Molecular methods play a critical role in the accurate diagnosis of leukemia by complementing morphologic, cytochemical, immunophenotypic, and cytogenetic analyses. We developed a multiplex RT-PCR method combined with liquid bead array cytometry for the rapid detection of genetic alterations associated with leukemia. Fusion transcripts corresponding to the most common recurrent chromosomal translocations were reproducibly detected in as low as 0.1 to 10 ng of total RNA with an analytical sensitivity of 0.01 to 1%. Multi-day, -lot, -operator, and -instrument precision studies for a total of 678 independent measures in 46 runs showed a very high reproducibility with 100% agreement between replicates. Using multiplex panels for four to twenty independent targets, we demonstrate the flexibility of the method to co-detect rare splicing isoforms, discriminate between multiple variants generated by unique cytogenetic abnormalities, identify distinct chromosomal partners involved with 11q23 or 17q21 rearrangements, and assess cryptic abnormalities not detectable by standard cytogenetics such as t(12;21), del(1p32), or NPM1 mutations. Overall, three different internal control transcripts and 34 variants resulting from eighteen abnormal chromosomal sites were evaluated. These results underscore the value of the multiplex assay system as a sensitive and reliable technology platform for the characterization of relevant genetic alterations in leukemia.
leukemia; fusion transcript; multiplex; RT-PCR; molecular diagnosis
Cytogenetics and multicolor flow cytometry (MFC) are useful tools for monitoring outcome of treatment in acute myeloid leukemia (AML). However, no data are available regarding the meaning of results when the two tests do not agree.
We analyzed 1464 pairs of concurrent cytogenetics and flow results from 424 patients, both pre- and post- hematopoietic cell transplantation (HCT), and compared the prognostic impact of discordant and concordant results.
Informative discordant results were found in 22% of patients. Compared with patients with double negative testing results, either positive result had a significant impact on overall survival (OS) and relapse-free survival (RFS). The hazard ratios (HR) with either cytogenetics or MFC positive pre-transplant were 3.1 (P = 0.009) and 2.5 (P = 0.0008), respectively, for reduced OS, and 2.7 (P = 0.01) and 4.1 (P < 0.0001), respectively, for decreased RFS. Similar findings were obtained post-transplant. Molecular cytogenetics, i.e. fluorescence in situ hybridization (FISH), further added value to the evaluation of discordant cases.
Detection of residual disease of AML by either cytogenetics or flow cytometry in HCT patients predicts early relapse and shortened survival.
Acute myeloid leukemia; Cytogenetics; Multicolor flow cytometry; Fluorescence in situ hybridization
Background & objectives:
Chronic myelogenous leukaemia (CML) is the commonest leukaemia in Asia. There is a paucity data on cytogenetic and molecular analyses of Indian CML patients. This apparently reflects the low availability of cytogenetic and molecular techniques in our country. This study aimed to document various types of BCR-ABL fusion transcripts in different phases of CML and to compare the Ph chromosome positivity/negativity vis-a-vis BCR-ABL fusion transcripts in adult CML patients.
Between June 2004 and February 2009, 208 patients were diagnosed as CML in chronic phase (CP), accelerated phase (AP) and blast crisis (BC), according to standard criteria. Cytogenetic and molecular genetic analyses were performed in all patients. Various types of BCR-ABL hybrid transcripts were compared with phases of CML and cytogenetic abnormalities.
Among 208 CML patients, b3a2 BCR-ABL transcripts were most commonly detected (66.82%) followed by b2a2 (28.84%), b3a2 + b2a2 (3.36%), b3a2 + e19a2 (0.48%) and b2a2 + e19a2 (0.48%). b3a2 transcripts were more frequently detected than b2a2 transcripts, in the whole group of 208 as well as in 183 CML-CP patients (P<0.0001). Ph chromosome was positive in 135 of 139 patients with b3a2 transcripts and 56 of 60 patients with b2a2 transcripts, difference not being significant. Additional cytogenetic abnormalities detected in 3.8 per cent patients in CML-CP and 44 per cent patients in CML-AP/BC, did not show predilection for any BCR-ABL transcript type.
Interpretation & conclusions:
This study documents higher Ph positivity (96.15%) by cytogenetic analysis among CML patients, as confirmed by qualitative reverse transcriptase-polymerase chain reaction (RT-PCR) analysis in a large patient group from north India. Both the techniques contribute towards understanding the disease biology, and have important implications for diagnosis and management of CML patients.
BCR-ABL fusion transcripts; chronic myelogenous leukaemia; cytogenetic analysis; polymerase chain reaction; reverse transcriptase
Gene expression profiling has shown its ability to identify with high accuracy low cytogenetic risk acute myeloid leukemia such as acute promyelocytic leukemia and leukemias with t(8;21) or inv(16). The aim of this gene expression profiling study was to evaluate to what extent suboptimal samples with low leukemic blast load (range, 2-59%) and/or poor quality control criteria could also be correctly identified.
Specific signatures were first defined so that all 71 acute promyelocytic leukemia, leukemia with t(8;21) or inv(16)-AML as well as cytogenetically normal acute myeloid leukemia samples with at least 60% blasts and good quality control criteria were correctly classified (training set). The classifiers were then evaluated for their ability to assign to the expected class 111 samples considered as suboptimal because of a low leukemic blast load (n = 101) and/or poor quality control criteria (n = 10) (test set).
With 10-marker classifiers, all training set samples as well as 97 of the 101 test samples with a low blast load, and all 10 samples with poor quality control criteria were correctly classified. Regarding test set samples, the overall error rate of the class prediction was below 4 percent, even though the leukemic blast load was as low as 2%. Sensitivity, specificity, negative and positive predictive values of the class assignments ranged from 91% to 100%. Of note, for acute promyelocytic leukemia and leukemias with t(8;21) or inv(16), the confidence level of the class assignment was influenced by the leukemic blast load.
Gene expression profiling and a supervised method requiring 10-marker classifiers enable the identification of favorable cytogenetic risk acute myeloid leukemia even when samples contain low leukemic blast loads or display poor quality control criterion.
We report a case of acute basophilic leukemia with two coexisting clonal abnormalities, t(9;22) and trisomy 19. The blast showed positive reaction with myeloperoxidase but negative reaction with chloroacetate esterase and acid phosphatase. Metachromatic features of the blast were observed with toluidine blue stain. Ultrastructure study showed the presence of azurophilic granules in basophils and blast mast cells. Conventional and molecular cytogenetic studies revealed, t(9;22) with BCR/ABL positive and trisomy 19 in all metaphase cells. To our knowledge, this paper here is the first to present acute basophilic leukemia with trisomy 19 and t(9;22).
The success of imatinib mesylate (STI571, Gleevec) in treating chronic myeloid leukemia (CML) is, to date, the crowning achievement of targeted molecular therapy in cancer. Nearly 90% of newly diagnosed patients treated with imatinib in the chronic phase of the disease achieve a complete cytogenetic response. However, more than 95% of these patients retain detectable levels of BCR-ABL mRNA and patients discontinuing imatinib therapy almost invariably relapse, demonstrating that an imatinib insensitive population of leukemia-initiating cells (LICs) persists in nearly all patients. These findings underscore the need for treatments specifically targeting the leukemia-initiating population of CML cells. While mounting evidence suggests that the LIC in the chronic phase of CML is the BCR-ABL positive hematopoietic stem cell, several recent publications suggest that during CML blast crisis, a granulocyte-macrophage progenitor (GMP) population also acquires LIC properties through activation of the β-catenin pathway. Characterization of these cells and evaluation of their sensitivity to imatinib is critical to our understanding and treatment of CML blast crisis.
chronic myeloid leukemia; BCR-ABL; p210; GMP; cancer stem cell; leukemia-initiating cell
Cytogenetics are an important prognostic factor for patients with MDS. However, existing cytogenetics grouping schemes are based on patients treated with supportive care, and may not be optimal for patients undergoing allogeneic stem cell transplantation (SCT). We previously proposed an SCT-specific cytogenetics grouping scheme for patients with MDS and AML arising from MDS, based on an analysis of patients transplanted at Dana-Farber Cancer Institute/Brigham and Women’s Hospital. Under this scheme, abnormalities of chromosome 7 and complex karyotype are considered adverse-risk, while all others are considered standard-risk. In the present retrospective study, we validated this scheme on an independent multicenter cohort of 546 patients. Adverse cytogenetics was the strongest prognostic factor for outcome in this cohort. Four-year relapse-free and overall survival were 42% and 46%, respectively, in the standard risk group, versus 21% and 23% in the adverse group (p<0.0001 for both comparisons). This grouping scheme retained its prognostic significance irrespective of patient age, disease type, prior leukemogenic therapy, and conditioning intensity. Therapy-related disease was not associated with increased mortality in this cohort, after taking cytogenetics into account. We propose that this SCT-specific cytogenetics grouping scheme be used for patients with MDS or AML arising from MDS who are considering or undergoing SCT.
In childhood acute lymphoblastic leukemia (ALL) genetic subtypes are recognized that determine the risk-group for further treatment. However, 25% of precursor BALL are currently genetically unclassified and have an intermediate prognosis. The present study used genome-wide strategies to reveal new biological insights and advance the prognostic classification of childhood ALL.
A classifier based on gene expression in ALL cells from 190 newly diagnosed pediatric cases was constructed using a double-loop cross-validation method and next, was validated on an independent cohort of 107 newly diagnosed pediatric ALL cases. Hierarchical cluster analysis using classifying gene probe sets then revealed a novel ALL subtype for which underlying genetic abnormalities were characterized by comparative genomic hybridization-arrays and molecular cytogenetics.
The prediction accuracy of the classifier was median 90% in the discovery cohort and 87.9% in the independent validation cohort. A significant part of the currently genetically unclassified cases clustered with BCR-ABL-positive cases in both the discovery and validation cohort. These BCR-ABL-like cases represent 15–20% of ALL cases and have a highly unfavorable outcome (5-year disease-free survival 59.5%, 95%CI: 37.1%–81.9%) compared to other precursor B-ALL cases (84.4%, 95%CI: 76.8%–92.1%; P=0.012), similar to the poor prognosis of BCR-ABL-positive ALL (51.9%, 95%CI: 23.1%–80.6%), as was confirmed in the validation cohort. Further genetic studies revealed that the BCR-ABL-like subtype is characterized by a high frequency of deletions in genes involved in B-cell development (82%), including IKAROS, E2A, EBF1, PAX5 and VPREB1, compared to other ALL cases (36%, p=0.0002). BCR-ABL-like leukemic cells were median >70-times resistant to L-asparaginase (p=0.001) and 1.6-times more resistant to daunorubicin (p=0.017) compared to other precursor B-ALL cases whereas the toxicity of prednisolone and vincristine did not significantly differ.
Classification by gene expression profiling identified a novel subtype of ALL not detected by current diagnostic procedures but which comprises the largest group of patients with a high-risk of treatment failure. New treatment strategies are needed to improve outcome for this novel high-risk subtype of ALL.
Dutch Cancer Society, Sophia Foundation for Medical Research, Pediatric Oncology Foundation Rotterdam, Center of Medical Systems Biology of the Netherlands Genomics Initiative/Netherlands Organisation for Scientific Research, American National Institute of Health, American National Cancer Institute and American Lebanese Syrian Associated Charities.
microarray; gene expression profiling; classification; genotype; novel subtype; class discovery; ALL
To identify gene-expression signatures predicting cytarabine response by an integrative analysis of multiple clinical and pharmacological end points in acute myeloid leukemia (AML) patients.
Materials & methods
We performed an integrated analysis to associate the gene expression of diagnostic bone marrow blasts from acute myeloid leukemia (AML) patients treated in the discovery set (AML97; n = 42) and in the independent validation set (AML02; n = 46) with multiple clinical and pharmacological end points. Based on prior biological knowledge, we defined a gene to show a therapeutically beneficial (detrimental) pattern of association of its expression positively (negatively) correlated with favorable phenotypes such as intracellular cytarabine 5´-triphosphate levels, morphological response and event-free survival, and negatively (positively) correlated with unfavorable end points such as post-cytarabine DNA synthesis levels, minimal residual disease and cytarabine LC50.
We identified 240 probe sets predicting a therapeutically beneficial pattern and 97 predicting detrimental pattern (p ≤ 0.005) in the discovery set. Of these, 60 were confirmed in the independent validation set. The validated probe sets correspond to genes involved in PIK3/PTEN/AKT/mTOR signaling, G-protein-coupled receptor signaling and leukemogenesis. This suggests that targeting these pathways as potential pharmacogenomic and therapeutic candidates could be useful for improving treatment outcomes in AML.
This study illustrates the power of integrated data analysis of genomic data as well as multiple clinical and pharmacologic end points in the identification of genes and pathways of biological relevance.
acute myeloid leukemia; cytarabine; gene-expression profiles; genetic signatures
Imatinib mesylate (Gleevec) is an effective treatment for chronic myeloid leukemia (CML). Though cytogenetic and molecular analyses are essential disease monitoring parameters in CML bone marrow morphological response is not well defined. We examined marrow samples from 40 patients with CML which have at least 2 or more follow-up marrow. A significant positive correlation with complete cytogenetic response shown for normalization of cellularity (P = 0.0097), absence of dry tap (P = 0.0368) and abnormal megakaryocytes (P = 0.005), reduction of blasts (P = 0.019), basophils (P = 0.031), M:E index (P = 0.018) and fibrosis (P = 0.018). Morphological criteria for complete cytogenetic response in CML patients treated with Imatinib can be defined.Morphologic response is also of potential clinical value in addition to cytogenetic and molecular response in patients of CML treated with Imatinib.
Morphology; Bone marrow; Chronic myeloid leukemia; Imatinib mesylate
Chronic Myeloid Leukemia (CML) is caused by the abnormal fusion protein BCR-ABL1, a constitutively active tyrosine kinase and product of the Philadelphia chromosome. Gleevec (Imatinib mesylate) is a selective inhibitor of this kinase. Treatment with this agent is known to result in hematologic, cytogenetic, and molecular responses. Patan hospital (Patan, Nepal) is one of the Gleevec International Patient Assistance Program (GIPAP) centers for patients with CML.
A total of 106 Philadelphia positive CML patients were enrolled in our center between Feb 2003 and Jun 2008, and 103 of them were eligible for cytogenetic and/or hematologic response analyses.
Out of 103 patients, 27% patients underwent cytogenetic analysis. Imatinib induced major cytogenetic responses in 89% and complete hematologic responses in almost 100% of the patients with confirmed CML. After a mean follow up of 27 months, an estimated 90% of the patients on imatinib remained in hematologic remission and more than 90% of the patients are still alive. About 30% of patients developed some form of manageable myelosuppression. A few patients developed non-hematologic toxic side effects such as edema and hepatotoxicity.
Our study demonstrates that imatinib is safe to use in a developing country. Furthermore, we demonstrate that imatinib is very effective and induced long lasting responses in a high proportion of patients with Ph chromosome/BCR-ABL1 positive CML. Imatinib is well tolerated by our patients. The lack of cytogenetic analysis in the majority of our patients hindered our ability to detect inadequate responses to imatinib and adjust therapy appropriately.
This study investigated the spectrum of chromosomal abnormalities in 325 leukemia patients and developed optimal profiles of leukemic fusion genes for multiplex RT-PCR. We prospectively analyzed blood and bone marrow specimens of patients with acute leukemia. Twenty types of chromosomal abnormalities were detected in 42% from all patients by commercially available multiplex RT-PCR for detecting 28 fusion genes and in 35% by cytogenetic analysis including FISH analysis. The most common cytogenetic aberrations in acute myeloid leukemia patients was PML/PARA, followed by AML1/MGT8 and MLL1, and in acute lymphoid leukemia patients was BCR/ABL, followed by TEL/AML1 and MLL1 gene rearrangement. Among the negative results for multiplex RT-PCR, clinically significant t(3;3)(q21;q26.2), t(8;14)(q24;q32) and i(17)(q10) were detected by conventional cytogenetics. The spectrum and frequency of chromosomal abnormalities in our leukemia patients are differed from previous studies, and may offer optimal profiles of leukemic fusion genes for the development of new molecular detection systems.
Leukemia; Chromosomal Abnormalities; Molecular Detection System
Accurate and standardized methods for the quantitative measurement of BCR–ABL1 are a prerequisite for monitoring of treatment response in t(9;22)-positive leukemia. Here, we describe a novel multiplex assay system based on the proven TaqMan and Armored RNA technologies and optimized for sensitive detection of three BCR–ABL1 fusion transcripts and ABL1 in a single reaction. Analytical experiments confirmed the absence of significant competition between the simultaneous amplification reactions and established the sensitivity, linearity and precision of the assay. Comparative studies with 115 clinical specimens resulted in high qualitative and quantitative agreement with independent singleplex laboratory-developed tests routinely used in clinical testing. Direct comparison with a reference laboratory calibrated to the international scale (IS) demonstrated minimal analytical bias between methods and an overall accuracy and precision within the performance range required for quantitative measurement of BCR–ABL1 on the IS. We conclude that detection of e1a2, b2a2, b3a2 and ABL1 can be achieved in a multiplex assay format compatible with IS reporting. Further clinical validation of the assay could improve the operational efficiency of clinical laboratories, increase their adherence to current recommendations for b2a2/b3a2 reporting on the IS and provide for the first time an opportunity to standardize e1a2-monitoring results.
BCR–ABL1; monitoring; tyrosine kinase inhibitor; international scale; e1a2
Background. There is a need for tools to assess dependency among persons with severe impairments. Objectives. The aim was to compare the Functional Independence Measure (FIM) and the Northwick Park Dependency Score (NPDS), in a sample from in-patient rehabilitation. Material and Methods. Data from 115 persons (20 to 65 years of age) with neurological impairments was gathered. Analyses were made of sensitivity, specificity, positive predictive value, and negative predictive value. Agreement of the scales was assessed with kappa and concordance with Goodman-Kruskal's gamma. Scale structures were explored using the Rank-Transformable Pattern of Agreement (RTPA). Content validation was performed. Results. The sensitivity of the NPDS as compared to FIM varied between 0.53 (feeding) and 1.0 (mobility) and specificity between 0.64 (mobility) and 1.0 (bladder). The positive predictive value varied from 0.62 (mobility) to 1.0 (bladder), and the negative predictive value varied from 0.48 (bowel) to 1.0 (mobility). Agreement between the scales was moderate to good (four items) and excellent (three items). Concordance was good, with a gamma of −.856, an asymptotic error (ase) of .025, and P < .000. The parallel reliability between the FIM and the NPDS showed a tendency for NPDS to be more sensitive (having more categories) when dependency is high. Conclusion. FIM and NPDS complement each other. NPDS can be used as a measure for severely injured patients who are sensitive when there is a high need of nursing time.
Tyrosine kinase inhibitors have changed the management and outcomes of chronic myeloid leukemia patients. Quantitative polymerase chain reaction is used to monitor molecular responses to tyrosine kinase inhibitors. Molecular monitoring represents the most sensitive tool to judge chronic myeloid leukemia disease course and allows early detection of relapse. Evidence of achieving molecular response is important for several reasons: 1. early molecular response is associated with major molecular response rates at 18-24 months; 2. patients achieving major molecular response are less likely to lose their complete cytogenetic response; 3. a durable, stable major molecular response is associated with increased progression-free survival. However, standardization of molecular techniques is still challenging.
Leukemia, myelogenous, chronic, BCR-ABL positive; Cytogenetic; Monitoring; Mutation; Polymerase chain reaction
A 68-year-old man was admitted to our hospital in September 2008 because of a left-sided chest pain. Bone marrow examination showed that 85.5% of leukemic cells were positive for myeloperoxidase (MPO) and were negative for esterase stain. Flow cytometric analysis (FCM) revealed the expression of CD19, CD79a, CD13, CD33, CD34, and HLA-DR on the blasts. Cytogenetic analysis of bone marrow cells using the G-banding technique demonstrated 47, XY, +X, t(4;11;7)(q21;q23;q22) in five of the 20 analyzed cells. The patient was diagnosed as having mixed biphenotypic acute leukemia according to the European Group for Immunologic Classification of Leukemia criteria. Mixed-phenotype acute leukemia is a rare, difficult to diagnose entity. Whether patients with mixed-phenotype acute leukemia should be treated with regimens designed for acute myeloid leukemia, acute lymphoblastic leukemia, or both remains unclear.
A sensitive, high-throughput method for monitoring pre-mRNA splicing on a genomic scale is needed to understand the spectrum of alternatively spliced mRNA in human cells.
We adapted Molecular Inversion Probes (MIPs), a padlock-probe based technology, for the multiplexed capture and quantitation of individual splice events in human tissues. Individual MIP capture probes can be quantified using either DNA microarrays or high-throughput sequencing, which permits independent assessment of each spliced junction. Using our methodology we successfully identified 100% of our positive controls and showed that there is a strong correlation between the data from our alternative splicing MIP (asMIP) assay and quantitative PCR.
The asMIP assay provides a sensitive, accurate and multiplexed means for measuring pre-mRNA splicing. Fully optimized, we estimate that the assay could accommodate a throughput of greater than 20,000 splice junctions in a single reaction. This would represent a significant improvement over existing technologies.
To evaluate the prognostic significance of CEBPA mutations in the context of established molecular markers in cytogenetically normal (CN) acute myeloid leukemia (AML) and gain biologic insights into leukemogenesis of the CN-AML molecular high-risk subset (FLT3 internal tandem duplication [ITD] positive and/or NPM1 wild type) that has a significantly higher incidence of CEBPA mutations than the molecular low-risk subset (FLT3-ITD negative and NPM1 mutated).
Patients and Methods
One hundred seventy-five adults age less than 60 years with untreated primary CN-AML were screened before treatment for CEBPA, FLT3, MLL, WT1, and NPM1 mutations and BAALC and ERG expression levels. Gene and microRNA (miRNA) expression profiles were obtained for the CN-AML molecular high-risk patients.
CEBPA mutations predicted better event-free (P = .007), disease-free (P = .014), and overall survival (P < .001) independently of other molecular and clinical prognosticators. Among patients with CEBPA mutations, 91% were in the CN-AML molecular high-risk group. Within this group, CEBPA mutations predicted better event-free (P < .001), disease-free (P = .004), and overall survival (P = .009) independently of other molecular and clinical characteristics and were associated with unique gene and miRNA expression profiles. The major features of these profiles were upregulation of genes (eg, GATA1, ZFPM1, EPOR, and GFI1B) and miRNAs (ie, the miR-181 family) involved in erythroid differentiation and downregulation of homeobox genes.
Pretreatment testing for CEBPA mutations identifies CN-AML patients with different outcomes, particularly in the molecular high-risk group, thus improving molecular risk-based classification of this large cytogenetic subset of AML. The gene and miRNA expression profiling provided insights into leukemogenesis of the CN-AML molecular high-risk group, indicating that CEBPA mutations are associated with partial erythroid differentiation.
We describe the
response of imatinib as lifesaving treatment of
chronic myeloid leukemia (CML) relapse in seven
patients who underwent allogeneic bone marrow
transplantation (alloBMT) at our institution
over a period of 4 years. Retrospective analysis
of their medical records revealed that a mean age at
transplant was 45.2 years. The median time to
diagnosis was 7.4 years after transplant. At
relapse, four, two, and one patients were
classified as having hematologic, major
molecular, and cytogenetic relapse, respectively.
At imatinib initiation, five had CML in a
chronic phase, while one patient was
diagnosed as having accelerated phase and blast
crisis. All these patients could be evaluated
for the therapeutic efficacy. At a mean of
follow-up of 1.9 years of therapy, all evaluable
patients achieved major molecular response
without compromising safety. Consistent with
available data, our results indicate that
imatinib is safe and effective treatment option
for patients with relapse after
Imatinib mesylate (Glivec®/Gleevec®) is the standard first-line therapy for the treatment of chronic myeloid leukemia due to its high hematologic, cytogenetic, and molecular response rates and favorable long-term safety profile. A copy version of imatinib is currently available in several countries. We report on two cases of CML who were originally treated with Glivec in Egypt and subsequently switched to the copy drug
Case one was a 35-year old female with chronic myeloid leukemia in blast crisis who began treatment with combination chemotherapy and Glivec. The patient achieved and maintained a complete hematologic response and continued on Glivec 400 mg/day. In March 2007, she was switched to the copy drug In September 2007, the patient presented in hematologic relapse. At this time, treatment with chemotherapy in combination with Glivec 400 mg/day was resumed. The patient quickly achieved, and maintained, complete hematologic response on Glivec 400 mg/day. The second patient was a 64-year old male with chronic myeloid leukemia in blast crisis who began treatment with truncated chemotherapy in combination with Glivec 400 mg/day. After 6 months, the patient achieved a partial hematologic response and continued on alternating cycles of chemotherapy with continuous administration of Glivec 400 mg/day. The patient received Glivec from January 2006 to February 2007, after which time he was switched to the copy drug. In November 2007, he presented with upper gastrointestinal bleeding and multiple gastric erosions and died the same day.
The safety and efficacy of the copy drug has not been established in randomized clinical trials. It is unknown whether patients, who respond to Glivec and then switch to copy versions of imatinib, will tolerate the copy drug and maintain their response.
Histone deacetylase (HDAC) inhibitors are a novel anti-tumor therapy. To determine whether HDAC inhibitors may be useful in the treatment of adult acute lymphoblastic leukemia (ALL), we examined the acetylation of histone H4 by immunohistochemistry in newly diagnosed ALL patients and evaluated the impact of acetylation on complete remission (CR) rate, relapse-free survival (RFS), and overall survival (OS).
Patients ≥18 years of age and an available diagnostic bone marrow biopsy were evaluated. Cox proportional hazards analysis was used to identify univariate and multivariate correlates of CR, RFS, and OS. The variables histone H4 acetylation (positive or negative), white blood count, cytogenetic (CG) risk group (CALGB criteria), and age were used in multivariate analysis.
On multivariate analysis, histone acetylation was associated with a trend towards an improved OS (for all CG risk groups) (HR = 0.51, p = 0.09). In patients without poor risk CG, there was an impressive association between the presence of histone acetylation and an improved CR rate (OR 3.43, p = 0.035), RFS (HR 0.07, p = 0.005), and OS (HR 0.24, p = 0.007). This association remained statistically significant in multivariate analysis.
These data provide a rationale for the design of novel regimens incorporating HDAC inhibitors in ALL.
Background: Acute lymphoblastic leukemia (ALL) is the sixth most common malignancy in Iran. Cytogenetic analysis of leukemic blasts plays an important role in classification and prognosis in ALL patients. The purpose of this study was to define the frequency of chromosomal abnormalities of ALL patients in adults and children in Fars province, Iran.
Methods: In this cross-sectional study, we evaluated karyotype results of bone marrow specimens in 168 Iranian patients with ALL (154 B-ALL and 14 T-ALL) in Fars Province using the conventional cytogenetic G-banding method.
Results: The frequency of cytogenetic abnormalities, including numerical and/or structural changes, was 61.7% and 53.8% in the B-ALL and T-ALL patients, respectively. Hyperdiploidy was the most common (32%) cytogenetic abnormality. Among structural abnormalities, the most common was t(9;22) in 11% of the patients. The children showed a higher incidence of hyperdiploidy and lower incidence of t(9;22) than adults (P<0.05). We found a lower incidence of recurrent abnormalities such as 11q23, t(1;19), and t(12;21) than those reported in previous studies.
Conclusion: Normal karyotype was more frequent in our study. The frequencies of some cytogenetic abnormalities such as hyperdiploidy and t(9;22) in our study were comparable to those reported in the literature. The results of this study in Fars Province can be used as baseline information for treatment decision and research purposes in ALL patients. We recommend the use of advanced molecular techniques in the future to better elucidate cryptic cytogenetic abnormalities.
Acute lymphoblastic leukemia; Cytogenetic analysis; Chromosomal abnormalities; Incidence; Iran
Background: Subtelomeric regions of the human genome are gene rich, with a high level of sequence polymorphism. A number of clinical conditions, including learning disability, have been attributed to subtelomeric deletions or duplications, but screening for deletion in these regions using conventional cytogenetic methods and fluorescence in situ hybridisation (FISH) is laborious. Here we report that a new method, multiplex amplifiable probe hybridisation (MAPH), can be used to screen for copy number at subtelomeric regions.
Methods: We have constructed a set of MAPH probes with each subtelomeric region represented at least once, so that one gel lane can assay copy number at all chromosome ends in one person. Each probe has been sequenced and, where possible, its position relative to the telomere determined by comparison with mapped clones.
Results: The sensitivity of the probes has been characterised on a series of cytogenetically verified positive controls and 83 normal controls were used to assess the frequency of polymorphic copy number with no apparent phenotypic effect. We have also used MAPH to test a cohort of 37 people selected from males referred for fragile X syndrome testing and found six changes that were confirmed by dosage PCR.
Conclusions: MAPH can be used to screen subtelomeric regions of chromosomes for deletions and duplications before confirmation by FISH or dosage PCR. The high throughput nature of this technique allows it to be used for large scale screening of subtelomeric copy number, before confirmation by FISH. In practice, the availability of a rapid and efficient screen may allow subtelomeric analysis to be applied to a wider selection of patients than is currently possible using FISH alone.
In this study, essential test characteristics of the recently described multiplex ligation-dependent probe amplification (MLPA) method are presented, using chromosome 22 as a model. This novel method allows the relative quantification of ~40–45 different target DNA sequences in a single reaction. For the purpose of this study, MLPA was performed in a blinded manner on a training set containing over 50 samples, including typical 22q11.2 deletions, various atypical deletions, duplications (trisomy and tetrasomy), and unbalanced translocations. All samples in the training set have been previously characterized by fluorescence in situ hybridization (FISH) with cosmid or BAC clones and/or cytogenetic studies. MLPA findings were consistent with cytogenetic and FISH studies, no rearrangement went undetected and repeated tests gave consistent results. At a relative change in comparative signal strength of 30% or more, sensitivity and specificity values were 0.95 and 0.99, respectively. Given that MLPA is likely to be used as an initial screening method, a higher sensitivity, at the cost of a lower specificity, was deemed more appropriate. A receiver operator characteristic (ROC) curve analysis was performed to calculate the most optimal threshold range, with associated sensitivity and specificity values of 0.99 and 0.97, respectively. Finally, performance of each individual probe was analyzed, providing further useful information for the interpretation of MLPA results. In conclusion, MLPA has proven to be a highly sensitive and accurate tool for detecting copy number changes in the 22q11.2 region, making it a fast and economic alternative to currently used methods. The current study provides valuable and detailed information on the characteristics of this novel method.
MLPA; atypical rearrangements; velocardiofacial syndrome; VCFS; DiGeorge; conotruncal anomaly; 22q11DS
The International Randomized Study of Interferon vs. STI571 (IRIS) trial that investigated the use of the tyrosine kinase inhibitor (TKI) imatinib (versus interferon) changed the treatment and outcome of chronic myeloid leukemia (CML). Long-term follow-up of IRIS patients has defined response parameters and methods of tracking residual disease with cytogenetic testing of bone marrow metaphases and molecular monitoring of BCR-ABL transcripts using quantitative reverse-transcriptase polymerase chain reaction. Cytogenetic and molecular responses are now considered useful surrogates for long-term outcome. Early and robust response to imatinib predicts positive long-term outcomes. However, 15–25% of patients fail initial treatment or become intolerant of imatinib and need increased doses or alternate treatment. Second-line treatment with the second-generation TKIs nilotinib and dasatinib have resulted in favorable rates of progression-free survival (PFS) and overall survival. Data from the ENESTnd (nilotinib) and DASISION (dasatinib) trials in newly diagnosed chronic-phase CML patients demonstrated more robust and rapid complete cytogenetic (77–80%) and major molecular responses (43–46%) at 12 months compared with imatinib (65–66% and 22–28%). The relationship between a complete cytogenetic response at 12 months and long-term PFS supports a role for second-generation TKIs as first-line treatment of newly diagnosed chronic-phase CML.
Chronic myeloid leukemia; cytogenetic response; molecular response; dasatinib; nilotinib; imatinib