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In acute myeloid leukemia (AML), molecular diagnosis for the optimal management of patients and for minimal residual disease (MRD) monitoring is of extreme importance. Cumulative data suggest that quantitative monitoring or MRD in AML with fusion transcripts corresponding to 5(I;21), inv(16), and t(15;17) is useful in distinguishing patients at high risk of relapse from those in durable remission. Real-time quantitative polymerase chain reaction (RQ-PCR) is by far the most sensitive assay in the context of MRD detection. We present herein an overview of the principles of RQ-PCR encompassing both the chemistries (double-stranded DNA detection or specific fragment detection) and the instruments. The absolute and relative quantification and the most commonly used methods for calculation of MRD results in absolute quantification are also described.
Methods Mol Med 2006
PMID:Overview of real-time RT-PCR strategies for quantification of gene rearrangements in the myeloid malignancies. 1650 77

The t(15;17) is the diagnostic hallmark of acute promyelocytic leukemia (APL). As a result, the RARA and the promyelocytic leukemia (PML) genes are fused. The use of reverse-transcription polymerase chain reaction (RT-PCR) for the detection of the PML-RARA and RARA-PML fusion genes is the only technique that defines the PML breakpoint type and that allows the definition of a correct strategy for subsequent minimal residual disease (MRD) monitoring. Standardized conditions for RT-PCR analysis of fusion transcripts from chromosome aberrations in acute leukemia, including APL, have recently been reported in the context of the Biomed-1 Concerted Action, and are described in detail in this chapter.
Methods Mol Med 2006
PMID:Diagnosis and monitoring of PML-RARA-positive acute promyelocytic leukemia by qualitative RT-PCR. 1650 81

The last 15 yr have produced dramatic improvements in the survival rate of patients with acute promyelocytic leukemia (APL). These improvements have been due mainly to the introduction of targeted therapies and improved methods for diagnosing and monitoring this disease. The underlying molecular lesion in APL involves a t(15:17) translocation which leads to the generation of PML-RARalpha fusion transcripts and proteins. The PML-RARalpha fusion transcripts have been shown to be useful markers for establishing the diagnosis and for monitoring the response to treatment. This manuscript describes the application of QZyme reverse-transcription polymerase chain reaction (RT-PCR) to the quantification of PML-RARalpha transcripts as a marker of APL. QZyme is a method for real time detection and quantification of target genes or transcripts. The principle of QZyme analysis is similar to other quantitative PCR systems; however, the mechanism is quite different. QZyme exploits the catalytic activity of DNAzymes (deoxyribozymes), which are oligonucleotides that can bind and cleave nucleic acid substrates. The approach is well suited to monitoring minimal residual disease (MRD) in patients with APL, as a result of its ability to detect low numbers of transcripts and accurately measure differences in concentration over a broad dynamic range. Further, its capacity for duplex analysis has multiple advantages for analysis of clinical specimens. Protocols for duplex, single-tube QZyme RT-PCR assays, which allow simultaneous quantification of PML-RARalpha fusion transcripts (either L-type and V-type, or S-type) and the internal control BCR transcript, are provided. These protocols can be used for analyzing patient RNA specimens and are suitable for clinical trial monitoring. For this type of work, it is recommended that investigators validate the assays to ensure reproducible, accurate, and specific results on the equipment in their own laboratories. Assay validation is critical for real-time quantitative RT-PCR (RQ-PCR) and is often overlooked. A guide to the steps involved in validation and recommendations for acceptance criteria is included in this chapter.
Methods Mol Med 2006
PMID:Diagnosis and monitoring of PML-RARalpha-positive acute promyelocytic leukemia by quantitative RT-PCR. 1650 82

Assessing the level of residual disease in leukemia is vital for evaluating patients' response to treatment and for identifying those at high risk of relapse. This should enable early preemptive intervention to prevent the onset of hematological relapse in those patients. One of the most common translocations in acute myeloid leukemia (AML) is the t(8;21). t(8;21) AML is characterized by a relatively good prognosis. This chapter discusses both qualitative and quantitative (real-time quantitative reverse-transcription polymerase chain reaction [RQ-PCR]) protocols for the diagnosis and minimal residual disease (MRD) monitoring in t(8;21) AML. It also discusses the importance of choosing appropriate controls for each assay. The chapter provides a simple equation for assessing the sensitivity/reliability of RQ-PCR assays, which enables scientists to assess the accuracy and reliability of their data.
Methods Mol Med 2006
PMID:Diagnosis and monitoring of AML1-MTG8 (ETO)-positive acute myeloid leukemia by qualitative and real-time quantitative RT-PCR. 1650 83

Chronic myelogenous leukemia (CML) is a clonal myeloproliferative disorder that is characterized by the presence of a reciprocal translocation between chromosomes 9 and 22 and results in the formation of the Philadelphia (Ph1) chromosome and is present in most of CML patients. The Ph1 chromosome forms a chimeric gene that encodes an abnormal P210 mRNA transcript in most CML patients. Surveillance for minimal residual disease by detection of BCR/ABL transcripts is currently done mostly by quantitative real-time reverse transcriptase polymerase chain reaction (RT-PCR). Quantitation of BCR/ABL transcripts can monitor tumor load and the outcome of therapy. Absolute quantification determines the input copy number of the transcript of interest, usually by plotting the amount of PCR product onto a standard curve based on serial dilutions of the same product cloned in plasmids. Relative quantification describes the change in expression of the target gene in the patient sample relative to that of a control transcript by using the 2-DeltaDeltaCt calculation. The results of real-time RT-PCR for BCR/ABL transcripts are often analyzed by using plasmid DNA standard curves. In the present study, 79 BCR/ABL transcript-positive samples from CML patients who were being monitored for minimal residual disease by real-time quantitative RT-PCR were studied to determine whether the 2-DeltaDeltaCt approach was equivalent to the plasmid standard curve method. BCR/ABL P210 transcripts were quantitated using both the plasmid standard curve method and the 2-DeltaDeltaCt calculation. The comparison of both methods revealed a highly significant and linear correlation between the plasmid standard curve method and the 2-DeltaDeltaCt calculation (R2=0.98, P<0.0001). Furthermore, there was a reduction of preparation time, contamination risk, and reagent usage. The 2-DeltaDeltaCt calculation is a convenient alternative method to derive accurate quantitative information from real time PCR assays.
Diagn Mol Pathol 2006 Mar
PMID:Validation of the 2-DeltaDeltaCt calculation as an alternate method of data analysis for quantitative PCR of BCR-ABL P210 transcripts. 1653 70

Universal Russian reagents for real time PCR were tested and compared with reference reagents provided by foreign companies. Testing was carried out on plasmids with cloning fragments (DNA-standards) of cDNA with chimeric (fusion) gene PML-RARalpha. Values of amplification efficiency of Russian and foreign reagents were measured on samples with serial dilutions (30-300000 copies) of cloned cDNA fragments of PML-RARalpha and internal control gene ABL. Amplification efficiencies of Russian and foreign reagents were found to be close one to another. Russian universal reagent kit RealityTM and ABI TaqMan Core Reagent Kit have amplification efficiencies 1.919 and 1.929, and correlation coefficients of copy numbers PML-RARalpha0.999 and 0.996, respectively. These values were determined by construction of a standard curve. To verify these results we studied also the samples of cDNA from blood and bone marrow of patients with acute promyelocytic leukemia. All samples posses translocation t(15;17), and appropriate chimeric gene PML-RARalpha. copy number in 1 microg of total RNA was in range 5.86 x 10(4)-8.315 x 10(5) before chemotherapy. No symptoms of minimal residual disease were found after 3.5 months since chemotherapy - fusion gene PML-RARalpha was not detected by real time PCR method. These results are in agreement with clinical data. Our investigations tend to show that application of RealityTM reagent set in real timePCR experiments gives correct results and may be used in molecular oncodiagnostics.
Mol Biol (Mosk)
PMID:[Characterization of the universal Russian reagent sets for real-time PCR and its application for molecular oncodiagnostic]. 1663 76

Oral cancer is a major health problem in many parts of the world including India. The molecular mechanisms involved in oral tumorigenesis are not completely understood. Although surgery continues to be the most common treatment modality for this cancer, survival rates of oral cancer patients have still not significantly improved over the last few decades. Classical diagnostic methods are still not sensitive enough in detecting completeness of surgery and assessing minimal residual disease. This study investigated the role of NF-kappaB and COX-2 both in oral cancer progression and assessment of minimal residual disease. Expression of NF-kappaB proteins and its inhibitory protein IkappaB-alpha was evaluated using immunohistochemistry, ELISA and EMSA, while RT-PCR was used to detect COX-2 expression. Cytoplasmic expression as well as nuclear translocation of NF-kappaB proteins increased with histological progression of oral cancer (from normal to leukoplakia to cancer). A similar pattern of expression was observed for COX-2 also. NF-kappaB proteins, both cytoplasmic and nuclear, had a significant negative correlation from tumor to surgical margin to extra margin; COX-2 paralleled the expression of NF-kappaB proteins. Our results thus point to NF-kappaB and COX-2 as participants in oral tumor progression and also to the validation of these two molecular markers in assessing minimal residual disease.
Exp Mol Pathol 2006 Oct
PMID:NF-kappaB and COX-2 during oral tumorigenesis and in assessment of minimal residual disease in surgical margins. 1682

Monitoring multiple myeloma patients for relapse requires sensitive methods to measure minimal residual disease and to establish a more precise prognosis. The present study aimed to standardize a real-time quantitative polymerase chain reaction (PCR) test for the IgH gene with a JH consensus self-quenched fluorescence reverse primer and a VDJH or DJH allele-specific sense primer (self-quenched PCR). This method was compared with allele-specific real-time quantitative PCR test for the IgH gene using a TaqMan probe and a JH consensus primer (TaqMan PCR). We studied nine multiple myeloma patients from the Spanish group treated with the MM2000 therapeutic protocol. Self-quenched PCR demonstrated sensitivity of >or=10(-4) or 16 genomes in most cases, efficiency was 1.71 to 2.14, and intra-assay and interassay reproducibilities were 1.18 and 0.75%, respectively. Sensitivity, efficiency, and residual disease detection were similar with both PCR methods. TaqMan PCR failed in one case because of a mutation in the JH primer binding site, and self-quenched PCR worked well in this case. In conclusion, self-quenched PCR is a sensitive and reproducible method for quantifying residual disease in multiple myeloma patients; it yields similar results to TaqMan PCR and may be more effective than the latter when somatic mutations are present in the JH intronic primer binding site.
J Mol Diagn 2006 Jul
PMID:Application of self-quenched JH consensus primers for real-time quantitative PCR of IGH gene to minimal residual disease evaluation in multiple myeloma. 1682 10

The minimal residual disease foci that beget breast cancer relapse after a period of disease dormancy remain uncharacterized despite their enormous clinical importance. To model dormant breast cancer in vivo, we employed a transgenic mouse model in which Wnt1-initiated mammary cancer is doxycycline dependent. After regression of Wnt-dependent cancers, subclinical disease lesions were propagated in vivo using classical tissue recombination techniques. Surprisingly, outgrowths derived from dormant malignant tissue reconstituted morphologically normal ductal trees in wild-type mammary fat pads. Whereas hyperplasia-derived outgrowths remained benign, outgrowths derived from dormant malignancy underwent a morphological transition suggesting single-step transformation following reactivation of Wnt signaling and rapidly yielded invasive mammary tumors. Remarkably, outgrowths derived from dormant malignancy could be serially propagated in vivo and retained the potential to undergo lobuloalveolar differentiation in response to hormones of pregnancy. Matching somatic H-Ras mutations shared by antecedent tumors and descendant mammary ductal outgrowths confirmed their clonal relatedness. Thus, propagation of epithelium that possesses a latent malignant growth program reveals impressive regenerative and developmental potential, supporting the notion that dormant mammary cancers harbor transformed mammary progenitor cells. Our results define an experimental paradigm for elucidating biological properties of dormant malignancy.
Mol Cell Biol 2007 Jan
PMID:Dormant Wnt-initiated mammary cancer can participate in reconstituting functional mammary glands. 1706 Apr 57

Achieving a specific diagnosis of polycythemia vera (PV) and other myeloproliferative disorders (MPDs) is often costly and complex. However, the recent identification of a V617F mutation in the JH2 domain of the JAK2 gene in a high proportion of patients suffering from MPDs may provide confirmation of a diagnosis. This is an acquired mutation and, as such, may only be present in a small number of cells within a sample. There is therefore a clinical need for highly sensitive detection techniques. We have developed a sensitive real-time polymerase chain reaction (PCR)-based approach for both detection and quantification of the JAK2 V671F mutation load, which allows determination of mutation status without the need for prior purification of granulocytes. We have performed a comparison of this assay with two previously published detection methods. Although an amplification refractory mutation system (ARMS) was shown to be slightly superior in terms of sensitivity, our real-time PCR method provides the potential for quantification of the JAK2 V617F mutation, having potential future applications in the monitoring of minimal residual disease or predicting outcome of disease severity.
J Mol Diagn 2007 Feb
PMID:Development of a quantitative real-time polymerase chain reaction assay for the detection of the JAK2 V617F mutation. 1725 34


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