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Zhou S, Sikorski D, Xu H, Zubarev A, Chergui M, Lagacé F, Miller WH, Redpath M, Ghazal S, Butler MO, Petrella TM, Claveau J, Nessim C, Salopek TG, Gniadecki R, Litvinov IV. Defining the Criteria for Reflex Testing for BRAF Mutations in Cutaneous Melanoma Patients. Cancers (Basel) 2021; 13:2282. [PMID: 34068774 PMCID: PMC8126223 DOI: 10.3390/cancers13092282] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 04/26/2021] [Accepted: 04/28/2021] [Indexed: 12/11/2022] Open
Abstract
Targeted therapy has been developed through an in-depth understanding of molecular pathways involved in the pathogenesis of melanoma. Approximately ~50% of patients with melanoma have tumors that harbor a mutation of the BRAF oncogene. Certain clinical features have been identified in BRAF-mutated melanomas (primary lesions located on the trunk, diagnosed in patients <50, visibly pigmented tumors and, at times, with ulceration or specific dermatoscopic features). While BRAF mutation testing is recommended for stage III-IV melanoma, guidelines differ in recommending mutation testing in stage II melanoma patients. To fully benefit from these treatment options and avoid delays in therapy initiation, advanced melanoma patients harboring a BRAF mutation must be identified accurately and quickly. To achieve this, clear definition and implementation of BRAF reflex testing criteria/methods in melanoma should be established so that patients with advanced melanoma can arrive to their first medical oncology appointment with a known biomarker status. Reflex testing has proven effective for a variety of cancers in selecting therapies and driving other medical decisions. We overview the pathophysiology, clinical presentation of BRAF-mutated melanoma, current guidelines, and present recommendations on BRAF mutation testing. We propose that reflex BRAF testing should be performed for every melanoma patient with stages ≥IIB.
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Affiliation(s)
- Sarah Zhou
- Division of Dermatology, McGill University, Montreal, QC H3A 0G4, Canada; (S.Z.); (D.S.); (A.Z.); (F.L.); (S.G.)
| | - Daniel Sikorski
- Division of Dermatology, McGill University, Montreal, QC H3A 0G4, Canada; (S.Z.); (D.S.); (A.Z.); (F.L.); (S.G.)
| | - Honghao Xu
- Division of Dermatology, Laval University, Quebec City, QC G1V 0A6, Canada; (H.X.); (J.C.)
| | - Andrei Zubarev
- Division of Dermatology, McGill University, Montreal, QC H3A 0G4, Canada; (S.Z.); (D.S.); (A.Z.); (F.L.); (S.G.)
| | - May Chergui
- Department of Pathology, McGill University, Montreal, QC H3A 0G4, Canada; (M.C.); (M.R.)
| | - François Lagacé
- Division of Dermatology, McGill University, Montreal, QC H3A 0G4, Canada; (S.Z.); (D.S.); (A.Z.); (F.L.); (S.G.)
| | - Wilson H. Miller
- Departments of Medicine and Oncology, McGill University, Montreal, QC H3A 0G4, Canada;
| | - Margaret Redpath
- Department of Pathology, McGill University, Montreal, QC H3A 0G4, Canada; (M.C.); (M.R.)
| | - Stephanie Ghazal
- Division of Dermatology, McGill University, Montreal, QC H3A 0G4, Canada; (S.Z.); (D.S.); (A.Z.); (F.L.); (S.G.)
| | - Marcus O. Butler
- Princess Margaret Cancer Centre, Department of Medical Oncology and Hematology, University of Toronto, Toronto, ON M5G 2C1, Canada;
| | - Teresa M. Petrella
- Odette Cancer Centre, Sunnybrook Health Sciences Centre, University of Toronto, Toronto, ON M4N 3M5, Canada;
| | - Joël Claveau
- Division of Dermatology, Laval University, Quebec City, QC G1V 0A6, Canada; (H.X.); (J.C.)
| | - Carolyn Nessim
- Division of General Surgery, University of Ottawa, Ottawa, ON K1N 6N5, Canada;
| | - Thomas G. Salopek
- Division of Dermatology, University of Alberta, Edmonton, AB T6G 2R3, Canada; (T.G.S.); (R.G.)
| | - Robert Gniadecki
- Division of Dermatology, University of Alberta, Edmonton, AB T6G 2R3, Canada; (T.G.S.); (R.G.)
| | - Ivan V. Litvinov
- Division of Dermatology, McGill University, Montreal, QC H3A 0G4, Canada; (S.Z.); (D.S.); (A.Z.); (F.L.); (S.G.)
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2
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Kassaza K, Long AC, McDaniels JM, Andre M, Fredrickson W, Nyehangane D, Orikiriza P, Operario DJ, Bazira J, Mwanga-Amumpaire JA, Moore CC, Guler JL, Boum Y. Surveillance of Plasmodium falciparum pfcrt haplotypes in southwestern uganda by high-resolution melt analysis. Malar J 2021; 20:114. [PMID: 33632242 PMCID: PMC7908690 DOI: 10.1186/s12936-021-03657-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2020] [Accepted: 02/18/2021] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND Chloroquine (CQ) resistance is conferred by mutations in the Plasmodium falciparum CQ resistance transporter (pfcrt). Following CQ withdrawal for anti-malarial treatment, studies across malaria-endemic countries have shown a range of responses. In some areas, CQ sensitive parasites re-emerge, and in others, mutant haplotypes persist. Active surveillance of resistance mutations in clinical parasites is essential to inform treatment regimens; this effort requires fast, reliable, and cost-effective methods that work on a variety of sample types with reagents accessible in malaria-endemic countries. METHODS Quantitative PCR followed by High-Resolution Melt (HRM) analysis was performed in a field setting to assess pfcrt mutations in two groups of clinical samples from Southwestern Uganda. Group 1 samples (119 in total) were collected in 2010 as predominantly Giemsa-stained slides; Group 2 samples (125 in total) were collected in 2015 as blood spots on filter paper. The Rotor-Gene Q instrument was utilized to assess the impact of different PCR-HRM reagent mixes and the detection of mixed haplotypes present in the clinical samples. Finally, the prevalence of the wild type (CVMNK) and resistant pfcrt haplotypes (CVIET and SVMNT) was evaluated in this understudied Southwestern region of Uganda. RESULTS The sample source (i.e. Giemsa-stained slides or blood spots) and type of LCGreen-based reagent mixes did not impact the success of PCR-HRM. The detection limit of 10- 5 ng and the ability to identify mixed haplotypes as low as 10 % was similar to other HRM platforms. The CVIET haplotype predominated in the clinical samples (66 %, 162/244); however, there was a large regional variation between the sample groups (94 % CVIET in Group 1 and 44 % CVIET in Group 2). CONCLUSIONS The HRM-based method exhibits the flexibility required to conduct reliable assessment of resistance alleles from various sample types generated during the clinical management of malaria. Large regional variations in CQ resistance haplotypes across Southwestern Uganda emphasizes the need for continued local parasite genotype assessment to inform anti-malarial treatment policies.
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Affiliation(s)
- Kennedy Kassaza
- Epicentre Mbarara Research Centre, Mbarara, Uganda
- Department of Microbiology, Mbarara University of Science and Technology, Mbarara, Uganda
| | - Anna C Long
- Department of Biology, University of Virginia, Box 400328, 22904, Charlottesville, VA, USA
| | - Jennifer M McDaniels
- Department of Biology, University of Virginia, Box 400328, 22904, Charlottesville, VA, USA
| | - Mharlove Andre
- Department of Biology, University of Virginia, Box 400328, 22904, Charlottesville, VA, USA
| | - Wasswa Fredrickson
- Department of Microbiology, Mbarara University of Science and Technology, Mbarara, Uganda
| | | | | | - Darwin J Operario
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, VA, 22904, USA
| | - Joel Bazira
- Department of Microbiology, Mbarara University of Science and Technology, Mbarara, Uganda
| | - Juliet A Mwanga-Amumpaire
- Epicentre Mbarara Research Centre, Mbarara, Uganda
- Department of Pediatrics and Child Health, Mbarara University of Science and Technology, Mbarara, Uganda
| | - Christopher C Moore
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, VA, 22904, USA
| | - Jennifer L Guler
- Department of Biology, University of Virginia, Box 400328, 22904, Charlottesville, VA, USA.
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, VA, 22904, USA.
| | - Yap Boum
- Epicentre Mbarara Research Centre, Mbarara, Uganda.
- Department of Microbiology, Mbarara University of Science and Technology, Mbarara, Uganda.
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Pham QT, Raad S, Mangahas CL, M'Callum MA, Raggi C, Paganelli M. High-throughput assessment of mutations generated by genome editing in induced pluripotent stem cells by high-resolution melting analysis. Cytotherapy 2020; 22:536-542. [PMID: 32768274 DOI: 10.1016/j.jcyt.2020.06.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Revised: 05/31/2020] [Accepted: 06/01/2020] [Indexed: 12/26/2022]
Abstract
BACKGROUND AND AIMS Genome editing of induced pluripotent stem cells (iPSCs) holds great potential for both disease modeling and regenerative medicine. Although clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 provides an efficient and precise genome editing tool, iPSCs are especially difficult to transfect, resulting in a small percentage of cells carrying the desired correction. A high-throughput method to identify edited clones is required to reduce the time and costs of such an approach. METHODS Here we assess high-resolution melting analysis (HRMA), a simple and efficient real-time polymerase chain reaction-based method, and compare it with more commonly used assays. RESULTS AND CONCLUSIONS Our data show that HRMA is a robust and highly sensitive method, allowing the cost-effective and time-saving screening of genome-edited iPSCs. Samples can be prepared directly from 96-well microtiter plates for high-throughput analysis, and amplicons can be further analyzed with downstream techniques for further confirmation, if needed.
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Affiliation(s)
- Quang T Pham
- Liver Tissue Engineering and Cell Therapy Laboratory, CHU Sainte-Justine, Montreal, Canada
| | - Suleen Raad
- Liver Tissue Engineering and Cell Therapy Laboratory, CHU Sainte-Justine, Montreal, Canada
| | - Chenicka-Lyn Mangahas
- Liver Tissue Engineering and Cell Therapy Laboratory, CHU Sainte-Justine, Montreal, Canada
| | - Marie-Agnès M'Callum
- Liver Tissue Engineering and Cell Therapy Laboratory, CHU Sainte-Justine, Montreal, Canada
| | - Claudia Raggi
- Liver Tissue Engineering and Cell Therapy Laboratory, CHU Sainte-Justine, Montreal, Canada
| | - Massimiliano Paganelli
- Liver Tissue Engineering and Cell Therapy Laboratory, CHU Sainte-Justine, Montreal, Canada; Pediatric Hepatology, CHU Sainte-Justine, Montreal, Canada; Department of Pediatrics, Université de Montréal, Montreal, Canada.
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Vanni I, Tanda ET, Spagnolo F, Andreotti V, Bruno W, Ghiorzo P. The Current State of Molecular Testing in the BRAF-Mutated Melanoma Landscape. Front Mol Biosci 2020; 7:113. [PMID: 32695793 PMCID: PMC7338720 DOI: 10.3389/fmolb.2020.00113] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Accepted: 05/13/2020] [Indexed: 01/19/2023] Open
Abstract
The incidence of melanoma, among the most lethal cancers, is widespread and increasing. Metastatic melanoma has a poor prognosis, representing about 90% of skin cancer mortality. The increased knowledge of tumor biology and the greater understanding of the immune system role in the anti-tumor response has allowed us to develop a more rational approach to systemic therapies. The discovery of activating BRAF mutations in half of all melanomas has led to the development of molecularly targeted therapy with BRAF and MEK inhibitors, which dramatically improved outcomes of patients with stage IV BRAF-mutant melanoma. More recently, the results of clinical phase III studies conducted in the adjuvant setting led to the combined administration of BRAF and MEK inhibitors also in patients with resected high-risk melanoma (stage III). Therefore, BRAF mutation testing has become a priority to determine the oncologist's choice and course of therapy. In this review, we will report the molecular biology-based strategies used for BRAF mutation detection with the main advantages and disadvantages of the most commonly used diagnostic strategies. The timing of such molecular assessment in patients with cutaneous melanoma will be discussed, and we will also examine considerations and approaches for accurate and effective BRAF testing.
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Affiliation(s)
- Irene Vanni
- Genetics of Rare Cancers, IRCCS Ospedale Policlinico San Martino, Genoa, Italy.,Genetics of Rare Cancers, Department of Internal Medicine and Medical Specialties, University of Genoa, Genoa, Italy
| | | | | | - Virginia Andreotti
- Genetics of Rare Cancers, IRCCS Ospedale Policlinico San Martino, Genoa, Italy.,Genetics of Rare Cancers, Department of Internal Medicine and Medical Specialties, University of Genoa, Genoa, Italy
| | - William Bruno
- Genetics of Rare Cancers, IRCCS Ospedale Policlinico San Martino, Genoa, Italy.,Genetics of Rare Cancers, Department of Internal Medicine and Medical Specialties, University of Genoa, Genoa, Italy
| | - Paola Ghiorzo
- Genetics of Rare Cancers, IRCCS Ospedale Policlinico San Martino, Genoa, Italy.,Genetics of Rare Cancers, Department of Internal Medicine and Medical Specialties, University of Genoa, Genoa, Italy
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5
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BRAF V600E mutation detection in hairy cell leukemia-utility of archival DNA from bone marrow aspirate/imprint smear and amplification refractory mutation system. Mol Biol Rep 2020; 47:4365-4372. [PMID: 32458259 DOI: 10.1007/s11033-020-05509-0] [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: 01/02/2020] [Accepted: 05/08/2020] [Indexed: 10/24/2022]
Abstract
BRAF V600E is a disease defining mutation for hairy cell leukemia (HCL), which helps in its diagnosis and differentiation from morphologically similar splenic marginal zone lymphoma (SMZL) and HCL-variant (HCL-v). Forty eight cases:HCL(n = 34), SMZL(n = 11) and HCL-v(n = 3) were included. Of these, 32 were retrospective and 16 were prospective. DNA was extracted, in retrospective cases from cells obtained by smears from bone marrow aspirate/trephine imprint (BMA/BMTx) slides, and in prospective cases from peripheral blood (PB)/BMA samples. BRAF V600E mutation testing was done using ARMS-PCR. BRAF V600E mutation was positive in all HCL and negative in all SMZL and HCL-v cases. DNA extracted from BMA/BMTx slides gave results comparable to DNA extracted from PB/BMA samples. Median age of presentation for HCL (53 years) and SMZL (56 years) were quite similar, however, HCL-v (71 years) cases presented at an older age. Statistically significant differences between the three groups were seen for total leucocyte, platelet, absolute lymphocyte and monocyte counts, bone marrow-infiltration pattern, reticulin fibrosis, and an expression of CD11c, CD25, CD103, CD123, and CD200. The use of BMA/BMTx smears for DNA extraction was found to be a useful alternative to DNA extraction from formalin-fixed paraffin-embedded biopsy sections. ARMS-PCR is an efficient and specific technique to detect BRAF V600E mutation in HCL patients.
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6
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Ju M, Bai X, Zhang T, Lin Y, Yang L, Zhou H, Chang X, Guan S, Ren X, Li K, Wang Y, Li G. Mutation spectrum of COL1A1/COL1A2 screening by high-resolution melting analysis of Chinese patients with osteogenesis imperfecta. J Bone Miner Metab 2020; 38:188-197. [PMID: 31414283 DOI: 10.1007/s00774-019-01039-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Accepted: 07/24/2019] [Indexed: 11/30/2022]
Abstract
High-resolution melting (HRM) analysis has been shown to be a time-saving method for the screening of genetic variants. To increase the precision of the diagnosis of osteogenesis imperfecta (OI), we used HRM to explore COL1A1/COL1A2 mutations in 87 Chinese OI patients and to perform population-based studies of the relationships between their genotypes and phenotypes. Peripheral blood samples were collected from the 87 non-consanguineous probands. The coding regions and exon boundaries of COL1A1/COL1A2 were detected by HRM and confirmed by Sanger sequencing. The functional effects of mutations were predicted through bioinformatic tools. Mutations were detected in 70.3% of familial cases and 40% of sporadic cases (p < 0.01). Compared with COL1A1 mutations, patients with COL1A2 mutations were more prone to severe phenotypes. Helical mutations (caused by substitution of the glycine within the Gly-X-Y triplet domain) were more likely to occur in patients with type III and IV (p < 0.05). Haploinsufficiency mutations (caused by frameshift, nonsense, and splice-site mutations) appeared more frequently in patients with type I (p < 0.05). Compared with the Sanger sequencing and whole exome sequencing (WES), HRM was found to reduce total costs by 78%- 80% in patients who had a positive HRM separate melting curve. Our findings suggest that HRM would greatly benefit small and understaffed hospitals and laboratories, and would facilitate the accurate diagnosis and early treatment of OI in remote and less developed regions.
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Affiliation(s)
- Mingyan Ju
- Department of Genetics, Tianjin Medical University, Tianjin, 300070, People's Republic of China
| | - Xue Bai
- Department of Medical Laboratory, Tianjin Hospital, Tianjin, 300000, People's Republic of China
| | - Tianke Zhang
- Colorectal Surgery, Tianjin People's Hospital, Tianjin, 300000, People's Republic of China
| | - Yunshou Lin
- School of Basic Medical Sciences, Tianjin Medical University, Tianjin, 300070, People's Republic of China
| | - Li Yang
- School of Basic Medical Sciences, Tianjin Medical University, Tianjin, 300070, People's Republic of China
| | - Huaiyu Zhou
- School of Basic Medical Sciences, Tianjin Medical University, Tianjin, 300070, People's Republic of China
| | - Xiaoli Chang
- Department of Medical Laboratory, Tianjin Hospital, Tianjin, 300000, People's Republic of China
| | - Shizhen Guan
- Department of Medical Laboratory, Tianjin Hospital, Tianjin, 300000, People's Republic of China
| | - Xiuzhi Ren
- Orthopedic Ward III, Wuqing People's Hospital, Tianjin, 300000, People's Republic of China
| | - Keqiu Li
- Department of Genetics, Tianjin Medical University, Tianjin, 300070, People's Republic of China
| | - Yi Wang
- Department of Medical Laboratory, Tianjin Hospital, Tianjin, 300000, People's Republic of China
| | - Guang Li
- Department of Genetics, Tianjin Medical University, Tianjin, 300070, People's Republic of China.
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Chen G, Chen R, Ding S, Li M, Wang J, Zou J, Du F, Dong J, Cui X, Huang X, Deng Y, Tang Z. Recombinase assisted loop-mediated isothermal DNA amplification. Analyst 2019; 145:440-444. [PMID: 31793929 DOI: 10.1039/c9an01701a] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Polymerase chain reaction (PCR) and isothermal amplification methods such as LAMP and RPA are widely used for genetic detection. However, there are some shortcomings of these methods such as dependence on thermocycler instruments for PCR, complexity of primer design, the possibility for nonspecific amplification in LAMP and complexity of components in RPA. We develop a novel isothermal DNA detection system named Recombinase Assisted Loop-mediated Amplification (RALA). Recombinase from Thermus thermophilus (TthRecA) was used to open target double-stranded DNA to initiate loop-mediated amplification under isothermal conditions, which simplified the primer design and circumvented pre-denaturation. A FRET sensor named ProofMan and a proofreading enzyme Pfu were introduced to produce fluorescence signals by cleaving the sensor from the 3' end. Consequently, sequence-specific detection based on the RALA system was achieved, and even a single nucleotide polymorphism (SNP) could be identified. By introducing additional loop primers, the fast RALA version can amplify 102 DNA targets in 30 minutes. In addition to high sensitivity and specificity, the flexibility of choosing different reporting sensors makes this method versatile in either quantitative or qualitative DNA detection.
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Affiliation(s)
- Gangyi Chen
- Natural Products Research Center, Chengdu Institution of Biology, Chinese Academy of Science, Chengdu 610041, P. R. China.
| | - Rong Chen
- Chengdu University of Traditional Chinese Medicine, Chengdu 611137, P. R. China
| | - Sheng Ding
- Natural Products Research Center, Chengdu Institution of Biology, Chinese Academy of Science, Chengdu 610041, P. R. China.
| | - Mei Li
- Natural Products Research Center, Chengdu Institution of Biology, Chinese Academy of Science, Chengdu 610041, P. R. China.
| | - Jiayu Wang
- Natural Products Research Center, Chengdu Institution of Biology, Chinese Academy of Science, Chengdu 610041, P. R. China.
| | - Jiawei Zou
- Natural Products Research Center, Chengdu Institution of Biology, Chinese Academy of Science, Chengdu 610041, P. R. China.
| | - Feng Du
- Natural Products Research Center, Chengdu Institution of Biology, Chinese Academy of Science, Chengdu 610041, P. R. China.
| | - Juan Dong
- Natural Products Research Center, Chengdu Institution of Biology, Chinese Academy of Science, Chengdu 610041, P. R. China.
| | - Xin Cui
- Natural Products Research Center, Chengdu Institution of Biology, Chinese Academy of Science, Chengdu 610041, P. R. China.
| | - Xin Huang
- Natural Products Research Center, Chengdu Institution of Biology, Chinese Academy of Science, Chengdu 610041, P. R. China.
| | - Yun Deng
- Chengdu University of Traditional Chinese Medicine, Chengdu 611137, P. R. China
| | - Zhuo Tang
- Natural Products Research Center, Chengdu Institution of Biology, Chinese Academy of Science, Chengdu 610041, P. R. China.
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8
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Ma Y, Chen Y, Lin J, Liu Y, Luo K, Cao Y, Wang T, Jin H, Su Z, Wu H, Chen X, Cheng J. Circulating miR-31 as an effective biomarker for detection and prognosis of human cancer: a meta-analysis. Oncotarget 2018; 8:28660-28671. [PMID: 28404921 PMCID: PMC5438681 DOI: 10.18632/oncotarget.15638] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Accepted: 01/29/2017] [Indexed: 12/26/2022] Open
Abstract
PURPOSE Circulating miR-31 was found to be associated with cancers detection and prognosis. The present meta-analysis aimed to explore the effect of circulating miR-31 on cancer detection and prognosis. METHOD The studies were accessed using multiple databases. RevMan5.3, Meta-DiSc 1.4, and STATA14.0 were used to estimate the pooled effects, heterogeneity among studies, and publication bias. RESULTS A total of 14 studies with 1397 cancer patients and 1039 controls were included. For the 12 prognostic tests, the adjusted pooled-AUC was 0.79 (95% CI: 0.73-0.86) as the pooled sensitivity, specificity, positive likelihood ratio (PLR), negative likelihood ratio (NLR), diagnostic odd ratio (DOR) from 10 tests was 0.79 (95% CI: 0.76-0.82), 0.79 (95% CI: 0.76-0.82), 3.81 (95% CI: 2.90-5.01), 0.26 (95% CI: 0.20-0.35), and 16.81 (95% CI: 9.67-29.25), respectively. For the 5 prognosis analyses, the pooled HR (hazard ratio) of overall survival (OS) was 1.55 (95% CI 1.30-1.86) for high versus low circulating miR-31 expression. However, high expression of circulating miR-31 did not significantly increase the risk of poor differentiation (pooled OR=1.39, 95% CI: 0.56-3.47) and LNM (pooled OR=3.46, 95% CI: 0.96-12.42) in lung cancer. CONCLUSION Circulating miR-31 is an effective biomarker and could be used as a component of miRs signature for cancer detection and prognosis surveillance.
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Affiliation(s)
- Yingjun Ma
- Respiratory Medicine, Guangming District People's Hospital of Shenzhen, Shenzhen, P.R. China
| | - Yunfang Chen
- Pain Department, The Eight Affiliated Hospital, Sun Yat-sen University, ShenZhen, P.R. China
| | - Jinbo Lin
- Medical oncology, Longgang District Central Hospital of Shenzhen, Shenzhen, P.R. China
| | - Yi Liu
- Center for Chronic Disease Control and Prevention, Shenzhen Guangming District Center for Disease Control and Prevention, Shenzhen, P.R. China
| | - Kai Luo
- Affiliated Cancer Hospital & Institute of Guangzhou Medical University, Guangzhou, P.R. China
| | - Yong Cao
- Center for Chronic Disease Control and Prevention, Shenzhen Guangming District Center for Disease Control and Prevention, Shenzhen, P.R. China
| | - Tieqiang Wang
- Center for Chronic Disease Control and Prevention, Shenzhen Guangming District Center for Disease Control and Prevention, Shenzhen, P.R. China
| | - Hongwei Jin
- Center for Chronic Disease Control and Prevention, Shenzhen Guangming District Center for Disease Control and Prevention, Shenzhen, P.R. China
| | - Zhan Su
- Center for Chronic Disease Control and Prevention, Shenzhen Guangming District Center for Disease Control and Prevention, Shenzhen, P.R. China
| | - Haolin Wu
- Center for Chronic Disease Control and Prevention, Shenzhen Guangming District Center for Disease Control and Prevention, Shenzhen, P.R. China
| | - Xiaoliang Chen
- Center for Chronic Disease Control and Prevention, Shenzhen Guangming District Center for Disease Control and Prevention, Shenzhen, P.R. China
| | - Jinquan Cheng
- Molecular Biology Laboratory, Shenzhen Center for Disease Control and Prevention, Shenzhen, P.R. China
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9
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Molecular testing for BRAF mutations to inform melanoma treatment decisions: a move toward precision medicine. Mod Pathol 2018; 31:24-38. [PMID: 29148538 PMCID: PMC5758899 DOI: 10.1038/modpathol.2017.104] [Citation(s) in RCA: 260] [Impact Index Per Article: 43.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Revised: 06/14/2017] [Accepted: 06/30/2017] [Indexed: 12/13/2022]
Abstract
Approximately one-half of advanced (unresectable or metastatic) melanomas harbor a mutation in the BRAF gene, with V600E being the most common mutation. Targeted therapy with BRAF and MEK inhibitors is associated with significant long-term treatment benefit in patients with BRAF V600-mutated melanoma. Therefore, molecular testing for BRAF mutations is a priority in determining the course of therapy. A literature search was performed using MEDLINE/PubMed and scientific congress databases using the terms 'BRAF,' 'mutation,' and 'cancer/tumor.' These results were filtered to include manuscripts that focused on diagnostic tests for determining BRAF mutation status. Numerous BRAF testing methods were identified, including DNA-based companion diagnostic tests and DNA- and protein-based laboratory-developed tests. Herein we review the characteristics of each method and highlight the strengths and weaknesses that should be considered before use and when interpreting results for each patient. Molecular profiling has shown that mutation load increases with melanoma tumor progression and that unique patterns of genetic changes and evolutionary trajectories for different melanoma subtypes can occur. Discordance in the BRAF mutational status between primary and metastatic lesions, as well as intratumoral heterogeneity, is known to occur. Additionally, the development of acquired resistance to combination BRAF and MEK inhibitor therapy is still a formidable obstacle. Therefore, tumor heterogeneity and the development of acquired resistance have important implications for molecular testing and ultimately the treatment of patients with advanced-stage melanoma. Overall, this information may help community oncologists more accurately and effectively interpret results of diagnostic tests within the context of recent data characterizing melanoma tumor progression.
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Zeng Y, Wang T, Liu Y, Su Z, Lu P, Chen X, Hu D. LncRNA PVT1 as an effective biomarker for cancer diagnosis and detection based on transcriptome data and meta-analysis. Oncotarget 2017; 8:75455-75466. [PMID: 29088881 PMCID: PMC5650436 DOI: 10.18632/oncotarget.20634] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Accepted: 08/17/2017] [Indexed: 01/16/2023] Open
Abstract
PURPOSE Long noncoding RNA (lncRNA) PVT1 was detected all types of cancer from Cancer Genome Atlas (TCGA) project; however, the role of PVT1 in cancer is not clear. This study aimed to reanalyze and determine the effect of PVT1 on cancer diagnosis, especially detection in serum. MATERIALS AND METHODS Differential expression of PVT1 between cancers and corresponding normal tissues and receiver operating characteristic (ROC) curve were analyzed for all types of cancers in TCGA database. RevMan5.3, Meta-DiSc1.4 and STATA14.0 were used to estimate pooled diagnostic effects of PVT1 in tissue as well as serum. RESULTS Compared to corresponding normal tissues, PVT1 expression was significantly upregulated in 18 types of cancer and further being an effective diagnosis biomarker in 16 of them. For the 23 diagnosis tests performed in tissue, the pooled AUC and diagnostic odd ratio (DOR) were estimated to be 0.81 (95% CI: 0.76-0.86) and 17.25 (95% CI: 8.43-35.27), when the pooled AUC and DOR were 0.83 (95%CI: 0.75-0.91) and 13.86 (95% CI: 4.70-40.66) for serum tests. Furthermore, the pooled sensitivity and specificity were 0.83 (95% CI: 0.76-0.89) and 0.74 (95% CI:0.70-0.84) for tissue as well as 0.81 (95% CI: 0.76-0.86) and 0.76 (95% CI:0.70-0.81) for serum. CONCLUSIONS PVT1, especially in serum, might be a usable biomarker for cancer diagnosis / detection.
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Affiliation(s)
- Yunhong Zeng
- Guangming District People's Hospital of Shenzhen, Shenzhen, Guangdong, P.R. China
| | - Tieqiang Wang
- Shenzhen Guangming District Center for Disease Control and Prevention, Shenzhen, Guangdong, P.R. China
| | - Yi Liu
- Shenzhen Guangming District Center for Disease Control and Prevention, Shenzhen, Guangdong, P.R. China
| | - Zhan Su
- Shenzhen Guangming District Center for Disease Control and Prevention, Shenzhen, Guangdong, P.R. China
| | - Pingtao Lu
- Guangming District People's Hospital of Shenzhen, Shenzhen, Guangdong, P.R. China
| | - Xiaoliang Chen
- Shenzhen Guangming District Center for Disease Control and Prevention, Shenzhen, Guangdong, P.R. China
| | - Dongsheng Hu
- Department of Preventive Medicine, Shenzhen University Health Science Center, Shenzhen, Guangdong, P.R. China
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Chen HX, Zhang X, Hou HT, Wang J, Yang Q, Wang XL, He GW. Identification of a novel and functional mutation in the TBX5 gene in a patient by screening from 354 patients with isolated ventricular septal defect. Eur J Med Genet 2017; 60:385-390. [DOI: 10.1016/j.ejmg.2017.04.011] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Revised: 02/23/2017] [Accepted: 04/17/2017] [Indexed: 11/16/2022]
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12
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Zaboikin M, Zaboikina T, Freter C, Srinivasakumar N. Non-Homologous End Joining and Homology Directed DNA Repair Frequency of Double-Stranded Breaks Introduced by Genome Editing Reagents. PLoS One 2017; 12:e0169931. [PMID: 28095454 PMCID: PMC5241150 DOI: 10.1371/journal.pone.0169931] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Accepted: 12/22/2016] [Indexed: 11/19/2022] Open
Abstract
Genome editing using transcription-activator like effector nucleases or RNA guided nucleases allows one to precisely engineer desired changes within a given target sequence. The genome editing reagents introduce double stranded breaks (DSBs) at the target site which can then undergo DNA repair by non-homologous end joining (NHEJ) or homology directed recombination (HDR) when a template DNA molecule is available. NHEJ repair results in indel mutations at the target site. As PCR amplified products from mutant target regions are likely to exhibit different melting profiles than PCR products amplified from wild type target region, we designed a high resolution melting analysis (HRMA) for rapid identification of efficient genome editing reagents. We also designed TaqMan assays using probes situated across the cut site to discriminate wild type from mutant sequences present after genome editing. The experiments revealed that the sensitivity of the assays to detect NHEJ-mediated DNA repair could be enhanced by selection of transfected cells to reduce the contribution of unmodified genomic DNA from untransfected cells to the DNA melting profile. The presence of donor template DNA lacking the target sequence at the time of genome editing further enhanced the sensitivity of the assays for detection of mutant DNA molecules by excluding the wild-type sequences modified by HDR. A second TaqMan probe that bound to an adjacent site, outside of the primary target cut site, was used to directly determine the contribution of HDR to DNA repair in the presence of the donor template sequence. The TaqMan qPCR assay, designed to measure the contribution of NHEJ and HDR in DNA repair, corroborated the results from HRMA. The data indicated that genome editing reagents can produce DSBs at high efficiency in HEK293T cells but a significant proportion of these are likely masked by reversion to wild type as a result of HDR. Supplying a donor plasmid to provide a template for HDR (that eliminates a PCR amplifiable target) revealed these cryptic DSBs and facilitated the determination of the true efficacy of genome editing reagents. The results indicated that in HEK293T cells, approximately 40% of the DSBs introduced by genome editing, were available for participation in HDR.
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Affiliation(s)
- Michail Zaboikin
- Division of Hematology/Oncology, Department of Internal Medicine, Saint Louis University, Saint Louis, Missouri, United States of America
| | - Tatiana Zaboikina
- Division of Hematology/Oncology, Department of Internal Medicine, Saint Louis University, Saint Louis, Missouri, United States of America
| | - Carl Freter
- Division of Hematology/Oncology, Department of Internal Medicine, Saint Louis University, Saint Louis, Missouri, United States of America
| | - Narasimhachar Srinivasakumar
- Division of Hematology/Oncology, Department of Internal Medicine, Saint Louis University, Saint Louis, Missouri, United States of America
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PCR-Based Detection Methods for Single-Nucleotide Polymorphism or Mutation: Real-Time PCR and Its Substantial Contribution Toward Technological Refinement. Adv Clin Chem 2017; 80:45-72. [PMID: 28431642 DOI: 10.1016/bs.acc.2016.11.002] [Citation(s) in RCA: 77] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Single-nucleotide polymorphisms (SNPs) and single-nucleotide mutations result from the substitution of only a single base. The SNP or mutation can be relevant to disease susceptibility, pathogenesis of disease, and efficacy of specific drugs. It is important to detect SNPs or mutations clinically. Methods to distinguish/detect SNPs or mutations should be highly specific and sensitive. In this regard, polymerase chain reaction (PCR) has provided the necessary analytical performance for many molecular analyses. PCR-based methods for SNP/mutation detection are broadly categorized into two types-(1) polymorphic or mutant allele-directed specific analysis using primers matched with substituted nucleotide or using oligonucleotides to block or clamp the nontargeted template, and (2) melting curve analysis, which is combined with the real-time PCR techniques using hydrolysis probes, hybridization probes, or double-stranded DNA-binding fluorescent dyes. Innovative and novel approaches as well as technical improvements have made SNP- or mutation-detection methods increasingly more sophisticated. These advances include DNA/RNA preparation and subsequent amplification steps, and miniaturization of PCR instruments such that testing may be performed with relative ease in clinical laboratories or as a point-of-care test in clinical settings.
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Karbalaie Niya MH, Basi A, Koochak A, Safarnezhad Tameshkel F, Rakhshani N, Zamani F, Imanzade F, Rezvani H, Adib Sereshki MM, Sohrabi MR. Sensitive High-Resolution Melting Analysis for Screening of KRAS and BRAF Mutations in Iranian Human Metastatic Colorectal Cancers. Asian Pac J Cancer Prev 2016; 17:5147-5152. [PMID: 28122448 PMCID: PMC5454650 DOI: 10.22034/apjcp.2016.17.12.5147] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Background: Investigations of methods for detection of mutations have uncovered major weaknesses of direct sequencing and pyrosequencing, with their high costs and low sensitivity in screening for both known and unknown mutations. High resolution melting (HRM) analysis is an alternative tool for the rapid detection of mutations. Here we describe the accuracy of HRM in screening for KRAS and BRAF mutations in metastatic colorectal cancer (mCRCs) samples. Materials and Methods: A total of 1000 mCRC patients in Mehr Hospital, Tehran, Iran, from Feb 2008 to May 2012 were examined for KRAS mutations and 242 of them were selected for further assessment of BRAF mutations by HRM analysis. In order to calculate the sensitivity and specificity, HRM results were checked by pyrosequencing as the golden standard and Dxs Therascreen as a further method. Results: In the total of 1,000 participants, there were 664 (66.4%) with wild type and 336 (33.6%) with mutant codons 12 and/or 13 of the KRAS gene. Among 242 samples randomly checked for the BRAF gene, all were wild type by HRM. Pyrosequencing and Dxs Therascreen results were in line with those of the HRM. In this regard, the sensitivity and specificity of HRM were evaluated as 100%. Conclusion: The findings suggest that the HRM, in comparison with DNA sequencing, is a more appropriate method for precise scanning of KRAS and BRAF mutations. It is also possible to state that HRM may be an attractive technique for the detection of known or unknown somatic mutations in other genes.
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15
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Yao Y, Liao Y, Han M, Li SL, Luo J, Zhang B. Two kinds of common prenatal screening tests for Down's syndrome: a systematic review and meta-analysis. Sci Rep 2016; 6:18866. [PMID: 26732706 PMCID: PMC4702166 DOI: 10.1038/srep18866] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2015] [Accepted: 11/11/2015] [Indexed: 12/18/2022] Open
Abstract
As the chromosomal examination of foetal cells for the prenatal diagnosis of Down's syndrome (DS) carries a risk of inducing miscarriage, serum screening tests are commonly used before invasive procedures. In this study, a total of 374 records from PubMed, EMBASE, and the ISI Science Citation Index databases were reviewed. As a result of duplication, insufficient data, and inappropriate article types, 18 independent articles containing 183,998 samples were used in the final systematic review and meta-analysis of the diagnostic performance of the serum triple screening test (STS) and the integrated screening test (INS). Data extracted from the selected studies were statistically analysed, and the presence of heterogeneity and publication bias was assessed using specific software. The overall sensitivity, specificity, positive likelihood ratio, negative likelihood ratio, diagnostic odds ratio, and the area under the curve for the STS were 0.77 (95% confidence interval = 0.73-0.81), 0.94 (0.94-0.94), 9.78 (6.87-13.93), 0.26 (0.22-0.31), 44.72 (30.77-65.01), and 0.9064, respectively. For the INS, these values were 0.93 (0.90-0.95), 0.93 (0.93-0.93), 22.38 (12.47-40.14), 0.08 (0.05-0.11), 289.81 (169.08-496.76), and 0.9781, respectively. These results indicate that the INS exhibits better diagnostic value for DS. However, further research is needed to identify other biomarkers to improve prenatal screening tests.
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Affiliation(s)
- Yuan Yao
- Department of Laboratory Medicine, Southwest Hospital, Third Military Medical University of PLA, Chongqing 400038, PR China
- Department of Laboratory Medicine, No. 191 Clinical Department of No. 303 Hospital of PLA, Guigang 537100, Guangxi, PR China
| | - Yang Liao
- Department of Laboratory Medicine, Guangzhou General Hospital of Guangzhou Military Command of PLA, Guangzhou 510010, Guangdong, PR China
| | - Mei Han
- Department of Laboratory Medicine, Southwest Hospital, Third Military Medical University of PLA, Chongqing 400038, PR China
| | - Sheng-Lan Li
- Department of Laboratory Medicine, Southwest Hospital, Third Military Medical University of PLA, Chongqing 400038, PR China
| | - Juan Luo
- Department of Laboratory Medicine, Southwest Hospital, Third Military Medical University of PLA, Chongqing 400038, PR China
| | - Bo Zhang
- Department of Laboratory Medicine, Southwest Hospital, Third Military Medical University of PLA, Chongqing 400038, PR China
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16
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Screening of the BRCA1 gene in Brazilian patients with breast and/or ovarian cancer via high-resolution melting reaction analysis. Fam Cancer 2015; 15:173-81. [DOI: 10.1007/s10689-015-9858-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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17
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Tschentscher A, Dekomien G, Ross S, Cremer K, Kukuk GM, Epplen JT, Hoffjan S. Analysis of the C19orf12 and WDR45 genes in patients with neurodegeneration with brain iron accumulation. J Neurol Sci 2015; 349:105-9. [DOI: 10.1016/j.jns.2014.12.036] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2014] [Revised: 11/24/2014] [Accepted: 12/24/2014] [Indexed: 12/14/2022]
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18
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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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Roma-Rodrigues C, Fernandes AR. Genetics of hypertrophic cardiomyopathy: advances and pitfalls in molecular diagnosis and therapy. APPLICATION OF CLINICAL GENETICS 2014; 7:195-208. [PMID: 25328416 PMCID: PMC4199654 DOI: 10.2147/tacg.s49126] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Hypertrophic cardiomyopathy (HCM) is a primary disease of the cardiac muscle that occurs mainly due to mutations (>1,400 variants) in genes encoding for the cardiac sarcomere. HCM, the most common familial form of cardiomyopathy, affecting one in every 500 people in the general population, is typically inherited in an autosomal dominant pattern, and presents variable expressivity and age-related penetrance. Due to the morphological and pathological heterogeneity of the disease, the appearance and progression of symptoms is not straightforward. Most HCM patients are asymptomatic, but up to 25% develop significant symptoms, including chest pain and sudden cardiac death. Sudden cardiac death is a dramatic event, since it occurs without warning and mainly in younger people, including trained athletes. Molecular diagnosis of HCM is of the outmost importance, since it may allow detection of subjects carrying mutations on HCM-associated genes before development of clinical symptoms of HCM. However, due to the genetic heterogeneity of HCM, molecular diagnosis is difficult. Currently, there are mainly four techniques used for molecular diagnosis of HCM, including Sanger sequencing, high resolution melting, mutation detection using DNA arrays, and next-generation sequencing techniques. Application of these methods has proven successful for identification of mutations on HCM-related genes. This review summarizes the features of these technologies, highlighting their strengths and weaknesses. Furthermore, current therapeutics for HCM patients are correlated with clinically observed phenotypes and are based on the alleviation of symptoms. This is mainly due to insufficient knowledge on the mechanisms involved in the onset of HCM. Tissue engineering alongside regenerative medicine coupled with nanotherapeutics may allow fulfillment of those gaps, together with screening of novel therapeutic drugs and target delivery systems.
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Affiliation(s)
- Catarina Roma-Rodrigues
- UCIBIO, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia da Universidade Nova de Lisboa, Campus de Caparica, Caparica, Portugal
| | - Alexandra R Fernandes
- UCIBIO, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia da Universidade Nova de Lisboa, Campus de Caparica, Caparica, Portugal ; Centro de Química Estrutural, Instituto Superior Técnico, Universidade de Lisboa, Lisboa, Portugal
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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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