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Wu M, Davis JD, Zhao C, Daley T, Oliver KE. Racial inequities and rare CFTR variants: Impact on cystic fibrosis diagnosis and treatment. J Clin Transl Endocrinol 2024; 36:100344. [PMID: 38765466 PMCID: PMC11099334 DOI: 10.1016/j.jcte.2024.100344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Revised: 02/21/2024] [Accepted: 04/14/2024] [Indexed: 05/22/2024] Open
Abstract
Cystic fibrosis (CF) has been traditionally viewed as a disease that affects White individuals. However, CF occurs among all races, ethnicities, and geographic ancestries. The disorder results from mutations in the CF transmembrane conductance regulator (CFTR). Varying incidence of CF is reported among Black, Indigenous, and People of Color (BIPOC), who typically exhibit worse clinical outcomes. These populations are more likely to carry rare CFTR variants omitted from newborn screening panels, leading to disparities in care such as delayed diagnosis and treatment. In this study, we present a case-in-point describing an individual of Gambian descent identified with CF. Patient genotype includes a premature termination codon (PTC) (c.2353C>T) and previously undescribed single nucleotide deletion (c.1970delG), arguing against effectiveness of currently available CFTR modulator-based interventions. Strategies for overcoming these two variants will likely include combinations of PTC suppressors, nonsense mediated decay inhibitors, and/or alternative approaches (e.g. gene therapy). Investigations such as the present study establish a foundation from which therapeutic treatments may be developed. Importantly, c.2353C>T and c.1970delG were not detected in the patient by traditional CFTR screening panels, which include an implicit racial and ethnic diagnostic bias as these tests are comprised of mutations largely observed in people of European ancestry. We suggest that next-generation sequencing of CFTR should be utilized to confirm or exclude a CF diagnosis, in order to equitably serve BIPOC individuals. Additional epidemiologic data, basic science investigations, and translational work are imperative for improving understanding of disease prevalence and progression, CFTR variant frequency, genotype-phenotype correlation, pharmacologic responsiveness, and personalized medicine approaches for patients with African ancestry and other historically understudied geographic lineages.
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Affiliation(s)
- Malinda Wu
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA
- Pediatric Institute, Children’s Healthcare of Atlanta, Atlanta, GA, USA
| | - Jacob D. Davis
- Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
| | - Conan Zhao
- Interdisciplinary Graduate Program in Quantitative Biosciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Tanicia Daley
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA
- Pediatric Institute, Children’s Healthcare of Atlanta, Atlanta, GA, USA
| | - Kathryn E. Oliver
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA
- Pediatric Institute, Children’s Healthcare of Atlanta, Atlanta, GA, USA
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2
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De Wachter E, De Boeck K, Sermet-Gaudelus I, Simmonds NJ, Munck A, Naehrlich L, Barben J, Boyd C, Veen SJ, Carr SB, Fajac I, Farrell PM, Girodon E, Gonska T, Grody WW, Jain M, Jung A, Kerem E, Raraigh KS, van Koningsbruggen-Rietschel S, Waller MD, Southern KW, Castellani C. ECFS standards of care on CFTR-related disorders: Towards a comprehensive program for affected individuals. J Cyst Fibros 2024; 23:388-397. [PMID: 38388234 DOI: 10.1016/j.jcf.2024.01.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 01/25/2024] [Accepted: 01/29/2024] [Indexed: 02/24/2024]
Abstract
After three publications defining an updated guidance on the diagnostic criteria for people with cystic fibrosis transmembrane conductance regulator (CFTR)-related disorders (pwCFTR-RDs), establishing its relationship to CFTR-dysfunction and describing the individual disorders, this fourth and last paper in the series addresses some critical challenges facing health care providers and pwCFTR-RD. Topics included are: 1) benefits and obstacles to collect data from pwCFTR-RD are discussed, together with the opportunity to integrate them into established CF-registries; 2) the potential of infants designated CRMS/CFSPID to develop a CFTR-RD and how to communicate this information; 3) a description of the challenges in genetic counseling, with particular regard to phenotypic variability, unknown long-term evolution, CFTR testing and pregnancy termination 4) a proposal for the assessment of potential barriers to the implementation and dissemination of the produced documents to health care professionals involved in the care of pwCFTR-RD and a process to monitor the implementation of the CFTR-RD recommendations; 5) clinical trials investigating the efficacy of CFTR modulators in CFTR-RD and how endpoints and outcomes might be adapted to the heterogeneity of these disorders.
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Affiliation(s)
- E De Wachter
- Cystic Fibrosis Center, Pediatric Pulmonology department, Universitair Ziekenhuis Brussel, Vrije Universiteit Brussel, Brussels, Belgium.
| | - K De Boeck
- Department of Pediatrics, University of Leuven, Leuven, Belgium
| | - I Sermet-Gaudelus
- INSERM U1151, Institut Necker Enfants Malades, Paris, France; Université de Paris, Paris, France; Centre de référence Maladies Rares, Mucoviscidose et maladies apparentées. Hôpital Necker Enfants malades, Paris, France
| | - N J Simmonds
- Adult Cystic Fibrosis Centre, Royal Brompton Hospital and Imperial College, London, UK
| | - A Munck
- Paediatric Cystic Fibrosis centre, Hôpital Necker Enfants Malades, AP-HP Paris, France
| | - L Naehrlich
- Department of Pediatrics, Justus-Liebig-University Giessen, Germany
| | - J Barben
- Paediatric Pulmonology & CF Centre, Children's Hospital of Eastern Switzerland, St. Gallen, Switzerland
| | | | | | - S B Carr
- Department of Paediatric Respiratory Medicine, Royal Brompton Hospital, and Imperial College, London, UK
| | - I Fajac
- Assistance Publique-Hôpitaux de Paris, Thoracic Department and National Cystic Fibrosis Reference Centre, Cochin Hospital, 75014 Paris, France; Université Paris Cité, Inserm U1016, Institut Cochin, 75014 Paris, France
| | - P M Farrell
- Departments of Pediatrics and Population Health Sciences, University of Wisconsin School of Medicine and Public Health, Madison, WI 53792, USA
| | - E Girodon
- Service de Médecine Génomique des Maladies de Système et d'Organe, APHP.Centre - Université de Paris Cité, Hôpital Cochin, Paris, France
| | - T Gonska
- Division of Pediatric Gastroenterology, Hepatology, Nutrition, Department of Pediatrics, University of Toronto, Toronto, Ontario, Canada; Program of Translational Medicine, Research institute, Hospital for Sick Children, Toronto, Canada
| | - W W Grody
- Departments of Pathology & Laboratory Medicine, Pediatrics, and Human Genetics, UCLA School of Medicine, Los Angeles, California 90095-1732, USA
| | - M Jain
- Northwestern University Feinberg School of Medicine, Pulmonary Critical Care, Chicago, Illinois, United States
| | - A Jung
- University Children`s Hospital Zurich, Steinwiesstrasse 75, CH-8032 Zurich, Switzerland
| | - E Kerem
- Department of Pediatrics and CF Center, Hadassah Hebrew University medical Center, Jerusalem, Israel
| | - K S Raraigh
- Department of Genetic Medicine, Johns Hopkins University, Baltimore, MD 21287, USA
| | | | - M D Waller
- Department of Adult Cystic Fibrosis and Respiratory Medicine, King's College Hospital NHS Foundation Trust, London, United Kingdom; Centre for Human & Applied Physiological Sciences, King's College London, London, United Kingdom
| | - K W Southern
- Department of Women's and Children's Health, University of Liverpool, Alder Hey Children's Hospital, Liverpool, UK
| | - C Castellani
- IRCCS Istituto Giannina Gaslini, Cystic Fibrosis Center, Genoa, Italy
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3
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Martínez-Hernández A, Mendoza-Caamal EC, Mendiola-Vidal NG, Barajas-Olmos F, Villafan-Bernal JR, Jiménez-Ruiz JL, Monge-Cazares T, García-Ortiz H, Cubas CC, Centeno-Cruz F, Alaez-Verson C, Ortega-Torres S, Luna-Castañeda ADC, Baca V, Lezana JL, Orozco L. CFTR pathogenic variants spectrum in a cohort of Mexican patients with cystic fibrosis. Heliyon 2024; 10:e28984. [PMID: 38601560 PMCID: PMC11004572 DOI: 10.1016/j.heliyon.2024.e28984] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 03/27/2024] [Accepted: 03/27/2024] [Indexed: 04/12/2024] Open
Abstract
Background Molecular diagnosis of cystic fibrosis (CF) is challenging in Mexico due to the population's high genetic heterogeneity. To date, 46 pathogenic variants (PVs) have been reported, yielding a detection rate of 77%. We updated the spectrum and frequency of PVs responsible for this disease in mexican patients. Methods We extracted genomic DNA from peripheral blood lymphocytes obtained from 297 CF patients and their parents. First, we analyzed the five most frequent PVs in the Mexican population using PCR-mediated site-directed mutagenesis. In patients with at least one identified allele, CFTR sequencing was performed using next-generation sequencing tools and multiplex ligation-dependent probe amplification. For variants not previously classified as pathogenic, we used a combination of in silico prediction, CFTR modeling, and clinical characteristics to determine a genotype-phenotype correlation. Results We identified 95 PVs, increasing the detection rate to 87.04%. The most frequent variants were p.(PheF508del) (42.7%), followed by p.(Gly542*) (5.6%), p.(Ser945Leu) (2.9%), p.(Trp1204*) and p.(Ser549Asn) (2.5%), and CFTRdel25-26 and p.(Asn386Ilefs*3) (2.3%). The remaining variants had frequencies of <2.0%, and some were exclusive to one family. We identified 10 novel PVs localized in different exons (frequency range: 0.1-0.8%), all of which produced structural changes, deletions, or duplications in different domains of the protein, resulting in dysfunctional ion flow. The use of different in silico software and American College of Medical Genetics and Genomics (ACMG) and the Association for Molecular Pathology (AMP) criteria allowed us to assume that all of these PVs were pathogenic, causing a severe phenotype. Conclusions In a highly heterogeneous population, combinations of different tools are needed to identify the variants responsible for CF and enable the establishment of appropriate strategies for CF diagnosis, prevention, and treatment.
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Affiliation(s)
- Angélica Martínez-Hernández
- Immunogenomics and Metabolic Disease Laboratory, Instituto Nacional de Medicina Genomica, SS, Tlalpan, 14610, Mexico City, Mexico
| | - Elvia C. Mendoza-Caamal
- Clinical Area, Instituto Nacional de Medicina Genómica, SS, Tlalpan, 14610, CDMX, Mexico City, Mexico
| | - Namibia G. Mendiola-Vidal
- Immunogenomics and Metabolic Disease Laboratory, Instituto Nacional de Medicina Genomica, SS, Tlalpan, 14610, Mexico City, Mexico
- Maestría en Ciencias Médicas. PMDCMOS. Sede: HGGEA, UNAM. Coyoacan, 04510, Mexico City, Mexico
| | - Francisco Barajas-Olmos
- Immunogenomics and Metabolic Disease Laboratory, Instituto Nacional de Medicina Genomica, SS, Tlalpan, 14610, Mexico City, Mexico
| | - José Rafael Villafan-Bernal
- Immunogenomics and Metabolic Disease Laboratory, Instituto Nacional de Medicina Genomica, SS, Tlalpan, 14610, Mexico City, Mexico
- Investigador por Mexico, Consejo Nacional de Humanidades, Ciencia y Tecnología (CONAHCYT), Benito Juarez, 03940, Mexico City, Mexico
| | - Juan Luis Jiménez-Ruiz
- Immunogenomics and Metabolic Disease Laboratory, Instituto Nacional de Medicina Genomica, SS, Tlalpan, 14610, Mexico City, Mexico
| | - Tulia Monge-Cazares
- Immunogenomics and Metabolic Disease Laboratory, Instituto Nacional de Medicina Genomica, SS, Tlalpan, 14610, Mexico City, Mexico
| | - Humberto García-Ortiz
- Immunogenomics and Metabolic Disease Laboratory, Instituto Nacional de Medicina Genomica, SS, Tlalpan, 14610, Mexico City, Mexico
| | - Cecilia Contreras- Cubas
- Immunogenomics and Metabolic Disease Laboratory, Instituto Nacional de Medicina Genomica, SS, Tlalpan, 14610, Mexico City, Mexico
| | - Federico Centeno-Cruz
- Immunogenomics and Metabolic Disease Laboratory, Instituto Nacional de Medicina Genomica, SS, Tlalpan, 14610, Mexico City, Mexico
| | - Carmen Alaez-Verson
- Genomic Diagnostic Laboratory, Instituto Nacional de Medicina Genomica, SS, Tlalpan, 14610, CDMX, Mexico City, Mexico
| | - Soraya Ortega-Torres
- Curso de Alta Especialidad en Medicina Genómica, Instituto Nacional de Medicina Genomica, Facultad de Medicina, Universidad Nacional Autonoma de Mexico, Coyoacan, 04510, Mexico City, Mexico
| | | | - Vicente Baca
- Rheumatology Department, Hospital de Pediatría, CMN Siglo XXI IMSS, Cuauhtemoc, 06720, Mexico City, Mexico
| | - José Luis Lezana
- Cystic Fibrosis Clinic and Pulmonary Physiology Laboratory. Hospital Infantil de Mexico Federico Gómez, SS, Cuauhtemoc, 06720, Mexico City, Mexico
- Asociacion Mexicana de Fibrosis Quistica, A.C. Benito Juarez, 03700, Mexico City, Mexico
| | - Lorena Orozco
- Immunogenomics and Metabolic Disease Laboratory, Instituto Nacional de Medicina Genomica, SS, Tlalpan, 14610, Mexico City, Mexico
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4
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Han Y, Zhao J, Liu W, Yang X, Zhang W, Xiao X, Liu X, Chen X, Tang L, Wang P, Ge W. Increased prevalence of CFTR variants and susceptibility to CRS: A real-world study based on Chinese children. Heliyon 2024; 10:e27681. [PMID: 38590877 PMCID: PMC10999871 DOI: 10.1016/j.heliyon.2024.e27681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 03/02/2024] [Accepted: 03/05/2024] [Indexed: 04/10/2024] Open
Abstract
Background Chronic Rhinosinusitis is a common disease in children. The main function of CFTR is to maintain the thickness of the mucous layer on the surface of the nasal mucosa. CFTR disease-causing variant can cause CFTR protein dysfunction and induce or aggravate chronic infection. However, the carrying status of the CFTR variants in the Chinese population is not clear. Objective To study the frequency and variants of CFTR in Chinese children with CRS and to analyze the CFTR variants and the clinical characteristics and susceptibility to CRS. Methods Whole Exome Sequencing was performed to analyze the CFTR genes in a total of 106 CRS children from the Chinese mainland area. The CFTR variants, frequency and clinical data were summarized and analyzed. Results A total of 31 CFTR variants were detected, of which the carrying rate of 7 sites was significantly higher than that of the population database. 88 patients carried more than 2 variants. 37 people carried variants (MAF < 0.05), of which 91.89% had a history of recurrent upper respiratory infections, 16 had nasal polyps, 5 had bronchiectasis, and 1 was diagnosed with CF-related disorders. Conclusion The carrying rate of CFTR variants in Chinese CRS children increased, and the highest rates of variants (MAF < 0.05) are p.I556V, p. E217G, c.1210-12[T]. Carrying multiple CFTR variants, especially p.E217G, p.I807 M, p.V920L and c.1210-12[T] may lead to increased susceptibility to CRS. There are CF-related disorders in patients with CRS.
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Affiliation(s)
- Yang Han
- Department of Otolaryngology, Head and Neck Surgery, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, 100045, China
| | - Jinhao Zhao
- Department of Otolaryngology, Head and Neck Surgery, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, 100045, China
| | - Wenjing Liu
- Department of Otolaryngology, Head and Neck Surgery, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, 100045, China
| | - Xiaojian Yang
- Department of Otolaryngology, Head and Neck Surgery, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, 100045, China
| | - Wei Zhang
- Department of Otolaryngology, Head and Neck Surgery, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, 100045, China
| | - Xiao Xiao
- Department of Otolaryngology, Head and Neck Surgery, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, 100045, China
| | - Xiaoge Liu
- Department of Otolaryngology, Head and Neck Surgery, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, 100045, China
| | - Xiaoxu Chen
- Department of Otolaryngology, Head and Neck Surgery, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, 100045, China
| | - Lixing Tang
- Department of Otolaryngology, Head and Neck Surgery, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, 100045, China
| | - Pengpeng Wang
- Department of Otolaryngology, Head and Neck Surgery, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, 100045, China
| | - Wentong Ge
- Department of Otolaryngology, Head and Neck Surgery, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, 100045, China
- Beijing Key Laboratory for Pediatric Diseases of Otolaryngology, Head and Neck Surgery, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, 100045, China
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5
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Ideozu JE, Liu M, Riley-Gillis BM, Paladugu SR, Rahimov F, Krishnan P, Tripathi R, Dorr P, Levy H, Singh A, Waring JF, Vasanthakumar A. Diversity of CFTR variants across ancestries characterized using 454,727 UK biobank whole exome sequences. Genome Med 2024; 16:43. [PMID: 38515211 PMCID: PMC10956269 DOI: 10.1186/s13073-024-01316-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Accepted: 03/15/2024] [Indexed: 03/23/2024] Open
Abstract
BACKGROUND Limited understanding of the diversity of variants in the cystic fibrosis transmembrane conductance regulator (CFTR) gene across ancestries hampers efforts to advance molecular diagnosis of cystic fibrosis (CF). The consequences pose a risk of delayed diagnoses and subsequently worsened health outcomes for patients. Therefore, characterizing the spectrum of CFTR variants across ancestries is critical for revolutionizing molecular diagnoses of CF. METHODS We analyzed 454,727 UK Biobank (UKBB) whole-exome sequences to characterize the diversity of CFTR variants across ancestries. Using the PanUKBB classification, the participants were assigned into six major groups: African (AFR), American/American Admixed (AMR), Central South Asia (CSA), East Asian (EAS), European (EUR), and Middle East (MID). We segregated ancestry-specific CFTR variants, including those that are CF-causing or clinically relevant. The ages of certain CF-causing variants were determined and analyzed for selective pressure effects, and curated phenotype analysis was performed for participants with clinically relevant CFTR genotypes. RESULTS We detected over 4000 CFTR variants, including novel ancestry-specific variants, across six ancestries. Europeans had the most unique CFTR variants [n = 2212], while the American group had the least unique variants [n = 23]. F508del was the most prevalent CF-causing variant found in all ancestries, except in EAS, where V520F was the most prevalent. Common EAS variants such as 3600G > A, V456A, and V520, which appeared approximately 270, 215, and 338 generations ago, respectively, did not show evidence of selective pressure. Sixteen participants had two CF-causing variants, with two being diagnosed with CF. We found 154 participants harboring a CF-causing and varying clinical consequences (VCC) variant. Phenotype analysis performed for participants with multiple clinically relevant variants returned significant associations with CF and its pulmonary phenotypes [Bonferroni-adjusted p < 0.05]. CONCLUSIONS We leveraged the UKBB database to comprehensively characterize the broad spectrum of CFTR variants across ancestries. The detection of over 4000 CFTR variants, including several ancestry-specific and uncharacterized CFTR variants, warrants the need for further characterization of their functional and clinical relevance. Overall, the presentation of classical CF phenotypes seen in non-CF diagnosed participants with more than one CF-causing variant indicates that they may benefit from current CFTR modulator therapies.
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Affiliation(s)
- Justin E Ideozu
- Genomic Medicine, Genomics Research Center, AbbVie, Chicago, IL, USA.
| | - Mengzhen Liu
- Human Genetics, Genomics Research Center, AbbVie, Chicago, IL, USA
| | | | - Sri R Paladugu
- Human Genetics, Genomics Research Center, AbbVie, Chicago, IL, USA
| | - Fedik Rahimov
- Human Genetics, Genomics Research Center, AbbVie, Chicago, IL, USA
| | | | | | | | - Hara Levy
- Department of Pediatrics, Division of Pulmonology and Sleep Medicine, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
| | | | - Jeffrey F Waring
- Genomic Medicine, Genomics Research Center, AbbVie, Chicago, IL, USA
- Human Genetics, Genomics Research Center, AbbVie, Chicago, IL, USA
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Diana A, Polizzi AM, De Luisi A, Pantaleo MG, Leonetti G, Simonetti S, Bukvic N, Iacoviello M, Bucci R, Gentile M, Resta N. First report of whole CFTR gene duplication in a healthy newborn carrying R74W and V855I variants on the same allele. J Cyst Fibros 2024:S1569-1993(24)00013-4. [PMID: 38320874 DOI: 10.1016/j.jcf.2024.01.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 11/16/2023] [Accepted: 01/29/2024] [Indexed: 02/08/2024]
Abstract
Cystic fibrosis (CF) is the most common severe autosomal recessive genetic disorder among Caucasians. The improvement of genetic techniques has allowed the identification of an increasing number of genetic variants, including large rearrangements such as duplications. We report the first case of a whole CFTR gene duplication in a healthy newborn, who had normal sweat test, also carrying R74W and V855I variants on the same allele. Familial segregation analysis and the observed frequencies of all the CFTR gene variants, revealed that R74W and V855I were probably both present in a cis arrangement on the allele also containing the duplication (i.e., in a double complex allele). Since R74W is a "variant of varying clinical consequence" its arrangement in trans with one pathogenic variant may not be sufficient to cause a classic CF disease phenotype. Moreover, its duplication could even be an advantage that could compensate for the effect of the alteration.
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Affiliation(s)
- Anna Diana
- Medical Genetics Section, Department of Precision and Regenerative Medicine and Ionian Area (DiMePRe-J), University Hospital Consortium Corporation Polyclinics of Bari, 70124 Bari, Italy
| | - Angela Maria Polizzi
- Medical Genetics Section, Department of Precision and Regenerative Medicine and Ionian Area (DiMePRe-J), University Hospital Consortium Corporation Polyclinics of Bari, 70124 Bari, Italy
| | - Annunziata De Luisi
- Medical Genetics Section, Department of Precision and Regenerative Medicine and Ionian Area (DiMePRe-J), University Hospital Consortium Corporation Polyclinics of Bari, 70124 Bari, Italy
| | - Maria Giuseppina Pantaleo
- Medical Genetics Section, Department of Precision and Regenerative Medicine and Ionian Area (DiMePRe-J), University Hospital Consortium Corporation Polyclinics of Bari, 70124 Bari, Italy
| | - Giuseppina Leonetti
- Cystic Fibrosis Regional Center, University Hospital Consortium Corporation Polyclinics of Bari, 70124 Bari, Italy
| | - Simonetta Simonetti
- Clinical Patology and Neonatal Screening, Hospital "Giovanni XXIII", University Hospital Consortium Corporation Polyclinics of Bari, Bari, Italy
| | - Nenad Bukvic
- Medical Genetics Section, Department of Precision and Regenerative Medicine and Ionian Area (DiMePRe-J), University Hospital Consortium Corporation Polyclinics of Bari, 70124 Bari, Italy
| | - Matteo Iacoviello
- Medical Genetics Section, Department of Precision and Regenerative Medicine and Ionian Area (DiMePRe-J), University Hospital Consortium Corporation Polyclinics of Bari, 70124 Bari, Italy
| | - Roberta Bucci
- Medical Genetics Section, Department of Precision and Regenerative Medicine and Ionian Area (DiMePRe-J), University Hospital Consortium Corporation Polyclinics of Bari, 70124 Bari, Italy; Medical Genetics Unit, Department of Human Reproductive Medicine, ASL Bari, Bari, Italy
| | - Mattia Gentile
- Medical Genetics Unit, Department of Human Reproductive Medicine, ASL Bari, Bari, Italy
| | - Nicoletta Resta
- Medical Genetics Section, Department of Precision and Regenerative Medicine and Ionian Area (DiMePRe-J), University Hospital Consortium Corporation Polyclinics of Bari, 70124 Bari, Italy.
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7
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Ahting S, Nährlich L, Held I, Henn C, Krill A, Landwehr K, Meister J, Nährig S, Nolde A, Remke K, Ruppel R, Sauer-Heilborn A, Schebek M, Schopper G, Schulte-Hubbert B, Schwarz C, Smaczny C, Wege S, Hentschel J. Every CFTR variant counts - Target-capture based next-generation-sequencing for molecular diagnosis in the German CF Registry. J Cyst Fibros 2023:S1569-1993(23)00928-1. [PMID: 37867076 DOI: 10.1016/j.jcf.2023.10.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 10/01/2023] [Accepted: 10/09/2023] [Indexed: 10/24/2023]
Abstract
BACKGROUND In times of genotype guided therapy options, a total of 3.2 % of people with CF (pwCF) in the German CF Registry[1] only have one or no CFTR-variant detected after genetic analysis. Additionally, genetic data in the Registry can be documented as free text and can therefore be prone to error. In order to allow the greatest possible amount of pwCF access to modern therapies, we conducted a re-evaluation of free text entries and established a custom-whole-CFTR-locus NGS-approach for all pwCF who remained without genetic confirmation afterwards. METHODS To this end, we assembled 731 free text variants of 655 pwCF in the German CF Registry. All variants were evaluated using ClinVar, HGMD and CFTR1/2, corrected in the Registries' database and uploaded to ClinVar. PwCF whose diagnosis remained uncertain as well as additional pwCF or pwCFTR-RD that were assembled through a nationwide call for testing of unclear cases were offered genetic analysis. Samples were analysed using a target-capture based NGS-custom-design-panel covering the entire CFTR-locus. RESULTS Evaluation of free text variants led to the discovery of 43 variants not formerly reported in the context of CF. The Registries' dropdown list was extended by 497 variants and over 500 pwCF were provided with their most up-to-date genotype. Samples of 47 pwCF/pwCFTR-RD were sequenced via NGS with an overall success rate of 61.7 %, resulting in implementation of entire CFTR-genotyping into routine diagnostics. CONCLUSION Entire CFTR-genotyping can greatly increase the genetic diagnostic rate of pwCF/pwCFTR-RD and should be considered after inconspicuous CFTR screening panels in CFTR-diagnostics.
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Affiliation(s)
- Simone Ahting
- Institute of Human Genetics, University Medical Center Leipzig, Leipzig, Germany.
| | - Lutz Nährlich
- Department of Pediatrics, Justus-Liebig-University Giessen, Giessen, Germany
| | - Inka Held
- Pediatric Practice Friesenweg, Cystic Fibrosis Center Altona, Hamburg, Germany
| | - Constance Henn
- Division of pediatric Pulmonology and Allergology, Hospital for children and adolescents, University Medical Center Leipzig, Leipzig, Germany
| | - Angelika Krill
- Division of Pneumology, University Medical Center Homburg, Homburg/Saar, Germany
| | - Kerstin Landwehr
- Division of Allergology and Pediatric Pneumology, University Children's Hospital Bethel, University Medical Center Ostwestfalen-Lippe, Bielefeld, Germany
| | - Jochen Meister
- Division of Pneumology, Allergology and Psychotherapy, Children's Hospital, Helios Hospital Aue, Aue, Germany
| | - Susanne Nährig
- Cystic Fibrosis Center for Adults, Med. Klinik V, University Hospital LMU, Munich, Germany
| | - Anna Nolde
- Division of Pneumology, II. Department of Medicine and University Transplant Center, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Katharina Remke
- Department for General Paediatrics, Neonatology and Paediatric Cardiology, University Hospital Düsseldorf, Düsseldorf, Germany
| | - Renate Ruppel
- University Children's Hospital, University Medical Center Erlangen, Erlangen, Germany
| | | | - Martin Schebek
- Division of Pediatric Pneumology, Center for Pediatric and Women's Medicine Kassel, Kassel, Germany
| | - Gudrun Schopper
- University Children's Hospital Schwabing, Technical University of Munich, Munich, Germany
| | - Bernhard Schulte-Hubbert
- Department of medical clinic I, Medical Center Carl Gustav Carus, Technical University of Dresden, Dresden, Germany
| | - Carsten Schwarz
- Department Medicine, HMU-Health and Medical University Potsdam and Director CF Center Westbrandenburg, Division Cystic Fibrosis, Clinic Westbrandenburg, Potsdam, Germany
| | - Christina Smaczny
- Christiane Herzog CF-centre Frankfurt/Main, University Medical Center Frankfurt, Goethe-University Frankfurt, Frankfurt/Main, Germany
| | - Sabine Wege
- Cystic Fibrosis Center, Thoraxklinik Heidelberg, University Medical Center Heidelberg, Heidelberg, Germany
| | - Julia Hentschel
- Institute of Human Genetics, University Medical Center Leipzig, Leipzig, Germany
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8
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Andreou SH, Davies JC. Cystic fibrosis to CFSPID: Burden of care vs need and rational approach to weaning therapies. Paediatr Respir Rev 2023; 47:27-29. [PMID: 37487798 DOI: 10.1016/j.prrv.2023.07.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Accepted: 07/10/2023] [Indexed: 07/26/2023]
Abstract
We present a case of a 10-year-old boy initially diagnosed with CF based on NBS guidelines. However, as CF genetics knowledge has advanced, he has been reclassified as CFSPID based on normal investigations and excellent general clinical status, in line with updated CFSPID guidelines. This case highlights the significance of reviewing CF diagnoses according to the latest understanding of CFTR mutation phenotypes, as well as the patient's clinical status. In order to identify opportunities to save patients from burdensome CF treatment and management, we review current CFSPID guidelines, emphasizing care tailored to each individual case.
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Affiliation(s)
| | - J C Davies
- Royal Brompton Hospital, Sydney St, London SW3 6NP, United Kingdom
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9
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Deignan JL, Gregg AR, Grody WW, Guo MH, Kearney H, Monaghan KG, Raraigh KS, Taylor J, Zepeda-Mendoza CJ, Ziats C. Updated recommendations for CFTR carrier screening: A position statement of the American College of Medical Genetics and Genomics (ACMG). Genet Med 2023; 25:100867. [PMID: 37310422 DOI: 10.1016/j.gim.2023.100867] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 04/20/2023] [Accepted: 04/24/2023] [Indexed: 06/14/2023] Open
Affiliation(s)
- Joshua L Deignan
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA
| | - Anthony R Gregg
- Division of Maternal Fetal Medicine, Department of Obstetrics and Gynecology, Prisma Health, Columbia, SC
| | - Wayne W Grody
- Departments of Pathology and Laboratory Medicine, Pediatrics, and Human Genetics, David Geffen School of Medicine, UCLA, Los Angeles, CA
| | - Michael H Guo
- Department of Neurology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Hutton Kearney
- Division of Laboratory Genetics and Genomics, Mayo Clinic, Rochester, MN
| | | | - Karen S Raraigh
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Jennifer Taylor
- American College of Medical Genetics and Genomics, Bethesda, MD
| | | | - Catherine Ziats
- Division of Genetics, Department of Pediatrics, Dell Medical School, University of Texas, Austin, TX
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10
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DeCelie-Germana JK, Bonitz L, Langfelder-Schwind E, Kier C, Diener BL, Berdella M. Diagnostic and Communication Challenges in Cystic Fibrosis Newborn Screening. Life (Basel) 2023; 13:1646. [PMID: 37629501 PMCID: PMC10455801 DOI: 10.3390/life13081646] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 07/14/2023] [Accepted: 07/25/2023] [Indexed: 08/27/2023] Open
Abstract
As of December 2009, cystic fibrosis (CF) newborn screening (NBS) is performed in all 50 US states and the District of Columbia. Widespread implementation of CF newborn screening (CFNBS) in the US and internationally has brought about new and varied challenges. Immunoreactive trypsinogen (IRT) remains the first, albeit imperfect, biomarker used universally in the screening process. Advances in genetic testing have provided an opportunity for newborn screening programs to add CFTR sequencing tiers to their algorithms. This in turn will enable earlier identification of babies with CF and improve longer-term outcomes through prompt treatment and intervention. CFTR sequencing has led to the ability to identify infants with CF from diverse ethnic and racial backgrounds more equitably while also identifying an increasing proportion of infants with inconclusive diagnoses. Using the evolution of the New York State CF newborn screening program as a guide, this review outlines the basic steps in a universal CF newborn screening program, considers how to reduce bias, highlights challenges, offers guidance to address these challenges and provides recommendations for future consideration.
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Affiliation(s)
- Joan Kathleen DeCelie-Germana
- Cohen Children’s Medical Center, Division of Pediatric Pulmonary and Cystic Fibrosis, Zucker School of Medicine at Hofstra/Northwell, New York, NY 11040, USA;
| | - Lynn Bonitz
- Cohen Children’s Medical Center, Division of Pediatric Pulmonary and Cystic Fibrosis, Zucker School of Medicine at Hofstra/Northwell, New York, NY 11040, USA;
| | - Elinor Langfelder-Schwind
- The Cystic Fibrosis Center, Department of Pulmonary Medicine, Lenox Hill Hospital, Northwell Health, New York, NY 10075, USA; (E.L.-S.); (M.B.)
| | - Catherine Kier
- Department of Pediatrics, Renaissance School of Medicine at Stony Brook, Stony Brook, New York, NY 11794, USA; (C.K.); (B.L.D.)
| | - Barry Lawrence Diener
- Department of Pediatrics, Renaissance School of Medicine at Stony Brook, Stony Brook, New York, NY 11794, USA; (C.K.); (B.L.D.)
| | - Maria Berdella
- The Cystic Fibrosis Center, Department of Pulmonary Medicine, Lenox Hill Hospital, Northwell Health, New York, NY 10075, USA; (E.L.-S.); (M.B.)
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11
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Lee EM, Verma M, Palaniappan N, Pope EM, Lee S, Blacher L, Neerumalla P, An W, Campbell T, Brown C, Hurst S, Marshall B, Hershey T, Nunes V, López de Heredia M, Urano F. Genotype and clinical characteristics of patients with Wolfram syndrome and WFS1-related disorders. Front Genet 2023; 14:1198171. [PMID: 37415600 PMCID: PMC10321297 DOI: 10.3389/fgene.2023.1198171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Accepted: 06/02/2023] [Indexed: 07/08/2023] Open
Abstract
Objective: Wolfram syndrome (WFS) is an autosomal recessive disorder associated with juvenile-onset diabetes mellitus, optic atrophy, diabetes insipidus, and sensorineural hearing loss. We sought to elucidate the relationship between genotypic and phenotypic presentations of Wolfram syndrome which would assist clinicians in classifying the severity and prognosis of Wolfram syndrome more accurately. Approach: Patient data from the Washington University International Registry and Clinical Study for Wolfram Syndrome and patient case reports were analyzed to select for patients with two recessive mutations in the WFS1 gene. Mutations were classified as being either nonsense/frameshift variants or missense/in-frame insertion/deletion variants. Missense/in-frame variants were further classified as transmembrane or non-transmembrane based on whether they affected amino acid residues predicted to be in transmembrane domains of WFS1. Statistical analysis was performed using Wilcoxon rank-sum tests with multiple test adjustment applied via the Bonferonni correction. Results: A greater number of genotype variants correlated with earlier onset and a more severe presentation of Wolfram syndrome. Secondly, non-sense and frameshift variants had more severe phenotypic presentations than missense variants, as evidenced by diabetes mellitus and optic atrophy emerging significantly earlier in patients with two nonsense/frameshift variants compared with zero or one nonsense/frameshift variants. In addition, the number of transmembrane in-frame variants demonstrated a statistically significant dose-effect on age of onset of diabetes mellitus and optic atrophy among patients with either one or two in-frame variants. Summary/Conclusion: The results contribute to our current understanding of the genotype-phenotype relationship of Wolfram syndrome, suggesting that alterations in coding sequences result in significant changes in the presentation and severity of Wolfram. The impact of these findings is significant, as the results will aid clinicians in predicting more accurate prognoses and pave the way for personalized treatments for Wolfram syndrome.
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Affiliation(s)
- Evan M. Lee
- Division of Endocrinology and Lipid Research, Department of Medicine, Washington University School of Medicine, St. Louis, MO, United States
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, United States
- Medical Scientist Training Program, Washington University School of Medicine, St. Louis, MO, United States
| | - Megha Verma
- Division of Endocrinology and Lipid Research, Department of Medicine, Washington University School of Medicine, St. Louis, MO, United States
- Saint Louis University School of Medicine, St. Louis, MO, United States
| | - Nila Palaniappan
- Division of Endocrinology and Lipid Research, Department of Medicine, Washington University School of Medicine, St. Louis, MO, United States
- School of Medicine, University of Missouri Kansas City, Kansas City, MO, United States
| | - Emiko M. Pope
- Division of Endocrinology and Lipid Research, Department of Medicine, Washington University School of Medicine, St. Louis, MO, United States
| | - Sammie Lee
- Division of Endocrinology and Lipid Research, Department of Medicine, Washington University School of Medicine, St. Louis, MO, United States
| | - Lindsey Blacher
- Division of Endocrinology and Lipid Research, Department of Medicine, Washington University School of Medicine, St. Louis, MO, United States
| | - Pooja Neerumalla
- Division of Endocrinology and Lipid Research, Department of Medicine, Washington University School of Medicine, St. Louis, MO, United States
| | - William An
- Division of Endocrinology and Lipid Research, Department of Medicine, Washington University School of Medicine, St. Louis, MO, United States
| | - Toko Campbell
- Division of Endocrinology and Lipid Research, Department of Medicine, Washington University School of Medicine, St. Louis, MO, United States
| | - Cris Brown
- Division of Endocrinology and Lipid Research, Department of Medicine, Washington University School of Medicine, St. Louis, MO, United States
| | - Stacy Hurst
- Division of Endocrinology and Lipid Research, Department of Medicine, Washington University School of Medicine, St. Louis, MO, United States
| | - Bess Marshall
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, United States
| | - Tamara Hershey
- Departments of Psychiatry and Radiology, Washington University School of Medicine, St. Louis, MO, United States
| | - Virginia Nunes
- Molecular Genetics Laboratory, Genes Disease and Therapy Program IDIBELL, L’Hospitalet de Llobregat, Barcelona, Spain
- Genetics Unit, Physiological Sciences Department, Health Sciences and Medicine Faculty University of Barcelona, L’Hospitalet de Llobregat, Barcelona, Spain
| | - Miguel López de Heredia
- Centre for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | - Fumihiko Urano
- Division of Endocrinology and Lipid Research, Department of Medicine, Washington University School of Medicine, St. Louis, MO, United States
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, United States
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12
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Lefferts JW, Boersma V, Nieuwenhuijze NDA, Suen SWF, Hajo K, Collantes NS, Vermeulen C, Groeneweg T, Hagemeijer MC, de Jonge HR, van der Ent CK, Splinter E, Beekman JM. Targeted locus amplification reveals heterogeneity between and within CFTR genotypes and association with CFTR function in patient-derived intestinal organoids. J Cyst Fibros 2023; 22:538-547. [PMID: 37100706 DOI: 10.1016/j.jcf.2023.04.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 03/31/2023] [Accepted: 04/07/2023] [Indexed: 04/28/2023]
Abstract
BACKGROUND Cystic fibrosis (CF) disease severity can be highly variable, even between people with CF (pwCF) with similar genotypes. Here we use patient-derived intestinal organoids to study the influence of genetic variation within the cystic fibrosis transmembrane conductance regulator (CFTR) gene on CFTR function. METHODS Organoids of F508del/class I, F508del/S1251N and pwCF with only one detected CF-causing mutation were cultured. Allele-specific CFTR variation was investigated using targeted locus amplification (TLA), CFTR function was measured using the forskolin-induced swelling assay and mRNA levels were quantified using RT-qPCR. RESULTS We were able to distinguish CFTR genotypes based on TLA data. Additionally, we observed heterogeneity within genotypes, which we were able to link to CFTR function for S1251N alleles. CONCLUSIONS Our results indicate that the paired analysis of CFTR intragenic variation and CFTR function can gain insights in the underlying CFTR defect for individuals where the disease phenotype does not match the CFTR mutations detected during diagnosis.
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Affiliation(s)
- J W Lefferts
- Department of Pediatric Respiratory Medicine, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht, the Netherlands; Regenerative Medicine Center, Center for Living Technologies, University Medical Center Utrecht, Utrecht, the Netherlands
| | - V Boersma
- Cergentis BV., Utrecht, the Netherlands
| | - N D A Nieuwenhuijze
- Department of Pediatric Respiratory Medicine, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht, the Netherlands; Regenerative Medicine Center, Center for Living Technologies, University Medical Center Utrecht, Utrecht, the Netherlands; Gastroenterology & Hepatology, Erasmus MC University Medical Center, Rotterdam, The Netherlands
| | - S W F Suen
- Department of Pediatric Respiratory Medicine, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht, the Netherlands; Regenerative Medicine Center, Center for Living Technologies, University Medical Center Utrecht, Utrecht, the Netherlands; Xilis BV, Utrecht, the Netherlands
| | - K Hajo
- Cergentis BV., Utrecht, the Netherlands
| | - N Sanchez Collantes
- Oncode Institute, Utrecht, the Netherlands; Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - C Vermeulen
- Oncode Institute, Utrecht, the Netherlands; Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - T Groeneweg
- Gastroenterology & Hepatology, Erasmus MC University Medical Center, Rotterdam, The Netherlands
| | - M C Hagemeijer
- Current affiliation: Center for Lysosomal and Metabolic Diseases, Department of Clinical Genetics, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - H R de Jonge
- Gastroenterology & Hepatology, Erasmus MC University Medical Center, Rotterdam, The Netherlands
| | - C K van der Ent
- Department of Pediatric Respiratory Medicine, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht, the Netherlands
| | | | - J M Beekman
- Department of Pediatric Respiratory Medicine, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht, the Netherlands; Regenerative Medicine Center, Center for Living Technologies, University Medical Center Utrecht, Utrecht, the Netherlands; Center for Living Technologies, Eindhoven-Wageningen-Utrecht Alliance, the Netherlands.
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13
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Makarova M, Nemtsova M, Danishevich A, Chernevskiy D, Belenikin M, Krinitsina A, Baranova E, Sagaydak O, Vorontsova M, Khatkov I, Zhukova L, Bodunova N, Nikolaev S, Byakhova M, Semenova A, Galkin V, Gadzhieva S. The CFTR Gene Germline Heterozygous Pathogenic Variants in Russian Patients with Malignant Neoplasms and Healthy Carriers: 11,800 WGS Results. Int J Mol Sci 2023; 24:ijms24097940. [PMID: 37175647 PMCID: PMC10178054 DOI: 10.3390/ijms24097940] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 04/14/2023] [Accepted: 04/25/2023] [Indexed: 05/15/2023] Open
Abstract
More than 275 million people in the world are carriers of a heterozygous mutation of the CFTR gene, associated with cystic fibrosis, the most common autosomal recessive disease among Caucasians. Some recent studies assessed the association between carriers of CFTR variants and some pathologies, including cancer risk. The aim of this study is to analyze the landscape of germline pathogenic heterozygous CFTR variants in patients with diagnosed malignant neoplasms. For the first time in Russia, we evaluated the frequency of CFTR pathogenic variants by whole-genome sequencing in 1800 patients with cancer and compared this with frequencies of CFTR variants in the control group (1825 people) adjusted for age and 10,000 healthy individuals. In the issue, 47 out of 1800 patients (2.6%) were carriers of CFTR pathogenic genetic variants: 0.028 (42/1525) (2.8%) among breast cancer patients, 0.017 (3/181) (1.7%) among colorectal cancer patients and 0.021 (2/94) (2.1%) among ovarian cancer patients. Pathogenic CFTR variants were found in 52/1825 cases (2.85%) in the control group and 221 (2.21%) in 10,000 healthy individuals. Based on the results of the comparison, there was no significant difference in the frequency and distribution of pathogenic variants of the CFTR gene, which is probably due to the study limitations. Obviously, additional studies are needed to assess the clinical significance of the heterozygous carriage of CFTR pathogenic variants in the development of various pathologies in the future, particularly cancer.
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Affiliation(s)
- Maria Makarova
- LLC Evogen, 115191 Moscow, Russia
- Federal State Budgetary Institution Russian Scientific Center of Roentgenoradiology of the Ministry of Healthcare of the Russian Federation, 117997 Moscow, Russia
| | - Marina Nemtsova
- LLC Evogen, 115191 Moscow, Russia
- Research Centre for Medical Genetics of N.P. Bochkov, 115522 Moscow, Russia
- Federal State Autonomous Educational Institution of Higher Education I.M. Sechenov of the Ministry of Health of Russian Federation, 119991 Moscow, Russia
| | | | | | | | | | - Elena Baranova
- LLC Evogen, 115191 Moscow, Russia
- Academy of Continuing Professional Education of the Ministry of Health of Russian Federation, 125993 Moscow, Russia
| | | | - Maria Vorontsova
- The National Medical Research Center for Endocrinology, 117292 Moscow, Russia
| | - Igor Khatkov
- SBHI Moscow Clinical Scientific Center Named after Loginov MHD, 111123 Moscow, Russia
| | - Lyudmila Zhukova
- SBHI Moscow Clinical Scientific Center Named after Loginov MHD, 111123 Moscow, Russia
| | - Natalia Bodunova
- SBHI Moscow Clinical Scientific Center Named after Loginov MHD, 111123 Moscow, Russia
| | - Sergey Nikolaev
- SBHI Moscow Clinical Scientific Center Named after Loginov MHD, 111123 Moscow, Russia
| | - Mariya Byakhova
- City Clinical Oncological Hospital No. 1, Moscow Department of Healthcare, 117152 Moscow, Russia
| | - Anna Semenova
- City Clinical Oncological Hospital No. 1, Moscow Department of Healthcare, 117152 Moscow, Russia
| | - Vsevolod Galkin
- City Clinical Oncological Hospital No. 1, Moscow Department of Healthcare, 117152 Moscow, Russia
| | - Saida Gadzhieva
- City Clinical Oncological Hospital No. 1, Moscow Department of Healthcare, 117152 Moscow, Russia
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14
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Lee EM, Verma M, Palaniappan N, Pope EM, Lee S, Blacher L, Neerumalla P, An W, Campbell T, Brown C, Hurst S, Marshall B, Hershey T, Nunes V, de Heredia ML, Urano F. Genotype and Clinical Characteristics of Patients with Wolfram Syndrome and WFS1-related Disorders. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.02.15.23284904. [PMID: 36824811 PMCID: PMC9949199 DOI: 10.1101/2023.02.15.23284904] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/18/2023]
Abstract
Objective Wolfram syndrome (WFS) is an autosomal recessive disorder associated with juvenile-onset diabetes mellitus, optic atrophy, diabetes insipidus, and sensorineural hearing loss. We sought to elucidate the relationship between genotypic and phenotypic presentations of Wolfram syndrome which would assist clinicians in classifying the severity and prognosis of Wolfram syndrome more accurately. Approach Patient data from the Washington University International Registry and Clinical Study for Wolfram Syndrome and patient case reports were analyzed to select for patients with two recessive mutations in the WFS1 gene. Mutations were classified as being either nonsense/frameshift variants or missense/in-frame insertion/deletion variants and statistical analysis was performed using unpaired and paired t-tests and one- and two-way ANOVA with Tukey's or Dunnett's tests. Results A greater number of genotype variants correlated with earlier onset and a more severe presentation of Wolfram syndrome. Secondly, non-sense and frameshift variants had more severe phenotypic presentations than missense variants, as evidenced by optic atrophy emerging significantly earlier in patients with 2 nonsense/frameshift alleles compared with 0 missense transmembrane variants. In addition, the number of transmembrane in-frame variants demonstrated a statistically significant dose-effect on age of onset of diabetes mellitus and optic atrophy. Summary / Conclusions The results contribute to our current understanding of the genotype-phenotype relationship of Wolfram syndrome, suggesting that alterations in coding sequences result in significant changes in the presentation and severity of Wolfram. The impact of these findings is significant, as the results will aid clinicians in predicting more accurate prognoses and pave the way for personalized treatments for Wolfram syndrome.
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Affiliation(s)
- Evan M. Lee
- Department of Medicine, Division of Endocrinology, Metabolism, and Lipid Research, Washington University School of Medicine, 660 South Euclid Avenue, St. Louis, MO 63110, USA
- Medical Scientist Training Program, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Megha Verma
- Department of Medicine, Division of Endocrinology, Metabolism, and Lipid Research, Washington University School of Medicine, 660 South Euclid Avenue, St. Louis, MO 63110, USA
- Saint Louis University School of Medicine, Saint Louis, MO, USA
| | - Nila Palaniappan
- Department of Medicine, Division of Endocrinology, Metabolism, and Lipid Research, Washington University School of Medicine, 660 South Euclid Avenue, St. Louis, MO 63110, USA
- University of Missouri Kansas City, Kansas City, MO, USA
| | - Emiko M. Pope
- Department of Medicine, Division of Endocrinology, Metabolism, and Lipid Research, Washington University School of Medicine, 660 South Euclid Avenue, St. Louis, MO 63110, USA
- Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Sammie Lee
- Department of Medicine, Division of Endocrinology, Metabolism, and Lipid Research, Washington University School of Medicine, 660 South Euclid Avenue, St. Louis, MO 63110, USA
- Cornell University, Ithaca, NY, USA
| | - Lindsey Blacher
- Department of Medicine, Division of Endocrinology, Metabolism, and Lipid Research, Washington University School of Medicine, 660 South Euclid Avenue, St. Louis, MO 63110, USA
| | - Pooja Neerumalla
- Department of Medicine, Division of Endocrinology, Metabolism, and Lipid Research, Washington University School of Medicine, 660 South Euclid Avenue, St. Louis, MO 63110, USA
| | - William An
- Department of Medicine, Division of Endocrinology, Metabolism, and Lipid Research, Washington University School of Medicine, 660 South Euclid Avenue, St. Louis, MO 63110, USA
| | - Toko Campbell
- Department of Medicine, Division of Endocrinology, Metabolism, and Lipid Research, Washington University School of Medicine, 660 South Euclid Avenue, St. Louis, MO 63110, USA
| | - Cris Brown
- Department of Medicine, Division of Endocrinology, Metabolism, and Lipid Research, Washington University School of Medicine, 660 South Euclid Avenue, St. Louis, MO 63110, USA
| | - Stacy Hurst
- Department of Medicine, Division of Endocrinology, Metabolism, and Lipid Research, Washington University School of Medicine, 660 South Euclid Avenue, St. Louis, MO 63110, USA
| | - Bess Marshall
- Department of Pediatrics, Washington University School of Medicine, 660 South Euclid Avenue, St. Louis, MO 63110, USA
| | - Tamara Hershey
- Departments of Psychiatry and Radiology, Washington University School of Medicine, 660 South Euclid Avenue, St. Louis, MO 63110, USA
| | - Virginia Nunes
- Molecular Genetics Laboratory. Genes, Disease and Therapy Program IDIBELL, l’Hospitalet de Llobregat, Barcelona, Spain
- Genetics Unit. Physiological Sciences Department. Health Sciences and Medicine Faculty. University of Barcelona, l’Hospitalet de Llobregat, Barcelona, Spain
| | - Miguel López de Heredia
- Centre for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | - Fumihiko Urano
- Department of Medicine, Division of Endocrinology, Metabolism, and Lipid Research, Washington University School of Medicine, 660 South Euclid Avenue, St. Louis, MO 63110, USA
- Department of Pathology and Immunology, Washington University School of Medicine, 660 South Euclid Avenue, St. Louis, MO 63110, USA
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15
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Standards of care for CFTR variant-specific therapy (including modulators) for people with cystic fibrosis. J Cyst Fibros 2023; 22:17-30. [PMID: 36916675 DOI: 10.1016/j.jcf.2022.10.002] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 10/06/2022] [Accepted: 10/10/2022] [Indexed: 11/11/2022]
Abstract
Cystic fibrosis (CF) has entered the era of variant-specific therapy, tailored to the genetic variants in the Cystic Fibrosis Transmembrane Conductance Regulator (CFTR) gene. CFTR modulators, the first variant-specific therapy available, have transformed the management of CF. The latest standards of care from the European CF Society (2018) did not include guidance on variant-specific therapy, as CFTR modulators were becoming established as a novel therapy. We have produced interim standards to guide healthcare professionals in the provision of variant-specific therapy for people with CF. Here we provide evidence-based guidance covering the spectrum of care, established using evidence from systematic reviews and expert opinion. Statements were reviewed by key stakeholders using Delphi methodology, with agreement (≥80%) achieved for all statements after one round of consultation. Issues around accessibility are discussed and there is clear consensus that all eligible people with CF should have access to variant-specific therapy.
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16
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Bergougnoux A, Billet A, Ka C, Heller M, Degrugillier F, Vuillaume ML, Thoreau V, Sasorith S, Bareil C, Thèze C, Ferec C, Gac GL, Bienvenu T, Bieth E, Gaston V, Lalau G, Pagin A, Malinge MC, Dufernez F, Lemonnier L, Koenig M, Fergelot P, Claustres M, Taulan-Cadars M, Kitzis A, Reboul MP, Becq F, Fanen P, Mekki C, Audrezet MP, Girodon E, Raynal C. The multi-faceted nature of 15 CFTR exonic variations: Impact on their functional classification and perspectives for therapy. J Cyst Fibros 2022:S1569-1993(22)01423-0. [PMID: 36567205 DOI: 10.1016/j.jcf.2022.12.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Revised: 09/30/2022] [Accepted: 12/05/2022] [Indexed: 12/24/2022]
Abstract
BACKGROUND The majority of variants of unknown clinical significance (VUCS) in the CFTR gene are missense variants. While change on the CFTR protein structure or function is often suspected, impact on splicing may be neglected. Such undetected splicing default of variants may complicate the interpretation of genetic analyses and the use of an appropriate pharmacotherapy. METHODS We selected 15 variants suspected to impact CFTR splicing after in silico predictions on 319 missense variants (214 VUCS), reported in the CFTR-France database. Six specialized laboratories assessed the impact of nucleotide substitutions on splicing (minigenes), mRNA expression levels (quantitative PCR), synthesis and maturation (western blot), cellular localization (immunofluorescence) and channel function (patch clamp) of the CFTR protein. We also studied maturation and function of the truncated protein, consecutive to in-frame aberrant splicing, on additional plasmid constructs. RESULTS Six of the 15 variants had a major impact on CFTR splicing by in-frame (n = 3) or out-of-frame (n = 3) exon skipping. We reclassified variants into: splicing variants; variants causing a splicing defect and the impairment of CFTR folding and/or function related to the amino acid substitution; deleterious missense variants that impair CFTR folding and/or function; and variants with no consequence on the different processes tested. CONCLUSION The 15 variants have been reclassified by our comprehensive approach of in vitro experiments that should be used to properly interpret very rare exonic variants of the CFTR gene. Targeted therapies may thus be adapted to the molecular defects regarding the results of laboratory experiments.
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Affiliation(s)
- A Bergougnoux
- Génétique Moléculaire, CHU Montpellier, Montpellier, France; PhyMedExp, INSERM, CNRS UMR, Montpellier, France; Université de Montpellier, Montpellier, France
| | - A Billet
- Laboratoire STIM, Université de Poitiers, Poitiers, France
| | - C Ka
- Service de génétique moléculaire, CHRU Brest, Brest, France; Université de Brest, Inserm, UMR 1078, GGB, Brest, France
| | - M Heller
- Service de Médecine Génomique des Maladies de Système et d'Organe, APHP Centre - Université de Paris, Hôpital Cochin, Paris, France
| | - F Degrugillier
- Université Paris-Est Créteil, INSERM, IMRB, Créteil F-94010, France
| | - M-L Vuillaume
- Génétique Moléculaire, CHU Bordeaux, Bordeaux, France
| | - V Thoreau
- Laboratoire NEUVACOD-3808, Université de Poitiers, Poitiers, France
| | - S Sasorith
- Génétique Moléculaire, CHU Montpellier, Montpellier, France; PhyMedExp, INSERM, CNRS UMR, Montpellier, France
| | - C Bareil
- Génétique Moléculaire, CHU Montpellier, Montpellier, France
| | - C Thèze
- Génétique Moléculaire, CHU Montpellier, Montpellier, France
| | - C Ferec
- Université de Brest, Inserm, UMR 1078, GGB, Brest, France
| | - G Le Gac
- Service de génétique moléculaire, CHRU Brest, Brest, France; Université de Brest, Inserm, UMR 1078, GGB, Brest, France
| | - T Bienvenu
- Service de Médecine Génomique des Maladies de Système et d'Organe, APHP Centre - Université de Paris, Hôpital Cochin, Paris, France
| | - E Bieth
- Génétique Médicale, CHU Toulouse, Toulouse, France
| | - V Gaston
- Génétique Médicale, CHU Toulouse, Toulouse, France
| | - G Lalau
- Biochimie et Biologie Moléculaire, CHU Lille, Lille, France
| | - A Pagin
- Biochimie et Biologie Moléculaire, CHU Lille, Lille, France
| | - M-C Malinge
- Biochimie et Génétique, CHU Angers, Angers, France
| | - F Dufernez
- Génétique, CHU Poitiers, Poitiers, France
| | - L Lemonnier
- Association Vaincre la Mucoviscidose, Paris, France
| | - M Koenig
- Génétique Moléculaire, CHU Montpellier, Montpellier, France; PhyMedExp, INSERM, CNRS UMR, Montpellier, France; Université de Montpellier, Montpellier, France
| | - P Fergelot
- MRGM, INSERM UMR 1211 Université de Bordeaux, Bordeaux, France
| | - M Claustres
- Université de Montpellier, Montpellier, France
| | - M Taulan-Cadars
- PhyMedExp, INSERM, CNRS UMR, Montpellier, France; Université de Montpellier, Montpellier, France
| | - A Kitzis
- Génétique, CHU Poitiers, Poitiers, France
| | - M-P Reboul
- Génétique Moléculaire, CHU Bordeaux, Bordeaux, France
| | - F Becq
- Laboratoire STIM, Université de Poitiers, Poitiers, France
| | - P Fanen
- AP-HP, Département de Biochimie-Biologie Moléculaire, Pharmacologie, Génétique Médicale, Hôpital Henri Mondor, Créteil F-94010, France
| | - C Mekki
- AP-HP, Département de Biochimie-Biologie Moléculaire, Pharmacologie, Génétique Médicale, Hôpital Henri Mondor, Créteil F-94010, France
| | - M-P Audrezet
- Service de génétique moléculaire, CHRU Brest, Brest, France; Université de Brest, Inserm, UMR 1078, GGB, Brest, France
| | - E Girodon
- Service de Médecine Génomique des Maladies de Système et d'Organe, APHP Centre - Université de Paris, Hôpital Cochin, Paris, France; INSERM U1151, Institut Necker Enfants Malades, Université de Paris, Paris, France
| | - C Raynal
- Génétique Moléculaire, CHU Montpellier, Montpellier, France; PhyMedExp, INSERM, CNRS UMR, Montpellier, France.
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17
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Sermet-Gaudelus I, Girodon E, Vermeulen F, Solomon G, Melotti P, Graeber S, Bronsveld I, Rowe S, Wilschanski M, Tümmler B, Cutting G, Gonska T. ECFS standards of care on CFTR-related disorders: Diagnostic criteria of CFTR dysfunction. J Cyst Fibros 2022; 21:922-936. [DOI: 10.1016/j.jcf.2022.09.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2022] [Revised: 09/06/2022] [Accepted: 09/14/2022] [Indexed: 11/06/2022]
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18
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ECFS standards of care on CFTR-related disorders: Updated diagnostic criteria. J Cyst Fibros 2022; 21:908-921. [DOI: 10.1016/j.jcf.2022.09.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 09/27/2022] [Accepted: 09/28/2022] [Indexed: 11/07/2022]
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19
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Splicing mutations in the CFTR gene as therapeutic targets. Gene Ther 2022; 29:399-406. [PMID: 35650428 PMCID: PMC9385490 DOI: 10.1038/s41434-022-00347-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 05/07/2022] [Accepted: 05/12/2022] [Indexed: 11/08/2022]
Abstract
The marketing approval, about ten years ago, of the first disease modulator for patients with cystic fibrosis harboring specific CFTR genotypes (~5% of all patients) brought new hope for their treatment. To date, several therapeutic strategies have been approved and the number of CFTR mutations targeted by therapeutic agents is increasing. Although these drugs do not reverse the existing disease, they help to increase the median life expectancy. However, on the basis of their CFTR genotype, ~10% of patients presently do not qualify for any of the currently available CFTR modulator therapies, particularly patients with splicing mutations (~12% of the reported CFTR mutations). Efforts are currently made to develop therapeutic agents that target disease-causing CFTR variants that affect splicing. This highlights the need to fully identify them by scanning non-coding regions and systematically determine their functional consequences. In this review, we present some examples of CFTR alterations that affect splicing events and the different therapeutic options that are currently developed and tested for splice switching.
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20
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Louis M, Staiano P, Micalo L, Chaudary N. Cystic Fibrosis and Sleep Circadian Rhythms. Pulm Ther 2022; 8:139-147. [PMID: 35149967 PMCID: PMC9098776 DOI: 10.1007/s41030-022-00184-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Accepted: 01/24/2022] [Indexed: 11/21/2022] Open
Abstract
Cystic fibrosis (CF) is due to a mutation in the cystic fibrosis transmembrane conductance regulator gene (CFTR), which leads to unusual water and chloride secretion across epithelial surfaces. The lungs are responsible for most morbidity, though other organs are frequently affected. Sleep abnormalities have long been recognized in CF. Abnormal ventilation and oxygenation, sinus disease, deconditioning due to muscle weakness and recurrent infections, and inflammation have been thought to play a role in sleep disorders in CF. However, there is evidence that CFTR gene dysregulation can affect circadian rhythms in CF. Early recognition and treatment of circadian rhythms may improve outcomes in CF.
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Affiliation(s)
- Mariam Louis
- Department of Pulmonary, Critical Care and Sleep Medicine, University of Florida, Jacksonville, FL, USA
| | - Peter Staiano
- Department of Pulmonary, Critical Care and Sleep Medicine, University of Florida, Jacksonville, FL, USA
| | - Lavender Micalo
- Division of Pulmonary Disease and Critical Care Medicine, Department of Medicine, Adult Cystic Fibrosis Center, Virginia Commonwealth University, 1200 East Broad Street, Box 980050, Richmond, VA, 23298, USA
| | - Nauman Chaudary
- Division of Pulmonary Disease and Critical Care Medicine, Department of Medicine, Adult Cystic Fibrosis Center, Virginia Commonwealth University, 1200 East Broad Street, Box 980050, Richmond, VA, 23298, USA.
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21
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Hatton A, Bergougnoux A, Zybert K, Chevalier B, Mesbahi M, Altéri JP, Walicka-Serzysko K, Postek M, Taulan-Cadars M, Edelman A, Hinzpeter A, Claustres M, Girodon E, Raynal C, Sermet-Gaudelus I, Sands D. Reclassifying inconclusive diagnosis after newborn screening for cystic fibrosis. Moving forward. J Cyst Fibros 2021; 21:448-455. [PMID: 34949556 DOI: 10.1016/j.jcf.2021.12.010] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 12/07/2021] [Accepted: 12/08/2021] [Indexed: 10/19/2022]
Abstract
BACKGROUND Newborn screening for Cystic Fibrosis (CF) is associated with situations where the diagnosis of CF or CFTR related disorders (CFTR-RD) cannot be clearly ruled out. MATERIALS/PATIENTS AND METHODS We report a case series of 23 children with unconclusive diagnosis after newborn screening for CF and a mean follow-up of 7.7 years (4-13). Comprehensive investigations including whole CFTR gene sequencing, in vivo intestinal current measurement (ICM), nasal potential difference (NPD), and in vitro functional studies of variants of unknown significance, helped to reclassify the patients. RESULTS Extensive genetic testing identified, in trans with a CF causing mutation, variants with varying clinical consequences and 3 variants of unknown significance (VUS). Eighteen deep intronic variants were identified by deep resequencing of the whole CFTR gene in 13 patients and were finally considered as non-pathogenic. All patients had normal CFTR dependent chloride transport in ICM. NPD differentiated 3 different profiles: CF-like tracings qualifying the patients as CF, such as F508del/D1152H patients; normal responses, suggesting an extremely low likelihood of developing a CFTR-RD such as F508del/TG11T5 patients; partial CFTR dysfunction above 20% of the normal, highlighting a remaining risk of developing CFTR-RD such as F508del/F1052V patients. The 3 VUS were reclassified as variant with defective maturation (D537N), defective expression (T582I) or with no clinical consequence (M952T). CONCLUSION This study demonstrates the usefulness of combining genetic and functional investigations to assess the possibility of evolving to CF or CFTR-RD in babies with inconclusive diagnosis at neonatal screening.
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Affiliation(s)
- Aurelie Hatton
- INSERM U1151, Institut Necker Enfants Malades, Université de Paris, 149 rue de Sévres, Paris 75015, France; Université de Paris, Paris, France
| | - Anne Bergougnoux
- PhyMedExp, INSERM U1046, CNRS UMR 9214, University of Montpellier, Montpellier, France; CHU de Montpellier, Laboratoire de Génétique Moléculaire, Montpellier, France
| | - Katarzyna Zybert
- Cystic Fibrosis Department, Institute of Mother and Child, Warsaw, Poland
| | - Benoit Chevalier
- INSERM U1151, Institut Necker Enfants Malades, Université de Paris, 149 rue de Sévres, Paris 75015, France; Université de Paris, Paris, France
| | - Myriam Mesbahi
- INSERM U1151, Institut Necker Enfants Malades, Université de Paris, 149 rue de Sévres, Paris 75015, France; Université de Paris, Paris, France
| | - Jean Pierre Altéri
- CHU de Montpellier, Laboratoire de Génétique Moléculaire, Montpellier, France
| | | | - Magdalena Postek
- Cystic Fibrosis Department, Institute of Mother and Child, Warsaw, Poland
| | - Magali Taulan-Cadars
- PhyMedExp, INSERM U1046, CNRS UMR 9214, University of Montpellier, Montpellier, France; Université de Montpellier, Montpellier, France
| | - Aleksander Edelman
- INSERM U1151, Institut Necker Enfants Malades, Université de Paris, 149 rue de Sévres, Paris 75015, France; Université de Paris, Paris, France
| | - Alexandre Hinzpeter
- INSERM U1151, Institut Necker Enfants Malades, Université de Paris, 149 rue de Sévres, Paris 75015, France; Université de Paris, Paris, France
| | | | - Emmanuelle Girodon
- INSERM U1151, Institut Necker Enfants Malades, Université de Paris, 149 rue de Sévres, Paris 75015, France; Laboratoire de Génétique et Biologie Moléculaires, Hôpital Cochin, APHP Centre, Université de Paris, Paris, France
| | - Caroline Raynal
- PhyMedExp, INSERM U1046, CNRS UMR 9214, University of Montpellier, Montpellier, France; CHU de Montpellier, Laboratoire de Génétique Moléculaire, Montpellier, France
| | - Isabelle Sermet-Gaudelus
- INSERM U1151, Institut Necker Enfants Malades, Université de Paris, 149 rue de Sévres, Paris 75015, France; Université de Paris, Paris, France; Centre de Référence Maladies Rares, Mucoviscidose et maladies apparentées, Hôpital Necker Enfants Malades, Paris, France; European Reference Network-Lung, France.
| | - Dorota Sands
- Cystic Fibrosis Department, Institute of Mother and Child, Warsaw, Poland
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22
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Noel S, Servel N, Hatton A, Golec A, Rodrat M, Ng DRS, Li H, Pranke I, Hinzpeter A, Edelman A, Sheppard DN, Sermet-Gaudelus I. Correlating genotype with phenotype using CFTR-mediated whole-cell Cl - currents in human nasal epithelial cells. J Physiol 2021; 600:1515-1531. [PMID: 34761808 DOI: 10.1113/jp282143] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Accepted: 11/01/2021] [Indexed: 12/20/2022] Open
Abstract
Dysfunction of the epithelial anion channel cystic fibrosis transmembrane conductance regulator (CFTR) causes a wide spectrum of disease, including cystic fibrosis (CF) and CFTR-related diseases (CFTR-RDs). Here, we investigate genotype-phenotype-CFTR function relationships using human nasal epithelial (hNE) cells from a small cohort of non-CF subjects and individuals with CF and CFTR-RDs and genotypes associated with either residual or minimal CFTR function using electrophysiological techniques. Collected hNE cells were either studied directly with the whole-cell patch-clamp technique or grown as primary cultures at an air-liquid interface after conditional reprogramming. The properties of cAMP-activated whole-cell Cl- currents in freshly isolated hNE cells identified them as CFTR-mediated. Their magnitude varied between hNE cells from individuals within the same genotype and decreased in the rank order: non-CF > CFTR residual function > CFTR minimal function. CFTR-mediated whole-cell Cl- currents in hNE cells isolated from fully differentiated primary cultures were identical to those in freshly isolated hNE cells in both magnitude and behaviour, demonstrating that conditional reprogramming culture is without effect on CFTR expression and function. For the cohort of subjects studied, CFTR-mediated whole-cell Cl- currents in hNE cells correlated well with CFTR-mediated transepithelial Cl- currents measured in vitro with the Ussing chamber technique, but not with those determined in vivo with the nasal potential difference assay. Nevertheless, they did correlate with the sweat Cl- concentration of study subjects. Thus, this study highlights the complexity of genotype-phenotype-CFTR function relationships, but emphasises the value of conditionally reprogrammed hNE cells in CFTR research and therapeutic testing. KEY POINTS: The genetic disease cystic fibrosis is caused by pathogenic variants in the cystic fibrosis transmembrane conductance regulator (CFTR), an ion channel, which controls anion flow across epithelia lining ducts and tubes in the body. This study investigated CFTR function in nasal epithelial cells from people with cystic fibrosis and CFTR variants with a range of disease severity. CFTR function varied widely in nasal epithelial cells depending on the identity of CFTR variants, but was unaffected by conditional reprogramming culture, a cell culture technique used to grow large numbers of patient-derived cells. Assessment of CFTR function in vitro in nasal epithelial cells and epithelia, and in vivo in the nasal epithelium and sweat gland highlights the complexity of genotype-phenotype-CFTR function relationships.
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Affiliation(s)
- Sabrina Noel
- INSERM U1151, Institut Necker-Enfants Malades, Paris, France.,Université de Paris, Paris, France
| | - Nathalie Servel
- INSERM U1151, Institut Necker-Enfants Malades, Paris, France.,Université de Paris, Paris, France
| | - Aurélie Hatton
- INSERM U1151, Institut Necker-Enfants Malades, Paris, France.,Université de Paris, Paris, France
| | - Anita Golec
- INSERM U1151, Institut Necker-Enfants Malades, Paris, France.,Université de Paris, Paris, France
| | - Mayuree Rodrat
- School of Physiology, Pharmacology and Neuroscience, University of Bristol, Bristol, UK.,Center of Research and Development for Biomedical Instrumentation, Institute of Molecular Biosciences, Mahidol University, Nakhon Pathom, Thailand
| | - Demi R S Ng
- School of Physiology, Pharmacology and Neuroscience, University of Bristol, Bristol, UK
| | - Hongyu Li
- School of Physiology, Pharmacology and Neuroscience, University of Bristol, Bristol, UK
| | - Iwona Pranke
- INSERM U1151, Institut Necker-Enfants Malades, Paris, France.,Université de Paris, Paris, France
| | - Alexandre Hinzpeter
- INSERM U1151, Institut Necker-Enfants Malades, Paris, France.,Université de Paris, Paris, France
| | - Aleksander Edelman
- INSERM U1151, Institut Necker-Enfants Malades, Paris, France.,Université de Paris, Paris, France
| | - David N Sheppard
- School of Physiology, Pharmacology and Neuroscience, University of Bristol, Bristol, UK
| | - Isabelle Sermet-Gaudelus
- INSERM U1151, Institut Necker-Enfants Malades, Paris, France.,Université de Paris, Paris, France.,Centre de Référence Maladies Rares, Mucoviscidose et Maladies Apparentées, Hôpital Necker-Enfants Malades, Paris, France.,European Reference Network on rare respiratory diseases, Frankfurt, Germany
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23
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Mikó Á, Kaposi A, Schnabel K, Seidl D, Tory K. Identification of incompletely penetrant variants and interallelic interactions in autosomal recessive disorders by a population-genetic approach. Hum Mutat 2021; 42:1473-1487. [PMID: 34405919 DOI: 10.1002/humu.24273] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 07/30/2021] [Accepted: 08/15/2021] [Indexed: 01/11/2023]
Abstract
We aimed to identify incompletely penetrant (IP) variants and interallelic interactions in autosomal recessive disorders by a population-genetic approach. Genotype and clinical data were collected from 9038 patients of European origin with ASL, ATP7B, CAPN3, CFTR, CTNS, DHCR7, GAA, GALNS, GALT, IDUA, MUT, NPHS1, NPHS2, PAH, PKHD1, PMM2, or SLC26A4-related disorders. We calculated the relative allele frequency of each pathogenic variant (n = 1936) to the loss-of-function (LOF) variants of the corresponding gene in the patient ( A C p t V / A C p t L O F ) and the general population ( AC gnomAD V / AC gnomAD LOF ) and estimated the penetrance of each variant by calculating their ratio: ( A C p t V / A C p t L O F ) ( A C g n o m A D V / A C g n o m A D L O F ) (V/LOF ratio). We classified all variants as null or hypomorphic based on the associated clinical phenotype. We found 25 variants, 29% of the frequent 85 variants, to be underrepresented in the patient population (V/LOF ratio <30% with p < 7.22 × 10-5 ), including 22 novel ones in the ASL, CAPN3, CFTR, GAA, GALNS, PAH, and PKHD1 genes. In contrast to the completely penetrant variants (CP), the majority of the IP variants were hypomorphic (IP: 16/18, 88%; CP: 177/933, 19.0%; p = 5.12 × 10-10 ). Among them, only the NPHS2 R229Q variant was subject to interallelic interactions. The proposed algorithm identifies frequent IP variants and estimates their penetrance and interallelic interactions in large patient cohorts.
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Affiliation(s)
- Ágnes Mikó
- MTA-SE Lendület Nephrogenetic Laboratory, Hungarian Academy of Sciences, Budapest, Hungary.,1st Department of Pediatrics, Semmelweis University, Budapest, Hungary
| | - Ambrus Kaposi
- MTA-SE Lendület Nephrogenetic Laboratory, Hungarian Academy of Sciences, Budapest, Hungary.,Department of Programming Languages and Compilers, Faculty of Informatics, Eötvös Loránd University, Budapest, Hungary
| | - Karolina Schnabel
- MTA-SE Lendület Nephrogenetic Laboratory, Hungarian Academy of Sciences, Budapest, Hungary.,1st Department of Pediatrics, Semmelweis University, Budapest, Hungary
| | - Dániel Seidl
- MTA-SE Lendület Nephrogenetic Laboratory, Hungarian Academy of Sciences, Budapest, Hungary.,1st Department of Pediatrics, Semmelweis University, Budapest, Hungary
| | - Kálmán Tory
- MTA-SE Lendület Nephrogenetic Laboratory, Hungarian Academy of Sciences, Budapest, Hungary.,1st Department of Pediatrics, Semmelweis University, Budapest, Hungary
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24
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Álvarez A, Loor K, Fernández-Alvarez P, Gartner S, Polverino E, Culebras M, Clofent D, García Arumí E, Tizzano EF, de Gracia J. Long-term Follow-up in Adult Patients with Cystic Fibrosis and Deep Intronic Splicing Variants. Arch Bronconeumol 2021; 57:501-503. [PMID: 35698963 DOI: 10.1016/j.arbr.2020.11.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Accepted: 11/02/2020] [Indexed: 06/15/2023]
Affiliation(s)
- Antonio Álvarez
- Department of Respiratory Medicine - Adult Cystic Fibrosis Unit, Vall d'Hebron Barcelona Hospital Campus, Universitat Autònoma de Barcelona, Passeig Vall d'Hebron 119-129, 08035 Barcelona, Spain; CIBER Enfermedades Respiratorias (Ciberes), Passeig Vall d'Hebron 119-129, 08035 Barcelona, Spain; Vall d'Hebron Institut de Recerca (VHIR), Passeig Vall d'Hebron 119-129, 08035 Barcelona, Spain.
| | - Karina Loor
- Department of Respiratory Medicine - Adult Cystic Fibrosis Unit, Vall d'Hebron Barcelona Hospital Campus, Universitat Autònoma de Barcelona, Passeig Vall d'Hebron 119-129, 08035 Barcelona, Spain; CIBER Enfermedades Respiratorias (Ciberes), Passeig Vall d'Hebron 119-129, 08035 Barcelona, Spain; Vall d'Hebron Institut de Recerca (VHIR), Passeig Vall d'Hebron 119-129, 08035 Barcelona, Spain
| | - Paula Fernández-Alvarez
- Department of Clinical and Molecular Genetics, Vall d'Hebron Barcelona Hospital Campus, Universitat Autònoma de Barcelona, Passeig Vall d'Hebron 119-129, 08035 Barcelona, Spain; Vall d'Hebron Institut de Recerca (VHIR), Passeig Vall d'Hebron 119-129, 08035 Barcelona, Spain
| | - Silvia Gartner
- Department of Pediatrics - Pediatric Cystic Fibrosis Unit, Vall d'Hebron Barcelona Hospital Campus, Universitat Autònoma de Barcelona, Passeig Vall d'Hebron 119-129, 08035 Barcelona, Spain; Vall d'Hebron Institut de Recerca (VHIR), Passeig Vall d'Hebron 119-129, 08035 Barcelona, Spain
| | - Eva Polverino
- Department of Respiratory Medicine - Adult Cystic Fibrosis Unit, Vall d'Hebron Barcelona Hospital Campus, Universitat Autònoma de Barcelona, Passeig Vall d'Hebron 119-129, 08035 Barcelona, Spain; CIBER Enfermedades Respiratorias (Ciberes), Passeig Vall d'Hebron 119-129, 08035 Barcelona, Spain; Vall d'Hebron Institut de Recerca (VHIR), Passeig Vall d'Hebron 119-129, 08035 Barcelona, Spain
| | - Mario Culebras
- Department of Respiratory Medicine - Adult Cystic Fibrosis Unit, Vall d'Hebron Barcelona Hospital Campus, Universitat Autònoma de Barcelona, Passeig Vall d'Hebron 119-129, 08035 Barcelona, Spain; CIBER Enfermedades Respiratorias (Ciberes), Passeig Vall d'Hebron 119-129, 08035 Barcelona, Spain; Vall d'Hebron Institut de Recerca (VHIR), Passeig Vall d'Hebron 119-129, 08035 Barcelona, Spain
| | - David Clofent
- Department of Respiratory Medicine - Adult Cystic Fibrosis Unit, Vall d'Hebron Barcelona Hospital Campus, Universitat Autònoma de Barcelona, Passeig Vall d'Hebron 119-129, 08035 Barcelona, Spain; CIBER Enfermedades Respiratorias (Ciberes), Passeig Vall d'Hebron 119-129, 08035 Barcelona, Spain; Vall d'Hebron Institut de Recerca (VHIR), Passeig Vall d'Hebron 119-129, 08035 Barcelona, Spain
| | - Elena García Arumí
- Department of Clinical and Molecular Genetics, Vall d'Hebron Barcelona Hospital Campus, Universitat Autònoma de Barcelona, Passeig Vall d'Hebron 119-129, 08035 Barcelona, Spain; Vall d'Hebron Institut de Recerca (VHIR), Passeig Vall d'Hebron 119-129, 08035 Barcelona, Spain
| | - Eduardo F Tizzano
- Department of Clinical and Molecular Genetics, Vall d'Hebron Barcelona Hospital Campus, Universitat Autònoma de Barcelona, Passeig Vall d'Hebron 119-129, 08035 Barcelona, Spain; Vall d'Hebron Institut de Recerca (VHIR), Passeig Vall d'Hebron 119-129, 08035 Barcelona, Spain
| | - Javier de Gracia
- Department of Respiratory Medicine - Adult Cystic Fibrosis Unit, Vall d'Hebron Barcelona Hospital Campus, Universitat Autònoma de Barcelona, Passeig Vall d'Hebron 119-129, 08035 Barcelona, Spain; CIBER Enfermedades Respiratorias (Ciberes), Passeig Vall d'Hebron 119-129, 08035 Barcelona, Spain; Vall d'Hebron Institut de Recerca (VHIR), Passeig Vall d'Hebron 119-129, 08035 Barcelona, Spain
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25
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Abstract
The discovery in 1989 that cystic fibrosis, the most common life-shortening hereditary disease in Caucasians, was caused by mutations in cystic fibrosis transmembrane conductance regulator (CFTR) gene, put in motion whole new areas of research, diagnosis, and therapeutic development. In this review, we focus on the most important advances in our understanding of the molecular basis of CFTR dysfunction. To date, over 2,000 CFTR mutations belonging to six protein-defect classes have been identified, increasing vastly our understanding of genotype/phenotype correlations. In the last 30 years, major achievements have been made in neonatal screening, antenatal diagnosis, and crucially with recent breakthroughs in the development of CFTR-directed therapies that may be effective for 90% of patients, paving the way for precision medicine.
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Affiliation(s)
- Claude Férec
- Univ Brest, Inserm UMR 1078, Génétique, génomique fonctionnelle et biotechnologies, Établissement français du sang - Bretagne, CHRU Brest, 22 avenue Camille Desmoulins, 29238 Brest Cedex 3 France
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26
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Munck A, Cheillan D, Audrezet MP, Guenet D, Huet F. [Newborn screening for cystic fibrosis in France]. Med Sci (Paris) 2021; 37:491-499. [PMID: 34003095 DOI: 10.1051/medsci/2021051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Neonatal screening for cystic fibrosis has optimised the prognosis for patients allowing very early multidisciplinary care. Over the past 20 years, screening programmes have undergone major international expansion. The performances of the French neonatal cystic fibrosis screening programme, established in 2002, has met European guideline standards, with positive predictive value of 0.31 (against a minimum of 0.30) and sensitivity value of 0.95 (against a minimum of 0.95). It is also important to highlight the very high percentage of sweat tests performed (95.5%), of mutations identified (96.6%), the 9:1 ratio of cystic fibrosis cases to cases of inconclusive diagnosis achieved and the effectiveness of the strategy implemented for the detection of false negative cases. A new organisation for cystic fibrosis neonatal screening has now been established in France. It is vital that effectiveness is maintained throughout the process, from newborn maternity care to diagnosis in cystic fibrosis care centres, and that further knowledge is gained through exhaustive data collection and validation.
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Affiliation(s)
- Anne Munck
- Société française de dépistage néonatal, Paris, France - Centre de ressource et de compétence de la mucoviscidose, Hopital Necker-Enfants malades, AP-HP, 149 rue de Sèvres, 75015 Paris, France
| | - David Cheillan
- Société française de dépistage néonatal, Paris, France - Service biochimie et biologie moléculaire Grand Est, Centre de biologie et de pathologie Est, Groupement hospitalier Est-Hospices civils de Lyon, 59 boulevard Pinel, 69677 Bron Cedex, France - Commission de biologie - Centre national de coordination du dépistage néonatal, Paris, France
| | - Marie-Pierre Audrezet
- Commission de biologie - Centre national de coordination du dépistage néonatal, Paris, France - Service de génétique médicale et biologie de la reproduction, CHRU de Brest, Inserm UMR1078 - Génétique, génomique et biotechnologies, F-29200, Brest, France
| | - David Guenet
- Laboratoire de biologie médicale, Centre régional de dépistage néonatal, Service de biochimie, CHU de Caen Normandie, Caen, France
| | - Frédéric Huet
- Société française de dépistage néonatal, Paris, France - Service de pédiatrie 1 et génétique médicale, 14 rue Paul Gaffarel, BP 77908, 21079 Dijon Cedex, France
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Precone V, Notarangelo A, Marceddu G, D'Agruma L, Cannarella R, Calogero AE, Cristofoli F, Guerri G, Paolacci S, Castori M, Bertelli M. A simultaneous next-generation sequencing approach to the diagnosis of couple infertility. Minerva Endocrinol (Torino) 2021; 47:4-10. [PMID: 33988008 DOI: 10.23736/s2724-6507.21.03477-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
BACKGROUND Infertility is a disorder of the male and/or female reproductive system, characterized by failure to establish a clinical pregnancy after 12 months of regular unprotected sexual intercourse. On a world basis, about one in six couplesare affected by infertility during their reproductive lifespan. Despite a comprehensive diagnostic work-up, infertility in about 50% of couples remains idiopathic. In this context, a next-generation sequencing (NGS) approach has been suggested to increase diagnostic yield. Accordingly, this study aimed to evaluate the effectiveness of a custom-made NGS gene panel for the simultaneous genetic diagnosis of both partners of a large population of infertile couples. METHODS We developed a custom-made NGS panel for 229 genes associated with male and female infertility. The panel targeted exons and their flanking regions and was used to screen 99 couples with idiopathic infertility. RESULTS NGS sequencing revealed five pathogenic variants in six couples and 17 likely pathogenic variants or variants with uncertain significance (VUS). The pathogenic variants were identified in the following genes: GNRHR, CCDC39, DNAH5, and CCDC103; likely pathogenic variants were identified in TAC3, PROKR2, and CFTR; VUS were identified in CATSPER2, FGFR1, LRRC6, DNAH5, DNAH11, TGFBR3, and DNAI1. CONCLUSIONS The panel of genes designed for this study allowed the identification of pathogenetic gene mutations and the presence of VUS in 6.1% and 17.2%, respectively, of couples with idiopathic infertility. This is the first study to successfully apply an NGS-based genetic screening including 229 genes known to play a role in both male and female infertility.
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Affiliation(s)
| | - Angelantonio Notarangelo
- Division of Medical Genetics, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Foggia, Italy
| | | | - Leonardo D'Agruma
- Division of Medical Genetics, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Foggia, Italy
| | - Rossella Cannarella
- Department of Clinical and Experimental Medicine, University of Catania, Catania, Italy
| | - Aldo E Calogero
- Department of Clinical and Experimental Medicine, University of Catania, Catania, Italy
| | | | | | | | - Marco Castori
- Division of Medical Genetics, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Foggia, Italy
| | - Matteo Bertelli
- MAGI Euregio, Bolzano, Italy.,MAGI'S LAB, Rovereto, Trento, Italy
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Mekki C, Aissat A, Mirlesse V, Mayer Lacrosniere S, Eche E, Le Floch A, Whalen S, Prud’Homme C, Remus C, Funalot B, Castaigne V, Fanen P, de Becdelièvre A. Prenatal Ultrasound Suspicion of Cystic Fibrosis in a Multiethnic Population: Is Extensive CFTR Genotyping Needed? Genes (Basel) 2021; 12:genes12050670. [PMID: 33946859 PMCID: PMC8145404 DOI: 10.3390/genes12050670] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 04/27/2021] [Accepted: 04/28/2021] [Indexed: 11/23/2022] Open
Abstract
In families without a Cystic Fibrosis (CF) history, fetal ultrasound bowel abnormalities can unexpectedly reveal the disease. Isolated or in association, the signs can be fetal bowel hyperechogenicity, intestinal loop dilatation and non-visualization of fetal gallbladder. In these cases, search for CF transmembrane conductance regulator (CFTR) gene mutations is part of the recommended diagnostic practices, with a search for frequent mutations according to ethnicity, and, in case of the triad of signs, with an exhaustive study of the gene. However, the molecular diagnosis remains a challenge in populations without well-known frequent pathogenic variants. We present a multiethnic cohort of 108 pregnancies with fetal bowel abnormalities in which the parents benefited from an exhaustive study of the CFTR gene. We describe the new homozygous p.Cys1410* mutation in a fetus of African origin. We did not observe the most frequent p.Phe508del mutation in our cohort but evidenced variants undetected by our frequent mutations kit. Thanks to the progress of sequencing techniques and despite the difficulties of interpretation occasionally encountered, we discuss the need to carry out a comprehensive CFTR study in all patients in case of fetal bowel abnormalities.
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Affiliation(s)
- Chadia Mekki
- Departement de Genetique, DMU Biologie-Pathologie, GH Mondor-Chenevier, AP-HP, F-94010 Creteil, France; (C.M.); (A.A.); (A.L.F.); (B.F.); (P.F.)
| | - Abdel Aissat
- Departement de Genetique, DMU Biologie-Pathologie, GH Mondor-Chenevier, AP-HP, F-94010 Creteil, France; (C.M.); (A.A.); (A.L.F.); (B.F.); (P.F.)
- INSERM, IMRB, Paris Est Creteil University, F-94010 Creteil, France
| | - Véronique Mirlesse
- Service D’echographie Gynecologique et Obstetricale, GH Bichat-C Bernard, AP-HP, F-75018 Paris, France; (V.M.); (E.E.)
- Service Medecine Fœtale, Centre Hospitalo Universitaire de Geneve (HUG), S-1205 Geneve, Switzerland
| | - Sophie Mayer Lacrosniere
- Département de Gastro-Enterologie, Pneumologie, Mucoviscidose et Nutrition Pediatrique, CRCM, Université Paris 7, Hopital Robert Debre, AP-HP, F-75019 Paris, France;
| | - Elsa Eche
- Service D’echographie Gynecologique et Obstetricale, GH Bichat-C Bernard, AP-HP, F-75018 Paris, France; (V.M.); (E.E.)
| | - Annick Le Floch
- Departement de Genetique, DMU Biologie-Pathologie, GH Mondor-Chenevier, AP-HP, F-94010 Creteil, France; (C.M.); (A.A.); (A.L.F.); (B.F.); (P.F.)
| | - Sandra Whalen
- Service de Genetique, Hopital Trousseau, AP-HP, F-75012 Paris, France; (S.W.); (C.P.)
| | - Cecile Prud’Homme
- Service de Genetique, Hopital Trousseau, AP-HP, F-75012 Paris, France; (S.W.); (C.P.)
| | - Christelle Remus
- Service de Genetique, Centre Hospitalier Intercommunal de Creteil, F-94010 Creteil, France;
| | - Benoit Funalot
- Departement de Genetique, DMU Biologie-Pathologie, GH Mondor-Chenevier, AP-HP, F-94010 Creteil, France; (C.M.); (A.A.); (A.L.F.); (B.F.); (P.F.)
- INSERM, IMRB, Paris Est Creteil University, F-94010 Creteil, France
- Service de Genetique, Centre Hospitalier Intercommunal de Creteil, F-94010 Creteil, France;
| | - Vanina Castaigne
- Service d’Obstetrique et Gynecologie, Centre Hospitalier Intercommunal de Creteil, F-94010 Creteil, France;
| | - Pascale Fanen
- Departement de Genetique, DMU Biologie-Pathologie, GH Mondor-Chenevier, AP-HP, F-94010 Creteil, France; (C.M.); (A.A.); (A.L.F.); (B.F.); (P.F.)
- INSERM, IMRB, Paris Est Creteil University, F-94010 Creteil, France
| | - Alix de Becdelièvre
- Departement de Genetique, DMU Biologie-Pathologie, GH Mondor-Chenevier, AP-HP, F-94010 Creteil, France; (C.M.); (A.A.); (A.L.F.); (B.F.); (P.F.)
- INSERM, IMRB, Paris Est Creteil University, F-94010 Creteil, France
- Correspondence:
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Hereditary pancreatitis in childhood: course of disease and complications. Wien Klin Wochenschr 2021; 133:669-673. [PMID: 33909107 DOI: 10.1007/s00508-021-01869-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Accepted: 03/31/2021] [Indexed: 10/21/2022]
Abstract
BACKGROUND Hereditary pancreatitis is rare. Pain therapy for juvenile symptom onset, child development and the risk of pancreatic carcinoma in adulthood must be considered. PATIENTS, MATERIAL AND METHODS Data from a cohort of 11 patients with disease onset in childhood (< 16 years) were analyzed retrospectively. The gene encoding cationic trypsinogen (PRSS1), serine protease inhibitor Kazal type 1 (SPINK1) and cystic fibrosis transmembrane conductance regulator (CFTR) genes were investigated as genetic factors. Treatment concept and complications were registered. Prognosis, treatment success and quality of life were objectified using the chronic pancreatitis prognosis score and a standardized questionnaire (KIDSCREEN-10 index). RESULTS The mean age of symptom onset was 7.5 ±4.2 years. The PRSS1 and SPINK1 mutations each occurred with 36.4%, 3 patients had a pancreas divisum and 2 a long common channel. The course of pancreatitis was obstructive in 90.9%. Exocrine pancreatic insufficiency occurred in seven patients so far (mean age 12.5 years). Stenting was performed in 72.7% and 18.2% needed pancreatic surgery. Currently the chronic prognosis score is on average 7.5 points, pain on numerical rating scale 0 (no pain). The mean KIDSCREEN‑T score of 66.9 confirms a very good quality of life. CONCLUSION Patients with genetically caused chronic pancreatitis are rare. Their care ranges from pain therapy in childhood and adolescence to questions concerning family planning and pancreatic cancer prevention from mid-adulthood onward. The disease is challenging for the interdisciplinary cooperation. We found the step-up strategy to be a good option for pain therapy. A national registry monitored by scientific societies with active recruitment for screening examinations will further improve and ensure care in the long term.
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Bieth E, Nectoux J, Girardet A, Gruchy N, Mittre H, Laurans M, Guenet D, Brouard J, Gerard M. Genetic counseling for cystic fibrosis: A basic model with new challenges. Arch Pediatr 2020; 27 Suppl 1:eS30-eS34. [PMID: 32172934 DOI: 10.1016/s0929-693x(20)30048-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
While the goals of genetic counseling for cystic fibrosis - delivering relevant information on the risk of recurrence and nondirectional support of couples at risk in their reproductive choices - have not changed fundamentally, the practice has evolved considerably in the last decade, growing more complex to face new challenges but also proving more effective. Many factors have contributed to this evolution: technical progress in the exploration of the genome (new generation sequencing) and in reproductive medicine, but also societal developments promoting access to genetic information and the professionalization of genetic counselors in France. The prospect of expanded pre-conception screening of at-risk couples makes genetic counselors major actors not only in medical care centers, but also in modern society by contributing to genetic education among citizens. © 2020 French Society of Pediatrics. Published by Elsevier Masson SAS. All rights reserved.
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Affiliation(s)
- E Bieth
- Génétique Médicale, CHU Toulouse, France.
| | - J Nectoux
- Service de génétique et biologie moléculaires, CHU Paris Centre - Hôpital Cochin, Site Cochin, Paris, France
| | - A Girardet
- Génétique Moléculaire, CHU Montpellier, France
| | - N Gruchy
- Génétique Médicale, CHR Clemenceau, CHU de Caen, Avenue Côte de Nacre, France
| | - H Mittre
- Génétique Médicale, CHR Clemenceau, CHU de Caen, Avenue Côte de Nacre, France
| | - M Laurans
- CRCM, CHU de Caen, Avenue Côte de Nacre, France
| | - D Guenet
- Laboratoire de Biochimie, Dépistage néonatal, CHU de Caen, Avenue Côte de Nacre, France
| | - J Brouard
- Pédiatrie, CHU de Caen, Avenue Côte de Nacre, France
| | - M Gerard
- Génétique Médicale, CHR Clemenceau, CHU de Caen, Avenue Côte de Nacre, France
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Abstract
Because CFTR gene studies now represent one of the most frequent genetic analyses routinely performed worldwide, the number of rare CFTR variants identified in various clinical situations, regularly increases. To provide appropriate diagnosis and prognosis to CF patients as well as appropriate genetic counseling to families, the clinical impact and the phenotypic spectrum of variants identified by diagnostic techniques need to be characterized. Three complementary locus specific databases, called CFTR1, CFTR2 and CFTR-France were developed to address these issues. Besides, the growing knowledge of the CF pathophysiology and the technical evolution in molecular biology allowed to identify candidate modifier genes, regulatory loci, epigenetic profiles and trans-regulators that could help to refine genotype-phenotype correlations at the individual level. These different factors may contribute to the large phenotypic variability between patients with CF, even when they carry identical CFTR variants, regarding lung function, meconium ileus susceptibility or the risk for developing CFTR-related diabetes and liver disease. Finally, the availability of new therapies that target the CFTR protein for numbers of CF patients led to the identification of 'good' and 'poor' responders, thus raising questions of pharmacogenetics factors that may influence treatment efficiency as a novel feature of the complexity of CF patients' management. © 2020 French Society of Pediatrics. Published by Elsevier Masson SAS. All rights reserved.
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32
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Bienvenu T, Nguyen-Khoa T. Current and future diagnosis of cystic fibrosis: Performance and limitations. Arch Pediatr 2020; 27 Suppl 1:eS19-eS24. [PMID: 32172931 DOI: 10.1016/s0929-693x(20)30046-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Cystic fibrosis (CF) is the most frequent genetic disorder in the Caucasian population benefiting from systematic newborn screening tests. It is also the most frequent indication of prenatal and preimplantation genetic diagnosis for a single gene disorder. During the past thirty years, thanks in part to the evolution of diagnostic techniques, our knowledge on CFTR genetics and pathophysiological mechanisms involved in CF have significantly improved. With the implementation of newborn screening in France and in several countries, the diagnosis now often occurs in clinically asymptomatic infants and this has modified the criteria for CF diagnosis. Recently, guidelines for CF diagnosis have been reformulated in Europe and the US, in regard to sweat chloride usual values and disease terminology. This review describes the methods and molecular approaches that are used in routine practice or are being developed to detect CFTR protein dysfunction and to identify disease-causing CFTR variants. Ultimately, an optimal use of all these functional and genetic resources may improve patient care and therapeutic decision-making. © 2020 French Society of Pediatrics. Published by Elsevier Masson SAS. All rights reserved.
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Affiliation(s)
- T Bienvenu
- Laboratoire de Génétique et Biologie Moléculaires, Hôpital Cochin, APHP. Centre Université de Paris, Paris.
| | - T Nguyen-Khoa
- Laboratoires de Biochimie Générale & du Centre Régional du Dépistage Néonatal Ile-de-France, Hôpital Necker-Enfants Malades, APHP. Centre Université de Paris, Paris; Centre de Ressources et de Compétences de la Mucoviscidose, Hôpital Necker-Enfants Malades, AP-HP. Centre Université de Paris, Paris; Institut Necker Enfants Malades/INSERM U1151, Mucoviscidose et autres maladies épithéliales respiratoires par défaut de repliement protéique, Université Paris Descartes, Paris
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33
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Martin N, Bergougnoux A, Baatallah N, Chevalier B, Varilh J, Baux D, Costes B, Fanen P, Raynal C, Sermet-Gaudelus I, Girodon E, Taulan-Cadars M, Hinzpeter A. Exon identity influences splicing induced by exonic variants and in silico prediction efficacy. J Cyst Fibros 2020; 20:464-472. [PMID: 33341408 DOI: 10.1016/j.jcf.2020.12.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Revised: 09/22/2020] [Accepted: 12/03/2020] [Indexed: 01/09/2023]
Abstract
BACKGROUND Minigenes and in silico prediction tools are commonly used to assess the impact on splicing of CFTR variants. Exon skipping is often neglected though it could impact the efficacy of targeted therapies. The aim of the study was to identify exon skipping associated with CFTR variants and to evaluate in silico predictions of seven freely available software. METHODS CFTR basal exon skipping was evaluated on endogenous mRNA extracted from non-CF nasal cells and on two CFTR minigene banks. In silico tools and minigene systems were used to evaluate the impact of CFTR exonic variants on exon skipping. RESULTS Data showed that out of 65 CFTR variants tested, 26 enhanced exon skipping and that in silico prediction efficacy was of 50%-66%. Some in silico tools presented predictions with a bias towards the occurrence of splicing events while others presented a bias towards the absence of splicing events (non-detection including true negatives and false negatives). Classification of exons depending on their basal exon skipping level increased prediction rates up to 80%. CONCLUSION This study indicates that taking basal exon skipping into account could orientate the choice of the in silico tools to improve prediction rates. It also highlights the need to validate effects using in vitro assays or mRNA studies in patients. Eventually, it shows that variant-guided therapy should also target exon skipping associated with variants.
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Affiliation(s)
- Natacha Martin
- INSERM, U955, Institut de Recherche Henri Mondor, IMRB, Créteil, France
| | - Anne Bergougnoux
- CHU de Montpellier, Laboratoire de Génétique Moléculaire, Montpellier, France; Université de Montpellier, Laboratoire de Génétique de Maladies Rares, EA7402 Montpellier, France
| | - Nesrine Baatallah
- INSERM U1151, Institut Necker Enfants Malades, INEM, Paris, France; Université Paris Descartes, Paris, France
| | - Benoit Chevalier
- INSERM U1151, Institut Necker Enfants Malades, INEM, Paris, France; Université Paris Descartes, Paris, France
| | - Jessica Varilh
- Université de Montpellier, Laboratoire de Génétique de Maladies Rares, EA7402 Montpellier, France
| | - David Baux
- CHU de Montpellier, Laboratoire de Génétique Moléculaire, Montpellier, France; Université de Montpellier, Laboratoire de Génétique de Maladies Rares, EA7402 Montpellier, France
| | - Bruno Costes
- INSERM, U955, Institut de Recherche Henri Mondor, IMRB, Créteil, France
| | - Pascale Fanen
- INSERM, U955, Institut de Recherche Henri Mondor, IMRB, Créteil, France; Department of Genetics, GH Henri Mondor, APHP, Créteil, France
| | - Caroline Raynal
- CHU de Montpellier, Laboratoire de Génétique Moléculaire, Montpellier, France; Université de Montpellier, Laboratoire de Génétique de Maladies Rares, EA7402 Montpellier, France
| | - Isabelle Sermet-Gaudelus
- INSERM U1151, Institut Necker Enfants Malades, INEM, Paris, France; Université Paris Descartes, Paris, France
| | - Emmanuelle Girodon
- INSERM U1151, Institut Necker Enfants Malades, INEM, Paris, France; Laboratoire de Génétique et Biologie Moléculaires, Hôpital Cochin, APHP Centre-Université de Paris, Paris, France
| | - Magali Taulan-Cadars
- Université de Montpellier, Laboratoire de Génétique de Maladies Rares, EA7402 Montpellier, France.
| | - Alexandre Hinzpeter
- INSERM U1151, Institut Necker Enfants Malades, INEM, Paris, France; Université Paris Descartes, Paris, France.
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Barben J, Castellani C, Munck A, Davies JC, de Winter-de Groot KM, Gartner S, Kashirskaya N, Linnane B, Mayell SJ, McColley S, Ooi CY, Proesmans M, Ren CL, Salinas D, Sands D, Sermet-Gaudelus I, Sommerburg O, Southern KW. Updated guidance on the management of children with cystic fibrosis transmembrane conductance regulator-related metabolic syndrome/cystic fibrosis screen positive, inconclusive diagnosis (CRMS/CFSPID). J Cyst Fibros 2020; 20:810-819. [PMID: 33257262 DOI: 10.1016/j.jcf.2020.11.006] [Citation(s) in RCA: 63] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Revised: 10/30/2020] [Accepted: 11/07/2020] [Indexed: 02/06/2023]
Abstract
Over the past two decades there has been considerable progress with the evaluation and management of infants with an inconclusive diagnosis following Newborn Screening (NBS) for cystic Fibrosis (CF). In addition, we have an increasing amount of evidence on which to base guidance on the management of these infants and, importantly, we have a consistent designation being used across the globe of CRMS/CFSPID. There is still work to be undertaken and research questions to answer, but these infants now receive more consistent and appropriate care pathways than previously. It is clear that the majority of these infants remain healthy, do not convert to a diagnosis of CF in childhood, and advice on management should reflect this. However, it is also clear that some will convert to a CF diagnosis and monitoring of these infants should facilitate their early recognition. Those infants that do not convert to a CF diagnosis have some potential of developing a CFTR-RD later in life. At present, it is not possible to quantify this risk, but families need to be provided with clear information of what to look out for. This paper contains a number of changes from previous guidance in light of developing evidence, but the major change is the recommendation of a detailed assessment of the child with CRMS/CFSPID in the sixth year of age, including respiratory function assessment and imaging. With these data, the CF team can discuss future care arrangements with the family and come to a shared decision on the best way forward, which may include discharge to primary care with appropriate information. Information is key for these families, and we recommend consideration of a further appointment when the individual is a young adult to directly communicate the implications of the CRMS/CFSPID designation.
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Affiliation(s)
- Jürg Barben
- Paediatric Pulmonology & CF Centre, Children's Hospital of Eastern Switzerland, St. Gallen, Switzerland.
| | - Carlo Castellani
- Istituto Giannina Gaslini, IRCCS Istituto Giannina Gaslini, Genova, Italy
| | - Anne Munck
- CF referent physician for the French Society of Newborn Screening, Hopital Necker Enfants-Malades, AP-HP, CF centre, Université Paris Descartes, France
| | - Jane C Davies
- National Heart & Lung Institute, Imperial College London, UK; Royal Brompton and Harefield NHS Foundation Trust, London, UK
| | - Karin M de Winter-de Groot
- Department of Paediatric Pulmonology & Allergology, Wilhelmina Children's Hospital/University Medical Centre Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Silvia Gartner
- Pediatric Pulmonology and Cystic Fibrosis Unit, Hospital Universitari Vall d´Hebron, Barcelona, Spain
| | - Nataliya Kashirskaya
- Laboratory of genetic epidemiology, Research Centre for Medical Genetics, Moscow, Russian Federation
| | - Barry Linnane
- Graduate Entry Medical School and Centre for Interventions in Infection, Inflammation & Immunity (4i), University of Limerick, Limerick, Ireland
| | - Sarah J Mayell
- Regional Paediatric CF Centre, Alder Hey Children's Hospital, Liverpool, UK
| | - Susanna McColley
- Department of Pediatrics, Northwestern University Feinberg School of Medicine, Stanley Manne Children's Research Institute, Ann and Robert H Lurie Children's Hospital of Chicago, USA
| | - Chee Y Ooi
- Discipline of Paediatrics, School of Women's and Children's Health, Faculty of Medicine, University of New South Wales, Australia; Department of Gastroenterology and Molecular and Integrative Cystic Fibrosis Research Centre, Sydney Children's Hospital, Randwick, NSW, Australia
| | - Marijke Proesmans
- Division of Woman and Child, Department of Pediatrics, University Hospitals Leuven, Leuven, Belgium
| | - Clement L Ren
- Department of Pediatrics, Indiana University School of Medicine, Division of Pediatric Pulmonology, Allergy and Sleep Medicine, Riley Hospital for Children, Indianapolis, USA
| | - Danieli Salinas
- Department of Pediatric Pulmonology, Children's Hospital Los Angeles, Keck School of Medicine, University of Southern California, USA
| | - Dorota Sands
- Cystic Fibrosis Department, Institute of Mother and Child, Warsaw, Poland
| | - Isabelle Sermet-Gaudelus
- Institut Necker Enfants Malades/INSERM U1151, Service de Pneumologie et Allergologie Pédiatriques Centre de Référence Maladies Rares, Mucoviscidose et maladies de CFTR, Hôpital Necker Enfants Malades Paris. Université de Paris. ERN Lung, France
| | - Olaf Sommerburg
- Paediatric Pulmonology, Allergology & CF Centre, Department of Paediatrics III, and Translational Lung Research Center, German Lung Research Center, University Hospital Heidelberg, Germany
| | - Kevin W Southern
- Department of Women's and Children's Health, University of Liverpool, UK
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Álvarez A, Loor K, Fernández-Alvarez P, Gartner S, Polverino E, Culebras M, Clofent D, García Arumí E, Tizzano EF, de Gracia J. Long-term Follow-up in Adult Patients with Cystic Fibrosis and Deep Intronic Splicing Variants. Arch Bronconeumol 2020; 57:S0300-2896(20)30519-6. [PMID: 33358537 DOI: 10.1016/j.arbres.2020.11.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Revised: 10/26/2020] [Accepted: 11/02/2020] [Indexed: 10/22/2022]
Affiliation(s)
- Antonio Álvarez
- Department of Respiratory Medicine - Adult Cystic Fibrosis Unit, Vall d'Hebron Barcelona Hospital Campus, Universitat Autònoma de Barcelona, Passeig Vall d'Hebron 119-129, 08035 Barcelona, Spain; CIBER Enfermedades Respiratorias (Ciberes), Passeig Vall d'Hebron 119-129, 08035 Barcelona, Spain; Vall d'Hebron Institut de Recerca (VHIR), Passeig Vall d'Hebron 119-129, 08035 Barcelona, Spain.
| | - Karina Loor
- Department of Respiratory Medicine - Adult Cystic Fibrosis Unit, Vall d'Hebron Barcelona Hospital Campus, Universitat Autònoma de Barcelona, Passeig Vall d'Hebron 119-129, 08035 Barcelona, Spain; CIBER Enfermedades Respiratorias (Ciberes), Passeig Vall d'Hebron 119-129, 08035 Barcelona, Spain; Vall d'Hebron Institut de Recerca (VHIR), Passeig Vall d'Hebron 119-129, 08035 Barcelona, Spain
| | - Paula Fernández-Alvarez
- Department of Clinical and Molecular Genetics, Vall d'Hebron Barcelona Hospital Campus, Universitat Autònoma de Barcelona, Passeig Vall d'Hebron 119-129, 08035 Barcelona, Spain; Vall d'Hebron Institut de Recerca (VHIR), Passeig Vall d'Hebron 119-129, 08035 Barcelona, Spain
| | - Silvia Gartner
- Department of Pediatrics - Pediatric Cystic Fibrosis Unit, Vall d'Hebron Barcelona Hospital Campus, Universitat Autònoma de Barcelona, Passeig Vall d'Hebron 119-129, 08035 Barcelona, Spain; Vall d'Hebron Institut de Recerca (VHIR), Passeig Vall d'Hebron 119-129, 08035 Barcelona, Spain
| | - Eva Polverino
- Department of Respiratory Medicine - Adult Cystic Fibrosis Unit, Vall d'Hebron Barcelona Hospital Campus, Universitat Autònoma de Barcelona, Passeig Vall d'Hebron 119-129, 08035 Barcelona, Spain; CIBER Enfermedades Respiratorias (Ciberes), Passeig Vall d'Hebron 119-129, 08035 Barcelona, Spain; Vall d'Hebron Institut de Recerca (VHIR), Passeig Vall d'Hebron 119-129, 08035 Barcelona, Spain
| | - Mario Culebras
- Department of Respiratory Medicine - Adult Cystic Fibrosis Unit, Vall d'Hebron Barcelona Hospital Campus, Universitat Autònoma de Barcelona, Passeig Vall d'Hebron 119-129, 08035 Barcelona, Spain; CIBER Enfermedades Respiratorias (Ciberes), Passeig Vall d'Hebron 119-129, 08035 Barcelona, Spain; Vall d'Hebron Institut de Recerca (VHIR), Passeig Vall d'Hebron 119-129, 08035 Barcelona, Spain
| | - David Clofent
- Department of Respiratory Medicine - Adult Cystic Fibrosis Unit, Vall d'Hebron Barcelona Hospital Campus, Universitat Autònoma de Barcelona, Passeig Vall d'Hebron 119-129, 08035 Barcelona, Spain; CIBER Enfermedades Respiratorias (Ciberes), Passeig Vall d'Hebron 119-129, 08035 Barcelona, Spain; Vall d'Hebron Institut de Recerca (VHIR), Passeig Vall d'Hebron 119-129, 08035 Barcelona, Spain
| | - Elena García Arumí
- Department of Clinical and Molecular Genetics, Vall d'Hebron Barcelona Hospital Campus, Universitat Autònoma de Barcelona, Passeig Vall d'Hebron 119-129, 08035 Barcelona, Spain; Vall d'Hebron Institut de Recerca (VHIR), Passeig Vall d'Hebron 119-129, 08035 Barcelona, Spain
| | - Eduardo F Tizzano
- Department of Clinical and Molecular Genetics, Vall d'Hebron Barcelona Hospital Campus, Universitat Autònoma de Barcelona, Passeig Vall d'Hebron 119-129, 08035 Barcelona, Spain; Vall d'Hebron Institut de Recerca (VHIR), Passeig Vall d'Hebron 119-129, 08035 Barcelona, Spain
| | - Javier de Gracia
- Department of Respiratory Medicine - Adult Cystic Fibrosis Unit, Vall d'Hebron Barcelona Hospital Campus, Universitat Autònoma de Barcelona, Passeig Vall d'Hebron 119-129, 08035 Barcelona, Spain; CIBER Enfermedades Respiratorias (Ciberes), Passeig Vall d'Hebron 119-129, 08035 Barcelona, Spain; Vall d'Hebron Institut de Recerca (VHIR), Passeig Vall d'Hebron 119-129, 08035 Barcelona, Spain
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MobiDetails: online DNA variants interpretation. Eur J Hum Genet 2020; 29:356-360. [PMID: 33161418 DOI: 10.1038/s41431-020-00755-z] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 10/22/2020] [Indexed: 11/08/2022] Open
Abstract
MobiDetails is an expert tool, online application which gathers useful data for the interpretation of DNA variants in the context of molecular diagnosis. It brings together in a single tool many sources of data, such as population genetics, various kinds of predictors, Human Genome Variation Society (HGVS) nomenclatures, curated databases, and access to various annotations. Accurate interpretation of DNA variants is crucial and can impact the patient care or have familial outcomes (prenatal diagnosis). Its importance will increase in the coming years with the expansion of the personalized medicine. MobiDetails is specifically designed to help with this task. Exonic or intronic substitutions and small insertions/deletions related to more than 18,000 human genes are easily submitted and annotated in real-time. It is a responsive website that can be accessed using mobiles or tablets during medical staff meetings. MobiDetails is based on publicly available resources, does not include any specific data on patients or phenotypes, and is freely available for academic use at https://mobidetails.iurc.montp.inserm.fr/MD/ .
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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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Laudus N, Audrézet MP, Girodon E, Morris MA, Radojkovic D, Raynal C, Seia M, Štambergová A, Torkler H, Yamamoto R, Dequeker EMC. Laboratory reporting on the clinical spectrum of CFTR p.Arg117His: Still room for improvement. J Cyst Fibros 2020; 19:969-974. [PMID: 32505523 DOI: 10.1016/j.jcf.2020.05.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 05/14/2020] [Accepted: 05/19/2020] [Indexed: 10/24/2022]
Abstract
BACKGROUND The clinical spectrum associated with cystic fibrosis transmembrane conductance regulator (CFTR) variant p.Arg117His is highly variable, ranging from full-blown cystic fibrosis (CF) in a small number of cases to CFTR-related disorders (CFTR-RDs) or no symptoms at all. Therefore, taking into account phenotype variability is essential for interpretation. External quality assessment (EQA) schemes can help laboratories to objectively assess the quality of genotyping and reporting by the laboratory. METHODS We performed a retrospective longitudinal data analysis on laboratory performance regarding the interpretation of p.Arg117His during CF EQA scheme participation. Completeness and accuracy of reporting on two mock clinical cases were each compared over time (case 1: 2005, 2007 and 2012; case 2: 2015 and 2018). These cases concerned subjects compound heterozygous for p.Phe508del and p.Arg117His in cis with 7T, but with different clinical backgrounds (family planning (case 1) versus diagnostic testing for a child (case 2)). Furthermore, we analyzed the influence of previous participations, annual test volume, accreditation status and laboratory setting on overall performance. RESULTS Overall performance improved over time, except during the 2007 CF EQA scheme. In addition, previous participations had a beneficial effect on laboratory performance. Accreditation status, annual test volume and laboratory setting did not significantly influence total interpretation scores. CONCLUSIONS In general, laboratories performed well on both cases, although reporting on the variable clinical spectrum of p.Arg117His in cis with 7T and on the disease liability of individual CFTR variants can still improve. Moreover, this study underlined the educational role of CF EQA schemes.
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Affiliation(s)
- Nele Laudus
- Biomedical Quality Assurance Research Unit, Department of Public Health and Primary Care, University of Leuven, Leuven, Belgium
| | | | - Emmanuelle Girodon
- Laboratoire de Génétique et Biologie Moléculaires, AP-HP.Centre-Université de Paris, Hôpital Cochin, Paris, France
| | | | - Dragica Radojkovic
- Laboratory for Molecular Biology, Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia
| | - Caroline Raynal
- Laboratoire de Génétique Moléculaire, CHU de Montpellier, Montpellier, France
| | - Manuela Seia
- Laboratorio di Genetica Medica - Settore di Genetica Molecolare, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Alexandra Štambergová
- Department of Biology and Medical Genetics, 2nd Faculty of Medicine, Charles University in Prague and Motol University Hospital, Prague, Czech Republic
| | - Heike Torkler
- MVZ Dr. Eberhard & Partner Dortmund, Dortmund, Germany
| | | | - Elisabeth M C Dequeker
- Biomedical Quality Assurance Research Unit, Department of Public Health and Primary Care, University of Leuven, Leuven, Belgium; Department of Medical Diagnostics, University Hospitals Leuven, Leuven, Belgium.
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Bienvenu T, Lopez M, Girodon E. Molecular Diagnosis and Genetic Counseling of Cystic Fibrosis and Related Disorders: New Challenges. Genes (Basel) 2020; 11:E619. [PMID: 32512765 PMCID: PMC7349214 DOI: 10.3390/genes11060619] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2020] [Revised: 05/28/2020] [Accepted: 06/02/2020] [Indexed: 11/16/2022] Open
Abstract
Identification of the cystic fibrosis transmembrane conductance regulator (CFTR) gene and its numerous variants opened the way to fantastic breakthroughs in diagnosis, research and treatment of cystic fibrosis (CF). The current and future challenges of molecular diagnosis of CF and CFTR-related disorders and of genetic counseling are here reviewed. Technological advances have enabled to make a diagnosis of CF with a sensitivity of 99% by using next generation sequencing in a single step. The detection of heretofore unidentified variants and ethnic-specific variants remains challenging, especially for newborn screening (NBS), CF carrier testing and genotype-guided therapy. Among the criteria for assessing the impact of variants, population genetics data are insufficiently taken into account and the penetrance of CF associated with CFTR variants remains poorly known. The huge diversity of diagnostic and genetic counseling indications for CFTR studies makes assessment of variant disease-liability critical. This is especially discussed in the perspective of wide genome analyses for NBS and CF carrier screening in the general population, as future challenges.
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Affiliation(s)
| | | | - Emmanuelle Girodon
- Molecular Genetics Laboratory, Cochin Hospital, APHP.Centre–Université de Paris, 75014 Paris, France; (T.B.); (M.L.)
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Boussaroque A, Audrézet MP, Raynal C, Sermet-Gaudelus I, Bienvenu T, Férec C, Bergougnoux A, Lopez M, Scotet V, Munck A, Girodon E. Penetrance is a critical parameter for assessing the disease liability of CFTR variants. J Cyst Fibros 2020; 19:949-954. [PMID: 32327388 DOI: 10.1016/j.jcf.2020.03.019] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Revised: 03/23/2020] [Accepted: 03/26/2020] [Indexed: 12/19/2022]
Abstract
BACKGROUND Major issues of newborn screening (NBS) for CF are the assessment of disease liability of variants and of the penetrance of clinical CF, notably in inconclusive diagnosis. The penetrance of CF is defined as the risk of a particular genotype to lead to a CF phenotype. METHODS We aimed to get insight into the penetrance of CF for fifteen CFTR variants: 5 frequent CF-causing and 10 classified as of varying clinical consequence (VCC) or associated with a CFTR-related disorder (CFTR-RD) in CFTR2 or CFTR-France databases. The penetrance was approached by: (1) comparison of variant allelic frequencies in CF patients (CFTR2) and in the general population; (2) estimation of the likelihood of a positive NBS test for the 14 compound heterozygous with F508del and the F508del homozygous genotypes, defined as the ratio of detected/expected number of neonates with a given genotype in the 2002-2017 period. RESULTS A full penetrance was observed for severe CF-causing variants. Five variants were more frequently found in the general population than in CF patients: TG11T5, TG12T5, TG13T5, L997F and R117H;T7. The likelihood of a positive NBS test was 0.03% for TG11T5, 0.3% for TG12T5, 1.9% for TG13T5, 0.6% for L997F, 11.7% for D1152H, and 17.8% for R117H;T7. Penetrance varied greatly for variants with discrepant classification between CFTR2 and CFTR-France: 5.1% for R117C, 12.3% for T338I, 43.5% for D110H and 52.6% for L206W. CONCLUSION These results illustrate the contribution of genetics population data to assess the disease liability of variants for diagnosis and genetic counselling purposes.
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Affiliation(s)
- A Boussaroque
- APHP.Centre-Université de Paris, Cochin Hospital, Molecular Genetics Laboratory, Paris, France
| | - M-P Audrézet
- Molecular Genetics Laboratory - CHRU Brest, Brest, France; Inserm UMR 1078, GGB, F-29200 Brest, France
| | - C Raynal
- Molecular Genetics Laboratory - CHU Montpellier, EA7402 Université de Montpellier, Montpellier, France
| | - I Sermet-Gaudelus
- APHP.Centre Université de Paris, Necker Enfants Malades Hospital, Cystic Fibrosis Center, Paris, France and INSERM U 1151, Paris, France
| | - T Bienvenu
- APHP.Centre-Université de Paris, Cochin Hospital, Molecular Genetics Laboratory, Paris, France
| | - C Férec
- Molecular Genetics Laboratory - CHRU Brest, Brest, France; Inserm UMR 1078, GGB, F-29200 Brest, France
| | - A Bergougnoux
- Molecular Genetics Laboratory - CHU Montpellier, EA7402 Université de Montpellier, Montpellier, France
| | - M Lopez
- APHP.Centre-Université de Paris, Cochin Hospital, Molecular Genetics Laboratory, Paris, France
| | - V Scotet
- Inserm UMR 1078, GGB, F-29200 Brest, France
| | - A Munck
- APHP.Centre Université de Paris, Necker Enfants Malades Hospital, Cystic Fibrosis Center, Paris, France and INSERM U 1151, Paris, France; Société francaise de dépistage néonatal
| | - E Girodon
- APHP.Centre-Université de Paris, Cochin Hospital, Molecular Genetics Laboratory, Paris, France.
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Girodon E, Fajac I. Preface. Arch Pediatr 2020; 27 Suppl 1:eS2-eS3. [PMID: 32172932 DOI: 10.1016/s0929-693x(20)30042-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Affiliation(s)
- E Girodon
- APHP, Centre-Université de Paris, Hôpital Cochin, Laboratoire de Génétique et Biologie Moléculaires, Paris, France.
| | - I Fajac
- AP-HP, Hôpital Cochin, Service de Physiologie et Explorations Fonctionnelles, Paris, France; Université Paris Descartes, Sorbonne Paris Cité, Paris, France
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Bergougnoux A, Lopez M, Girodon E. The Role of Extended CFTR Gene Sequencing in Newborn Screening for Cystic Fibrosis. Int J Neonatal Screen 2020; 6:23. [PMID: 33073020 PMCID: PMC7422980 DOI: 10.3390/ijns6010023] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Accepted: 03/19/2020] [Indexed: 01/25/2023] Open
Abstract
There has been considerable progress in the implementation of newborn screening (NBS) programs for cystic fibrosis (CF), with DNA analysis being part of an increasing number of strategies. Thanks to advances in genomic sequencing technologies, CFTR-extended genetic analysis (EGA) by sequencing its coding regions has become affordable and has already been included as part of a limited number of core NBS programs, to the benefit of admixed populations. Based on results analysis of existing programs, the values and challenges of EGA are reviewed in the perspective of its implementation on a larger scale. Sensitivity would be increased at best by using EGA as a second tier, but this could be at the expense of positive predictive value, which improves, however, if EGA is applied after testing a variant panel. The increased detection of babies with an inconclusive diagnosis has proved to be a major drawback in programs using EGA. The lack of knowledge on pathogenicity and penetrance associated with numerous variants hinders the introduction of EGA as a second tier, but EGA with filtering for all known CF variants with full penetrance could be a solution. The issue of incomplete knowledge is a real challenge in terms of the implemention of NBS extended to many genetic diseases.
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Affiliation(s)
- Anne Bergougnoux
- Molecular Genetics Laboratory, CHU Montpellier, EA7402 University of Montpellier, 34093 Montpellier CEDEX 5, France;
| | - Maureen Lopez
- Molecular Genetics Laboratory, Cochin Hospital, APHP. Centre, University of Paris, 75014 Paris, France;
| | - Emmanuelle Girodon
- Molecular Genetics Laboratory, Cochin Hospital, APHP. Centre, University of Paris, 75014 Paris, France;
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Bieth E, Hamdi SM, Mieusset R. Genetics of the congenital absence of the vas deferens. Hum Genet 2020; 140:59-76. [PMID: 32025909 PMCID: PMC7864840 DOI: 10.1007/s00439-020-02122-w] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 01/28/2020] [Indexed: 01/19/2023]
Abstract
Congenital absence of the vas deferens (CAVD) may have various clinical presentations depending on whether it is bilateral (CBAVD) or unilateral (CUAVD), complete or partial, and associated or not with other abnormalities of the male urogenital tract. CBAVD is usually discovered in adult men either during the systematic assessment of cystic fibrosis or other CFTR-related conditions, or during the exploration of isolated infertility with obstructive azoospermia. The prevalence of CAVDs in men is reported to be approximately 0.1%. However, this figure is probably underestimated, because unilateral forms of CAVD in asymptomatic fertile men are not usually diagnosed. The diagnosis of CAVDs is based on clinical, ultrasound, and sperm examinations. The majority of subjects with CAVD carry at least one cystic fibrosis-causing mutation that warrants CFTR testing and in case of a positive result, genetic counseling prior to conception. Approximately 2% of the cases of CAVD are hemizygous for a loss-of-function mutation in the ADGRG2 gene that may cause a familial form of X-linked infertility. However, despite this recent finding, 10–20% of CBAVDs and 60–70% of CUAVDs remain without a genetic diagnosis. An important proportion of these unexplained CAVDs coexist with a solitary kidney suggesting an early organogenesis disorder (Wolffian duct), unlike CAVDs related to CFTR or ADGRG2 mutations, which might be the result of progressive degeneration that begins later in fetal life and probably continues after birth. How the dysfunction of CFTR, ADGRG2, or other genes such as SLC29A3 leads to this involution is the subject of various pathophysiological hypotheses that are discussed in this review.
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Affiliation(s)
- Eric Bieth
- Service de Génétique Médicale, Hôpital Purpan, CHU, 31059, Toulouse, France.
| | - Safouane M Hamdi
- Service de Biochimie, Institut Fédératif de Biologie, CHU, 31059, Toulouse, France.,EA3694 (Groupe de Recherche en Fertilité Humaine), Université Toulouse III, 31059, Toulouse, France
| | - Roger Mieusset
- EA3694 (Groupe de Recherche en Fertilité Humaine), Université Toulouse III, 31059, Toulouse, France.,Département d'Andrologie (Groupe Activité Médecine de la Reproduction), CHU, 31059, Toulouse, France
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Castellani C. Conclusion and Prospects: Genetics of cystic fibrosis – an agenda for the next ten years. Arch Pediatr 2020; 27 Suppl 1:eS45-eS47. [DOI: 10.1016/s0929-693x(20)30051-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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45
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Han ST, Cutting GR. Molecular Genetics of Cystic Fibrosis. Respir Med 2020. [DOI: 10.1007/978-3-030-42382-7_23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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Pagin A, Bergougnoux A, Girodon E, Reboul MP, Willoquaux C, Kesteloot M, Raynal C, Bienvenu T, Humbert M, Lalau G, Bieth E. Novel ADGRG2 truncating variants in patients with X-linked congenital absence of vas deferens. Andrology 2019; 8:618-624. [PMID: 31845523 DOI: 10.1111/andr.12744] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Revised: 12/10/2019] [Accepted: 12/11/2019] [Indexed: 11/30/2022]
Abstract
BACKGROUND Congenital absence of vas deferens (CAVD) represents a major cause of obstructive azoospermia and is mainly related to biallelic alteration of the CFTR gene, also involved in cystic fibrosis. Using whole exome sequencing, we recently identified hemizygous loss-of-function mutations in the Adhesion G Protein-coupled Receptor G2 gene (ADGRG2) as responsible of isolated CAVD in the absence of associated unilateral renal agenesis. OBJECTIVES The objective of this study was to retrospectively perform ADGRG2 sequencing on a large cohort of patients with CAVD, and 0 or only 1 CFTR defective allele identified after comprehensive testing in order to (a) define more precisely the spectrum and the frequency of ADGRG2 mutations within Caucasian population (b) explore the possibility of co-occurrence of CFTR and ADGRG2 mutations. MATERIALS AND METHODS We collected 53 DNA samples from CAVD patients with 0 (n = 23) or 1 (n = 30) alteration identified after comprehensive CFTR testing in order to perform ADGRG2 sequencing. Twenty patients had normal ultrasonographic renal examination, and renal status was not documented for 33 patients. RESULTS We identified six new truncating ADGRG2 mutations in 8 patients including two twin brothers: c.251C > G (p.Ser84*), c.1013delC (p.Pro338Hisfs*4), c.1460delG (p.Gly487Alafs*9), c.2096dupT (p.Phe700Ilefs*29), c.2473C > T (p.Arg825*), and c.1731_1839 + 373del (p.Asn578Thrfs*12), which is a 596 base pair deletion affecting the last five bases of exon 21 and the whole exon 22. Five of the eight patients also harbored an heterozygous CFTR mutation which we consider as incidental regarding the high penetrance expected for ADGRG2 truncating variants. The frequency of ADGRG2 truncating mutation was 26% (5/19 unrelated patients) when presence of both kidneys was attested by ultrasonography and 6.1% (2/33) among patients with unknown renal status. DISCUSSION & CONCLUSION Our results confirm the interest of ADGRG2 sequencing in patients with CAVD not formerly related to CFTR dysfunction, especially in the absence of associated unilateral renal agenesis.
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Affiliation(s)
- Adrien Pagin
- CHU Lille, Service de Toxicologie et Génopathies, Lille, France
| | - Anne Bergougnoux
- Laboratoire de Génétique Moléculaire, Centre Hospitalier Universitaire de Montpellier, EA7402 Laboratoire de Génétique de Maladies Rares, Université de Montpellier, Montpellier, France
| | - Emmanuelle Girodon
- Service de Génétique et Biologie Moléculaires, AP-HP.5, Groupe Hospitalier HUPC, Paris, France
| | - Marie-Pierre Reboul
- Service de Génétique Médicale, Centre Hospitalier Régional Universitaire, Bordeaux, France
| | | | | | - Caroline Raynal
- Laboratoire de Génétique Moléculaire, Centre Hospitalier Universitaire de Montpellier, EA7402 Laboratoire de Génétique de Maladies Rares, Université de Montpellier, Montpellier, France
| | - Thierry Bienvenu
- Service de Génétique et Biologie Moléculaires, AP-HP.5, Groupe Hospitalier HUPC, Paris, France
| | - Mathilde Humbert
- Service de Biologie de la Reproduction, Centre Hospitalier Régional Universitaire, Bordeaux, France
| | - Guy Lalau
- CHU Lille, Service de Toxicologie et Génopathies, Lille, France
| | - Eric Bieth
- Service de Génétique Médicale, Centre Hospitalier Universitaire, Toulouse, France
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Sharma N, Cutting GR. The genetics and genomics of cystic fibrosis. J Cyst Fibros 2019; 19 Suppl 1:S5-S9. [PMID: 31879237 DOI: 10.1016/j.jcf.2019.11.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Revised: 11/06/2019] [Accepted: 11/08/2019] [Indexed: 02/07/2023]
Abstract
Genetics is the branch of biology concerned with study of individual genes and how they work whereas genomics is involved with the analysis of all genes and their interactions. Both of these approaches have been applied extensively to CF. Identification of the CFTR gene initiated the dissection of CF genetics at the molecular level. Subsequently, thousands of variants were found in the gene and the functional consequences of a subset have been studied in detail. The completion of the human genome ushered in a new phase of study where the role of genes beyond CFTR could be evaluated for their contribution to the severity of CF. This will be a brief overview of the contribution of these complementary methods to our understanding of CF pathogenesis.
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Affiliation(s)
- N Sharma
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, United States of America
| | - G R Cutting
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, United States of America.
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Sasorith S, Baux D, Bergougnoux A, Paulet D, Lahure A, Bareil C, Taulan-Cadars M, Roux AF, Koenig M, Claustres M, Raynal C. The CYSMA web server: An example of integrative tool for in silico analysis of missense variants identified in Mendelian disorders. Hum Mutat 2019; 41:375-386. [PMID: 31674704 DOI: 10.1002/humu.23941] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Revised: 10/02/2019] [Accepted: 10/30/2019] [Indexed: 12/17/2022]
Abstract
Exome sequencing used for molecular diagnosis of Mendelian disorders considerably increases the number of missense variants of unclear significance, whose pathogenicity can be assessed by a variety of prediction tools. As the performance of algorithms may vary according to the datasets, complementary specific resources are needed to improve variant interpretation. As a model, we were interested in the cystic fibrosis transmembrane conductance regulator gene (CFTR) causing cystic fibrosis, in which at least 40% of missense variants are reported. Cystic fibrosis missense analysis (CYSMA) is a new web server designed for online estimation of the pathological relevance of CFTR missense variants. CYSMA generates a set of computationally derived data, ranging from evolutionary conservation to functional observations from three-dimensional structures, provides all available allelic frequencies, clinical observations, and references for functional studies. Compared to software classically used in analysis pipelines on a dataset of 141 well-characterized missense variants, CYSMA was the most efficient tool to discriminate benign missense variants, with a specificity of 85%, and very good sensitivity of 89%. These results suggest that such integrative tools could be adapted to numbers of genes involved in Mendelian disorders to improve the interpretation of missense variants identified in the context of diagnosis.
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Affiliation(s)
- Souphatta Sasorith
- Laboratoire de Génétique Moléculaire, CHU de Montpellier, Montpellier, France.,EA 7402, Université de Montpellier, Montpellier, France
| | - David Baux
- Laboratoire de Génétique Moléculaire, CHU de Montpellier, Montpellier, France.,EA 7402, Université de Montpellier, Montpellier, France
| | - Anne Bergougnoux
- Laboratoire de Génétique Moléculaire, CHU de Montpellier, Montpellier, France.,EA 7402, Université de Montpellier, Montpellier, France
| | - Damien Paulet
- EA 7402, Université de Montpellier, Montpellier, France
| | - Alan Lahure
- EA 7402, Université de Montpellier, Montpellier, France
| | - Corinne Bareil
- Laboratoire de Génétique Moléculaire, CHU de Montpellier, Montpellier, France.,EA 7402, Université de Montpellier, Montpellier, France
| | | | - Anne-Françoise Roux
- Laboratoire de Génétique Moléculaire, CHU de Montpellier, Montpellier, France.,EA 7402, Université de Montpellier, Montpellier, France
| | - Michel Koenig
- Laboratoire de Génétique Moléculaire, CHU de Montpellier, Montpellier, France.,EA 7402, Université de Montpellier, Montpellier, France
| | | | - Caroline Raynal
- Laboratoire de Génétique Moléculaire, CHU de Montpellier, Montpellier, France.,EA 7402, Université de Montpellier, Montpellier, France
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49
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Boussaroque A, Bergougnoux A, Raynal C, Audrézet M, Sasorith S, Férec C, Bienvenu T, Girodon E. Pitfalls in the interpretation of
CFTR
variants in the context of incidental findings. Hum Mutat 2019; 40:2239-2246. [DOI: 10.1002/humu.23884] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Revised: 07/24/2019] [Accepted: 07/24/2019] [Indexed: 12/29/2022]
Affiliation(s)
- Agathe Boussaroque
- Laboratoire de Génétique et Biologie Moléculaires, AP‐HP, Hôpital CochinHUPC Paris France
| | - Anne Bergougnoux
- Laboratoire de Génétique MoléculaireCHU de Montpellier Montpellier France
| | - Caroline Raynal
- Laboratoire de Génétique MoléculaireCHU de Montpellier Montpellier France
| | | | - Souphatta Sasorith
- Laboratoire de Génétique MoléculaireCHU de Montpellier Montpellier France
| | - Claude Férec
- Laboratoire de Génétique MoléculaireCHU de Brest Brest France
| | - Thierry Bienvenu
- Laboratoire de Génétique et Biologie Moléculaires, AP‐HP, Hôpital CochinHUPC Paris France
| | - Emmanuelle Girodon
- Laboratoire de Génétique et Biologie Moléculaires, AP‐HP, Hôpital CochinHUPC Paris France
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50
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Raynal C, Girodon E, Audrezet M, Cabet F, Pagin A, Reboul M, Dufernez F, Fergelot P, Bergougnoux A, Fanen P, Ferec C, Bienvenu T. CFTR
gene variants: a predisposition factor to aquagenic palmoplantar keratoderma. Br J Dermatol 2019; 181:1097-1099. [DOI: 10.1111/bjd.18162] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- C. Raynal
- Laboratoire de Génétique Moléculaire IURC CHU Montpellier Montpellier France
| | - E. Girodon
- Laboratoire de Génétique et Biologie Moléculaires APHP.5, HUPC, Hôpital Cochin Paris France
| | | | - F. Cabet
- Laboratoire de Génétique Moléculaire Hospices civils de Lyon France
| | - A. Pagin
- Service de Toxicologie et Génopathies Institut de Biochimie et Biologie Moléculaire CHRU Lille Lille France
| | - M.P. Reboul
- Service de Génétique Médicale CHU de Bordeaux Bordeaux France
| | - F. Dufernez
- Laboratoire de Génétique Biologique CHU Poitiers Poitiers France
| | - P. Fergelot
- Service de Génétique Médicale CHU de Bordeaux Bordeaux France
| | - A. Bergougnoux
- Laboratoire de Génétique Moléculaire IURC CHU Montpellier Montpellier France
| | - P. Fanen
- Laboratoire de Génétique Moléculaire Hôpital Henri‐Mondor Créteil France
| | - C. Ferec
- Centre de Biogénétique Brest France
| | - T. Bienvenu
- Laboratoire de Génétique et Biologie Moléculaires APHP.5, HUPC, Hôpital Cochin Paris France
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