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HRM method for identification of TP53 exon 5 and 8 mutations in human prostate cancer patients. Meta Gene 2022. [DOI: 10.1016/j.mgene.2022.101020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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2
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Fonseca AS, Ramão A, Bürger MC, de Souza JES, Zanette DL, de Molfetta GA, de Araújo LF, de Barros E Lima Bueno R, Aguiar GM, Plaça JR, Alves CDP, Dos Santos ARD, Vidal DO, Silva GEB, Panepucci RA, Peria FM, Feres O, da Rocha JJR, Zago MA, Silva WA. ETV4 plays a role on the primary events during the adenoma-adenocarcinoma progression in colorectal cancer. BMC Cancer 2021; 21:207. [PMID: 33648461 PMCID: PMC7919324 DOI: 10.1186/s12885-021-07857-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Accepted: 01/31/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Colorectal cancer (CRC) is one of the most common cancers worldwide; it is the fourth leading cause of death in the world and the third in Brazil. Mutations in the APC, DCC, KRAS and TP53 genes have been associated with the progression of sporadic CRC, occurring at defined pathological stages of the tumor progression and consequently modulating several genes in the corresponding signaling pathways. Therefore, the identification of gene signatures that occur at each stage during the CRC progression is critical and can present an impact on the diagnosis and prognosis of the patient. In this study, our main goal was to determine these signatures, by evaluating the gene expression of paired colorectal adenoma and adenocarcinoma samples to identify novel genetic markers in association to the adenoma-adenocarcinoma stage transition. METHODS Ten paired adenoma and adenocarcinoma colorectal samples were subjected to microarray gene expression analysis. In addition, mutations in APC, KRAS and TP53 genes were investigated by DNA sequencing in paired samples of adenoma, adenocarcinoma, normal tissue, and peripheral blood from ten patients. RESULTS Gene expression analysis revealed a signature of 689 differentially expressed genes (DEG) (fold-change> 2, p< 0.05), between the adenoma and adenocarcinoma paired samples analyzed. Gene pathway analysis using the 689 DEG identified important cancer pathways such as remodeling of the extracellular matrix and epithelial-mesenchymal transition. Among these DEG, the ETV4 stood out as one of the most expressed in the adenocarcinoma samples, further confirmed in the adenocarcinoma set of samples from the TCGA database. Subsequent in vitro siRNA assays against ETV4 resulted in the decrease of cell proliferation, colony formation and cell migration in the HT29 and SW480 colorectal cell lines. DNA sequencing analysis revealed KRAS and TP53 gene pathogenic mutations, exclusively in the adenocarcinomas samples. CONCLUSION Our study identified a set of genes with high potential to be used as biomarkers in CRC, with a special emphasis on the ETV4 gene, which demonstrated involvement in proliferation and migration.
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Affiliation(s)
- Aline Simoneti Fonseca
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, Av Bandeirantes, 3900, CEP: 14049-900, Monte Alegre, Ribeirão Preto, SP, Brazil.
- Center for Cell Based Therapy and National Institute of Science and Technology in Stem Cell and Cell Therapy, Ribeirão Preto, SP, Brazil.
- Center for Integrative Systems Biology - CISBi, NAP/USP, Ribeirão Preto, SP, Brazil.
- Research Institute Pelé Pequeno Príncipe, Av Silva Jardim, 1632, CEP: 80250-060, Água Verde, Curitiba, PR, Brazil.
| | - Anelisa Ramão
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, Av Bandeirantes, 3900, CEP: 14049-900, Monte Alegre, Ribeirão Preto, SP, Brazil
- Center for Cell Based Therapy and National Institute of Science and Technology in Stem Cell and Cell Therapy, Ribeirão Preto, SP, Brazil
| | - Matheus Carvalho Bürger
- Center for Cell Based Therapy and National Institute of Science and Technology in Stem Cell and Cell Therapy, Ribeirão Preto, SP, Brazil
| | - Jorge Estefano Santana de Souza
- Center for Cell Based Therapy and National Institute of Science and Technology in Stem Cell and Cell Therapy, Ribeirão Preto, SP, Brazil
| | - Dalila Lucíola Zanette
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, Av Bandeirantes, 3900, CEP: 14049-900, Monte Alegre, Ribeirão Preto, SP, Brazil
- Center for Cell Based Therapy and National Institute of Science and Technology in Stem Cell and Cell Therapy, Ribeirão Preto, SP, Brazil
- Center for Integrative Systems Biology - CISBi, NAP/USP, Ribeirão Preto, SP, Brazil
- Laboratory of Applied Science and Technology in Health (LASTH), Instituto Carlos Chagas, Fundação Oswaldo Cruz, Curitiba, PR, Brazil
| | - Greice Andreotti de Molfetta
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, Av Bandeirantes, 3900, CEP: 14049-900, Monte Alegre, Ribeirão Preto, SP, Brazil
- Center for Cell Based Therapy and National Institute of Science and Technology in Stem Cell and Cell Therapy, Ribeirão Preto, SP, Brazil
- Center for Integrative Systems Biology - CISBi, NAP/USP, Ribeirão Preto, SP, Brazil
| | - Luiza Ferreira de Araújo
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, Av Bandeirantes, 3900, CEP: 14049-900, Monte Alegre, Ribeirão Preto, SP, Brazil
- Center for Cell Based Therapy and National Institute of Science and Technology in Stem Cell and Cell Therapy, Ribeirão Preto, SP, Brazil
- Center for Integrative Systems Biology - CISBi, NAP/USP, Ribeirão Preto, SP, Brazil
| | - Rafaela de Barros E Lima Bueno
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, Av Bandeirantes, 3900, CEP: 14049-900, Monte Alegre, Ribeirão Preto, SP, Brazil
- Center for Cell Based Therapy and National Institute of Science and Technology in Stem Cell and Cell Therapy, Ribeirão Preto, SP, Brazil
| | - Graziela Moura Aguiar
- Center for Cell Based Therapy and National Institute of Science and Technology in Stem Cell and Cell Therapy, Ribeirão Preto, SP, Brazil
| | - Jessica Rodrigues Plaça
- Center for Cell Based Therapy and National Institute of Science and Technology in Stem Cell and Cell Therapy, Ribeirão Preto, SP, Brazil
| | - Cleidson de Pádua Alves
- Center for Cell Based Therapy and National Institute of Science and Technology in Stem Cell and Cell Therapy, Ribeirão Preto, SP, Brazil
| | - Anemari Ramos Dinarte Dos Santos
- Center for Cell Based Therapy and National Institute of Science and Technology in Stem Cell and Cell Therapy, Ribeirão Preto, SP, Brazil
| | - Daniel Onofre Vidal
- Center for Cell Based Therapy and National Institute of Science and Technology in Stem Cell and Cell Therapy, Ribeirão Preto, SP, Brazil
| | - Gyl Eanes Barros Silva
- Laboratory of Immunofluorescence and Electron Microscopy (LIME), Presidente Dutra University Hospital (HUUFMA), São Luís, MA, Brazil
| | - Rodrigo Alexandre Panepucci
- Center for Cell Based Therapy and National Institute of Science and Technology in Stem Cell and Cell Therapy, Ribeirão Preto, SP, Brazil
| | - Fernanda Maris Peria
- Departament of Medical Clinic, Medical School of Ribeirão Preto, University of São Paulo, USP, Ribeirão Preto, SP, Brazil
| | - Omar Feres
- Department of Surgery and Anatomy, School of Medicine of Ribeirão Preto, University of São Paulo, Sao Paulo, Brazil
| | | | - Marco Antonio Zago
- Center for Cell Based Therapy and National Institute of Science and Technology in Stem Cell and Cell Therapy, Ribeirão Preto, SP, Brazil
| | - Wilson Araújo Silva
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, Av Bandeirantes, 3900, CEP: 14049-900, Monte Alegre, Ribeirão Preto, SP, Brazil.
- Center for Cell Based Therapy and National Institute of Science and Technology in Stem Cell and Cell Therapy, Ribeirão Preto, SP, Brazil.
- Center for Integrative Systems Biology - CISBi, NAP/USP, Ribeirão Preto, SP, Brazil.
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Pileckyte R, Valceckiene V, Stoskus M, Matuzeviciene R, Sejoniene J, Zvirblis T, Griskevicius L. Dose Intensive Rituximab and High-Dose Methylprednisolone in Elderly or Unfit Patients with Relapsed Chronic Lymphocytic Leukemia. ACTA ACUST UNITED AC 2019; 55:medicina55110719. [PMID: 31671877 PMCID: PMC6915691 DOI: 10.3390/medicina55110719] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Revised: 10/18/2019] [Accepted: 10/25/2019] [Indexed: 11/29/2022]
Abstract
Background and Objectives: BTK and BCL2 inhibitors have changed the treatment paradigms of high-risk and elderly patients with chronic lymphocytic leukemia (CLL), but their long-term efficacy and toxicity are still unknown and the costs are considerable. Our previous data showed that Rituximab (Rtx) and high-dose methylprednisolone (HDMP) can be an effective and safe treatment option for relapsed high-risk CLL patients. Materials and Methods: We explored the efficacy and safety of a higher Rtx dose in combination with a shorter (3-day) schedule of HDMP in relapsed elderly or unfit CLL patients. Results: Twenty-five patients were included in the phase-two, single-arm trial. The median progression free survival (PFS) was 11 months (range 10–12). Median OS was 68 (range 47–89) months. Adverse events (AE) were mainly grade I–II° (77%) and no deaths occurred during the treatment period. Conclusions: 3-day HDMP and Rtx was associated with clinically meaningful improvement in most patients. The median PFS in 3-day and 5-day HDMP studies was similar and the toxicity of the 3-day HDMP schedule proved to be lower. The HDMP and Rtx combination can still be applied in some relapsed high-risk and elderly or unfit CLL patients if new targeted therapies are contraindicated or unavailable. (ClinicalTrials.gov identifier: NCT01576588).
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Affiliation(s)
- Regina Pileckyte
- Hematology, Oncology and Transfusion Medicine Center, Vilnius University Hospital Santaros Klinikos, 08661 Vilnius, Lithuania.
- Institute of Clinical Medicine, Vilnius University, 08661 Vilnius, Lithuania.
| | - Vilma Valceckiene
- Hematology, Oncology and Transfusion Medicine Center, Vilnius University Hospital Santaros Klinikos, 08661 Vilnius, Lithuania.
| | - Mindaugas Stoskus
- Hematology, Oncology and Transfusion Medicine Center, Vilnius University Hospital Santaros Klinikos, 08661 Vilnius, Lithuania.
| | - Reda Matuzeviciene
- Laboratory Diagnostics Centre, Vilnius University Hospital Santaros Klinikos, 08661 Vilnius, Lithuania.
| | - Jurgita Sejoniene
- Radiology and Nuclear Medicine Center, Vilnius University Hospital Santaros Klinikos, 08661 Vilnius, Lithuania.
| | - Tadas Zvirblis
- Hematology, Oncology and Transfusion Medicine Center, Vilnius University Hospital Santaros Klinikos, 08661 Vilnius, Lithuania.
| | - Laimonas Griskevicius
- Hematology, Oncology and Transfusion Medicine Center, Vilnius University Hospital Santaros Klinikos, 08661 Vilnius, Lithuania.
- Institute of Clinical Medicine, Vilnius University, 08661 Vilnius, Lithuania.
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Mutation screening of TP53, CHEK2 and BRCA genes in patients at high risk for hereditary breast and ovarian cancer (HBOC) in Brazil. Breast Cancer 2018; 26:397-405. [DOI: 10.1007/s12282-018-00938-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Accepted: 11/30/2018] [Indexed: 10/27/2022]
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Eskandari F, Mohaghegh MA, Mirzaei F, Ghomashlooyan M, Hejazi SH. Molecular Characteristics of Echinococcus granulosus Strains Isolated from Iranian Camel Using High Resolution Melting Analysis of atp6 and cox1 Genes. ACTA ACUST UNITED AC 2017. [DOI: 10.34172/ajcmi.2018.03] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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Bousquet G, El Bouchtaoui M, Leboeuf C, Battistella M, Varna M, Ferreira I, Plassa LF, Hamdan D, Bertheau P, Feugeas JP, Damotte D, Janin A. Tracking sub-clonal TP53 mutated tumor cells in human metastatic renal cell carcinoma. Oncotarget 2016; 6:19279-89. [PMID: 26002555 PMCID: PMC4662490 DOI: 10.18632/oncotarget.4220] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2014] [Accepted: 04/10/2015] [Indexed: 11/25/2022] Open
Abstract
Renal Cell Carcinomas (RCCs) are heterogeneous tumors with late acquisition of TP53 abnormalities during their evolution. They harbor TP53 abnormalities in their metastases. We aimed to study TP53 gene alterations in tissue samples from primary and metastatic RCCs in 36 patients followed up over a median of 4.2 years, and in xenografted issued from primary RCCs. In 36 primary RCCs systematically xenografted in mice, and in biopsies of metastases performed whenever possible during patient follow-up, we studied p53-expressing tumor cells and TP53 gene abnormalities.We identified TP53 gene alterations in primary tumors, metastases and xenografts. Quantification of tumors cells with TP53 gene alterations showed a significant increase in the metastases compared to the primary RCCs, and, strikingly, the xenografts were similar to the metastases and not to the primary RCCs from which they were derived.Using laser-microdissection of p53-expressing tumor cells, we identified TP53-mutated tumor cells in the xenografts derived from the primary RCC, and in a lung metastasis later developed in one patient. The mutation enabled us to track back their origin to a minority sub-clone in the primary heterogeneous RCC. Combining in situ and molecular analyses, we demonstrated a clonal expansion in a living patient with metastatic RCC.
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Affiliation(s)
- Guilhem Bousquet
- Université Paris Diderot, Sorbonne Paris Cité, Laboratoire de Pathologie, Paris, France.,INSERM, Paris, France.,AP-HP-Hôpital Saint-Louis, Service d'Oncologie Médicale, Paris, France
| | - Morad El Bouchtaoui
- INSERM, Paris, France.,AP-HP-Hôpital Saint-Louis, Service d'Oncologie Médicale, Paris, France
| | - Christophe Leboeuf
- Université Paris Diderot, Sorbonne Paris Cité, Laboratoire de Pathologie, Paris, France.,INSERM, Paris, France
| | - Maxime Battistella
- Université Paris Diderot, Sorbonne Paris Cité, Laboratoire de Pathologie, Paris, France.,INSERM, Paris, France.,AP-HP-Hôpital Saint-Louis, Service de Pathologie, Paris, France
| | | | - Irmine Ferreira
- Université Paris Diderot, Sorbonne Paris Cité, Laboratoire de Pathologie, Paris, France.,INSERM, Paris, France
| | | | - Diaddin Hamdan
- Centre Hospitalier de Marne-la-Vallée, Service d'Oncologie Médicale, Jossigny, France
| | - Philippe Bertheau
- Université Paris Diderot, Sorbonne Paris Cité, Laboratoire de Pathologie, Paris, France.,INSERM, Paris, France.,AP-HP-Hôpital Saint-Louis, Service de Pathologie, Paris, France
| | | | - Diane Damotte
- AP-HP-Hôtel-Dieu, Service de Pathologie, Paris, France
| | - Anne Janin
- Université Paris Diderot, Sorbonne Paris Cité, Laboratoire de Pathologie, Paris, France.,INSERM, Paris, France.,AP-HP-Hôpital Saint-Louis, Service de Pathologie, Paris, France
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Fitarelli-Kiehl M, Macedo GS, Schlatter RP, Koehler-Santos P, Matte UDS, Ashton-Prolla P, Giacomazzi J. Comparison of multiple genotyping methods for the identification of the cancer predisposing founder mutation p.R337H in TP53. Genet Mol Biol 2016; 39:203-9. [PMID: 27275664 PMCID: PMC4910550 DOI: 10.1590/1678-4685-gmb-2014-0351] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2014] [Accepted: 09/22/2015] [Indexed: 01/04/2023] Open
Abstract
Germline mutations in the TP53 gene are associated with Li-Fraumeni and Li-Fraumeni-Like Syndromes, characterized by increased predisposition to early-onset cancers. In Brazil, the prevalence of the TP53-p.R337H germline mutation is exceedingly high in the general population and in cancer-affected patients, probably as result of a founder effect. Several genotyping methods are used for the molecular diagnosis of LFS/LFL, however Sanger sequencing is still considered the gold standard. We compared performance, cost and turnaround time of Sanger sequencing, PCR-RFLP, TaqMan-PCR and HRM in the p.R337H genotyping. The performance was determined by analysis of 95 genomic DNA samples and results were 100% concordant for all methods. Sequencing was the most expensive method followed by TaqMan-PCR, PCR-RFLP and HRM. The overall cost of HRM increased with the prevalence of positive samples, since confirmatory sequencing must be performed when a sample shows an abnormal melting profile, but remained lower than all other methods when the mutation prevalence was less than 2.5%. Sequencing had the highest throughput and the longest turnaround time, while TaqMan-PCR showed the lowest turnaround and hands-on times. All methodologies studied are suitable for the detection of p.R337H and the choice will depend on the application and clinical scenario.
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Affiliation(s)
- Mariana Fitarelli-Kiehl
- Programa de Pós-Graduação em Genética e Biologia Molecular,
Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil
- Laboratório de Medicina Genômica, Centro de Pesquisa Experimental,
Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre, RS, Brazil
| | - Gabriel S. Macedo
- Programa de Pós-Graduação em Genética e Biologia Molecular,
Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil
- Laboratório de Medicina Genômica, Centro de Pesquisa Experimental,
Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre, RS, Brazil
| | - Rosane Paixão Schlatter
- Grupo de Pesquisa e Pós-Graduação (GPPG), Hospital de Clínicas de
Porto Alegre, and Programa de Pós Graduação em Cardiologia, UFRGS Porto Alegre, RS,
Brazil
| | - Patricia Koehler-Santos
- Unidade de Análises Moleculares e de Proteínas (UAMP), Centro de
Pesquisa Experimental, Hospital de Clínicas de Porto Alegre, Porto Alegre, RS,
Brazil
| | - Ursula da Silveira Matte
- Programa de Pós-Graduação em Genética e Biologia Molecular,
Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil
- Unidade de Análises Moleculares e de Proteínas (UAMP), Centro de
Pesquisa Experimental, Hospital de Clínicas de Porto Alegre, Porto Alegre, RS,
Brazil
- Departamento de Genética, Universidade Federal do Rio Grande do Sul
(UFRGS), Porto Alegre, RS, Brazil
| | - Patricia Ashton-Prolla
- Programa de Pós-Graduação em Genética e Biologia Molecular,
Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil
- Laboratório de Medicina Genômica, Centro de Pesquisa Experimental,
Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre, RS, Brazil
- Departamento de Genética, Universidade Federal do Rio Grande do Sul
(UFRGS), Porto Alegre, RS, Brazil
| | - Juliana Giacomazzi
- Laboratório de Medicina Genômica, Centro de Pesquisa Experimental,
Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre, RS, Brazil
- Departamento de Genética, Universidade Federal do Rio Grande do Sul
(UFRGS), Porto Alegre, RS, Brazil
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Kanderian S, Jiang L, Knight I. Automated Classification and Cluster Visualization of Genotypes Derived from High Resolution Melt Curves. PLoS One 2015; 10:e0143295. [PMID: 26605797 PMCID: PMC4659556 DOI: 10.1371/journal.pone.0143295] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2015] [Accepted: 11/03/2015] [Indexed: 11/19/2022] Open
Abstract
Introduction High Resolution Melting (HRM) following PCR has been used to identify DNA genotypes. Fluorescent dyes bounded to double strand DNA lose their fluorescence with increasing temperature, yielding different signatures for different genotypes. Recent software tools have been made available to aid in the distinction of different genotypes, but they are not fully automated, used only for research purposes, or require some level of interaction or confirmation from an analyst. Materials and Methods We describe a fully automated machine learning software algorithm that classifies unknown genotypes. Dynamic melt curves are transformed to multidimensional clusters of points whereby a training set is used to establish the distribution of genotype clusters. Subsequently, probabilistic and statistical methods were used to classify the genotypes of unknown DNA samples on 4 different assays (40 VKORC1, CYP2C9*2, CYP2C9*3 samples in triplicate, and 49 MTHFR c.665C>T samples in triplicate) run on the Roche LC480. Melt curves of each of the triplicates were genotyped separately. Results Automated genotyping called 100% of VKORC1, CYP2C9*3 and MTHFR c.665C>T samples correctly. 97.5% of CYP2C9*2 melt curves were genotyped correctly with the remaining 2.5% given a no call due to the inability to decipher 3 melt curves in close proximity as either homozygous mutant or wild-type with greater than 99.5% posterior probability. Conclusions We demonstrate the ability to fully automate DNA genotyping from HRM curves systematically and accurately without requiring any user interpretation or interaction with the data. Visualization of genotype clusters and quantification of the expected misclassification rate is also available to provide feedback to assay scientists and engineers as changes are made to the assay or instrument.
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Affiliation(s)
- Sami Kanderian
- Canon U.S. Life Sciences, Rockville, MD, United States of America
- * E-mail:
| | - Lingxia Jiang
- Canon U.S. Life Sciences, Rockville, MD, United States of America
| | - Ivor Knight
- Canon U.S. Life Sciences, Rockville, MD, United States of America
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Kim HJ, Jeon BS. Hypothesis: somatic mosaicism and Parkinson disease. Exp Neurobiol 2014; 23:271-6. [PMID: 25548528 PMCID: PMC4276799 DOI: 10.5607/en.2014.23.4.271] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2014] [Revised: 09/29/2014] [Accepted: 09/29/2014] [Indexed: 12/18/2022] Open
Abstract
Mutations causing genetic disorders can occur during mitotic cell division after fertilization, which is called somatic mutations. This leads to somatic mosaicism, where two or more genetically distinct cells are present in one individual. Somatic mutations are the most well studied in cancer where it plays an important role and also have been associated with some neurodegenerative disorders. The study of somatic mosaicism in Parkinson disease (PD) is only in its infancy, and a case with somatic mutation has not yet been described. However, we can speculate that a somatic mutation affecting cells in the central nervous system including substantia nigra dopaminergic neurons could lead to the development of PD through the same pathomechanisms of genetic PD even in the absence of a germ-line mutation. Theoretically, a number of genes could be candidates for genetic analysis for the presence of somatic mosaicism. Among them, SNCA and PARK2 could be the best candidates to analyze. Because analyzing brain tissues in living patients is impossible, alternative tissues could be used to indicate the genetic status of the brain. Performance of the technology is another factor to consider when analyzing the tissues.
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Affiliation(s)
- Han-Joon Kim
- Department of Neurology and Movement Disorder Center, Parkinson Study Group, and Neuroscience Research Institute, College of Medicine, Seoul National University, Seoul, Korea
| | - Beom S Jeon
- Department of Neurology and Movement Disorder Center, Parkinson Study Group, and Neuroscience Research Institute, College of Medicine, Seoul National University, Seoul, Korea
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Cury NM, Ferraz VE, Silva WA. TP53 p.R337H prevalence in a series of Brazilian hereditary breast cancer families. Hered Cancer Clin Pract 2014; 12:8. [PMID: 24625245 PMCID: PMC3995619 DOI: 10.1186/1897-4287-12-8] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2013] [Accepted: 02/27/2014] [Indexed: 02/07/2023] Open
Abstract
Background Approximately 5-10% of breast cancers are hereditary. Among hereditary syndromes, Hereditary Breast and Ovarian Cancer Syndrome (HBOC) and Li-Fraumeni Syndrome (LFS) have received the most attention. HBOC is due to mutations in the BRCA1 and BRCA2 genes and is characterized by breast adenocarcinoma and/or epithelial ovarian carcinoma. LFS is associated with germline mutations in TP53; the most frequent cancer types associated with this syndrome are sarcoma, breast cancer, leukemia, brain tumors and adrenocortical carcinomas. Other cancers related to LFS are found at lower frequencies. In Brazil, especially in the southern part of the country, a specific mutation in the TP53 gene, TP53 p.R337H, occurs at a high frequency in childhood adrenocortical tumors. It has been proposed that this mutation increases breast cancer risk in southern Brazilian women. Methods We carried out a case-control study to determine the prevalence of the TP53 p.R337H mutation in 28 female cancer patients attended at the Cancer Genetic Counseling Service of the General Hospital of the University of São Paulo Medical School of Ribeirão Preto who fulfilled Hereditary Breast and Ovary Cancer Syndrome genetic test criteria compared to healthy woman (controls). TP53 p.R337H mutation status was determined using the High Resolution Melting (HRM) method, followed by DNA sequencing. Fisher’s test was used to compare the prevalence of TP53 p.R337H in the patient and control groups. Results Two of the breast cancer cases (7.1%) and none of the controls carried the TP53 p.R337H mutation. At the time of the investigation, both cases fulfilled testing criteria for Hereditary Breast and Ovary Cancer Syndrome but not Li-Fraumeni or Li-Fraumeni-like Syndrome, based on genetic testing criteria of NCCN Clinical Practice Guidelines in Oncology (v.1.2010). Conclusions We suggest that genetic screening of Brazilian breast cancer patients who fulfill Hereditary Breast and Ovary Cancer Syndrome criteria and have a family history that includes other tumors of the LFS/LFL spectrum be tested for the TP53 p.R337H mutation.
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Affiliation(s)
| | - Victor Ef Ferraz
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo (FMRP/USP), São Paulo, Brazil.
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Chen D, Wang YY, Chuai ZR, Huang JF, Wang YX, Liu K, Zhang LQ, Yang Z, Shi DC, Liu Q, Huang Q, Fu WL. High-resolution melting analysis for accurate detection of BRAF mutations: a systematic review and meta-analysis. Sci Rep 2014; 4:4168. [PMID: 24566771 PMCID: PMC3933866 DOI: 10.1038/srep04168] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2013] [Accepted: 02/03/2014] [Indexed: 12/24/2022] Open
Abstract
The high-resolution melting curve analysis (HRMA) might be a good alternative method for rapid detection of BRAF mutations. However, the accuracy of HRMA in detection of BRAF mutations has not been systematically evaluated. We performed a systematic review and meta-analysis involving 1324 samples from 14 separate studies. The overall sensitivity of HRMA was 0.99 (95% confidence interval (CI) = 0.75–0.82), and the overall specificity was very high at 0.99 (95% CI = 0.94–0.98). The values for the pooled positive likelihood ratio, negative likelihood ratio, and diagnostic odds ratio were 68.01 (95% CI = 25.33–182.64), 0.06 (95% CI = 0.03–0.11), and1263.76 (95% CI = 393.91–4064.39), respectively. The summary receiver operating characteristic curve for the same data shows an area of 1.00 and a Q* value of 0.97. The high sensitivity and specificity, simplicity, low cost, less labor or time and rapid turnaround make HRMA a good alternative method for rapid detection of BRAF mutations in the clinical practice.
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Affiliation(s)
- Dong Chen
- Department of Laboratory Medicine, Southwest Hospital, Third Military Medical University, Chongqing, PR China
| | - Yan-Yan Wang
- Research and service centre of laboratory medicine, Chengdu Military general Hospital, Chengdu, PR China
| | - Zheng-Ran Chuai
- Department of Laboratory Medicine, Southwest Hospital, Third Military Medical University, Chongqing, PR China
| | - Jun-Fu Huang
- Department of Laboratory Medicine, Southwest Hospital, Third Military Medical University, Chongqing, PR China
| | - Yun-Xia Wang
- Department of Laboratory Medicine, Southwest Hospital, Third Military Medical University, Chongqing, PR China
| | - Kai Liu
- Research Center for Nutrition and Food Safety, Institute of Military Preventive Medicine, Third Military Medical University, Chongqing, PR China
| | - Li-Qun Zhang
- Department of Laboratory Medicine, Southwest Hospital, Third Military Medical University, Chongqing, PR China
| | - Zhao Yang
- Department of Laboratory Medicine, Southwest Hospital, Third Military Medical University, Chongqing, PR China
| | - Da-Chuan Shi
- Department of Laboratory Medicine, Southwest Hospital, Third Military Medical University, Chongqing, PR China
| | - Qian Liu
- Department of Laboratory Medicine, Southwest Hospital, Third Military Medical University, Chongqing, PR China
| | - Qing Huang
- Department of Laboratory Medicine, Southwest Hospital, Third Military Medical University, Chongqing, PR China
| | - Wei-Ling Fu
- Department of Laboratory Medicine, Southwest Hospital, Third Military Medical University, Chongqing, PR China
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Verneuil L, Varna M, Ratajczak P, Leboeuf C, Plassa LF, Elbouchtaoui M, Schneider P, Sandid W, Lebbé C, Peraldi MN, Sigaux F, de Thé H, Janin A. Human skin carcinoma arising from kidney transplant-derived tumor cells. J Clin Invest 2013; 123:3797-801. [PMID: 23979160 DOI: 10.1172/jci66721] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2012] [Accepted: 05/23/2013] [Indexed: 01/04/2023] Open
Abstract
Tumor cells with donor genotype have been identified in human skin cancer after allogeneic transplantation; however, the donor contribution to the malignant epithelium has not been established. Kidney transplant recipients have an increased risk of invasive skin squamous cell carcinoma (SCC), which is associated with accumulation of the tumor suppressor p53 and TP53 mutations. In 21 skin SCCs from kidney transplant recipients, we systematically assessed p53 expression and donor/recipient origin in laser-microdissected p53+ tumor cells. In one patient, molecular analyses demonstrated that skin tumor cells had the donor genotype and harbored a TP53 mutation in codon 175. In a kidney graft biopsy performed 7 years before the skin SCC diagnosis, we found p53+ cells in the renal tubules. We identified the same TP53 mutation in these p53+ epithelial cells from the kidney transplant. These findings provide evidence for a donor epithelial cell contribution to the malignant skin epithelium in the recipient in the setting of allogeneic kidney transplantation. This finding has theoretical implications for cancer initiation and progression and clinical implications in the context of prolonged immunosuppression and longer survival of kidney transplant patients.
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13
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Rostami S, Talebi S, Babaei Z, Sharbatkhori M, Ziaali N, Rostami H, Harandi MF. High resolution melting technique for molecular epidemiological studies of cystic echinococcosis: differentiating G1, G3, and G6 genotypes of Echinococcus granulosus sensu lato. Parasitol Res 2013; 112:3441-7. [PMID: 23832641 DOI: 10.1007/s00436-013-3523-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2013] [Accepted: 06/25/2013] [Indexed: 10/26/2022]
Abstract
Reliable and rapid genotyping of large number of Echinococcus granulosus sensu lato isolates is crucial for understanding the epidemiology and transmission of cystic echinococcosis. We have developed a method for distinguishing and discriminating common genotypes of E. granulosus s.l. (G1, G3, and G6) in Iran. This method is based on polymerase chain reaction coupled with high resolution melting curve (HRM), ramping from 70 to 86 °C with fluorescence data acquisition set at 0.1 °C increments and continuous fluorescence monitoring. Consistency of this technique was assessed by inter- and intra-assays. Assessment of intra- and inter-assay variability showed low and acceptable coefficient of variations ranging from 0.09 to 0.17 %. Two hundred and eighty E. granulosus s.l. isolates from sheep, cattle, and camel were used to evaluate the applicability and accuracy of the method. The isolates were categorized as G1 (93, 94, and 25%), G3 (7, 4, and 4%), and G6 (0, 2, and 71%) for sheep, cattle, and camel, respectively. HRM results were completely compatible with those obtained from sequencing and rostellar hook measurement. This method proved to be a valuable screening tool for large-scale molecular epidemiological studies.
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Affiliation(s)
- Sima Rostami
- Research Center of Tropical and Infectious Diseases, Kerman University of Medical Sciences, Kerman, Iran
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14
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Pindurová E, Zourková A, Zrůstová J, Juřica J, Pavelka A. Alternative reliable method for cytochrome P450 2D6 poor metabolizers genotyping. Mol Biotechnol 2013; 53:29-40. [PMID: 22367691 DOI: 10.1007/s12033-012-9510-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
High-resolution melting curve analysis (HRM) of polymerase chain reaction (PCR) amplicons has been described as a fast, cheap, and reliable closed-tube method of genotyping with no need for labeled primers or labeled probes. We adapted this melting analysis assay for the detection of the most common nonfunctional alleles of cytochrome P-450 (CYP) 2D6 in the Caucasian population that affect the metabolism of many commonly used drugs. We used this method to genotype 91 patients under paroxetine therapy. The presence and the constitution of the most common single-nucleotide polymorphisms (1846G>A, 2988G>A, 100C>T, 2549delA, 2615_2617delAAG, and 1707delT) in poor and intermediate metabolizers from the Caucasian population were detected in short amplicons (≤148 bp). After fluorescence normalization, the wild-type, homozygous, and heterozygous samples were easily distinguishable from each other by their specific melting curve shape. A total of 92.6% of the 1846G>A heterozygotes, 96% of the 100C>T heterozygotes, and 100% of the 2988G>A, 2549delA, 2615_2617delAAG, and 1707delT heterozygotes have been correctly distinguished from the wild types. One hundred percent of all the homozygotes in this group of patients have been detected without any error. HRM of short amplicons is a simple tool for effective, rapid, and reliable CYP2D6 genotyping that does not require real-time PCR, labeled probes, processing or any separations after PCR. The reaction is performed in a closed-tube system and is highly specific and sensitive. We proved that this technique is highly reliable for use in routine diagnostics.
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Affiliation(s)
- E Pindurová
- Department of Applied Neuroscience, Faculty of Medicine, Central European Institute of Technology (CEITEC), Brno, Czech Republic.
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Proukakis C, Houlden H, Schapira AH. Somatic alpha-synuclein mutations in Parkinson's disease: hypothesis and preliminary data. Mov Disord 2013; 28:705-12. [PMID: 23674490 PMCID: PMC3739940 DOI: 10.1002/mds.25502] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2012] [Revised: 03/13/2013] [Accepted: 04/01/2013] [Indexed: 02/02/2023] Open
Abstract
Alpha-synuclein (SNCA) is crucial in the pathogenesis of Parkinson's disease (PD), yet mutations in the SNCA gene are rare. Evidence for somatic genetic variation in normal humans, also involving the brain, is increasing, but its role in disease is unknown. Somatic SNCA mutations, arising in early development and leading to mosaicism, could contribute to PD pathogenesis and yet be absent or undetectable in DNA derived from peripheral lymphocytes. Such mutations could underlie the widespread pathology in PD, with the precise clinical outcome dependent on their type and the timing and location of their occurrence. We recently reported a novel SNCA mutation (c.150T>G, p.H50Q) in PD brain-derived DNA. To determine if there was mosaicism for this, a PCR and cloning strategy was used to take advantage of a nearby heterozygous intronic polymorphism. No evidence of mosaicism was found. High-resolution melting curve analysis of SNCA coding exons, which was shown to be sensitive enough to detect low proportions of 2 known mutations, did not reveal any further mutations in DNA from 28 PD brain-derived samples. We outline the grounds that make the somatic SNCA mutation hypothesis consistent with genetic, embryological, and pathological data. Further studies of brain-derived DNA are warranted and should include DNA from multiple regions and methods for detecting other types of genomic variation. © 2013 Movement Disorder Society
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Affiliation(s)
- Christos Proukakis
- Department of Clinical Neuroscience, Institute of Neurology, University College London, London, United Kingdom.
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Li BS, Wang XY, Xu AG, Ma FL, Ma QY, Li Z, Liu JH, Gan AH, Yu ZJ, Zhang XH, Jiang B. High-Resolution Melting Assay (HRMA) is a Simple and Sensitive Stool-Based DNA Test for the Detection of Mutations in Colorectal Neoplasms. Clin Colorectal Cancer 2012; 11:280-90. [DOI: 10.1016/j.clcc.2012.04.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2011] [Revised: 03/14/2012] [Accepted: 04/12/2012] [Indexed: 01/04/2023]
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17
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Anasagasti A, Irigoyen C, Barandika O, López de Munain A, Ruiz-Ederra J. Current mutation discovery approaches in Retinitis Pigmentosa. Vision Res 2012; 75:117-29. [PMID: 23022136 DOI: 10.1016/j.visres.2012.09.012] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2012] [Revised: 09/08/2012] [Accepted: 09/13/2012] [Indexed: 12/22/2022]
Abstract
With a worldwide prevalence of about 1 in 3500-5000 individuals, Retinitis Pigmentosa (RP) is the most common form of hereditary retinal degeneration. It is an extremely heterogeneous group of genetically determined retinal diseases leading to progressive loss of vision due to impairment of rod and cone photoreceptors. RP can be inherited as an autosomal-recessive, autosomal-dominant, or X-linked trait. Non-Mendelian inheritance patterns such as digenic, maternal (mitochondrial) or compound heterozygosity have also been reported. To date, more than 65 genes have been implicated in syndromic and non-syndromic forms of RP, which account for only about 60% of all RP cases. Due to this high heterogeneity and diversity of inheritance patterns, the molecular diagnosis of syndromic and non-syndromic RP is very challenging, and the heritability of 40% of total RP cases worldwide remains unknown. However new sequencing methodologies, boosted by the human genome project, have contributed to exponential plummeting in sequencing costs, thereby making it feasible to include molecular testing for RP patients in routine clinical practice within the coming years. Here, we summarize the most widely used state-of-the-art technologies currently applied for the molecular diagnosis of RP, and address their strengths and weaknesses for the molecular diagnosis of such a complex genetic disease.
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Affiliation(s)
- Ander Anasagasti
- Division of Neurosciences, Instituto Biodonostia, San Sebastián, Gipuzkoa, Spain
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18
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Obul J, Itoga S, Abliz M, Sato K, Ishige T, Utsuno E, Matsushita K, Matsubara H, Nomura F. High-resolution melting analyses for gene scanning of APC, MLH1, MSH2, and MSH6 associated with hereditary colorectal cancer. Genet Test Mol Biomarkers 2012; 16:406-11. [PMID: 22283331 DOI: 10.1089/gtmb.2011.0166] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Hereditary colorectal cancer accounts for approximately 4-5% of all colorectal cancers. The causative genes for familial adenomatous polyposis and hereditary nonpolyposis colorectal cancer are large, making comprehensive analyses difficult. Therefore, high-throughput and practical methods are required to make an early diagnosis of hereditary colorectal cancers and identify high-risk individuals. For this purpose, we developed a novel gene scanning method by high-resolution melting (HRM) analysis. METHODS High-resolution melting (HRM) analysis is a promising prescreening method for nucleic acid sequence variants because of its high sensitivity and high-throughput capability. We evaluated HRM for screening APC, MLH1, MSH2, and MSH6 genes for point mutations, small deletions, and insertions. Simultaneously, we evaluated quantitative polymerase chain reaction-HRM (qPCR-HRM) for screening the MSH2 gene for large rearrangements. RESULTS All 28 point mutations and 1 large rearrangement were successfully detected by qPCR-HRM analysis. CONCLUSIONS A fast and reliable mutation detection strategy with HRM and qPCR-HRM was used to diagnose hereditary colorectal cancers. Because this method is simple and economical, it may be useful in diagnostic laboratories.
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Affiliation(s)
- Jurat Obul
- Department of Molecular Diagnosis, Graduate School of Medicine, Chiba University, Chiba, Japan.
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19
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Pileckyte R, Jurgutis M, Valceckiene V, Stoskus M, Gineikiene E, Sejoniene J, Degulys A, Zvirblis T, Griskevicius L. Dose-dense high-dose methylprednisolone and rituximab in the treatment of relapsed or refractory high-risk chronic lymphocytic leukemia. Leuk Lymphoma 2011; 52:1055-65. [PMID: 21599591 DOI: 10.3109/10428194.2011.562572] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
This study evaluated the efficacy and safety of dose-dense high-dose methylprednisolone (HDMP) plus rituximab (Rtx) in patients with high-risk CLL. Twenty-nine patients with relapsed or progressive CLL with adverse cytogenetics (17p deletion, TP53 mutation, 11q deletion, and/or trisomy 12) and/or progression within 12 months of fludarabine treatment were included. HDMP (1 g/m(2)) was administered daily for 5 days of each treatment course. Rtx was administered on days 1 (375 mg/m(2)) and 5 (500 mg/m(2)) of the first treatment course, on days 1 (500 mg/m(2)) and 5 (500 mg/m(2)) of the second course, and on day 1 (500 mg/m(2)) of courses 3-6. The cycles were repeated every 21 days. The overall response rate (ORR) was 62%, and 28% of patients had stable disease. In 13 patients with 17p deletion/TP53 mutation, ORR was 69%. After 22 months, the median progression-free and overall survivals were 12 and 31 months, respectively. The most frequent toxicity was hyperglycemia, and three deaths occurred in the study. Dose-dense treatment with HDMP and Rtx is an effective therapy with a favorable safety profile in patients with high-risk CLL, including those with 17p deletion/TP53 mutation.
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Affiliation(s)
- Regina Pileckyte
- Department of Hematology, Hematology, Oncology and Transfusion Medicine Center, Vilnius University Hospital Santariskiu Clinics, Vilnius, Lithuania.
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20
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Milbury CA, Chen CC, Mamon H, Liu P, Santagata S, Makrigiorgos GM. Multiplex amplification coupled with COLD-PCR and high resolution melting enables identification of low-abundance mutations in cancer samples with low DNA content. J Mol Diagn 2011; 13:220-32. [PMID: 21354058 DOI: 10.1016/j.jmoldx.2010.10.008] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2010] [Revised: 09/09/2010] [Accepted: 10/18/2010] [Indexed: 01/18/2023] Open
Abstract
Thorough screening of cancer-specific biomarkers, such as DNA mutations, can require large amounts of genomic material; however, the amount of genomic material obtained from some specimens (such as biopsies, fine-needle aspirations, circulating-DNA or tumor cells, and histological slides) may limit the analyses that can be performed. Furthermore, mutant alleles may be at low-abundance relative to wild-type DNA, reducing detection ability. We present a multiplex-PCR approach tailored to amplify targets of interest from small amounts of precious specimens, for extensive downstream detection of low-abundance alleles. Using 3 ng of DNA (1000 genome-equivalents), we amplified the 1 coding exons (2-11) of TP53 via multiplex-PCR. Following multiplex-PCR, we performed COLD-PCR (co-amplification of major and minor alleles at lower denaturation temperature) to enrich low-abundance variants and high resolution melting (HRM) to screen for aberrant melting profiles. Mutation-positive samples were sequenced. Evaluation of mutation-containing dilutions revealed improved sensitivities after COLD-PCR over conventional-PCR. COLD-PCR improved HRM sensitivity by approximately threefold to sixfold. Similarly, COLD-PCR improved mutation identification in sequence-chromatograms over conventional PCR. In clinical specimens, eight mutations were detected via conventional-PCR-HRM, whereas 12 were detected by COLD-PCR-HRM, yielding a 33% improvement in mutation detection. In summary, we demonstrate an efficient approach to increase screening capabilities from limited DNA material via multiplex-PCR and improve mutation detection sensitivity via COLD-PCR amplification.
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Affiliation(s)
- Coren A Milbury
- Department of Radiation Oncology, Dana-Farber/Brigham and Women's Cancer Center, Harvard Medical School, Boston, Massachusetts 02115, USA
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21
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Romero A, Pérez-Segura P, Tosar A, García-Saenz JA, Díaz-Rubio E, Caldés T, de la Hoya M. A HRM-based screening method detects RAD51C germ-line deleterious mutations in Spanish breast and ovarian cancer families. Breast Cancer Res Treat 2011; 129:939-46. [PMID: 21537932 DOI: 10.1007/s10549-011-1543-x] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2011] [Accepted: 04/20/2011] [Indexed: 11/30/2022]
Abstract
The RAD51C gene has been recently proposed as a high-penetrance breast and ovarian cancer gene. However, early replication studies have failed to confirm the finding. Thus, further studies in larger cohorts should be conducted in order to clarify the role of RAD51C as a cancer susceptibility gene. Here, we describe a high-resolution melting analysis (HRMA)-based method developed for presequence screening of RAD51C sequence variants. We have screened RAD51C sequence variants by HRMA in 492 breast cancer patients with family history of breast and/or ovarian cancer that were previously tested negative for BRCA1/2. All variants were confirmed by direct sequencing. We have detected 12 different RAD51C germ-line sequence variants, including eight transitions, two transversion, and two indels (insA, and delT). All these variants generated melting profiles which differ from wild type homozygous controls. Interestingly, we have identified one clearly pathogenic mutation (c.774delT) in the subset of 101 breast and ovarian cancer families, supporting that RAD51C is a human breast and ovarian cancer susceptibility gene.
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Affiliation(s)
- Atocha Romero
- Laboratorio de Oncología Molecular, Planta baja sur. Hospital Clínico San Carlos, c/Martín Lagos s/n, 28040 Madrid, Spain
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22
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Janavičius R, Andrėkutė K, Mickys U, Rudaitis V, Brasiūnienė B, Griškevičius L. Apparently "BRCA-related" breast and ovarian cancer patient with germline TP53 mutation. Breast J 2011; 17:409-15. [PMID: 21535297 DOI: 10.1111/j.1524-4741.2011.01088.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Germline TP53 gene mutations are associated with complex cancer predisposition syndrome, the Li--Fraumeni syndrome, and are not as rare as were previously thought. Currently, the identification of Li--Fraumeni syndrome is mostly based on a conformance to descriptive criteria, which recently were amended to include wider spectrum of malignancies. The presence of very young age-onset breast cancers in TP53 mutations families is a feature that overlaps with hereditary breast/ovarian cancer families with BRCA1/2 genes mutations. Peri-diagnostic germline TP53 testing results in breast cancer patients can significantly affect surgical and adjuvant radiotherapy choices. The aim of this case report is to emphasize the importance of peri-diagnostic germline TP53 molecular testing in patients with early-onset breast cancer and its effect on the management and outcome of the disease. We present the apparent BRCA1-related, although mutation negative, breast and ovarian cancer patient who subsequently was confirmed to be TP53 c.817C>T (p.R273C) mutation carrier and discuss the importance of peri-diagnostic oncogenetic TP53 testing in early breast cancer cases. Histopathology and genetic modifiers (MDM2 SNP309G; TP53 R72P, PIN3) data are also addressed.
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Affiliation(s)
- Ramūnas Janavičius
- Department of Molecular and Regenerative Medicine, Hematology, Oncology and Transfusion Medicine Center, Vilnius University Hospital Santariskiu Clinics, Vilnius, Lithuania.
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23
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Arrabal L, Teresa L, Sánchez-Alcudia R, Castro M, Medrano C, Gutiérrez-Solana L, Roldán S, Ormazábal A, Pérez-Cerdá C, Merinero B, Pérez B, Artuch R, Ugarte M, Desviat LR. Genotype–phenotype correlations in sepiapterin reductase deficiency. A splicing defect accounts for a new phenotypic variant. Neurogenetics 2011; 12:183-91. [DOI: 10.1007/s10048-011-0279-4] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2011] [Accepted: 02/18/2011] [Indexed: 12/25/2022]
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Li BS, Wang XY, Ma FL, Jiang B, Song XX, Xu AG. Is high resolution melting analysis (HRMA) accurate for detection of human disease-associated mutations? A meta analysis. PLoS One 2011; 6:e28078. [PMID: 22194806 PMCID: PMC3237421 DOI: 10.1371/journal.pone.0028078] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2011] [Accepted: 10/31/2011] [Indexed: 01/15/2023] Open
Abstract
BACKGROUND High Resolution Melting Analysis (HRMA) is becoming the preferred method for mutation detection. However, its accuracy in the individual clinical diagnostic setting is variable. To assess the diagnostic accuracy of HRMA for human mutations in comparison to DNA sequencing in different routine clinical settings, we have conducted a meta-analysis of published reports. METHODOLOGY/PRINCIPAL FINDINGS Out of 195 publications obtained from the initial search criteria, thirty-four studies assessing the accuracy of HRMA were included in the meta-analysis. We found that HRMA was a highly sensitive test for detecting disease-associated mutations in humans. Overall, the summary sensitivity was 97.5% (95% confidence interval (CI): 96.8-98.5; I(2) = 27.0%). Subgroup analysis showed even higher sensitivity for non-HR-1 instruments (sensitivity 98.7% (95%CI: 97.7-99.3; I(2) = 0.0%)) and an eligible sample size subgroup (sensitivity 99.3% (95%CI: 98.1-99.8; I(2) = 0.0%)). HRMA specificity showed considerable heterogeneity between studies. Sensitivity of the techniques was influenced by sample size and instrument type but by not sample source or dye type. CONCLUSIONS/SIGNIFICANCE These findings show that HRMA is a highly sensitive, simple and low-cost test to detect human disease-associated mutations, especially for samples with mutations of low incidence. The burden on DNA sequencing could be significantly reduced by the implementation of HRMA, but it should be recognized that its sensitivity varies according to the number of samples with/without mutations, and positive results require DNA sequencing for confirmation.
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Affiliation(s)
- Bing-Sheng Li
- Department of Gastroenterology, Nanfang Hospital, Southern Medical University, Guangzhou, People's Republic of China
- Guangdong Provincial Key Laboratory of Gastroenterology, Guangzhou, People's Republic of China
| | - Xin-Ying Wang
- Department of Gastroenterology, Nanfang Hospital, Southern Medical University, Guangzhou, People's Republic of China
- Guangdong Provincial Key Laboratory of Gastroenterology, Guangzhou, People's Republic of China
| | - Feng-Li Ma
- Department of Gastroenterology, Nanfang Hospital, Southern Medical University, Guangzhou, People's Republic of China
- Guangdong Provincial Key Laboratory of Gastroenterology, Guangzhou, People's Republic of China
| | - Bo Jiang
- Department of Gastroenterology, Nanfang Hospital, Southern Medical University, Guangzhou, People's Republic of China
- Guangdong Provincial Key Laboratory of Gastroenterology, Guangzhou, People's Republic of China
| | - Xiao-Xiao Song
- School of Public Health, Kunming Medical University, Kunming, People's Republic of China
| | - An-Gao Xu
- Huizhou Medicine Institute, Huizhou First Hospital, Huizhou, Guangdong, People's Republic of China
- * E-mail:
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25
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Janavicius R, Matiukaite D, Jakubauskas A, Griskevicius L. Microsatellite instability detection by high-resolution melting analysis. Clin Chem 2010; 56:1750-7. [PMID: 20852132 DOI: 10.1373/clinchem.2010.150680] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
BACKGROUND Microsatellite instability (MSI) is an important marker for screening for hereditary nonpolyposis colorectal cancer (Lynch syndrome) as well as a prognostic and predictive marker for sporadic colorectal cancer (CRC). The mononucleotide microsatellite marker panel is a well-established and superior alternative to the traditional Bethesda MSI analysis panel, and does not require testing for corresponding normal DNA. The most common MSI detection techniques-fluorescent capillary electrophoresis and denaturing HPLC (DHPLC)-both have advantages and drawbacks. A new high-resolution melting (HRM) analysis method enables rapid identification of heteroduplexes in amplicons by their lower thermal stability, a technique that overcomes the main shortcomings of capillary electrophoresis and DHPLC. METHODS We investigated the straightforward application of HRM for the detection of MSI in 70 archival CRC samples. HRM analysis for 2 MSI markers (BAT25 and BAT26) was evaluated, and 2 different HRM-enabled instruments were compared-the LightCycler® 480 (Roche Diagnostics) and the LightScanner(TM) (Idaho Technology). We also determined the analytical sensitivity and specificity of the HRM assay on both instruments using 11 known MSI-positive and 54 microsatellite-stable CRC samples. RESULTS All MSI-positive samples were detected on both instruments (100% analytical sensitivity). The LightScanner performed better for analytical specificity, giving a combined specificity value of 99.1% compared with 92.3% on the LightCycler 480. CONCLUSIONS We expanded the application of the HRM analysis method as an effective MSI detection technique for clinical samples.
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Affiliation(s)
- Ramunas Janavicius
- Department of Molecular and Regenerative Medicine, Hematology, Oncology and Transfusion Medicine Center, Vilnius University Hospital Santariskiu Clinics, Vilnius, Lithuania.
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26
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Montgomery JL, Sanford LN, Wittwer CT. High-resolution DNA melting analysis in clinical research and diagnostics. Expert Rev Mol Diagn 2010; 10:219-40. [PMID: 20214540 DOI: 10.1586/erm.09.84] [Citation(s) in RCA: 146] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Among nucleic acid analytical methods, high-resolution melting analysis is gaining more and more attention. High-resolution melting provides simple, homogeneous solutions for variant scanning and genotyping, addressing the needs of today's overburdened laboratories with rapid turnaround times and minimal cost. The flexibility of the technique has allowed it to be adopted by a wide range of disciplines for a variety of applications. In this review we examine the broad use of high-resolution melting analysis, including gene scanning, genotyping (including small amplicon, unlabeled probe and snapback primers), sequence matching and methylation analysis. Four major application arenas are examined to demonstrate the methods and approaches commonly used in particular fields. The appropriate usage of high-resolution melting analysis is discussed in the context of known constraints, such as sample quality and quantity, with a particular focus placed on proper experimental design in order to produce successful results.
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Affiliation(s)
- Jesse L Montgomery
- Department of Pathology, University of Utah Health Sciences Center, Salt Lake City, UT 84132, USA
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27
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Guan M, Zhang J, Chen Y, Liu W, Kong N, Zou H. High-resolution melting analysis for the rapid detection of an intronic single nucleotide polymorphism in SLC22A12 in male patients with primary gout in China. Scand J Rheumatol 2010; 38:276-81. [PMID: 19306160 DOI: 10.1080/03009740802572483] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
OBJECTIVES The human urate transporter 1 (URAT1, encoded by SLC22A12) was recently identified as the major absorptive urate transporter protein in the kidney responsible for regulating blood urate levels. The present study was designed to investigate the rs893006 polymorphism (GG, GT, and TT) in SLC22A12 in a total of 292 Chinese male subjects. Differences of clinical characteristics among the genotype groups were analysed. METHODS A total of 124 consecutive patients with diagnosis of primary gout and 168 healthy male volunteers were enrolled in this study. Demographic and clinical data were obtained from the patients and controls. DNA was purified from peripheral blood and the rs893006 polymorphism was determined with sequencing analysis. In addition, DNA samples were detected by high-resolution melting (HRM) analysis. Melting curves were analysed as fluorescence difference plots. The shift and curve shapes of melting profiles were used to distinguish the different genotypes. RESULTS GG, GT, and TT genotypes were unambiguously distinguished with HRM technology. Genotyping based on HRM analysis was fully concordant with the sequencing. Serum uric acid levels in the TT genotype subjects were significantly lower than those in the GG and GT genotypes. However, no differences among the groups were found in body mass index (BMI), blood pressure, creatinine, total cholesterol, and triglycerides. The TT genotype was observed more frequently among the low uric acid group than the high uric acid group. CONCLUSIONS HRM analysis is a simple, rapid and accurate one-tube assay for genotyping the SLCSSA12 gene. The rs893006 polymorphism in SLC22CA12 was confirmed to be a genetic risk for hyperuricaemia among the Chinese male population.
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Affiliation(s)
- M Guan
- Department of Laboratory Medicine, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, P. R. China
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Li J, Milbury CA, Li C, Makrigiorgos GM. Two-round coamplification at lower denaturation temperature-PCR (COLD-PCR)-based sanger sequencing identifies a novel spectrum of low-level mutations in lung adenocarcinoma. Hum Mutat 2010; 30:1583-90. [PMID: 19760750 DOI: 10.1002/humu.21112] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Reliable identification of cancer-related mutations in TP53 is often problematic, as these mutations can be randomly distributed throughout numerous codons and their relative abundance in clinical samples can fall below the sensitivity limits of conventional sequencing. To ensure the highest sensitivity in mutation detection, we adapted the recently described coamplification at lower denaturation temperature-PCR (COLD-PCR) method to employ two consecutive rounds of COLD-PCR followed by Sanger sequencing. Using this highly sensitive approach we screened 48 nonmicrodissected lung adenocarcinoma samples for TP53 mutations. Twenty-four missense/frameshift TP53 mutations throughout exons 5 to 8 were identified in 23 out of 48 (48%) lung adenocarcinoma samples examined, including eight low-level mutations at an abundance of approximately 1 to 17%, most of which would have been missed using conventional methodologies. The identified alterations include two rare lung adenocarcinoma mutations, one of which is a "disruptive" mutation currently undocumented in the lung cancer mutation databases. A sample harboring a low-level mutation ( approximately 2% abundance) concurrently with a clonal mutation (80% abundance) revealed intratumoral TP53 mutation heterogeneity. The ability to identify and sequence low-level mutations in the absence of elaborate microdissection, via COLD-PCR-based Sanger sequencing, provides a platform for accurate mutation profiling in clinical specimens and the use of TP53 as a prognostic/predictive biomarker, evaluation of cancer risk, recurrence, and further understanding of cancer biology.
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Affiliation(s)
- Jin Li
- Department of Radiation Oncology, Division of DNA Repair and Genome Stability, Dana-Farber/Brigham and Women's Cancer Center, Harvard Medical School, Boston, Massachusetts 02115, USA
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Richard E, Jorge-Finnigan A, Garcia-Villoria J, Merinero B, Desviat LR, Gort L, Briones P, Leal F, Pérez-Cerdá C, Ribes A, Ugarte M, Pérez B. Genetic and cellular studies of oxidative stress in methylmalonic aciduria (MMA) cobalamin deficiency type C (cblC) with homocystinuria (MMACHC). Hum Mutat 2010; 30:1558-66. [PMID: 19760748 DOI: 10.1002/humu.21107] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Methylmalonic aciduria (MMA) cobalamin deficiency type C (cblC) with homocystinuria (MMACHC) is the most frequent genetic disorder of vitamin B(12) metabolism. The aim of this work was to identify the mutational spectrum in a cohort of cblC-affected patients and the analysis of the cellular oxidative stress and apoptosis processes, in the presence or absence of vitamin B(12). The mutational spectrum includes nine previously described mutations: c.3G>A (p.M1L), c.217C>T (p.R73X), c.271dupA (p.R91KfsX14), c.331C>T (p.R111X), c.394C>T (p.R132X), c.457C>T (p.R153X), c.481C>T (p.R161X), c.565C>A (p.R189S), and c.615C>G (p.Y205X), and two novel changes, c.90G>A (p.W30X) and c.81+2T>G (IVS1+2T>G). The most frequent change was the known c.271dupA mutation, which accounts for 85% of the mutant alleles characterized in this cohort of patients. Owing to its high frequency, a real-time PCR and subsequent high-resolution melting (HRM) analysis for this mutation has been established for diagnostic purposes. All cell lines studied presented a significant increase of intracellular reactive oxygen species (ROS) content, and also a high rate of apoptosis, suggesting that elevated ROS levels might induce apoptosis in cblC patients. In addition, ROS levels decreased in hydroxocobalamin-incubated cells, indicating that cobalamin might either directly or indirectly act as a scavenger of ROS. ROS production might be considered as a phenotypic modifier in cblC patients, and cobalamin supplementation or additional antioxidant drugs might suppress apoptosis and prevent cellular damage in these patients.
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Affiliation(s)
- Eva Richard
- Centro de Diagnóstico de Enfermedades Moleculares, Centro de Biología Molecular-Severo Ochoa (SO) Universidad Autónoma de Madrid (UAM)-Consejo Superior de Investigaciones Científicas (CSIC), Universidad Autónoma de Madrid, Campus de Cantoblanco, Madrid, Spain
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van Eijk R, van Puijenbroek M, Chhatta AR, Gupta N, Vossen RHAM, Lips EH, Cleton-Jansen AM, Morreau H, van Wezel T. Sensitive and specific KRAS somatic mutation analysis on whole-genome amplified DNA from archival tissues. J Mol Diagn 2009; 12:27-34. [PMID: 19959798 DOI: 10.2353/jmoldx.2010.090028] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Kirsten RAS (KRAS) is a small GTPase that plays a key role in Ras/mitogen-activated protein kinase signaling; somatic mutations in KRAS are frequently found in many cancers. The most common KRAS mutations result in a constitutively active protein. Accurate detection of KRAS mutations is pivotal to the molecular diagnosis of cancer and may guide proper treatment selection. Here, we describe a two-step KRAS mutation screening protocol that combines whole-genome amplification (WGA), high-resolution melting analysis (HRM) as a prescreen method for mutation carrying samples, and direct Sanger sequencing of DNA from formalin-fixed, paraffin-embedded (FFPE) tissue, from which limited amounts of DNA are available. We developed target-specific primers, thereby avoiding amplification of homologous KRAS sequences. The addition of herring sperm DNA facilitated WGA in DNA samples isolated from as few as 100 cells. KRAS mutation screening using high-resolution melting analysis on wgaDNA from formalin-fixed, paraffin-embedded tissue is highly sensitive and specific; additionally, this method is feasible for screening of clinical specimens, as illustrated by our analysis of pancreatic cancers. Furthermore, PCR on wgaDNA does not introduce genotypic changes, as opposed to unamplified genomic DNA. This method can, after validation, be applied to virtually any potentially mutated region in the genome.
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Affiliation(s)
- Ronald van Eijk
- Department of Pathology, Leiden University Medical Center, Leiden, The Netherlands
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Milbury CA, Li J, Makrigiorgos GM. COLD-PCR-enhanced high-resolution melting enables rapid and selective identification of low-level unknown mutations. Clin Chem 2009; 55:2130-43. [PMID: 19815609 DOI: 10.1373/clinchem.2009.131029] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
BACKGROUND Analysis of clinical samples often necessitates identification of low-level somatic mutations within wild-type DNA; however, the selectivity and sensitivity of the methods are often limiting. COLD-PCR (coamplification at lower denaturation temperature-PCR) is a new form of PCR that enriches mutation-containing amplicons to concentrations sufficient for direct sequencing; nevertheless, sequencing itself remains an expensive mutation-screening approach. Conversely, high-resolution melting (HRM) is a rapid, inexpensive scanning method, but it cannot specifically identify the detected mutation. To enable enrichment, quick scanning, and identification of low-level unknown mutations, we combined COLD-PCR with HRM mutation scanning, followed by sequencing of positive samples. METHODS Mutation-containing cell-line DNA serially diluted into wild-type DNA and DNA samples from human lung adenocarcinomas containing low-level mutations were amplified via COLD-PCR and via conventional PCR for TP53 (tumor protein p53) exons 6-8, and the 2 approaches were compared. HRM analysis was used to screen amplicons for mutations; mutation-positive amplicons were sequenced. RESULTS Dilution experiments indicated an approximate 6- to 20-fold improvement in selectivity with COLD-PCR/HRM. Conventional PCR/HRM exhibited mutation-detection limits of approximately 2% to 10%, whereas COLD-PCR/HRM exhibited limits from approximately 0.1% to 1% mutant-to-wild-type ratio. After HRM analysis of lung adenocarcinoma samples, we detected 7 mutations by both PCR methods in exon 7; however, in exon 8 we detected 9 mutations in COLD-PCR amplicons, compared with only 6 mutations in conventional-PCR amplicons. Furthermore, 94% of the HRM-detected mutations were successfully sequenced with COLD-PCR amplicons, compared with 50% with conventional-PCR amplicons. CONCLUSIONS COLD-PCR/HRM improves the mutation-scanning capabilities of HRM and combines high selectivity, convenience, and low cost with the ability to sequence unknown low-level mutations in clinical samples.
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Affiliation(s)
- Coren A Milbury
- Department of Radiation Oncology, Division of Medical Physics and Biophysics, and Division of Genome Stability and DNA Repair, Dana-Farber/Brigham and Women's Cancer Center, Harvard Medical School, Boston, MA, USA
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Dobrowolski SF, Hendrickx ATM, van den Bosch BJC, Smeets HJM, Gray J, Miller T, Sears M. Identifying sequence variants in the human mitochondrial genome using high-resolution melt (HRM) profiling. Hum Mutat 2009; 30:891-8. [PMID: 19370763 DOI: 10.1002/humu.21003] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Identifying mitochondrial DNA (mtDNA) sequence variants in human diseases is complicated. Many pathological mutations are heteroplasmic, with the mutant allele represented at highly variable percentages. High-resolution melt (HRM or HRMA) profiling was applied to comprehensive assessment of the mitochondrial genome and targeted assessment of recognized pathological mutations. The assay panel providing comprehensive coverage of the mitochondrial genome utilizes 36 overlapping fragments (301-658 bp) that employ a common PCR protocol. The comprehensive assay identified heteroplasmic mutation in 33 out of 33 patient specimens tested. Allele fraction among the specimens ranged from 1 to 100%. The comprehensive assay panel was also used to assess 125 mtDNA specimens from healthy donors, which identified 431 unique sequence variants. Utilizing the comprehensive mtDNA panel, the mitochondrial genome of a patient specimen may be assessed in less than 1 day using a single 384-well plate or two 96-well plates. Specific assays were used to identify the myopathy, encephalopathy, lactic acidosis and stroke-like episodes (MELAS) mutation m.3243A>G, myoclonus epilepsy, ragged red fibers (MERRF) mutation m.8344A>G, and m.1555A>G associated with aminoglycoside hearing loss. These assays employ a calibrated, amplicon-based strategy that is exceedingly simple in design, utilization, and interpretation, yet provides sensitivity to detect variants at and below 10% heteroplasmy. Turnaround time for the genotyping tests is about 1 hr.
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Diagnostic method validation: High resolution melting (HRM) of small amplicons genotyping for the most common variants in the MTHFR gene. Clin Biochem 2009; 42:1308-16. [DOI: 10.1016/j.clinbiochem.2009.04.015] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2008] [Revised: 03/29/2009] [Accepted: 04/24/2009] [Indexed: 11/23/2022]
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Abstract
Mutation scanning techniques are used to detect sequence variants without the need for prior knowledge of the identity or precise location of the variant, in contrast with genotyping techniques, which determine the status of a specific variant. High-resolution melting is a recently developed method that shows great potential as a mutation scanning technique. Sensitivity and specificity for mutation detection are extremely high and the technique also has advantages of cost and throughput. Practical considerations for successful mutation scanning by high-resolution melting are also discussed in this review.
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Abstract
LightCycler technology combines rapid-cycle polymerase chain reaction with real-time fluorescent monitoring and melting curve analysis. Since its introduction in 1997, it is now used in many areas of molecular pathology, including oncology (solid tumors and hematopathology), inherited disease, and infectious disease. By monitoring product accumulation during rapid amplification, quantitative polymerase chain reaction in a closed-tube system is possible in 15 to 30 minutes. Furthermore, melting curve analysis of probes and/or amplicons provides genotyping and even haplotyping. Novel mutations are identified by unexpected melting temperature or curve shape changes. Melting probe designs include adjacent hybridization probes, single labeled probes, unlabeled probes, and snapback primers. High-resolution melting allows mutation scanning by detecting all heterozygous changes. This review describes the major advances throughout the last 15 years regarding LightCycler technology and its application in clinical laboratories.
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Affiliation(s)
- Elaine Lyon
- Department of Pathology, University of Utah, Salt Lake City, Utah, USA.
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Garritano S, Gemignani F, Voegele C, Nguyen-Dumont T, Le Calvez-Kelm F, De Silva D, Lesueur F, Landi S, Tavtigian SV. Determining the effectiveness of High Resolution Melting analysis for SNP genotyping and mutation scanning at the TP53 locus. BMC Genet 2009; 10:5. [PMID: 19222838 PMCID: PMC2648999 DOI: 10.1186/1471-2156-10-5] [Citation(s) in RCA: 95] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2008] [Accepted: 02/17/2009] [Indexed: 12/22/2022] Open
Abstract
Background Together single nucleotide substitutions and small insertion/deletion variants are the most common form of sequence variation in the human gene pool. High-resolution SNP profile and/or haplotype analyses enable the identification of modest-risk susceptibility genes to common diseases, genes that may modulate responses to pharmaceutical agents, and SNPs that can affect either their expression or function. In addition, sensitive techniques for germline or somatic mutation detection are important tools for characterizing sequence variations in genes responsible for tumor predisposition. Cost-effective methods are highly desirable. Many of the recently developed high-throughput technologies are geared toward industrial scale genetic studies and arguably do not provide useful solutions for small laboratory investigator-initiated projects. Recently, the use of new fluorescent dyes allowed the high-resolution analysis of DNA melting curves (HRM). Results Here, we compared the capacity of HRM, applicable to both genotyping and mutation scanning, to detect genetic variations in the tumor suppressor gene TP53 with that of mutation screening by full resequencing. We also assessed the performance of a variety of available HRM-based genotyping assays by genotyping 30 TP53 SNPs. We describe a series of solutions to handle the difficulties that may arise in large-scale application of HRM to mutation screening and genotyping at the TP53 locus. In particular, we developed specific HRM assays that render possible genotyping of 2 or more, sometimes closely spaced, polymorphisms within the same amplicon. We also show that simultaneous genotyping of 2 SNPs from 2 different amplicons using a multiplex PCR reaction is feasible; the data can be analyzed in a single HRM run, potentially improving the efficiency of HRM genotyping workflows. Conclusion The HRM technique showed high sensitivity and specificity (1.0, and 0.8, respectively, for amplicons of <400 bp) for mutation screening and provided useful genotyping assays as assessed by comparing the results with those obtained with Sanger sequencing. Thus, HRM is particularly suitable for either performing mutation scanning of a large number of samples, even in the situation where the amplicon(s) of interest harbor a common variant that may disturb the analysis, or in a context where gathering common SNP genotypes is of interest.
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Affiliation(s)
- Sonia Garritano
- Department of Biology, Genetics via Derna 1, University of Pisa, Pisa, Italy.
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Cho MH, Ciulla D, Klanderman BJ, Raby BA, Silverman EK. High-Resolution Melting Curve Analysis of Genomic and Whole-Genome Amplified DNA. Clin Chem 2008; 54:2055-8. [DOI: 10.1373/clinchem.2008.109744] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Abstract
Background: High-resolution melting curve analysis is an accurate method for mutation detection in genomic DNA. Few studies have compared the performance of high-resolution DNA melting curve analysis (HRM) in genomic and whole-genome amplified (WGA) DNA.
Methods: In 39 paired genomic and WGA samples, 23 amplicons from 9 genes were PCR amplified and analyzed by high-resolution melting curve analysis using the 96-well LightScanner (Idaho Technology). We used genotyping and bidirectional resequencing to verify melting curve results.
Results: Melting patterns were concordant between the genomic and WGA samples in 823 of 863 (95%) analyzed sample pairs. Of the discordant patterns, there was an overrepresentation of alternate melting curve patterns in the WGA samples, suggesting the presence of a mutation (false positives). Targeted resequencing in 135 genomic and 136 WGA samples revealed 43 single nucleotide polymorphisms (SNPs). All SNPs detected in genomic samples were also detected in WGA. Additional genotyping and sequencing allowed the classification of 628 genomic and 614 WGA amplicon samples. Heterozygous variants were identified by non–wild-type melting pattern in 98% of genomic and 97% of WGA samples (P = 0.11). Wild types were correctly classified in 99% of genomic and 91% of WGA samples (P < 0.001).
Conclusions: In WGA DNA, high-resolution DNA melting curve analysis is a sensitive tool for SNP discovery through detection of heterozygote variants; however, it may misclassify a greater number of wild-type samples.
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Affiliation(s)
- Michael H Cho
- Channing Laboratory, Brigham and Women’s Hospital, Boston, MA
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women’s Hospital, Boston, MA; and
- Harvard Medical School, Boston, MA
| | - Dawn Ciulla
- Channing Laboratory, Brigham and Women’s Hospital, Boston, MA
| | - Barbara J Klanderman
- Channing Laboratory, Brigham and Women’s Hospital, Boston, MA
- Harvard Medical School, Boston, MA
| | - Benjamin A Raby
- Channing Laboratory, Brigham and Women’s Hospital, Boston, MA
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women’s Hospital, Boston, MA; and
- Harvard Medical School, Boston, MA
| | - Edwin K Silverman
- Channing Laboratory, Brigham and Women’s Hospital, Boston, MA
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women’s Hospital, Boston, MA; and
- Harvard Medical School, Boston, MA
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