或复杂核型异常的Ph阳性白血病患者骨髓细胞进行间期FISH检测.结果 所有单纯t(9;22)(q34;q11)易位的白血病患者应用两种探针均检测到BCR/ABL阳性信号,ES-FISH探针显示2个橙色信号、1个绿色信号和1个黄色信号模式,而D-FISH探针显示1个橙色信号、1个绿色信号和2个黄色信号模式.ES-FISH探针在9例(12.2%)Ph阳性白血病患者中识别次要BCR断裂位点(1个橙色信号、1个绿色信号和2个黄色信号),而D-FISH探针不能识别主要BCR和次要BCR断裂位点;D-FISH探针在8例(10.8%)Ph阳性白血病中区分ABL基因单独缺失(1个橙色信号、2个绿色信号、1个黄色信号)和ABL、BCR基因共同缺失(1个橙色信号、1个绿色信号和1个黄色信号),ES-FISH则不能区分之.检测变异Ph易位和含Ph易位的复杂核型异常时,两种探针的信号模式分别有4种和6种之多,且以不典型者居多,对于它们的精确解释必须依赖常规染色体分析和中期FISH结果 .结论 ES-FISH及D-FISH探针由于BCR探针大小及覆盖区域不同,在Ph阳性白血病的FISH检测中显示不同信号模式,可分别作为Ph+急性淋巴细胞白血病和慢性髓系白血病患者FISH检测的首选.若采用伊马替尼治疗,主要BCR断裂点和次要BCR断裂点、伴或不伴有衍生9号染色体部分序列缺失均不影响预后,但鉴于ES-FISH探针性价比优于D-FISH探针,推荐其作为Ph阳性白血病FISH检测的首选.     

两种BCR/ABL探针在Ph阳性白血病荧光原位杂交检测中的不同信号模式及其意义

目的 比较BCR/ABL双色额外信号探针(dual color extra-signal BCR/ABL probe,ESFISH探针)及BCR/ABL双色双融合探针(dual color dual fusion BCR/ABL probe,D-FISH探针)在Ph阳性白血病荧光原位杂交(fluorescence in situ hybridization,FISH)检测中信号模式的差异,探讨它们的诊断价值.方法 分别采用D-FISH和ES-FISH探针对74例伴有单纯t(9;22)(q34;q11)及37例伴有变异Ph易位或复杂核型异常的Ph阳性白血病患者骨髓细胞进行间期FISH检测.结果 所有单纯t(9;22)(q34;q11)易位的白血病患者应用两种探针均检测到BCR/ABL阳性信号,ES-FISH探针显示2个橙色信号、1个绿色信号和1个黄色信号模式,而D-FISH探针显示1个橙色信号、1个绿色信号和2个黄色信号模式.ES-FISH探针在9例(12.2%)Ph阳性白血病患者中识别次要BCR断裂位点(1个橙色信号、1个绿色信号和2个黄色信号),而D-FISH探针不能识别主要BCR和次要BCR断裂位点;D-FISH探针在8例(10.8%)Ph阳性白血病中区分ABL基因单独缺失(1个橙色信号、2个绿色信号、1个黄色信号)和ABL、BCR基因共同缺失(1个橙色信号、1个绿色信号和1个黄色信号),ES-FISH则不能区分之.检测变异Ph易位和含Ph易位的复杂核型异常时,两种探针的信号模式分别有4种和6种之多,且以不典型者居多,对于它们的精确解释必须依赖常规染色体分析和中期FISH结果 .结论 ES-FISH及D-FISH探针由于BCR探针大小及覆盖区域不同,在Ph阳性白血病的FISH检测中显示不同信号模式,可分别作为Ph+急性淋巴细胞白血病和慢性髓系白血病患者FISH检测的首选.若采用伊马替尼治疗,主要BCR断裂点和次要BCR断裂点、伴或不伴有衍生9号染色体部分序列缺失均不影响预后,但鉴于ES-FISH探针性价比优于D-FISH探针,推荐其作为Ph阳性白血病FISH检测的首选.     

A near‐haploid clone harboring a BCR/ABL1 gene fusion in an adult patient with newly diagnosed B‐lymphoblastic leukemia

The detection of recurrent genetic abnormalities in B‐lymphoblastic leukemia (B‐ALL) is critical for risk stratification and therapy‐related decisions. Near‐haploidy (24‐30 chromosomes), a subgroup of hypodiploidy (<46 chromosomes), and BCR/ABL1 gene fusions are both recurrent genetic abnormalities in B‐ALL and are considered adverse prognostic findings, although outcomes in BCR/ABL1‐positive patients have improved with tyrosine kinase inhibitor therapy. While near‐haploid clones are primarily observed in children and rarely harbor structural abnormalities, BCR/ABL1‐positive B‐ALL is primarily observed in adults. Importantly, recurrent genetic abnormalities are considered mutually exclusive and rarely exist within the same neoplastic clone. We report only the second case to our knowledge of a near‐haploid clone that harbors a BCR/ABL1 fusion in an adult with newly diagnosed B‐ALL. Conventional chromosome studies revealed a near‐haploid clone (27 chromosomes) along with a der(22)t(9;22)(q34.1;q11.2) in 17 of 20 metaphases analyzed. Our B‐ALL fluorescence in situ hybridization (FISH) panel confirmed the BCR/ABL1 fusion and monosomies consistent with chromosome studies in approximately 95% of interphase nuclei. Moreover, no evidence of a “doubled” near‐haploid clone was observed by chromosome or FISH studies. This highly unusual case illustrates that while rare, recurrent genetic abnormalities in B‐ALL can exist within the same neoplastic clone.     

Acquisition of a Ph chromosome with minor BCR/ABL fusion in treatment-related myelodysplastic syndrome with chromosome 7 abnormalities in a patient treated for Hodgkin disease

The patient reported in this study originally had Hodgkin disease that was treated heavily with multiple courses of combined chemotherapy and radiotherapy. Secondary myelodysplastic syndrome (MDS) with a complex karyotype with monosomy 7, deletion 7q31, and double deletion 7q31 developed 8 years later. During the course of the disease, conventional cytogenetics and interphase FISH (I-FISH) analysis detected a Ph chromosome and BCR/ABL fusion with mBCR rearrangement. Using a multiparametric cell scanning system that enables combined analysis with probes specific for 7/7q- and BCR/ABL in a single cell, we were able to demonstrate the presence of the BCR/ABL fusion only in cells with monosomy of chromosome 7 and 7q31 deletion, but not in cells with a normal chromosome 7 or with a double deletion of 7q31. We propose two possible models that may explain the appearance of the BCR/ABL fusion in the pre-existing treatment-related MDS clones characterized by chromosome 7 rearrangements.     

Studies of complex Ph translocations in cases with chronic myelogenous leukemia and one with acute lymphoblastic leukemia

The BCR/ABL gene fusion, the hallmark of chronic myelogenous leukemia (CML) is generated in 2-10% of patients by a variant Ph translocation involving 9q34, 22q11.2, and one or more additional genomic regions. The objective of this study was the characterization by conventional and molecular cytogenetics of complex variant Ph translocations present at diagnosis. FISH studies were performed in 7 cases using the LSI BCR/ABL ES probe allowing the detection of the fusion BCR/ABL gene on the Ph chromosome in all of them and 9q34 deletions in 2 cases. Three cryptic complex rearrangements were detected by FISH studies. The third and the fourth chromosome regions involved in the 8 complex variant translocations were: 1q21, 1p36, 5q31, 11q13, 12q13, 12p13, and 20q12. In conclusion, FISH studies have been useful in the detection of the BCR/ABL rearrangements and 9q34 deletions, and to identify complex rearrangements that differ from the ones previously established by conventional cytogenetics.     

Complex chromosome 9, 20, and 22 rearrangements in acute lymphoblastic leukemia with duplication of BCR and ABL sequences

Cytogenetic analysis was performed on bone marrow cells from a 28-year-old woman who was diagnosed with acute lymphoblastic leukemia (ALL). Her karyotype was: 46,XX,t(9;22)(q34;q11)[6]/47, XX,+8,t(9;22)(q34;q11)[4]/47,XX,+8,t(9;22)(q34;q11),del(20)(q11)[2]/46, XX,t(9;22)(q34;q11),del[20](q11)[7]/45,XX,der(9)t(9;22)(q34;q11),-20,-22 , +mar1[8]/45,XX,der(9)t(9;22)(q34;q11),-20,-22,+mar2[3]. Both marker chromosomes are dicentric and have the same size and banding pattern but different primary constrictions. Fluorescence in situ hybridization (FISH) demonstrated that both markers were derived from chromosomes 9, 20, and 22. FISH with the bcr/abl probe showed fusion of the BCR gene with the ABL gene; however, this fusion signal was present in duplicate on both marker chromosomes. To our knowledge, duplication of the BCR/ABL fusion signal on a single chromosome arm has not been reported before, except for the extensive amplification of BCR/ABL fusion signals in the leukemic cell line K-562. These data demonstrate that the marker chromosomes are the result of complex genomic rearrangements. At the molecular level, the BCR/ABL fusion gene encodes the p190 fusion protein. Similar findings have never been observed in any case of ALL.     

Complete cytogenetic and molecular response after imatinib treatment for chronic myeloid leukemia in a patient with atypical karyotype and BCR-ABL b2a3 transcript

The molecular hallmark of CML is the BCR-ABL fusion gene, usually with specific breakpoints within ABL intron 1 and BCR introns b2, b3, and e19. The amplification of the BCR-ABL hybrid gene resulting from additional copies of the Ph chromosome has been identified as a mechanism for imatinib (IM) resistance. Cytogenetic clonal evolution correlates with the accelerated phase of leukemia, whereas deletions in the derivative chromosome 9 are associated with a poor prognosis. Relevance in IM therapy is unclear. We report a case of a 39-year-old male with chronic phase CML. Cytogenetic studies showed a complex karyotype with additional copies of the Ph chromosome, sextasomy 8, and ASS gene deletion. An unusual aberrant fusion gene product was derived from the joining of BCR exon 13 (b2) and ABL exon 3 (a3). During IM treatment, the patient was monitored in 3- to 6-month intervals. Major cytogenetic response was achieved after 5 months; complete cytogenetic and molecular remission was reached after 8 months; after 22 months, normal karyotype and absence of the BCR-ABL product continued. Our data seem to confirm the data of others in regards to the b2a3 breakpoint, suggesting a better prognosis, regardless of other unfavorable factors.     

Gene expression analysis of BCR/ABL1-dependent transcriptional response reveals enrichment for genes involved in negative feedback regulation

Philadelphia (Ph) chromosome-positive leukemia is characterized by the BCR/ABL1 fusion protein that affects a wide range of signal transduction pathways. The knowledge about its downstream target genes is, however, still quite limited. To identify novel BCR/ABL1-regulated genes we used global gene expression profiling of several Ph-positive and Ph-negative cell lines treated with imatinib. Following imatinib treatment, the Ph-positive cells showed decreased growth, viability, and reduced phosphorylation of BCR/ABL1 and STAT5. In total, 142 genes were identified as being dependent on BCR/ABL1-mediated signaling, mainly including genes involved in signal transduction, e.g. the JAK/STAT, MAPK, TGFB, and insulin signaling pathways, and in regulation of metabolism. Interestingly, BCR/ABL1 was found to activate several genes involved in negative feedback regulation (CISH, SOCS2, SOCS3, PIM1, DUSP6, and TNFAIP3), which may act to indirectly suppress the tumor promoting effects exerted by BCR/ABL1. In addition, several genes identified as deregulated upon BCR/ABL1 expression could be assigned to the TGFB and NFkB signaling pathways, as well as to reflect the metabolic adjustments needed for rapidly growing cells. Apart from providing important pathogenetic insights into BCR/ABL1-mediated leukemogenesis, the present study also provides a number of pathways/individual genes that may provide attractive targets for future development of targeted therapies. This article contains Supplementary Material available at http://www.interscience.wiley.com/jpages/1045-2257/suppmat.     

BCR/ABL fusion gene detected on 9q34 by fluorescence in situ hybridization in an acute leukemia with two BCR/ABL positive clones, one Ph-negative and one Ph-positive.

We report cytogenetic, fluorescence in situ hybridization (FISH), and molecular analyses in the first reported case of an acute leukemia with two BCR-positive clones: one cell Ph-positive and all others Ph-negative. A BCR/ABL fusion gene on 9q34 was detected only with a BCR/ABL dual color translocation probe. These FISH interphase signals must be confirmed on a metaphase to avoid an erroneous interpretation. This observation appears to indicate a 2-step mechanism for this aberrant fusion gene localization: first, a classical t(9;22), and then the transfer of the fusion gene formed on chromosome 22 to chromosome 9 by a second translocation between the long arms of the derivative chromosomes 9q+ and 22q-, masking the first chromosome exchange.     

Deletion of any part of the BCR or ABL gene on the derivative chromosome 9 is a poor prognostic marker in chronic myelogenous leukemia

To evaluate the prognostic significance of submicroscopic deletions of the ABL or BCR gene associated with t(9;22) in chronic myelogenous leukemia (CML), we investigated the incidence of an ABL or BCR deletion on derivative chromosome 9 using fluorescence in situ hybridization (FISH). FISH was performed using the LSI BCR/ABL dual-fusion translocation probe on bone marrow cells of 86 patients with CML. Of 86 patients, ABL deletion was detected in 13 (15.1%) patients and BCR deletion in 8 patients (9.3%). Patients with ABL deletion showed shorter event-free survival time (EFS) than those without ABL deletion (P = 0.020). Patients with BCR deletion showed significantly short overall survival time (OS; P = 0.039). Patients with ABL and/or BCR deletion (14/86 patients, 16.3%) showed significantly short OS and EFS (median OS, 43.0 months; median EFS, 40.0 months), compared to the patients without any BCR or ABL gene deletions (median OS, 94.0 months; median EFS, 90.0 months; P = 0.041 for OS, P = 0.008 for EFS). All the patients with BCR deletion, except for one, had a concomitant ABL deletion, suggesting that BCR deletion occurs in conjunction with ABL deletion. In patients with ABL deletion only, BCR/ABL rearrangement with b2a2 mRNA type tended to be more frequent than in patients without any deletion of the two genes (P = 0.073). Deletion of any of the BCR or ABL genes on derivative chromosome 9 was associated with both short OS and EFS. We conclude that deletion of not only the ABL gene, but also of the BCR gene, is a poor prognostic marker that indicates rapid disease progression in CML.