Beyond Molecular Monitoring: Cytogenetic Testing and Mutational Analysis in Chronic Myeloid Leukemia

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The question is: What impact do these [chromosomal] abnormalities have on the long-term outcome of patients?

— Jorge Cortes, MD

Cytogenetic analysis remains an important component of patient monitoring until a complete cytogenetic response is achieved. In addition, the ability of conventional cytogenetics to identify additional chromosomal abnormalities not detected by fluorescence in situ hybridization is noteworthy. Jorge Cortes, MD, Professor of Medicine in the Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, introduced the case of a 74-year-old male patient with chronic myeloid leukemia (CML) who presented with a loss of chromosome Y and translocation t(9;9;22) to illustrate these points.

Differing Criteria for Chronic- vs Accelerated-phase CML

There was some disagreement among audience members regarding classification of the patient as being in chronic- (54%; 66/122) vs accelerated-phase CML (44%; 54/122), mainly due to the various criteria that are used to define accelerated-phase CML (eg, the International Bone Marrow Transplant Registry, the World Health Organization [WHO], and MD Anderson Cancer Center).1 One of the distinct features of the WHO classification is that the presence of additional cytogenetic abnormalities in Philadelphia chromosome–positive cells (clonal evolution) at the time of diagnosis is not considered to be a feature of accelerated-phase CML. Dr. Cortes pointed out that in the European LeukemiaNet recommendations, which the majority of respondents indicated that they most frequently use in their practice, clonal evolution at the time of diagnosis is considered to be just a warning sign. Nevertheless, half of respondents (80/159) said they would treat the patient with standard-dose imatinib (Gleevec), with the remainder using second-generation tyrosine kinase inhibitors.

Variant Philadelphia Chromosome Translocations

An important question is: Does the presence of chromosomal abnormalities at diagnosis affect prognosis? According to an analysis of data on 809 patients treated with imatinib at MD Anderson, the complete cytogenetic response rate was similar in patients with clonal evolution at diagnosis and those with chronic-phase CML (86% and 76%, respectively), and both groups had similar 3-year progression-free survival rates (92% and 89%, respectively).2 Likewise, a multivariate analysis of earlier data on patients receiving imatinib at MD Anderson (n = 721) showed that variant Philadelphia chromosome translocations involving chromosomes other than 9 and 22 (variant Philadelphia chromosome) had no impact on response rate, duration of response, or overall survival compared with patients with classic Philadelphia chromosome translocations.3 Similar findings were reported last year by the GIMEMA CML Working Party, who showed there was no impact of variant Philadelphia chromosome translocations on cytogenetic and molecular response and survival outcomes in 559 patients with early chronic-phase CML receiving imatinib therapy.4 Together, these data suggest that patients with variant translocations do not constitute a “warning” category in the imatinib era.

Impact of Y-chromosome Loss

Males have a tendency to lose the Y chromosome with aging, and the frequency of loss is slightly increased in individuals with hematologic malignancies. The next question is: Does loss of the Y chromosome constitute clonal evolution, and how does it affect outcome? In a series of 724 patients with chronic-phase CML treated with imatinib at MD Anderson, Y-chromosome loss was infrequent, being seen in only 2% of patients (10 at diagnosis, 5 during treatment).5 Although the major cytogenetic response rate was equivalent in patients with chronic-phase CML both with and without the Y chromosome (80%), the complete cytogenetic response rate was substantially lower in patients who lacked the Y chromosome (20% vs 74%). In addition, event-free survival was lower in patients with chronic-phase CML with loss of  the Y chromosome compared with patients with chronic-phase CML who have a Y chromosome, and with patients with accelerated-phase CML (ie, clonal evolution). Thus, although uncommon, loss of the Y chromosome did appear to have an impact on outcome in this study.

In contrast, long-term observation of a large series of patients from CML Study IV (n = 1,151) showed no impact of loss of the Y chromosome on 5-year overall survival.6 In addition, a trend toward shorter survival was observed in patients with variant Philadelphia chromosome, which is also contrary to the earlier data presented. Thus, the impact of these chromosomal abnormalities is not totally clear.

In general, Dr. Cortes feels that most physicians would not treat patients with loss of the Y chromosome any differently than they would normally treat chronic-phase CML. In the case presented, the patient did indeed receive imatinib (800 mg/d) and achieved a complete cytogenetic response by 3 months and sustained 4-log molecular response (MR4; BCR-ABL/ABL 0.01% International Scale) by 12 months. At that time, cytogenetic analysis still showed the loss of the Y chromosome, but now also showed loss of chromosome 8 in 80% of metaphases, with no Philadelphia chromosome present. Other than moderate fluid retention requiring diuretics, the patient is doing well. When asked if therapy should be changed based on these findings, almost half of respondents (45%; 71/158) said they would continue the current treatment, 30% (47/158) would reduce the dose of imatinib to address the edema, and 25% (39/158) would switch to nilotinib (Tasigna) or dasatinib (Sprycel). Only 1% (1/158) indicated they would proceed to stem cell transplant.

Long-term Effects

According to Dr. Cortes, chromosomal abnormalities appear in Philadelphia chromosome–negative metaphases in approximately 10% to 15% of patients with CML treated with imatinib. Such chromosomal abnormalities are not unique to imatinib but are seen with all tyrosine kinase inhibitors, including newer and investigational agents. However, patients are less likely to lose their response with second-generation tyrosine kinase inhibitors.

“Curiously, these abnormalities tend to be more frequently the kind of abnormalities we see in myelodysplastic syndromes [MDS]: trisomy 8, –5, 20q–, etc,” noted Dr. Cortes. “The question is: What impact do these abnormalities have on the long-term outcome of patients?” One of the fears is that these changes may lead to the development of MDS or acute leukemia.

In the few reported cases of MDS/acute leukemia developing in Philadelphia chromosome–negative CML treated with imatinib, –7 is often seen, but a variety of other chromosomal abnormalities are also noted. As such, Dr. Cortes feels that there is always a need to follow up on such abnormalities, but they are not necessarily an indication to treat. An analysis of patients who developed chromosomal abnormalities in Philadelphia chromosome–negative metaphases with imatinib after interferon failure showed a low (0.4%) incidence of MDS.7 In addition, the presence of chromosomal abnormalities did not significantly impact overall survival or progression-free survival in patients achieving a major cytogenetic response in this study. An analysis of chromosomal abnormalities in Philadelphia chromosome–negative metaphases after front-line imatinib undertaken at MD Anderson showed only one case of acute myeloid leukemia (0.4%), but revealed slightly lower overall survival and progression-free survival in patients developing chromosomal abnormalities.8 When progression did occur, Dr. Cortes noted that it mainly consisted of loss of response rather than transformation or non–CML-related death. However, there is not enough evidence at this time to indicate that a change in therapy would be warranted.

Increasing Transcript Levels

Dr. Cortes concluded his session with a brief discussion on the clinical significance of increasing transcript levels in CML, citing the landmark 2004 paper by Branford et al, showing that a greater than twofold rise can indicate the presence of BCR-ABL kinase domain mutations.9 A recent mutational data analysis performed by the GIMEMA CML Working Party to validate updated European LeukemiaNet recommendations for mutational analysis indicated a 27% incidence of mutations in patients for whom imatinib fails (European LeukemiaNet response criteria), confirming the importance of mutational analysis in these cases.10 A low 4% incidence of mutations was seen in patients with suboptimal response losing a major molecular response, so mutational analysis may not be needed in this instance. ■


1. Quintas-Cardama A, Cortes JE: Chronic myeloid leukemia: Diagnosis and treatment. Mayo Clin Proc 81:973-988, 2006.

2. Cortes JE, Talpaz, M, O’Brien S, et al: Staging of chronic myeloid leukemia in the imatinib era: An evaluation of the World Health Organization proposal. Cancer 106:1306-1315, 2006.

3. El-Zimaity MM, Kantarjian H, Talpaz M, et al: Results of imatinib mesylate therapy in chronic myelogenous leukaemia with variant Philadelphia chromosome. Br J Haematol 125:187-195, 2004.

4. Marzocchi G, Castagenetti F, Luatti S, et al: Variant Philadelphia translocations: Molecular-cytogenetic characterization and prognostic influence on frontline imatinib therapy, a GIMEMA Working Party on CML analysis. Blood 117:6793-6800, 2011.

5. Jabbour E, Kantarjian H, Ravandi-Kashani F, et al: Clinical significance of loss of chromosome Y (–Y) in patients with chronic myeloid leukemia (CML): Is it clonal evolution? Blood 108(suppl 11):Abstract 2117, 2006.

6. Fabarius A, Leitner A, Hochhaus A, et al: Impact of additional cytogenetic aberrations at diagnosis on prognosis of CML: Long-term observation of 1151 patients from the randomized CML Study IV. Blood 118:6760-6768, 2011.

7. Deininger MWN, Cortes J, Paquete R, et al: The prognosis for patients with chronic myeloid leukemia who have clonal cytogenetic abnormalities in Philadelphia chromosome–negative cells. Cancer 110:1509-1519, 2007.

8. Jabbour E, Kantarjian HM, Abruzzo LV, et al: Chromosomal abnormalities in Philadelphia chromosome–negative metaphases appearing during imatinib mesylate therapy in patients with newly diagnosed chronic myeloid leukemia in chronic phase. Blood 110:2991-2995, 2007.

9. Branford S, Rudzki Z, Parkinson I, et al: Real-time quantitative PCR analysis can be used as a primary screen to identify patients with CML treated with imatinib who have BCR-ABL kinase domain mutations. Blood 104:2926-2932, 2004.

10. Soverini S, Gnani A, De Benedittis C, et al: Validation of the new European LeukemiaNet (ELN) recommendations for Bcr-Abl kinase domain mutation analysis in chronic myeloid leukemia: An analysis of the GIMEMA CML Working Party studies. Blood 118(suppl 21):Abstract 112, 2011.