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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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Zhou J, Ma R, Luo R, Sun Y, He X, Sun W, Tang W, Yao X. Primary exploration of CDR3 spectratyping and molecular features of TCR β chain in the peripheral blood and tissue of patients with colorectal carcinoma. Cancer Epidemiol 2010; 34:733-40. [DOI: 10.1016/j.canep.2010.06.010] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2010] [Revised: 05/26/2010] [Accepted: 06/20/2010] [Indexed: 11/25/2022]
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Yang JZ, Li MW, Wang JG, Lu HF, Yao XS, He JQ, Li LJ. Rapid detection of clonal expansion of T-cell receptor-beta gene in patients with HBV using the real-time PCR with DNA melting curve analysis. Hepatol Res 2010; 40:407-14. [PMID: 20070405 DOI: 10.1111/j.1872-034x.2009.00600.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/08/2022]
Abstract
AIM The gene melting spectral pattern (GMSP) of PCR products from 24 T-cell receptor beta chain variable (TCRBV) gene families was developed to determine sequence bias and feature of TCRBV CDR3 gene family. METHODS The assay was based on reverse transcript quantitative polymerase chain reaction and their DNA melting curves. RESULTS We discovered that the relatively conserved amino acid sequences X-Q and X-G are present in TCRBV CDR3 from patients with HBV. Further, the X of the X-Q motif is preferentially E (glutamic acid), P (proline) or T (threonine) when accompanied by the BJ2.7, BJ1.5, or BJ2.3, respectively. The frequency of sequence bias in the TCRBV gene family showed a positive correlation with the T cell receptor excision circles (TRECs) content, and an inverse correlation with the HBV DNA loading. CONCLUSION These results suggest that the GMSP assay could be used to monitor the features of TCRBV gene distribution quickly, and facilitate the further study of HBV-specific T cell in patients with HBV.
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Affiliation(s)
- Jie-Zuan Yang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Department of Infectious Diseases, the First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou
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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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Jabeen R, Payne D, Wiktorowicz J, Mohammad A, Petersen J. Capillary electrophoresis and the clinical laboratory. Electrophoresis 2006; 27:2413-38. [PMID: 16718719 DOI: 10.1002/elps.200500948] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Over the past 15 years, CE as an analytical tool has shown great promise in replacing many conventional clinical laboratory methods, such as electrophoresis and HPLC. CE's appeal was that it was fast, used very small amounts of sample and reagents, was extremely versatile, and was able to separate large and small analytes, whether neutral or charged. Because of this versatility, numerous methods have been developed for analytes that are of clinical interest. Other than molecular diagnostic and forensic laboratories CE has not been able to make a major impact in the United States. In contrast, in Europe and Japan an increasing number of clinical laboratories are using CE. Now that automated multicapillary instruments are commercially available along with cost-effective test kits, CE may yet be accepted as an instrument that will be routinely used in the clinical laboratories. This review will focus on areas where CE has the potential to have the greatest impact on the clinical laboratory. These include analyses of proteins found in serum and urine, hemoglobin (A1c and variants), carbohydrate-deficient transferrin, forensic and therapeutic drug screening, and molecular diagnostics.
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Affiliation(s)
- Rukhsana Jabeen
- University of Texas Medical Branch--Pathology, Galveston, TX 77555-0551, USA
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Tamura K, Yagihara H, Isotani M, Ono K, Washizu T, Bonkobara M. Development of the polymerase chain reaction assay based on the canine genome database for detection of monoclonality in B cell lymphoma. Vet Immunol Immunopathol 2006; 110:163-7. [PMID: 16325266 DOI: 10.1016/j.vetimm.2005.10.009] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2005] [Revised: 10/06/2005] [Accepted: 10/07/2005] [Indexed: 11/29/2022]
Abstract
From the canine genome database and its bioinformatic analysis, we identified conserved sequences within the vast majority of 61 variable segments and 1 joining segment of the immunoglobulin heavy chain (IgH) gene, and designed optimal primers for polymerase chain reaction (PCR) amplification directed at these conserved sequences to evaluate the monoclonality of IgH in canine B cell lymphoma. Using the primers, a PCR-based assay was performed on fine-needle aspiration samples of normal, hyperplasia, and malignant lymph nodes and lymphoma cell lines. All fine-needle aspiration samples of five B cell lymphoma cases and the B cell lymphoma line GL-1 exhibited clonal amplification, whereas no amplification was observed in the samples from normal and hyperplasia lymph nodes, cases of T cell lymphoma, and the T cell lymphoma line CL-1. The primers we designed clearly distinguished malignant B lymphocytes from normal, reactive, and malignant T lymphocytes, indicating a potential utility of the primers for PCR-based routine clinical examination for canine B cell lymphoma.
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Affiliation(s)
- K Tamura
- Department of Veterinary Clinical Pathology, Nippon Veterinary and Animal Science University, 1-7-1 Kyonan-cho, Musashino-shi, Tokyo 180-8602, Japan
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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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