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Qi M, Stenson PD, Ball EV, Tainer JA, Bacolla A, Kehrer-Sawatzki H, Cooper DN, Zhao H. Distinct sequence features underlie microdeletions and gross deletions in the human genome. Hum Mutat 2021; 43:328-346. [PMID: 34918412 PMCID: PMC9069542 DOI: 10.1002/humu.24314] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 11/02/2021] [Accepted: 12/14/2021] [Indexed: 11/18/2022]
Abstract
Microdeletions and gross deletions are important causes (~20%) of human inherited disease and their genomic locations are strongly influenced by the local DNA sequence environment. This notwithstanding, no study has systematically examined their underlying generative mechanisms. Here, we obtained 42,098 pathogenic microdeletions and gross deletions from the Human Gene Mutation Database (HGMD) that together form a continuum of germline deletions ranging in size from 1 to 28,394,429 bp. We analyzed the DNA sequence within 1 kb of the breakpoint junctions and found that the frequencies of non‐B DNA‐forming repeats, GC‐content, and the presence of seven of 78 specific sequence motifs in the vicinity of pathogenic deletions correlated with deletion length for deletions of length ≤30 bp. Further, we found that the presence of DR, GQ, and STR repeats is important for the formation of longer deletions (>30 bp) but not for the formation of shorter deletions (≤30 bp) while significantly (χ2, p < 2E−16) more microhomologies were identified flanking short deletions than long deletions (length >30 bp). We provide evidence to support a functional distinction between microdeletions and gross deletions. Finally, we propose that a deletion length cut‐off of 25–30 bp may serve as an objective means to functionally distinguish microdeletions from gross deletions.
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Affiliation(s)
- Mengling Qi
- Department of Medical Research Center, Sun Yat-sen Memorial Hospital; Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangzhou, China
| | - Peter D Stenson
- Institute of Medical Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK
| | - Edward V Ball
- Institute of Medical Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK
| | - John A Tainer
- Departments of Cancer Biology and of Molecular and Cellular Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Albino Bacolla
- Departments of Cancer Biology and of Molecular and Cellular Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | | | - David N Cooper
- Institute of Medical Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK
| | - Huiying Zhao
- Department of Medical Research Center, Sun Yat-sen Memorial Hospital; Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangzhou, China
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2
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Validation of a Custom Next-Generation Sequencing Assay for Cystic Fibrosis Newborn Screening. Int J Neonatal Screen 2021; 7:ijns7040073. [PMID: 34842611 PMCID: PMC8628990 DOI: 10.3390/ijns7040073] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 10/20/2021] [Accepted: 10/28/2021] [Indexed: 11/16/2022] Open
Abstract
Newborn screening (NBS) for Cystic Fibrosis (CF) is associated with improved outcomes. All US states screen for CF; however, CF NBS algorithms have high false positive (FP) rates. In New York State (NYS), the positive predictive value of CF NBS improved from 3.7% to 25.2% following the implementation of a three-tier IRT-DNA-SEQ approach using commercially available tests. Here we describe a modification of the NYS CF NBS algorithm via transition to a new custom next-generation sequencing (NGS) platform for more comprehensive cystic fibrosis transmembrane conductance regulator (CFTR) gene analysis. After full gene sequencing, a tiered strategy is used to first analyze only a specific panel of 338 clinically relevant CFTR variants (second-tier), followed by unblinding of all sequence variants and bioinformatic assessment of deletions/duplications in a subset of samples requiring third-tier analysis. We demonstrate the analytical and clinical validity of the assay and the feasibility of use in the NBS setting. The custom assay has streamlined our molecular workflow, increased throughput, and allows for bioinformatic customization of second-tier variant panel content. NBS aims to identify those infants with the highest disease risk. Technological molecular improvements can be applied to NBS algorithms to reduce the burden of FP referrals without loss of sensitivity.
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3
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Harris A. Human molecular genetics and the long road to treating cystic fibrosis. Hum Mol Genet 2021; 30:R264-R273. [PMID: 34245257 DOI: 10.1093/hmg/ddab191] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 07/04/2021] [Accepted: 07/06/2021] [Indexed: 11/13/2022] Open
Abstract
The causative gene in cystic fibrosis was identified in 1989, three years before the publication of the first issue of Human Molecular Genetics. CFTR was among the first genes underlying a common inherited disorder to be cloned, and hence its subsequent utilization towards a cure for CF provides a roadmap for other monogenic diseases. Over the past 30 years the advances that built upon knowledge of the gene and the CFTR protein to develop effective therapeutics have been remarkable, and yet the setbacks have also been challenging. Technological progress in other fields has often circumvented the barriers. This review focuses on key aspects of CF diagnostics and current approaches to develop new therapies for all CFTR mutations. It also highlights the major research advances that underpinned progress towards treatments, and considers the remaining obstacles.
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Affiliation(s)
- Ann Harris
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH, 44106, USA
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4
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Abstract
Pathogenic variants of the CFTR gene are responsible for a broad phenotypic spectrum characterized by malfunction of some exocrine tissues, with an autosomal recessive mode of inheritance. More than 2,000 variants, distributed throughout the CFTR gene, have been identified, with different effects on the gene and protein expression and function. Genotype-phenotype correlation studies have associated severe variants with a typical multi-organ form of cystic fibrosis, while mild variants are involved in monosymptomatic or adult-onset diseases, called CFTR-related disorders. However, the interpretation of rare variants remains challenging. This review presents an overview of the epidemiology of CFTR variants worldwide and in France and describes the functional classification. Finally, some frequent cystic fibrosis-causing and mild CFTR variants are used as example to depict the molecular pathology of the CFTR locus. Finally, we give the recommendations concerning nomenclature and classification that are useful for appropriate genetic counseling. © 2020 French Society of Pediatrics. Published by Elsevier Masson SAS. All rights reserved.
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Affiliation(s)
- C Bareil
- Laboratoire de Génétique Moléculaire, CHU de Montpellier, Montpellier, France
| | - A Bergougnoux
- Laboratoire de Génétique Moléculaire, CHU de Montpellier, Montpellier, France; EA7402 Laboratoire de Génétique de Maladies Rares, Institut Universitaire de Recherche Clinique, Université de Montpellier, Montpellier, France..
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5
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Analysis of rearrangements of the CFTR gene in patients from Turkey with CFTR-related disorders: frequent exon 2 deletion. J Hum Genet 2020; 66:315-320. [PMID: 33093640 DOI: 10.1038/s10038-020-00859-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 09/23/2020] [Accepted: 10/06/2020] [Indexed: 11/09/2022]
Abstract
Cystic fibrosis is a hereditary disease that mostly affects the sweat glands, respiratory system, digestive system, and reproductive system. Many and various types of mutations have been reported in CFTR in different ethnicities and countries/regions. Analysis of CFTR gene rearrangements is recommended in patients with unidentified mutated alleles in CFTR sequencing analysis. We collected MLPA analyses of 527 patients from Turkey who had at least one unidentified mutation in CFTR sequence analysis. Heterozygous/homozygous deletions were detected in the CFTR gene in 49 individuals (9.2%) from 35 families. Twelve different single/multi exon deletions were demonstrated, two of which were not previously reported in the literature. Mutations have previously reported in patients from various regions including Asia, Europe, and Africa, and Turkey is located at a crossroads between them. The most frequent mutation was the exon 2 deletion, accounting for 60%. Moreover, patients with exon 2 deletions, were especially originated from northern Turkey. This finding is valuable in leading and shaping planned screening programs in Turkey. Our study, the most comprehensive study for rearrangement analysis in patients from Tukey, revealed a candidate hotspot region of patients suspected of having CFTR-related disorders from Turkey.
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Ma C, Wang R, Li T, Li H, Wang B. Analysis of CNVs of CFTR gene in Chinese Han population with CBAVD. Mol Genet Genomic Med 2020; 8:e1506. [PMID: 32951344 PMCID: PMC7667304 DOI: 10.1002/mgg3.1506] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 08/28/2020] [Accepted: 08/31/2020] [Indexed: 01/09/2023] Open
Abstract
Background Congenital bilateral absence of vas deferens (CBAVD) is an important disease of male infertility, which affects 1%–2% of infertile population. In addition to common mutations of CFTR, copy number variants (CNVs) have also been implicated as one of the pathogenesis of CBAVD. The present study aimed to investigate the genetic contribution of CFTR CNVs in Chinese Han population with CBAVD. Methods Two hundred and sixty‐three CBAVD patients were recruited. Genomic DNA was extracted from peripheral blood samples. The Multiplex Ligation‐dependent Probe Amplification assay was performed which targets the region of the CFTR gene. Results Among 263 Chinese men affected with CBAVD in this study, 5 (1.90%) patients were detected for copy number variants in the region of CFTR gene (4 of them carried partial deletions and 1 of them carried partial duplication of CFTR gene). Conclusions The study showed that the rate of CFTR CNVs in Chinese population with CBAVD were basically consistent with the previous reports. And the study first revealed genetic risk of CNVs of CFTR on a large sample size of CBAVD patients in Chinese Han population, which prompted that it was necessary to detect CNVs of CFTR in Chinese Han people with CBAVD.
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Affiliation(s)
- Chengquan Ma
- Department of Urology, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, P. R. China.,Graduate School of Peking Union Medical College, Beijing, P. R. China
| | - Ruyi Wang
- Graduate School of Peking Union Medical College, Beijing, P. R. China.,Center for Genetics, National Research Institute for Family Planning, Beijing, P. R. China
| | - Tengyan Li
- Center for Genetics, National Research Institute for Family Planning, Beijing, P. R. China
| | - Hongjun Li
- Department of Urology, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, P. R. China
| | - Binbin Wang
- Graduate School of Peking Union Medical College, Beijing, P. R. China.,Center for Genetics, National Research Institute for Family Planning, Beijing, P. R. China
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Paranjapye A, Ruffin M, Harris A, Corvol H. Genetic variation in CFTR and modifier loci may modulate cystic fibrosis disease severity. J Cyst Fibros 2020; 19 Suppl 1:S10-S14. [PMID: 31734115 PMCID: PMC7036019 DOI: 10.1016/j.jcf.2019.11.001] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Revised: 11/04/2019] [Accepted: 11/07/2019] [Indexed: 12/11/2022]
Abstract
In patients with cystic fibrosis (CF), genetic variants within and outside the CFTR locus contribute to the variability of the disease severity. CFTR transcription is tightly regulated by cis-regulatory elements (CREs) that control the three-dimensional structure of the locus, chromatin accessibility and transcription factor recruitment. Variants within these CREs may contribute to the pathophysiology and to the phenotypic heterogeneity by altering CFTR transcript abundance. In addition to the CREs, variants outside the CFTR locus, namely "modifiers genes", may also be associated with the clinical variability. This review addresses variants at the CFTR locus itself and CFTR CREs, together with the outcomes of the latest modifier gene studies with respect to the different CF phenotypes.
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Affiliation(s)
- Alekh Paranjapye
- Department of Genetics and Genome Sciences, Case Western Reserve University Medical School, 10900 Euclid Avenue, Cleveland, OH, USA
| | - Manon Ruffin
- Sorbonne Université, INSERM, Centre de Recherche Saint-Antoine, CRSA, Paris, France
| | - Ann Harris
- Department of Genetics and Genome Sciences, Case Western Reserve University Medical School, 10900 Euclid Avenue, Cleveland, OH, USA.
| | - Harriet Corvol
- Sorbonne Université, INSERM, Centre de Recherche Saint-Antoine, CRSA, Paris, France; AP-HP, Hôpital Trousseau, Service de Pneumologie Pédiatrique, Paris, France.
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8
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Martins RDS, Campos Junior M, Dos Santos Moreira A, Marques Zembrzuski V, da Fonseca ACP, Abreu GDM, Cabello PH, de Cabello GMK. Identification of a novel large deletion and other copy number variations in the CFTR gene in patients with Cystic Fibrosis from a multiethnic population. Mol Genet Genomic Med 2019; 7:e00645. [PMID: 31199594 PMCID: PMC6625342 DOI: 10.1002/mgg3.645] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Revised: 02/13/2019] [Accepted: 02/20/2019] [Indexed: 11/30/2022] Open
Abstract
Background Cystic fibrosis (CF) is caused by mutations in the cystic fibrosis transmembrane conductance regulator gene (CFTR). There are over 2000 different pathogenic and non‐pathogenic variants described in association with a broad clinical heterogeneity. The most common types of mutations in this gene are single nucleotide substitutions or small deletions and insertions. However, large rearrangements, such as large duplications or deletions, are also a possible cause of CF; these variations are rarely tested in routine screenings, and much of them remain unidentified in some populations, especially those with high ethnic heterogeneity. Methods The present study utilized the Multiplex Ligation‐dependent Probe Amplification (MLPA) technique for the detection of duplications and deletions in 165 CF patients from the Rio de Janeiro State (Brazil), which after extensive mutational screening, still exhibited one or two unidentified CF alleles. Results Five patients with alterations in MLPA signals were detected. After validation, we identified three copy number variations, one large duplication (CFTRdup2‐3) and two large deletions (CFTRdel25‐26 and CFTRdel25‐27‐CTTNBP2). Two detected deletions were not validated. They were false positives caused by a small deletion of 18 base pairs (232del18) and a point mutation (S168L) in the probe binding site. Conclusion Our results highlight the importance of screening for large rearrangements in CF cases with no or only one CFTR mutation defined.
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Affiliation(s)
- Raisa da Silva Martins
- Human Genetics Laboratory, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro, Brazil.,Molecular and Cellular Biology Graduate Program (PPGBMC), Federal University of the State of Rio de Janeiro (UNIRIO), Rio de Janeiro, Brazil
| | - Mario Campos Junior
- Human Genetics Laboratory, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro, Brazil
| | - Aline Dos Santos Moreira
- Laboratory of Functional Genomics and Bioinformatics, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro, Brazil
| | | | | | | | - Pedro Hernan Cabello
- Human Genetics Laboratory, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro, Brazil.,Genetics Laboratory, Grande Rio University (UNIGRANRIO), Rio de Janeiro, Brazil
| | - Giselda Maria Kalil de Cabello
- Human Genetics Laboratory, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro, Brazil.,Molecular and Cellular Biology Graduate Program (PPGBMC), Federal University of the State of Rio de Janeiro (UNIRIO), Rio de Janeiro, Brazil
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9
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Kerschner JL, Ghosh S, Paranjapye A, Cosme WR, Audrézet MP, Nakakuki M, Ishiguro H, Férec C, Rommens J, Harris A. Screening for Regulatory Variants in 460 kb Encompassing the CFTR Locus in Cystic Fibrosis Patients. J Mol Diagn 2018; 21:70-80. [PMID: 30296588 DOI: 10.1016/j.jmoldx.2018.08.011] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2018] [Revised: 07/18/2018] [Accepted: 08/10/2018] [Indexed: 12/30/2022] Open
Abstract
It is estimated that up to 5% of cystic fibrosis transmembrane conductance regulator (CFTR) pathogenic alleles are unidentified. Some of these errors may lie in noncoding regions of the locus and affect gene expression. To identify regulatory element variants in the CFTR locus, SureSelect targeted enrichment of 460 kb encompassing the gene was optimized to deep sequence genomic DNA from 80 CF patients with an unequivocal clinical diagnosis but only one or no CFTR-coding region pathogenic variants. Bioinformatics tools were used to identify sequence variants and predict their impact, which were then assayed in transient reporter gene luciferase assays. The effect of five variants in the CFTR promoter and four in an intestinal enhancer of the gene were assayed in relevant cell lines. The initial analysis of sequence data revealed previously known CF-causing variants, validating the robustness of the SureSelect design, and showed that 85 of 160 CF alleles were undefined. Of a total 1737 variants revealed across the extended 460-kb CFTR locus, 51 map to known CFTR cis-regulatory elements, and many of these are predicted to alter transcription factor occupancy. Four promoter variants and all those in the intestinal enhancer significantly repress reporter gene activity. These data suggest that CFTR regulatory elements may harbor novel CF disease-causing variants that warrant further investigation, both for genetic screening protocols and functional assays.
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Affiliation(s)
- Jenny L Kerschner
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, Ohio
| | - Sujana Ghosh
- Human Molecular Genetics Program, Lurie Children's Research Center, Chicago, Illinois; Department of Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Alekh Paranjapye
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, Ohio
| | - Wilmel R Cosme
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, Ohio
| | | | - Miyuki Nakakuki
- Department of Human Nutrition, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Hiroshi Ishiguro
- Department of Human Nutrition, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | | | - Johanna Rommens
- Program in Genetics and Genome Biology, Research Institute, The Hospital for Sick Children, Toronto, Ontario, Canada; Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Ann Harris
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, Ohio; Human Molecular Genetics Program, Lurie Children's Research Center, Chicago, Illinois; Department of Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, Illinois.
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10
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Claustres M, Thèze C, des Georges M, Baux D, Girodon E, Bienvenu T, Audrezet MP, Dugueperoux I, Férec C, Lalau G, Pagin A, Kitzis A, Thoreau V, Gaston V, Bieth E, Malinge MC, Reboul MP, Fergelot P, Lemonnier L, Mekki C, Fanen P, Bergougnoux A, Sasorith S, Raynal C, Bareil C. CFTR-France, a national relational patient database for sharing genetic and phenotypic data associated with rare CFTR variants. Hum Mutat 2017; 38:1297-1315. [PMID: 28603918 DOI: 10.1002/humu.23276] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Revised: 05/31/2017] [Accepted: 06/04/2017] [Indexed: 11/09/2022]
Abstract
Most of the 2,000 variants identified in the CFTR (cystic fibrosis transmembrane regulator) gene are rare or private. Their interpretation is hampered by the lack of available data and resources, making patient care and genetic counseling challenging. We developed a patient-based database dedicated to the annotations of rare CFTR variants in the context of their cis- and trans-allelic combinations. Based on almost 30 years of experience of CFTR testing, CFTR-France (https://cftr.iurc.montp.inserm.fr/cftr) currently compiles 16,819 variant records from 4,615 individuals with cystic fibrosis (CF) or CFTR-RD (related disorders), fetuses with ultrasound bowel anomalies, newborns awaiting clinical diagnosis, and asymptomatic compound heterozygotes. For each of the 736 different variants reported in the database, patient characteristics and genetic information (other variations in cis or in trans) have been thoroughly checked by a dedicated curator. Combining updated clinical, epidemiological, in silico, or in vitro functional data helps to the interpretation of unclassified and the reassessment of misclassified variants. This comprehensive CFTR database is now an invaluable tool for diagnostic laboratories gathering information on rare variants, especially in the context of genetic counseling, prenatal and preimplantation genetic diagnosis. CFTR-France is thus highly complementary to the international database CFTR2 focused so far on the most common CF-causing alleles.
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Affiliation(s)
- Mireille Claustres
- Laboratoire de Génétique Moléculaire, Centre Hospitalier Universitaire et Université de Montpellier, Montpellier, France
| | - Corinne Thèze
- Laboratoire de Génétique Moléculaire, Centre Hospitalier Universitaire et Université de Montpellier, Montpellier, France
| | - Marie des Georges
- Laboratoire de Génétique Moléculaire, Centre Hospitalier Universitaire et Université de Montpellier, Montpellier, France
| | - David Baux
- Laboratoire de Génétique Moléculaire, Centre Hospitalier Universitaire et Université de Montpellier, Montpellier, France
| | - Emmanuelle Girodon
- Service de Génétique et Biologie Moléculaires, Groupe Hospitalier Cochin-Broca-Hotel Dieu, Paris, France
| | - Thierry Bienvenu
- Service de Génétique et Biologie Moléculaires, Groupe Hospitalier Cochin-Broca-Hotel Dieu, Paris, France
| | - Marie-Pierre Audrezet
- Laboratoire de Génétique Moléculaire et d'Histocompatibilité, Centre Hospitalier Régional Universitaire, Brest, France
| | - Ingrid Dugueperoux
- Laboratoire de Génétique Moléculaire et d'Histocompatibilité, Centre Hospitalier Régional Universitaire, Brest, France
| | - Claude Férec
- Laboratoire de Génétique Moléculaire et d'Histocompatibilité, Centre Hospitalier Régional Universitaire, Brest, France
| | - Guy Lalau
- Centre de Biologie Pathologie Génétique, Centre Hospitalier Régional Universitaire, Lille, France
| | - Adrien Pagin
- Centre de Biologie Pathologie Génétique, Centre Hospitalier Régional Universitaire, Lille, France
| | - Alain Kitzis
- Département de Génétique, Centre Hospitalier Universitaire, Poitiers, France
| | - Vincent Thoreau
- Département de Génétique, Centre Hospitalier Universitaire, Poitiers, France
| | - Véronique Gaston
- Service de Génétique Médicale, Centre Hospitalier Universitaire, Toulouse, France
| | - Eric Bieth
- Service de Génétique Médicale, Centre Hospitalier Universitaire, Toulouse, France
| | - Marie-Claire Malinge
- Département de Biochimie Génétique, Institut de Biologie en Santé, Centre Hospitalier Universitaire, Angers, France
| | - Marie-Pierre Reboul
- Laboratoire de Génétique Moléculaire, Centre Hospitalier Régional Universitaire, Bordeaux, France
| | - Patricia Fergelot
- Laboratoire Maladies Rares, Génétique et Métabolisme, Bordeaux, France
| | - Lydie Lemonnier
- Registre français de la mucoviscidose, Vaincre la Mucoviscidose, Paris, France
| | - Chadia Mekki
- Laboratoire de Génétique, Hôpital Henri Mondor, Créteil, France
| | - Pascale Fanen
- Laboratoire de Génétique, Hôpital Henri Mondor, Créteil, France
| | - Anne Bergougnoux
- Laboratoire de Génétique Moléculaire, Centre Hospitalier Universitaire et Université de Montpellier, Montpellier, France
| | - Souphatta Sasorith
- Laboratoire de Génétique Moléculaire, Centre Hospitalier Universitaire et Université de Montpellier, Montpellier, France
| | - Caroline Raynal
- Laboratoire de Génétique Moléculaire, Centre Hospitalier Universitaire et Université de Montpellier, Montpellier, France
| | - Corinne Bareil
- Laboratoire de Génétique Moléculaire, Centre Hospitalier Universitaire et Université de Montpellier, Montpellier, France
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11
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Abstract
Cystic fibrosis (CF) is the most frequent lethal genetic disorder among Caucasians, but is considered to be a very rare disease in Chinese population. Here, we present an 11-year-old Chinese CF patient with disseminated bronchiectasis and salty sweat, for whom exon sequencing followed by multiplex ligation-dependent probe amplification analysis of the CFTR gene was applied for mutation screening. A homozygous deletion involving exon 20 of CFTR was observed in the patient's genome. Molecular characterization of the breakpoints indicated that both alleles of this locus had an identical novel complex rearrangement (c.3140-454_c.3367+249del931ins13, p.R1048_G1123del), leading to an in-frame removal of 76 amino acid residues in the second transmembrane domains of the CFTR protein. Although a same haplotype containing this complex rearrangement was observed on both of the maternal and paternal alleles, the parents denied any blood relationship as far as they know. Genome-wide homozygosity mapping was performed through SNP microarray and only a single homozygous interval of ~14.1 Mb at chromosome 7 containing the CFTR gene was observed, indicating the possible origin of the deletion from a common ancestor many generations ago. This study expands the mutation spectrum of CFTR in patients of Chinese origin and further emphasizes the necessity of MLPA analysis in mutation screening for CF patients.
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12
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Improving newborn screening for cystic fibrosis using next-generation sequencing technology: a technical feasibility study. Genet Med 2015; 18:231-8. [PMID: 25674778 DOI: 10.1038/gim.2014.209] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2014] [Accepted: 12/22/2014] [Indexed: 11/09/2022] Open
Abstract
PURPOSE Many regions have implemented newborn screening (NBS) for cystic fibrosis (CF) using a limited panel of cystic fibrosis transmembrane regulator (CFTR) mutations after immunoreactive trypsinogen (IRT) analysis. We sought to assess the feasibility of further improving the screening using next-generation sequencing (NGS) technology. METHODS An NGS assay was used to detect 162 CFTR mutations/variants characterized by the CFTR2 project. We used 67 dried blood spots (DBSs) containing 48 distinct CFTR mutations to validate the assay. NGS assay was retrospectively performed on 165 CF screen-positive samples with one CFTR mutation. RESULTS The NGS assay was successfully performed using DNA isolated from DBSs, and it correctly detected all CFTR mutations in the validation. Among 165 screen-positive infants with one CFTR mutation, no additional disease-causing mutation was identified in 151 samples consistent with normal sweat tests. Five infants had a CF-causing mutation that was not included in this panel, and nine with two CF-causing mutations were identified. CONCLUSION The NGS assay was 100% concordant with traditional methods. Retrospective analysis results indicate an IRT/NGS screening algorithm would enable high sensitivity, better specificity and positive predictive value (PPV). This study lays the foundation for prospective studies and for introducing NGS in NBS laboratories.
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13
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Aygun N. Correlations between long inverted repeat (LIR) features, deletion size and distance from breakpoint in human gross gene deletions. Sci Rep 2015; 5:8300. [PMID: 25657065 PMCID: PMC4319165 DOI: 10.1038/srep08300] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2014] [Accepted: 01/14/2015] [Indexed: 11/09/2022] Open
Abstract
Long inverted repeats (LIRs) have been shown to induce genomic deletions in yeast. In this study, LIRs were investigated within ±10 kb spanning each breakpoint from 109 human gross deletions, using Inverted Repeat Finder (IRF) software. LIR number was significantly higher at the breakpoint regions, than in control segments (P < 0.001). In addition, it was found that strong correlation between 5' and 3' LIR numbers, suggesting contribution to DNA sequence evolution (r = 0.85, P < 0.001). 138 LIR features at ±3 kb breakpoints in 89 (81%) of 109 gross deletions were evaluated. Significant correlations were found between distance from breakpoint and loop length (r = -0.18, P < 0.05) and stem length (r = -0.18, P < 0.05), suggesting DNA strands are potentially broken in locations closer to bigger LIRs. In addition, bigger loops cause larger deletions (r = 0.19, P < 0.05). Moreover, loop length (r = 0.29, P < 0.02) and identity between stem copies (r = 0.30, P < 0.05) of 3' LIRs were more important in larger deletions. Consequently, DNA breaks may form via LIR-induced cruciform structure during replication. DNA ends may be later repaired by non-homologous end-joining (NHEJ), with following deletion.
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Affiliation(s)
- Nevim Aygun
- Department of Medical Biology, Faculty of Medicine, Dokuz Eylul University, Inciralti, Izmir, Turkey
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Molecular Analysis of Cystic Fibrosis Patients in Hungary - An Update to the Mutational Spectrum. J Med Biochem 2014; 34:46-51. [PMID: 28356823 PMCID: PMC4922332 DOI: 10.2478/jomb-2014-0055] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2014] [Accepted: 05/25/2014] [Indexed: 11/21/2022] Open
Abstract
BACKGROUND In this study the authors present an update to the CFTR mutation profile in Hungary, utilizing data from a selected cohort of 45 cystic fibrosis (CF) patients from different regions of the country. METHODS Depending on the preceding analysis, four different mutation detection methods were used. A commercial assay targeting the most common CF-causing mutations was performed as the first test followed by an allele specific PCR for CFTRdele2,3(21kb), Sanger sequencing and MLPA analysis of the coding region of the CFTR gene. RESULTS In our recent study 27 different mutations were detected, including 2 novel ones (c.1037_1038insA and c.1394C>T). Besides F508del (c.1521_1523delCTT), the following mutations were found at a frequency of ≥ 4.0%: W1282X (c.3846G>A), N1303K (c.3909C>G), CFTRdele2,3(21kb) (c.54-5940_273+10250del21kb) and 2184insA (c.2052_2053insA). In addition, four mutations (G542X, Y1092X, 621+1G>T, and 2143delT) were found in more than one allele. CONCLUSIONS The updated database of Hungarian mutations not only enables to increase the efficiency of the existing diagnostic approach, but also provides a further refined basis for the introduction of the molecular newborn screening (NBS) program in Hungary.
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15
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Does Integration of Various Ion Channel Measurements Improve Diagnostic Performance in Cystic Fibrosis? Ann Am Thorac Soc 2014; 11:562-70. [DOI: 10.1513/annalsats.201311-412oc] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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16
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Ooi CY, Dupuis A, Ellis L, Jarvi K, Martin S, Ray PN, Steele L, Kortan P, Gonska T, Dorfman R, Solomon M, Zielenski J, Corey M, Tullis E, Durie P. Does extensive genotyping and nasal potential difference testing clarify the diagnosis of cystic fibrosis among patients with single-organ manifestations of cystic fibrosis? Thorax 2013; 69:254-60. [PMID: 24149827 DOI: 10.1136/thoraxjnl-2013-203832] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
BACKGROUND The phenotypic spectrum of cystic fibrosis (CF) has expanded to include patients affected by single-organ diseases. Extensive genotyping and nasal potential difference (NPD) testing have been proposed to assist in the diagnosis of CF when sweat testing is inconclusive. However, the diagnostic yield of extensive genotyping and NPD and the concordance between NPD and the sweat test have not been carefully evaluated. METHODS We evaluated the diagnostic outcomes of genotyping (with 122 mutations included as disease causing), sweat testing and NPD in a prospectively ascertained cohort of undiagnosed patients who presented with chronic sino-pulmonary disease (RESP), chronic/recurrent pancreatitis (PANC) or obstructive azoospermia (AZOOSP). RESULTS 202 patients (68 RESP, 42 PANC and 92 AZOOSP) were evaluated; 17.3%, 22.8% and 59.9% had abnormal, borderline and normal sweat chloride results, respectively. Only 17 (8.4%) patients were diagnosable as having CF by genotyping. Compared to sweat testing, NPD identified more patients as having CF (33.2%) with fewer borderline results (18.8%). The level of agreement according to kappa statistics (and the observed percentage of agreement) between sweat chloride and NPD in RESP, PANC and AZOOSP subjects was 'moderate' (65% observed agreement), 'poor' (33% observed agreement) and 'fair' (28% observed agreement), respectively. The degree of agreement only improved marginally when subjects with borderline sweat chloride results were excluded from the analysis. CONCLUSIONS The diagnosis of CF or its exclusion is not always straightforward and may remain elusive even with comprehensive evaluation, particularly among individuals who present at an older age with single-organ manifestations suggestive of CF.
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Affiliation(s)
- Chee Y Ooi
- Physiology and Experimental Medicine, Research Institute, The Hospital for Sick Children, , Toronto, Canada
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17
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Rouzier C, Chaussenot A, Serre V, Fragaki K, Bannwarth S, Ait-El-Mkadem S, Attarian S, Kaphan E, Cano A, Delmont E, Sacconi S, Mousson de Camaret B, Rio M, Lebre AS, Jardel C, Deschamps R, Richelme C, Pouget J, Chabrol B, Paquis-Flucklinger V. Quantitative multiplex PCR of short fluorescent fragments for the detection of large intragenic POLG rearrangements in a large French cohort. Eur J Hum Genet 2013; 22:542-50. [PMID: 23921535 DOI: 10.1038/ejhg.2013.171] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2012] [Revised: 05/21/2013] [Accepted: 06/19/2013] [Indexed: 01/03/2023] Open
Abstract
Polymerase gamma (POLG) is the gene most commonly involved in mitochondrial disorders with mitochondrial DNA instability and causes a wide range of diseases with recessive or dominant transmission. More than 170 mutations have been reported. Most of them are missense mutations, although nonsense mutations, splice-site mutations, small deletions and insertions have also been identified. However, to date, only one large-scale rearrangement has been described in a child with Alpers syndrome. Below, we report a large cohort of 160 patients with clinical, molecular and/or biochemical presentation suggestive of POLG deficiency. Using sequencing, we identified POLG variants in 22 patients (18 kindreds) including five novel pathogenic mutations. Two patients with novel mutations had unusual clinical presentation: the first exhibited an isolated ataxic neuropathy and the second was a child who presented with endocrine signs. We completed the sequencing step by quantitative multiplex PCR of short fluorescent fragments (QMPSF) analysis in 37 patients with either only one POLG heterozygous variant or a family history suggesting a dominant transmission. We identified a large intragenic deletion encompassing part of intron 21 and exon 22 of POLG in a child with refractory epilepsia partialis continua. In conclusion, we describe the first large French cohort of patients with POLG mutations, expanding the wide clinical and molecular spectrum observed in POLG disease. We confirm that large deletions in the POLG gene are rare events and we highlight the importance of QMPSF in patients with a single heterozygous POLG mutation, particularly in severe infantile phenotypes.
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Affiliation(s)
- Cécile Rouzier
- 1] Department of Medical Genetics, National Centre for Mitochondrial diseases, Nice Teaching Hospital, Nice, France [2] IRCAN, CNRS UMR 7284/INSERM U1081/UNS, School of Medicine, Nice Sophia-Antipolis University, Nice, France
| | - Annabelle Chaussenot
- Department of Medical Genetics, National Centre for Mitochondrial diseases, Nice Teaching Hospital, Nice, France
| | - Valérie Serre
- Jacques Monod Institute, CNRS-University Paris Diderot, Sorbonne, Paris, France
| | - Konstantina Fragaki
- 1] Department of Medical Genetics, National Centre for Mitochondrial diseases, Nice Teaching Hospital, Nice, France [2] IRCAN, CNRS UMR 7284/INSERM U1081/UNS, School of Medicine, Nice Sophia-Antipolis University, Nice, France
| | - Sylvie Bannwarth
- 1] Department of Medical Genetics, National Centre for Mitochondrial diseases, Nice Teaching Hospital, Nice, France [2] IRCAN, CNRS UMR 7284/INSERM U1081/UNS, School of Medicine, Nice Sophia-Antipolis University, Nice, France
| | - Samira Ait-El-Mkadem
- 1] Department of Medical Genetics, National Centre for Mitochondrial diseases, Nice Teaching Hospital, Nice, France [2] IRCAN, CNRS UMR 7284/INSERM U1081/UNS, School of Medicine, Nice Sophia-Antipolis University, Nice, France
| | - Shahram Attarian
- Department of Neurology, Timone Hospital, Marseille Teaching Hospital, Marseille, France
| | - Elsa Kaphan
- Department of Neurology, Timone Hospital, Marseille Teaching Hospital, Marseille, France
| | - Aline Cano
- Department of Neuropediatrics, Timone Hospital, Marseille Teaching Hospital, Marseille, France
| | - Emilien Delmont
- Department of Neurology, Nice Teaching Hospital, Nice, France
| | - Sabrina Sacconi
- Department of Neurology, Nice Teaching Hospital, Nice, France
| | | | - Marlène Rio
- Department of Medical Genetics, Necker Hospital, Paris Teaching Hospital, Paris, France
| | - Anne-Sophie Lebre
- Department of Medical Genetics, Necker Hospital, Paris Teaching Hospital, Paris, France
| | - Claude Jardel
- Department of Molecular and Chromosomal Genetics, Pitié-Salpétrière Hospital, Paris Teaching Hospital, Paris, France
| | - Romain Deschamps
- Department of Neuromuscular disorders, Fort-de-France Teaching Hospital, Martinique, France
| | - Christian Richelme
- Department of Pediatrics, Lenval Hospital, Nice Teaching Hospital, Nice, France
| | - Jean Pouget
- Department of Neurology, Timone Hospital, Marseille Teaching Hospital, Marseille, France
| | - Brigitte Chabrol
- Department of Neuropediatrics, Timone Hospital, Marseille Teaching Hospital, Marseille, France
| | - Véronique Paquis-Flucklinger
- 1] Department of Medical Genetics, National Centre for Mitochondrial diseases, Nice Teaching Hospital, Nice, France [2] IRCAN, CNRS UMR 7284/INSERM U1081/UNS, School of Medicine, Nice Sophia-Antipolis University, Nice, France
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Trujillano D, Ramos MD, González J, Tornador C, Sotillo F, Escaramis G, Ossowski S, Armengol L, Casals T, Estivill X. Next generation diagnostics of cystic fibrosis and CFTR-related disorders by targeted multiplex high-coverage resequencing of CFTR. J Med Genet 2013; 50:455-62. [PMID: 23687349 DOI: 10.1136/jmedgenet-2013-101602] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
BACKGROUND Here we have developed a novel and much more efficient strategy for the complete molecular characterisation of the cystic fibrosis (CF) transmembrane regulator (CFTR) gene, based on multiplexed targeted resequencing. We have tested this approach in a cohort of 92 samples with previously characterised CFTR mutations and polymorphisms. METHODS After enrichment of the pooled barcoded DNA libraries with a custom NimbleGen SeqCap EZ Choice array (Roche) and sequencing with a HiSeq2000 (Illumina) sequencer, we applied several bioinformatics tools to call mutations and polymorphisms in CFTR. RESULTS The combination of several bioinformatics tools allowed us to detect all known pathogenic variants (point mutations, short insertions/deletions, and large genomic rearrangements) and polymorphisms (including the poly-T and poly-thymidine-guanine polymorphic tracts) in the 92 samples. In addition, we report the precise characterisation of the breakpoints of seven genomic rearrangements in CFTR, including those of a novel deletion of exon 22 and a complex 85 kb inversion which includes two large deletions affecting exons 4-8 and 12-21, respectively. CONCLUSIONS This work is a proof-of-principle that targeted resequencing is an accurate and cost-effective approach for the genetic testing of CF and CFTR-related disorders (ie, male infertility) amenable to the routine clinical practice, and ready to substitute classical molecular methods in medical genetics.
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Affiliation(s)
- D Trujillano
- Genetic Causes of Disease Group, Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), Doctor Aiguader 88, Barcelona, Catalonia 08003, Spain
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Vasson A, Leroux C, Orhant L, Boimard M, Toussaint A, Leroy C, Commere V, Ghiotti T, Deburgrave N, Saillour Y, Atlan I, Fouveaut C, Beldjord C, Valleix S, Leturcq F, Dodé C, Bienvenu T, Chelly J, Cossée M. Custom oligonucleotide array-based CGH: a reliable diagnostic tool for detection of exonic copy-number changes in multiple targeted genes. Eur J Hum Genet 2013; 21:977-87. [PMID: 23340513 PMCID: PMC3746255 DOI: 10.1038/ejhg.2012.279] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2012] [Revised: 10/31/2012] [Accepted: 11/13/2012] [Indexed: 11/09/2022] Open
Abstract
The frequency of disease-related large rearrangements (referred to as copy-number mutations, CNMs) varies among genes, and search for these mutations has an important place in diagnostic strategies. In recent years, CGH method using custom-designed high-density oligonucleotide-based arrays allowed the development of a powerful tool for detection of alterations at the level of exons and made it possible to provide flexibility through the possibility of modeling chips. The aim of our study was to test custom-designed oligonucleotide CGH array in a diagnostic laboratory setting that analyses several genes involved in various genetic diseases, and to compare it with conventional strategies. To this end, we designed a 12-plex CGH array (135k; 135 000 probes/subarray) (Roche Nimblegen) with exonic and intronic oligonucleotide probes covering 26 genes routinely analyzed in the laboratory. We tested control samples with known CNMs and patients for whom genetic causes underlying their disorders were unknown. The contribution of this technique is undeniable. Indeed, it appeared reproducible, reliable and sensitive enough to detect heterozygous single-exon deletions or duplications, complex rearrangements and somatic mosaicism. In addition, it improves reliability of CNM detection and allows determination of boundaries precisely enough to direct targeted sequencing of breakpoints. All of these points, associated with the possibility of a simultaneous analysis of several genes and scalability 'homemade' make it a valuable tool as a new diagnostic approach of CNMs.
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Affiliation(s)
- Aurélie Vasson
- Assistance Publique-Hôpitaux de Paris, Laboratoire de Biochimie et Génétique Moléculaire, Hôpital Cochin, APHP, Paris, France
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20
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Tang S, Moonnumakal SP, Stevens B, Douglas G, Mason S, Schmitt ES, Eng CM, Katz M, Fang P. Characterization of a recurrent 3.8kb deletion involving exons 17a and 17b within the CFTR gene. J Cyst Fibros 2012; 12:290-4. [PMID: 22998936 DOI: 10.1016/j.jcf.2012.08.017] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2012] [Revised: 08/29/2012] [Accepted: 08/29/2012] [Indexed: 12/17/2022]
Abstract
BACKGROUND Large deletions within CFTR have been estimated to constitute 1-2% pathogenic alleles, but the occurrence could be much higher in classical cystic fibrosis (CF) patients with one mutation detectable by the routine screening/sequencing work-up. Currently, evaluation of major CFTR rearrangements is not included in the mutation analysis for the reproductive partner of a CF patient/carrier. METHODS Exon sequencing and Multiplex Ligation-dependent Amplification (MLPA) analyses were used to make a molecular diagnosis of two unrelated CF patients. Long PCR, restriction mapping, cloning, and hot start sequencing were employed to accurately annotate the rearrangement junctions. RESULTS Both patients had a heterozygous single amino acid deletion mutation identified by sequencing, and a heterozygous deletion of CFTR exons 17a and 17b detected by MLPA. Molecular characterization of the rearrangement breakpoints indicated that the two patients had an identical complex c.2988+1616_c.3367+356del3796ins62 change, flanked by a pair of perfectly inverted repeats of 32 nucleotides. CONCLUSIONS The c.2988+1616_c.3367+356del3796ins62 complex rearrangement is a recurrent mutation from patients of different ethnic backgrounds. This mutation can be detected through a simple PCR based analysis.
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Affiliation(s)
- Sha Tang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX77030, United States
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21
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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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22
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Identification of a novel duplication CFTRdup2 and functional impact of large rearrangements identified in the CFTR gene. Gene 2012; 500:194-8. [DOI: 10.1016/j.gene.2012.03.043] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2011] [Revised: 02/13/2012] [Accepted: 03/04/2012] [Indexed: 11/23/2022]
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Vargas-Poussou R, Dahan K, Kahila D, Venisse A, Riveira-Munoz E, Debaix H, Grisart B, Bridoux F, Unwin R, Moulin B, Haymann JP, Vantyghem MC, Rigothier C, Dussol B, Godin M, Nivet H, Dubourg L, Tack I, Gimenez-Roqueplo AP, Houillier P, Blanchard A, Devuyst O, Jeunemaitre X. Spectrum of mutations in Gitelman syndrome. J Am Soc Nephrol 2011; 22:693-703. [PMID: 21415153 DOI: 10.1681/asn.2010090907] [Citation(s) in RCA: 154] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Gitelman's syndrome (GS) is a rare, autosomal recessive, salt-losing tubulopathy caused by mutations in the SLC12A3 gene, which encodes the thiazide-sensitive NaCl cotransporter (NCC). Because 18 to 40% of suspected GS patients carry only one SLC12A3 mutant allele, large genomic rearrangements may account for unidentified mutations. Here, we directly sequenced genomic DNA from a large cohort of 448 unrelated patients suspected of having GS. We found 172 distinct mutations, of which 100 were unreported previously. In 315 patients (70%), we identified two mutations; in 81 patients (18%), we identified one; and in 52 patients (12%), we did not detect a mutation. In 88 patients, we performed a search for large rearrangements by multiplex ligation-dependent probe amplification (MLPA) and found nine deletions and two duplications in 24 of the 51 heterozygous patients. A second technique confirmed each rearrangement. Based on the breakpoints of seven deletions, nonallelic homologous recombination by Alu sequences and nonhomologous end-joining probably favor these intragenic deletions. In summary, missense mutations account for approximately 59% of the mutations in Gitelman's syndrome, and there is a predisposition to large rearrangements (6% of our cases) caused by the presence of repeated sequences within the SLC12A3 gene.
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Affiliation(s)
- Rosa Vargas-Poussou
- Assistance Publique-Hôpitaux de Paris, Hôpital Européen Georges Pompidou, Service de Génétique, Paris, France.
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Marsman RF, Bardai A, Postma AV, Res JCJ, Koopmann TT, Beekman L, van der Wal AC, Pinto YM, Lekanne Deprez RH, Wilde AAM, Jordaens LJ, Bezzina CR. A complex double deletion in LMNA underlies progressive cardiac conduction disease, atrial arrhythmias, and sudden death. ACTA ACUST UNITED AC 2011; 4:280-7. [PMID: 21406687 DOI: 10.1161/circgenetics.110.959221] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
BACKGROUND Cardiac conduction disease is a clinically and genetically heterogeneous disorder characterized by defects in electrical impulse generation and conduction and is associated with sudden cardiac death. METHODS AND RESULTS We studied a 4-generation family with autosomal dominant progressive cardiac conduction disease, including atrioventricular conduction block and sinus bradycardia, atrial arrhythmias, and sudden death. Genome-wide linkage analysis mapped the disease locus to chromosome 1p22-q21. Multiplex ligation-dependent probe amplification analysis of the LMNA gene, which encodes the nuclear-envelope protein lamin A/C, revealed a novel gene rearrangement involving a 24-bp inversion flanked by a 3.8-kb deletion upstream and a 7.8-kb deletion downstream. The presence of short inverted sequence homologies at the breakpoint junctions suggested a mutational event involving serial replication slippage in trans during DNA replication. CONCLUSIONS We identified for the first time a complex LMNA gene rearrangement involving a double deletion in a 4-generation Dutch family with progressive conduction system disease. Our findings underscore the fact that if conventional polymerase chain reaction-based direct sequencing approaches for LMNA analysis are negative in suggestive pedigrees, mutation detection techniques capable of detecting gross genomic lesions involving deletions and insertions should be considered.
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Affiliation(s)
- Roos F Marsman
- Heart Failure Research Center, Department of Experimental Cardiology, Amsterdam, The Netherlands
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Ooi CY, Dorfman R, Cipolli M, Gonska T, Castellani C, Keenan K, Freedman SD, Zielenski J, Berthiaume Y, Corey M, Schibli S, Tullis E, Durie PR. Type of CFTR mutation determines risk of pancreatitis in patients with cystic fibrosis. Gastroenterology 2011; 140:153-61. [PMID: 20923678 DOI: 10.1053/j.gastro.2010.09.046] [Citation(s) in RCA: 174] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/18/2010] [Revised: 08/20/2010] [Accepted: 09/17/2010] [Indexed: 12/12/2022]
Abstract
BACKGROUND & AIMS Different mutations in the cystic fibrosis gene (CFTR) are associated with different functional status of the exocrine pancreas. We investigated whether CFTR genotypes determine the risk of pancreatitis in patients with cystic fibrosis (CF). METHODS Patients with pancreatic-sufficient CF were identified from 2 CF population-based databases (N = 277; 62 with pancreatitis and 215 without pancreatitis); patients' genotypes and clinical characteristics were analyzed. The loss of pancreatic function associated with each CFTR genotype was determined based on the pancreatic insufficiency prevalence (PIP) score. RESULTS Patients with pancreatitis were more likely to have genotypes associated with mild (70%) than moderate-severe (30%) PIP scores (P = .004). The cumulative proportion of patients who developed pancreatitis through to the age of 50 years was significantly greater for genotypes associated with mild (50%) than moderate-severe (27%) PIP scores (P = .006). The genotype associated with mild PIP scores had a hazard ratio of 2.4 for pancreatitis (95% confidence interval, 1.3-4.5; P = .006). Patients with pancreatitis were diagnosed with CF at an older median age than those without pancreatitis (14.9 years [interquartile range, 9.5-27.7] vs 9.3 years [interquartile range, 1.5-21.4]; P = .003) and had lower mean levels of sweat chloride than patients without pancreatitis (74.5 ± 26.2 mmol/L vs 82.8 ± 25.2 mmol/L; P = .03). CONCLUSIONS Specific CFTR genotypes are significantly associated with pancreatitis. Patients with genotypes associated with mild phenotypic effects have a greater risk of developing pancreatitis than patients with genotypes associated with moderate-severe phenotypes. This observation provides further insight into the complex pathogenesis of pancreatitis.
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Affiliation(s)
- Chee Y Ooi
- Physiology and Experimental Medicine, The Research Institute, Department of Pediatrics, The Hospital for Sick Children, Toronto, Ontario, Canada
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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: 1.3] [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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Makukh H, Křenková P, Tyrkus M, Bober L, Hančárová M, Hnateyko O, Macek M. A high frequency of the Cystic Fibrosis 2184insA mutation in Western Ukraine: Genotype–phenotype correlations, relevance for newborn screening and genetic testing. J Cyst Fibros 2010; 9:371-5. [DOI: 10.1016/j.jcf.2010.06.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2010] [Revised: 06/02/2010] [Accepted: 06/07/2010] [Indexed: 11/25/2022]
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Ramos MD, Masvidal L, Giménez J, Bieth E, Seia M, Georges MD, Armengol L, Casals T. CFTR Rearrangements in Spanish Cystic Fibrosis Patients: First New Duplication (35kb) Characterised in the Mediterranean Countries. Ann Hum Genet 2010; 74:463-9. [DOI: 10.1111/j.1469-1809.2010.00591.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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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: 2.1] [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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31
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de Becdelièvre A, Costa C, LeFloch A, Legendre M, Jouannic JM, Vigneron J, Bresson JL, Gobin S, Martin J, Goossens M, Girodon E. Notable contribution of large CFTR gene rearrangements to the diagnosis of cystic fibrosis in fetuses with bowel anomalies. Eur J Hum Genet 2010; 18:1166-9. [PMID: 20512161 DOI: 10.1038/ejhg.2010.80] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Grade III fetal bowel hyperechogenicity and/or loop dilatation observed at the second trimester of pregnancy can be due to several disease conditions, including cystic fibrosis (CF). Screening for frequent CF mutations is performed as a first step and, in certain situations, such as when a frequent CF mutation is found in the fetus, the increased risk of CF justifies an in-depth study of the second allele. To determine the contribution of large CFTR gene rearrangements in such cases, detected using a semiquantitative fluorescent multiplex PCR (QFM-PCR) assay, we collated data on 669 referrals related to suspicion of CF in fetuses from 1998 to 2009. Deletions were found in 5/70 cases in which QFM-PCR was applied, dele19, dele22_23, dele2_6b, dele14b_15 and dele6a_6b, of which the last three remain undescribed. In 3/5 cases, hyperechogenicity was associated with dilatation and/or gallbladder anomalies. Of the total cases of CF recognized in the subgroup of first-hand referrals, deletions represent 16.7% of CF alleles. Our study thus strengthens the need to consider large CFTR gene rearrangements in the diagnosis strategy of fetal bowel anomalies, in particular in the presence of multiple anomalies.
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Affiliation(s)
- Alix de Becdelièvre
- Service de Biochimie-Génétique et Inserm U955 Equipe 11, Groupe Hospitalier Henri Mondor-Albert Chenevier, APHP, Créteil, France
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32
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Masson E, Paliwal S, Bhaskar S, Prakash S, Scotet V, Reddy DN, Le Maréchal C, Ratan Chandak G, Chen JM, Férec C. Genetic analysis of the glycoprotein 2 gene in patients with chronic pancreatitis. Pancreas 2010; 39:353-8. [PMID: 20335779 DOI: 10.1097/mpa.0b013e3181bb9620] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
OBJECTIVES The aim of this study was to evaluate whether variations in the glycoprotein 2 gene (GP2) may potentially affect the risk of chronic pancreatitis. METHODS Six hundred sixty-one French white patients (idiopathic chronic pancreatitis, n = 590; familial chronic pancreatitis, n = 42; hereditary pancreatitis, n = 29), 445 Dravidian patients from India (tropical calcific pancreatitis, n = 306; idiopathic chronic pancreatitis, n = 139), and 962 unrelated healthy subjects (French white, n = 500; Dravidian, n = 462) participated in this case-control association study. The entire coding sequence of the GP2 gene was searched for conventional genetic variations by direct sequencing, whereas all 12 exons of the GP2 gene were screened for copy number variations by quantitative fluorescent multiplex-polymerase chain reaction. RESULTS Only 3 rare missense mutations (p.A137T, p.E250D, and p.V432M; only p.E250D was not detected in any control subjects) and 3 common synonymous polymorphisms (c.348C>T, c.714G>C, and c.1275A>G) were identified. The c.348C>T and c.1275A>G variations were found to be contradictorily associated with the disease (ranging from protective effects to disease-predisposing effects) in the French white and Indian populations. CONCLUSION The paucity of patient-specific missense mutations and contradictory findings with respect to 2 common polymorphisms in the 2 contrasting populations suggest that the GP2 gene is unlikely to play a major role in the etiology of chronic pancreatitis.
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Affiliation(s)
- Emmanuelle Masson
- Institut National de la Santé et de la Recherche Médicale (INSERM), U613, 29218 Brest, France
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33
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Walsh AC, Rault G, Li Z, Scotet V, Duguépéroux I, Férec C, Roussey M, Laxova A, Farrell PM. Pulmonary outcome differences in U.S. and French cystic fibrosis cohorts diagnosed through newborn screening. J Cyst Fibros 2010; 9:44-50. [PMID: 19926349 PMCID: PMC2818431 DOI: 10.1016/j.jcf.2009.10.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2009] [Revised: 10/07/2009] [Accepted: 10/26/2009] [Indexed: 10/20/2022]
Abstract
BACKGROUND A comparison of the longitudinal progression of lung disease in cystic fibrosis patients identified through newborn screening (NBS) in cohorts located in two different countries has never been performed and was the primary objective of this study. METHODS The study included 56 patients in Brittany diagnosed through NBS between 1989 and 1994 and 69 similar patients in Wisconsin between 1985 and 1994. The onset and progression of lung disease was radiographically quantified using the Wisconsin Chest X-ray (WCXR) scoring system. A single pediatric pulmonologist blinded to all identifiers scored the films. RESULTS Generalized estimating equation analyses adjusted for age, genotype, sex, pancreatic insufficiency, and meconium ileus showed worse WCXR scores in Brittany patients compared to Wisconsin patients (average score difference=4.48; p<0.001). Percent predicted FEV1 was also worse among Brittany patients (p<0.001). CONCLUSIONS The finding of milder radiographically-quantified lung disease using the WCXR scoring system, as well as better FEV1 values, may be explained by variations in nutrition, environmental exposures, or healthcare delivery.
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Affiliation(s)
- Aimee C Walsh
- School of Medicine and Public Health, University of Wisconsin, Madison, Wisconsin, USA
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34
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Prenatal diagnosis of hemoglobin disorders: Present and future strategies. Clin Biochem 2009; 42:1767-79. [DOI: 10.1016/j.clinbiochem.2009.07.001] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2009] [Revised: 06/24/2009] [Accepted: 07/02/2009] [Indexed: 12/14/2022]
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35
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Detection and characterisation of large SERPINC1 deletions in type I inherited antithrombin deficiency. Hum Genet 2009; 127:45-53. [DOI: 10.1007/s00439-009-0742-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2009] [Accepted: 09/05/2009] [Indexed: 10/20/2022]
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36
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Chauvin A, Chen JM, Quemener S, Masson E, Kehrer-Sawatzki H, Ohmle B, Cooper DN, Le Marechal C, Ferec C. Elucidation of the complex structure and origin of the human trypsinogen locus triplication. Hum Mol Genet 2009; 18:3605-14. [DOI: 10.1093/hmg/ddp308] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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37
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Bickmann JK, Kamin W, Wiebel M, Häuser F, Wenzel JJ, Neukirch C, Stuhrmann M, Lackner KJ, Rossmann H. A Novel Approach to CFTR Mutation Testing by Pyrosequencing-Based Assay Panels Adapted to Ethnicities. Clin Chem 2009; 55:1083-91. [DOI: 10.1373/clinchem.2008.120220] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Abstract
Background: Cystic fibrosis (CF) is a common autosomal recessive genetic disorder caused by a variety of sequence alterations in the CFTR gene [cystic fibrosis transmembrane conductance regulator (ATP-binding cassette sub-family C, member 7)]. Because the relative prevalence of mutations strongly depends on the ethnic background, first-level testing of CF as defined by recent consensus recommendations ought to be adaptable to the ethnicity of patients.
Methods: We therefore developed and implemented a diagnostic approach to first-level testing for CF based on published mutation frequencies and Pyrosequencing (PSQ) technology that we complemented with standard procedures of mutation detection at the second level.
Results: The current test system of PSQ assays for 46 target CF mutations [including CFTRdele2,3 (21 kb) and 1342-6 (T)n (5T/7T/9T)] permits recombinations of single assays to optimize sensitivities for certain ethnicities. By easy expansion of the original mutation panel, the first-level test sensitivities with other ethnic groups would be increased, provided that the mutation frequencies are known. The test was validated with our local, ethnically mixed, but mainly German population (155 patients). The mutation-detection rate for the 92 patients whose CF was confirmed by the sweat test was 89.0% for the patients of German descent (73 of the 92 patients) and 73.7% for the patients of any other origin (19 of the 92 patients). Ethnicity-adapted testing panels for our foreign CF patients would increase the sensitivities for the respective groups by approximately 5%.
Conclusions: PSQ-based genotyping is a reliable, convenient, highly flexible, and inexpensive alternative to conventional methods for first-level testing of CFTR, facilitating flexible adaptation of the analyzed mutation panel to any local ethnic group.
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Affiliation(s)
| | - Wolfgang Kamin
- CF Center of the Children’s Hospital, Johannes Gutenberg University Mainz, Mainz, Germany
| | - Matthias Wiebel
- Department of Pulmonology, Thorax Clinic of the University Clinic of Heidelberg, Heidelberg, Germany
| | | | | | | | | | - Karl J Lackner
- Department of Clinical Chemistry and Laboratory Medicine, and
| | - Heidi Rossmann
- Department of Clinical Chemistry and Laboratory Medicine, and
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Hantash FM, Rebuyon A, Peng M, Redman JB, Sun W, Strom CM. Apparent homozygosity of a novel frame shift mutation in the CFTR gene because of a large deletion. J Mol Diagn 2009; 11:253-6. [PMID: 19324987 DOI: 10.2353/jmoldx.2009.080117] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Patients develop cystic fibrosis because of a variety of homozygous recessive mutations, including single nucleotide polymorphisms, insertions, and deletions, in the cystic fibrosis transmembrane regulator (CFTR) gene, or because of compound heterozygosity for two mutations in the CFTR gene. A false determination of homozygosity for a particular CFTR mutation could negatively affect both carrier screens for a patient's family as well as researchers' ability to study the physiological implications of a particular mutation. We argued previously that homozygosity for rare or novel mutations in the CFTR gene could result from a mutation on one allele and the presence of a large deletion encompassing the same sequence region on the second allele. We present here a patient with classic cystic fibrosis who has a novel microdeletion in exon 7 on one allele and a large deletion encompassing exon 7 on the second allele. These data highlight the need to prevent misdiagnosis of homozygous mutations, which can lead to misinterpretation of mutation penetrance and its effects on protein function.
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Affiliation(s)
- Feras M Hantash
- Department of Molecular Genetics, Quest Diagnostics Nichols Institute, San Juan Capistrano, California 92690, USA.
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39
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A microhomology-mediated break-induced replication model for the origin of human copy number variation. PLoS Genet 2009; 5:e1000327. [PMID: 19180184 PMCID: PMC2621351 DOI: 10.1371/journal.pgen.1000327] [Citation(s) in RCA: 627] [Impact Index Per Article: 39.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
Chromosome structural changes with nonrecurrent endpoints associated with genomic disorders offer windows into the mechanism of origin of copy number variation (CNV). A recent report of nonrecurrent duplications associated with Pelizaeus-Merzbacher disease identified three distinctive characteristics. First, the majority of events can be seen to be complex, showing discontinuous duplications mixed with deletions, inverted duplications, and triplications. Second, junctions at endpoints show microhomology of 2–5 base pairs (bp). Third, endpoints occur near pre-existing low copy repeats (LCRs). Using these observations and evidence from DNA repair in other organisms, we derive a model of microhomology-mediated break-induced replication (MMBIR) for the origin of CNV and, ultimately, of LCRs. We propose that breakage of replication forks in stressed cells that are deficient in homologous recombination induces an aberrant repair process with features of break-induced replication (BIR). Under these circumstances, single-strand 3′ tails from broken replication forks will anneal with microhomology on any single-stranded DNA nearby, priming low-processivity polymerization with multiple template switches generating complex rearrangements, and eventual re-establishment of processive replication.
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40
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Dorfman R, Nalpathamkalam T, Taylor C, Gonska T, Keenan K, Yuan XW, Corey M, Tsui LC, Zielenski J, Durie P. Do common in silico tools predict the clinical consequences of amino-acid substitutions in the CFTR gene? Clin Genet 2009; 77:464-73. [PMID: 20059485 DOI: 10.1111/j.1399-0004.2009.01351.x] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Computational methods are used to predict the molecular consequences of amino-acid substitutions on the basis of evolutionary conservation or protein structure, but their utility in clinical diagnosis or prediction of disease outcome has not been well validated. We evaluated three popular computer programs, namely, PANTHER, SIFT and PolyPhen, by comparing the predicted clinical outcomes for a group of known CFTR missense mutations against the diagnosis of cystic fibrosis (CF) and clinical manifestations in cohorts of subjects with CF-disease and CFTR-related disorders carrying these mutations. Owing to poor specificity, none of tools reliably distinguished between individual mutations that confer CF disease from mutations found in subjects with a CFTR-related disorder or no disease. Prediction scores for CFTR mutations derived from PANTHER showed a significant overall statistical correlation with the spectrum of disease severity associated with mutations in the CFTR gene. In contrast, PolyPhen- and SIFT-derived scores only showed significant differences between CF-causing and non-CF variants. Current computational methods are not recommended for establishing or excluding a CF diagnosis, notably as a newborn screening strategy or in patients with equivocal test results.
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Affiliation(s)
- R Dorfman
- Genetics and Genome Biology, Hospital for Sick Children, Toronto, Canada
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41
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Saillour Y, Cossée M, Leturcq F, Vasson A, Beugnet C, Poirier K, Commere V, Sublemontier S, Viel M, Letourneur F, Barbot JC, Deburgrave N, Chelly J, Bienvenu T. Detection of exonic copy-number changes using a highly efficient oligonucleotide-based comparative genomic hybridization-array method. Hum Mutat 2008; 29:1083-90. [PMID: 18683213 DOI: 10.1002/humu.20829] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Genomic copy-number variations (CNVs) involving large DNA segments are known to cause many genetic disorders. Depending on the changes, they are predicted to lead either to decreased or an increased gene expression. However, the ability to detect smaller exonic copy-number changes has not been explored. Here we describe a new oligonucleotide-based comparative genomic hybridization (CGH)-array approach for high-throughput detection of exonic deletions or duplications and its application to deletion/duplication analyses of the genes encoding CFTR, six sarcoglycans (SGCA, SGCB, SGCG, SGCD, SGCE, and SGCZ), and DMD. In this work we show the successful development of an array format containing 158 exons that collectively span eight genes and its clinical application for the rapid screening of deletions and duplications in a diagnostic setting. We have analyzed a series of 35 DNA samples from patients affected with cystic fibrosis (CF), Duchenne and Becker muscular dystrophies (DMD/BMD), or sarcoglycanopathies, and have characterized exonic copy-number changes that have been validated with other methods. Interestingly, even heterozygous deletions and duplications of only one exon, as well as mosaic deletions, were detected by this CGH approach. Our results showed that the resolution is very high, as abnormalities of about 1.5-2 kb could be detected. Since this approach is completely scalable, this new molecular tool will allow the screening of combinations of genes involved in a particular group of clinically and genetically heterogeneous disorders such as mental retardation, muscular dystrophies and brain malformations.
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Affiliation(s)
- Yoann Saillour
- Institut Cochin, Université Paris Descartes, Paris, France
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42
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Consensus on the use and interpretation of cystic fibrosis mutation analysis in clinical practice. J Cyst Fibros 2008; 7:179-96. [PMID: 18456578 DOI: 10.1016/j.jcf.2008.03.009] [Citation(s) in RCA: 396] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2007] [Accepted: 03/14/2008] [Indexed: 02/06/2023]
Abstract
It is often challenging for the clinician interested in cystic fibrosis (CF) to interpret molecular genetic results, and to integrate them in the diagnostic process. The limitations of genotyping technology, the choice of mutations to be tested, and the clinical context in which the test is administered can all influence how genetic information is interpreted. This paper describes the conclusions of a consensus conference to address the use and interpretation of CF mutation analysis in clinical settings. Although the diagnosis of CF is usually straightforward, care needs to be exercised in the use and interpretation of genetic tests: genotype information is not the final arbiter of a clinical diagnosis of CF or CF transmembrane conductance regulator (CFTR) protein related disorders. The diagnosis of these conditions is primarily based on the clinical presentation, and is supported by evaluation of CFTR function (sweat testing, nasal potential difference) and genetic analysis. None of these features are sufficient on their own to make a diagnosis of CF or CFTR-related disorders. Broad genotype/phenotype associations are useful in epidemiological studies, but CFTR genotype does not accurately predict individual outcome. The use of CFTR genotype for prediction of prognosis in people with CF at the time of their diagnosis is not recommended. The importance of communication between clinicians and medical genetic laboratories is emphasized. The results of testing and their implications should be reported in a manner understandable to the clinicians caring for CF patients.
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43
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des Georges M, Guittard C, Templin C, Altiéri JP, de Carvalho C, Ramsay M, Claustres M. WGA allows the molecular characterization of a novel large CFTR rearrangement in a black South African cystic fibrosis patient. J Mol Diagn 2008; 10:544-8. [PMID: 18832460 DOI: 10.2353/jmoldx.2008.080028] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
By performing extensive scanning of whole coding and flanking sequences of the cystic fibrosis (CF) transmembrane conductance regulator (CFTR) gene, we had previously identified the CF-causing mutations in black South African patients of different ethnic groups suspected with the disease. Of ten samples analyzed, there were six remaining that had either one (n = 2) or two (n = 4) unidentified CFTR alleles that have now been tested for large rearrangements using a semiquantitative fluorescent PCR assay. A novel deletion encompassing CFTR exon 2 was detected in one patient who was heterozygous for the mutation 3120+1G>A. The Caucasian deletion involving the same exon [c.54-5811_c.164+2186del8108ins182] was ruled out. The DNA had been stored for more than 12 years and only minute quantities remained. We thus used a whole-genome amplification method based on multiple displacement amplification to generate sufficient amounts of DNA to characterize the intronic breakpoints and identify the deletion at the genomic level. Mapping and sequencing the breakpoint junctions revealed a novel large deletion [c.54-1161_c.164+1603del2875]. We have designed a simple test to specifically detect the presence or absence of this large rearrangement. This study reports the first large CFTR rearrangement in a black South African CF patient, further defining the molecular spectrum of CF that will be useful for improving genetic testing and counseling in this region.
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44
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Gouas L, Goumy C, Véronèse L, Tchirkov A, Vago P. Gene dosage methods as diagnostic tools for the identification of chromosome abnormalities. ACTA ACUST UNITED AC 2008; 56:345-53. [DOI: 10.1016/j.patbio.2008.03.010] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2008] [Accepted: 03/14/2008] [Indexed: 10/22/2022]
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45
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Dequeker E, Stuhrmann M, Morris MA, Casals T, Castellani C, Claustres M, Cuppens H, des Georges M, Ferec C, Macek M, Pignatti PF, Scheffer H, Schwartz M, Witt M, Schwarz M, Girodon E. Best practice guidelines for molecular genetic diagnosis of cystic fibrosis and CFTR-related disorders--updated European recommendations. Eur J Hum Genet 2008. [PMID: 18685558 DOI: 10.1038/+ejhg.2008.136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
The increasing number of laboratories offering molecular genetic analysis of the CFTR gene and the growing use of commercial kits strengthen the need for an update of previous best practice guidelines (published in 2000). The importance of organizing regional or national laboratory networks, to provide both primary and comprehensive CFTR mutation screening, is stressed. Current guidelines focus on strategies for dealing with increasingly complex situations of CFTR testing. Diagnostic flow charts now include testing in CFTR-related disorders and in fetal bowel anomalies. Emphasis is also placed on the need to consider ethnic or geographic origins of patients and individuals, on basic principles of risk calculation and on the importance of providing accurate laboratory reports. Finally, classification of CFTR mutations is reviewed, with regard to their relevance to pathogenicity and to genetic counselling.
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Affiliation(s)
- Els Dequeker
- Center for Human Genetics, Campus Gasthuisberg, KULeuven, Belgium
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46
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Distribution of CFTR mutations in Saguenay- Lac-Saint-Jean: proposal of a panel of mutations for population screening. Genet Med 2008; 10:201-6. [PMID: 18344710 DOI: 10.1097/gim.0b013e318164cb1c] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
PURPOSE Saguenay-Lac-Saint-Jean is a region located in the northeastern part of the Province of Quebec, Canada, and is characterized by a founder effect. In this region, it has been documented that the incidence of cystic fibrosis reached 1/902 live births between 1975 and 1988, three times higher than the average incidence of 1/2500 live births reported in other Caucasian populations. This corresponds to a carrier rate of 1/15. METHODS Using genotyping data from the Canadian Consortium for Cystic Fibrosis Genetic Studies, this article describes the cystic fibrosis transmembrane conductance regulator profile of the cystic fibrosis population living in the Saguenay-Lac-Saint-Jean region and compares it with cystic fibrosis populations living in three other regions of the Province of Quebec. RESULTS Significant differences in allelic frequencies of common mutations (as DeltaF508, 621 + 1G>T and A455E), and in percentage of covered allele with three or six mutations, were found in Saguenay-Lac-Saint-Jean compared to other regions. Based on this result, two mutation panels exceeding 90% sensitivity threshold are now proposed for cystic fibrosis carrier screening in this region. CONCLUSION The implementation of the proposed carrier screening program could diminish the incidence of this disease in this region and allow future parents to make informed decisions about family planning.
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47
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Best practice guidelines for molecular genetic diagnosis of cystic fibrosis and CFTR-related disorders--updated European recommendations. Eur J Hum Genet 2008; 17:51-65. [PMID: 18685558 DOI: 10.1038/ejhg.2008.136] [Citation(s) in RCA: 159] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
The increasing number of laboratories offering molecular genetic analysis of the CFTR gene and the growing use of commercial kits strengthen the need for an update of previous best practice guidelines (published in 2000). The importance of organizing regional or national laboratory networks, to provide both primary and comprehensive CFTR mutation screening, is stressed. Current guidelines focus on strategies for dealing with increasingly complex situations of CFTR testing. Diagnostic flow charts now include testing in CFTR-related disorders and in fetal bowel anomalies. Emphasis is also placed on the need to consider ethnic or geographic origins of patients and individuals, on basic principles of risk calculation and on the importance of providing accurate laboratory reports. Finally, classification of CFTR mutations is reviewed, with regard to their relevance to pathogenicity and to genetic counselling.
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48
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Schrijver I, Rappahahn K, Pique L, Kharrazi M, Wong LJ. Multiplex ligation-dependent probe amplification identification of whole exon and single nucleotide deletions in the CFTR gene of Hispanic individuals with cystic fibrosis. J Mol Diagn 2008; 10:368-75. [PMID: 18556774 DOI: 10.2353/jmoldx.2008.080004] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
A disparity between Caucasian and Hispanic mutation detection for cystic fibrosis continues to exist, although the carrier frequency is only moderately lower in Hispanics. We aimed to identify exonic rearrangements that remained undetected by conventional methods. In seven of 32 cystic fibrosis-affected self-identified Hispanics for whom only one or no mutations were identified by extensive molecular testing, exon deletions appeared to be present with a multiplex ligation-dependent probe amplification (MLPA) assay. Two recurrent deletions (of exons 2-3 and exons 22-23) were identified in one and three patients, respectively (12.5%, 11.1% of unidentified alleles). Two apparently novel deletions (exons 6b and 20) were identified in three additional patients. Subsequent sequencing to characterize deletion breakpoints, however, identified single nucleotide deletions at the probe binding sites close to the ligation point. All resulted in false positive MLPA deletion signals. Interestingly, these mutations were not common in Caucasians, and one (935delA) was common in U.S. Hispanics. On examination of all probe binding sites, we identified a total of 76 reported mutations and five silent variants that immediately surrounded the MLPA ligation sites, with 22 occurring in non-Caucasians. These mutations are not all rare. Thus, apparent exon deletions by MLPA may indicate the presence of both large deletions and point mutations, with important implications for pan-ethnic MLPA testing in cystic fibrosis and other genetic conditions.
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Affiliation(s)
- Iris Schrijver
- Department of Pathology L235, Stanford University Medical Center, 300 Pasteur Drive, Stanford, CA 94305, USA.
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49
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von Salomé J, Kukkonen JP. Sequence features of HLA-DRB1 locus define putative basis for gene conversion and point mutations. BMC Genomics 2008; 9:228. [PMID: 18489735 PMCID: PMC2408603 DOI: 10.1186/1471-2164-9-228] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2007] [Accepted: 05/19/2008] [Indexed: 11/10/2022] Open
Abstract
Background HLA/MHC class II molecules show high degree of polymorphism in the human population. The individual polymorphic motifs have been suggested to be propagated and mixed by transfer of genetic material (recombination, gene conversion) between alleles, but no clear molecular basis for this has been identified as yet. A large number of MHC class II allele sequences is publicly available and could be used to analyze the sequence features behind the recombination, revealing possible basis for such recombination processes both in HLA class II genes and other genes, which recombination acts upon. Results In this study we analyzed the vast dataset of human allelic variants (49 full coding sequences, 374 full exon 2 sequences) of the most polymorphic MHC class II locus, HLA-DRB1, and identified many previously unknown sequence features possibly contributing to the recombination. The CpG-dinucleotide content of exon 2 (containing the antigen-binding sites and subsequently a high degree of polymorphism) was much elevated as compared to the other exons despite similar overall G+C content. Furthermore, the CpG pattern was highly conserved. We also identified more complex, highly conserved sequence motifs in exon 2. Some of these can be identified as putative recombination motifs previously found in other genes, but most are previously unidentified. Conclusion The identified sequence features could putatively act in recombination allowing either less (CpG dinucleotides) or more specific DNA cleavage (complex sequences) or homologous recombination (complex sequences).
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Affiliation(s)
- Jenny von Salomé
- University of Helsinki, Department of Basic Veterinary Sciences, Helsinki, Finland.
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Lakeman P, Gille JJ, Dankert-Roelse JE, Heijerman HG, Munck A, Iron A, Grasemann H, Schuster A, Cornel MC, ten Kate LP. CFTR Mutations in Turkish and North African Cystic Fibrosis Patients in Europe: Implications for Screening. ACTA ACUST UNITED AC 2008; 12:25-35. [DOI: 10.1089/gte.2007.0046] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Phillis Lakeman
- Department of Clinical Genetics, VU University Medical Center, Amsterdam, The Netherlands
- Department of EMGO Institute, VU University Medical Center, Amsterdam, The Netherlands
| | - Johan J.P. Gille
- Department of Clinical Genetics, VU University Medical Center, Amsterdam, The Netherlands
| | | | | | - Anne Munck
- Department of Paediatric Gastroenterology and Nutrition, Hôpital Robert Debré, Paris, France
| | - Albert Iron
- Service de Génétique Médicale, CHU Pellegrin, Bordeaux, France
| | - Hartmut Grasemann
- Paediatric Respiratory Medicine, Hospital for Sick Children, Toronto, Canada
| | - Antje Schuster
- Department of Paediatrics, Heinrich Heine University, Düsseldorf, Germany
| | - Martina C. Cornel
- Department of Clinical Genetics, VU University Medical Center, Amsterdam, The Netherlands
- Department of EMGO Institute, VU University Medical Center, Amsterdam, The Netherlands
| | - Leo P. ten Kate
- Department of Clinical Genetics, VU University Medical Center, Amsterdam, The Netherlands
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