Comparison of FISH and quantitative RT-PCR for the diagnosis and follow-up of BCR-ABL-positive leukemias

Pediatric chronic myeloid leukemia in myeloid blast crisis

Chronic myeloid leukemia (CML) accounts for 2-3% of childhood leukemias. About 5% of cases present in a blastic phase of CML which clinically and morphologically mimics more common acute leukemias of childhood. We report a case of a 3-year-old male who presented with gradual onset swelling of the abdomen and extremities along with generalized weakness. Examination revealed massive splenomegaly, pallor, and pedal edema. Initial workup showed anemia, thrombocytopenia, and leukocytosis (120,000/uL) with a blast percentage of 35%. Blasts were positive for CD13, CD33, CD117, CD34 and HLA-DR, and stained negative for Myeloperoxidase and Periodic Acid Schiff. Fluorescence in situ hybridization was positive for b3a2/e14a2 junction BCR-ABL1 transcript and negative for RUNX1-RUNX1T1/t(8;21), clinching the diagnosis of CML in myeloid blast crisis. The patient expired within 17 days of diagnosis and initiation of therapy.

Detection of 22 common leukemic fusion genes using a single-step multiplex qRT-PCR-based assay

Background

Fusion genes generated from chromosomal translocation play an important role in hematological malignancies. Detection of fusion genes currently employ use of either conventional RT-PCR methods or fluorescent in situ hybridization (FISH), where both methods involve tedious methodologies and require prior characterization of chromosomal translocation events as determined by cytogenetic analysis. In this study, we describe a real-time quantitative reverse transcription PCR (qRT-PCR)-based multi-fusion gene screening method with the capacity to detect 22 fusion genes commonly found in leukemia. This method does not require pre-characterization of gene translocation events, thereby facilitating immediate diagnosis and therapeutic management.

Methods

We performed fluorescent qRT-PCR (F-qRT-PCR) using a commercially-available multi-fusion gene detection kit on a patient cohort of 345 individuals comprising 108 cases diagnosed with acute myeloid leukemia (AML) for initial evaluation; remaining patients within the cohort were assayed for confirmatory diagnosis. Results obtained by F-qRT-PCR were compared alongside patient analysis by cytogenetic characterization.

Results

Gene translocations detected by F-qRT-PCR in AML cases were diagnosed in 69.4% of the patient cohort, which was comparatively similar to 68.5% as diagnosed by cytogenetic analysis, thereby demonstrating 99.1% concordance. Overall gene fusion was detected in 53.7% of the overall patient population by F-qRT-PCR, 52.9% by cytogenetic prediction in leukemia, and 9.1% in non-leukemia patients by both methods. The overall concordance rate was calculated to be 99.0%. Fusion genes were detected by F-qRT-PCR in 97.3% of patients with CML, followed by 69.4% with AML, 33.3% with acute lymphoblastic leukemia (ALL), 9.1% with myelodysplastic syndromes (MDS), and 0% with chronic lymphocytic leukemia (CLL).

Conclusions

We describe the use of a F-qRT-PCR-based multi-fusion gene screening method as an efficient one-step diagnostic procedure as an effective alternative to lengthy conventional diagnostic procedures requiring both cytogenetic analysis followed by targeted quantitative reverse transcription (qRT-PCR) methods, thus allowing timely patient management.

Novel BCR-ABL1 fusion and leukemic mutations of SETBP1, PAX5, and TP53 detected by next generation sequencing in chronic myeloid leukemia

Patients with BCR-ABL1 fusion genes are potential candidates for targeted therapy with tyrosine kinase inhibitor (TKI) imatinib. However, novel BCR-ABL1 fusion variants can be undetected by qRT-PCR-based routine molecular screening, affecting immediate patient management and proper treatment selection. In this study, we describe a case of chronic myeloid leukemia (CML) harboring a novel BCR-ABL1 variant gene. Although Fluorescent In situ Hybridization (FISH) analysis suggested Philadelphia (Ph) translocation, qRT-PCR screening failed to detect the presence of a functional fusion transcript, which is critical for selecting targeted therapy against BCR-ABL1 fusion with aberrant kinase activity. Meanwhile, G-band cytogenetic analysis was performed twice without a solid conclusion. To overcome the uncertainty whether TKIs should be used to treat this patient effectively, we performed whole genome sequencing (WGS) in a next-generation sequencing (NGS) platform and discovered an unusual e13a2-like BCR-ABL1 fusion with 9 ABL1 intron 1 nucleotides incorporated into the broken BCR exon 13 to form a novel chimeric exon, which has never been described previously based on the best of our knowledge. Based on FISH and NGS results, the patient was treated with imatinib, showing significant improvement. Moreover, we also detected novel genetic mutations in the known leukemic genes SETBP1, PAX5, and TP53, while their role in the leukemogenesis remains to be determined. In summary, we have identified BCR-ABL1 fusion and other genetic mutations in a diagnostically difficult case of CML, demonstrating that NGS is a powerful diagnostic tool when routine procedures are challenged.

Nanotools and molecular techniques to rapidly identify and fight bacterial infections

Reducing the emergence and spread of antibiotic-resistant bacteria is one of the major healthcare issues of our century. In addition to the increased mortality, infections caused by multi-resistant bacteria drastically enhance the healthcare costs, mainly because of the longer duration of illness and treatment. While in the last 20years, bacterial identification has been revolutionized by the introduction of new molecular techniques, the current phenotypic techniques to determine the susceptibilities of common Gram-positive and Gram-negative bacteria require at least two days from collection of clinical samples. Therefore, there is an urgent need for the development of new technologies to determine rapidly drug susceptibility in bacteria and to achieve faster diagnoses. These techniques would also lead to a better understanding of the mechanisms that lead to the insurgence of the resistance, greatly helping the quest for new antibacterial systems and drugs. In this review, we describe some of the tools most currently used in clinical and microbiological research to study bacteria and to address the challenge of infections. We discuss the most interesting advancements in the molecular susceptibility testing systems, with a particular focus on the many applications of the MALDI-TOF MS system. In the field of the phenotypic characterization protocols, we detail some of the most promising semi-automated commercial systems and we focus on some emerging developments in the field of nanomechanical sensors, which constitute a step towards the development of rapid and affordable point-of-care testing devices and techniques. While there is still no innovative technique that is capable of completely substituting for the conventional protocols and clinical practices, many exciting new experimental setups and tools could constitute the basis of the standard testing package of future microbiological tests.

Qualitative and quantitative evaluation of the BCR-ABL fusion gene in chronic myelogenous leukemia by flourescence in situ hybridization and molecular genetic methods

AIMS

Fluorescence in situ hybridization (FISH) and quantitative real-time polymerase chain reaction (QRT-PCR) were used to diagnose or screen for minimal residual disease (MRD) in Philadelphia (Ph) chromosome-positive leukemia. We compared the diagnostic utility of FISH and QRT-PCR at various time points in the course of chronic myelogenous leukemia (CML) and to determine the mean initial values for patients whose QRT-PCR results were not known at the time of diagnosis.

RESULTS

We analyzed 135 results for 78 CML patients tested by FISH and QRT-PCR for the Ph chromosomal translocation. All newly diagnosed cases were positive by both methods. On follow-up following treatment, 1 case was FISH positive and QRT-PCR negative; 61 cases were FISH negative and QRT-PCR positive. Overall concordance was 54.1%. There was good concordance between QRT-PCR results and cytogenetic response categories.

CONCLUSIONS

We confirmed that QRT-PCR allows precise measurement of low levels of BCR-ABL transcripts and can serve as a sensitive indicator of MRD. We also demonstrated 100% correlation between QRT-PCR and FISH in newly diagnosed CML.

Standard treatment of Ph+ CML in 2010: how, when and where not to use what BCR/ABL1 kinase inhibitor?

Chronic myeloid leukaemia (CML) is a haematopoietic neoplasm characterised by the BCR/ABL1 oncoprotein. In chronic phase CML, the neoplastic clone exhibits multilineage differentiation and maturation capacity. The BCR/ABL1 kinase blocker imatinib shows major antileukaemic effects in most patients and is considered standard frontline therapy. However, not all patients have a long-lasting response to imatinib. Notably, resistance to imatinib has been recognised as an emerging problem and challenge in CML. Whereas CML stem cells are considered to exhibit intrinsic resistance, acquired resistance may, in addition, develop in subclones over time, resulting in an overt relapse. A key trigger of resistance in subclones are BCR/ABL1 mutations. For such patients, novel multikinase inhibitors such as nilotinib, dasatinib, bosutinib or bafetinib, which block the kinase activity of various BCR/ABL1 mutants, have been developed and reportedly exert antileukaemic effects in drug-resistant cells. For highly resistant patients, haematopoietic stem cell transplantation is an alternative option. Treatment decisions and the selection of drugs are based on the presence and type of BCR/ABL1 mutation(s), phase of disease, other disease-related variables and patient-related factors including age, compliance and co-morbidity. The current review provides an overview on standards in the diagnosis and therapy in CML, with special reference to novel BCR/ABL1 inhibitors.

Flow cytometric assay of phosphotyrosine levels in Bcr-Abl-positive chronic myelogenous leukemias: a potential prognostic marker

Assay of phosphotyrosine levels using flow cytometry has been used to identify patients with chronic myelogenous leukemia positive for the Bcr-Abl fusion gene. We hypothesized that clinical monitoring could identify treatment response through reductions in intragranulocyte phosphotyrosine. Initially, we studied cell lines FDC-P1 and HL60 (Bcr-Abl-negative) and FDrv210 and K562 (Bcr-Abl-positive) with our technique. A fluorescein isothiocyanate-conjugated monoclonal antibody was used along with fluorescence-conjugated microspheres for reference (ratio of sample fluorescence: bead fluorescence = relative fluorescence unit [RFU]). Samples from 20 controls and 32 patients undergoing treatment were analyzed using the same method. Bcr-Abl status for each patient was confirmed using fluorescent in situ hybridization or polymerase chain reaction gene amplification (PCR). Testing of cell lines consistently produced expected results. Patient values were found to be significantly higher than control values (P < 0.001) and values for patients with advanced disease were significantly higher than for patients with chronic-phase disease (P < 0.05). Results of clinical monitoring were consistent with results from PCR. Two patients who received allogeneic stem cell transplantation had molecular remission confirmed by PCR and had a marked decrease in RFU value (from 62 to five and from 131 to 23). No such fluorescence change was observed in patients who achieved clinical remission. Flow cytometric analysis of phosphotyrosine levels is a reliable and convenient adjuvant technique for diagnosis of Bcr-Abl-positive leukemias and shows promise for serial evaluation of patients undergoing treatment.