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Sande CM, Yang G, Mohamed A, Legendre BL, Pion D, Ferro SL, Grimm K, Elenitoba-Johnson KSJ. High-resolution melting assay for rapid, simultaneous detection of JAK2, MPL and CALR variants. J Clin Pathol 2024; 77:639-644. [PMID: 37156613 DOI: 10.1136/jcp-2023-208861] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2023] [Accepted: 04/30/2023] [Indexed: 05/10/2023]
Abstract
AIMS Identification of recurrent genetic alterations in JAK2, MPL and CALR remains crucial in the diagnosis of Philadelphia-negative myeloproliferative neoplasms (MPNs). Current laboratory testing algorithms may entail batching and/or sequential testing, involving multiple testing modalities and sometimes send-out testing that increase the technical and economic demands on laboratories while delaying patient diagnoses. To address this gap, an assay based on PCR and high-resolution melting (HRM) analysis was developed for simultaneous evaluation of JAK2 exons 12-14, MPL exon 10 and CALR exon 9, embodied in the HemeScreen® (hereafter 'HemeScreen') MPN assay. METHODS The HemeScreen MPN assay was validated with blood and bone marrow samples from 982 patients with clinical suspicion for MPN. The HRM assay and Sanger sequencing were performed in independent Clinical Laboratory Improvement Amendments (CLIA)-certified laboratories with Sanger sequencing (supported by droplet digital PCR) serving as the gold standard. RESULTS HRM and Sanger sequencing had an overall concordance of 99.4% with HRM detecting 133/139 (96%) variants confirmed by sequencing (9/10 MPL, 25/25 CALR, 99/104 JAK2), including 114 single nucleotide variants and 25 indels (3-52 bp). Variants consisted of disease-associated (DA) variants (89%), variants of unclear significance (2%) and non-DA variants (9%) with a positive predictive value of 92.3% and negative predictive value of 99.5%. CONCLUSIONS These studies demonstrate the exquisite accuracy, sensitivity and specificity of the HRM-based HemeScreen MPN assay, which serves as a powerful, clinically applicable platform for rapid, simultaneous detection of clinically relevant, somatic disease variants.
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Affiliation(s)
- Christopher M Sande
- Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Guang Yang
- Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | | | | | | | | | - Kate Grimm
- Precipio Inc, New Haven, Connecticut, USA
| | - Kojo S J Elenitoba-Johnson
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
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Jeong J, Yang Y, Song MS, Won HY, Han AT, Kim S. High-Resolution Melting (HRM) analysis of DNA methylation using semiconductor chip-based digital PCR. Genes Genomics 2024; 46:909-915. [PMID: 38849705 DOI: 10.1007/s13258-024-01527-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2024] [Accepted: 05/26/2024] [Indexed: 06/09/2024]
Abstract
BACKGROUND Digital PCR (dPCR) technology allows absolute quantification and detection of disease-associated rare variants, and thus the use of dPCR technology has been increasing in clinical research and diagnostics. The high-resolution melting curve analysis (HRM) of qPCR is widely used to distinguish true positives from false positives and detect rare variants. In particular, qPCR-HRM is commonly used for methylation assessment in research and diagnostics due to its simplicity and high reproducibility. Most dPCR instruments have limited fluorescence channels available and separate heating and imaging systems. Therefore, it is difficult to perform HRM analysis using dPCR instruments. OBJECTIVE A new digital real-time PCR instrument (LOAA) has been recently developed to integrate partitioning, thermocycling, and imaging in a single dPCR instrument. In addition, a new technique to perform HRM analysis is utilized in LOAA. The aim of the present study is to evaluate the efficiency and accuracy of LOAA dPCR on HRM analysis for the detection of methylation. METHODS In this study, comprehensive comparison with Bio-Rad qRT-PCR and droplet-based dPCR equipment was performed to verify the HRM analysis-based methylation detection efficiency of the LOAA digital PCR equipment. Here, sodium bisulfite modification method was applied to detect methylated DNA sequences by each PCR method. RESULTS Melting curve analysis detected four different Tm values using LOAA and qPCR, and found that LOAA, unlike qPCR, successfully distinguished between different Tm values when the Tm values were very similar. In addition, melting temperatures increased by each methylation were about 0.5℃ for qPCR and about 0.2 ~ 0.6℃ for LOAA. The melting temperature analyses of methylated and unmethylated DNA samples were conducted using LOAA dPCR with TaqMan probes and EvaGreen, and the result found that Tm values of methylated DNA samples are higher than those of unmethylated DNA samples. CONCLUSION The present study shows that LOAA dPCR could detect different melting temperatures according to methylation status of target sequences, indicating that LOAA dPCR would be useful for diagnostic applications that require the accurate quantification and assessment of DNA methylation.
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Affiliation(s)
- Jinuk Jeong
- Center for Bio-Medical Engineering Core Facility, Dankook University, Cheonan, 31116, Republic of Korea
- Smart Animal Bio Institute, Dankook University, Cheonan, 31116, Republic of Korea
| | - Yongsu Yang
- Department of Microbiology, College of Bio-Convergence, Dankook University, Cheonan, 31116, Republic of Korea
| | - Min-Sik Song
- BIO Institute, OPTOLANE Technologies Inc, Seongnam, South Korea
| | - Hee-Young Won
- BIO Institute, OPTOLANE Technologies Inc, Seongnam, South Korea
| | - Andrew T Han
- BIO Institute, OPTOLANE Technologies Inc, Seongnam, South Korea
| | - Songmi Kim
- Smart Animal Bio Institute, Dankook University, Cheonan, 31116, Republic of Korea.
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Ghorbani M, Namazi S, Dehghani M, Razi F, Khalvati B, Dehshahri A. Gene polymorphisms of TACR1 serve as the potential pharmacogenetic predictors of response to the neurokinin-1 receptor antagonist-based antiemetic regimens: a candidate-gene association study in breast cancer patients. Cancer Chemother Pharmacol 2024:10.1007/s00280-024-04661-9. [PMID: 38678150 DOI: 10.1007/s00280-024-04661-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Accepted: 02/20/2024] [Indexed: 04/29/2024]
Abstract
PURPOSE The current candidate gene association study aims to investigate tag SNPs from the TACR1 gene as pharmacogenetic predictors of response to the antiemetic guidelines-recommended, NK-1 receptor antagonist-based, triple antiemetic regimens. METHODS A set of eighteen tag SNPs of TACR1 were genotyped in breast cancer patients receiving anthracycline and cyclophosphamide (with/without docetaxel) applying real-time PCR-HRMA. Data analysis for 121 ultimately enrolled patients was initiated by defining haplotype blocks using PHASE v.2.1. The association of each tag SNP and haplotype alleles with failure to achieve the defined antiemetic regimen efficacy endpoints was tested using PLINK (v.1.9 and v.1.07, respectively) based on the logistic regression, adjusting for the previously known chemotherapy-induced nausea and vomiting (CINV) prognostic factors. All reported p-values were corrected using the permutation test (n = 100,000). RESULTS Four variants of rs881, rs17010730, rs727156, and rs3755462, as well as haplotypes containing the mentioned variants, were significantly associated with failure to achieve at least one of the defined efficacy endpoints. Variant annotation via in-silico studies revealed that the non-seed sequence variant, rs881, is located in the miRNA (hsa-miR-613) binding site. The other three variants or a variant in complete linkage disequilibrium with them overlap a region of high H3K9ac-promoter-like signature or regions of high enhancer-like signature in the brain or gastrointestinal tissue. CONCLUSION Playing an essential role in regulating TACR1 expression, gene polymorphisms of TACR1 serve as the potential pharmacogenetic predictors of response to the NK-1 receptor antagonist-based, triple antiemetic regimens. If clinically approved, modifying the NK-1 receptor antagonist dose leads to better management of CINV in risk-allele carriers.
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Affiliation(s)
- Marziyeh Ghorbani
- Department of Pharmaceutical Biotechnology, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Soha Namazi
- Research Center for Rational Use of Drugs, Tehran University of Medical Sciences (TUMS), Tehran, Iran
| | - Mehdi Dehghani
- Department of Hematology and Medical Oncology, Hematology Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Farideh Razi
- Metabolomics and Genomics Research Center, Endocrinology and Metabolism Molecular-Cellular Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Bahman Khalvati
- Cellular and Molecular Research Center, Yasuj University of Medical Sciences, Yasuj, Iran
- Biological Mass Spectrometry Center, Stony Brook Medicine, Stony Brook University, Stony Brook, NY, USA
| | - Ali Dehshahri
- Department of Pharmaceutical Biotechnology, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran.
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Alirezaei M, Mosawi SH, Afgar A, Zarean M, Movahhed TK, Abbasi V, Fotouhi-Ardakani R. Discrimination of human papillomavirus genotypes using innovative technique nested-high resolution melting. Sci Rep 2022; 12:13943. [PMID: 35977949 PMCID: PMC9382607 DOI: 10.1038/s41598-022-14730-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 06/13/2022] [Indexed: 11/09/2022] Open
Abstract
The prompt detection of human papillomavirus and discrimination of its genotypes by combining conventional methods in new molecular laboratories is essential to achieve the global call of eliminating cervical cancer. After predicting the melting temperature of an approximately 221 bp region of the L1 gene from different HPV genotypes by bioinformatics software, an innovative technique based on the nested- high resolution melting was designed with three approaches and using conventional PCR, qPCR, and diagnostic standards. HPV-positive samples identified by microarray along with diagnostic standards were evaluated by qPCR-HRM and discordant results were subjected to sequencing and analyzed in silico using reference types. In addition to screening for human papillomavirus, nested-qPCR-HRM is one of the modified HRM techniques which can discriminate some genotypes, including 6, 16, 18, 52, 59, 68 and 89. Despite the differences in diagnostic capabilities among HRM, microarray and sequencing, a number of similarities between HRM, and sequencing were diagnostically identified as the gold standard method. However, the bioinformatics analysis and melting temperature studies of the selected region in different HPV genotypes showed that it could be predicted. With numerous HPV genotypes and significant genetic diversity among them, determining the virus genotype is important. Therefore, our goal in this design was to use the specific molecular techniques with several specific primers to increase sensitivity and specificity for discriminating a wide range of HPV genotypes. This approach led to new findings to evaluate the ability of different approaches and procedures in accordance with bioinformatics.
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Affiliation(s)
- Melika Alirezaei
- Cellular and Molecular Research Center, Qom University of Medical Sciences, Qom, 3736175513, Iran
| | | | - Ali Afgar
- Research Center for Hydatid Disease in Iran, Kerman University of Medical Sciences, Kerman, Iran
| | - Mehdi Zarean
- Department of Parasitology and Mycology, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Tahereh Komeili Movahhed
- Cellular and Molecular Research Center, Qom University of Medical Sciences, Qom, 3736175513, Iran
| | - Vajiheh Abbasi
- Cellular and Molecular Research Center, Qom University of Medical Sciences, Qom, 3736175513, Iran
| | - Reza Fotouhi-Ardakani
- Cellular and Molecular Research Center, Qom University of Medical Sciences, Qom, 3736175513, Iran. .,Department of Medical Biotechnology, School of Medicine, Qom University of Medical Sciences, Qom, Iran.
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Smith RA, Lam AK. Single Nucleotide Polymorphisms in Papillary Thyroid Carcinoma: Clinical Significance and Detection by High-Resolution Melting. Methods Mol Biol 2022; 2534:149-159. [PMID: 35670974 DOI: 10.1007/978-1-0716-2505-7_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Single nucleotide polymorphisms (SNPs) can have a variety of implications for the progression and development of papillary thyroid carcinomas (PTCs). Identification of SNPs, either as germline variants or mutations occurring in tumor tissue, can thus have useful implications for patient management. There are many potential methods that can be used to identify a specific SNP or other genetic variant, and among these is high-resolution melting (HRM). HRM can be used to detect the presence of a genetic variant in a single sealed tube, involving undertaking a polymerase chain reaction (PCR) in the presence of a saturating intercalating dye. Once PCR is complete, the amplicons produced can be melted through incremental raising of the temperature and the genotype of individual samples determined by changes in the change in fluorescence as the fluorescent dye is released by the melting DNA. In this chapter, we detail a method for the genotyping of DNA samples using HRM.
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Affiliation(s)
- Robert A Smith
- Genomics Research Centre, Centre for Genomics and Personalised Health, Queensland University of Technology, Kelvin Grove, QLD, Australia.
- Cancer Molecular Pathology of School of Medicine and Dentistry, Menzies Health Institute Queensland, Griffith University, Gold Coast, QLD, Australia.
| | - Alfred K Lam
- Cancer Molecular Pathology of School of Medicine and Dentistry, Menzies Health Institute Queensland, Griffith University, Gold Coast, QLD, Australia
- Pathology Queensland, Gold Coast University Hospital, Southport, QLD, Australia
- Faculty of Medicine, University of Queensland, Herston, QLD, Australia
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6
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Riba FRG, Gomes MES, Rabelo NC, Zuma MCC, Llerena JC, Mencalha AL, Gonzalez S. High-Resolution Melting Analysis for Rapid Detection of Mutations in Patients with FGFR3-Related Skeletal Dysplasias. Genet Test Mol Biomarkers 2021; 25:674-682. [PMID: 34672771 DOI: 10.1089/gtmb.2020.0330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Background: Mutations in the fibroblast growth factor receptor 3 (FGFR3) gene are related to skeletal dysplasias (SDs): acondroplasia (ACH), hypochodroplasia (HCH) and type I (TDI) and II (TDII) tanatophoric dysplasias. This study was designed to standardize and implement a high-resolution melting (HRM) technique to identify mutations in patients with these phenotypes. Methods: Initially, FGFR3 gene segments from 84 patients were PCR amplified and subjected to Sanger sequencing. Samples from 29 patients positive for mutations were analyzed by HRM. Results: Twelve of the patients FGFR3 mutations had ACH (six g.16081 G > A, three g.16081 G > C and three g.16081 G > A + g.16002 C > T); thirteen of patients with HCH had FGFR3 mutations (eight g.17333 C > A, five g.17333 C > G and five were negative); and four patients with DTI had FGFR3 mutations (three g.13526 C > T and one g.16051G > T and two patients with DTII (presented mutation g.17852 A > G). When analyzing the four SDs altogether, an overlap of the dissociation curves was observed, making genotyping difficult. When analyzed separately, however, the HRM analysis method proved to be efficient for discriminating among the mutations for each SD type, except for those patients carrying additional polymorphism concomitant to the recurrent mutation. Conclusion: We conclude that for recurrent mutations in the FGFR3 gene, that the HRM technique can be used as a faster, reliable and less expensive genotyping routine for the diagnosis of these pathologies than Sanger sequencing.
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Affiliation(s)
- Fernanda Rolemberg G Riba
- Laboratório de Medicina Genômica and Centro de Genética Médica-Serviço de Referência em Doenças Raras/IFF/FIOCRUZ, Rio de Janeiro, Brasil
| | - Maria E S Gomes
- Laboratório de Medicina Genômica and Centro de Genética Médica-Serviço de Referência em Doenças Raras/IFF/FIOCRUZ, Rio de Janeiro, Brasil
| | - Natana Chaves Rabelo
- Laboratório de Medicina Genômica and Centro de Genética Médica-Serviço de Referência em Doenças Raras/IFF/FIOCRUZ, Rio de Janeiro, Brasil
| | - Maria Celia C Zuma
- Laboratório de Medicina Genômica and Centro de Genética Médica-Serviço de Referência em Doenças Raras/IFF/FIOCRUZ, Rio de Janeiro, Brasil
| | - Juan C Llerena
- Unidade de Genética Clínica, Centro de Genética Médica-Serviço de Referência em Doenças Raras/IFF/FIOCRUZ, Rio de Janeiro, Brasil
| | - André Luiz Mencalha
- Departamento de Biofísica e Biometria, Instituto de Biologia Roberto Alcântara Gomes, Universidade do Estado do Rio de Janeiro (UERJ), Rio de Janeiro, Brasil
| | - Sayonara Gonzalez
- Laboratório de Medicina Genômica and Centro de Genética Médica-Serviço de Referência em Doenças Raras/IFF/FIOCRUZ, Rio de Janeiro, Brasil
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Wang NY, Gama AB, Marin MV, Peres NA. Development of a Multiplex High-Throughput Diagnostic Assay for the Detection of Strawberry Crown Rot Diseases Using High-Resolution Melting Analysis. PHYTOPATHOLOGY 2021; 111:1470-1483. [PMID: 33754805 DOI: 10.1094/phyto-12-20-0556-r] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Rapid and accurate disease diagnosis is a prerequisite for an effective disease management program in strawberry production. In Florida, Colletotrichum spp., Phytophthora spp., and Macrophomina phaseolina are the primary microorganisms causing strawberry crown rot. Even though the diseases can be caused by different pathogens, symptoms are indistinguishable and equally devastating. To inform strawberry growers in a timely fashion of diagnostic results for effective deployment of chemical control practices, we developed a multiplex high-resolution melting (HRM) assay to rapidly and accurately detect the abovementioned pathogens. The multiplex HRM assays using three predesigned primer pairs showed high specificity for individual species by generating specific melting peaks without cross-reaction between primers or with other common strawberry pathogens. The amplification limit of the assay was 1 pg of Colletotrichum and Phytophthora and 100 pg of M. phaseolina DNA per 10-μl reaction. However, the presence of different melting peaks was observed in mixed DNA samples and was concentration and target DNA dependent. A crude DNA extraction protocol was developed to allow high-throughput screening by minimizing the inhibitory effects. Moreover, we applied the HRM assay to 522 plant samples and found high correlations between conventional pathogen isolation and HRM and between singleplex and multiplex assays. Altogether, this multiplex HRM assay is specific, cost effective, and reliable for the timely detection of strawberry crown rot pathogens.
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Affiliation(s)
- Nan-Yi Wang
- Gulf Coast Research and Education Center, Plant Pathology Department, Institute of Food and Agricultural Sciences, University of Florida, Wimauma, FL 33598
| | - Andre Bueno Gama
- Gulf Coast Research and Education Center, Plant Pathology Department, Institute of Food and Agricultural Sciences, University of Florida, Wimauma, FL 33598
| | - Marcus Vinicius Marin
- Gulf Coast Research and Education Center, Plant Pathology Department, Institute of Food and Agricultural Sciences, University of Florida, Wimauma, FL 33598
| | - Natalia A Peres
- Gulf Coast Research and Education Center, Plant Pathology Department, Institute of Food and Agricultural Sciences, University of Florida, Wimauma, FL 33598
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Comparison of high-resolution melting analysis with direct sequencing for detection of FLT3-TKD, FLT3-ITD and WT1 mutations in acute myeloid leukemia. Cancer Treat Res Commun 2021; 28:100432. [PMID: 34303121 DOI: 10.1016/j.ctarc.2021.100432] [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: 04/04/2021] [Revised: 05/28/2021] [Accepted: 07/06/2021] [Indexed: 11/20/2022]
Abstract
BACKGROUND Acute Myeloid Leukemia (AML) is a group of hematologic diseases characterized by a variety of clinically important genetic alterations. Genetic mutations affecting the FMS-like receptor tyrosine kinase-3 (FLT3) and Wilm's tumor (WT-1) genes are associated with poor prognosis in AML. In this work, efficiency of HRM method for detection of FLT3-ITD, FLT3-TKD, and WT-1 mutations was assessed in comparison with direct sequencing. METHOD A total of 58 formalin-fixed, paraffin-embedded BM biopsy specimens of AML patients were analyzed. Mutation detection was performed by HRM method and the results were consequently compared with direct sequencing RESULTS: FLT3 and WT-1 mutations were detected in 21 (36.2%) and 3 (5.17%) samples, respectively. Among all FLT3 mutations, 10 (17.2%) and 11 (18.2%) samples were harboring the FLT3-ITD and-TKD gene mutations, respectively. Frequency of the FLT3-ITD was not statistically different in females (51%) and males (49%). Also, FLT3-TKD was more common in males although the differences in gender distribution were not statistically significant (P = 0.721 and P = 0.626, respectively). CONCLUSIONS Regarded as the desirable characteristic, the present study is generally distinguished by the similar previous ones due to assessing the FFPE BM tissue from the perspective of the type of assessed sample. This discrepancy between our results and those in prior studies may be due to the disparity of the studied population size, adopted methods as well as the sample type. In this survey, regarding to low amount of extracted DNA from the paraffinized samples, the HRM method was efficient in determining the mentioned mutations.
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Neoadjuvant Chemotherapy of Triple-Negative Breast Cancer: Evaluation of Early Clinical Response, Pathological Complete Response Rates, and Addition of Platinum Salts Benefit Based on Real-World Evidence. Cancers (Basel) 2021; 13:cancers13071586. [PMID: 33808149 PMCID: PMC8036281 DOI: 10.3390/cancers13071586] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 03/25/2021] [Accepted: 03/26/2021] [Indexed: 12/17/2022] Open
Abstract
Simple Summary Neoadjuvant chemotherapy (NACT) is the standard treatment for early-stage triple-negative breast cancer (TNBC). Achieving pathological complete response (pCR) is considered an essential prognostic factor with favorable long-term outcomes. The administration of NACT regimens with platinum salts is associated with a higher pCR rate. However, with unclear treatment guidelines and at the expense of a higher incidence of adverse events. Identifying patients and circumstances in which the benefits of platinum NACT outweigh inconveniences is still an ongoing challenge. Considering early clinical response (ECR) after the initial standard NACT cycles together with other suitable predictors could be useful to decide about the administration of platinum salts in clinical practice. The results of this large single institutional retrospective study of consecutive patients showed the significant role of adding platinum salts in older patients with high-proliferative early responded tumors and persisted lymph nodes involvement regardless of BRCA1/2 status. Abstract Pathological complete response (pCR) achievement is undoubtedly the essential goal of neoadjuvant therapy for breast cancer, directly affecting survival endpoints. This retrospective study of 237 triple-negative breast cancer (TNBC) patients with a median follow-up of 36 months evaluated the role of adding platinum salts into standard neoadjuvant chemotherapy (NACT). After the initial four standard NACT cycles, early clinical response (ECR) was assessed and used to identify tumors and patients generally sensitive to NACT. BRCA1/2 mutation, smaller unifocal tumors, and Ki-67 ≥ 65% were independent predictors of ECR. The total pCR rate was 41%, the achievement of pCR was strongly associated with ECR (OR = 15.1, p < 0.001). According to multivariable analysis, the significant benefit of platinum NACT was observed in early responders ≥45 years, Ki-67 ≥ 65% and persisted lymph node involvement regardless of BRCA1/2 status. Early responders with pCR had a longer time to death (HR = 0.28, p < 0.001) and relapse (HR = 0.26, p < 0.001). The pCR was achieved in only 7% of non-responders. However, platinum salts favored non-responders’ survival outcomes without statistical significance. Toxicity was significantly often observed in patients with platinum NACT (p = 0.003) but not for grade 3/4 (p = 0.155). These results based on real-world evidence point to the usability of ECR in NACT management, especially focusing on the benefit of platinum salts.
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Xu X, Zheng J, Zou Q, Wang C, Zhang X, Wang X, Liu Y, Shu J. Rapid screening of UPB1 gene variations by high resolution melting curve analysis. Exp Ther Med 2021; 21:403. [PMID: 33692834 PMCID: PMC7938451 DOI: 10.3892/etm.2021.9834] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Accepted: 10/08/2020] [Indexed: 12/12/2022] Open
Abstract
The present study aimed to analyze gene mutations in patients with β-ureidopropinoase deficiency and establish a rapid detection method for β-ureidopropinoase (UPB1) pathogenic variations by high resolution melting (HRM) analysis. DNA samples with known UPB1 mutations in three patients with β-ureidopropinoase deficiency were utilized to establish a rapid detection method for UPB1 pathogenic variations by HRM analysis. Further rapid screening was performed on two patients diagnosed with β-ureidopropinoase deficiency and 50 healthy control individuals. The results showed that all known UPB1 gene mutations can be analyzed by a specially designed HRM assay. Each mutation has specific HRM profiles which could be used in rapid screening. The HRM method could correctly identify all genetic mutations in two children with β-ureidopropinoase deficiency. In addition, the HRM assay also recognized four unknown mutations. To conclude, the results support future studies of applying HRM analysis as a diagnostic approach for β-ureidopropinoase deficiency and a rapid screening method for UPB1 mutation carriers.
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Affiliation(s)
- Xiaowei Xu
- Tianjin Pediatric Research Institute, Tianjin Children's Hospital, Tianjin 300134, P.R. China.,Tianjin Key Laboratory of Prevention and Treatment of Birth Defects, Tianjin Children's Hospital, Tianjin 300134, P.R. China
| | - Jie Zheng
- Graduate College, Tianjin Medical University, Tianjin 300070, P.R. China
| | - Qianqian Zou
- Graduate College, Tianjin Medical University, Tianjin 300070, P.R. China
| | - Chao Wang
- Tianjin Pediatric Research Institute, Tianjin Children's Hospital, Tianjin 300134, P.R. China.,Tianjin Key Laboratory of Prevention and Treatment of Birth Defects, Tianjin Children's Hospital, Tianjin 300134, P.R. China
| | - Xinjie Zhang
- Tianjin Pediatric Research Institute, Tianjin Children's Hospital, Tianjin 300134, P.R. China.,Tianjin Key Laboratory of Prevention and Treatment of Birth Defects, Tianjin Children's Hospital, Tianjin 300134, P.R. China
| | - Xuetao Wang
- Tianjin Pediatric Research Institute, Tianjin Children's Hospital, Tianjin 300134, P.R. China.,Tianjin Key Laboratory of Prevention and Treatment of Birth Defects, Tianjin Children's Hospital, Tianjin 300134, P.R. China
| | - Yang Liu
- Department of Neonatology, Tianjin Children's Hospital, Tianjin 300134, P.R. China
| | - Jianbo Shu
- Tianjin Pediatric Research Institute, Tianjin Children's Hospital, Tianjin 300134, P.R. China.,Tianjin Key Laboratory of Prevention and Treatment of Birth Defects, Tianjin Children's Hospital, Tianjin 300134, P.R. China
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High Resolution Melting Analysis for Evaluation of mir-612 (Rs12803915) Genetic Variant with Susceptibility to Pediatric Acute Lymphoblastic Leukemia. Rep Biochem Mol Biol 2021; 9:385-393. [PMID: 33969131 DOI: 10.52547/rbmb.9.4.385] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Background Acute lymphoblastic leukemia (ALL) is a highly heterogeneous malignancy that accounts for nearly 75% of leukemias in children. While the exact mechanism of ALL is not fully understood, some genetic variants have been implicated as associated with ALL susceptibility. The association between some genetic variants in miRNA genes and ALL risk has been described previously. A previous study suggested that mir-612 rs12803915 G> A may be associated with pediatric ALL risk. High-resolution melting (HRM) analysis is a reliable method that can be applied for polymorphism detection. Methods This retrospective study was performed on 100 B-ALL patients (52 males and 48 females; age 4.6 ± 3.2 years) and 105 age- and sex-matched healthy controls (48 males and 57 females; age 5.1 ± 3 years). We used HRM to identify mir-612 rs12803915 genotypes. Sanger sequencing was applied to validate the HRM results. Results High resolution melting analysis was used to genotype the mir-612 rs12803915 polymorphism. We found no association between rs12803915 allele A and B-ALL risk in any inheritance models (p> 0.05). Conclusion HRM is a suitable method to detect SNP rs12803915 in the mir-612 gene; however, we found no significant association between the rs12803915 polymorphism and ALL risk.
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12
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Bidla G, Rosenblatt DS, Gilfix BM. Identification of Variants in Alpha-1-Antitrypsin by High Resolution Melting. J Appl Lab Med 2020; 6:715-728. [PMID: 33331634 DOI: 10.1093/jalm/jfaa191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Accepted: 09/28/2020] [Indexed: 11/14/2022]
Abstract
BACKGROUND Alpha-1-antitrypsin deficiency (AATD) is one of the most common hereditary disorders occurring in populations of European origin and is due to variants in SERPINA1, which encodes a protease inhibitor of neutrophil elastase, limiting lung damage from this enzyme. The World Health Organization has recommended that individuals with chronic obstructive pulmonary disease and asthma be tested for AATD. The development of inexpensive and simple genetic testing will help to meet this goal. METHODS Primers and synthetic SERPINA1 gene fragments (gBlocks) were designed for 5 AATD-associated variants. PCR was run on a CFX96 Thermal Cycler with High Resolution Melting (HRM) capacity and data analyzed using the supplied HRM-analysis software. Genomic DNA from individuals (n = 86) genotyped for the S and Z variants were used for validation. HRM-analysis was performed on 3 additional samples with low alpha-1-antitrypsin levels inconsistent with the genotype determined in our clinical laboratory. RESULTS Unique normalized melt curve and difference curve patterns were identified for the AAT variants Z, S, I, F, and MMalton using gBlocks. Similar curve shapes were seen when these primers were used to analyze the gDNA samples. HRM identified the genotypes of the gDNA correctly with 100% concordance. The curve shapes of some samples did not match the melting patterns of the targeted variant. Sequencing was used to identify the variants, including rare AATD variants c.1108_1115delinsAAAAACA (p.Glu370Lysfs*31) and c.1130dup (p.Leu377fs). CONCLUSION We developed a rapid and inexpensive HRM-analysis method for genotyping of Z, S, MMalton, I, and F variants that was also capable of detecting other variants.
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Affiliation(s)
- Gawa Bidla
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada
| | - David S Rosenblatt
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada.,Divisions of Medical Genetics, Department of Specialized Medicine, McGill University Health Centre, Montreal, Quebec, Canada.,Medical Biochemistry, Department of Specialized Medicine, McGill University Health Centre, Montreal, Quebec, Canada
| | - Brian M Gilfix
- Medical Biochemistry, Department of Specialized Medicine, McGill University Health Centre, Montreal, Quebec, Canada
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Ababneh M, Ababneh O, Al-Zghoul MB. High-resolution melting curve analysis for infectious bronchitis virus strain differentiation. Vet World 2020; 13:400-406. [PMID: 32367941 PMCID: PMC7183480 DOI: 10.14202/vetworld.2020.400-406] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Accepted: 01/13/2020] [Indexed: 11/19/2022] Open
Abstract
Background and Aim: Belonging to the Coronaviridae family, avian infectious bronchitis virus (IBV) causes respiratory, reproductive, and renal diseases in poultry. Preventative measures lie mainly in vaccination, while the gold standard for IBV classification and differentiation is based on the sequence analysis of the spike 1 (S1) gene. In this study, we tested a new assay for IBV strain classification that is less expensive and requires reduced time and effort to perform. We carried out a quantitative real-time polymerase chain reaction followed by high-resolution melting (qRT-PCR/HRM) curve analysis. Materials and Methods: In this study, qRT-PCR was conducted on a partial fragment S1 gene followed by a high resolution melting curve analysis (qRT-PCR/HRM) on 23 IBV-positive samples in Jordan. For this assay, we utilized the most common IBV vaccine strains (Mass and 4/91) as a reference in the HRM assay. To evaluate the discrimination power of the qRT-PCR/HRM, we did the sequencing of the partial S1 gene. Results: It was shown that HRM was able to classify IBV samples into four clusters based on the degree of similarity between their melting points: The first cluster exhibited the highest similarity to the 4/91 strain, while the second was similar to the Mass-related IBV strain. Although the third cluster contained the highest number of samples, it displayed no similarity to any of the reference vaccine strains, and, after comparing them with the sequencing results, we found that the samples in the third cluster were similar to the variant II-like (IS-1494-06) IBV field strain. Finally, the fourth cluster comprised one unique sample that was found to belong to the Q1 IBV strain. Conclusion: Our developed qRT-PCR/HRM curve analysis was able to detect and rapidly identify novel and vaccine-related IBV strains as confirmed by S1 gene nucleotide sequences, making it a rapid and cost-effective tool.
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Affiliation(s)
- Mustafa Ababneh
- Department of Basic Medical Veterinary Sciences, Jordan University of Science and Technology, Irbid 22110, Jordan
| | - Ola Ababneh
- Department of Basic Medical Veterinary Sciences, Jordan University of Science and Technology, Irbid 22110, Jordan
| | - Mohammad Borhan Al-Zghoul
- Department of Basic Medical Veterinary Sciences, Jordan University of Science and Technology, Irbid 22110, Jordan
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Diagnosis of genetic amyloidosis through the analysis of transthyretin gene mutation using high-resolution melting. Int J Cardiol 2020; 301:220-225. [PMID: 31740141 DOI: 10.1016/j.ijcard.2019.10.028] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/09/2019] [Revised: 10/09/2019] [Accepted: 10/15/2019] [Indexed: 01/22/2023]
Abstract
Transthyretin amyloidosis can be either the wild-type (ATTR-wt) or the hereditary form (ATTR-m) with autosomal dominant inheritance. ATTR seems to be an underdiagnosed disease, despite now being recognized as one of the most frequent causes of heart failure (HF) with preserved ejection fraction. The confirmation of diagnosis includes a genetic analysis as a critical step to distinguish between ATTR-wt and hereditary amyloidosis. The present study aimed to evaluate the potential application of High-Resolution Melting (HRM) analysis for identifying gene mutations in patients with suspected ATTR-m. We have adapted and validated the use of HRM for TTR mutations. We, therefore, sequenced the TTR gene and used HRM in a group of 134 patients suspected of suffering from amyloidosis. Seven patients were diagnosed with mutations in the TTR gene (p.Glu74Gln, heterozygous p.Val142Ile, and homozygous p.Val142Ile). HRM is capable of clearly detecting these TTR mutations, including the heterozygous and homozygous variants. The results show a 100% correlation between the HRM study and TTR sequencing. These results support future studies of applying HRM analysis as a diagnostic approach for ATTR-m, mainly for epidemiological studies.
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15
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Yang MJ, Hou YL, Yang XL, Wang CX, Zhi LX, You CG. Development and application of a PCR-HRM molecular diagnostic method of SNPs linked with TNF inhibitor efficacy. ACTA ACUST UNITED AC 2020; 6:277-286. [PMID: 30511928 DOI: 10.1515/dx-2018-0062] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Accepted: 10/03/2018] [Indexed: 01/21/2023]
Abstract
Background Clinical evidence indicates that genetic variations may interfere with the mechanism of drug action. Recently, it has been reported that the single nucleotide polymorphisms (SNPs) of STAT4, PTPN2, PSORS1C1 and TRAF3IP2RA genes are associated with the clinical efficacy of tumor necrosis factor (TNF) inhibitors in the treatment of rheumatoid arthritis (RA) patients. Therefore, the detection of the SNPs linked with TNF inhibitor efficacy may provide an important basis for the treatment of RA. This study intended to establish molecular diagnostic methods for genotyping the linked SNPs based on high resolution melting (HRM) curve analysis. Methods The polymerase chain reaction-HRM (PCR-HRM) curve analysis detecting systems were established by designing the primers of the four SNPs, rs7574865G>T, rs7234029A>G, rs2233945C>A and rs33980500C>T, and the performance and clinical applicability of which were evaluated by using the Sanger sequencing method and genotyping test for 208 clinical samples. Results The self-developed molecular diagnostic methods of PCR-HRM were confirmed to be able to correctly genotype the four SNPs, the sensitivity and specificity of which were 100% in this study. The repeatability and reproducibility tests showed that there is little variable in intra-assay and inter-assay (the coefficient of variation ranged from 0.01% to 0.07%). The slight changes of DNA template and primer concentrations, PCR cycle number and reaction system volume had no significant effect on the genotyping performance of the method. The PCR-HRM assays were also applied to other PCR thermocyclers with HRM function and use different saturation fluorescent dyes. Conclusions The PCR-HRM genotyping method established in this study can be applied to the routine molecular diagnosis of rs7574865, rs7234029, rs2233945 and rs33980500.
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Affiliation(s)
- Mei-Juan Yang
- Department of Clinical Laboratory, Lanzhou University Second Hospital, Lanzhou, Gansu, P.R. China
| | - Yan-Long Hou
- Department of Clinical Laboratory, Lanzhou University Second Hospital, Lanzhou, Gansu, P.R. China
| | - Xiao-Lan Yang
- Department of Clinical Laboratory, The First People's Hospital of Baiyin, Baiyin, P.R. China
| | - Chun-Xia Wang
- Department of Clinical Laboratory, The First People's Hospital of Lanzhou City, Lanzhou, P.R. China
| | - Li-Xia Zhi
- Department of Clinical Laboratory, The Second People's Hospital of Lanzhou City, Lanzhou, P.R. China
| | - Chong-Ge You
- Department of Clinical Laboratory, Lanzhou University Second Hospital, Lanzhou, No. 82 Cuiyingmen Road, Lanzhou, Gansu, 730000, P.R. China, Phone: +86-0931-8943093
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16
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Ariza MJ, Pérez-López C, Almagro F, Sánchez-Tévar AM, Muñiz-Grijalvo O, Álvarez-Sala Walter LA, Rioja J, Sánchez-Chaparro MÁ, Valdivielso P. Genetic variants in the LPL and GPIHBP1 genes, in patients with severe hypertriglyceridaemia, detected with high resolution melting analysis. Clin Chim Acta 2019; 500:163-171. [PMID: 31669931 DOI: 10.1016/j.cca.2019.10.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Revised: 10/02/2019] [Accepted: 10/14/2019] [Indexed: 12/30/2022]
Abstract
INTRODUCTION Pathogenic variants in lipoprotein lipase (LPL) and glycosylphosphatidylinositol-anchored high-density lipoprotein-binding protein 1 (GPIHBP1) have been described in patients with severe hypertriglyceridaemia. We aimed to optimise high resolution melting (HRM) assays to detect the presence of functional variants in these genes. METHODS One hundred and sixteen patients with severe hypertriglyceridaemia were studied. HRM assays were optimised to scan exons and splice junctions in LPL and GPIHBP1. Sanger sequencing was the reference method. Next-generation-sequencing (NGS) was performed in five patients, including one with Familial Chylomicronemia syndrome (FCS). RESULTS We identified 15 different variants in LPL and 6 in GPIHBP1. The variants revealed with NGS were also detected with HRM, including a rare premature stop codon in LPL (p.Trp421*) and two LPL pathogenic variants in the patient with FCS (p.His80Arg + p.Gly215Glu). Having multiple functional variant alleles was associated with pancreatitis onset at younger ages and higher baseline triglycerides. CONCLUSIONS Our HRM assays detected the presence of functional gene variants that were confirmed with Sanger and NGS sequencing. The presence of multiple functional variant alleles was associated with differences in the clinical profile. Therefore, these assays represent a reliable, cost-effective tool that can be used to complement the NGS approach for gene scanning.
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Affiliation(s)
- María José Ariza
- Department of Medicine and Dermatology, Lipids and Atherosclerosis Laboratory, Centro de Investigaciones Médico Sanitarias (CIMES), Instituto de Investigación Biomédica de Málaga (IBIMA), University of Málaga, C/Marqués de Beccaria n° 3, 29010 Málaga, Spain.
| | - Carmen Pérez-López
- Internal Medicine Unit, University Hospital Virgen de la Victoria, Campus de Teatinos, S/N, 29010 Málaga, Spain
| | - Fátima Almagro
- Lipids Unit, Internal Medicine, University Hospital Donostia, San Sebastian, Begiristain Doktorea Pasealekua, 107-115, 20014 Donostia, Gipuzkoa, Spain
| | - Ana María Sánchez-Tévar
- Department of Medicine and Dermatology, Lipids and Atherosclerosis Laboratory, Centro de Investigaciones Médico Sanitarias (CIMES), Instituto de Investigación Biomédica de Málaga (IBIMA), University of Málaga, C/Marqués de Beccaria n° 3, 29010 Málaga, Spain
| | - Ovidio Muñiz-Grijalvo
- UCERV-UCAMI, Internal Medicine Department, University Hospital Virgen del Rocío, Av. Manuel Siurot, S/n, 41013 Sevilla, Spain
| | - Luis Antonio Álvarez-Sala Walter
- Lipids Unit, Internal Medicine, Hospital General Universitario Gregorio Marañón, IiSGM, Calle del Dr. Esquerdo, 46, 28007 Madrid, Spain; Department of Medicine, School of Medicine, Universidad Complutense, Av. Séneca, 2, 28040 Madrid, Spain
| | - José Rioja
- Department of Medicine and Dermatology, Lipids and Atherosclerosis Laboratory, Centro de Investigaciones Médico Sanitarias (CIMES), Instituto de Investigación Biomédica de Málaga (IBIMA), University of Málaga, C/Marqués de Beccaria n° 3, 29010 Málaga, Spain
| | - Miguel Ángel Sánchez-Chaparro
- Department of Medicine and Dermatology, Lipids and Atherosclerosis Laboratory, Centro de Investigaciones Médico Sanitarias (CIMES), Instituto de Investigación Biomédica de Málaga (IBIMA), University of Málaga, C/Marqués de Beccaria n° 3, 29010 Málaga, Spain; Internal Medicine Unit, University Hospital Virgen de la Victoria, Campus de Teatinos, S/N, 29010 Málaga, Spain
| | - Pedro Valdivielso
- Department of Medicine and Dermatology, Lipids and Atherosclerosis Laboratory, Centro de Investigaciones Médico Sanitarias (CIMES), Instituto de Investigación Biomédica de Málaga (IBIMA), University of Málaga, C/Marqués de Beccaria n° 3, 29010 Málaga, Spain; Internal Medicine Unit, University Hospital Virgen de la Victoria, Campus de Teatinos, S/N, 29010 Málaga, Spain
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17
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Chen SW, Shen WC, Chen WTL, Hsieh TC, Yen KY, Chang JG, Kao CH. Metabolic Imaging Phenotype Using Radiomics of [ 18F]FDG PET/CT Associated with Genetic Alterations of Colorectal Cancer. Mol Imaging Biol 2019; 21:183-190. [PMID: 29948642 DOI: 10.1007/s11307-018-1225-8] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
PURPOSE To understand the association between genetic mutations and radiomics of 2-deoxy-2-[18F]fluoro-D-glucose ([18F]FDG) positron emission tomography (PET)/x-ray computed tomography (CT) in patients with colorectal cancer (CRC). PROCEDURES This study included 74 CRC patients who had undergone preoperative [18F]FDG PET/CT. A total of 65 PET/CT-related features including intensity, volume-based, histogram, and textural features were calculated. High-resolution melting methods were used for genetic mutation analysis. RESULTS Genetic mutants were found in 21 KRAS tumors (28 %), 31 TP53 tumors (42 %), and 17 APC tumors (23 %). Tumors with a mutated KRAS had an increased value at the 25th percentile of maximal standardized uptake value (SUVmax) within their metabolic tumor volume (MTV) (P < .0001; odds ratio [OR] 1.99; 95 % confidence interval [CI] 1.37-2.90) and their contrast from the gray-level cooccurrence matrix (P = .005; OR 1.52; 95 % CI 1.14-2.04). A mutated TP53 was associated with an increased value of short-run low gray-level emphasis derived from the gray-level run length matrix (P = .001; OR 243006.0; 95 % CI 59.2-996,872,313). APC mutants exhibited lower low gray-level zone emphasis derived from the gray-level zone length matrix (P = .006; OR < .0001; 95 % CI 0.000-0.22). CONCLUSION PET/CT-derived radiomics can provide supplemental information to determine KRAS, TP53, and APC genetic alterations in CRC.
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Affiliation(s)
- Shang-Wen Chen
- Department of Radiation Oncology, China Medical University Hospital, Taichung, Taiwan.,Graduate Institute of Clinical Medical Science, School of Medicine, College of Medicine, China Medical University, No. 2, Yuh-Der Road, Taichung, 404, Taiwan.,Department of Radiology, School of Medicine, Taipei Medical University, Taipei, Taiwan
| | - Wei-Chih Shen
- Department of Computer Science and Information Engineering, Asia University, Taichung, Taiwan
| | - William Tzu-Liang Chen
- Graduate Institute of Clinical Medical Science, School of Medicine, College of Medicine, China Medical University, No. 2, Yuh-Der Road, Taichung, 404, Taiwan.,Department of Surgery, China Medical University Hospital, Taichung, Taiwan
| | - Te-Chun Hsieh
- Department of Nuclear Medicine and PET Center, China Medical University Hospital, Taichung, Taiwan.,Department of Biomedical Imaging and Radiological Science, China Medical University, Taichung, Taiwan
| | - Kuo-Yang Yen
- Department of Nuclear Medicine and PET Center, China Medical University Hospital, Taichung, Taiwan.,Department of Biomedical Imaging and Radiological Science, China Medical University, Taichung, Taiwan
| | - Jan-Gowth Chang
- Graduate Institute of Clinical Medical Science, School of Medicine, College of Medicine, China Medical University, No. 2, Yuh-Der Road, Taichung, 404, Taiwan.,Department of Laboratory Medicine, Chine Medical University Hospital, Taichung, Taiwan
| | - Chia-Hung Kao
- Graduate Institute of Clinical Medical Science, School of Medicine, College of Medicine, China Medical University, No. 2, Yuh-Der Road, Taichung, 404, Taiwan. .,Department of Nuclear Medicine and PET Center, China Medical University Hospital, Taichung, Taiwan. .,Department of Bioinformatics and Medical Engineering, Asia University, Taichung, Taiwan.
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Darvishi FZ, Boroumand F, Saadat M. Genotyping of a 50 bp insertion/deletion genetic variation at promoter region of the superoxide dismutase 1 (SOD1) using high resolution melting analysis. GENE REPORTS 2019. [DOI: 10.1016/j.genrep.2019.100367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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19
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Buddhachat K, Chontananarth T. Is species identification of Echinostoma revolutum using mitochondrial DNA barcoding feasible with high-resolution melting analysis? Parasitol Res 2019; 118:1799-1810. [PMID: 31028468 DOI: 10.1007/s00436-019-06322-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Accepted: 04/09/2019] [Indexed: 01/22/2023]
Abstract
The taxonomic evaluation of Echinostoma species is controversial. Echinostoma species are recognized as complex, leading to problems associated with accurate identification of these species. The aim of this study was to test the feasibility of using DNA barcoding of cytochrome c oxidase subunit I (COI) and NADH dehydrogenase subunit 1 (ND1) conjugated with high-resolution melting (HRM) analysis to identify Echinostoma revolutum. HRM using COI and ND1 was unable to differentiate between species in the "revolutum complex" but did distinguish between two isolates of 37-collar-spined echinostome species, including E. revolutum (Asian lineage) and Echinostoma sp. A from different genera, e.g., Hypoderaeum conoideum, Haplorchoides mehrai, Fasciola gigantica, and Thapariella anastomusa, based on the Tm values derived from HRM analysis. Through phylogenetic analysis, a new clade of the cryptic species known as Echinostoma sp. A was identified. In addition, we found that the E. revolutum clade of ND1 phylogeny obtained from the Thailand strain was from a different lineage than the Eurasian lineage. These findings reveal the complexity of the clade, which is composed of 37-collar-spined echinostome species found in Southeast Asia. Taken together, the systematic aspects of the complex revolutum group are in need of extensive investigation by integrating morphological, biological, and molecular features in order to clarify them, particularly in Southeast Asia.
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Affiliation(s)
- Kittisak Buddhachat
- Department of Biology, Faculty of Science, Naresuan University, Phitsanulok, 65000, Thailand.,Excellence Center in Veterinary Biosciences, Chiang Mai University, Chiang Mai, 50200, Thailand
| | - Thapana Chontananarth
- Applied Parasitology Research Laboratory, Department of Biology, Faculty of Science, Srinakharinwirot University, Bangkok, 10110, Thailand. .,Center of Excellence in Animal, Plant and Parasite Biotechnology, Srinakharinwirot University, Bangkok, 10110, Thailand.
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20
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De Bonis M, De Paolis E, Scaglione GL, Fania L, Lavieri MM, Mazzanti C, Di Zenzo G, Minucci A, Capoluongo E. High-resolution melting analysis to screen the ST18 gene functional risk variant for pemphigus vulgaris: The occasion to open a debate on its usefulness in clinical setting. Exp Mol Pathol 2019; 108:57-63. [PMID: 30926339 DOI: 10.1016/j.yexmp.2019.03.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Accepted: 03/25/2019] [Indexed: 01/09/2023]
Abstract
The ST18 -497-65050 T > C polymorphisms (rs17315309) exhibit a very strong association in the pathogenesis of Pemphigus Vulgaris (PV) and could represent a new potential molecular target for the treatment of disease. The present study aimed to establish a low-cost, sensitive and reliable assay using high-resolution melting curve analysis (HRMA) on magnetic induction rotor-based platform, the Magnetic Induction Cycler (MIC) (Bio molecular Systems). HRMA assay was able to identify easily and unambiguously the c.-497-65050 T > C genotypes evaluating melting curve shape and melting temperature (Tm). The results of HRMA were validated by direct DNA sequencing. The HRMA is rapid, sensitive, low-cost and high-throughput assay to screen the rs17315309 variant and could be used in clinical diagnostic laboratories.
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Affiliation(s)
- Maria De Bonis
- UOC Laboratory Medicine, Genetics and Toxicology, IDI IRCCS, Fondazione Luigi Maria Monti, Via Monti di Creta 104, Rome, Italy; Polo Scienze per Immagini, di Laboratorio e Infettivologiche, "Fondazione Policlinico Agostino Gemelli" - IRCCS, Rome, Italy.
| | - Elisa De Paolis
- UOC Laboratory Medicine, Genetics and Toxicology, IDI IRCCS, Fondazione Luigi Maria Monti, Via Monti di Creta 104, Rome, Italy; Polo Scienze per Immagini, di Laboratorio e Infettivologiche, "Fondazione Policlinico Agostino Gemelli" - IRCCS, Rome, Italy
| | - Giovanni Luca Scaglione
- UOC Laboratory Medicine, Genetics and Toxicology, IDI IRCCS, Fondazione Luigi Maria Monti, Via Monti di Creta 104, Rome, Italy
| | - Luca Fania
- Department of Dermatology - IDI IRCCS, Fondazione Luigi Maria Monti, Via Monti di Creta 104, Rome, Italy
| | | | - Cinzia Mazzanti
- Department of Dermatology - IDI IRCCS, Fondazione Luigi Maria Monti, Via Monti di Creta 104, Rome, Italy
| | - Giovanni Di Zenzo
- Molecular and Cell Biology Laboratory IDI-IRCCS, FLMM, Fondazione Luigi Maria Monti, Via Monti di Creta 104, Rome, Italy
| | - Angelo Minucci
- Polo Scienze per Immagini, di Laboratorio e Infettivologiche, "Fondazione Policlinico Agostino Gemelli" - IRCCS, Rome, Italy
| | - Ettore Capoluongo
- UOC Laboratory Medicine, Genetics and Toxicology, IDI IRCCS, Fondazione Luigi Maria Monti, Via Monti di Creta 104, Rome, Italy; Polo Scienze per Immagini, di Laboratorio e Infettivologiche, "Fondazione Policlinico Agostino Gemelli" - IRCCS, Rome, Italy.
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Liu Z, Bingga G, Zhang C, Shao J, Shen H, Sun J, Zhang J. Application of Duplex Fluorescence Melting Curve Analysis (FMCA) to Identify Canine Parvovirus Type 2 Variants. Front Microbiol 2019; 10:419. [PMID: 30891024 PMCID: PMC6411689 DOI: 10.3389/fmicb.2019.00419] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Accepted: 02/18/2019] [Indexed: 11/15/2022] Open
Abstract
Canine parvovirus (CPV-2) is an enteric virus causing morbidity and mortality in dogs worldwide. Since CPV-2 emerged as canine pathogen, the original CPV-2 strain has constantly evolved, and its primary variants (CPV-2a, CPV-2b, and CPV-2c) co-circulate to varying extents in canine populations worldwide. Thus, rapid and accurate laboratory diagnoses of CPV-2 variants are crucial to monitor CPV-2 evolution. Conventional methods for CPV-2 genotyping are laborious, time consuming, and determining the genotype of a CPV-2 variant often requires two or more reaction tubes. The present study developed a probe-based fluorescence melting curve analysis (FMCA) for genotyping six different CPV-2 variants (original CPV-2, CPV-2a, CPV-2b, CPV-2c, and vaccine strains of CPVpf and CPVint) in a single reaction tube using only two TaqMan probes. One of the TaqMan probes (FAM labeled) was designed to perfectly match with the target sequence of CPV-2a, this probe allows a 1-bp mismatched hybridization with the CPV-2b VP2 gene region (A4062G), and a 2-bp mismatched hybridization for CPV-2c (A4062G and T4064A); Another TaqMan probe (HEX labeled) was produced to perfectly match with the target sequence of original CPV-2, this probe enables 1-bp mismatched hybridization with the other CPV-2 variants (A3045T). Using the two TaqMan probes, all six CPV-2 variants were readily distinguished by their respective melting temperature values in a single reaction tube. The detection limits of this assay were 1–10 copies per reaction for six CPV-2 construction plasmids and no cross reactions were observed with several other common canine viruses. In this assay, co-infected samples were also directly identified via probe-based FMCA without using a mixing control; only a pure control is required. The clinical evaluation of this assay was demonstrated by analyzing 83 clinical fecal samples, among which 41 (49.39%), 8 (9.63%), and 14 (16.87%) samples were found to be positive for CPV-2a, CPV-2b, and CPV-2c, respectively. The concordance rate between probe-based FMCA and Sanger sequencing was 100%. Thus, the duplex FMCA is effective, rapid, simple, high-throughput, and straightforward for genotyping CPV-2 variants, and is useful to effectively diagnose and monitor CPV-2 epidemiology.
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Affiliation(s)
- Zhicheng Liu
- Scientific Observation and Experiment Station of Veterinary Drugs and Diagnostic Techniques of Guangdong Province, Ministry of Agriculture, Key Laboratory of Livestock Disease Prevention of Guangdong Province, Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Gali Bingga
- Vocational and Technical College of Inner Mongolia Agricultural University, Baotou, China
| | - Chunhong Zhang
- Scientific Observation and Experiment Station of Veterinary Drugs and Diagnostic Techniques of Guangdong Province, Ministry of Agriculture, Key Laboratory of Livestock Disease Prevention of Guangdong Province, Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Junjie Shao
- Changzhou Wumu Animal Hospital, Changzhou, China
| | - Haiyan Shen
- Scientific Observation and Experiment Station of Veterinary Drugs and Diagnostic Techniques of Guangdong Province, Ministry of Agriculture, Key Laboratory of Livestock Disease Prevention of Guangdong Province, Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Junying Sun
- Scientific Observation and Experiment Station of Veterinary Drugs and Diagnostic Techniques of Guangdong Province, Ministry of Agriculture, Key Laboratory of Livestock Disease Prevention of Guangdong Province, Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Jianfeng Zhang
- Scientific Observation and Experiment Station of Veterinary Drugs and Diagnostic Techniques of Guangdong Province, Ministry of Agriculture, Key Laboratory of Livestock Disease Prevention of Guangdong Province, Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Guangzhou, China
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Fakhri O, Hartley CA, Devlin JM, Browning GF, Noormohammadi AH, Lee SW. Development and application of high-resolution melting analysis for the classification of infectious laryngotracheitis virus strains and detection of recombinant progeny. Arch Virol 2018; 164:427-438. [PMID: 30421085 PMCID: PMC6373279 DOI: 10.1007/s00705-018-4086-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Accepted: 10/15/2018] [Indexed: 12/15/2022]
Abstract
Live attenuated vaccines against infectious laryngotracheitis virus (ILTV) are widely used in the poultry industry to control disease and help prevent economic losses. Molecular epidemiological studies of currently circulating strains of ILTV within poultry flocks in Australia have demonstrated the presence of highly virulent viruses generated by genomic recombination events between vaccine strains. In this study, high-resolution melting (HRM) analysis was used to develop a tool to classify ILTV isolates and to investigate ILTV recombination. The assay was applied to plaque-purified progeny viruses generated after co-infection of chicken embryo kidney (CEK) monolayers with the A20 and Serva ILT vaccine strains and also to viruses isolated from field samples. The results showed that the HRM analysis is a suitable tool for the classification of ILTV isolates and can be used to detect recombination between ILTV vaccine strains in vitro. This method can be used to classify a broad range of ILTV strains to facilitate the classification and genotyping of ILTV and help to further understand recombination in these viruses.
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Affiliation(s)
- Omid Fakhri
- Asia-Pacific Centre for Animal Health, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC, Australia.
| | - Carol A Hartley
- Asia-Pacific Centre for Animal Health, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC, Australia
| | - Joanne M Devlin
- Asia-Pacific Centre for Animal Health, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC, Australia
| | - Glenn F Browning
- Asia-Pacific Centre for Animal Health, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC, Australia
| | - Amir H Noormohammadi
- Asia-Pacific Centre for Animal Health, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Werribee, VIC, Australia
| | - Sang-Won Lee
- Asia-Pacific Centre for Animal Health, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC, Australia.,College of Veterinary Medicine, Konkuk University, Seoul, Republic of Korea
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Ceri A, Pavic M, Horvat I, Radic Antolic M, Zadro R. Development and validation of a rapid method for genotyping three P-selectin gene polymorphisms based on high resolution melting analysis. J Clin Lab Anal 2018; 33:e22698. [PMID: 30350887 DOI: 10.1002/jcla.22698] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Revised: 09/21/2018] [Accepted: 09/25/2018] [Indexed: 01/13/2023] Open
Abstract
BACKGROUND High resolution melting (HRM) analysis is one of the newer, reliable, and sensitive genotyping techniques, which offers considerable time and cost savings. P-selectin is an adhesion molecule that has a role in the initial phases of leukocyte adhesion to stimulated platelets and endothelial cells in inflammation. Multiple polymorphisms in P-selectin gene (SELP) that affect the protein sequence have been described. The aim of this study was to design, optimize, and validate a simple and rapid in-house HRM-based method for genotyping the NM_003005.3:c.992G>A (c.992G>A), NM_003005.3:c.1918G>T (c.1918G>T), and NM_003005.3:c.2266A>C (c.2266A>C) SELP polymorphisms. METHODS Initial genotyping of three SELP polymorphisms was performed by applying polymerase chain reaction (PCR) with sequence-specific primers (SSP), which was used as a reference method for determination of analytical sensitivity. PCR-HRM was performed with primers for c.2266A>C reported in the literature. Primers for the remaining two polymorphisms were designed using Primer-BLAST. Precision testing was performed using three samples with different genotypes. For accuracy, analytical sensitivity and specificity testing, 20 wild type, 10 heterozygous, and 10 homozygous samples were chosen per polymorphism. Results were expressed as percentage of concordance with the acceptability criterion ≥95%. RESULTS Agreement of results was 100% for all validation parameters except for analytical sensitivity for c.1918G>T and c.2266A>C, with agreement of 90%. Repeated analysis using both methods revealed an error in initial genotyping and correct genotyping by PCR-HRM, which was confirmed by Sanger sequencing. CONCLUSION The validation confirmed PCR-HRM as a precise, accurate, and specific method for genotyping the c.992G>A, c.1918G>T, and c.2266A>C SELP polymorphisms.
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Affiliation(s)
- Andrea Ceri
- Faculty of Pharmacy and Biochemistry, Department of Medical Biochemistry and Haematology, University of Zagreb, Zagreb, Croatia
| | - Marina Pavic
- Clinical Institute of Chemistry, Department of Laboratory Diagnostics in Traumatology and Orthopaedics, Sestre milosrdnice University Hospital Centre, Zagreb, Croatia
| | - Ivana Horvat
- Department of Laboratory Diagnosis, Zagreb University Hospital Centre, Zagreb, Croatia
| | | | - Renata Zadro
- Faculty of Pharmacy and Biochemistry, Department of Medical Biochemistry and Haematology, University of Zagreb, Zagreb, Croatia.,Department of Laboratory Diagnosis, Zagreb University Hospital Centre, Zagreb, Croatia
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Nettore IC, Desiderio S, De Nisco E, Cacace V, Albano L, Improda N, Ungaro P, Salerno M, Colao A, Macchia PE. High-resolution melting analysis (HRM) for mutational screening of Dnajc17 gene in patients affected by thyroid dysgenesis. J Endocrinol Invest 2018; 41:711-717. [PMID: 29159607 DOI: 10.1007/s40618-017-0795-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Accepted: 11/14/2017] [Indexed: 02/01/2023]
Abstract
BACKGROUND Congenital hypothyroidism is a frequent disease occurring with an incidence of about 1/1500 newborns/year. In about 75% of the cases, CH is caused by alterations in thyroid morphogenesis, defined "thyroid dysgenesis" (TD). TD is generally a sporadic disease but in about 5% of the cases a genetic origin has been demonstrated. Previous studies indicate that Dnajc17 as a candidate modifier gene for hypothyroidism, since it is expressed in the thyroid bud, interacts with NKX2.1 and PAX8 and it has been associated to the hypothyroid phenotype in mice carrying a single Nkx2.1 and Pax8 genes (double heterozygous knock-out). PURPOSE The work evaluates the possible involvement of DNAJC17 in the pathogenesis of TD. METHODS High-resolution DNA melting analysis (HRM) and direct sequencing have been used to screen for mutations in the DNAJC17 coding sequence in 89 patients with TD. RESULTS Two mutations have been identified in the coding sequence of DNAJC17 gene, one in exon 5 (c.350A>C; rs79709714) and one in exon 9 (c.610G>C; rs117485355). The last one is a rare variant, while the rs79709714 is a polymorphism. Both are present in databases and the frequency of the alleles is not different between TD patients and controls. CONCLUSIONS DNAJC17 mutations are not frequently present in patients with TD.
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Affiliation(s)
- I C Nettore
- Dipartimento di Medicina Clinica e Chirurgia, Università degli Studi di Napoli "Federico II", Via S. Pansini, 5, 80131, Naples, Italy
| | - S Desiderio
- Dipartimento di Medicina Clinica e Chirurgia, Università degli Studi di Napoli "Federico II", Via S. Pansini, 5, 80131, Naples, Italy
| | - E De Nisco
- Dipartimento di Medicina Clinica e Chirurgia, Università degli Studi di Napoli "Federico II", Via S. Pansini, 5, 80131, Naples, Italy
| | - V Cacace
- Dipartimento di Medicina Clinica e Chirurgia, Università degli Studi di Napoli "Federico II", Via S. Pansini, 5, 80131, Naples, Italy
- TIGEM, Via Campi Flegrei 34, 80078, Pozzuoli, NA, Italy
| | - L Albano
- Dipartimento di Scienze Mediche Traslazionali, Università degli Studi di Napoli "Federico II", Via S. Pansini, 5, 80131, Naples, Italy
| | - N Improda
- Dipartimento di Scienze Mediche Traslazionali, Università degli Studi di Napoli "Federico II", Via S. Pansini, 5, 80131, Naples, Italy
| | - P Ungaro
- IEOS, Istituto per l'Endocrinologia e l'Oncologia Sperimentale, "Gaetano Salvatore" Consiglio Nazionale delle Ricerche, Via S. Pansini, 5, 80131, Naples, Italy
| | - M Salerno
- Dipartimento di Scienze Mediche Traslazionali, Università degli Studi di Napoli "Federico II", Via S. Pansini, 5, 80131, Naples, Italy
| | - A Colao
- Dipartimento di Medicina Clinica e Chirurgia, Università degli Studi di Napoli "Federico II", Via S. Pansini, 5, 80131, Naples, Italy
| | - P E Macchia
- Dipartimento di Medicina Clinica e Chirurgia, Università degli Studi di Napoli "Federico II", Via S. Pansini, 5, 80131, Naples, Italy.
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De Paolis E, Minucci A, De Bonis M, Scaglione GL, Gervasoni J, Primiano A, Ferraro PM, Cappellani D, Marcocci C, Gambaro G, Capoluongo E. A rapid screening of a recurrent CYP24A1 pathogenic variant opens the way to molecular testing for Idiopathic Infantile Hypercalcemia (IIH). Clin Chim Acta 2018; 482:8-13. [PMID: 29574006 DOI: 10.1016/j.cca.2018.03.024] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2018] [Revised: 03/09/2018] [Accepted: 03/20/2018] [Indexed: 12/18/2022]
Abstract
INTRODUCTION Loss-of-function mutations in cytochrome P450 family 24 subfamily A member 1 (CYP24A1) gene are associated with Idiopathic Infantile Hypercalcemia (IIH) and adult kidney stone disease. The enzyme deficiency leads to an impaired vitamin D catabolism pathway, resulting in a syndrome characterized by recurrent hypercalcemia, hypercalciuria and suppressed parathyroid hormone (PTH) levels. In these patients, the genetic evaluation of CYP24A1 is an important diagnostic tool, allowing the definitive diagnosis of IIH. METHODS A rapid CYP24A1 gene testing based on High Resolution Melting Analysis (HRMA) was designed in order to detect the CYP24A1 c.428_430delAAG (p.Glu143del), a recurrent IIH-associated variant. RESULTS HRMA method was able to identify c.428_430delAAG genotypes evaluating melting curve shape and melting temperature (Tm). Heterozygous samples exhibited a typical melting profile while homozygous samples showed a specific Tm shift. CONCLUSIONS We provide evidence about application of HRMA in unambiguous genotyping of the CYP24A1 c.428_430delAAG variant, making this method useful in clinical molecular diagnostics. This approach opens the way to a helpful molecular analysis of CYP24A1 gene in IIH diagnosis, to an improved pharmacological treatment strategy and to a reduced risk of recurrent stones and worsening nephrocalcinosis.
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Affiliation(s)
- Elisa De Paolis
- Polo Scienze delle Immagini, di Laboratorio ed Infettivologiche, Università Cattolica del Sacro Cuore, Fondazione Policlinico Universitario Agostino Gemelli, Roma, Italy
| | - Angelo Minucci
- Polo Scienze delle Immagini, di Laboratorio ed Infettivologiche, Università Cattolica del Sacro Cuore, Fondazione Policlinico Universitario Agostino Gemelli, Roma, Italy
| | - Maria De Bonis
- Polo Scienze delle Immagini, di Laboratorio ed Infettivologiche, Università Cattolica del Sacro Cuore, Fondazione Policlinico Universitario Agostino Gemelli, Roma, Italy
| | - Giovanni Luca Scaglione
- Laboratory of Molecular Oncology, "Giovanni Paolo II" Foundation, Catholic University of Sacred Heart, Campobasso, Italy
| | - Jacopo Gervasoni
- Polo Scienze delle Immagini, di Laboratorio ed Infettivologiche, Università Cattolica del Sacro Cuore, Fondazione Policlinico Universitario Agostino Gemelli, Roma, Italy
| | - Aniello Primiano
- Polo Scienze delle Immagini, di Laboratorio ed Infettivologiche, Università Cattolica del Sacro Cuore, Fondazione Policlinico Universitario Agostino Gemelli, Roma, Italy
| | - Pietro Manuel Ferraro
- Polo di Scienze Reumatologiche, Dermatologiche, Immuno-Allergologiche, Urologiche e Nefrologiche, Istituto di Medicina Interna e Geriatria. Università Cattolica del Sacro Cuore, Fondazione Policlinico Universitario Agostino Gemelli, Roma, Italy
| | - Daniele Cappellani
- Department of Clinical and Experimental Medicine, Section of Endocrinology, University of Pisa, Pisa, Italy
| | - Claudio Marcocci
- Department of Clinical and Experimental Medicine, Section of Endocrinology, University of Pisa, Pisa, Italy
| | - Giovanni Gambaro
- Polo di Scienze Reumatologiche, Dermatologiche, Immuno-Allergologiche, Urologiche e Nefrologiche, Istituto di Medicina Interna e Geriatria. Università Cattolica del Sacro Cuore, Fondazione Policlinico Universitario Agostino Gemelli, Roma, Italy
| | - Ettore Capoluongo
- Laboratory of Clinical Pathology and Advanced Molecular Diagnostics, Istituto Dermopatico dell'Immacolata -IRCCS, Rome, Italy; Università Cattolica del Sacro Cuore, Fondazione Policlinico Universitario Agostino Gemelli, Roma, Italy.
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Yanus G, Akhapkina T, Ivantsov A, Preobrazhenskaya E, Aleksakhina S, Bizin I, Sokolenko A, Mitiushkina N, Kuligina E, Suspitsin E, Venina A, Holmatov M, Zaitseva O, Yatsuk O, Pashkov D, Belyaev A, Togo A, Imyanitov E, Iyevleva A. Spectrum of APC and MUTYH germ-line mutations in Russian patients with colorectal malignancies. Clin Genet 2018; 93:1015-1021. [DOI: 10.1111/cge.13228] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2017] [Revised: 01/28/2018] [Accepted: 01/31/2018] [Indexed: 12/14/2022]
Affiliation(s)
- G.A. Yanus
- N.N. Petrov Institute of Oncology, Laboratory of Molecular Oncology; St.-Petersburg 197758 Russia
- St.-Petersburg Pediatric Medical University, Department of Medical Genetics; St.-Petersburg 194100 Russia
| | - T.A. Akhapkina
- N.N. Petrov Institute of Oncology, Laboratory of Molecular Oncology; St.-Petersburg 197758 Russia
- St.-Petersburg Pediatric Medical University, Department of Medical Genetics; St.-Petersburg 194100 Russia
| | - A.O. Ivantsov
- N.N. Petrov Institute of Oncology, Laboratory of Molecular Oncology; St.-Petersburg 197758 Russia
- St.-Petersburg Pediatric Medical University, Department of Medical Genetics; St.-Petersburg 194100 Russia
| | - E.V. Preobrazhenskaya
- N.N. Petrov Institute of Oncology, Laboratory of Molecular Oncology; St.-Petersburg 197758 Russia
- St.-Petersburg Pediatric Medical University, Department of Medical Genetics; St.-Petersburg 194100 Russia
| | - S.N. Aleksakhina
- N.N. Petrov Institute of Oncology, Laboratory of Molecular Oncology; St.-Petersburg 197758 Russia
| | - I.V. Bizin
- Peter the Great St.-Petersburg Polytechnic University, Department of Bioinformatics; St.-Petersburg 195251 Russia
| | - A.P. Sokolenko
- N.N. Petrov Institute of Oncology, Laboratory of Molecular Oncology; St.-Petersburg 197758 Russia
- St.-Petersburg Pediatric Medical University, Department of Medical Genetics; St.-Petersburg 194100 Russia
| | - N.V. Mitiushkina
- N.N. Petrov Institute of Oncology, Laboratory of Molecular Oncology; St.-Petersburg 197758 Russia
| | - E.Sh. Kuligina
- N.N. Petrov Institute of Oncology, Laboratory of Molecular Oncology; St.-Petersburg 197758 Russia
| | - E.N. Suspitsin
- N.N. Petrov Institute of Oncology, Laboratory of Molecular Oncology; St.-Petersburg 197758 Russia
- St.-Petersburg Pediatric Medical University, Department of Medical Genetics; St.-Petersburg 194100 Russia
| | - A.R. Venina
- N.N. Petrov Institute of Oncology, Laboratory of Molecular Oncology; St.-Petersburg 197758 Russia
| | - M.M. Holmatov
- N.N. Petrov Institute of Oncology, Laboratory of Molecular Oncology; St.-Petersburg 197758 Russia
- St.-Petersburg Pediatric Medical University, Department of Medical Genetics; St.-Petersburg 194100 Russia
| | - O.A. Zaitseva
- N.N. Petrov Institute of Oncology, Laboratory of Molecular Oncology; St.-Petersburg 197758 Russia
| | - O.S. Yatsuk
- N.N. Petrov Institute of Oncology, Laboratory of Molecular Oncology; St.-Petersburg 197758 Russia
| | - D.V. Pashkov
- S.M. Kirov Military Medical Academy, Department of Surgery; St.-Petersburg 194044 Russia
| | - A.M. Belyaev
- N.N. Petrov Institute of Oncology, Laboratory of Molecular Oncology; St.-Petersburg 197758 Russia
- S.M. Kirov Military Medical Academy, Department of Surgery; St.-Petersburg 194044 Russia
| | - A.V. Togo
- N.N. Petrov Institute of Oncology, Laboratory of Molecular Oncology; St.-Petersburg 197758 Russia
| | - E.N. Imyanitov
- N.N. Petrov Institute of Oncology, Laboratory of Molecular Oncology; St.-Petersburg 197758 Russia
- St.-Petersburg Pediatric Medical University, Department of Medical Genetics; St.-Petersburg 194100 Russia
- I.I. Mechnikov North-Western Medical University, Department of Oncology; St.-Petersburg 191015 Russia
- St.-Petersburg State University, Faculty of Medicine, Department of Oncology; St.-Petersburg 199034 Russia
| | - A.G. Iyevleva
- N.N. Petrov Institute of Oncology, Laboratory of Molecular Oncology; St.-Petersburg 197758 Russia
- St.-Petersburg Pediatric Medical University, Department of Medical Genetics; St.-Petersburg 194100 Russia
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Słomka M, Sobalska-Kwapis M, Wachulec M, Bartosz G, Strapagiel D. High Resolution Melting (HRM) for High-Throughput Genotyping-Limitations and Caveats in Practical Case Studies. Int J Mol Sci 2017; 18:ijms18112316. [PMID: 29099791 PMCID: PMC5713285 DOI: 10.3390/ijms18112316] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2017] [Revised: 10/06/2017] [Accepted: 10/31/2017] [Indexed: 01/02/2023] Open
Abstract
High resolution melting (HRM) is a convenient method for gene scanning as well as genotyping of individual and multiple single nucleotide polymorphisms (SNPs). This rapid, simple, closed-tube, homogenous, and cost-efficient approach has the capacity for high specificity and sensitivity, while allowing easy transition to high-throughput scale. In this paper, we provide examples from our laboratory practice of some problematic issues which can affect the performance and data analysis of HRM results, especially with regard to reference curve-based targeted genotyping. We present those examples in order of the typical experimental workflow, and discuss the crucial significance of the respective experimental errors and limitations for the quality and analysis of results. The experimental details which have a decisive impact on correct execution of a HRM genotyping experiment include type and quality of DNA source material, reproducibility of isolation method and template DNA preparation, primer and amplicon design, automation-derived preparation and pipetting inconsistencies, as well as physical limitations in melting curve distinction for alternative variants and careful selection of samples for validation by sequencing. We provide a case-by-case analysis and discussion of actual problems we encountered and solutions that should be taken into account by researchers newly attempting HRM genotyping, especially in a high-throughput setup.
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Affiliation(s)
- Marcin Słomka
- Biobank Lab, Department of Molecular Biophysics, Faculty of Biology and Environmental Protection, University of Łódź, Pilarskiego 14/16, 90-231 Łódź, Poland.
- BBMRI.pl Consortium, 54-066 Wrocław, Poland.
| | - Marta Sobalska-Kwapis
- Biobank Lab, Department of Molecular Biophysics, Faculty of Biology and Environmental Protection, University of Łódź, Pilarskiego 14/16, 90-231 Łódź, Poland.
- BBMRI.pl Consortium, 54-066 Wrocław, Poland.
| | - Monika Wachulec
- Department of Molecular Biophysics, Faculty of Biology and Environmental Protection, University of Łódź, Pomorska 141/143, 90-236 Łódź, Poland.
| | - Grzegorz Bartosz
- Department of Molecular Biophysics, Faculty of Biology and Environmental Protection, University of Łódź, Pomorska 141/143, 90-236 Łódź, Poland.
| | - Dominik Strapagiel
- Biobank Lab, Department of Molecular Biophysics, Faculty of Biology and Environmental Protection, University of Łódź, Pilarskiego 14/16, 90-231 Łódź, Poland.
- BBMRI.pl Consortium, 54-066 Wrocław, Poland.
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Minucci A, De Bonis M, De Paolis E, Gentile L, Santonocito C, Concolino P, Mignone F, Capoluongo E. High Resolution Melting Analysis is Very Useful to Identify BRCA1 c.4964_4982del19 (rs80359876) Founder Calabrian Pathogenic Variant on Peripheral Blood and Buccal Swab DNA. Mol Diagn Ther 2017; 21:217-223. [PMID: 28161869 DOI: 10.1007/s40291-017-0262-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
INTRODUCTION Detection of pathogenic variants in hereditary breast and ovarian cancer-related breast cancer type 1 and type 2 susceptibility proteins (BRCA1/2) genes is an effective strategy in cancer prevention and treatment. Some ethnic and geographical regions show different BRCA1/2 mutation spectrum and prevalence. In Italy, elucidation of founder effect in BRCA1/2 genes can have an impact on the management of hereditary cancer families on a healthcare system level, making genetic testing more affordable and cost effective in certain regions. METHODS The purpose of this paper is to develop a rapid, low-cost, high-throughput single-tube technology for genotyping the Italian founder mutation c.4964_4982del19 (rs80359876) in the BRCA1 gene, starting from peripheral blood and/or buccal swab DNA. RESULTS Heterozygote samples for c.4964_4982del19 variant were easily and unambiguously identified by the altered shape of the melting curves and were clearly distinguished by a change in melting temperature that differed by approximately 5 °C. The same results were obtained both with DNA from peripheral blood than buccal swab. CONCLUSIONS We provide evidence about application of high-resolution melting analysis (HRMA) in unambiguously genotyping of the founder BRCA1 c.4964_4982del19 variant (rs80359876) in individuals from the Calabria region of Italy. In fact, HRMA was confirmed to be particularly suitable for the identification of BRCA1 c.4964_4982del19 variant, making this approach useful in clinical molecular diagnostics.
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Affiliation(s)
- Angelo Minucci
- Laboratory of Clinical Molecular and Personalized Diagnostics, Institute of Biochemistry and Clinical Biochemistry, Teaching and Research Hospital 'Agostino Gemelli' Foundation, Rome, Italy.
| | - Maria De Bonis
- Laboratory of Clinical Molecular and Personalized Diagnostics, Institute of Biochemistry and Clinical Biochemistry, Teaching and Research Hospital 'Agostino Gemelli' Foundation, Rome, Italy
| | - Elisa De Paolis
- Laboratory of Clinical Molecular and Personalized Diagnostics, Institute of Biochemistry and Clinical Biochemistry, Teaching and Research Hospital 'Agostino Gemelli' Foundation, Rome, Italy
| | - Leonarda Gentile
- Laboratory of Clinical Molecular and Personalized Diagnostics, Institute of Biochemistry and Clinical Biochemistry, Teaching and Research Hospital 'Agostino Gemelli' Foundation, Rome, Italy
| | - Concetta Santonocito
- Laboratory of Clinical Molecular and Personalized Diagnostics, Institute of Biochemistry and Clinical Biochemistry, Teaching and Research Hospital 'Agostino Gemelli' Foundation, Rome, Italy
| | - Paola Concolino
- Laboratory of Clinical Molecular and Personalized Diagnostics, Institute of Biochemistry and Clinical Biochemistry, Teaching and Research Hospital 'Agostino Gemelli' Foundation, Rome, Italy
| | - Flavio Mignone
- Laboratory of Clinical Molecular and Personalized Diagnostics, Institute of Biochemistry and Clinical Biochemistry, Teaching and Research Hospital 'Agostino Gemelli' Foundation, Rome, Italy
| | - Ettore Capoluongo
- Laboratory of Clinical Molecular and Personalized Diagnostics, Institute of Biochemistry and Clinical Biochemistry, Teaching and Research Hospital 'Agostino Gemelli' Foundation, Rome, Italy.
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Xu JJ, Yao FR, Jiang M, Zhang YT, Guo F. High-resolution melting analysis for rapid and sensitive NOTCH1 screening in chronic lymphocytic leukemia. Int J Mol Med 2017; 39:415-422. [PMID: 28075457 DOI: 10.3892/ijmm.2017.2849] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2016] [Accepted: 12/14/2016] [Indexed: 11/05/2022] Open
Abstract
Chronic lymphocytic leukemia (CLL) is a biological and clinical heterogeneous disease. Activating mutations of NOTCH1 have been implicated to be associated with adverse prognosis in CLL. The objective of the present study was to develop an effective high-resolution melting (HRM) assay for detecting NOTCH1 mutations. Genomic DNA (gDNA) extracted from 133 CLL patients was screened by HRM assay, and the results were compared with the data obtained using direct sequencing. The relative sensitivity of the HRM assay and direct sequencing was evaluated using diluted gDNA with different NOTCH1 mutational frequencies. The HRM assay was able to detect and discriminate samples with NOTCH1 mutations from the wild-type template in CLL. Eight of the 133 CLL patients (6.02%) were scored positively for NOTCH1 mutations in the HRM assay. The results of the NOTCH1 mutations detected by HRM analysis achieved 100% concordance with those determined from direct sequencing. HRM had a higher sensitivity (1%) and shorter turn-around time (TAT), compared to direct sequencing. In conclusion, the HRM assay developed by us was confirmed to be a rapid, sensitive, and promising approach for high-throughput prognostic NOTCH1 screening in CLL. It enables real-time NOTCH1 evaluation, which is of great significance in clinical practice and may facilitate the decision-making of clinicians in CLL.
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Affiliation(s)
- Jing-Jing Xu
- Center for Clinical Laboratory, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu 215006, P.R. China
| | - Fei-Rong Yao
- Department of Radiology, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu 215006, P.R. China
| | - Min Jiang
- Department of Blood Transfusion, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu 215006, P.R. China
| | - You-Tao Zhang
- Center for Clinical Laboratory, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu 215006, P.R. China
| | - Feng Guo
- Center for Clinical Laboratory, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu 215006, P.R. China
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High-resolution Melting Analysis for Gene Scanning of Adenomatous Polyposis Coli (APC) Gene With Oral Squamous Cell Carcinoma Samples. Appl Immunohistochem Mol Morphol 2016; 24:97-104. [PMID: 26447891 DOI: 10.1097/pai.0000000000000158] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
BACKGROUND There have been many different mutations reported for the large adenomatous polyposis coli (APC) tumor suppressor gene. APC mutations result in inactivation of APC tumor suppressor action, allowing the progression of tumorigenesis. The present study utilized a highly efficient method to identify APC mutations and investigated the association between the APC genetic variants Y486Y, A545A, T1493T, and D1822V and susceptibility to oral squamous cell carcinoma (OSCC). METHODS High-resolution melting (HRM) analysis was used to characterize APC mutations. Genomic DNA was extracted from 83 patient specimens of OSCC and 50 blood samples from healthy control subjects. The 14 exons and mutation cluster region of exon 15 were screened by HRM analysis. All mutations were confirmed by direct DNA sequencing. RESULTS Three mutations and 4 single nucleotide polymorphisms (SNPs) were found in this study. The mutations were c.573T>C (Y191Y) in exon 5, c.1005A>G (L335L) in exon 9, and c.1488A>T (T496T) in exon 11. Two SNPs, c.4479G>A (T1493T) and c.5465A>T (D1822V), were located in exon 15, whereas c.1458T>C (Y486Y) and c.1635G>A (A545A) were located in exon 11 and 13, respectively. There was no observed association between OSCC risk and genotype for any of the 4 APC SNPs. CONCLUSIONS The mutation of APC is rare in Taiwanese patients with OSCC. HRM analysis is a reliable, accurate, and fast screening method for APC mutations.
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González-Giraldo Y, Rodríguez-Dueñas M, Forero DA. Development of Novel High-Resolution Melting-Based Assays for Genotyping Two Alu Insertion Polymorphisms (FXIIIB and PV92). Mol Biotechnol 2016; 58:197-201. [PMID: 26843017 DOI: 10.1007/s12033-016-9915-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Insertion/Deletion polymorphisms (InDels) are a common type of genetic variation, with a growing role in population genetics and applied genomics. There is the need for the development of novel cost-effective assays for genotyping InDels of high importance. The main objective of this study was to develop high-resolution melting-based assays for genotyping two commonly studied Alu insertion polymorphisms: FXIIIB and PV92 (rs70942849 and rs3138523). Three primers (two forward and one reverse) were designed for each marker, and high-resolution melting (HRM) analyses in a qPCR platform were performed, using EvaGreen fluorescent dye. For each one of the two Alu insertion polymorphisms, HRM analyses identified distinguishable peaks for the three genotypes, allowing a robust genotyping. Results were validated using 96 DNA samples previously genotyped and the assays worked with different DNA concentrations. In this study, we developed novel cost-effective assays, using qPCR, for genotyping two Alu insertion polymorphisms (widely used as ancestry markers). Our results highlight the feasibility of using HRM analyses for genotyping InDel polymorphisms of medical and biotechnological importance.
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Affiliation(s)
- Yeimy González-Giraldo
- Department of Nutrition and Biochemistry, School of Sciences, Pontificia Universidad Javeriana, Bogotá, Colombia.,Laboratory of NeuroPsychiatric Genetics, Biomedical Sciences Research Group, School of Medicine, Universidad Antonio Nariño, Bogotá, Colombia
| | - Marisol Rodríguez-Dueñas
- Laboratory of NeuroPsychiatric Genetics, Biomedical Sciences Research Group, School of Medicine, Universidad Antonio Nariño, Bogotá, Colombia.,Faculty of Science, Universidad Antonio Nariño, Bogotá, Colombia
| | - Diego A Forero
- Laboratory of NeuroPsychiatric Genetics, Biomedical Sciences Research Group, School of Medicine, Universidad Antonio Nariño, Bogotá, Colombia.
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Lin CY, Ho CM, Tamamyan G, Yang SF, Peng CT, Chang JG. Validating the Sensitivity of High-Resolution Melting Analysis for JAK2 V617F Mutation in the Clinical Setting. J Clin Lab Anal 2016; 30:838-844. [PMID: 27169616 DOI: 10.1002/jcla.21945] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2014] [Revised: 01/05/2016] [Accepted: 01/13/2016] [Indexed: 01/10/2023] Open
Abstract
BACKGROUND Janus kinase 2 (JAK2) plays an important role in normal hematopoietic growth factor signaling. The detection of the JAK2 V617F mutation (c.1849GNT, GTC → TTC) is crucial for the diagnosis of myeloproliferative neoplasm (MPN) and has become the essential criteria for diagnosis of MPN by the WHO. High-resolution melt (HRM) curve analysis is a nongel-based, closed-tube method, in which PCR amplification and subsequent analysis are sequentially performed in the well, making it more convenient than other scanning methodologies. METHODS We evaluated JAK2 V617F mutation by HRM. Twenty-nine patients diagnosed with MPN were examined. We studied the analytical sensitivity of the HRM analysis using real-time polymerase chain reaction (PCR) for identifying the JAK2 V617F mutation. Additionally, the sensitivity of HRM analysis and allele-specific PCR (AS-PCR) assay was compared. RESULTS The JAK2 V617F mutation was successfully discriminated at an abundance of 6% or above in HRM analysis. Both HRM analysis and AS-PCR showed 100% accuracy with detection limits of 6% and 2.5%, respectively. CONCLUSION HRM analysis is a fast, simple, reliable, and nonexpensive method for the detection of the JAK2 V617F mutation. However, more validation of the detection limits of HRM analysis should be performed before declaration of the analytic sensitivity of the method.
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Affiliation(s)
- Chien-Yu Lin
- Graduate Institute of Clinical Medical Sciences, China Medical University, Taichung, Taiwan.,Department of Laboratory Medicine, China Medical University Hospital, Taichung, Taiwan.,Epigenome Research Center, China Medical University Hospital, Taichung, Taiwan
| | - Cheng-Mao Ho
- Department of Laboratory Medicine, China Medical University Hospital, Taichung, Taiwan.,Department of Nursing, Hungkuang University, Taichung, Taiwan
| | - Gevorg Tamamyan
- Department of Pediatric Hemato/Oncology, Complex Clinic of Chemotherapy, Yerevan State Medical University "Muratsan" Hospital, Yerevan, Armenia
| | - Shu-Fen Yang
- Department of Laboratory Medicine, China Medical University Hospital, Taichung, Taiwan.,Epigenome Research Center, China Medical University Hospital, Taichung, Taiwan
| | - Ching-Tien Peng
- Division of Pediatric Hemato/Oncology, China Medical University Children's Hospital, Taichung, Taiwan. .,Department of Biotechnology, Asia University, Taichung, Taiwan.
| | - Jan-Gowth Chang
- Department of Laboratory Medicine, China Medical University Hospital, Taichung, Taiwan. .,Epigenome Research Center, China Medical University Hospital, Taichung, Taiwan. .,College of Medicine, China Medical University, Taichung, Taiwan.
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Ke T, Han M, Zhao M, Wang QK, Zhang H, Zhao Y, Ruan X, Li H, Xu C, Sun T. Alpha-actin-2 mutations in Chinese patients with a non-syndromatic thoracic aortic aneurysm. BMC MEDICAL GENETICS 2016; 17:45. [PMID: 27431987 PMCID: PMC4950238 DOI: 10.1186/s12881-016-0310-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/01/2015] [Accepted: 06/30/2016] [Indexed: 12/12/2022]
Abstract
Background Aortic aneurysms and/or dissection (AADs) in the aorta are a leading cause of human morbidity and mortality. To date, data on non-syndromic thoracic AADs (TAADs) have been mainly derived from Caucasians, and the genetic basis of TAADs remains to be elucidated. In this study, we assessed gene mutations in a Chinese population with TAADs. Methods A cohort of 68 non-syndromic familial TAAD Chinese patients was screened for the most common TAAD-causing genes (ACTA2, MYH11, TGFBR1, TGFBR2, and SMAD3) using high-resolution melting (HRM) analysis. Thereafter, 142 unrelated non-syndromic sporadic cases were recruited and further analyzed using HRM analysis to estimate the prevalence of disease-causing mutations in these candidate genes. Results Two novel ACTA2 mutations (N117I and L348R) were identified in each familial TAAD proband separately, and an additional novel ACTA2 mutation (Y168N) was identified in one patient with sporadic TAADs. In contrast, none of the three mutations occurred in 480 control subjects. Also, no other gene mutations were identified in this cohort of Chinese TAAD patients. Conclusions The current study identified three novel ACTA2 mutations in Chinese TAAD patients, and these mutations represented the most predominant genes responsible for non-syndromic TAADs. In addition, HRM analysis was shown to be a sensitive and high-throughput method for screening gene mutations.
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Affiliation(s)
- Tie Ke
- The Key Laboratory of Molecular Biophysics of Chinese Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China.,Center for Human Genome Research, Cardio-X Institute, Huazhong University of Science and Technology, Wuhan, China
| | - Meng Han
- The Key Laboratory of Molecular Biophysics of Chinese Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China.,Center for Human Genome Research, Cardio-X Institute, Huazhong University of Science and Technology, Wuhan, China
| | - Miao Zhao
- The Key Laboratory of Molecular Biophysics of Chinese Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China.,Center for Human Genome Research, Cardio-X Institute, Huazhong University of Science and Technology, Wuhan, China
| | - Qing Kenneth Wang
- The Key Laboratory of Molecular Biophysics of Chinese Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China.,Center for Human Genome Research, Cardio-X Institute, Huazhong University of Science and Technology, Wuhan, China.,Department of Molecular Cardiology, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, 44195, USA.,Center for Cardiovascular Genetics, Cleveland Clinic, Cleveland, OH, 44195, USA
| | - Huazhi Zhang
- The Key Laboratory of Molecular Biophysics of Chinese Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China.,Center for Human Genome Research, Cardio-X Institute, Huazhong University of Science and Technology, Wuhan, China
| | - Yuanyuan Zhao
- The Key Laboratory of Molecular Biophysics of Chinese Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China.,Center for Human Genome Research, Cardio-X Institute, Huazhong University of Science and Technology, Wuhan, China
| | - Xinlong Ruan
- Department of Cardiovascular Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Hui Li
- The Key Laboratory of Molecular Biophysics of Chinese Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China.,Center for Human Genome Research, Cardio-X Institute, Huazhong University of Science and Technology, Wuhan, China
| | - Chengqi Xu
- The Key Laboratory of Molecular Biophysics of Chinese Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China.,Center for Human Genome Research, Cardio-X Institute, Huazhong University of Science and Technology, Wuhan, China
| | - Tucheng Sun
- Department of Cardiovascular Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
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Chassanidis C, Boutou E, Voskaridou E, Balassopoulou A. Development of a High-Resolution Melting Approach for Scanning Beta Globin Gene Point Mutations in the Greek and Other Mediterranean Populations. PLoS One 2016; 11:e0157393. [PMID: 27351925 PMCID: PMC4924799 DOI: 10.1371/journal.pone.0157393] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Accepted: 05/27/2016] [Indexed: 12/22/2022] Open
Abstract
Beta-thalassaemia is one of the most common autosomal recessive disorders worldwide. The disease’s high incidence, which is observed in the broader Mediterranean area has led to the establishment of molecular diagnostics’ assays to prevent affected births. Therefore, the development of a reliable, cost-effective and rapid scanning method for β globin gene point mutations, easily adapted to a routine laboratory, is absolutely essential. Here, we describe, for the first time, the development of a High-Resolution Melting Analysis (HRMA) approach, suitable for scanning the particularly heterogeneous beta globin gene mutations present in the Greek population, and thus adaptable to the Mediterranean and other areas where these mutations have been identified. Within this context, β globin gene regions containing mutations frequently identified in the Greek population were divided in ten overlapping amplicons. Our reactions’ setup allowed for the simultaneous amplification of multiple primer sets and partial multiplexing, thereby resulting in significant reduction of the experimental time. DNA samples from β-thalassaemia patients/carriers with defined genotypes were tested. Distinct genotypes displayed distinguishable melting curves, enabling accurate detection of mutations. The described HRMA can be adapted to a high-throughput level. It represents a rapid, simple, cost-effective, reliable, highly feasible and sensitive method for β-thalassaemia gene scanning.
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Affiliation(s)
- Christos Chassanidis
- Molecular Genetics Laboratory, Thalassaemia and Hemoglobinopathies Center, Laiko General Hospital, Athens, Greece
- * E-mail: (AB); (CC)
| | - Effrossyni Boutou
- Molecular Genetics Laboratory, Thalassaemia and Hemoglobinopathies Center, Laiko General Hospital, Athens, Greece
| | - Ersi Voskaridou
- Thalassaemia and Hemoglobinopathies Center, Laiko General Hospital, Athens, Greece
| | - Angeliki Balassopoulou
- Molecular Genetics Laboratory, Thalassaemia and Hemoglobinopathies Center, Laiko General Hospital, Athens, Greece
- * E-mail: (AB); (CC)
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Rapid Identification of FGFR2 Gene Mutations in Taiwanese Patients With Endometrial Cancer Using High-resolution Melting Analysis. Appl Immunohistochem Mol Morphol 2016; 23:532-7. [PMID: 25517871 DOI: 10.1097/pai.0000000000000114] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
OBJECTIVES Mutations in fibroblast growth factor receptor 2 (FGFR2) gene have been reported in endometrial cancer and mutant FGFR2 has been pointed out as a potential therapeutic target. The aim of the current study was to use a high-resolution melting (HRM) analysis to identify FGFR2 hotspot mutations and to investigate the occurrence of these mutations in the Taiwanese population with endometrial cancer. DESIGN AND METHODS HRM analysis was designed to characterize the FGFR2 hotspot mutations. DNAs were extracted from 72 cases of fresh-frozen endometrial cancer tissues for FGFR2 mutational analysis by HRM analysis. The 6 exons of FGFR2 were screened by HRM analysis. All results were confirmed by direct sequencing. RESULTS We have identified the 6 reported mutations in the FGFR2 gene. The mutation c.879C>T (p.Q289P) was first reported in endometrial cancer. Each mutation could be readily and accurately identified in the difference plot curves. The frequency of FGFR2 hotspot mutations is 9.7% (7/72) in patients with endometrial cancer in the Taiwanese population. CONCLUSIONS HRM analysis is rapid, feasible, and a reliable diagnostic method for the detection of FGFR2 mutations in a clinical setting. Our results indicated the prevalence of FGFR2 mutational status in the Taiwanese population with endometrial cancer.
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Somatic Mutations and Genetic Variants of NOTCH1 in Head and Neck Squamous Cell Carcinoma Occurrence and Development. Sci Rep 2016; 6:24014. [PMID: 27035284 PMCID: PMC4817511 DOI: 10.1038/srep24014] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2015] [Accepted: 03/15/2016] [Indexed: 12/28/2022] Open
Abstract
A number of genetic variants have been associated with cancer occurrence, however it may be the acquired somatic mutations (SMs) that drive cancer development. This study investigates the potential SMs and related genetic variants associated with the occurrence and development of head and neck squamous cell carcinoma (HNSCC). We identified several SMs in NOTCH1 from whole-exome sequencing and validated them in a 13-year cohort of 128 HNSCC patients using a high-resolution melting analysis and resequencing. Patients who have NOTCH1 SMs show higher 5-year relapse-free recurrence (P = 0.0013) and lower survival proportion (P = 0.0447) when the risk-associated SMs were analysed by Cox proportional hazard models. Interestingly, the NOTCH1 gene rs139994842 that shares linkage with SMs is associated with HNSCC risk (OR = 3.46), increasing when SMs in NOTCH1 are involved (OR = 7.74), and furthermore when there are SMs in conjunction to betel quid chewing (OR = 32.11), which is a related independent environmental risk factor after adjusting for substances use (alcohol, betel quid, cigarettes) and age. The findings indicate that betel quid chewing is highly associated with NOTCH1 SMs (especially with changes in EGF-like domains), and that rs139994842 may potentially serve as an early predictive and prognostic biomarker for the occurrence and development of HNSCC.
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Chang YS, Lin CY, Yang SF, Ho CM, Chang JG. Analysing the mutational status of adenomatous polyposis coli (APC) gene in breast cancer. Cancer Cell Int 2016; 16:23. [PMID: 27028212 PMCID: PMC4810512 DOI: 10.1186/s12935-016-0297-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2014] [Accepted: 03/10/2016] [Indexed: 02/06/2023] Open
Abstract
Background Breast cancer is a heterogeneous disorder for which the underlying genetic basis remains unclear. We developed a method for identifying adenomatous polyposis coli (APC) mutations and we evaluated the possible association between APC genetic variants and breast cancer susceptibility. Methods Genomic DNA was extracted from tumor and matched peripheral blood samples collected from 89 breast cancer patients and from peripheral blood samples collected from 50 controls. All samples were tested for mutations in exons 1–14 and the mutation cluster region of exon 15 by HRM analysis. All mutations were confirmed by direct DNA sequencing. Results We identified a new single nucleotide polymorphism (SNP), c.465A>G (K155K), in exon 4 and seven known SNPs: c.573T>C (Y191Y) in exon 5, c.1005A>G (L335L) in exon 9, c.1458T>C (Y486Y) and c.1488A>T (T496T) in exon 11, c.1635G>A (A545A) in exon 13, and c.4479G>A (T1493T) and c.5465T>A (V1822D) in exon 15. The following alterations were found in 2, 1, 2, and 1 patients, respectively: c.465A>G, c.573T>C, c.1005A>G, and c.1488A>T. There was no observed association between breast cancer risk and any of these APC SNPs. Conclusions APC mutations occur at a low frequency in Taiwanese breast cancer cases. HRM analysis is a powerful method for the detection of APC mutations in breast. Electronic supplementary material The online version of this article (doi:10.1186/s12935-016-0297-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ya-Sian Chang
- Epigenome Research Center, China Medical University Hospital, 2 Yuh-Der Road, Taichung, 404 Taiwan ; Department of Laboratory Medicine, China Medical University Hospital, Taichung, Taiwan
| | - Chien-Yu Lin
- Department of Laboratory Medicine, China Medical University Hospital, Taichung, Taiwan
| | - Shu-Fen Yang
- Department of Laboratory Medicine, China Medical University Hospital, Taichung, Taiwan
| | - Cheng-Mao Ho
- Department of Laboratory Medicine, China Medical University Hospital, Taichung, Taiwan
| | - Jan-Gowth Chang
- Epigenome Research Center, China Medical University Hospital, 2 Yuh-Der Road, Taichung, 404 Taiwan ; Department of Laboratory Medicine, China Medical University Hospital, Taichung, Taiwan ; School of Medicine, China Medical University, Taichung, Taiwan
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Chang YC, Chang YS, Chang CC, Liu TC, Ko YC, Lee CC, Chang SJ, Chang JG. Development of a high-resolution melting method for the screening of TNFAIP3 gene mutations. Oncol Rep 2016; 35:2936-42. [PMID: 26986245 DOI: 10.3892/or.2016.4662] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2015] [Accepted: 12/23/2015] [Indexed: 11/06/2022] Open
Abstract
Tumor necrosis factor, α-induced protein 3 (TNFAIP3) which encodes a ubiquitin-modifying enzyme (A20), acts as a negative regulator of the NF-κB pathway, and in lymphoma and autoimmune diseases it is frequently inactivated by mutations and/or deletions. We investigated the prevalence of the inactivation of TNFAIP3 in oral squamous cell carcinoma (OSCC). DNA was extracted from 81 cases of OSCC and 50 peripheral blood samples from normal controls. A high-resolution melting (HRM) analysis was used to characterize TNFAIP3 mutations, and the results were confirmed by direct DNA sequencing. Three mutations and three single-nucleotide polymorphisms (SNPs) were found to be associated with OSCC; the TNFAIP3 mutation occurred in 3.7% (3/81) of the OSCC cases examined. All mutations were in exon 7 [c.1081G>A (p.E361K), c.1398C>G (p.S466R) (rs200878487) and c.1760C>T (p.P587L) (rs150056192)], and p.E361K was identified as a novel mutation. We further used SIFT and PolyPhen-2 software to assess potentially functional mutations. Two SNPs, c.296‑20_296-18delCTC (rs71670547) and c.380T>G (p.F127C) (rs2230926), were located in exon 3, and c.2140C>T (p.P714S) was located in exon 9. A novel SNP, p.P714S differed from the one reported previously (p.P714A) (rs369155845) at that site. We also identified five SNPs in 50 normal Taiwanese individuals, and two of them [c.296‑15C>T (rs377482653) and c.305A>G (p.N102S) (rs146534657)] were not found in our OSCC tissue. HRM facilitated the screening of genetic changes. In addition, our results indicate that the prevalence of the TNFAIP3 mutation is low in OSCC.
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Affiliation(s)
- Yuli Christine Chang
- Graduate Institute of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan, R.O.C
| | - Ya-Sian Chang
- Epigenome Research Center, China Medical University Hospital, Taichung, Taiwan, R.O.C
| | - Chun-Chi Chang
- Division of Chest Medicine, Department of Internal Medicine, Changhua Christian Hospital, Changhua, Taiwan, R.O.C
| | - Ta-Chih Liu
- Graduate Institute of Clinical Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan, R.O.C
| | - Ying-Chin Ko
- Environment-Omics‑Disease Research Center, China Medical University Hospital, Taichung, Taiwan, R.O.C
| | - Chien-Chin Lee
- Epigenome Research Center, China Medical University Hospital, Taichung, Taiwan, R.O.C
| | - Shun-Jen Chang
- Department of Kinesiology, Health and Leisure Studies, National University of Kaohsiung, Kaohsiung, Taiwan, R.O.C
| | - Jan-Gowth Chang
- Epigenome Research Center, China Medical University Hospital, Taichung, Taiwan, R.O.C
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Abstract
Inborn errors of metabolism are single gene disorders resulting from the defects in the biochemical pathways of the body. Although these disorders are individually rare, collectively they account for a significant portion of childhood disability and deaths. Most of the disorders are inherited as autosomal recessive whereas autosomal dominant and X-linked disorders are also present. The clinical signs and symptoms arise from the accumulation of the toxic substrate, deficiency of the product, or both. Depending on the residual activity of the deficient enzyme, the initiation of the clinical picture may vary starting from the newborn period up until adulthood. Hundreds of disorders have been described until now and there has been a considerable clinical overlap between certain inborn errors. Resulting from this fact, the definite diagnosis of inborn errors depends on enzyme assays or genetic tests. Especially during the recent years, significant achievements have been gained for the biochemical and genetic diagnosis of inborn errors. Techniques such as tandem mass spectrometry and gas chromatography for biochemical diagnosis and microarrays and next-generation sequencing for the genetic diagnosis have enabled rapid and accurate diagnosis. The achievements for the diagnosis also enabled newborn screening and prenatal diagnosis. Parallel to the development the diagnostic methods; significant progress has also been obtained for the treatment. Treatment approaches such as special diets, enzyme replacement therapy, substrate inhibition, and organ transplantation have been widely used. It is obvious that by the help of the preclinical and clinical research carried out for inborn errors, better diagnostic methods and better treatment approaches will high likely be available.
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Ha BH, Park J, Destgeer G, Jung JH, Sung HJ. Generation of Dynamic Free-Form Temperature Gradients in a Disposable Microchip. Anal Chem 2015; 87:11568-74. [DOI: 10.1021/acs.analchem.5b03457] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Byung Hang Ha
- Department
of Mechanical
Engineering, KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Korea
| | - Jinsoo Park
- Department
of Mechanical
Engineering, KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Korea
| | - Ghulam Destgeer
- Department
of Mechanical
Engineering, KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Korea
| | - Jin Ho Jung
- Department
of Mechanical
Engineering, KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Korea
| | - Hyung Jin Sung
- Department
of Mechanical
Engineering, KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Korea
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Destouni A, Poulou M, Kakourou G, Vrettou C, Tzetis M, Traeger-Synodinos J, Kitsiou-Tzeli S. Single-cell high resolution melting analysis: A novel, generic, pre-implantation genetic diagnosis (PGD) method applied to cystic fibrosis (HRMA CF-PGD). J Cyst Fibros 2015; 15:163-70. [PMID: 26493493 DOI: 10.1016/j.jcf.2015.09.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2015] [Revised: 07/15/2015] [Accepted: 09/23/2015] [Indexed: 02/04/2023]
Abstract
BACKGROUND Institutions offering CF-PGD face the challenge of developing and optimizing single cell genotyping protocols that should cover for the extremely heterogeneous CF mutation spectrum. Here we report the development and successful clinical application of a generic CF-PGD protocol to facilitate direct detection of any CFTR nucleotide variation(s) by HRMA and simultaneous confirmation of diagnosis through haplotype analysis. METHODS A multiplex PCR was optimized supporting co-amplification of any CFTR exon-region, along with 6 closely linked STRs. Single cell genotypes were established through HRM analysis following melting of the 2nd round PCR products and were confirmed by STR haplotype analysis of the 1st PCR products. The protocol was validated pre-clinically, by testing 208 single lymphocytes, isolated from whole blood samples from 4 validation family trios. Fifteen PGD cycles were performed and 103 embryos were biopsied. RESULTS In 15 clinical PGD cycles, genotypes were achieved in 88/93 (94.6%) embryo biopsy samples, of which 57/88 (64.8%) were deemed genetically suitable for embryo transfer. Amplification failed at all loci for 10/103 blastomeres biopsied from poor quality embryos. Six clinical pregnancies were achieved (2 twin, 4 singletons). PGD genotypes were confirmed following conventional amniocentesis or chorionic villus sampling in all achieved pregnancies. CONCLUSIONS The single cell HRMA CF-PGD protocol described herein is a flexible, generic, low cost and robust genotyping method, which facilitates the analysis of any CFTR genotype combination. Single-cell HRMA can be beneficial to other clinical settings, for example the detection of single nucleotide variants in single cells derived from clinical tumor samples.
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Affiliation(s)
- A Destouni
- Department of Medical Genetics, University of Athens, St Sophia's Children's Hospital, Athens, Greece
| | - M Poulou
- Department of Medical Genetics, University of Athens, St Sophia's Children's Hospital, Athens, Greece.
| | - G Kakourou
- Department of Medical Genetics, University of Athens, St Sophia's Children's Hospital, Athens, Greece
| | - C Vrettou
- Department of Medical Genetics, University of Athens, St Sophia's Children's Hospital, Athens, Greece
| | - M Tzetis
- Department of Medical Genetics, University of Athens, St Sophia's Children's Hospital, Athens, Greece
| | - J Traeger-Synodinos
- Department of Medical Genetics, University of Athens, St Sophia's Children's Hospital, Athens, Greece
| | - S Kitsiou-Tzeli
- Department of Medical Genetics, University of Athens, St Sophia's Children's Hospital, Athens, Greece
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Berenstein R. Class III Receptor Tyrosine Kinases in Acute Leukemia - Biological Functions and Modern Laboratory Analysis. Biomark Insights 2015; 10:1-14. [PMID: 26309392 PMCID: PMC4527365 DOI: 10.4137/bmi.s22433] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2015] [Revised: 07/02/2015] [Accepted: 07/04/2015] [Indexed: 12/12/2022] Open
Abstract
Acute myeloid leukemia (AML) is a complex disease caused by deregulation of multiple signaling pathways. Mutations in class III receptor tyrosine kinases (RTKs) have been implicated in alteration of cell signals concerning the growth and differentiation of leukemic cells. Point mutations, insertions, or deletions of RTKs as well as chromosomal translocations induce constitutive activation of the receptor, leading to uncontrolled proliferation of undifferentiated myeloid blasts. Aberrations can occur in all domains of RTKs causing either the ligand-independent activation or mimicking the activated conformation. The World Health Organization recommended including RTK mutations in the AML classification since their detection in routine laboratory diagnostics is a major factor for prognostic stratification of patients. Polymerase chain reaction (PCR)-based methods are well-validated for the detection of fms-related tyrosine kinase 3 (FLT3) mutations and can easily be applied for other RTKs. However, when methodological limitations are reached, accessory techniques can be applied. For a higher resolution and more quantitative approach compared to agarose gel electrophoresis, PCR fragments can be separated by capillary electrophoresis. Furthermore, high-resolution melting and denaturing high-pressure liquid chromatography are reliable presequencing screening methods that reduce the sample amount for Sanger sequencing. Because traditional DNA sequencing is time-consuming, next-generation sequencing (NGS) is an innovative modern possibility to analyze a high amount of samples simultaneously in a short period of time. At present, standardized procedures for NGS are not established, but when this barrier is resolved, it will provide a new platform for rapid and reliable laboratory diagnostic of RTK mutations in patients with AML. In this article, the biological and physiological role of RTK mutations in AML as well as possible laboratory methods for their detection will be reviewed.
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Affiliation(s)
- Rimma Berenstein
- Department of Hematology, Oncology and Tumourimmunology, Charité Universitätsmedizin Berlin, Berlin, Germany
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Capper RL, Jin YK, Lundgren PB, Peplow LM, Matz MV, van Oppen MJH. Quantitative high resolution melting: two methods to determine SNP allele frequencies from pooled samples. BMC Genet 2015; 16:62. [PMID: 26070466 PMCID: PMC4465018 DOI: 10.1186/s12863-015-0222-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2015] [Accepted: 05/27/2015] [Indexed: 01/06/2023] Open
Abstract
Background The advent of next-generation sequencing has brought about an explosion of single nucleotide polymorphism (SNP) data in non-model organisms; however, profiling these SNPs across multiple natural populations still requires substantial time and resources. Results Here, we introduce two cost-efficient quantitative High Resolution Melting (qHRM) methods for measuring allele frequencies at known SNP loci in pooled DNA samples: the “peaks” method, which can be applied to large numbers of SNPs, and the “curves” method, which is more labor intensive but also slightly more accurate. Using the reef-building coral Acropora millepora, we show that both qHRM methods can recover the allele proportions from mixtures prepared using two or more individuals of known genotype. We further demonstrate advantages of each method over previously published methods; specifically, the “peaks” method can be rapidly scaled to screen several hundred SNPs at once, whereas the “curves” method is better suited for smaller numbers of SNPs. Conclusions Compared to genotyping individual samples, these methods can save considerable effort and genotyping costs when relatively few candidate SNPs must be profiled across a large number of populations. One of the main applications of this method could be validation of SNPs of interest identified in population genomic studies. Electronic supplementary material The online version of this article (doi:10.1186/s12863-015-0222-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Roxana L Capper
- Department of Cell and Molecular Biology, University of Texas at Austin, Austin, TX, 78712, USA.
| | - Young K Jin
- School of Marine and Tropical Biology, James Cook University, Townsville, Qld, 4811, Australia. .,Australian Institute of Marine Science, PMB3, Townsville MC, Qld, 4810, Australia.
| | - Petra B Lundgren
- Department of Anatomy and Developmental Biology, School of Biomedical Sciences, Monash University, Clayton, VIC, 3800, Australia.
| | - Lesa M Peplow
- Australian Institute of Marine Science, PMB3, Townsville MC, Qld, 4810, Australia.
| | - Mikhail V Matz
- Department of Cell and Molecular Biology, University of Texas at Austin, Austin, TX, 78712, USA.
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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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Abstract
The technology of Single Nucleotide Polymorphism (SNP) detection has evolved steadily through mobility shift studies, mass cleavage product evaluations, heterodimer differences in chemical, conformational, and enzymatic properties, mass spectroscopy and sequencing, to allele-specific hybridization probe methods. Each method presented challenges of labor intensity, unreliable efficiencies, complicated optimizations, and issues of sample quantity and quality. Concurrently the value of SNP detection in basic research and personalized medicine has continued to grow. Accessing the secrets of genetic individuality is the next frontier in moving medicine from the description of very low frequency and highly deleterious nucleotide changes to the study of very low frequency polymorphisms, lower penetrance polymorphisms, and polymorphisms with public health importance. High-Resolution Melting (HRM) analysis of SNP status became an option for high throughput settings with the development of double-stranded dyes that do not interfere with PCR amplification in saturation, eliminate dye jumping, and nearest neighbor sequence changes influence melt temperature via amplicon strand locking chemistry. This method is able to distinguish transitions, transversions, and identify novel changes at or near the SNP of interest rapidly, inexpensively, and without post-amplification assay techniques or extensive technical interpretation of data. For probe or solid matrix based assays, the investigator initially defines a set of target sequences for binding. These assays are not only difficult due to the optimization of binding conditions but are unable to detect sequences that were not included in the design, often have marginalized binding due to a "one size fits all" reaction, and are not distinct in the case of heterozygotes.
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Affiliation(s)
- Carol M Bruzzone
- Department of Medicine, University of Minnesota Medical School, Minneapolis, MN, USA,
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Chang YS, Yang YW, Lin YN, Lin KH, Chang KC, Chang JG. Mutation Analysis of KCNQ1, KCNH2 and SCN5A Genes in Taiwanese Long QT Syndrome Patients. Int Heart J 2015; 56:450-3. [PMID: 26118593 DOI: 10.1536/ihj.14-428] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Affiliation(s)
- Ya-Sian Chang
- Epigenome Research Center, China Medical University Hospital
- Department of Laboratory Medicine, China Medical University Hospital
| | - Yi-Wen Yang
- Department of Laboratory Medicine, China Medical University Hospital
| | - Yen-Nien Lin
- Division of Cardiology, Department of Internal Medicine, China Medical University Hospital
| | - Kuo-Hung Lin
- Division of Cardiology, Department of Internal Medicine, China Medical University Hospital
| | - Kuan-Cheng Chang
- Division of Cardiology, Department of Internal Medicine, China Medical University Hospital
- School of Medicine, China Medical University
| | - Jan-Gowth Chang
- Epigenome Research Center, China Medical University Hospital
- Department of Laboratory Medicine, China Medical University Hospital
- School of Medicine, China Medical University
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High-resolution melting of 12S rRNA and cytochrome b DNA sequences for discrimination of species within distinct European animal families. PLoS One 2014; 9:e115575. [PMID: 25531439 PMCID: PMC4274031 DOI: 10.1371/journal.pone.0115575] [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: 08/08/2014] [Accepted: 11/29/2014] [Indexed: 11/19/2022] Open
Abstract
The cheap and easy identification of species is necessary within multiple fields of molecular biology. The use of high-resolution melting (HRM) of DNA provides a fast closed-tube method for analysis of the sequence composition of the mitochondrial genes 12S rRNA and cytochrome b. We investigated the potential use of HRM for species identification within eleven different animal groups commonly found in Europe by animal-group-specific DNA amplification followed by DNA melting. Influence factors as DNA amount, additional single base alterations, and the existence of mixed samples were taken into consideration. Visual inspection combined with mathematical evaluation of the curve shapes did resolve nearly all species within an animal group. The assay can therefore not only be used for identification of animal groups and mixture analysis but also for species identification within the respective groups. The use of a universal 12S rRNA system additionally revealed a possible approach for species discrimination, mostly by exclusion. The use of the HRM assay showed to be a reliable, fast, and cheap method for species discrimination within a broad range of different animal species and can be used in a flexible "modular" manner depending on the question to be solved.
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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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Prajantasen T, Fucharoen S, Fucharoen G. High resolution melting analytical platform for rapid prenatal and postnatal diagnosis of β-thalassemia common among Southeast Asian population. Clin Chim Acta 2014; 441:56-62. [PMID: 25526804 DOI: 10.1016/j.cca.2014.12.015] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2014] [Revised: 11/30/2014] [Accepted: 12/12/2014] [Indexed: 12/01/2022]
Abstract
BACKGROUND High resolution melting (HRM) analysis is a powerful technology for scanning sequence alteration. We have applied this HRM assay to screen common β-thalassemia mutations found among Southeast Asian population. METHODS Known DNA samples with 8 common mutations were used in initial development of the methods including -28 A-G, codon 17 A-T, IVSI-1G-T, IVSI-5G-C, codon 26G-A (Hb E), codons 41/42 -TTCT, codons 71/72+A and IVSII-654 C-T. Further validation was done on 60 postnatal and 6 prenatal diagnoses of β-thalassemia. RESULTS Each mutation has specific HRM profile which could be used in rapid screening. Apart from those with DNA deletions, the results of HRM assay matched 100% with those of routine diagnosis made by routine allele specific PCR. In addition, the HRM assay could initially recognize three unknown mutations including a hitherto un-described one in Thai population. CONCLUSIONS The established HRM assay should prove useful for rapid and high throughput platform for screening and prenatal diagnosis of β-thalassemia common in the region.
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Affiliation(s)
- Thanet Prajantasen
- Biomedical Science Program, Graduate School, Khon Kaen University, Thailand; Centre for Research and Development of Medical Diagnostic Laboratories, Faculty of Associated Medical Sciences, Khon Kaen University, Khon Kaen, Thailand; Faculty of Medical Technology, Prince of Songkla University, Hat Yai, Songkhla, Thailand
| | - Supan Fucharoen
- Centre for Research and Development of Medical Diagnostic Laboratories, Faculty of Associated Medical Sciences, Khon Kaen University, Khon Kaen, Thailand.
| | - Goonnapa Fucharoen
- Centre for Research and Development of Medical Diagnostic Laboratories, Faculty of Associated Medical Sciences, Khon Kaen University, Khon Kaen, Thailand
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