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Díez Rodríguez GR, Figueredo Lago JE, Armas Cayarga A, González González YJ, García de la Rosa I, Collazo Mesa T, López Reyes I, Batista Lozada Y, Rodríguez Calá FR, García Sánchez JB. A novel high-resolution melting analysis strategy for detecting cystic fibrosis-causing variants. Lab Med 2024; 55:185-197. [PMID: 37417450 DOI: 10.1093/labmed/lmad058] [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: 07/08/2023] Open
Abstract
Cystic fibrosis (CF), an autosomal recessive disease, is caused by variants in both alleles of the CF transmembrane conductance regulator (CFTR) gene. A new assay based on allele-specific polymerase chain reaction and high-resolution melting analysis was developed for the detection of 18 CF-causing CFTR variants previously identified in Cuba and Latin America. The assay is also useful for zygosity determination of mutated alleles and includes internal controls. The reaction mixtures were normalized and evaluated using blood samples collected on filter paper. The evaluation of analytical parameters demonstrated the specificity and sensitivity of the method to detect the included CFTR variants. Internal and external validations yielded a 100% agreement between the new assay and the used reference tests. This assay can complement CF newborn screening not only in Cuba but also in Latin America.
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Affiliation(s)
| | | | | | | | | | - Teresa Collazo Mesa
- National Center of Medical Genetics, Medical University of Havana, Playa, Havana, Cuba
| | - Ixchel López Reyes
- National Center of Medical Genetics, Medical University of Havana, Playa, Havana, Cuba
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Muller N, Sarantitis I, Rouanet M, de Mestier L, Halloran C, Greenhalf W, Férec C, Masson E, Ruszniewski P, Lévy P, Neoptolemos J, Buscail L, Rebours V. Natural history of SPINK1 germline mutation related-pancreatitis. EBioMedicine 2019; 48:581-591. [PMID: 31628023 PMCID: PMC6838417 DOI: 10.1016/j.ebiom.2019.09.032] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Revised: 09/29/2019] [Accepted: 09/30/2019] [Indexed: 02/09/2023] Open
Abstract
BACKGROUND The aim was to describe genetic, clinical and morphological features in a large, multicentre European cohort of patients with SPINK1 related pancreatitis, in comparison with patients with idiopathic pancreatitis (IP). METHODS All SPINK1 mutation carriers with pancreatic symptoms from two French and one English centers were included. Patients with IP were included in a control group. Genetic, clinical, radiological and biochemical data were collected. FINDINGS 209 and 302 patients were included in the SPINK1 and control groups (median follow-up: 8.3 years (3.7-17.4) vs 5.3 (2.5-8.8)). The median age at onset of symptoms was 20.1 years (17.5-22.8) in the SPINK1 group versus 41.2 (35.2-45.2). The age of exocrine pancreatic insufficiency (EPI) onset in the SPINK1 group was 49.5 (44.5-54.6) years vs. 65.2 (62.1-68.3), p < 0.001. SPINK1 patients with EPI were 5.3%, 14.7%, 28.3% and 52.4% at 20, 30, 40 and 50 years. Diabetes occurred 37.7 (33.3-42.1) years following the onset of symptoms in the SPINK1 group vs. 30.6 (17.3-43.8) (p = 0.002). SPINK1 patients with diabetes were 7.8%, 13.4%, 26.3% and 43.4% at 30, 40, 50 and 60 years. Seven patients (3.3%) developed pancreatic cancer in the SPINK1 group (versus 3 (0.99%), p = 0.1), at a median age of 60 vs 66 years. The cancer risk was 0.8% before 50 years, 11.9%, 27.7%, 51.8% at 60, 70 and 80 years and was 12 times higher than in controls (Cox HR 12.0 (3.0-47.8), p < 0.001). INTERPRETATION SPINK1 related pancreatitis is associated with earlier onset and pancreatic insufficiencies. p.N34S SPINK1 may well be associated with cancer.
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Affiliation(s)
- Nelly Muller
- Department of Gastroenterology and Pancreatology, Beaujon Hospital, APHP, Clichy, and Paris-Diderot University, Paris, France
| | - Ioannis Sarantitis
- Department of Molecular and Clinical Cancer Medicine, Institute of Translational Medicine, University of Liverpool, Royal Liverpool University Hospital, Liverpool, England United Kingdom
| | - Marie Rouanet
- Department of Gastroenterology and Pancreatology, INSERM U1037, University of Toulouse 3, CHU Rangueil, Toulouse, France
| | - Louis de Mestier
- Department of Gastroenterology and Pancreatology, Beaujon Hospital, APHP, Clichy, and Paris-Diderot University, Paris, France
| | - Christopher Halloran
- Department of Molecular and Clinical Cancer Medicine, Institute of Translational Medicine, University of Liverpool, Royal Liverpool University Hospital, Liverpool, England United Kingdom
| | - William Greenhalf
- Department of Molecular and Clinical Cancer Medicine, Institute of Translational Medicine, University of Liverpool, Royal Liverpool University Hospital, Liverpool, England United Kingdom
| | - Claude Férec
- UMR1078 Génétique, Génomique Fonctionnelle et Biotechnologies, INSERM, EFS - Bretagne, Université de Brest, CHRU Brest, Brest, France
| | - Emmanuelle Masson
- UMR1078 Génétique, Génomique Fonctionnelle et Biotechnologies, INSERM, EFS - Bretagne, Université de Brest, CHRU Brest, Brest, France
| | - Philippe Ruszniewski
- Department of Gastroenterology and Pancreatology, Beaujon Hospital, APHP, Clichy, and Paris-Diderot University, Paris, France
| | - Philippe Lévy
- Department of Gastroenterology and Pancreatology, Beaujon Hospital, APHP, Clichy, and Paris-Diderot University, Paris, France
| | - John Neoptolemos
- Department of General Surgery and transplantation, University of Heidelberg, Heidelberg, Germany
| | - Louis Buscail
- Department of Gastroenterology and Pancreatology, INSERM U1037, University of Toulouse 3, CHU Rangueil, Toulouse, France
| | - Vinciane Rebours
- Department of Gastroenterology and Pancreatology, Beaujon Hospital, APHP, Clichy, and Paris-Diderot University, Paris, France.
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Zou F, Ruan Q, Lin X, Zhang M, Song Y, Zhou L, Zhu Z, Lin S, Wang W, Yang CJ. Rapid, real-time chemiluminescent detection of DNA mutation based on digital microfluidics and pyrosequencing. Biosens Bioelectron 2019; 126:551-557. [DOI: 10.1016/j.bios.2018.09.092] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Revised: 09/17/2018] [Accepted: 09/27/2018] [Indexed: 02/07/2023]
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Bergougnoux A, Taulan-Cadars M, Claustres M, Raynal C. Current and future molecular approaches in the diagnosis of cystic fibrosis. Expert Rev Respir Med 2018; 12:415-426. [PMID: 29580110 DOI: 10.1080/17476348.2018.1457438] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
INTRODUCTION Cystic Fibrosis is among the first diseases to have general population genetic screening tests and one of the most common indications of prenatal and preimplantation genetic diagnosis for single gene disorders. During the past twenty years, thanks to the evolution of diagnostic techniques, our knowledge of CFTR genetics and pathophysiological mechanisms involved in cystic fibrosis has significantly improved. Areas covered: Sanger sequencing and quantitative methods greatly contributed to the identification of more than 2,000 sequence variations reported worldwide in the CFTR gene. We are now entering a new technological age with the generalization of high throughput approaches such as Next Generation Sequencing and Droplet Digital PCR technologies in diagnostics laboratories. These powerful technologies open up new perspectives for scanning the entire CFTR locus, exploring modifier factors that possibly influence the clinical evolution of patients, and for preimplantation and prenatal diagnosis. Expert commentary: Such breakthroughs would, however, require powerful bioinformatics tools and relevant functional tests of variants for analysis and interpretation of the resulting data. Ultimately, an optimal use of all those resources may improve patient care and therapeutic decision-making.
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Affiliation(s)
- Anne Bergougnoux
- a Laboratoire de Génétique Moléculaire , Centre Hospitalier Universitaire de Montpellier , Montpellier , France.,b EA 7402 , Université de Montpellier , Montpellier , France
| | | | | | - Caroline Raynal
- a Laboratoire de Génétique Moléculaire , Centre Hospitalier Universitaire de Montpellier , Montpellier , France
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Figueredo Lago JE, Armas Cayarga A, González González YJ, Collazo Mesa T. A simple, fast and inexpensive method for mutation scanning of CFTR gene. BMC MEDICAL GENETICS 2017; 18:58. [PMID: 28545452 PMCID: PMC5445409 DOI: 10.1186/s12881-017-0420-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/27/2016] [Accepted: 05/09/2017] [Indexed: 11/10/2022]
Abstract
BACKGROUND Mutation scanning methods in Cystic Fibrosis Transmembrane Conductance Regulator (CFTR) gene may not distinguish between a Cystic Fibrosis (CF) causing mutation and a benign variant. We have developed a simple and fast method for scanning 14 selected CF-causing mutations which have high frequency in Latin America. METHODS In a group of 35 samples coming from CF patients previously characterized and using two allele-specific real-time multiplex PCRs targeting wild-type and mutant alleles respectively, we detect the presence of mutations by analyzing the Ct variation. Twenty-five samples without mutations considered non-carrier samples, were also included in this study. High Resolution Melting Analysis (HRMA) was performed to confirm the result of the scanning method and in most cases allowed the genotype determination. RESULTS The results validate this method for CF diagnosis. A least one CFTR gene mutation was detected in the samples of CF patients, as predicted by their ΔCt values. The ΔCt value also indicated the zygosity of the sample according to the distribution of CFTR gene mutations. In most cases, HRMA allowed the identification of the mutation(s), thereby confirming the efficiency of this scanning strategy. CONCLUSIONS This strategy simplifies the detection of CF, reducing the analysis of 14 CF-causing mutations to two parallel reactions and making the procedure compatible with the analysis of a large number of samples. As the method is fast, inexpensive and highly reliable, it is advisable for scanning CFTR gene mutations in newborns, patients with a clinical suspicion of CF as well as in the preconception carrier screening.
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Affiliation(s)
| | - Anny Armas Cayarga
- Department of Molecular Biology, Immunoassay Center (CIE) Cubanacan, Playa, Havana, Cuba
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Obliosca JM, Cheng SY, Chen YA, Llanos MF, Liu YL, Imphean DM, Bell DR, Petty JT, Ren P, Yeh HC. LNA Thymidine Monomer Enables Differentiation of the Four Single-Nucleotide Variants by Melting Temperature. J Am Chem Soc 2017; 139:7110-7116. [PMID: 28463488 DOI: 10.1021/jacs.7b03395] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
High-resolution melting (HRM) analysis of DNA is a closed-tube single-nucleotide polymorphism (SNP) detection method that has shown many advantages in point-of-care diagnostics and personalized medicine. While recently developed melting probes have demonstrated significantly improved discrimination of mismatched (mutant) alleles from matched (wild-type) alleles, no effort has been made to design a simple melting probe that can reliably distinguish all four SNP alleles in a single experiment. Such a new probe could facilitate the discovery of rare genetic mutations at lower cost. Here we demonstrate that a melting probe embedded with a single locked thymidine monomer (tL) can reliably differentiate the four SNP alleles by four distinct melting temperatures (termed the "4Tm probe"). This enhanced discriminatory power comes from the decreased melting temperature of the tL·C mismatched hybrid as compared to that of the t·C mismatched hybrid, while the melting temperatures of the tL-A, tL·G and tL·T hybrids are increased or remain unchanged as compared to those of their canonical counterparts. This phenomenon is observed not only in the HRM experiments but also in the molecular dynamics simulations.
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Affiliation(s)
- Judy M Obliosca
- Department of Biomedical Engineering, Cockrell School of Engineering, University of Texas at Austin , Austin, Texas 78712, United States
| | - Sara Y Cheng
- Department of Physics, College of Natural Sciences, University of Texas at Austin , Austin, Texas 78712, United States
| | - Yu-An Chen
- Department of Biomedical Engineering, Cockrell School of Engineering, University of Texas at Austin , Austin, Texas 78712, United States
| | - Mariana F Llanos
- Department of Chemistry, Department of Chemistry, Furman University , Greenville, South Carolina 29613, United States
| | - Yen-Liang Liu
- Department of Biomedical Engineering, Cockrell School of Engineering, University of Texas at Austin , Austin, Texas 78712, United States
| | - Darren M Imphean
- Department of Biomedical Engineering, Cockrell School of Engineering, University of Texas at Austin , Austin, Texas 78712, United States
| | - David R Bell
- Department of Biomedical Engineering, Cockrell School of Engineering, University of Texas at Austin , Austin, Texas 78712, United States
| | - Jeffrey T Petty
- Department of Chemistry, Department of Chemistry, Furman University , Greenville, South Carolina 29613, United States
| | - Pengyu Ren
- Department of Biomedical Engineering, Cockrell School of Engineering, University of Texas at Austin , Austin, Texas 78712, United States
| | - Hsin-Chih Yeh
- Department of Biomedical Engineering, Cockrell School of Engineering, University of Texas at Austin , Austin, Texas 78712, United States
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Siji A, Pardeshi VC, Ravindran S, Vasudevan A, Vasudevan A. Screening of WT1 mutations in exon 8 and 9 in children with steroid resistant nephrotic syndrome from a single centre and establishment of a rapid screening assay using high-resolution melting analysis in a clinical setting. BMC MEDICAL GENETICS 2017; 18:3. [PMID: 28068926 PMCID: PMC5223455 DOI: 10.1186/s12881-016-0362-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Accepted: 12/08/2016] [Indexed: 11/22/2022]
Abstract
BACKGROUND Mutations in Wilm's tumor 1 (WT1) gene is one of the commonly reported genetic mutations in children with steroid resistant nephrotic syndrome (SRNS). We report the results of direct sequencing of exons 8 and 9 of WT1 gene in 100 children with SRNS from a single centre. We standardized and validated High Resolution Melt (HRM) as a rapid and cost effective screening step to identify individuals with normal sequence and distinguish it from those with a potential mutation. Since only mutation positive samples identified by HRM will be further processed for sequencing it will help in reducing the sequencing burden and speed up the screening process. METHODS One hundred SRNS children were screened for WT1 mutations in Exon 8 and 9 using Sanger sequencing. HRM assay was standardized and validated by performing analysis for exon 8 and 9 on 3 healthy control and 5 abnormal variants created by site directed mutagenesis and verified by sequencing. To further test the clinical applicability of the assay, we screened additional 91 samples for HRM testing and performed a blinded assessment. RESULTS WT1 mutations were not observed in the cohort of children with SRNS. The results of HRM analysis were concordant with the sequencing results. CONCLUSION The WT1 gene mutations were not observed in the SRNS cohort indicating it has a low prevalence. We propose applying this simple, rapid and cost effective assay using HRM technique as the first step for screening the WT1 gene hot spot region in a clinical setting.
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Affiliation(s)
- Annes Siji
- Division of Molecular Medicine, St. John's Research Institute, Bangalore, India
| | | | - Shilpa Ravindran
- Division of Molecular Medicine, St. John's Research Institute, Bangalore, India
| | - Ambily Vasudevan
- Division of Molecular Medicine, St. John's Research Institute, Bangalore, India
| | - Anil Vasudevan
- Division of Molecular Medicine, St. John's Research Institute, Bangalore, India.
- Department of Pediatric Nephrology, St. John's Medical College Hospital, Bangalore, 560034, India.
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Audrézet MP, Munck A, Scotet V, Claustres M, Roussey M, Delmas D, Férec C, Desgeorges M. Comprehensive CFTR gene analysis of the French cystic fibrosis screened newborn cohort: implications for diagnosis, genetic counseling, and mutation-specific therapy. Genet Med 2014; 17:108-16. [DOI: 10.1038/gim.2014.113] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2014] [Accepted: 05/06/2014] [Indexed: 11/09/2022] Open
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Knez K, Spasic D, Janssen KPF, Lammertyn J. Emerging technologies for hybridization based single nucleotide polymorphism detection. Analyst 2014; 139:353-70. [PMID: 24298558 DOI: 10.1039/c3an01436c] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Detection of single nucleotide polymorphisms (SNPs) is a crucial challenge in the development of a novel generation of diagnostic tools. Accurate detection of SNPs can prove elusive, as the impact of a single variable nucleotide on the properties of a target sequence is limited, even if this sequence consists of only a few nucleotides. New, accurate and facile strategies for the detection of point mutations are therefore absolutely necessary for the increased adoption of point-of-care molecular diagnostics. Currently, PCR and sequencing are mostly applied for diagnosing SNPs. However these methods have serious drawbacks as routine diagnostic tools because of their labour intensity and cost. Several new, more suitable methods can be applied to enable sensitive detection of mutations based on specially designed hybridization probes, mutation recognizing enzymes and thermal denaturation. Here, an overview is presented of the most recent advances in the field of fast and sensitive SNP detection assays with strong potential for integration in point-of-care tests.
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Affiliation(s)
- Karel Knez
- KU Leuven, BIOSYST-MeBioS, Willem de Croylaan 42, Leuven, Belgium.
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García-Mendiola T, Barreiro Martínez T, Pariente F, Molano J, Lorenzo E. Screening of Specific Gene Mutations Associated with Cystic Fibrosis. ELECTROANAL 2014. [DOI: 10.1002/elan.201400042] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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Masson E, Chen JM, Audrézet MP, Cooper DN, Férec C. A conservative assessment of the major genetic causes of idiopathic chronic pancreatitis: data from a comprehensive analysis of PRSS1, SPINK1, CTRC and CFTR genes in 253 young French patients. PLoS One 2013; 8:e73522. [PMID: 23951356 PMCID: PMC3738529 DOI: 10.1371/journal.pone.0073522] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2013] [Accepted: 07/30/2013] [Indexed: 12/21/2022] Open
Abstract
Idiopathic chronic pancreatitis (ICP) has traditionally been defined as chronic pancreatitis in the absence of any obvious precipitating factors (e.g. alcohol abuse) and family history of the disease. Studies over the past 15 years have revealed that ICP has a highly complex genetic architecture involving multiple gene loci. Here, we have attempted to provide a conservative assessment of the major genetic causes of ICP in a sample of 253 young French ICP patients. For the first time, conventional types of mutation (comprising coding sequence variants and variants at intron/exon boundaries) and gross genomic rearrangements were screened for in all four major pancreatitis genes, PRSS1, SPINK1, CTRC and CFTR. For the purposes of the study, synonymous, intronic and 5'- or 3'-untranslated region variants were excluded from the analysis except where there was persuasive evidence of functional consequences. The remaining sequence variants/genotypes were classified into causative, contributory or neutral categories by consideration of (i) their allele frequencies in patient and normal control populations, (ii) their presumed or experimentally confirmed functional effects, (iii) the relative importance of their associated genes in the pathogenesis of chronic pancreatitis and (iv) gene-gene interactions wherever applicable. Adoption of this strategy allowed us to assess the pathogenic relevance of specific variants/genotypes to their respective carriers to an unprecedented degree. The genetic cause of ICP could be assigned in 23.7% of individuals in the study group. A strong genetic susceptibility factor was also present in an additional 24.5% of cases. Taken together, up to 48.2% of the studied ICP patients were found to display evidence of a genetic basis for their pancreatitis. Whereas these particular proportions may not be extrapolable to all ICP patients, the approach employed should serve as a useful framework for acquiring a better understanding of the role of genetic factors in causing this oligogenic disease.
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Affiliation(s)
- Emmanuelle Masson
- Institut National de la Santé et de la Recherche Médicale, U1078, Brest, France
- Laboratoire de Génétique Moléculaire et d’Histocompatibilité, Centre Hospitalier Régional Universitaire Brest, Hôpital Morvan, Brest, France
| | - Jian-Min Chen
- Institut National de la Santé et de la Recherche Médicale, U1078, Brest, France
- Etablissement Français du sang – Bretagne, Brest, France
- * E-mail: (J-MC); (CF)
| | - Marie-Pierre Audrézet
- Institut National de la Santé et de la Recherche Médicale, U1078, Brest, France
- Laboratoire de Génétique Moléculaire et d’Histocompatibilité, Centre Hospitalier Régional Universitaire Brest, Hôpital Morvan, Brest, France
| | - David N. Cooper
- Institute of Medical Genetics, School of Medicine, Cardiff University, Cardiff, United Kingdom
| | - Claude Férec
- Institut National de la Santé et de la Recherche Médicale, U1078, Brest, France
- Laboratoire de Génétique Moléculaire et d’Histocompatibilité, Centre Hospitalier Régional Universitaire Brest, Hôpital Morvan, Brest, France
- Etablissement Français du sang – Bretagne, Brest, France
- Faculté de Médecine et des Sciences de la Santé, Université de Bretagne Occidentale, Brest, France
- * E-mail: (J-MC); (CF)
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Masson E, Hammel P, Garceau C, Bénech C, Quéméner-Redon S, Chen JM, Férec C. Characterization of two deletions of the CTRC locus. Mol Genet Metab 2013; 109:296-300. [PMID: 23721890 DOI: 10.1016/j.ymgme.2013.04.022] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/26/2013] [Revised: 04/30/2013] [Accepted: 04/30/2013] [Indexed: 12/26/2022]
Abstract
Novel variants associated with chronic pancreatitis are being increasingly reported. However, most studies have so far only analyzed point mutations and small insertions or deletions. Here we report the characterization of two distinct deletions of the CTRC locus. Variants in four chronic pancreatitis genes, PRSS1, SPINK1, CTRC and CFTR, were systematically analyzed in the studied cases. Copy number change of the CTRC gene was analyzed by quantitative fluorescent multiplex PCR (QFM-PCR). Walking QFM-PCR followed by long-range PCR and direct sequencing were employed to identify the deletion breakpoints at the nucleotide level. A heterozygous CTRC-deleting complex rearrangement, which was co-inherited with different trans variants in SPINK1, CFTR or PRSS1, is associated with variable phenotypes (chronic pancreatitis; pancreatic cancer and chronic pancreatitis; and type 1 diabetes). Moreover, a different homozygous deletion of the CTRC locus was found in an unrelated patient with asymptomatic chronic pancreatitis. Our findings revealed a hitherto unrecognized level of complexity of genotype-phenotype correlation in chronic pancreatitis. The CTRC-deleting complex rearrangement probably resulted from LINE-1-mediated Alu insertion, which represents a novel mutational mechanism causing chronic pancreatitis.
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Affiliation(s)
- Emmanuelle Masson
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1078, Brest, France
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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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Zhou L, Palais RA, Ye F, Chen J, Montgomery JL, Wittwer CT. Symmetric snapback primers for scanning and genotyping of the cystic fibrosis transmembrane conductance regulator gene. Clin Chem 2013; 59:1052-61. [PMID: 23503723 DOI: 10.1373/clinchem.2013.202689] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
BACKGROUND High-resolution melting of PCR products is an efficient and analytically sensitive method to scan for sequence variation, but detected variants must still be identified. Snapback primer genotyping uses a 5' primer tail complementary to its own extension product to genotype the resulting hairpin via melting. If the 2 methods were combined to analyze the same PCR product, the residual sequencing burden could be reduced or even eliminated. METHODS The 27 exons and neighboring splice sites of the CFTR [cystic fibrosis transmembrane conductance regulator (ATP-binding cassette sub-family C, member 7)] gene were amplified by the PCR in 39 fragments. Primers included snapback tails for genotyping 7 common variants and the 23 CFTR mutations recommended for screening by the American College of Medical Genetics. After symmetric PCR, the amplicons were analyzed by high-resolution melting to scan for variants. Then, a 5-fold excess of H2O was added to each reaction to produce intramolecular hairpins for snapback genotyping by melting. Each melting step required <10 min. Of the 133 DNA samples analyzed, 51 were from CFTR patient samples or cell lines. RESULTS As expected, the analytical sensitivity of heterozygote detection in blinded studies was 100%. Snapback genotyping reduced the need for sequencing from 7.9% to 0.5% of PCR products; only 1 amplicon every 5 patients required sequencing to identify nonanticipated rare variants. We identified 2 previously unreported variants: c.3945A>G and c.4243-5C>T. CONCLUSIONS CFTR analysis by sequential scanning and genotyping with snapback primers is a good match for targeted clinical genetics, for which high analytical accuracy and rapid turnaround times are important.
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Affiliation(s)
- Luming Zhou
- Department of Pathology, School of Medicine, University of Utah, Salt Lake City, UT 84132, USA.
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Ferec C, Cutting GR. Assessing the Disease-Liability of Mutations in CFTR. Cold Spring Harb Perspect Med 2012; 2:a009480. [PMID: 23209179 DOI: 10.1101/cshperspect.a009480] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Over 1900 mutations have been reported in the cystic fibrosis transmembrane conductance regulator (CFTR), the gene defective in patients with cystic fibrosis. These mutations have been discovered primarily in individuals who have features consistent with the diagnosis of CF. In some cases, it has been recognized that the mutations are not causative of cystic fibrosis but are responsible for disorders with features similar to CF, and these conditions have been termed CFTR-related disorders or CFTR-RD. There are also mutations in CFTR that do not contribute to any known disease state. Distinguishing CFTR mutations according to their penetrance for an abnormal phenotype is important for clinical management, structure/function analysis of CFTR, and understanding the molecular and cellular mechanisms underlying CF.
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Affiliation(s)
- Claude Ferec
- Faculté de Médecine et des Sciences de la Santé, Université de Bretagne Occidentale; Centre Hospitalier Universitaire (CHU), Hôpital Morvan; INSERM, U1078 Brest, France
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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: 50] [Impact Index Per Article: 4.2] [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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Abstract
Cystic fibrosis (CF) is defined as the most common life shortening genetic disorder in the Caucasian populations. The cloning of the gene responsible for the disease - the CFTR (Cystic Fibrosis Transmembrane conductance Regulator) gene - twenty years ago has greatly improved our knowledge of the pathophysiology of CF. That disease is characterized by a highly phenotypic variability and the CFTR mutations cannot explain all the variability observed in the disease severity. The possible influence of the environment and modifier genes has therefore been evocated. Several genetic variants coding for genes involved in the physiopathology of the disease have been studied, like genes involve in the immunity and the inflammatory response. Some of these genes have indeed been shown to influence the disease severity. A new approach has also been developed, analyzing the whole genome. This review summarizes the genetic basis of CF in its classical and atypical forms, as well as the work performed in the field of modifier genes.
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Santos S, Marques V, Pires M, Silveira L, Oliveira H, Lança V, Brito D, Madeira H, Esteves JF, Freitas A, Carreira IM, Gaspar IM, Monteiro C, Fernandes AR. High resolution melting: improvements in the genetic diagnosis of hypertrophic cardiomyopathy in a Portuguese cohort. BMC MEDICAL GENETICS 2012; 13:17. [PMID: 22429680 PMCID: PMC3359199 DOI: 10.1186/1471-2350-13-17] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/24/2011] [Accepted: 03/19/2012] [Indexed: 02/01/2023]
Abstract
BACKGROUND Hypertrophic Cardiomyopathy (HCM) is a complex myocardial disorder with a recognized genetic heterogeneity. The elevated number of genes and mutations involved in HCM limits a gene-based diagnosis that should be considered of most importance for basic research and clinical medicine. METHODOLOGY In this report, we evaluated High Resolution Melting (HRM) robustness, regarding HCM genetic testing, by means of analyzing 28 HCM-associated genes, including the most frequent 4 HCM-associated sarcomere genes, as well as 24 genes with lower reported HCM-phenotype association. We analyzed 80 Portuguese individuals with clinical phenotype of HCM allowing simultaneously a better characterization of this disease in the Portuguese population. RESULTS HRM technology allowed us to identify 60 mutated alleles in 72 HCM patients: 49 missense mutations, 3 nonsense mutations, one 1-bp deletion, one 5-bp deletion, one in frame 3-bp deletion, one insertion/deletion, 3 splice mutations, one 5'UTR mutation in MYH7, MYBPC3, TNNT2, TNNI3, CSRP3, MYH6 and MYL2 genes. Significantly 22 are novel gene mutations. CONCLUSIONS HRM was proven to be a technique with high sensitivity and a low false positive ratio allowing a rapid, innovative and low cost genotyping of HCM. In a short return, HRM as a gene scanning technique could be a cost-effective gene-based diagnosis for an accurate HCM genetic diagnosis and hopefully providing new insights into genotype/phenotype correlations.
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Affiliation(s)
- Susana Santos
- Centro de Química Estrutural, Instituto Superior Técnico, Technical University of Lisbon, Lisbon, Portugal
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Duno M, Schwartz M, Larsen PL, Rosenberg T. Phenotypic and genetic spectrum of Danish patients with ABCA4-related retinopathy. Ophthalmic Genet 2012; 33:225-31. [PMID: 22229821 DOI: 10.3109/13816810.2011.643441] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
BACKGROUND Pathogenic variations in the ABCA4 gene were originally recognized as genetic background for the autosomal recessive disorders Stargardt disease and fundus flavimaculatus, but have expanded to embrace a diversity of retinal diseases, giving rise to the new diagnostic term, ABCA4-related retinopathy. Diagnostic genotyping of ABCA4 is complicated by the large size of the gene and the existence of approximately 600 known pathogenic variations, along with numerous rare polymorphisms. A commercial diagnostic array-based assay has been developed targeting known mutations, however a conclusive genetic diagnosis must rely on a comprehensive genetic screening as the mutation spectrum of ABCA4-related retinopathies continues to expand. MATERIAL AND METHODS Among 161 patients with a Stargardt-related phenotype previously assessed with the commercial ABCA4 mutation microarray, we analyzed the ABCA4 gene with High-resolution melting (HRM) in patients in whom the array analysis identified either a heterozygous mutation (n = 50) or no mutation (n = 30). RESULTS The HRM method detected each of the already known mutations and polymorphisms. We identified the second ABCA4 mutation in 31 of 50 heterozygous patients (62%). Several novel mutations were identified of which four were identified multiple times. The recurrent novel mutations were subsequently assessed among the 30 patients with possible ABCA4-related diseases, previously found to be negative for known ABCA4 mutations by array analysis. In total, 30 different mutations were identified of which 21 have not been described before. CONCLUSION Scandinavian patients with ABCA4-related retinopathy appear to have a distinct mutation spectrum, which can be identified in patients of diverse clinical phenotypes.
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Affiliation(s)
- Morten Duno
- Department of Clinical Genetics, Rigshospitalet, Copenhagen University Hospital, Denmark.
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Benej M, Bendlova B, Vaclavikova E, Poturnajova M. Establishing high resolution melting analysis: method validation and evaluation for c-RET proto-oncogene mutation screening. Clin Chem Lab Med 2012; 50:51-60. [DOI: 10.1515/cclm.2011.730] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2011] [Accepted: 09/05/2011] [Indexed: 11/15/2022]
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Duguépéroux I, Scotet V, Audrézet MP, Saliou AH, Collet M, Blayau M, Schmitt S, Kitzis A, Fresquet F, Müller F, Férec C. Nonvisualization of fetal gallbladder increases the risk of cystic fibrosis. Prenat Diagn 2011; 32:21-8. [PMID: 22052729 DOI: 10.1002/pd.2866] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2011] [Revised: 08/18/2011] [Accepted: 08/18/2011] [Indexed: 01/23/2023]
Abstract
OBJECTIVE The aim of our study is to evaluate the prevalence of cystic fibrosis (CF) in fetuses referred for genetic testing because of ultrasonographic sign (nonvisualized fetal gallbladder--NVFGB). METHOD We reviewed the results of CFTR gene analysis over the period 2002 to 2009 in all consecutive cases referred because of NVFGB in Western France. We correlated these data with the presence of a more classical ultrasonographic finding (fetal echogenic bowel - FEB). RESULTS Cystic fibrosis was diagnosed in 5 of the 37 fetuses with NVFGB (13.5%, 95% confidence interval (CI): [2.5%; 24.5%]) and in only 9 of the 229 other cases referred because of FEB (3.9%, 95% CI: [3.2%; 14.7%]). In our series, all CF-affected fetuses with NVFGB also had FEB. The risk of CF was 11.6-fold higher in fetuses with both indications (NVFGB + FEB) than in fetuses with isolated FEB (45.5% vs 3.9%, RR = 11.6, 95% CI: [4.7%; 28.8%], p = 0.0001). We also estimated that the residual risk of CF was less than 1 in 68 (1.5%) when a single mutation was identified in the fetus by our molecular protocol. CONCLUSION Ultrasonographic evidence of NVFGB is an additional risk factor for CF in cases with FEB.
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Tricarico R, Crucianelli F, Alvau A, Orlando C, Sestini R, Tonelli F, Valanzano R, Genuardi M. High resolution melting analysis for a rapid identification of heterozygous and homozygous sequence changes in the MUTYH gene. BMC Cancer 2011; 11:305. [PMID: 21777424 PMCID: PMC3156810 DOI: 10.1186/1471-2407-11-305] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2011] [Accepted: 07/21/2011] [Indexed: 11/29/2022] Open
Abstract
Background MUTYH-associated polyposis (MAP) is an autosomal recessive form of intestinal polyposis predisposing to colorectal carcinoma. High resolution melting analysis (HRMA) is a mutation scanning method that allows detection of heterozygous sequence changes with high sensitivity, whereas homozygosity for a nucleotide change may not lead to significant curve shape or melting temperature changes compared to homozygous wild-type samples. Therefore, HRMA has been mainly applied to the detection of mutations associated with autosomal dominant or X-linked disorders, while applications to autosomal recessive conditions are less common. Methods MUTYH coding sequence and UTRs were analyzed by both HRMA and sequencing on 88 leukocyte genomic DNA samples. Twenty-six samples were also examined by SSCP. Experiments were performed both with and without mixing the test samples with wild-type DNA. Results The results show that all MUTYH sequence variations, including G > C and A > T homozygous changes, can be reliably identified by HRMA when a condition of artificial heterozygosity is created by mixing test and reference DNA. HRMA had a sensitivity comparable to sequencing and higher than SSCP. Conclusions The availability of a rapid and inexpensive method for the identification of MUTYH sequence variants is relevant for the diagnosis of colorectal cancer susceptibility, since the MAP phenotype is highly variable.
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Affiliation(s)
- Rossella Tricarico
- Department of Clinical Pathophysiology, Medical Genetics Unit, University of Florence, Florence, Italy
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Chen N, Tranebjærg L, Rendtorff ND, Schrijver I. Mutation analysis of SLC26A4 for Pendred syndrome and nonsyndromic hearing loss by high-resolution melting. J Mol Diagn 2011; 13:416-26. [PMID: 21704276 PMCID: PMC3123795 DOI: 10.1016/j.jmoldx.2011.03.003] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2010] [Revised: 02/15/2011] [Accepted: 03/16/2011] [Indexed: 02/04/2023] Open
Abstract
Pendred syndrome and DFNB4 (autosomal recessive nonsyndromic congenital deafness, locus 4) are associated with autosomal recessive congenital sensorineural hearing loss and mutations in the SLC26A4 gene. Extensive allelic heterogeneity, however, necessitates analysis of all exons and splice sites to identify mutations for individual patients. Although Sanger sequencing is the gold standard for mutation detection, screening methods supplemented with targeted sequencing can provide a cost-effective alternative. One such method, denaturing high-performance liquid chromatography, was developed for clinical mutation detection in SLC26A4. However, this method inherently cannot distinguish homozygous changes from wild-type sequences. High-resolution melting (HRM), on the other hand, can detect heterozygous and homozygous changes cost-effectively, without any post-PCR modifications. We developed a closed-tube HRM mutation detection method specific for SLC26A4 that can be used in the clinical diagnostic setting. Twenty-eight primer pairs were designed to cover all 21 SLC26A4 exons and splice junction sequences. Using the resulting amplicons, initial HRM analysis detected all 45 variants previously identified by sequencing. Subsequently, a 384-well plate format was designed for up to three patient samples per run. Blinded HRM testing on these plates of patient samples collected over 1 year in a clinical diagnostic laboratory accurately detected all variants identified by sequencing. In conclusion, HRM with targeted sequencing is a reliable, simple, and cost-effective method for SLC26A4 mutation screening and detection.
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Affiliation(s)
- Neng Chen
- Department of Pathology, Stanford University School of Medicine, Stanford, California
| | - Lisbeth Tranebjærg
- Department of Audiology, Bispebjerg Hospital, Copenhagen, Denmark
- Wilhelm Johannsen Center of Functional Genomics, Institute of Molecular Medicine, ICMM, The Panum Institute, University of Copenhagen, Copenhagen, Denmark
| | - Nanna Dahl Rendtorff
- Wilhelm Johannsen Center of Functional Genomics, Institute of Molecular Medicine, ICMM, The Panum Institute, University of Copenhagen, Copenhagen, Denmark
| | - Iris Schrijver
- Department of Pathology, Stanford University School of Medicine, Stanford, California
- Department of Pediatrics, Stanford University School of Medicine, Stanford, California
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A novel exon duplication of the cystic fibrosis transmembrane conductance regulator in a patient presenting with adult-onset recurrent pancreatitis. Pancreas 2011; 40:773-7. [PMID: 21673536 DOI: 10.1097/mpa.0b013e3182156e47] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Pancreatitis is a rare occurrence in patients with cystic fibrosis (CF) affecting 1.2% of all patients, but it can be the first presenting sign in approximately 15% of adults with pancreatic sufficiency and a milder CF phenotype. We report a case of a woman with recurrent pancreatitis who has one cystic fibrosis-causing mutation (G551D) and the first known description of a pathologic duplication of exon 19 of the CF transmembrane conductance regulator (CFTR). A 30-year-old white woman with 30 attacks of pancreatitis over a 5-year period starting at age 25 presented to the genetics department. She was found to have a mutation in the SPINK1 gene, IVS3+184T>A, and one cystic fibrosis-causing mutation (G551D) prompting full gene sequencing of the CFTR, revealing an additional duplication of exon 19. Sweat chloride testing was elevated at 97 and 106 mmol/L. Despite normal growth parameters and lung function, it is important to be aware of recurrent pancreatitis as a presenting sign of CF. Comprehensive CF gene analysis is necessary to detect a second CF-causing mutation that may put patients at risk for more severe symptoms of pancreatitis. There is a significant difference in the prevalence of heterozygote mutations between available testing methods.
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Lin TC, Jiang SS, Chou WC, Hou HA, Lin YM, Chang CL, Hsu CA, Tien HF, Lin LI. Rapid assessment of the heterogeneous methylation status of CEBPA in patients with acute myeloid leukemia by using high-resolution melting profile. J Mol Diagn 2011; 13:514-9. [PMID: 21723418 DOI: 10.1016/j.jmoldx.2011.05.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2010] [Revised: 04/28/2011] [Accepted: 05/02/2011] [Indexed: 11/25/2022] Open
Abstract
Epigenetic inactivation of tumor-suppressor genes, often in association with aberrant DNA methylation of CpG islands in the promoter region of these genes, is a key factor in tumorigenesis. CCAAT/enhancer binding protein alpha (CEBPA) methylation is a favorable prognostic biomarker for acute myeloid leukemia; however, rather than the complete methylation observed in inherited disorders, CEBPA methylation is heterogeneous. In this study, we established an algorithm called the "methylation index," deduced from high-resolution melting profiles, which includes Tm shifting (ΔTm) and Tm width ratio (fold of width), to evaluate the heterogeneous methylation status. The methylation index was highly correlated with the exact methylation levels detected by using the MassARRAY method (R(2) = 0.80; P < 0.001). Within-run reproducibility for the methylation index was 0.9% as the coefficient of variation, and between-run reproducibility was 2.6%. It was determined that with a cutoff methylation index of 1.412, the best measures of sensitivity and specificity could be obtained (97.14% and 95.89%, respectively) to discern low or high CEBPA methylation status. This novel algorithm for calculation of the methylation index from high-resolution melting profiles for CEBPA methylation is compatible with measurement of the methylation level as assayed using MassARRAY and could be a simple and efficient screening method for determination of CEBPA methylation status in acute myeloid leukemia.
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Affiliation(s)
- Tsung-Chin Lin
- Department of Clinical Laboratory Sciences and Medical Biotechnology, National Taiwan University, Taipei, Taiwan
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Kauvar EF, Hu P, Pineda-Alvarez DE, Solomon BD, Dutra A, Pak E, Blessing B, Proud V, Shanske AL, Stevens CA, Rosenfeld JA, Shaffer LG, Roessler E, Muenke M. Minimal evidence for a direct involvement of twisted gastrulation homolog 1 (TWSG1) gene in human holoprosencephaly. Mol Genet Metab 2011; 102:470-80. [PMID: 21227728 PMCID: PMC3152819 DOI: 10.1016/j.ymgme.2010.12.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/13/2010] [Revised: 12/14/2010] [Accepted: 12/14/2010] [Indexed: 10/18/2022]
Abstract
Holoprosencephaly (HPE) is the most common disorder of human forebrain and facial development. Presently understood etiologies include both genetic and environmental factors, acting either alone, or more likely, in combination. The majority of patients without overt chromosomal abnormalities or recognizable associated syndromes have unidentified etiologies. A potential candidate gene, Twisted Gastrulation Homolog 1 (TWSG1), was previously suggested as a contributor to the complex genetics of human HPE based on (1) cytogenetic studies of patients with 18p deletions, (2) animal studies of TWSG1 deficient mice, and (3) the relationship of TWSG1 to bone morphogenetic protein (BMP) signaling, which modulates the primary pathway implicated in HPE, Sonic Hedgehog (SHH) signaling. Here we present the first analysis of a large cohort of patients with HPE for coding sequence variations in TWSG1. We also performed fine mapping of 18p for a subset of patients with partial 18p deletions. Surprisingly, minimal evidence for alterations of TWSG1 was found, suggesting that sequence alterations of TWSG1 are neither a common direct cause nor a frequent modifying factor for human HPE pathologies.
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Affiliation(s)
- Emily F. Kauvar
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
- Howard Hughes Medical Institute – National Institutes of Health Research Scholars Program, Bethesda, MD, USA
| | - Ping Hu
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Daniel E. Pineda-Alvarez
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Benjamin D. Solomon
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Amalia Dutra
- Genetic Disease Research Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Evgenia Pak
- Genetic Disease Research Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Brooke Blessing
- Division of Medical Genetics, Children’s Hospital of The King’s Daughters, Norfolk, VA, USA
| | - Virginia Proud
- Division of Medical Genetics, Children’s Hospital of The King’s Daughters, Norfolk, VA, USA
| | - Alan L. Shanske
- Center for Craniofacial Disorders, Children’s Hospital at Montefiore Medical Center, Bronx, NY, USA
| | - Cathy A. Stevens
- Department of Pediatrics, University of Tennessee College of Medicine, Chattanooga, TN, USA
| | | | | | - Erich Roessler
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Maximilian Muenke
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
- Corresponding author: Address: 35 Convent Drive, MSC 3717, Bldg 35, Rm 1B-203, Bethesda, MD, 20892-3717, USA. Tel: (301) 402-8167. Fax: (301) 480-7876. (M. Muenke)
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Development of a high resolution melting method for the detection of genetic variations in Long QT Syndrome. Clin Chim Acta 2011; 412:203-7. [DOI: 10.1016/j.cca.2010.09.013] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2010] [Revised: 09/08/2010] [Accepted: 09/10/2010] [Indexed: 11/22/2022]
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Scotet V, Duguépéroux I, Audrézet MP, Audebert-Bellanger S, Muller M, Blayau M, Férec C. Focus on cystic fibrosis and other disorders evidenced in fetuses with sonographic finding of echogenic bowel: 16-year report from Brittany, France. Am J Obstet Gynecol 2010; 203:592.e1-6. [PMID: 20932506 DOI: 10.1016/j.ajog.2010.08.033] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2010] [Revised: 04/30/2010] [Accepted: 08/17/2010] [Indexed: 12/22/2022]
Abstract
OBJECTIVE Pregnancies medical follow-up and ultrasonography development have enabled detection of fetal echogenic bowel, a sign associated with various pathologies, including cystic fibrosis. Based on the long experience of a region where cystic fibrosis is frequent (Brittany, France), we describe disorders diagnosed in fetal echogenic bowel fetuses and assess ultrasonography ability in detecting cystic fibrosis in utero. STUDY DESIGN We reviewed the cases of fetal echogenic bowel diagnosed in pregnant women living in Brittany and referred for CFTR gene analysis over the 1992-2007 period (n = 289). RESULTS A disorder was diagnosed in 32.2% of the fetuses, cystic fibrosis being the most commonly identified (7.6%). We also found digestive malformations (7.0%), chromosomal abnormalities (3.7%), and maternofetal infections (3.7%). Combining these data with our ongoing newborn screening program since 1989 showed that ultrasonography enabled diagnosis of 10.7% of the cystic fibrosis cases. CONCLUSION This study highlights the importance of pregnancy ultrasound examinations and their efficiency in detecting cystic fibrosis.
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Sheridan MB, Hefferon TW, Wang N, Merlo C, Milla C, Borowitz D, Green ED, Mogayzel PJ, Cutting GR. CFTR transcription defects in pancreatic sufficient cystic fibrosis patients with only one mutation in the coding region of CFTR. J Med Genet 2010; 48:235-41. [PMID: 21097845 DOI: 10.1136/jmg.2010.083287] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
BACKGROUND Patients with cystic fibrosis (CF) manifest a multisystem disease due to deleterious mutations in each gene encoding the cystic fibrosis transmembrane conductance regulator (CFTR). However, the role of dysfunctional CFTR is uncertain in individuals with mild forms of CF (ie, pancreatic sufficiency) and mutation in only one CFTR gene. METHODS Eleven pancreatic sufficient (PS) CF patients with only one CFTR mutation identified after mutation screening (three patients), mutation scanning (four patients) or DNA sequencing (four patients) were studied. Bi-directional sequencing of the coding region of CFTR was performed in patients who had mutation screening or scanning. If a second CFTR mutation was not identified, CFTR mRNA transcripts from nasal epithelial cells were analysed to determine if any PS-CF patients harboured a second CFTR mutation that altered RNA expression. RESULTS Sequencing of the coding regions of CFTR identified a second deleterious mutation in five of the seven patients who previously had mutation screening or mutation scanning. Five of the remaining six patients with only one deleterious mutation identified in the coding region of one CFTR gene had a pathologic reduction in the amount of RNA transcribed from their other CFTR gene (8.4-16% of wild type). CONCLUSIONS These results show that sequencing of the coding region of CFTR followed by analysis of CFTR transcription could be a useful diagnostic approach to confirm that patients with mild forms of CF harbour deleterious alterations in both CFTR genes.
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Affiliation(s)
- Molly B Sheridan
- McKusick-Nathans Institute of Genetic Medicine, 733 North Broadway, Johns Hopkins Medical Institutions, Baltimore, MD 21205, USA
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Li R, Liao C, Li D, Li J. High-Resolution Melting Analysis of the Three Common Nondeletional α-Thalassemia Mutations in the Chinese Population: Hbs Constant Spring, Quong Sze and Westmead. Hemoglobin 2010; 34:587-93. [DOI: 10.3109/03630269.2010.526881] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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Millat G, Chanavat V, Créhalet H, Rousson R. Development of a high resolution melting method for the detection of genetic variations in hypertrophic cardiomyopathy. Clin Chim Acta 2010; 411:1983-91. [PMID: 20800588 DOI: 10.1016/j.cca.2010.08.017] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2010] [Revised: 08/10/2010] [Accepted: 08/10/2010] [Indexed: 01/09/2023]
Abstract
BACKGROUND Hypertrophic cardiomyopathy (HCM) is the most common genetic cardiac disease affecting 1 in 500 people. Due to large cohorts to investigate, the number of disease-causing genes, the size of the 2 prevalent mutated genes, and the presence of a large spectrum of private mutations, mutational screening must be performed using an extremely sensitive and specific scanning method. METHODS High Resolution Melting (HRM) analysis was developed for prevalent HCM-causing genes (MYBPC3, MYH7, TNNT2, and TNNI3) using control DNAs and DNAs carrying previously identified gene variants. A cohort of 34 HCM patients was further blindly screened. To evaluate HRM sensitivity, this cohort was also screened using an optimized DHPLC methodology. RESULTS All gene variants detected by DHPLC were also readily identified as abnormal by HRM analysis. Mutational screening of a cohort of 34 HCM cases led to identification of 19 mutated alleles. Complete molecular investigation was completed two times faster and cheaper than using DHPLC strategy. CONCLUSIONS HRM analysis represents an inexpensive, highly sensitive and high-throughput method to allow identification of mutations in the coding sequences of prevalent HCM genes. Identification of more HCM mutations will provide new insights into genotype/phenotype relationships and will allow a better knowledge of the HCM physiopathology.
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Affiliation(s)
- Gilles Millat
- Laboratoire de Cardiogénétique Moléculaire, Centre de Biologie et Pathologie Est, Hospices Civils de Lyon, Lyon, France.
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Quemener S, Chen JM, Chuzhanova N, Bénech C, Casals T, Macek M, Bienvenu T, McDevitt T, Farrell PM, Loumi O, Messaoud T, Cuppens H, Cutting GR, Stenson PD, Giteau K, Audrézet MP, Cooper DN, Férec C. Complete ascertainment of intragenic copy number mutations (CNMs) in the CFTR gene and its implications for CNM formation at other autosomal loci. Hum Mutat 2010; 31:421-8. [PMID: 20052766 DOI: 10.1002/humu.21196] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Over the last 20 years since the discovery of the cystic fibrosis transmembrane conductance regulator (CFTR) gene, more than 1,600 different putatively pathological CFTR mutations have been identified. Until now, however, copy number mutations (CNMs) involving the CFTR gene have not been methodically analyzed, resulting almost certainly in the underascertainment of CFTR gene duplications compared with deletions. Here, high-resolution array comparative genomic hybridization (averaging one interrogating probe every 95 bp) was used to analyze the entire length of the CFTR gene (189 kb) in 233 cystic fibrosis chromosomes lacking conventional mutations. We succeeded in identifying five duplication CNMs that would otherwise have been refractory to analysis. Based upon findings from this and other studies, we propose that deletion and duplication CNMs in the human autosomal genome are likely to be generated in the proportion of approximately 2-3:1. We further postulate that intragenic gene duplication CNMs in other disease loci may have been routinely underascertained. Finally, our analysis of +/-20 bp flanking each of the 40 CFTR breakpoints characterized at the DNA sequence level provide support for the emerging concept that non-B DNA conformations in combination with specific sequence motifs predispose to both recurring and nonrecurring genomic rearrangements.
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Affiliation(s)
- Sylvia Quemener
- INSERM U613, and Université de Bretagne Occidentale, 46 rue Félix Le Dantec, Brest, France
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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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Abstract
Acute pancreatitis and chronic pancreatitis are complex inflammatory disorders of the pancreas with unpredictable severity, complications, and clinical courses. Growing evidence for genetic risk and modifying factors, plus strong evidence that only a minority of patients with these disorders are heavy alcohol drinkers, has revolutionized our concept of these diseases. Once considered a self-inflicted injury, pancreatitis is now recognized as a complex inflammatory condition like inflammatory bowel disease. Genetic linkage and candidate gene studies have identified six pancreas-targeting factors that are associated with changes in susceptibility to acute and/or chronic pancreatitis, including cationic trypsinogen (PRSS1), anionic trypsinogen (PRSS2), serine protease inhibitor Kazal 1 (SPINK1), cystic fibrosis transmembrane conductance regulator (CFTR), chymotrypsinogen C (CTRC) and calcium-sensing receptor (CASR). Patients with mutations in these genes are at increased risk of pancreatitis caused by a variety of stresses including hyperlipidemia and hypercalcemia. Multiple studies are reporting new polymorphisms, as well as complex gene x gene and gene x environmental interactions.
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Affiliation(s)
- David C Whitcomb
- Division of Gastroenterology, Hepatology and Nutrition, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania 15213, USA.
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Lince SL, Kluivers KB, Dijkstra JR, Janssen MJ, Vierhout ME, van Kempen LC. Reliable Identification of the Type III Collagen Gene Polymorphism rs1800255 with the Use of High Resolution Melting Analysis. Lab Med 2009. [DOI: 10.1309/lmua5cs39fulvwem] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
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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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Duno M, Quinlivan R, Vissing J, Schwartz M. High-resolution Melting Facilitates Mutation Screening ofPYGMin Patients with McArdle Disease. Ann Hum Genet 2009; 73:292-7. [DOI: 10.1111/j.1469-1809.2009.00512.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Millat G, Chanavat V, Rodriguez-Lafrasse C, Rousson R. Rapid, sensitive and inexpensive detection of SCN5A genetic variations by high resolution melting analysis. Clin Biochem 2009; 42:491-9. [DOI: 10.1016/j.clinbiochem.2008.10.014] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2008] [Revised: 10/06/2008] [Accepted: 10/20/2008] [Indexed: 12/19/2022]
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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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Millat G, Chanavat V, Julia S, Crehalet H, Bouvagnet P, Rousson R. Validation of high-resolution DNA melting analysis for mutation scanning of the LMNA gene. Clin Biochem 2009; 42:892-8. [PMID: 19318026 DOI: 10.1016/j.clinbiochem.2009.01.016] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2008] [Revised: 01/13/2009] [Accepted: 01/24/2009] [Indexed: 11/29/2022]
Abstract
OBJECTIVES LMNA mutations lead to a wide spectrum of disorders now called laminopathies. Due to large cohorts to investigate, mutational screening must be performed using an extremely sensitive and specific scanning method. DESIGN AND METHODS High Resolution Melting (HRM) analysis was developed for LMNA mutation detection. A cohort of 64 patients with dilated cardiomyopathy was prospectively screened using both HRM and DHPLC methodologies. RESULTS All gene variants detected by DHPLC or by direct sequencing were also readily identified as abnormal by HRM analysis. Mutations were identified in 7 patients (approximately 11%). Complete molecular LMNA investigation was completed two times faster and cheaper than using DHPLC strategy. CONCLUSIONS HRM analysis represents an inexpensive, highly sensitive and high-throughput method to identify LMNA genetic variants. The discovery of novel LMNA mutations will provide new insights into the pathophysiology of dilated cardiomyopathy and in all other laminopathies.
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Affiliation(s)
- Gilles Millat
- Laboratoire de Cardiogénétique Moléculaire, Centre de Biologie et Pathologie Est, Hospices Civils de Lyon, Bron, France.
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