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Kim M, Savsani K, Dakshanamurthy S. A Peptide Vaccine Design Targeting KIT Mutations in Acute Myeloid Leukemia. Pharmaceuticals (Basel) 2023; 16:932. [PMID: 37513844 PMCID: PMC10383192 DOI: 10.3390/ph16070932] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 06/06/2023] [Accepted: 06/21/2023] [Indexed: 07/30/2023] Open
Abstract
Acute myeloid leukemia (AML) is a leading blood cancer subtype that can be caused by 27 gene mutations. Previous studies have explored potential vaccine and drug treatments against AML, but many were proven immunologically insignificant. Here, we targeted this issue and applied various clinical filters to improve immune response. KIT is an oncogenic gene that can cause AML when mutated and is predicted to be a promising vaccine target because of its immunogenic responses when activated. We designed a multi-epitope vaccine targeting mutations in the KIT oncogene using CD8+ and CD4+ epitopes. We selected the most viable vaccine epitopes based on thresholds for percentile rank, immunogenicity, antigenicity, half-life, toxicity, IFNγ release, allergenicity, and stability. The efficacy of data was observed through world and regional population coverage of our vaccine design. Then, we obtained epitopes for optimized population coverage from PCOptim-CD, a modified version of our original Java-based program code PCOptim. Using 24 mutations on the KIT gene, 12 CD8+ epitopes and 21 CD4+ epitopes were obtained. The CD8+ dataset had a 98.55% world population coverage, while the CD4+ dataset had a 65.14% world population coverage. There were five CD4+ epitopes that overlapped with the top CD8+ epitopes. Strong binding to murine MHC molecules was found in four CD8+ and six CD4+ epitopes, demonstrating the feasibility of our results in preclinical murine vaccine trials. We then created three-dimensional (3D) models to visualize epitope-MHC complexes and TCR interactions. The final candidate is a non-toxic and non-allergenic multi-epitope vaccine against KIT mutations that cause AML. Further research would involve murine trials of the vaccine candidates on tumor cells causing AML.
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Affiliation(s)
- Minji Kim
- College of Human Ecology, Cornell University, Ithaca, NY 14850, USA
| | - Kush Savsani
- College of Humanities and Sciences, Virginia Commonwealth University, Richmond, VA 23284, USA
| | - Sivanesan Dakshanamurthy
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC 20057, USA
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Chen OJ, Castellsagué E, Moustafa-Kamal M, Nadaf J, Rivera B, Fahiminiya S, Wang Y, Gamache I, Pacifico C, Jiang L, Carrot-Zhang J, Witkowski L, Berghuis AM, Schönberger S, Schneider D, Hillmer M, Bens S, Siebert R, Stewart CJR, Zhang Z, Chao WCH, Greenwood CMT, Barford D, Tischkowitz M, Majewski J, Foulkes WD, Teodoro JG. Germline Missense Variants in CDC20 Result in Aberrant Mitotic Progression and Familial Cancer. Cancer Res 2022; 82:3499-3515. [PMID: 35913887 DOI: 10.1158/0008-5472.can-21-3956] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 04/12/2022] [Accepted: 07/26/2022] [Indexed: 11/16/2022]
Abstract
CDC20 is a coactivator of the anaphase promoting complex/cyclosome (APC/C) and is essential for mitotic progression. APC/CCDC20 is inhibited by the spindle assembly checkpoint (SAC), which prevents premature separation of sister chromatids and aneuploidy in daughter cells. Although overexpression of CDC20 is common in many cancers, oncogenic mutations have never been identified in humans. Using whole-exome sequencing, we identified heterozygous missense CDC20 variants (L151R and N331K) that segregate with ovarian germ cell tumors in two families. Functional characterization showed these mutants retain APC/C activation activity but have impaired binding to BUBR1, a component of the SAC. Expression of L151R and N331K variants promoted mitotic slippage in HeLa cells and primary skin fibroblasts derived from carriers. Generation of mice carrying the N331K variant using CRISPR-Cas9 showed that, although homozygous N331K mice were nonviable, heterozygotes displayed accelerated oncogenicity of Myc-driven cancers. These findings highlight an unappreciated role for CDC20 variants as tumor-promoting genes. SIGNIFICANCE Two germline CDC20 missense variants that segregate with cancer in two families compromise the spindle assembly checkpoint and lead to aberrant mitotic progression, which could predispose cells to transformation. See related commentary by Villarroya-Beltri and Malumbres, p. 3432.
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Affiliation(s)
- Owen J Chen
- Goodman Cancer Institute, McGill University, Montréal, Québec, Canada
- Department of Biochemistry, McGill University, Montréal, Québec, Canada
| | - Ester Castellsagué
- Department of Human Genetics, McGill University, Montréal, Québec, Canada
- Division of Medical Genetics and Cancer Axis, Lady Davis Institute, Segal Cancer Centre, Jewish General Hospital, Montréal, Québec, Canada
- Translational Research Laboratory, Catalan Institute of Oncology, Bellvitge Institute for Biomedical Research, L'Hospitalet de Llobregat, Barcelona, Spain
| | - Mohamed Moustafa-Kamal
- Goodman Cancer Institute, McGill University, Montréal, Québec, Canada
- Department of Biochemistry, McGill University, Montréal, Québec, Canada
| | - Javad Nadaf
- McGill University and Génome Québec Innovation Centre, Montréal, Québec, Canada
| | - Barbara Rivera
- Cancer Axis, Lady Davis Institute, Jewish General Hospital, Montréal, Québec, Canada
- Hereditary Cancer Programme, Catalan Institute of Oncology, Bellvitge Institute for Biomedical Research, L'Hospitalet de Llobregat, Barcelona, Spain
- Gerald Bronfman Department of Oncology, McGill University, Montréal, Québec, Canada
| | - Somayyeh Fahiminiya
- Department of Human Genetics, McGill University, Montréal, Québec, Canada
- Cancer Research Program, Research Institute of the McGill University Health Centre, Montréal, Québec, Canada
| | - Yilin Wang
- Goodman Cancer Institute, McGill University, Montréal, Québec, Canada
- Department of Biochemistry, McGill University, Montréal, Québec, Canada
| | - Isabelle Gamache
- Goodman Cancer Institute, McGill University, Montréal, Québec, Canada
| | - Caterina Pacifico
- Goodman Cancer Institute, McGill University, Montréal, Québec, Canada
- Department of Biology, McGill University, Montréal, Québec, Canada
| | - Lai Jiang
- Cancer Axis, Lady Davis Institute, Jewish General Hospital, Montréal, Québec, Canada
- Department of Epidemiology, Biostatistics & Occupational Health, McGill University, Montréal, Québec, Canada
| | - Jian Carrot-Zhang
- Department of Human Genetics, McGill University, Montréal, Québec, Canada
- Cancer Research Program, Research Institute of the McGill University Health Centre, Montréal, Québec, Canada
| | - Leora Witkowski
- Department of Human Genetics, McGill University, Montréal, Québec, Canada
- Division of Medical Genetics and Cancer Axis, Lady Davis Institute, Segal Cancer Centre, Jewish General Hospital, Montréal, Québec, Canada
| | - Albert M Berghuis
- Department of Biochemistry, McGill University, Montréal, Québec, Canada
- Centre de Recherche en Biologie Structurale, McGill University, Montréal, Québec, Canada
- Department of Microbiology and Immunology, Montréal, Québec, Canada
| | - Stefan Schönberger
- Department of Pediatric Hematology and Oncology, Pediatrics III, University Hospital of Essen, University of Duisburg-Essen, Essen, Germany
| | - Dominik Schneider
- Clinic of Pediatrics, Dortmund Municipal Hospital, Dortmund, Germany
| | - Morten Hillmer
- Institute of Human Genetics, University of Ulm & Ulm University Medical Center, Ulm, Germany
| | - Susanne Bens
- Institute of Human Genetics, University of Ulm & Ulm University Medical Center, Ulm, Germany
| | - Reiner Siebert
- Institute of Human Genetics, University of Ulm & Ulm University Medical Center, Ulm, Germany
| | - Colin J R Stewart
- Department of Histopathology, King Edward Memorial Hospital, and School for Women's and Infants' Health, University of Western Australia, Perth, Australia
| | - Ziguo Zhang
- Institute of Cancer Research, London, United Kingdom
| | - William C H Chao
- Faculty of Health Sciences, University of Macau, Macau SAR, China
| | - Celia M T Greenwood
- Cancer Axis, Lady Davis Institute, Jewish General Hospital, Montréal, Québec, Canada
- Department of Epidemiology, Biostatistics & Occupational Health, McGill University, Montréal, Québec, Canada
- Departments of Oncology and Human Genetics, McGill University, Montréal, Québec, Canada
| | - David Barford
- Institute of Cancer Research, London, United Kingdom
| | - Marc Tischkowitz
- Department of Medical Genetics, National Institute for Health Research Cambridge Biomedical Research Centre, University of Cambridge, Cambridge, United Kingdom
| | - Jacek Majewski
- Department of Human Genetics, McGill University, Montréal, Québec, Canada
- Cancer Research Program, Research Institute of the McGill University Health Centre, Montréal, Québec, Canada
| | - William D Foulkes
- Department of Human Genetics, McGill University, Montréal, Québec, Canada
- Division of Medical Genetics and Cancer Axis, Lady Davis Institute, Segal Cancer Centre, Jewish General Hospital, Montréal, Québec, Canada
- Program in Cancer Genetics, Department of Oncology and Human Genetics, McGill University, Montréal, Québec, Canada
- Division of Medical Genetics and Cancer Research Program, Research Institute of the McGill University Health Centre, Montréal, Québec, Canada
| | - Jose G Teodoro
- Goodman Cancer Institute, McGill University, Montréal, Québec, Canada
- Department of Biochemistry, McGill University, Montréal, Québec, Canada
- Department of Microbiology and Immunology, Montréal, Québec, Canada
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Alonso CM, Llop M, Sargas C, Pedrola L, Panadero J, Hervás D, Cervera J, Such E, Ibáñez M, Ayala R, Martínez-López J, Onecha E, de Juan I, Palanca S, Martínez-Cuadrón D, Rodríguez-Veiga R, Boluda B, Montesinos P, Sanz G, Sanz MA, Barragán E. Clinical Utility of a Next-Generation Sequencing Panel for Acute Myeloid Leukemia Diagnostics. J Mol Diagn 2019; 21:228-240. [DOI: 10.1016/j.jmoldx.2018.09.009] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2017] [Revised: 09/06/2018] [Accepted: 09/20/2018] [Indexed: 10/27/2022] Open
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Badr P, Elsayed GM, Eldin DN, Riad BY, Hamdy N. Detection of KIT mutations in core binding factor acute myeloid leukemia. Leuk Res Rep 2018; 10:20-25. [PMID: 30112273 PMCID: PMC6092444 DOI: 10.1016/j.lrr.2018.06.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Revised: 06/05/2018] [Accepted: 06/29/2018] [Indexed: 11/30/2022] Open
Abstract
We have investigated the frequency and the effect of KIT mutations on the outcome of patients with CBF-AML. 69 patients (34 pediatrics and 35 adults) with CBF-AML were enrolled in the study. The frequency of KIT mutations was higher in adults compared to pediatrics (22.9% and 14.7%, p = 0.38) respectively. Leukocytosis ≥ 20 × 109 /L was significantly associated with pediatrics compared to adults. t(8;21)(q22;22) was significantly associated with thrombocytopenia in adults. We conclude that no significant difference is found between KIT mutated and unmutated CBF-AML in adults and pediatrics. Children with CBF-AML present with leukocytosis. t(8;21) is associated with thrombocytopenia.
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Affiliation(s)
- Passant Badr
- BSc Biotechnology, Faculty of Science, Cairo University, Cairo, Egypt
| | - Ghada M Elsayed
- Professor of Clinical Pathology and Oncologic Laboratory Medicine, National Cancer institute, Cairo University, Cairo, Egypt
| | - Dalia Negm Eldin
- Lecturer of biostatistics, Department of Biostatistics and Cancer Epidemiology, National Cancer Institute, Cairo University, Cairo, Egypt
| | - Bahia Y Riad
- Professor of Organic Chemistry, Faculty of Science, Cairo University, Cairo, Egypt
| | - Nayera Hamdy
- Professor of Clinical Pathology and Oncologic Laboratory Medicine, National Cancer institute, Cairo University, Cairo, Egypt
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ElNahass YH, Mahmoud HK, Mattar MM, Fahmy OA, Samra MA, Abdelfattah RM, ElRefaey FA, Fahmy HM, Fathy GM, Abdulgawad A, AbdelKader M, Elleithy HN, Gamil M, Talaat M, Nader HA, ElMetnawy WH. MPN10 score and survival of molecularly annotated myeloproliferative neoplasm patients. Leuk Lymphoma 2017; 59:844-854. [DOI: 10.1080/10428194.2017.1365852] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | - Mona Gamil
- Faculty of Medicine, Cairo University, Cairo, Egypt
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Ayatollahi H, Shajiei A, Sadeghian MH, Sheikhi M, Yazdandoust E, Ghazanfarpour M, Shams SF, Shakeri S. Prognostic Importance of C-KIT Mutations in Core Binding Factor Acute Myeloid Leukemia: A Systematic Review. Hematol Oncol Stem Cell Ther 2016; 10:1-7. [PMID: 27613372 DOI: 10.1016/j.hemonc.2016.08.005] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Revised: 08/07/2016] [Accepted: 08/10/2016] [Indexed: 11/16/2022] Open
Abstract
OBJECTIVE/BACKGROUND Acute myeloid leukemia (AML) is defined as leukemic blast reproduction in bone marrow. Chromosomal abnormalities form different subgroups with joint clinical specifications and results. t(8;21)(q22;q22) and inv(16)(p13;q22) form core binding factor-AML (CBF-AML). c-kit mutation activation occurs in 12.8-46.1% of adults with CBF leukemia. These mutations occur in 20-25% of t(8;21) and 30% of inv(16) cases. METHODS In this systematic review, we searched different databases, including PubMed, Scopus, and Embase. Selected articles were measured based on the inclusion criteria of this study and initially compared in terms of titles or abstracts. Finally, articles relevant to the subject of this review were retrieved in full text. Twenty-two articles matched the inclusion criteria and were selected for this review. RESULTS In this study, c-kit mutations were associated with poor prognosis in AML patients with t(8;21) and inv(16). In addition, these mutations had better prognostic effects on AML patients with inv(16) compared with those with t(8;21). CONCLUSION According to the results of this study, c-kit mutations have intense, harmful effects on the relapse and white blood cell increase in CBF-AML adults. However, these mutations have no significant prognostic effects on patients.
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Affiliation(s)
- Hossein Ayatollahi
- Cancer Molecular Pathology Research Center, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Arezoo Shajiei
- Department of Hematology and Blood Bank, Cancer Molecular Pathology Research Center, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Mohammad Hadi Sadeghian
- Department of Hematology and Blood Bank, Cancer Molecular Pathology Research Center, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Maryam Sheikhi
- Cancer Molecular Pathology Research Center, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran.
| | - Ehsan Yazdandoust
- Department of Hematology and Blood Bank, Cancer Molecular Pathology Research Center, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Masumeh Ghazanfarpour
- Department of Midwifery, School of Nursing and Midwifery, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Seyyede Fatemeh Shams
- Department of Hematology and Blood Bank, Cancer Molecular Pathology Research Center, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Sepideh Shakeri
- Department of Hematology and Blood Bank, Cancer Molecular Pathology Research Center, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
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Rybicka M, Stalke P, Bielawski KP. Current molecular methods for the detection of hepatitis B virus quasispecies. Rev Med Virol 2016; 26:369-81. [PMID: 27506508 DOI: 10.1002/rmv.1897] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2016] [Revised: 06/16/2016] [Accepted: 06/22/2016] [Indexed: 01/20/2023]
Abstract
Chronic HBV infection affects more than 240 million people worldwide and is associated with a broad range of clinical manifestations including liver cirrhosis, liver failure and hepatocellular carcinoma. Because of the lack of an efficient cure for chronic hepatitis B, the main goal of antiviral therapy is the prevention of liver disease progression coupled with prolonged survival of patients. Because HBV viral load has been shown to be a crucial determinant of the progression of liver damage, these goals can be achieved as long as HBV replication can be suppressed. Unfortunately, long-term therapy with the low-to-moderate genetic barrier drugs, which are still recommended in a majority of developing countries, are strongly associated with HBV resistance development and treatment failure. In such cases, the precise and accurate determination of drug-resistant variants in an individual patient before treatment is important for a proper choice of first-line potent therapy. Nowadays, a number of techniques are available to study HBV quasispecies evolution. This review describes the advantages and limitations of various assays detecting drug-resistant HBV variants. Copyright © 2016 John Wiley & Sons, Ltd.
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Affiliation(s)
- Magda Rybicka
- Intercollegiate Faculty of Biotechnology, University of Gdansk and Medical University of Gdansk, Gdansk, Poland.
| | - Piotr Stalke
- Department of Infectious Diseases, Medical University of Gdansk, Gdansk, Poland
| | - Krzysztof Piotr Bielawski
- Intercollegiate Faculty of Biotechnology, University of Gdansk and Medical University of Gdansk, Gdansk, Poland
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Ziai JM, Siddon AJ. Pathology Consultation on Gene Mutations in Acute Myeloid Leukemia. Am J Clin Pathol 2015; 144:539-54. [PMID: 26386075 DOI: 10.1309/ajcp77zfpuqgygwy] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
OBJECTIVES Acute myeloid leukemia (AML) is a rapidly fatal disease without the use of aggressive chemotherapy regimens. Cytogenetic and molecular studies are commonly used to classify types of AML based on prognosis, as well as to determine therapeutic regimens. METHODS Although there are several AML classifications determined by particular translocations, cytogenetically normal AML represents a molecularly, as well as clinically, heterogeneous group of diseases. Laboratory evaluation of AML will become increasingly important as new mutations with both prognostic and therapeutic implications are being recognized. Moreover, because many patients with AML are being treated more effectively, these mutations may become increasingly useful as markers of minimal residual disease, which can be interpreted in an individualized approach. RESULTS Current laboratory studies of gene mutations in AML include analysis of NPM1, FLT3, CEBPA, and KIT. In addition to these genes, many other genes are emerging as potentially useful in determining patients' prognosis, therapy, and disease course. CONCLUSIONS This article briefly reviews the current most clinically relevant gene mutations and their clinical and immunophenotypic features, prognostic information, and methods used for detection.
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Affiliation(s)
| | - Alexa J. Siddon
- Departments of Pathology, Yale School of Medicine, New Haven, CT
- Laboratory Medicine, Yale School of Medicine, New Haven, CT
- VA Connecticut Healthcare, West Haven, CT
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Liu YP, Wu HY, Yang X, Xu HQ, Chen D, Huang Q, Fu WL. Diagnostic accuracy of high resolution melting analysis for detection of KRAS mutations: a systematic review and meta-analysis. Sci Rep 2014; 4:7521. [PMID: 25515911 PMCID: PMC4268648 DOI: 10.1038/srep07521] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2014] [Accepted: 11/27/2014] [Indexed: 01/01/2023] Open
Abstract
Increasing evidence points to a negative correlation between KRAS mutations and patients' responses to anti-EGFR monoclonal antibody treatment. Therefore, patients must undergo KRAS mutation detection to be eligible for treatment. High resolution melting analysis (HRM) is gaining increasing attention in KRAS mutation detection. However, its accuracy has not been systematically evaluated. We conducted a meta-analysis of published articles, involving 13 articles with 1,520 samples, to assess its diagnostic accuracy compared with DNA sequencing. The quality of included articles was assessed using the revised Quality Assessment for Studies of Diagnostic Accuracy (QUADAS-2) tools. Random effects models were applied to analyze the performance of pooled characteristics. The overall sensitivity and specificity of HRM were 0.99 (95% confidence interval [CI]: 0.98-1.00) and 0.96 (95%CI: 0.94-0.97), respectively. The area under the summary receiver operating characteristic curve was 0.996. High sensitivity and specificity, less labor, rapid turn-around and the closed-tube format of HRM make it an attractive choice for rapid detection of KRAS mutations in clinical practice. The burden of DNA sequencing can be reduced dramatically by the implementation of HRM, but positive results still need to be sequenced for diagnostic confirmation.
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Affiliation(s)
- Yue-Ping Liu
- 1] Department of Laboratory Medicine, Southwest Hospital, Third Military Medical University, Chongqing, 400038, PR China [2] Department of Laboratory Medicine, 477TH Hospital of PLA, Xiangyang City, 400013, Hubei Province, PR China
| | - Hai-Yan Wu
- Department of Laboratory Medicine, Southwest Hospital, Third Military Medical University, Chongqing, 400038, PR China
| | - Xiang Yang
- Department of Laboratory Medicine, Southwest Hospital, Third Military Medical University, Chongqing, 400038, PR China
| | - Han-Qing Xu
- Department of Laboratory Medicine, Southwest Hospital, Third Military Medical University, Chongqing, 400038, PR China
| | - Dong Chen
- Department of Laboratory Medicine, Southwest Hospital, Third Military Medical University, Chongqing, 400038, PR China
| | - Qing Huang
- Department of Laboratory Medicine, Southwest Hospital, Third Military Medical University, Chongqing, 400038, PR China
| | - Wei-Ling Fu
- Department of Laboratory Medicine, Southwest Hospital, Third Military Medical University, Chongqing, 400038, PR China
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Bilbao-Sieyro C, Santana G, Moreno M, Torres L, Santana-Lopez G, Rodriguez-Medina C, Perera M, Bellosillo B, de la Iglesia S, Molero T, Gomez-Casares MT. High resolution melting analysis: a rapid and accurate method to detect CALR mutations. PLoS One 2014; 9:e103511. [PMID: 25068507 PMCID: PMC4113452 DOI: 10.1371/journal.pone.0103511] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2014] [Accepted: 06/30/2014] [Indexed: 01/23/2023] Open
Abstract
Background The recent discovery of CALR mutations in essential thrombocythemia (ET) and primary myelofibrosis (PMF) patients without JAK2/MPL mutations has emerged as a relevant finding for the molecular diagnosis of these myeloproliferative neoplasms (MPN). We tested the feasibility of high-resolution melting (HRM) as a screening method for rapid detection of CALR mutations. Methods CALR was studied in wild-type JAK2/MPL patients including 34 ET, 21 persistent thrombocytosis suggestive of MPN and 98 suspected secondary thrombocytosis. CALR mutation analysis was performed through HRM and Sanger sequencing. We compared clinical features of CALR-mutated versus 45 JAK2/MPL-mutated subjects in ET. Results Nineteen samples showed distinct HRM patterns from wild-type. Of them, 18 were mutations and one a polymorphism as confirmed by direct sequencing. CALR mutations were present in 44% of ET (15/34), 14% of persistent thrombocytosis suggestive of MPN (3/21) and none of the secondary thrombocytosis (0/98). Of the 18 mutants, 9 were 52 bp deletions, 8 were 5 bp insertions and other was a complex mutation with insertion/deletion. No mutations were found after sequencing analysis of 45 samples displaying wild-type HRM curves. HRM technique was reproducible, no false positive or negative were detected and the limit of detection was of 3%. Conclusions This study establishes a sensitive, reliable and rapid HRM method to screen for the presence of CALR mutations.
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Affiliation(s)
- Cristina Bilbao-Sieyro
- Hematology Department, Hospital Universitario de Gran Canaria Dr. Negrin, Las Palmas de Gran Canaria, Spain
- Morfology Department, Universidad de Las Palmas de Gran Canaria, Las Palmas de Gran Canaria, Spain
| | - Guillermo Santana
- Hematology Department, Hospital Universitario de Gran Canaria Dr. Negrin, Las Palmas de Gran Canaria, Spain
| | - Melania Moreno
- Hematology Department, Hospital Universitario de Gran Canaria Dr. Negrin, Las Palmas de Gran Canaria, Spain
| | - Laura Torres
- Hematology Department, Hospital Universitario de Gran Canaria Dr. Negrin, Las Palmas de Gran Canaria, Spain
| | - Gonzalo Santana-Lopez
- Preventive Medicine Department, Hospital Universitario de Gran Canaria Dr. Negrin, Las Palmas de Gran Canaria, Spain
| | - Carlos Rodriguez-Medina
- Hematology Department, Hospital Universitario de Gran Canaria Dr. Negrin, Las Palmas de Gran Canaria, Spain
| | - María Perera
- Hematology Department, Hospital Universitario de Gran Canaria Dr. Negrin, Las Palmas de Gran Canaria, Spain
| | - Beatriz Bellosillo
- Laboratori de Biologia Molecular Servei de Patologia, Hospital del Mar, Barcelona, Spain
| | - Silvia de la Iglesia
- Hematology Department, Hospital Universitario de Gran Canaria Dr. Negrin, Las Palmas de Gran Canaria, Spain
| | - Teresa Molero
- Hematology Department, Hospital Universitario de Gran Canaria Dr. Negrin, Las Palmas de Gran Canaria, Spain
- Medical Sciences Department, Universidad de Las Palmas de Gran Canaria, Las Palmas de Gran Canaria, Spain
| | - Maria Teresa Gomez-Casares
- Hematology Department, Hospital Universitario de Gran Canaria Dr. Negrin, Las Palmas de Gran Canaria, Spain
- * E-mail:
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Lu Q, Huang X, Chen H, Zhao X. A novel melting curve-based method for detecting c-kit mutations in acute myeloid leukemia. Oncol Lett 2014; 8:99-104. [PMID: 24959227 PMCID: PMC4063585 DOI: 10.3892/ol.2014.2128] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2013] [Accepted: 04/03/2014] [Indexed: 01/30/2023] Open
Abstract
The c-kit gene encodes a class III tyrosine kinase receptor. Specific somatic mutations in c-kit have been associated with acute myeloid leukemia (AML) and are markers of a poor prognosis in AML. Various methods have been used to detect the c-kit gene mutation; however, the suitability of these methods in the clinical management of AML remains unclear. The current study developed a novel method, using modified hybridization probes and melting curve analysis, for detecting c-kit mutations in exon 17. Dual-labeled self-quenched oligonucleotide probes containing two segments, labeled with carboxyrhodamine or hexachlorofluorescein, were designed to detect sequences around the D816 or N820/N822 mutation hot spots in exon 17 of c-kit. The exon 17 region of c-kit was amplified by polymerase chain reaction using control plasmids carrying wild-type or mutant sequences, or genomic DNA derived from AML patients. Melting curve analysis of the amplification products was performed using a self-quenched probe. The results showed that the detection sensitivity, assayed using mutation-positive control plasmids, was 10% for the N820G mutation and 5% for the six other mutations; N822K(A), N822K(G), D816V, D816Y, D816H and D816F. In addition, c-kit mutations were identified in six of the 12 samples from the core-binding factor (CBF)-AML patients. This demonstrates that the novel method developed in the present study, is simple, rapid, specific and highly sensitive, and may facilitate the diagnosis and treatment of CBF-AML.
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Affiliation(s)
- Quanyi Lu
- Department of Hematology, Zhongshan Hospital of Xiamen University, Xiamen, Fujian 361004, P.R. China
| | - Xiao Huang
- Department of Hematology, Zhongshan Hospital of Xiamen University, Xiamen, Fujian 361004, P.R. China
| | - Huaying Chen
- Department of Hematology, Zhongshan Hospital of Xiamen University, Xiamen, Fujian 361004, P.R. China
| | - Xiaomin Zhao
- Department of Hematology, Zhongshan Hospital of Xiamen University, Xiamen, Fujian 361004, P.R. China
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Liu Y, Tang J, Wakamatsu P, Xue H, Chen J, Gaynon PS, Shen S, Sun W. High-resolution melting curve analysis, a rapid and affordable method for mutation analysis in childhood acute myeloid leukemia. Front Pediatr 2014; 2:96. [PMID: 25250304 PMCID: PMC4158872 DOI: 10.3389/fped.2014.00096] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/20/2014] [Accepted: 08/24/2014] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Molecular genetic alterations with prognostic significance have been described in childhood acute myeloid leukemia (AML). The aim of this study was to establish cost-effective techniques to detect mutations of FMS-like tyrosine kinase 3 (FLT3), nucleophosmin 1 (NPM1), and a partial tandem duplication within the mixed-lineage leukemia (MLL-PTD) genes in childhood AML. PROCEDURE Ninety-nine children with newly diagnosed AML were included in this study. We developed a fluorescent dye SYTO-82 based high-resolution melting (HRM) curve analysis to detect FLT3 internal tandem duplication (FLT3-ITD), FLT3 tyrosine kinase domain (FLT3-TKD), and NPM1 mutations. MLL-PTD was screened by real-time quantitative PCR. RESULTS The HRM methodology correlated well with gold standard Sanger sequencing with less cost. Among the 99 patients studied, the FLT3-ITD mutation was associated with significantly worse event-free survival (EFS). Patients with the NPM1 mutation had significantly better EFS and overall survival. However, HRM was not sensitive enough for minimal residual disease monitoring. CONCLUSION High-resolution melting was a rapid and efficient method for screening of FLT3 and NPM1 gene mutations. It was both affordable and accurate, especially in resource underprivileged regions. Our results indicated that HRM could be a useful clinical tool for rapid and cost-effective screening of the FLT3 and NPM1 mutations in AML patients.
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Affiliation(s)
- Yin Liu
- Department of Hematology/Oncology, Shanghai Children's Medical Center, Shanghai Jiaotong University School of Medicine , Shanghai , China
| | - Jingyan Tang
- Department of Hematology/Oncology, Shanghai Children's Medical Center, Shanghai Jiaotong University School of Medicine , Shanghai , China
| | - Peter Wakamatsu
- Division of Hematology, Oncology and Blood and Marrow Transplantation, Children's Center for Cancer and Blood Disease, Children's Hospital Los Angeles, Keck School of Medicine, University of Southern California , Los Angeles, CA , USA
| | - Huiliang Xue
- Department of Hematology/Oncology, Shanghai Children's Medical Center, Shanghai Jiaotong University School of Medicine , Shanghai , China
| | - Jing Chen
- Department of Hematology/Oncology, Shanghai Children's Medical Center, Shanghai Jiaotong University School of Medicine , Shanghai , China
| | - Paul S Gaynon
- Division of Hematology, Oncology and Blood and Marrow Transplantation, Children's Center for Cancer and Blood Disease, Children's Hospital Los Angeles, Keck School of Medicine, University of Southern California , Los Angeles, CA , USA
| | - Shuhong Shen
- Department of Hematology/Oncology, Shanghai Children's Medical Center, Shanghai Jiaotong University School of Medicine , Shanghai , China
| | - Weili Sun
- Division of Hematology, Oncology and Blood and Marrow Transplantation, Children's Center for Cancer and Blood Disease, Children's Hospital Los Angeles, Keck School of Medicine, University of Southern California , Los Angeles, CA , USA
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Huss S, Künstlinger H, Wardelmann E, Kleine MA, Binot E, Merkelbach-Bruse S, Rüdiger T, Mittler J, Hartmann W, Büttner R, Schildhaus HU. A subset of gastrointestinal stromal tumors previously regarded as wild-type tumors carries somatic activating mutations in KIT exon 8 (p.D419del). Mod Pathol 2013; 26:1004-12. [PMID: 23599150 PMCID: PMC3701292 DOI: 10.1038/modpathol.2013.47] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2012] [Revised: 01/02/2013] [Accepted: 01/02/2013] [Indexed: 01/11/2023]
Abstract
About 10-15% of gastrointestinal stromal tumors (GISTs) carry wild-type sequences in all hot spots of KIT and platelet-derived growth factor receptor alpha (PDGFRA) (wt-GISTs). These tumors are currently defined by having no mutations in exons 9, 11, 13, and 17 of the KIT gene and exons 12, 14, and 18 of the PDGFRA gene. Until now, the analysis of further exons is not recommended. However, we have previously published a report on a KIT exon 8 germline mutation, which was associated with familial GIST and mastocytosis. We therefore investigated whether KIT exon 8 mutations might also occur in sporadic GIST. We screened a cohort of 145 wt-GISTs from a total of 1351 cases from our registry for somatic mutations in KIT exon 8. Two primary GISTs with an identical exon 8 mutation (p.D419del) were detected, representing 1.4% of all the cases analyzed. Based on all GISTs from our registry, the overall frequency of KIT exon 8 mutations was 0.15%. The first tumor originating in the small bowel of a 53-year-old male patient had mostly a biphasic spindled-epithelioid pattern with a high proliferative activity (14 mitoses/50 HPF) combined with a second low proliferative spindle cell pattern (4/50 HPF). The patient developed multiple peritoneal metastases 29 months later. The second case represented a jejunal GIST in a 67-year old woman who is relapse-free under adjuvant imatinib treatment. We conclude that about 1-2% of GISTs being classified as 'wild type' so far might, in fact, carry KIT mutations in exon 8. Moreover, this mutational subtype was shown to be activating and imatinib sensitive in vitro. We therefore propose that screening for KIT exon 8 mutations should become a routine in the diagnostic work-up of GIST and that patients with an exon 8 mutation and a significant risk for tumor progression should be treated with imatinib.
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Affiliation(s)
- Sebastian Huss
- Institute of Pathology, University of Cologne, Medical Center, Cologne, Germany
| | - Helen Künstlinger
- Institute of Pathology, University of Cologne, Medical Center, Cologne, Germany
| | - Eva Wardelmann
- Institute of Pathology, University of Cologne, Medical Center, Cologne, Germany
| | - Michaela A Kleine
- Institute of Pathology, University of Cologne, Medical Center, Cologne, Germany
| | - Elke Binot
- Institute of Pathology, University of Cologne, Medical Center, Cologne, Germany
| | | | - Thomas Rüdiger
- Städtisches Klinikum Karlsruhe, Institute of Pathology, Karlsruhe, Germany
| | - Jens Mittler
- Department of General and Abdominal Surgery, University Hospital Mainz, Mainz, Germany
| | - Wolfgang Hartmann
- Institute of Pathology, University of Cologne, Medical Center, Cologne, Germany
| | - Reinhard Büttner
- Institute of Pathology, University of Cologne, Medical Center, Cologne, Germany
| | - Hans-Ulrich Schildhaus
- Institute of Pathology, University of Cologne, Medical Center, Cologne, Germany,Institute of Pathology, University of Cologne, Medical Center, Kerpener Strasse 62, Cologne D-50924, Germany.
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Cairoli R, Beghini A, Turrini M, Bertani G, Nadali G, Rodeghiero F, Castagnola C, Lazzaroni F, Nichelatti M, Ferrara F, Pizzolo G, Pogliani E, Rossi G, Martinelli G, Morra E. Old and new prognostic factors in acute myeloid leukemia with deranged core-binding factor beta. Am J Hematol 2013; 88:594-600. [PMID: 23619823 DOI: 10.1002/ajh.23461] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2013] [Revised: 04/04/2013] [Accepted: 04/08/2013] [Indexed: 02/06/2023]
Abstract
Acute myeloid leukemia (AML) with deranged core-binding factor beta (CBFβ) is usually associated with a favorable prognosis with 50-70% of patients cured using contemporary treatments. We analyzed the prognostic significance of clinical features on 58 patients with CBFβ-AML aged ≤60 years. Increasing age was the only predictor for survival (P <0.001), with an optimal cut-point at 43 years. White blood cells (WBCs) at diagnosis emerged as an independent risk factor for relapse incidence (P = 0.017), with 1.1% increase of hazard for each 1.0 × 10(9) /L WBC increment. KIT mutations lacked prognostic value for survival and showed only a trend for relapse incidence (P = 0.069).
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Affiliation(s)
- Roberto Cairoli
- Division of Haematology; Niguarda Hospital; Milan Italy
- Division of Haematology; Department of Internal Medicine; Valduce Hospital; Como Italy
| | - Alessandro Beghini
- Department of Medical Biotechnology and Translational Medicine; University of Milan; Milan Italy
| | - Mauro Turrini
- Division of Haematology; Niguarda Hospital; Milan Italy
| | | | - Gianpaolo Nadali
- Department of Clinical and Experimental Medicine; University of Verona; Verona Italy
| | | | - Carlo Castagnola
- Department of Haematology Oncology; University of Pavia & Fondazione IRCCS Policlinico San Matteo; Pavia Italy
| | - Francesca Lazzaroni
- Department of Medical Biotechnology and Translational Medicine; University of Milan; Milan Italy
| | | | - Felicetto Ferrara
- Division of Haematology and Stem Cell Transplantation Unit; Cardarelli General Hospital; Naples Italy
| | - Giovanni Pizzolo
- Department of Clinical and Experimental Medicine; University of Verona; Verona Italy
| | - Enrico Pogliani
- Division of Hematology and Bone Marrow Transplantation Unit; San Gerardo University Hospital; Monza Italy
| | - Giuseppe Rossi
- Department of Haematology; Spedali Civili; Brescia Italy
| | | | - Enrica Morra
- Division of Haematology; Niguarda Hospital; Milan Italy
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Li BS, Wang XY, Xu AG, Ma FL, Ma QY, Li Z, Liu JH, Gan AH, Yu ZJ, Zhang XH, Jiang B. High-Resolution Melting Assay (HRMA) is a Simple and Sensitive Stool-Based DNA Test for the Detection of Mutations in Colorectal Neoplasms. Clin Colorectal Cancer 2012; 11:280-90. [DOI: 10.1016/j.clcc.2012.04.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2011] [Revised: 03/14/2012] [Accepted: 04/12/2012] [Indexed: 01/04/2023]
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Kristensen T, Preiss B, Broesby-Olsen S, Vestergaard H, Friis L, Møller MB. Systemic mastocytosis is uncommon inKITD816V mutation positive core-binding factor acute myeloid leukemia. Leuk Lymphoma 2012; 53:1338-44. [DOI: 10.3109/10428194.2011.647314] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
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Chen N, Tranebjærg L, Rendtorff ND, Schrijver I. Mutation analysis of SLC26A4 for Pendred syndrome and nonsyndromic hearing loss by high-resolution melting. J Mol Diagn 2011; 13:416-26. [PMID: 21704276 PMCID: PMC3123795 DOI: 10.1016/j.jmoldx.2011.03.003] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2010] [Revised: 02/15/2011] [Accepted: 03/16/2011] [Indexed: 02/04/2023] Open
Abstract
Pendred syndrome and DFNB4 (autosomal recessive nonsyndromic congenital deafness, locus 4) are associated with autosomal recessive congenital sensorineural hearing loss and mutations in the SLC26A4 gene. Extensive allelic heterogeneity, however, necessitates analysis of all exons and splice sites to identify mutations for individual patients. Although Sanger sequencing is the gold standard for mutation detection, screening methods supplemented with targeted sequencing can provide a cost-effective alternative. One such method, denaturing high-performance liquid chromatography, was developed for clinical mutation detection in SLC26A4. However, this method inherently cannot distinguish homozygous changes from wild-type sequences. High-resolution melting (HRM), on the other hand, can detect heterozygous and homozygous changes cost-effectively, without any post-PCR modifications. We developed a closed-tube HRM mutation detection method specific for SLC26A4 that can be used in the clinical diagnostic setting. Twenty-eight primer pairs were designed to cover all 21 SLC26A4 exons and splice junction sequences. Using the resulting amplicons, initial HRM analysis detected all 45 variants previously identified by sequencing. Subsequently, a 384-well plate format was designed for up to three patient samples per run. Blinded HRM testing on these plates of patient samples collected over 1 year in a clinical diagnostic laboratory accurately detected all variants identified by sequencing. In conclusion, HRM with targeted sequencing is a reliable, simple, and cost-effective method for SLC26A4 mutation screening and detection.
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Affiliation(s)
- Neng Chen
- Department of Pathology, Stanford University School of Medicine, Stanford, California
| | - Lisbeth Tranebjærg
- Department of Audiology, Bispebjerg Hospital, Copenhagen, Denmark
- Wilhelm Johannsen Center of Functional Genomics, Institute of Molecular Medicine, ICMM, The Panum Institute, University of Copenhagen, Copenhagen, Denmark
| | - Nanna Dahl Rendtorff
- Wilhelm Johannsen Center of Functional Genomics, Institute of Molecular Medicine, ICMM, The Panum Institute, University of Copenhagen, Copenhagen, Denmark
| | - Iris Schrijver
- Department of Pathology, Stanford University School of Medicine, Stanford, California
- Department of Pediatrics, Stanford University School of Medicine, Stanford, California
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Ultrasensitive detection of drug-resistant pandemic 2009 (H1N1) influenza A virus by rare-variant-sensitive high-resolution melting-curve analysis. J Clin Microbiol 2011; 49:2602-9. [PMID: 21543559 DOI: 10.1128/jcm.00277-11] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Oseltamivir (Tamiflu), an oral neuraminidase inhibitor, has been widely used to treat pandemic 2009 (H1N1) influenza A. Although a majority of 2009 (H1N1) influenza A virus remains oseltamivir susceptible, the threat of resistance due to the His275Tyr mutation is highlighted by the limitations of alternative therapies and the potential for rapid, global fixation of this mutation in the circulating influenza A virus population. In order to better understand the emergence of resistance, we developed a rare-variant-sensitive high-resolution melting-curve analysis method (RVS-HRM) that is able to detect the His275Tyr oseltamivir resistance mutation to 0.5% in a background of susceptible virus. We applied RVS-HRM to clinical specimens from patients who developed oseltamivir resistance and demonstrated the ultrasensitive detection of influenza A virus N1 neuraminidase quasispecies. Interestingly, we were unable to detect the oseltamivir resistance mutation in pretreatment samples, suggesting that resistant virus does not reach even this very low detection threshold until exposed to selective drug pressure. Thus, patients naive to oseltamivir are most likely to be susceptible when this drug is used as a first-line treatment modality.
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Li BS, Wang XY, Ma FL, Jiang B, Song XX, Xu AG. Is high resolution melting analysis (HRMA) accurate for detection of human disease-associated mutations? A meta analysis. PLoS One 2011; 6:e28078. [PMID: 22194806 PMCID: PMC3237421 DOI: 10.1371/journal.pone.0028078] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2011] [Accepted: 10/31/2011] [Indexed: 01/15/2023] Open
Abstract
BACKGROUND High Resolution Melting Analysis (HRMA) is becoming the preferred method for mutation detection. However, its accuracy in the individual clinical diagnostic setting is variable. To assess the diagnostic accuracy of HRMA for human mutations in comparison to DNA sequencing in different routine clinical settings, we have conducted a meta-analysis of published reports. METHODOLOGY/PRINCIPAL FINDINGS Out of 195 publications obtained from the initial search criteria, thirty-four studies assessing the accuracy of HRMA were included in the meta-analysis. We found that HRMA was a highly sensitive test for detecting disease-associated mutations in humans. Overall, the summary sensitivity was 97.5% (95% confidence interval (CI): 96.8-98.5; I(2) = 27.0%). Subgroup analysis showed even higher sensitivity for non-HR-1 instruments (sensitivity 98.7% (95%CI: 97.7-99.3; I(2) = 0.0%)) and an eligible sample size subgroup (sensitivity 99.3% (95%CI: 98.1-99.8; I(2) = 0.0%)). HRMA specificity showed considerable heterogeneity between studies. Sensitivity of the techniques was influenced by sample size and instrument type but by not sample source or dye type. CONCLUSIONS/SIGNIFICANCE These findings show that HRMA is a highly sensitive, simple and low-cost test to detect human disease-associated mutations, especially for samples with mutations of low incidence. The burden on DNA sequencing could be significantly reduced by the implementation of HRMA, but it should be recognized that its sensitivity varies according to the number of samples with/without mutations, and positive results require DNA sequencing for confirmation.
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Affiliation(s)
- Bing-Sheng Li
- Department of Gastroenterology, Nanfang Hospital, Southern Medical University, Guangzhou, People's Republic of China
- Guangdong Provincial Key Laboratory of Gastroenterology, Guangzhou, People's Republic of China
| | - Xin-Ying Wang
- Department of Gastroenterology, Nanfang Hospital, Southern Medical University, Guangzhou, People's Republic of China
- Guangdong Provincial Key Laboratory of Gastroenterology, Guangzhou, People's Republic of China
| | - Feng-Li Ma
- Department of Gastroenterology, Nanfang Hospital, Southern Medical University, Guangzhou, People's Republic of China
- Guangdong Provincial Key Laboratory of Gastroenterology, Guangzhou, People's Republic of China
| | - Bo Jiang
- Department of Gastroenterology, Nanfang Hospital, Southern Medical University, Guangzhou, People's Republic of China
- Guangdong Provincial Key Laboratory of Gastroenterology, Guangzhou, People's Republic of China
| | - Xiao-Xiao Song
- School of Public Health, Kunming Medical University, Kunming, People's Republic of China
| | - An-Gao Xu
- Huizhou Medicine Institute, Huizhou First Hospital, Huizhou, Guangdong, People's Republic of China
- * E-mail:
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López-Villar I, Ayala R, Wesselink J, Morillas JD, López E, Marín JC, Díaz-Tasende J, González S, Robles L, Martínez-López J. Simplifying the detection of MUTYH mutations by high resolution melting analysis. BMC Cancer 2010; 10:408. [PMID: 20687945 PMCID: PMC2924853 DOI: 10.1186/1471-2407-10-408] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2010] [Accepted: 08/05/2010] [Indexed: 11/10/2022] Open
Abstract
Background MUTYH-associated polyposis (MAP) is a disorder caused by bi-allelic germline MUTYH mutation, characterized by multiple colorectal adenomas. In order to identify mutations in MUTYH gene we applied High Resolution Melting (HRM) genotyping. HRM analysis is extensively employed as a scanning method for the detection of heterozygous mutations. Therefore, we applied HRM to show effectiveness in detecting homozygous mutations for these clinically important and frequent patients. Methods In this study, we analyzed phenotype and genotype data from 82 patients, with multiple (>= 10) synchronous (19/82) or metachronous (63/82) adenomas and negative APC study (except one case). Analysis was performed by HRM-PCR and direct sequencing, in order to identify mutations in MUTYH exons 7, 12 and 13, where the most prevalent mutations are located. In monoallelic mutation carriers, we evaluated entire MUTYH gene in search of another possible alteration. HRM-PCR was performed with strict conditions in several rounds: the first one to discriminate the heteroduplex patterns and homoduplex patterns and the next ones, in order to refine and confirm parameters. The genotypes obtained were correlated to phenotypic features (number of adenomas (synchronous or metachronous), colorectal cancer (CRC) and family history). Results MUTYH germline mutations were found in 15.8% (13/82) of patients. The hot spots, Y179C (exon 7) and G396D (exon 13), were readily identified and other mutations were also detected. Each mutation had a reproducible melting profile by HRM, both heterozygous mutations and homozygous mutations. In our study of 82 patients, biallelic mutation is associated with being a carrier of ≥10 synchronous polyps (p = 0.05) and there is no association between biallelic mutation and CRC (p = 0.39) nor family history (p = 0.63). G338H non-pathogenic polymorphism (exon 12) was found in 23.1% (19/82) of patients. In all cases there was concordance between HRM (first and subsequent rounds) and sequencing data. Conclusions Here, we describe a screening method, HRM, for the detection of both heterozygous and homozygous mutations in the gene encoding MUTYH in selected samples of patients with phenotype of MAP. We refine the capabilities of HRM-PCR and apply it to a gene not yet analyzed by this tool. As clinical decisions will increasingly rely on molecular medicine, the power of identifying germline mutations must be continuously evaluated and improved.
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Affiliation(s)
- Isabel López-Villar
- Department of Molecular Biology, 12 De Octubre University Hospital, Madrid, E-28041, Spain.
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