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Henrich M, Scheffold S, Hecht W, Reinacher M. High resolution melting analysis (HRM) for the assessment of clonality in feline B-cell lymphomas. Vet Immunol Immunopathol 2018; 200:59-68. [DOI: 10.1016/j.vetimm.2018.04.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Revised: 03/20/2018] [Accepted: 04/21/2018] [Indexed: 01/10/2023]
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Schöpper I, Ohmura S, Rütgen B, Tsujimoto H, Weber K, Hirschberger J. Melting curve analysis in canine lymphoma by calculating maximum fluorescence decrease. Vet Comp Oncol 2016; 15:563-575. [DOI: 10.1111/vco.12200] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2015] [Revised: 10/18/2015] [Accepted: 10/30/2015] [Indexed: 01/25/2023]
Affiliation(s)
- I. Schöpper
- Clinic of Small Animal Medicine, Center for Clinical Veterinary Medicine; Ludwig-Maximilians-University; Munich Germany
| | - S. Ohmura
- Clinic of Small Animal Medicine, Center for Clinical Veterinary Medicine; Ludwig-Maximilians-University; Munich Germany
| | - B. Rütgen
- Department of Pathobiology, Clinical Pathology; University of Veterinary Medicine; Vienna Austria
| | - H. Tsujimoto
- Department of Veterinary Internal Medicine, Graduate School of Agricultural Life Sciences; The University of Tokyo; Tokyo Japan
| | - K. Weber
- Clinic of Small Animal Medicine, Center for Clinical Veterinary Medicine; Ludwig-Maximilians-University; Munich Germany
| | - J. Hirschberger
- Clinic of Small Animal Medicine, Center for Clinical Veterinary Medicine; Ludwig-Maximilians-University; Munich Germany
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Xu D, Yang Z, Zhang D, Wu W, Guo Y, Chen Q, Xu D, Cui W. Rapid detection of immunoglobulin heavy chain gene rearrangement by PCR and melting curve analysis using combined FR2 and FR3 primers. Diagn Pathol 2015; 10:140. [PMID: 26255311 PMCID: PMC4529721 DOI: 10.1186/s13000-015-0370-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2015] [Accepted: 07/27/2015] [Indexed: 11/18/2022] Open
Abstract
Background Immunoglobulin heavy chain (IgH) gene rearrangement test is a standard tool in diagnosing B-cell lymphoma. The BIOMED-2 multiplex PCR protocol has become the most commonly used laboratory method for detecting clonal IgH gene rearrangement. However, post-PCR procedure requires manual transfer of PCR product for analysis and is time-consuming. A novel strategy using LightCycler to continuously monitor fluorescence during melting curve analysis (MCA) can overcome these shortcomings. The previous studies published on this method were all restricted to FR3 primers of BIOMED-2. Methods Real-time PCR and subsequent MCA were performed on 71 clinical DNA samples from formalin-fixed, paraffin-embedded tissues, including 40 with B-cell non-Hodgkin lymphomas and 31 with reactive lymphoid hyperplasia. We optimized the current method using FR3 primers and applied FR2 primers for the first time into MCA to detect IgH gene rearrangement. Polyacrylamide gel electrophoresis and capillary gel electrophoresis were also performed on all lymphoma samples with the identical FR2 primers. Results MCA of combined FR2 and FR3 primer sets yielded the sensitivity and the specificity equal to 70 % (28/40) and 100 % (31/31), respectively. Addition of FR2 primers increased the sensitivity by 12.5 % (5/40) comparing to FR3 primers alone. MCA was slightly more sensitive than polyacrylamide gel electrophoresis and comparable to capillary gel electrophoresis to detect clonal IgH gene rearrangement. Conclusions Combined PCR and DNA melting curve analysis in a closed system can reduce cross-contamination risk. This method can test 96 samples simultaneously within 90 min and therefore, it is high-throughput and faster. PCR-MCA in the LightCycler system has potential for evaluating monoclonal IgH gene rearrangement in a clinical environment.
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Affiliation(s)
- Danfei Xu
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, 100730, China.
| | - Zhuo Yang
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, 100730, China.
| | - Donghong Zhang
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, 100730, China.
| | - Wei Wu
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, 100730, China.
| | - Ye Guo
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, 100730, China.
| | - Qian Chen
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, 100730, China.
| | - Dongsheng Xu
- Hematopathology Program, CBL Path, Inc., Rye Brook, NY, 10753, USA.
| | - Wei Cui
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, 100730, China.
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Detection of clonal antigen receptor gene rearrangement in dogs with lymphoma by real-time polymerase chain reaction and melting curve analysis. BMC Vet Res 2014; 10:1. [PMID: 24383544 PMCID: PMC3904468 DOI: 10.1186/1746-6148-10-1] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2013] [Accepted: 12/27/2013] [Indexed: 11/25/2022] Open
Abstract
Background Molecular techniques that detect canine lymphoma cells by their clonal antigen receptor gene rearrangement play an increasing role for diagnosis as well as for monitoring minimal residual disease during and after cytostatic therapy. However, the methods currently available are time-consuming and/or cost-intensive thus impeding the use in clinical routine. The aim of the present study was to develop and evaluate a real-time polymerase chain reaction (PCR) with subsequent melting curve analysis (MCA) for the detection of clonally rearranged antigen receptor genes in dogs with B and T cell lymphoma on non formalin-fixed and paraffin-embedded lymph node samples. Results In lymph node aspirates from 30 dogs with multicentric B cell lymphoma, real-time PCR with MCA detected clonal rearrangement in 100% and conventional PCR with polyacrylamide gel electrophoresis (PAGE) in 93% of samples. Both methods correctly identified clonality in 80% of lymph node aspirates of 10 dogs with T cell lymphoma. None of the two PCR systems detected clonal rearrangement in samples from 9 dogs with lymph node hyperplasia. Using a dilutional series with regular lymphoid desoxyribonucleic acid (DNA), detection limits of lymphoma DNA were as low as 0.8% and 6.25% for B and T cell clonal rearrangement with real-time PCR and MCA and at 3.13% and 12.5% with the conventional system. Median absolute detection limits of lymphoma DNA were shown to be at 0.1 ng and 1 ng for the B and T cell immunophenotype with the real-time PCR system and at 10 ng each with conventional PCR and PAGE. Conclusions Real-time PCR with MCA is a convenient and reliable method with a good analytical sensitivity. Thus, the method may assist the detection of clonal antigen receptor gene rearrangement in canine lymphoma patients in a clinical setting also in the presence of small amounts of neoplastic cells.
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Kummalue T, Chuphrom A, Sukpanichanant S, Pongpruttipan T, Sukpanichanant S. Detection of monoclonal immunoglobulin heavy chain gene rearrangement (FR3) in Thai malignant lymphoma by High Resolution Melting curve analysis. Diagn Pathol 2010; 5:31. [PMID: 20482846 PMCID: PMC2886000 DOI: 10.1186/1746-1596-5-31] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2009] [Accepted: 05/19/2010] [Indexed: 11/10/2022] Open
Abstract
UNLABELLED Malignant lymphoma, especially non-Hodgkin lymphoma, is one of the most common hematologic malignancies in Thailand. The diagnosis of malignant lymphoma is often problematic, especially in early stages of the disease. Detection of antigen receptor gene rearrangement including T cell receptor (TCR) and immunoglobulin heavy chain (IgH) by polymerase chain reaction followed by heteroduplex has currently become standard whereas fluorescent fragment analysis (GeneScan) has been used for confirmation test. In this study, three techniques had been compared: thermocycler polymerase chain reaction (PCR) followed by heteroduplex and polyacrylamide gel electrophoresis, GeneScan analysis, and real time PCR with High Resolution Melting curve analysis (HRM). The comparison was carried out with DNA extracted from paraffin embedded tissues diagnosed as B- cell non-Hodgkin lymphoma. Specific PCR primers sequences for IgH gene variable region 3, including fluorescence labeled IgH primers were used and results were compared with HRM. In conclusion, the detection IgH gene rearrangement by HRM in the LightCycler System showed potential for distinguishing monoclonality from polyclonality in B-cell non-Hodgkin lymphoma. INTRODUCTION Malignant lymphoma, especially non-Hodgkin lymphoma, is one of the most common hematologic malignancies in Thailand. The incidence rate as reported by Ministry of Public Health is 3.1 per 100,000 population in female whereas the rate in male is 4.5 per 100,000 population 1. At Siriraj Hospital, the new cases diagnosed as malignant lymphoma were 214.6 cases/year 2. The diagnosis of malignant lymphoma is often problematic, especially in early stages of the disease. Therefore, detection of antigen receptor gene rearrangement including T cell receptor (TCR) and immunoglobulin heavy chain (IgH) by polymerase chain reaction (PCR) assay has recently become a standard laboratory test for discrimination of reactive from malignant clonal lymphoproliferation 34. Analyzing DNA extracted from formalin-fixed, paraffin-embedded tissues by multiplex PCR techniques is more rapid, accurate and highly sensitive. Measuring the size of the amplicon from PCR analysis could be used to diagnose malignant lymphoma with monoclonal pattern showing specific and distinct bands detected on acrylamide gel electrophoresis. However, this technique has some limitations and some patients might require a further confirmation test such as GeneScan or fragment analysis 56.GeneScan technique or fragment analysis reflects size and peak of DNA by using capillary gel electrophoresis. This technique is highly sensitive and can detect 0.5-1% of clonal lymphoid cells. It measures the amplicons by using various fluorescently labeled primers at forward or reverse sides and a specific size standard. Using a Genetic Analyzer machine and GeneMapper software (Applied Bioscience, USA), the monoclonal pattern revealed one single, sharp and high peak at the specific size corresponding to acrylamide gel pattern, whereas the polyclonal pattern showed multiple and small peak condensed at the same size standard. This technique is the most sensitive and accurate technique; however, it usually requires high technical experience and is also of high cost 7. Therefore, rapid and more cost effective technique are being sought.LightCycler PCR performs the diagnostic detection of amplicon via melting curve analysis within 2 hours with the use of a specific dye 89. This dye consists of two types: one known as SYBR-Green I which is non specific and the other named as High Resolution Melting analysis (HRM) which is highly sensitive, more accurate and stable. Several reports demonstrated that this new instrument combined with DNA intercalating dyes can be used to discriminate sequence changes in PCR amplicon without manual handling of PCR product 1011. Therefore, current investigations using melting curve analysis are being developed 1213.In this study, three different techniques were compared to evaluate the suitability of LightCycler PCR with HRM as the clonal diagnostic tool for IgH gene rearrangement in B-cell non-Hogdkin lymphoma, i.e. thermocycler PCR followed by heteroduplex analysis and PAGE, GeneScan analysis and LightCycler PCR with HRM.
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Affiliation(s)
- Tanawan Kummalue
- Department of Clinical Pathology, Faculty of Medicine Siriraj Hospital, Bangkok 10700, Thailand.
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Screening for residual disease in pediatric burkitt lymphoma using consensus primer pools. Adv Hematol 2009; 2009:412163. [PMID: 19890467 PMCID: PMC2771857 DOI: 10.1155/2009/412163] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2008] [Accepted: 01/25/2009] [Indexed: 11/17/2022] Open
Abstract
Assessing molecular persistent or minimal residual disease (PD/MRD) in childhood Burkitt lymphoma (BL) is challenging because access to original tumor is usually needed to design patient-specific primers (PSPs). Because BL is characterized by rearranged immunoglobulin heavy chain (IgVH) genes, IgVH primer pools from IgVH1–IgVH7 regions were tested to detect PD/MRD, thus eliminating the need for original tumor. The focus of the current study was to assess the feasibility of using IgVH primer pools to detect disease in clinical specimens. Fourteen children diagnosed with B-NHL had follow-up repository specimens available to assess PD/MRD. Of the 14 patients, 12 were PD/MRD negative after 2 months of therapy and remained in remission at the end of therapy; 2/14 patients were PD/MRD positive at 2-3 months and later relapsed. PSP-based assays from these 14 patients showed 100% concordance with the current assay. This feasibility study warrants further investigation to assess PD/MRD using IgVH primer pools, which could have clinical significance as a real-time assessment tool to monitor pediatric BL and possibly other B-cell non-Hodgkin lymphoma therapy.
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Retamales E, Rodriguez L, Guzman L, Aguayo F, Palma M, Backhouse C, Argandona J, Riquelme E, Corvalan A. Analytical detection of immunoglobulin heavy chain gene rearrangements in gastric lymphoid infiltrates by peak area analysis of the melting curve in the LightCycler System. J Mol Diagn 2007; 9:351-7. [PMID: 17591935 PMCID: PMC1899425 DOI: 10.2353/jmoldx.2007.050129] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Because it is difficult to differentiate gastric mucosa-associated lymphoid tissue (MALT) lymphoma from chronic gastritis in gastric lymphoid infiltrates, molecular detection of monoclonality through immunoglobulin heavy chain (IgH) gene rearrangements is commonly performed. However, heterogeneity in the performance and results obtained from IgH gene rearrangements has been reported. To improve the accuracy in the diagnosis of gastric lymphoid infiltrates, we developed an analytical approach based on one-peak area analysis of the melting curve in the LightCycler System. Using a training-testing approach, the likelihood ratio method was selected to find a discriminative function of 4.64 in the training set (10 gastric MALT lymphomas and 10 chronic gastritis cases). This discriminative function was validated in the testing set (five gastric MALT lymphomas, six abnormal lymphocytic infiltrates with subsequently demonstrated gastric MALT lymphomas, and six cases of chronic gastritis). All but one case of gastric MALT lymphoma, as well as abnormal lymphocytic infiltrates, clustered under 4.64, and all chronic gastritis cases clustered above 4.64. These results were validated by conventional electrophoreses confirming one or two sharp bands in cases of gastric MALT lymphomas and a smear of multiple bands in cases of chronic gastritis. Analytical detection of IgH gene rearrangement in gastric lymphoid infiltrates by one-peak area analysis correctly distinguishes gastric MALT lymphomas from chronic gastritis, even in cases with diagnosis of abnormal lymphocytic infiltrates.
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MESH Headings
- Biopsy
- Chronic Disease
- Diagnosis, Differential
- Gastritis/diagnosis
- Gastritis/genetics
- Gastritis/immunology
- Gastritis/pathology
- Gene Rearrangement, B-Lymphocyte, Heavy Chain
- Genes, Immunoglobulin Heavy Chain
- Humans
- Lymphocytes, Tumor-Infiltrating
- Lymphoma, B-Cell, Marginal Zone/diagnosis
- Lymphoma, B-Cell, Marginal Zone/genetics
- Lymphoma, B-Cell, Marginal Zone/immunology
- Nucleic Acid Denaturation
- Polymerase Chain Reaction/instrumentation
- Polymerase Chain Reaction/methods
- Transition Temperature
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Affiliation(s)
- Eduardo Retamales
- Departamento Laboratorio de Salud, Instituto Salud Publica de Chile, Santiago, Chile
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Uemura A, Mori S, Sugahara K, Akamatsu N, Tsuruda K, Tsukasaki K, Hirakata Y, Atogami S, Hasegawa H, Yamada Y, Kamihira S. Rapid and high-resolution detection of IgH gene rearrangements using PCR and melting curve analysis. Int J Lab Hematol 2007; 29:200-7. [PMID: 17474898 DOI: 10.1111/j.1751-553x.2006.00832.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
The analytical methods of Southern blot hybridization (SBH) and the polymerase chain reaction (PCR) for complementarity determining region-3 (CDR3) are fundamental for detecting IgH gene rearrangement. However, there are problems stemming from the characteristics of both methods; especially, the long turn around time (TAT) because of the complex process in the SBH, and the low analytical sensitivity for amplicons in the PCR. Thus, to improve the PCR procedure, we investigated the application of detecting the clonal amplicons based on the different melting Temperature (T(m)) in internal melting domains corresponding to the CDR3 hypervariable region. Our new protocol is based on the combination of a LightCycler Technology with high-speed amplification, and Idaho-Technology with rapid and high-resolution melting curve analysis (MCA), designated PCR-MCA. This method can provide the results within 3 h with an analytical sensitivity of 10(-3). The diagnostic sensitivity and specificity relative to the results documented with the SBH analysis were 89.2% and 100%, respectively. This indicates that the new protocol of PCR-MCA is acceptable for clinical testing; especially, PCR-MCA is relevant in terms of the rapid and sensitive detection of IgH clonality within amplicons.
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Affiliation(s)
- A Uemura
- Department of Laboratory Medicine, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki University Hospital, Nagasaki City, Nagasaki, Japan
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UEMURA A, MORI S, SUGAHARA K, AKAMATSU N, TSURUDA K, TSUKASAKI K, HIRAKATA Y, ATOGAMI S, HASEGAWA H, YAMADA Y, KAMIHIRA SHIMERU. Rapid and high-resolution detection of IgH gene rearrangements using PCR and melting curve analysis. Int J Lab Hematol 2006. [DOI: 10.1111/j.1365-2257.2006.00832.x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Olsen RJ, Tang Z, Farkas DH, Bernard DW, Zu Y, Chang CC. Detection of the JAK2(V617F) mutation in myeloproliferative disorders by melting curve analysis using the LightCycler system. Arch Pathol Lab Med 2006; 130:997-1003. [PMID: 16831057 DOI: 10.5858/2006-130-997-dotjmi] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
CONTEXT A specific mutation, JAK2(V617F), was recently recognized as having diagnostic value for myeloproliferative disorders. No practical assay is currently available for routine use in a clinical laboratory. OBJECTIVE We report the development of a real-time polymerase chain reaction melting curve analysis assay that is appropriate for molecular diagnostics testing. DESIGN Specific primers and fluorescence resonance energy transfer probes were designed, and patients with a previously diagnosed myeloproliferative disorder, de novo acute myeloid leukemia, or reactive condition were selected. The DNA was extracted from fresh and archived peripheral blood and bone marrow specimens, and real-time polymerase chain reaction melting curve analysis was performed on the LightCycler platform (Roche Applied Science, Indianapolis, Ind). RESULTS The JAK2 region was successfully amplified, and wild-type amplicons were reproducibly discriminated from JAK2(V617F) amplicons. Titration studies using homozygous wild-type and mutant cell lines showed the relative areas under a melting curve were proportional to allele proportion, and the assay reliably detected one mutant in 20 total cells. JAK2(V617F) was identified in patients previously diagnosed with a myeloproliferative disorder or acute myeloid leukemia transformed from myeloproliferative disorder, whereas a wild-type genotype was identified in patients with reactive conditions or de novo acute myeloid leukemia. CONCLUSIONS These findings demonstrate the suitability of this assay for identifying JAK2(V617F) in a clinical laboratory setting. Furthermore, the semiquantitative detection of JAK2(V617F) in archived specimens provides a new tool for studying the prognostic significance of this mutation.
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Affiliation(s)
- Randall J Olsen
- Department of Pathology, Baylor College of Medicine, Houston, Texas, USA
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Steiff JN, Neubauer A, Stolte M, Wündisch T. Clonality analyses in gastric MALT (mucosa-associated lymphoid tissue). Pathol Res Pract 2006; 202:503-7. [PMID: 16687216 DOI: 10.1016/j.prp.2006.02.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/09/2005] [Accepted: 02/22/2006] [Indexed: 11/16/2022]
Abstract
B-cell clonality, assessed by PCR for amplification of the VDJ region of the immunoglobulin heavy chain gene (IgH), is used to support the diagnosis of gastric mucosa-associated lymphoid tissue (MALT) lymphoma (GML). It has also been described in simple gastritis cases, without any histological hint for lymphoma, especially in the presence of lymphoid follicles. We analyzed a randomly selected series of 130 gastric biopsies with histologically described lymphoid follicle formation and investigated these for the prevalence of B-cell clonality using different PCR-based methods to discuss its usefulness in the differential diagnosis of GML. A seminested PCR for the IgH gene was performed and evaluated by agarose gel electrophoresis, GeneScan technique, and melting-curve analysis. The majority of cases revealed histologically chronic active Helicobacter pylori gastritis. Monoclonality was detected in 7.5% (10 of 130) and 7% (9 of 130) of samples using GeneScan technique and melting-curve analysis, respectively. In eight of eight samples investigated, monoclonality was not demonstrated in deeper sections of the same biopsy using GeneScan technique, favoring the diagnosis of a reactive process rather than overt lymphoma. Electrophoresis proved more difficult to interpret and revealed clonal cases in 14% (18 of 130). We conclude that GeneScan technique and melting curve analysis are the methods of choice for clonality analysis in gastric biopsies. Analyses of different deep sections with advanced PCR technology might be the method of choice for future analyses. In our opinion, the question of whether detected monoclonality can be interpreted as malignant lymphoma is still open.
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Affiliation(s)
- Johannes N Steiff
- Dept. of Hematology, Oncology and Immunology, Philipps University, Marburg, Germany
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Mori S, Sugahara K, Uemura A, Akamatsu N, Tutsumi R, Kuroki T, Hirakata Y, Atogami S, Hasegawa H, Yamada Y, Kamihira S. Rapid, Simple, and Accurate Detection of K-ras Mutations From Body Fluids Using Real-Time PCR and DNA Melting Curve Analysis. Lab Med 2006. [DOI: 10.1309/6507kah8ev592mj4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
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Cho YK, Kim J, Lee Y, Kim YA, Namkoong K, Lim H, Oh KW, Kim S, Han J, Park C, Pak YE, Ki CS, Choi JR, Myeong HK, Ko C. Clinical evaluation of micro-scale chip-based PCR system for rapid detection of hepatitis B virus. Biosens Bioelectron 2005; 21:2161-9. [PMID: 16290126 DOI: 10.1016/j.bios.2005.10.005] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2005] [Revised: 09/30/2005] [Accepted: 10/07/2005] [Indexed: 12/18/2022]
Abstract
The polymerase chain reaction (PCR) is widely used to amplify a small amount of DNA in samples for genetic analysis. Rapid and accurate amplification is prerequisite for broad applications including molecular diagnostics of diseases, food safety, and biological warfare tests. We have developed a rapid real-time micro-scale chip-based PCR system, which consists of six individual thermal cycling modules capable of independent control of PCR protocols. The PCR volume is 1 microl and it takes less than 20 min to complete 40 thermal cycles. To test utility of a chip-based PCR system as a molecular diagnostic device, we have conducted the first large-scale clinical evaluation study. Three independent clinical evaluation studies (n = 563) for screening the hepatitis B virus (HBV) infection, the most popular social epidemic disease in Asia, showed an excellent sensitivity, e.g. 94%, and specificity, e.g. 93%, demonstrating micro-scale chip-based PCR can be applied in molecular diagnostics.
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Affiliation(s)
- Yoon-Kyoung Cho
- Bio Lab, Samsung Advanced Institute of Technology, P.O. Box 111, Suwon 440-600, Republic of Korea
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Yang XY, Xu D, Du J, Kamino H, Rakeman J, Ratech H. Rapid detection of clonal T-cell receptor-beta gene rearrangements in T-Cell lymphomas using the LightCycler-polymerase chain reaction with DNA melting curve analysis. J Mol Diagn 2005; 7:81-8. [PMID: 15681478 PMCID: PMC1867496 DOI: 10.1016/s1525-1578(10)60012-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
Abstract
Various molecular methods have been developed to diagnose clonal T-cell receptor (TCR) gene rearrangements in clinical samples. Most polymerase chain reaction strategies for detecting clonal TCR gene rearrangements rely on either gel or capillary electrophoresis. However, a cumbersome manual transfer step separates amplification from analysis. Recently, we developed a novel polymerase chain reaction assay using the LightCycler system to detect clonal immunoglobulin heavy chain gene rearrangement. In the current study, we extend this work to include the TCR. We report that clonal TCR-beta (TCR-beta) gene rearrangements can be detected in less than 1 hour after preparing the DNA by measuring DNA melting immediately after amplification in a single closed capillary tube. We retrospectively studied 52 fresh-frozen tissue samples from patients clinically suspected of T-cell malignancy. A clonal TCR-beta gene rearrangement was detected in 14 samples by DNA melting curve analysis. When DNA melting was compared to the gold standard methods of Southern blot or denaturing gradient gel electrophoresis, it achieved a sensitivity equal to 71% and a specificity equal to 94%. We also compared melting curve analysis and polyacrylamide gel electrophoresis: melting curve analysis reached a sensitivity equal to 100% and a specificity equal to 97%. We conclude that DNA melting curve analysis in the LightCycler system has potential for clinical use as a new, ultra-fast method for the initial diagnosis of clonal TCR-beta gene rearrangements.
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Affiliation(s)
- Xiao Yan Yang
- Department of Pathology, Montefiore Medical Center, Albert Einstein College of Medicine, North 4, 111 East 210th St., Bronx, NY 10467, USA
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Xu D, Du J, Kamino H, Ratech H. Rapid diagnosis of clonal immunoglobulin heavy chain gene rearrangements in cutaneous B-cell lymphomas using the LightCycler-Polymerase Chain Reaction with DNA melting curve analysis. Am J Dermatopathol 2005; 26:385-9. [PMID: 15365370 DOI: 10.1097/00000372-200410000-00007] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
We have recently developed a novel Immunoglobulin heavy chain gene rearrangement (IgH-R) assay that combines polymerase chain reaction (PCR) amplification and analysis in the same closed capillary tube using the LightCycler System. IgH-R can be identified by DNA melting curve analysis within 40 minutes after DNA preparation and amplification. To test the clinical utility of this new IgH-R assay for rapidly diagnosing cutaneous B-cell lymphomas, we prospectively analyzed 44 formalin-fixed, paraffin-embedded tissues suspected of B-cell malignant lymphoma: skin (n = 31), lymph node (n = 7), stomach (n = 3), spleen (n = 1), colon (n = 1), and soft tissue (n = 1). We detected IgH-R in 12 DNA samples, including 8 skin biopsies, with the following diagnoses: B-cell chronic lymphocytic leukemia (n = 4), extranodal marginal zone B-cell lymphoma (n = 4), diffuse large B-cell lymphoma (n = 2), Burkitt lymphoma (n = 1), and precursor B-lymphoblastic lymphoma (n = 1). DNA melting curve analysis, compared with polyacrylamide gel electrophoresis, achieved a sensitivity equal to 92.3% and a specificity equal to 100%. There was a single false negative result because DNA melting curve analysis could not detect less than 10.0% clonal B-cells. We conclude that this new, rapid PCR assay for detecting IgH-R based on DNA melting curve analysis can be clinically useful for confirming the initial diagnosis of B-cell malignant lymphoma.
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Affiliation(s)
- Dongsheng Xu
- Department of Pathology, Albert Einstein College of Medicine/Montefiore Medical Center, Bronx, New York 10467, USA
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Plachý R, Hamal P, Raclavský V. McRAPD as a new approach to rapid and accurate identification of pathogenic yeasts. J Microbiol Methods 2005; 60:107-13. [PMID: 15567230 DOI: 10.1016/j.mimet.2004.09.003] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2004] [Revised: 08/28/2004] [Accepted: 09/07/2004] [Indexed: 11/19/2022]
Abstract
Despite advances in antifungal prophylaxis and therapy, morbidity and mortality incurred by yeasts remain a significant burden. As pathogenic yeast species vary in their susceptibilities to antifungal agents, clinical microbiology laboratories face an important challenge to identify them rapidly and accurately. Although a vast array of phenotyping and genotyping methods has been developed, these are either unable to cover the whole spectrum of potential yeast pathogens or can do this only in a rather costly or laborious way. Random amplified polymorphic DNA (RAPD) fingerprinting was repeatedly demonstrated to be a convenient tool for species identification in pathogenic yeasts. However, its wider acceptance has been limited mainly due to special expertise and software needed for analysis and comparison of the resulting banding patterns. Based on a pilot study, we demonstrate here that a simple and rapid melting curve analysis of RAPD products can provide data for identification of five of the most medically important Candida species. We have termed this new approach melting curve of random amplified polymorphic DNA (McRAPD) to emphasize its rapidity and potential for automation, highly desirable features for a routine laboratory test.
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Affiliation(s)
- Radek Plachý
- Department of Microbiology, Faculty of Medicine, Palacký University, Hnvotínská 3, CZ-775 15 Olomouc, Czech Republic
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Avery PR, Avery AC. Molecular methods to distinguish reactive and neoplastic lymphocyte expansions and their importance in transitional neoplastic states. Vet Clin Pathol 2004; 33:196-207. [PMID: 15570556 DOI: 10.1111/j.1939-165x.2004.tb00374.x] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Although lymphoma and leukemia usually can be diagnosed by routine cytology and histology, some cases present a diagnostic challenge for pathologists and clinicians. Often the dilemma lies in determining whether a population of lymphocytes is reactive or neoplastic. We review currently available methods for analyzing lymphocyte populations by immunophenotyping and by identifying clonally rearranged immunoglobulin and T-cell receptor genes and discuss how these tests can be used to clarify such diagnostic dilemmas. We also describe the detection of chromosomal abnormalities and methods on the horizon, such as gene expression profiling, to identify diagnostically useful oncogenes. Finally, we review the emerging concept of transitional neoplastic states, in which reactive lymphocytes transform to neoplastic lymphocytes in the presence of continued antigenic stimulation, such as that caused by infection with Helicobacter pylori. The existence of transitional neoplastic states underscores the need for an array of molecular diagnostic tools that would improve our ability to characterize lymphocyte populations in human and animal patients and enhance early detection of neoplastic lymphocytes such that eradication of the infectious or inflammatory stimulus could lead to cure.
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Affiliation(s)
- Paul R Avery
- Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Fort Collins, CO 80523, USA
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Dobbs LJ, Earls L. Clonality analysis of B-cell lymphoproliferative disorders using PCR and melting curve analysis. ACTA ACUST UNITED AC 2004; 12:212-23. [PMID: 14639107 DOI: 10.1097/00019606-200312000-00005] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Detection of a monoclonal immunoglobulin heavy chain gene (IgH gene) rearrangement is commonly used to support the diagnosis of B-cell non-Hodgkin lymphoma. We investigated the application of melting curve analysis as a substitute for polyacrylamide gel electrophoresis (PAGE) in the detection of monoclonal IgH gene rearrangements after PCR. A total of 140 cases were selected for this study, including 63 B-cell malignancies with a previously documented monoclonal IgH gene rearrangement. These 140 specimens were tested using PCR with melting curve analysis, and the results obtained were compared with PAGE results to calculate the relative sensitivity and specificity of melting curve analysis. Melting curve analysis detected monoclonal rearrangements in 56 of 63 specimens (relative sensitivity 88.9%). No false positives were detected (relative specificity = 100%). False-negative results were obtained only when a weak monoclonal band was present on PAGE. These results show that a positive result on melting curve analysis is specific for a monoclonal IgH gene rearrangement. However, with a sensitivity of only 88.9%, the majority of negative results would require further evaluation of the amplicons using PAGE. The application of melting curve analysis in the detection of monoclonal IgH gene rearrangements in the clinical laboratory setting is discussed.
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Affiliation(s)
- Larry J Dobbs
- Brody School of Medicine at East Carolina University, Greenville, NC 27858, USA.
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