1
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Anwar S, Peng JL, Zahid KR, Zhou YM, Ali Q, Qiu CR. Cystic Fibrosis: Understanding Cystic Fibrosis Transmembrane Regulator Mutation Classification and Modulator Therapies. Adv Respir Med 2024; 92:263-277. [PMID: 39051188 PMCID: PMC11270331 DOI: 10.3390/arm92040026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2024] [Revised: 07/16/2024] [Accepted: 07/17/2024] [Indexed: 07/27/2024]
Abstract
A common life-threatening hereditary disease, Cystic Fibrosis (CF), affects primarily Caucasian infants. High sweat-salt levels are observed as a result of a single autosomal mutation in chromosome 7 that affects the critical function of the cystic fibrosis transmembrane regulator (CFTR). For establishing tailored treatment strategies, it is important to understand the broad range of CFTR mutations and their impacts on disease pathophysiology. This study thoroughly investigates the six main classes of classification of CFTR mutations based on their functional effects. Each class is distinguished by distinct molecular flaws, such as poor protein synthesis, misfolding, gating defects, conduction defects, and decreased CFTR expression at the apical membrane. Furthermore, this paper focuses on the emerging field of CFTR modulators, which intend to restore CFTR function or mitigate its consequences. These modulators, which are characterized by the mode of action and targeted mutation class, have the potential to provide personalized therapy regimens in CF patients. This review provides valuable insights into the genetic basis of CF pathology, and highlights the potential for precision medicine methods in CF therapy by thoroughly investigating CFTR mutation classification and related modulators.
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Affiliation(s)
- Saba Anwar
- Centre for Applied Molecular Biology, University of the Punjab Lahore, Lahore 53700, Pakistan;
| | - Jin-Liang Peng
- Department of Emergency, The Affiliated Ganzhou Hospital of Nanchang University, Ganzhou 341000, China; (J.-L.P.); (Y.-M.Z.)
| | - Kashif Rafiq Zahid
- Department of Radiation Oncology, Melvin and Bren Simon Comprehensive Cancer Center, Indiana University School of Medicine, Indianaapolis, IN 46202, USA;
| | - Yu-Ming Zhou
- Department of Emergency, The Affiliated Ganzhou Hospital of Nanchang University, Ganzhou 341000, China; (J.-L.P.); (Y.-M.Z.)
| | - Qurban Ali
- Department of Plant Breeding and Genetics, Faculty of Agricultural Sciences, University of the Punjab, Lahore 54590, Pakistan
| | - Chong-Rong Qiu
- Department of Emergency, The Affiliated Ganzhou Hospital of Nanchang University, Ganzhou 341000, China; (J.-L.P.); (Y.-M.Z.)
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2
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Kaluzna-Mlynarczyk A, Pucher B, Sroczynski J, Kotowski M, Jonczyk-Potoczna K, Szydlowski J. The development of paranasal sinuses in patients with cystic fibrosis: sinuses volume analysis. Eur Arch Otorhinolaryngol 2024; 281:795-803. [PMID: 37882847 PMCID: PMC10796702 DOI: 10.1007/s00405-023-08236-x] [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: 08/05/2023] [Accepted: 09/08/2023] [Indexed: 10/27/2023]
Abstract
BACKGROUND Cystic fibrosis (CF) is a severe systemic disease that affects many aspects of patients' lives. It is known that the progression of the disease adversely affects lower and upper airways including the paranasal sinuses. However, its impact on sinus development in the pediatric population is not fully examined. The purpose of this study was to evaluate the development of the paranasal sinuses in a pediatric population with CF and compare it to a control group consisting of healthy children. METHODS The results of computed tomography (CT) scans of children with the disease and the control group were evaluated. The study included 114 CT images of children in the study group and 126 images of healthy children aged 0-18 years. The volumes of maxillary, frontal, and sphenoid sinuses were analyzed. The obtained results were compared with those of the control group and analyzed statistically. RESULTS The volume and the development of the paranasal sinuses in both groups increased with age, but statistically significant differences were found between the study and the control group. CONCLUSIONS The obtained results provide valuable knowledge regarding the impact of the CF on sinuses development. Also, they may be important in understanding the progression of the disease and its influence on the quality and length of life of patients. The results may contribute to enhanced diagnostics and have implications for improving therapy for patients with chronic sinusitis associated with CF.
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Affiliation(s)
- Agata Kaluzna-Mlynarczyk
- Department of Pediatric Otolaryngology, Institute of Pediatrics, Poznan University of Medical Sciences, Szpitalna 27/33, 60-572, Poznań, Poland.
- Doctoral School, Poznan University of Medical Sciences, Bukowska 70, 60-812, Poznań, Poland.
| | - Beata Pucher
- Department of Pediatric Otolaryngology, Institute of Pediatrics, Poznan University of Medical Sciences, Szpitalna 27/33, 60-572, Poznań, Poland
| | - Jakub Sroczynski
- Department of Pediatric Otolaryngology, Institute of Pediatrics, Poznan University of Medical Sciences, Szpitalna 27/33, 60-572, Poznań, Poland
| | - Michal Kotowski
- Department of Pediatric Otolaryngology, Institute of Pediatrics, Poznan University of Medical Sciences, Szpitalna 27/33, 60-572, Poznań, Poland
| | - Katarzyna Jonczyk-Potoczna
- Department of Pediatric Radiology, Institute of Pediatrics, Poznan University of Medical Sciences, Szpitalna 27/33, 60-572, Poznań, Poland
| | - Jarosław Szydlowski
- Department of Pediatric Otolaryngology, Institute of Pediatrics, Poznan University of Medical Sciences, Szpitalna 27/33, 60-572, Poznań, Poland
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3
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Hartzler AL, Bartlett LE, Hobler MR, Reid N, Pryor JB, Kapnadak SG, Berry DL, Lober WB, Goss CH, Ramos KJ. Take on transplant: human-centered design of a patient education tool to facilitate informed discussions about lung transplant among people with cystic fibrosis. J Am Med Inform Assoc 2022; 30:26-37. [PMID: 36173364 PMCID: PMC9748576 DOI: 10.1093/jamia/ocac176] [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: 04/01/2022] [Revised: 09/10/2022] [Accepted: 09/23/2022] [Indexed: 12/15/2022] Open
Abstract
OBJECTIVE Lung transplant (LTx) saves lives in cystic fibrosis (CF). However, many potential candidates express uncertainty about LTx and die before receiving this treatment. CF guidelines recommend LTx education and clinical discussions well before the need for LTx arises, but limited patient resources exist. MATERIALS AND METHODS We engaged people with CF and CF physicians in human-centered design of "Take On Transplant" (TOT), a web-based education tool to prepare patients for LTx discussions. Across 3 phases, needs assessment, design groups, and iterative user testing of TOT, we refined TOT from wireframe prototypes, to an interactive website, to a fully functional intervention ready for clinical trials. RESULTS Fifty-five people with CF and 105 physicians identified information needs to prepare for LTx discussions. Design groups (n = 14 participants) then established core requirements: didactic education ("Resource Library"), patient narratives ("CF Stories"), frequently asked questions ("FAQ"), and self-assessment to tailor content ("My CF Stage"). Iterative usability testing (n = 39) optimized the design of CF Stories and prototype layout. We then developed the TOT website and demonstrated feasibility and preliminary efficacy of use through 2-week field testing (n = 9). DISCUSSION Our human-centered design process provided guidance for educational tools to serve the evolving needs of potential LTx candidates. Our findings support the process of patient deliberation as a foundation for shared decision-making in CF, and inform educational tools that could potentially translate beyond LTx. CONCLUSION TOT fills a critical gap in preparing people with CF for shared decision-making about LTx and may serve as a model for educational tools for other preference-sensitive decisions.
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Affiliation(s)
- Andrea L Hartzler
- Department of Biomedical Informatics and Medical Education, School of Medicine, University of Washington, Seattle, Washington, USA
| | - Lauren E Bartlett
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine, School of Medicine, University of Washington, Seattle, Washington, USA
| | - Mara R Hobler
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine, School of Medicine, University of Washington, Seattle, Washington, USA
| | - Nick Reid
- Department of Biomedical Informatics and Medical Education, School of Medicine, University of Washington, Seattle, Washington, USA
| | - Joseph B Pryor
- Department of General Internal Medicine, School of Medicine, University of Washington, Seattle, Washington, USA
| | - Siddhartha G Kapnadak
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine, School of Medicine, University of Washington, Seattle, Washington, USA
| | - Donna L Berry
- Biobehavioral Nursing and Health Informatics, School of Nursing, University of Washington, Seattle, Washington, USA
| | - William B Lober
- Department of Biomedical Informatics and Medical Education, School of Medicine, University of Washington, Seattle, Washington, USA
- Biobehavioral Nursing and Health Informatics, School of Nursing, University of Washington, Seattle, Washington, USA
| | - Christopher H Goss
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine, School of Medicine, University of Washington, Seattle, Washington, USA
| | - Kathleen J Ramos
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine, School of Medicine, University of Washington, Seattle, Washington, USA
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4
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Guidelines for Cystic Fibrosis Carrier Screening in the Prenatal/Preconception Period. Obstet Gynecol Surv 2022; 77:606-610. [DOI: 10.1097/ogx.0000000000001062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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5
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Boardman F, Clark C. 'We're kind of like genetic nomads': Parents' experiences of biographical disruption and uncertainty following in/conclusive results from newborn cystic fibrosis screening. Soc Sci Med 2022; 301:114972. [PMID: 35430463 DOI: 10.1016/j.socscimed.2022.114972] [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: 09/30/2021] [Revised: 03/02/2022] [Accepted: 04/08/2022] [Indexed: 11/26/2022]
Abstract
As whole genome sequencing is being considered as a tool to deliver expanded newborn screening (NBS) globally, the range of equivocal results it could produce are gaining increased attention. For cystic fibrosis (CF) screening, the use of next generation sequencing within existing UK NBS programmes would increase the number of uncertain designations returned within results, including that of Cystic Fibrosis Screen Positive Inconclusive Diagnosis (CFSPID). However, the experiences of families already living with this designation have been under-explored. This study uses in-depth interviews to explore the perspectives of sixteen parents who received positive results from CF NBS, with varying degrees of prognostic un/certainty; parents with a child diagnosed with CF (n = 6), CF carrier status (n = 3) and those with the CFSPID designation (n = 7). The biographically disruptive nature of positive NBS results-regardless of immediate relevance to the child-dominated early experiences of positive results across all groups. For those with CF, biographical reparation involved becoming 'a CF family', underscoring biological kinship bonds and reinforcing familial identity. For those with uncertain results, biographical re-calibration was more complex. Diagnostic and prognostic uncertainty posed a barrier to entry for both the 'CF world' and the 'healthy kid' world, leading parents to attempt to minimise its role, either through rejection, or re-interpretation of their child's result. Other parents, however, experienced biographical reparation more dynamically. The concept of 'genetic nomadism' captures accounts of oscillation between the two worlds; movements that were responsive to evolving health experiences, as well as social, environmental and temporal factors. Through the concept of genetic nomadism, this paper delineates both the productive, as well as divisive, nature of uncertainty for biographical reparation in the aftermath of NBS, as well as the strategies parents use to harness it, in order to successfully navigate the world with a child with an ambiguous genetic future.
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Affiliation(s)
- Felicity Boardman
- Warwick Medical School, Gibbet Hill Road, Coventry, CV4 7AL, United Kingdom.
| | - Corinna Clark
- Warwick Medical School, Gibbet Hill Road, Coventry, CV4 7AL, United Kingdom
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6
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Shaughnessy CA, Zeitlin PL, Bratcher PE. Net benefit of ivacaftor during prolonged tezacaftor/elexacaftor exposure in vitro. J Cyst Fibros 2022; 21:637-643. [DOI: 10.1016/j.jcf.2022.02.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 01/05/2022] [Accepted: 02/16/2022] [Indexed: 11/17/2022]
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7
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Morel D. Special Needs Insurance: More Stability for a Growing Family's Budget. J Insur Med 2021; 49:1-31. [PMID: 34788842 DOI: 10.17849/insm-49-s1-1-31.1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Accepted: 10/21/2020] [Indexed: 11/20/2022]
Abstract
OBJECTIVE.— To propose an insurance product called special needs insurance. The insurance will pay parents a lump sum up to $100,000 if they have a child that is born with or develops a special needs condition such as Down syndrome, cerebral palsy or autism. BACKGROUND.— Raising a child is expensive; raising a child with a special need can be hundreds of thousands of dollars more expensive. These additional costs include direct costs that are not covered by health insurance and indirect costs such as the loss of earnings when a working parent must tend to a special needs child. METHOD.— We analyze a gamut of birth and early childhood disabilities, both physical and cognitive, from the medico-actuarial perspective. We describe each condition using relevant medical literature and calculate prevalence rates from epidemiological studies (appendix A1-A15). After accounting for multiple births, we develop a final premium. RESULTS.— We find that physical impairments are sufficiently well understood to guarantee a fixed payout, whereas cognitive impairments such as autism are less understood, and so for these we propose a cognitive fund that does not guarantee a fixed payout. We find that an average single premium of $4,600 allows the insurer to profitably pay out the proposed benefits. CONCLUSIONS.— Raising a special needs child can put a significant strain on the affected family's budget. We propose an insurance product that provides relief through a large lump sum payout. Although no new insurance product can be guaranteed success, our analysis of this product gives an interested insurer reasonable justification to take on this new risk.
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8
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Two Siblings Homozygous for F508del-CFTR Have Varied Disease Phenotypes and Protein Biomarkers. Int J Mol Sci 2021; 22:ijms22052631. [PMID: 33807880 PMCID: PMC7961721 DOI: 10.3390/ijms22052631] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Revised: 02/20/2021] [Accepted: 03/01/2021] [Indexed: 12/01/2022] Open
Abstract
Two siblings with CF are homozygous for F508del (referred to as Subject A and Subject B). Despite having the same CFTR genotype and similar environment, these two subjects exhibited different disease phenotypes. We analyzed their medical records and CF Foundation Registry data and measured inflammatory protein mediators in their sputum samples. Then, we examined the longitudinal relationships between inflammatory markers and disease severity for each subject and compared between them. Subject A presented a more severe disease than Subject B. During the study period, Subject A had two pulmonary exacerbations (PEs) whereas Subject B had one mild PE. The forced expiratory volume in 1 s (FEV1, % predicted) values for Subject A were between 34–45% whereas for Subject B varied between 48–90%. Inflammatory protein mediators associated with neutrophils, Th1, Th2, and Th17 responses were elevated in sputum of Subject A compared with Subject B, and also in samples collected prior to and during PEs for both subjects. Neutrophilic elastase (NE) seemed to be the most informative biomarkers. The infectious burden between these two subjects was different.
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9
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Abstract
Cystic fibrosis (CF) is a rare autosomal-recessive disorder manifested as multisystem organ dysfunction. The cystic fibrosis transmembrane conductance regulator (CFTR) protein functions as an ion transporter on the epithelium of exocrine glands, regulating secretion viscosity. The CFTR gene, encoded on chromosome 7, is required for the production and trafficking of the intact and functional CFTR protein. Literally thousands of human CFTR allelic mutations have been identified, each with varying impact on protein quality and quantity. As a result, individuals harboring CFTR mutations present with a spectrum of symptoms ranging from CF to normal phenotypes. Those with loss of function but without full CF may present with CFTR-related disorders (CFTR-RDs) including male infertility, sinusitis, pancreatitis, atypical asthma and bronchitis. Studies have demonstrated associations between higher rates of CFTR mutations and oligospermia, epididymal obstruction, congenital bilateral absence of the vas deferens (CBAVD), and idiopathic ejaculatory duct obstruction (EDO). Genetic variants are detected in over three-quarters of men with CBAVD, the reproductive abnormality most classically associated with CFTR aberrations. Likewise, nearly all men with clinical CF will have CBAVD. Current guidelines from multiple groups recommend CFTR screening in all men with clinical CF or CBAVD though a consensus on the minimum number of variants for which to test is lacking. CFTR testing is not recommended as routine screening for men with other categories of infertility. While available CFTR panels include 30 to 96 of the most common variants, complete gene sequencing should be considered if there is a high index of suspicion in a high-risk couple (e.g., partner is CFTR mutation carrier). CF treatments to date have largely targeted end-organ complications. Novel CFTR-modulator treatments aim to directly target CFTR protein dysfunction, effectively circumventing downstream complications, and possibly preventing symptoms like vasal atresia at a young age. Future gene therapies may also hold promise in preventing or reversing genetic changes that lead to CF and CFTR-RD.
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Affiliation(s)
- Jared M Bieniek
- Tallwood Urology & Kidney Institute, Hartford HealthCare, Hartford, CT, USA
| | - Craig D Lapin
- Division of Pediatric Pulmonology, Connecticut Children's Medical Center, Hartford, CT, USA.,Department of Pediatrics, University of Connecticut, Farmington, CT, USA
| | - Keith A Jarvi
- Division of Urology, Department of Surgery, Mount Sinai Hospital and Institute of Medical Sciences, University of Toronto, Toronto, ON, Canada
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10
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Pelzman DL, Hwang K. Genetic testing for men with infertility: techniques and indications. Transl Androl Urol 2021; 10:1354-1364. [PMID: 33850771 PMCID: PMC8039607 DOI: 10.21037/tau-19-725] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Genetic testing is an integral component in the workup of male infertility as genetic conditions may be responsible for up to 15% of all cases. Currently, three genetic tests are commonly performed and recommended by major urologic associations: karyotype analysis (KA), Y-chromosome microdeletion testing, and CFTR mutation testing. Despite widespread adoption of these tests, an etiology for infertility remains elusive in up to 80% of cases. Recent work has identified intriguing new targets for genetic testing which may soon see clinical relevance. This review will discuss the indications and techniques for currently offered genetic tests and briefly explore ongoing research directions within this field.
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Affiliation(s)
- Daniel L Pelzman
- Department of Urology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Kathleen Hwang
- Department of Urology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
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11
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F1099L-CFTR (c.3297C>G) has Impaired Channel Function and Associates with Mild Disease Phenotypes in Two Pediatric Patients. Life (Basel) 2021; 11:life11020131. [PMID: 33567498 PMCID: PMC7915716 DOI: 10.3390/life11020131] [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: 12/24/2020] [Revised: 02/03/2021] [Accepted: 02/05/2021] [Indexed: 11/18/2022] Open
Abstract
(1) Background: many rare cystic fibrosistransmembrane conductance regulator (CFTR) mutations remain poorly characterized with regard to functional consequences of the mutation. We present the clinical features of two pediatric cystic fibrosis (CF) subjects who are heterozygous for F1099L (c.3297C>G), one with G551D (a class III mutation) and one with 3849 + 10kbC->T (a class V mutation). We also identified the molecular defect(s) that are associated with F1099L mutation to correlate with the clinical features that we observed; (2) Methods: clinical findings and history were extracted from the electronic medical record and de-identified. F1099L-CFTR protein expression level and maturation status, channel function, and the effects of CFTR modulation on these characteristics were investigated using western blotting and iodide efflux assay; (3) Results: these two subjects have mild CF phenotypes when F1099L is combined with two known disease-causing mutations. F1099L-CFTR has a moderate defect in processing and maturation, causing fewer CFTR channels at the cell surface and, therefore, impaired channel activities. These defects could be effectively corrected using VX-809 (lumacaftor); and, (4) Conclusions: our biochemical data correlate with the disease manifestations and suggest that F1099L is potentially a CF-causing mutation. The study expands our knowledge of rare CFTR mutations and may help in developing effective therapies for subjects with F1099L mutation.
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12
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Abstract
Cystic fibrosis (CF) is one of the most commonly diagnosed genetic disorders. Clinical characteristics include progressive obstructive lung disease, sinusitis, exocrine pancreatic insufficiency leading to malabsorption and malnutrition, liver and pancreatic dysfunction, and male infertility. Although CF is a life-shortening disease, survival has continued to improve to a median age of 46.2 years due to earlier diagnosis through routine newborn screening, promulgation of evidence-based guidelines to optimize nutritional and pulmonary health, and the development of CF-specific interdisciplinary care centers. Future improvements in health and quality of life for individuals with CF are likely with the recent development of mutation-specific modulator therapies. In this review, we will cover the current understanding of the disease manifestations, diagnosis, and management as well as common complications seen in individuals with CF.
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Affiliation(s)
- Kimberly M. Dickinson
- Johns Hopkins University, School of Medicine, Eudowood Division of Pediatric Respiratory Sciences, Baltimore, MD
| | - Joseph M. Collaco
- Johns Hopkins University, School of Medicine, Eudowood Division of Pediatric Respiratory Sciences, Baltimore, MD
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13
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A chaotic viewpoint-based approach to solve haplotype assembly using hypergraph model. PLoS One 2020; 15:e0241291. [PMID: 33120403 PMCID: PMC7595403 DOI: 10.1371/journal.pone.0241291] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2020] [Accepted: 10/12/2020] [Indexed: 12/30/2022] Open
Abstract
Decreasing the cost of high-throughput DNA sequencing technologies, provides a huge amount of data that enables researchers to determine haplotypes for diploid and polyploid organisms. Although various methods have been developed to reconstruct haplotypes in diploid form, their accuracy is still a challenging task. Also, most of the current methods cannot be applied to polyploid form. In this paper, an iterative method is proposed, which employs hypergraph to reconstruct haplotype. The proposed method by utilizing chaotic viewpoint can enhance the obtained haplotypes. For this purpose, a haplotype set was randomly generated as an initial estimate, and its consistency with the input fragments was described by constructing a weighted hypergraph. Partitioning the hypergraph specifies those positions in the haplotype set that need to be corrected. This procedure is repeated until no further improvement could be achieved. Each element of the finalized haplotype set is mapped to a line by chaos game representation, and a coordinate series is defined based on the position of mapped points. Then, some positions with low qualities can be assessed by applying a local projection. Experimental results on both simulated and real datasets demonstrate that this method outperforms most other approaches, and is promising to perform the haplotype assembly.
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14
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McCravy MS, Quinney NL, Cholon DM, Boyles SE, Jensen TJ, Aleksandrov AA, Donaldson SH, Noone PG, Gentzsch M. Personalised medicine for non-classic cystic fibrosis resulting from rare CFTR mutations. Eur Respir J 2020; 56:13993003.00062-2020. [PMID: 32265312 DOI: 10.1183/13993003.00062-2020] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2020] [Accepted: 03/16/2020] [Indexed: 01/04/2023]
Affiliation(s)
- Matthew S McCravy
- Dept of Medicine, University of North Carolina, Chapel Hill, NC, USA
| | - Nancy L Quinney
- Marsico Lung Institute/Cystic Fibrosis Research Center, University of North Carolina, Chapel Hill, NC, USA
| | - Deborah M Cholon
- Marsico Lung Institute/Cystic Fibrosis Research Center, University of North Carolina, Chapel Hill, NC, USA
| | - Susan E Boyles
- Marsico Lung Institute/Cystic Fibrosis Research Center, University of North Carolina, Chapel Hill, NC, USA
| | - Timothy J Jensen
- Marsico Lung Institute/Cystic Fibrosis Research Center, University of North Carolina, Chapel Hill, NC, USA
| | - Andrei A Aleksandrov
- Marsico Lung Institute/Cystic Fibrosis Research Center, University of North Carolina, Chapel Hill, NC, USA.,Dept of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC, USA
| | - Scott H Donaldson
- Dept of Medicine, University of North Carolina, Chapel Hill, NC, USA.,Division of Pulmonary Diseases and Critical Care Medicine, University of North Carolina, Chapel Hill, NC, USA
| | - Peadar G Noone
- Dept of Medicine, University of North Carolina, Chapel Hill, NC, USA.,Division of Pulmonary Diseases and Critical Care Medicine, University of North Carolina, Chapel Hill, NC, USA.,M. Gentzsch and P.G. Noone contributed equally to this article as lead authors and supervised the work
| | - Martina Gentzsch
- Marsico Lung Institute/Cystic Fibrosis Research Center, University of North Carolina, Chapel Hill, NC, USA .,Dept of Cell Biology and Physiology, University of North Carolina, Chapel Hill, NC, USA.,M. Gentzsch and P.G. Noone contributed equally to this article as lead authors and supervised the work
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15
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Characterization of Ancestral Origin of Cystic Fibrosis of Patients with New Reported Mutations in CFTR. BIOMED RESEARCH INTERNATIONAL 2020; 2020:9074760. [PMID: 32596391 PMCID: PMC7288203 DOI: 10.1155/2020/9074760] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Accepted: 05/06/2020] [Indexed: 11/17/2022]
Abstract
The incidence of cystic fibrosis (CF) and the frequency of the variants reported for CFTR depend on the population; furthermore, CF symptomatology is characterized by obstructive lung disease and pancreatic insufficiency among other symptoms, which are reliant on the individual's genotype. The Ecuadorian population is a mixture of Native Americans, Europeans, and Africans. That population admixture could be the reason for the new mutations reported in a previous study by Ruiz et al. (2019). A panel of 46 Ancestry Informative Markers was used to estimate the ancestral proportions of each available sample (12 samples in total). As a result, the Native American ancestry proportion was the most prevalent in almost all individuals, except for three patients from Guayaquil with the mutation [c.757G>A:p.Gly253Arg; c.1352G>T:p.Gly451Val] who had the highest European composition.
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16
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Al-Qahtani W, Abdel Jabar M, Masood A, Jacob M, Nizami I, Dasouki M, Abdel Rahman AM. Dried Blood Spot-Based Metabolomic Profiling in Adults with Cystic Fibrosis. J Proteome Res 2020; 19:2346-2357. [PMID: 32312052 DOI: 10.1021/acs.jproteome.0c00031] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Mucoviscidosis of the respiratory, gastrointestinal, and genitourinary tracts is the major pathology in patients with cystic fibrosis (CF), a lethal monogenic panethnic and multisystemic disease most commonly identified in Caucasians. Currently, the measurement of immuno reactive trypsinogen in dry blood spots (DBSs) is the gold-standard method for initial newborn screening for CF, followed by targeted CF transmembrane regulator (CFTR) mutation analysis, and ultimate confirmation with abnormally elevated sweat chloride. Previous metabolomics studies in patients with CF reported on different biomarkers such as breath 2-aminoacetophenone produced during acute and chronic infection in human tissues, including the lungs of CF patients. Herein, we used liquid and gas chromatography-mass spectrometry-based targeted metabolomics profiling to identify potentially reliable, sensitive, and specific biomarkers in DBSs collected from 69 young and adult people including CF patients (n = 39) and healthy control (n = 30). A distinctive metabolic profile including 26 significantly differentially expressed metabolites involving amino acids, glycolysis, mitochondrial and peroxisomal metabolism, and sorbitol pathways was identified. Specifically, the osmolyte (sorbitol) was remarkably downregulated in CF patients compared to healthy controls indicating perturbation in the sorbitol pathway, which may be responsible for the mucoviscidosis seen in patients with CF. The significance of our findings is supported by the clinical utility of inhaled mannitol and hypertonic saline in patients with CF. The systemic administration of sorbitol in such patients may confer additional benefits beyond the respiratory system, especially in those with misfolded CFTR proteins.
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Affiliation(s)
- Wafa Al-Qahtani
- Department of Genetics, King Faisal Specialist Hospital and Research Centre (KFSHRC), Zahrawi Street, Al Maather, Riyadh 11211, Saudi Arabia.,Department of Biochemistry and Molecular Medicine, College of Medicine, Al Faisal University, Riyadh 11533, Saudi Arabia
| | - Mai Abdel Jabar
- Department of Genetics, King Faisal Specialist Hospital and Research Centre (KFSHRC), Zahrawi Street, Al Maather, Riyadh 11211, Saudi Arabia
| | - Afshan Masood
- Proteomics Resource Unit, Obesity Research Center, College of Medicine, King Saud University, P.O. Box 2925 (98), Riyadh 11461, Saudi Arabia
| | - Minnie Jacob
- Department of Genetics, King Faisal Specialist Hospital and Research Centre (KFSHRC), Zahrawi Street, Al Maather, Riyadh 11211, Saudi Arabia
| | - Imran Nizami
- Lung Transplant Section, Organ Transplant Center, King Faisal Specialist Hospital and Research Center, Zahrawi Street, Al Maather, Riyadh 11211, Saudi Arabia
| | - Majed Dasouki
- Department of Genetics, King Faisal Specialist Hospital and Research Centre (KFSHRC), Zahrawi Street, Al Maather, Riyadh 11211, Saudi Arabia
| | - Anas M Abdel Rahman
- Department of Genetics, King Faisal Specialist Hospital and Research Centre (KFSHRC), Zahrawi Street, Al Maather, Riyadh 11211, Saudi Arabia.,Department of Biochemistry and Molecular Medicine, College of Medicine, Al Faisal University, Riyadh 11533, Saudi Arabia.,Department of Chemistry, Memorial University of Newfoundland, St. John's, Newfoundland A1B 3X7, Canada
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17
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Januska MN, Marx L, Walker PA, Berdella MN, Langfelder-Schwind E. The CFTR variant profile of Hispanic patients with cystic fibrosis: Impact on access to effective screening, diagnosis, and personalized medicine. J Genet Couns 2020; 29:607-615. [PMID: 32227567 DOI: 10.1002/jgc4.1271] [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: 12/04/2019] [Revised: 02/25/2020] [Accepted: 02/26/2020] [Indexed: 11/11/2022]
Abstract
Hispanic patients comprise an appreciable and increasing proportion of patients with cystic fibrosis (CF) in the United States (US). Hispanic patients with CF are known to have increased morbidity and mortality compared to non-Hispanic white patients with CF, and ongoing investigations are underway to identify contributing factors amenable to intervention in order to address the disparate health outcomes. One contributing factor is the different CF transmembrane conductance regulator (CFTR) variant profile observed in Hispanic patients with CF. The most common CFTR variant, p.Phe508del (legacy name F508del), is proportionally underrepresented in Hispanic patients with CF. This difference has implications for prenatal screening, newborn screening (NBS), and CFTR variant-specific therapeutic options. In particular, the recent approval of a highly effective CFTR modulator for patients carrying at least one copy of F508del, elexacaftor/tezacaftor/ivacaftor triple combination therapy, underscores the potential for unequal access to personalized treatment for Hispanic patients with CF. We report the CFTR variant profiles of Hispanic patients with CF and non-CF Hispanic infants with a false-positive New York State CF NBS at a single center in New York City over a 5-year study period, as an opportunity to address the racial and ethnic disparities that currently exist in CF screening, diagnosis, and treatment. In addition to the previously documented disparate prevalence of the CFTR variant F508del in Hispanic patients, we observed two CFTR variants, p.His609Arg (legacy name H609R) and p.Thr1036Asn (legacy name T1036N), frequently identified in our Hispanic patients of Ecuadorian and Mexican ancestry, respectively, that are not well-described in the US population. The presence of population-specific and individually rare CFTR variants in Hispanic patients with CF further accentuates the disparity in health outcomes, as these CFTR variants are often absent from prenatal and NBS CFTR variant panels, potentially delaying diagnosis, and without an approved CFTR variant-specific therapy.
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Affiliation(s)
- Megan N Januska
- Department of Pulmonary, Critical Care, and Sleep Medicine, The Cystic Fibrosis Center at Mount Sinai Beth Israel, New York City, New York.,Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York City, New York
| | - Laura Marx
- Department of Pulmonary, Critical Care, and Sleep Medicine, The Cystic Fibrosis Center at Mount Sinai Beth Israel, New York City, New York.,Department of Pediatrics, Genetics and Metabolic Clinic, St. Luke's Children's Hospital, Boise, Idaho
| | - Patricia A Walker
- Department of Pulmonary, Critical Care, and Sleep Medicine, The Cystic Fibrosis Center at Mount Sinai Beth Israel, New York City, New York
| | - Maria N Berdella
- Department of Pulmonary, Critical Care, and Sleep Medicine, The Cystic Fibrosis Center at Mount Sinai Beth Israel, New York City, New York.,Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York City, New York
| | - Elinor Langfelder-Schwind
- Department of Pulmonary, Critical Care, and Sleep Medicine, The Cystic Fibrosis Center at Mount Sinai Beth Israel, New York City, New York
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18
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Neri M, Rossi R, Trabanelli C, Mauro A, Selvatici R, Falzarano MS, Spedicato N, Margutti A, Rimessi P, Fortunato F, Fabris M, Gualandi F, Comi G, Tedeschi S, Seia M, Fiorillo C, Traverso M, Bruno C, Giardina E, Piemontese MR, Merla G, Cau M, Marica M, Scuderi C, Borgione E, Tessa A, Astrea G, Santorelli FM, Merlini L, Mora M, Bernasconi P, Gibertini S, Sansone V, Mongini T, Berardinelli A, Pini A, Liguori R, Filosto M, Messina S, Vita G, Toscano A, Vita G, Pane M, Servidei S, Pegoraro E, Bello L, Travaglini L, Bertini E, D'Amico A, Ergoli M, Politano L, Torella A, Nigro V, Mercuri E, Ferlini A. The Genetic Landscape of Dystrophin Mutations in Italy: A Nationwide Study. Front Genet 2020; 11:131. [PMID: 32194622 PMCID: PMC7063120 DOI: 10.3389/fgene.2020.00131] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Accepted: 02/03/2020] [Indexed: 12/11/2022] Open
Abstract
Dystrophinopathies are inherited diseases caused by mutations in the dystrophin (DMD) gene for which testing is mandatory for genetic diagnosis, reproductive choices and eligibility for personalized trials. We genotyped the DMD gene in our Italian cohort of 1902 patients (BMD n = 740, 39%; DMD n =1162, 61%) within a nationwide study involving 11 diagnostic centers in a 10-year window (2008–2017). In DMD patients, we found deletions in 57%, duplications in 11% and small mutations in 32%. In BMD, we found deletions in 78%, duplications in 9% and small mutations in 13%. In BMD, there are a higher number of deletions, and small mutations are more frequent than duplications. Among small mutations that are generally frequent in both phenotypes, 44% of DMD and 36% of BMD are nonsense, thus, eligible for stop codon read-through therapy; 63% of all out-of-frame deletions are eligible for single exon skipping. Patients were also assigned to Italian regions and showed interesting regional differences in mutation distribution. The full genetic characterization in this large, nationwide cohort has allowed us to draw several correlations between DMD/BMD genotype landscapes and mutation frequency, mutation types, mutation locations along the gene, exon/intron architecture, and relevant protein domain, with effects on population genetic characteristics and new personalized therapies.
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Affiliation(s)
- Marcella Neri
- Unit of Medical Genetics, Department of Medical Sciences, University of Ferrara, Ferrara, Italy
| | - Rachele Rossi
- Unit of Medical Genetics, Department of Medical Sciences, University of Ferrara, Ferrara, Italy
| | - Cecilia Trabanelli
- Unit of Medical Genetics, Department of Medical Sciences, University of Ferrara, Ferrara, Italy
| | - Antonio Mauro
- Unit of Medical Genetics, Department of Medical Sciences, University of Ferrara, Ferrara, Italy
| | - Rita Selvatici
- Unit of Medical Genetics, Department of Medical Sciences, University of Ferrara, Ferrara, Italy
| | - Maria Sofia Falzarano
- Unit of Medical Genetics, Department of Medical Sciences, University of Ferrara, Ferrara, Italy
| | - Noemi Spedicato
- Unit of Medical Genetics, Department of Medical Sciences, University of Ferrara, Ferrara, Italy
| | - Alice Margutti
- Unit of Medical Genetics, Department of Medical Sciences, University of Ferrara, Ferrara, Italy
| | - Paola Rimessi
- Unit of Medical Genetics, Department of Medical Sciences, University of Ferrara, Ferrara, Italy
| | - Fernanda Fortunato
- Unit of Medical Genetics, Department of Medical Sciences, University of Ferrara, Ferrara, Italy
| | - Marina Fabris
- Unit of Medical Genetics, Department of Medical Sciences, University of Ferrara, Ferrara, Italy
| | - Francesca Gualandi
- Unit of Medical Genetics, Department of Medical Sciences, University of Ferrara, Ferrara, Italy
| | - Giacomo Comi
- Neuroscience Section, Department of Pathophysiology and Transplantation, Dino Ferrari Center, University of Milan, Milan, Italy
| | - Silvana Tedeschi
- Laboratory of Medical Genetics, IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Manuela Seia
- Laboratory of Medical Genetics, IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Chiara Fiorillo
- Paediatric Neurology and Muscular Diseases Unit, University of Genoa and G. Gaslini Institute, Genoa, Italy
| | - Monica Traverso
- Paediatric Neurology and Muscular Diseases Unit, University of Genoa and G. Gaslini Institute, Genoa, Italy
| | - Claudio Bruno
- Center of Translational and Experimental Myology, IRCCS Gaslini, Genova, Italy
| | - Emiliano Giardina
- Molecular Genetics Laboratory UILDM, Santa Lucia Foundation, Rome, Italy
| | | | - Giuseppe Merla
- Division of Medical Genetics, IRCCS Casa Sollievo della Sofferenza, Foggia, Italy
| | - Milena Cau
- Laboratory of Genetics and Genomics, Department of Medical Science and Public Health, University of Cagliari, Cagliari, Italy
| | - Monica Marica
- Clinica Pediatrica e Malattie Rare, Brotzu, Cagliari, Italy
| | - Carmela Scuderi
- Unit of Neuromuscular Diseases, Oasi Research Institute-IRCCS, Troina, Italy
| | - Eugenia Borgione
- Unit of Neuromuscular Diseases, Oasi Research Institute-IRCCS, Troina, Italy
| | - Alessandra Tessa
- Department of Molecular Medicine, IRCCS Fondazione Stella Maris, Pisa, Italy
| | - Guia Astrea
- Department of Molecular Medicine, IRCCS Fondazione Stella Maris, Pisa, Italy
| | | | - Luciano Merlini
- Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna, Italy
| | - Marina Mora
- Neuromuscular Diseases and Neuroimmunology Unit, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Pia Bernasconi
- Neuromuscular Diseases and Neuroimmunology Unit, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Sara Gibertini
- Neuromuscular Diseases and Neuroimmunology Unit, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Valeria Sansone
- Neurorehabilitation Unit, Department Biomedical Sciences for Health, University of Milan, Milan, Italy
| | - Tiziana Mongini
- Neuromuscular Center, AOU Città della Salute e della Scienza, University of Turin, Turin, Italy
| | - Angela Berardinelli
- Child Neurology and Psychiatry Unit, "Casimiro Mondino" Foundation, Pavia, Italy
| | - Antonella Pini
- Child Neurology Unit, IRCCS Istituto delle Scienze Neurologiche, Bologna, Italy
| | - Rocco Liguori
- Department of Biomedical and Neuro Motor Sciences, University of Bologna, Bologna, Italy
| | - Massimiliano Filosto
- Laboratory of Medical Genetics, IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Sonia Messina
- Department of Clinical and Experimental Medicine, University of Messina and Nemo Sud Clinical Center, Messina, Italy
| | - Gianluca Vita
- Department of Clinical and Experimental Medicine, University of Messina and Nemo Sud Clinical Center, Messina, Italy
| | - Antonio Toscano
- Department of Clinical and Experimental Medicine, University of Messina and Nemo Sud Clinical Center, Messina, Italy
| | - Giuseppe Vita
- Department of Clinical and Experimental Medicine, University of Messina and Nemo Sud Clinical Center, Messina, Italy
| | - Marika Pane
- Centro Clinico Nemo, Policlinico A. Gemelli, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | - Serenella Servidei
- UOC Neurofisiopatologia, Fondazione Policlinico Universitario A. Gemelli IRCCS, Institute of Neurology, Catholic University of Sacred Heart, Rome, Italy
| | - Elena Pegoraro
- Department of Neurosciences, University of Padua, Padua, Italy
| | - Luca Bello
- Department of Neurosciences, University of Padua, Padua, Italy
| | - Lorena Travaglini
- Unit of Neuromuscular and Neurodegenerative Disorders, Department of Neurosciences, Bambino Gesu Children's Research Hospital IRCCS, Rome, Italy
| | - Enrico Bertini
- Unit of Neuromuscular and Neurodegenerative Disorders, Department of Neurosciences, Bambino Gesu Children's Research Hospital IRCCS, Rome, Italy
| | - Adele D'Amico
- Unit of Neuromuscular and Neurodegenerative Disorders, Department of Neurosciences, Bambino Gesu Children's Research Hospital IRCCS, Rome, Italy
| | - Manuela Ergoli
- Cardiomiology and Medical Genetics, University of Campania "Luigi Vanvitelli, Naples, Italy
| | - Luisa Politano
- Cardiomiology and Medical Genetics, University of Campania "Luigi Vanvitelli, Naples, Italy
| | - Annalaura Torella
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli, Naples, Italy
| | - Vincenzo Nigro
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli, Naples, Italy
| | - Eugenio Mercuri
- Centro Clinico Nemo, Policlinico A. Gemelli, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy.,Pediatric Neurology, Catholic University, Rome, Italy
| | - Alessandra Ferlini
- Unit of Medical Genetics, Department of Medical Sciences, University of Ferrara, Ferrara, Italy.,Dubowitz Neuromuscular Unit, Institute of Child Health, University College London, London, United Kingdom
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19
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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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20
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Holt MR, Kasperbauer SH, Koelsch TL, Daley CL. Similar characteristics of nontuberculous mycobacterial pulmonary disease in men and women. Eur Respir J 2019; 54:13993003.00252-2019. [PMID: 30956208 DOI: 10.1183/13993003.00252-2019] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Accepted: 03/24/2019] [Indexed: 11/05/2022]
Affiliation(s)
- Michael R Holt
- Division of Mycobacterial and Respiratory Infections, Dept of Medicine, National Jewish Health, Denver, CO, USA .,Dept of Medicine, University of Colorado Denver, Aurora, CO, USA
| | - Shannon H Kasperbauer
- Division of Mycobacterial and Respiratory Infections, Dept of Medicine, National Jewish Health, Denver, CO, USA.,Dept of Medicine, University of Colorado Denver, Aurora, CO, USA
| | | | - Charles L Daley
- Division of Mycobacterial and Respiratory Infections, Dept of Medicine, National Jewish Health, Denver, CO, USA.,Dept of Medicine, University of Colorado Denver, Aurora, CO, USA
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21
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Abstract
Risk of disease is multifactorial and can be shaped by socio-economic, demographic, cultural, environmental and genetic factors. Our understanding of the genetic determinants of disease risk has greatly advanced with the advent of genome-wide association studies (GWAS), which detect associations between genetic variants and complex traits or diseases by comparing populations of cases and controls. However, much of this discovery has occurred through GWAS of individuals of European ancestry, with limited representation of other populations, including from Africa, The Americas, Asia and Oceania. Population demography, genetic drift and adaptation to environments over thousands of years have led globally to the diversification of populations. This global genomic diversity can provide new opportunities for discovery and translation into therapies, as well as a better understanding of population disease risk. Large-scale multi-ethnic and representative biobanks and population health resources provide unprecedented opportunities to understand the genetic determinants of disease on a global scale.
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22
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Bezzerri V, Piacenza F, Caporelli N, Malavolta M, Provinciali M, Cipolli M. Is cellular senescence involved in cystic fibrosis? Respir Res 2019; 20:32. [PMID: 30764828 PMCID: PMC6376730 DOI: 10.1186/s12931-019-0993-2] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Accepted: 01/31/2019] [Indexed: 02/06/2023] Open
Abstract
Pulmonary disease is the main cause of the morbidity and mortality of patients affected by cystic fibrosis (CF). The lung pathology is dominated by excessive recruitment of neutrophils followed by an exaggerated inflammatory process that has also been reported to occur in the absence of apparent pathogenic infections. Airway surface dehydration and mucus accumulation are the driving forces of this process. The continuous release of reactive oxygen species and proteases by neutrophils contributes to tissue damage, which eventually leads to respiratory insufficiency. CF has been considered a paediatric problem for several decades. Nevertheless, during the last 40 years, therapeutic options for CF have been greatly improved, turning CF into a chronic disease and extending the life expectancy of patients. Unfortunately, chronic inflammatory processes, which are characterized by a substantial release of cytokines and chemokines, along with ROS and proteases, can accelerate cellular senescence, leading to further complications in adulthood. The alterations and mechanisms downstream of CFTR functional defects that can stimulate cellular senescence remain unclear. However, while there are correlative data suggesting that cellular senescence may be implicated in CF, a causal or consequential relationship between cellular senescence and CF is still far from being established. Senescence can be both beneficial and detrimental. Senescence may suppress bacterial infections and cooperate with tissue repair. Additionally, it may act as an effective anticancer mechanism. However, it may also promote a pro-inflammatory environment, thereby damaging tissues and leading to chronic age-related diseases. In this review, we present the most current knowledge on cellular senescence and contextualize its possible involvement in CF.
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Affiliation(s)
- Valentino Bezzerri
- Cystic Fibrosis Center, Azienda Ospedaliera Universitaria Ospedali Riuniti, 60121, Ancona, Italy
| | - Francesco Piacenza
- Advanced Technology Center for Aging Research, Scientific Technological Area, IRCCS INRCA, 60121, Ancona, Italy
| | - Nicole Caporelli
- Cystic Fibrosis Center, Azienda Ospedaliera Universitaria Ospedali Riuniti, 60121, Ancona, Italy
| | - Marco Malavolta
- Advanced Technology Center for Aging Research, Scientific Technological Area, IRCCS INRCA, 60121, Ancona, Italy
| | - Mauro Provinciali
- Advanced Technology Center for Aging Research, Scientific Technological Area, IRCCS INRCA, 60121, Ancona, Italy
| | - Marco Cipolli
- Cystic Fibrosis Center, Azienda Ospedaliera Universitaria Ospedali Riuniti, 60121, Ancona, Italy.
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23
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Ivanov M, Matsvay A, Glazova O, Krasovskiy S, Usacheva M, Amelina E, Chernyak A, Ivanov M, Musienko S, Prodanov T, Kovalenko S, Baranova A, Khafizov K. Targeted sequencing reveals complex, phenotype-correlated genotypes in cystic fibrosis. BMC Med Genomics 2018; 11:13. [PMID: 29504914 PMCID: PMC5836842 DOI: 10.1186/s12920-018-0328-z] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Background Cystic fibrosis (CF) is one of the most common life-threatening genetic disorders. Around 2000 variants in the CFTR gene have been identified, with some proportion known to be pathogenic and 300 disease-causing mutations have been characterized in detail by CFTR2 database, which complicates its analysis with conventional methods. Methods We conducted next-generation sequencing (NGS) in a cohort of 89 adult patients negative for p.Phe508del homozygosity. Complete clinical and demographic information were available for 84 patients. Results By combining MLPA with NGS, we identified disease-causing alleles in all the CF patients. Importantly, in 10% of cases, standard bioinformatics pipelines were inefficient in identifying causative mutations. Class IV-V mutations were observed in 38 (45%) cases, predominantly ones with pancreatic sufficient CF disease; rest of the patients had Class I-III mutations. Diabetes was seen only in patients homozygous for class I-III mutations. We found that 12% of the patients were heterozygous for more than two pathogenic CFTR mutations. Two patients were observed with p.[Arg1070Gln, Ser466*] complex allele which was associated with milder pulmonary obstructions (FVC 107 and 109% versus 67%, CI 95%: 63-72%; FEV 90 and 111% versus 47%, CI 95%: 37-48%). For the first time p.[Phe508del, Leu467Phe] complex allele was reported, observed in four patients (5%). Conclusion NGS can be a more information-gaining technology compared to standard methods. Combined with its equivalent diagnostic performance, it can therefore be implemented in the clinical practice, although careful validation is still required. Electronic supplementary material The online version of this article (10.1186/s12920-018-0328-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Maxim Ivanov
- Moscow Institute of Physics and Technology, Department of Biological and Medical Physics, Dolgoprudny, Moscow Region, Russian Federation, 141700. .,Atlas Biomed Group, Moscow, Russian Federation, 121069.
| | - Alina Matsvay
- Moscow Institute of Physics and Technology, Department of Biological and Medical Physics, Dolgoprudny, Moscow Region, Russian Federation, 141700.,Central Research Scientific Institute of Epidemiology, Moscow, Russian Federation, 111123
| | - Olga Glazova
- Moscow Institute of Physics and Technology, Department of Biological and Medical Physics, Dolgoprudny, Moscow Region, Russian Federation, 141700
| | | | - Mariya Usacheva
- Federal Pulmonology Research Institute, Moscow, Russian Federation, 105077
| | - Elena Amelina
- Federal Pulmonology Research Institute, Moscow, Russian Federation, 105077
| | - Aleksandr Chernyak
- Federal Pulmonology Research Institute, Moscow, Russian Federation, 105077
| | - Mikhail Ivanov
- Moscow Institute of Physics and Technology, Department of Biological and Medical Physics, Dolgoprudny, Moscow Region, Russian Federation, 141700
| | | | - Timofey Prodanov
- Department of Mathematics and Information Technology, St. Petersburg Academic University, St. Petersburg, Russian Federation, 195251
| | - Sergey Kovalenko
- The Institute of Molecular Biology and Biophysics, Novosibirsk, Russian Federation, 630117.,Novosibirsk State University, Novosibirsk, Russian Federation, 630090
| | - Ancha Baranova
- Moscow Institute of Physics and Technology, Department of Biological and Medical Physics, Dolgoprudny, Moscow Region, Russian Federation, 141700.,Atlas Biomed Group, Moscow, Russian Federation, 121069.,Research Centre for Medical Genetics, Moscow, Russia.,Center for the Study of Chronic Metabolic Diseases, School of Systems Biology, George Mason University, Fairfax, VA, USA
| | - Kamil Khafizov
- Moscow Institute of Physics and Technology, Department of Biological and Medical Physics, Dolgoprudny, Moscow Region, Russian Federation, 141700.,Central Research Scientific Institute of Epidemiology, Moscow, Russian Federation, 111123
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24
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Futuristic Look at Genetic and Birth Defect Diagnoses and Treatments. Clin Obstet Gynecol 2017; 60:867-877. [PMID: 28990982 DOI: 10.1097/grf.0000000000000327] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
One aim of prenatal care is to provide information to prospective parents. The information provided encompasses prenatal care, intrapartum and postpartum care. Learning the genetic constitution of the parents pre-conception or the ongoing pregnancy allows parents to make decisions and set expectations. Offering screening and diagnostic testing has been the main in satisfying the desire for prenatal genetic information. With rapid advances in genomics and genome sequencing, screening during an ongoing pregnancy may become obsolete. Preconception risk will be determined by whole exome sequencing and chromosomal microarray of prospective parents and a number of approaches to alter pregnancy outcome can be considered when genome variations are identified. Therapeutic approaches include mitochondrial transfer and gene editing, two technologies that are in early stages, but showing promise as tools to alter outcomes.
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25
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Zhang W, Zhang X, Zhang YH, Strokes DC, Naren AP. Lumacaftor/ivacaftor combination for cystic fibrosis patients homozygous for Phe508del-CFTR. DRUGS OF TODAY (BARCELONA, SPAIN : 1998) 2016; 52:229-37. [PMID: 27252987 DOI: 10.1358/dot.2016.52.4.2467205] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Cystic fibrosis (CF) is a life-shortening inherited disease caused by the loss or dysfunction of the CF transmembrane conductance regulator (CFTR) channel activity resulting from mutations in the CFTR gene. Phe508del is the most prevalent mutation, with approximately 90% of all CF patients carrying it on at least one allele. Over the past two or three decades, significant progress has been made in understanding the pathogenesis of CF, and in the development of effective CF therapies. The approval of Orkambi® (lumacaftor/ivacaftor) marks another milestone in CF therapeutics development, which, with the advent of personalized medicine, could potentially revolutionize CF care and management. This article reviews the rationale, progress and future direction in the development of lumacaftor/ivacaftor combination to treat CF patients homozygous for the Phe508del-CFTR mutation.
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Affiliation(s)
- W Zhang
- Department of Pediatrics, Physiology, University of Tennessee Health Science Center, and University of Tennessee Cystic Fibrosis Care and Research Center at Le Bonheur Children's Hospital-Methodist University Hospital, Memphis, Tennessee, USA
| | - X Zhang
- Department of Pediatrics, University of Tennessee Health Science Center, and University of Tennessee Cystic Fibrosis Care and Research Center at Le Bonheur Children's Hospital-Methodist University Hospital, Memphis, Tennessee, USA
| | - Y H Zhang
- Department of Bioscience Research, University of Tennessee Health Science Center, Memphis, Tennessee, USA
| | - D C Strokes
- Department of Pediatrics, University of Tennessee Health Science Center, and University of Tennessee Cystic Fibrosis Care and Research Center at Le Bonheur Children's Hospital-Methodist University Hospital, Memphis, Tennessee, USA
| | - A P Naren
- Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA.
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26
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Zhang X, Hothi JS, Zhang YH, Srinivasan S, Stokes DC, Zhang W. c.3623G > A mutation encodes a CFTR protein with impaired channel function. Respir Res 2016; 17:8. [PMID: 26800689 PMCID: PMC4724100 DOI: 10.1186/s12931-016-0326-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2015] [Accepted: 01/19/2016] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND The aims of this study were to characterize clinical features of a pediatric African-American cystic fibrosis (CF) patient heterozygous for F508del and a novel c.3623G > A mutation, and to identify the molecular defect(s) associated with c.3623G > A mutation. METHODS The medical record of this patient was analyzed retrospectively. Western blotting and iodide efflux assay were used to study mutant CFTR protein expression level, maturation status, channel function, and the effects of CFTR modulation on these characteristics. RESULTS The encoding protein of c.3623G > A mutation, G1208D-CFTR, has a moderate processing defect and exhibits impaired channel function, which were partially rescued by using VX-809 or exposed to low temperature (28 °C). The patient has mild CF disease manifestations. CONCLUSIONS Our biochemical findings correlate with the clinical phenotype and suggest that c.3623G > A is a CF-causing mutation. The study helps expand our knowledge of rare CFTR mutations in a minority population and may have important clinical implications for personalized therapeutic intervention.
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Affiliation(s)
- Xiaoying Zhang
- Department of Pediatrics, University of Tennessee Health Science Center, 50 North Dunlap Street, Memphis, TN, 38103, USA.,University of Tennessee Cystic Fibrosis Care and Research Center, Le Bonheur Children's Hospital-Methodist University Hospital, Memphis, TN, 38103, USA
| | - Jaspal S Hothi
- Department of Pediatrics, University of Tennessee Health Science Center, 50 North Dunlap Street, Memphis, TN, 38103, USA.,University of Tennessee Cystic Fibrosis Care and Research Center, Le Bonheur Children's Hospital-Methodist University Hospital, Memphis, TN, 38103, USA
| | - Yanhui H Zhang
- Department of Bioscience Research, University of Tennessee Health Science Center, 875 Union Avenue, Memphis, TN, 38163, USA
| | - Saumini Srinivasan
- Department of Pediatrics, University of Tennessee Health Science Center, 50 North Dunlap Street, Memphis, TN, 38103, USA.,University of Tennessee Cystic Fibrosis Care and Research Center, Le Bonheur Children's Hospital-Methodist University Hospital, Memphis, TN, 38103, USA
| | - Dennis C Stokes
- Department of Pediatrics, University of Tennessee Health Science Center, 50 North Dunlap Street, Memphis, TN, 38103, USA.,University of Tennessee Cystic Fibrosis Care and Research Center, Le Bonheur Children's Hospital-Methodist University Hospital, Memphis, TN, 38103, USA
| | - Weiqiang Zhang
- Department of Pediatrics, University of Tennessee Health Science Center, 50 North Dunlap Street, Memphis, TN, 38103, USA. .,Department of Physiology, University of Tennessee Health Science Center, 50 North Dunlap Street, Room 309R, Memphis, TN, 38103, USA. .,University of Tennessee Cystic Fibrosis Care and Research Center, Le Bonheur Children's Hospital-Methodist University Hospital, Memphis, TN, 38103, USA.
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Exploring the landscape of pathogenic genetic variation in the ExAC population database: insights of relevance to variant classification. Genet Med 2015; 18:850-4. [PMID: 26681313 DOI: 10.1038/gim.2015.180] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2015] [Accepted: 10/30/2015] [Indexed: 11/08/2022] Open
Abstract
PURPOSE We evaluated the Exome Aggregation Consortium (ExAC) database as a control cohort to classify variants across a diverse set of genes spanning dominant and recessively inherited disorders. METHODS The frequency of pathogenic variants in ExAC was compared with the estimated maximal pathogenic allele frequency (MPAF), based on the disease prevalence, penetrance, inheritance, allelic and locus heterogeneity of each gene. Additionally, the observed carrier frequency and the ethnicity-specific variant distribution were compared between ExAC and the published literature. RESULTS The carrier frequency and ethnic distribution of pathogenic variants in ExAC were concordant with reported estimates. Of 871 pathogenic/likely pathogenic variants across 19 genes, only 3 exceeded the estimated MPAF. Eighty-four percent of variants with ExAC frequencies above the estimated MPAF were classified as "benign." Additionally, 20% of the cardiac and 19% of the Lynch syndrome gene variants originally classified as "VUS" occurred with ExAC frequencies above the estimated MPAF, making these suitable for reassessment. CONCLUSIONS The ExAC database is a useful source for variant classification and is not overrepresented for pathogenic variants in the genes evaluated. However, the mutational spectrum, pseudogenes, genetic heterogeneity, and paucity of literature should be considered in deriving meaningful classifications using ExAC.Genet Med 18 8, 850-854.
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Kondo S, Fujiki K, Ko SBH, Yamamoto A, Nakakuki M, Ito Y, Shcheynikov N, Kitagawa M, Naruse S, Ishiguro H. Functional characteristics of L1156F-CFTR associated with alcoholic chronic pancreatitis in Japanese. Am J Physiol Gastrointest Liver Physiol 2015; 309:G260-9. [PMID: 26089335 PMCID: PMC4537928 DOI: 10.1152/ajpgi.00015.2014] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/10/2014] [Accepted: 06/09/2015] [Indexed: 01/31/2023]
Abstract
Although cystic fibrosis is rare in Japanese, measurement of sweat Cl(-) has suggested mild dysfunction of cystic fibrosis transmembrane conductance regulator (CFTR) in some patients with chronic pancreatitis. In the present study, we have investigated the association of CFTR variants and chronic pancreatitis in Japanese and the functional characteristics of a Japanese- and pancreatitis-specific CFTR variant, L1156F. Seventy patients with alcoholic chronic pancreatitis, 18 patients with idiopathic chronic pancreatitis, and 180 normal subjects participated. All exons and their boundaries and promoter region of the CFTR gene were sequenced. Human embryonic kidney-293 cells were transfected with three CFTR variants (M470V, L1156F, and M470V+L1156F), and the protein expression was examined. Xenopus laevis oocytes were injected with the CFTR variants, and bicarbonate (HCO3 (-)) transport activity was examined. CFPAC-1 cells were transfected with the CFTR variants and Cl(-)/HCO3 (-) exchange activity was examined. Six variants (E217G, I556V, M470V, L1156F, Q1352H, and R1453W) were identified in the coding region of the CFTR gene. Cystic fibrosis-causing mutations were not found. The allele frequencies of L1156F and Q1352H in alcoholic chronic pancreatitis (5.0 and 7.9%) were significantly (P < 0.01) higher than those in normal subjects (0.6 and 1.9%). L1156F was linked with a worldwide CFTR variant, M470V. Combination of M470V and L1156F significantly reduced CFTR expression to ∼60%, impaired CFTR-mediated HCO3 (-)/Cl(-) transport activity to 50-60%, and impaired CFTR-coupled Cl(-)/HCO3 (-) exchange activity to 20-30%. The data suggest that the Japanese-specific CFTR variant L1156F causes mild dysfunction of CFTR and increases the risk of alcoholic chronic pancreatitis in Japanese.
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Affiliation(s)
- Shiho Kondo
- Department of Human Nutrition, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Kotoyo Fujiki
- Department of Nutrition, Nagoya University of Arts and Sciences, Nisshin, Japan
| | - Shigeru B H Ko
- Department of Systems Medicine, Keio University School of Medicine, Tokyo, Japan
| | - Akiko Yamamoto
- Department of Human Nutrition, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Miyuki Nakakuki
- Department of Human Nutrition, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Yasutomo Ito
- Division for Medical Research Engineering, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Nikolay Shcheynikov
- Epithelial Signaling and Transport Section, National Institute of Dental and Craniofacial Research, Bethesda, Maryland; and
| | - Motoji Kitagawa
- Department of Nutrition, Nagoya University of Arts and Sciences, Nisshin, Japan
| | | | - Hiroshi Ishiguro
- Department of Human Nutrition, Nagoya University Graduate School of Medicine, Nagoya, Japan;
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29
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Kay DM, Langfelder-Schwind E, DeCelie-Germana J, Sharp JK, Maloney B, Tavakoli NP, Saavedra-Matiz CA, Krein LM, Caggana M, Kier C. Utility of a very high IRT/No mutation referral category in cystic fibrosis newborn screening. Pediatr Pulmonol 2015; 50:771-80. [PMID: 26098992 DOI: 10.1002/ppul.23222] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/13/2014] [Revised: 04/17/2015] [Accepted: 05/08/2015] [Indexed: 11/11/2022]
Abstract
Newborn screening for Cystic Fibrosis (CF) began in New York in October, 2002 using immunoreactive trypsinogen (IRT)/DNA methodology. Infants with at least one CFTR mutation or very high IRT and no mutations (VHIRT) are referred for sweat testing. In a preliminary analysis, we noted a very low positive predictive value (PPV) and preponderance of Hispanic infants in the group of infants with CF referred for VHIRT, which led to a decision to revise, but not eliminate, the VHIRT category. Automatic referral for specimens with VHIRT collected on the day of birth was eliminated, and the VHIRT threshold was raised from 0.2% to 0.1%. In this report, we describe outcomes from VHIRT referrals among 2.4 million infants screened between March 2003 and February 2013. Following the algorithm change, referrals decreased by 37.8% overall (annual mean 1,485 vs. 923), and the VHIRT PPV improved (0.6-1.0%). The number of infants diagnosed has remained consistent at 1 in 4,400 births. The proportion of Black/Hispanic/Asian/Other infants with confirmed CF, CFTR-related metabolic syndrome (CRMS), or possible CF/CRMS was 21.3% in infants with 1-2 mutations, but 75.8% in the VHIRT group. In conclusion, although the PPV among VHIRT referrals remains low, had this category never been implemented, 24 infants with confirmed CF, and 9 infants with CRMS or possible CF/CRMS, most of whom were Hispanic, would have been missed over the 10 years. Information from this study may be helpful in assessing the need for the VHIRT category and algorithm changes in other screening programs.
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Affiliation(s)
- Denise M Kay
- Division of Genetics, Wadsworth Center, New York State Department of Health, Albany, New York
| | | | | | - Jack K Sharp
- Departments of Pediatrics, Duke University, Durham, NC and State University of New York (SUNY) at Buffalo, Buffalo, New York
| | - Breanne Maloney
- Division of Genetics, Wadsworth Center, New York State Department of Health, Albany, New York
| | - Norma P Tavakoli
- Division of Genetics, Wadsworth Center, New York State Department of Health, Albany, New York.,Department of Biomedical Sciences, University at Albany, Albany, New York
| | - Carlos A Saavedra-Matiz
- Division of Genetics, Wadsworth Center, New York State Department of Health, Albany, New York
| | - Lea M Krein
- Division of Genetics, Wadsworth Center, New York State Department of Health, Albany, New York
| | - Michele Caggana
- Division of Genetics, Wadsworth Center, New York State Department of Health, Albany, New York
| | - Catherine Kier
- University Medical Center at Stony Brook, Stony Brook, New York
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30
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Attitudes of cystic fibrosis patients and parents toward carrier screening and related reproductive issues. Eur J Hum Genet 2015. [PMID: 26220700 DOI: 10.1038/ejhg.2015.160] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Cystic fibrosis (CF) is a life-limiting autosomal recessive disorder affecting ~1 in 2500-4000 Caucasians. As most CF patients have no family history of the disorder, carrier screening for CF has the potential to prospectively identify couples at risk of conceiving an affected child. At-risk couples may consequently choose to act on the provided information and take steps to avoid the birth of a child with CF. Although carrier screening is widely believed to enhance reproductive autonomy of prospective parents, the practice also raises important ethical questions. A written questionnaire was administered to adult patients and parents of children with CF with the aim to explore participants' attitudes toward CF carrier screening and related reproductive issues. The study population was recruited from a CF patient registry in Belgium and comprised 111 participants (64 parents, 47 patients aged 16 or older). We found that more than 80% of all participants were in favor of preconception carrier screening for CF. However, some were concerned over potential negative consequences of population-wide CF carrier screening. Regarding future reproductive intentions, 43% of the participants indicated a desire to have children. Among these, preimplantation genetic diagnosis was found to be the most preferred reproductive option, closely followed by spontaneous pregnancy and prenatal diagnosis. Although the findings of our study suggest that patients and parents of children with CF support a population-based carrier screening program for CF, they also highlight some issues deserving particular attention when implementing such a program.
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31
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Distribution of Cystic Fibrosis Transmembrane Conductance Regulator (CFTR) Mutations in a Cohort of Patients Residing in Palestine. PLoS One 2015. [PMID: 26208274 PMCID: PMC4514804 DOI: 10.1371/journal.pone.0133890] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Cystic fibrosis (CF) is an autosomal recessive inherited life-threatening disorder that causes severe damage to the lungs and the digestive system. In Palestine, mutations in the Cystic Fibrosis Transmembrane Conductance Regulator gene (CFTR) that contributes to the clinical presentation of CF are ill defined. A cohort of thirty three clinically diagnosed CF patients from twenty one different Palestinian families residing in the central and southern part of Palestine were incorporated in this study. Sweat chloride testing was performed using the Sweat Chek Conductivity Analyzer (ELITECH Group, France) to confirm the clinical diagnosis of CF. In addition, nucleic acid from the patients’ blood samples was extracted and the CFTR mutation profiles were assessed by direct sequencing of the CFTR 27 exons and the intron-exon boundaries. For patient’s DNA samples where no homozygous or two heterozygous CFTR mutations were identified by exon sequencing, DNA samples were tested for deletions or duplications using SALSA MLPA probemix P091-D1 CFTR assay. Sweat chloride testing confirmed the clinical diagnosis of CF in those patients. All patients had NaCl conductivity >60mmol/l. In addition, nine different CFTR mutations were identified in all 21 different families evaluated. These mutations were c.1393-1G>A, F508del, W1282X, G85E, c.313delA, N1303K, deletion exons 17a-17b-18, deletion exons 17a-17b and Q1100P. c.1393-1G>A was shown to be the most frequent occurring mutation among tested families. We have profiled the underling mutations in the CFTR gene of a cohort of 21 different families affected by CF. Unlike other studies from the Arab countries where F508del was reported to be the most common mutation, in southern/central Palestine, the c.1393-1G>A appeared to be the most common. Further studies are needed per sample size and geographic distribution to account for other possible CFTR genetic alterations and their frequencies. Genotype/phenotype assessments are also recommended and finally carrier frequency should be ascertained.
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32
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Targeted mutation screening panels expose systematic population bias in detection of cystic fibrosis risk. Genet Med 2015; 18:174-9. [PMID: 25880441 DOI: 10.1038/gim.2015.52] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2014] [Accepted: 03/04/2015] [Indexed: 12/23/2022] Open
Abstract
PURPOSE Carrier screening for mutations contributing to cystic fibrosis (CF) is typically accomplished with panels composed of variants that are clinically validated primarily in patients of European descent. This approach has created a static genetic and phenotypic profile for CF. An opportunity now exists to reevaluate the disease profile of CFTR at a global population level. METHODS CFTR allele and genotype frequencies were obtained from a nonpatient cohort with more than 60,000 unrelated personal genomes collected by the Exome Aggregation Consortium. Likely disease-contributing mutations were identified with the use of public database annotations and computational tools. RESULTS We identified 131 previously described and likely pathogenic variants and another 210 untested variants with a high probability of causing protein damage. None of the current genetic screening panels or existing CFTR mutation databases covered a majority of deleterious variants in any geographical population outside of Europe. CONCLUSIONS Both clinical annotation and mutation coverage by commercially available targeted screening panels for CF are strongly biased toward detection of reproductive risk in persons of European descent. South and East Asian populations are severely underrepresented, in part because of a definition of disease that preferences the phenotype associated with European-typical CFTR alleles.
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33
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Janssens S, Kalokairinou L, Chokoshvilli D, Binst C, Mahieu I, Henneman L, De Paepe A, Borry P. Attitudes of cystic fibrosis patients and their parents towards direct-to-consumer genetic testing for carrier status. Per Med 2015; 12:99-107. [DOI: 10.2217/pme.14.75] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Background: An increasing number of direct-to-consumer (DTC) genetic testing companies have started offering tests for carrier status of autosomal recessive disorders. Materials & Methods: A written questionnaire was administered to 47 patients and 65 parents of children with Cystic Fibrosis (CF), a common severe autosomal recessive disorder, to assess their views about the offer of DTC carrier tests. All participants were recruited from a CF patient registry in Belgium. Results & Conclusion: We found that very few patients and parents were aware of the offer of DTC genetic testing for carrier status, and were generally skeptical. A strong preference for the healthcare system over commercial companies as the provider of the test was observed. However, many participants believe people should have a right to access DTC genetic tests provided by commercial companies.
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Affiliation(s)
- Sandra Janssens
- Centre for Medical Genetics, Ghent University Hospital, Ghent, De Pintelaan 185, 9000 Ghent, Belgium
| | - Louiza Kalokairinou
- Centre for Biomedical Ethics & Law, Department of Public Health and Primary Care, University of Leuven, Kapucijnenvoer 35 BOX 7001 3000 Leuven, Belgium
| | - Davit Chokoshvilli
- Centre for Medical Genetics, Ghent University Hospital, Ghent, De Pintelaan 185, 9000 Ghent, Belgium
- Centre for Biomedical Ethics & Law, Department of Public Health and Primary Care, University of Leuven, Kapucijnenvoer 35 BOX 7001 3000 Leuven, Belgium
| | - Carmen Binst
- Department of Life Sciences & Medicine, University of Ghent, Ghent, Belgium
| | - Inge Mahieu
- Department of Life Sciences & Medicine, University of Ghent, Ghent, Belgium
| | - Lidewij Henneman
- Community Genetics Section, Department of Clinical Genetics, EMGO Institute for Health & Care Research, VU University Medical Center, Van der Boechorststraat 7, 1081 BT Amsterdam, The Netherlands
| | - Anne De Paepe
- Centre for Medical Genetics, Ghent University Hospital, Ghent, De Pintelaan 185, 9000 Ghent, Belgium
| | - Pascal Borry
- Centre for Biomedical Ethics & Law, Department of Public Health and Primary Care, University of Leuven, Kapucijnenvoer 35 BOX 7001 3000 Leuven, Belgium
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Langlois S, Benn P, Wilkins-Haug L. Current controversies in prenatal diagnosis 4: pre-conception expanded carrier screening should replace all current prenatal screening for specific single gene disorders. Prenat Diagn 2015; 35:23-8. [DOI: 10.1002/pd.4532] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2014] [Revised: 11/02/2014] [Accepted: 11/07/2014] [Indexed: 12/21/2022]
Affiliation(s)
- Sylvie Langlois
- University of British Columbia; Medical Genetics; Vancouver British Columbia Canada
| | - Peter Benn
- University of Connecticut Health Center; Division of Human Genetics; Farmington CT United States
| | - Louise Wilkins-Haug
- Brigham and Women's Hospital; OB/GYN, Division of Division of Maternal Fetal Medicine; Boston MA United States
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35
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VanWort TA, Lee JA, Karvir H, Whitehouse MC, Beim PY, Copperman AB. Female cystic fibrosis mutation carriers and assisted reproductive technology: does carrier status affect reproductive outcomes? Fertil Steril 2014; 102:1324-30. [DOI: 10.1016/j.fertnstert.2014.07.1234] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2014] [Revised: 07/08/2014] [Accepted: 07/14/2014] [Indexed: 12/31/2022]
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Boyd SD, Galli SJ, Schrijver I, Zehnder JL, Ashley EA, Merker JD. A Balanced Look at the Implications of Genomic (and Other "Omics") Testing for Disease Diagnosis and Clinical Care. Genes (Basel) 2014; 5:748-66. [PMID: 25257203 PMCID: PMC4198929 DOI: 10.3390/genes5030748] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2014] [Revised: 07/20/2014] [Accepted: 08/18/2014] [Indexed: 11/16/2022] Open
Abstract
The tremendous increase in DNA sequencing capacity arising from the commercialization of "next generation" instruments has opened the door to innumerable routes of investigation in basic and translational medical science. It enables very large data sets to be gathered, whose interpretation and conversion into useful knowledge is only beginning. A challenge for modern healthcare systems and academic medical centers is to apply these new methods for the diagnosis of disease and the management of patient care without unnecessary delay, but also with appropriate evaluation of the quality of data and interpretation, as well as the clinical value of the insights gained. Most critically, the standards applied for evaluating these new laboratory data and ensuring that the results and their significance are clearly communicated to patients and their caregivers should be at least as rigorous as those applied to other kinds of medical tests. Here, we present an overview of conceptual and practical issues to be considered in planning for the integration of genomic methods or, in principle, any other type of "omics" testing into clinical care.
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Affiliation(s)
- Scott D Boyd
- Department of Pathology, Stanford University, Stanford, CA 94305, USA.
| | - Stephen J Galli
- Department of Pathology, Stanford University, Stanford, CA 94305, USA.
| | - Iris Schrijver
- Department of Pathology, Stanford University, Stanford, CA 94305, USA.
| | - James L Zehnder
- Department of Pathology, Stanford University, Stanford, CA 94305, USA.
| | - Euan A Ashley
- Department of Medicine, Stanford University, Stanford, CA 94305, USA.
| | - Jason D Merker
- Department of Pathology, Stanford University, Stanford, CA 94305, USA.
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Chen N, Prada AE. Development of allele-specific multiplex PCR to determine the length of poly-T in intron 8 of CFTR. PeerJ 2014; 2:e468. [PMID: 25071991 PMCID: PMC4103085 DOI: 10.7717/peerj.468] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2014] [Accepted: 06/13/2014] [Indexed: 11/23/2022] Open
Abstract
Cystic fibrosis transmembrane conductance regulator (CFTR) gene mutation analysis has been implemented for Cystic Fibrosis (CF) carrier screening, and molecular diagnosis of CF and congenital bilateral absence of the vas deferens (CBAVD). Although poly-T allele analysis in intron 8 of CFTR is required when a patient is positive for R117H, it is not recommended for routine carrier screening. Therefore, commercial kits for CFTR mutation analysis were designed either to mask the poly-T allele results, unless a patient is R117H positive, or to have the poly-T analysis as a standalone reflex test using the same commercial platform. There are other standalone assays developed to detect poly-T alleles, such as heteroduplex analysis, High Resolution Melting (HRM) curve analysis, allele-specific PCR (AS-PCR) and Sanger sequencing. In this report, we developed a simple and easy-to-implement multiplex AS-PCR assay using unlabeled standard length primers, which can be used as a reflex or standalone test for CFTR poly-T track analysis. Out of 115 human gDNA samples tested, results from our new AS-PCR matched to the previous known poly-T results or results from Sanger sequencing.
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Affiliation(s)
- Neng Chen
- Department of Pathology and Laboratory Medicine, Beaumont Health System , Royal Oak, MI , USA ; Department of Pathology and Laboratory Medicine, Oakland University William Beaumont School of Medicine , Royal Oak, MI , USA
| | - Anne E Prada
- Department of Pathology and Laboratory Medicine, Beaumont Health System , Royal Oak, MI , USA
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Grosu DS, Hague L, Chelliserry M, Kruglyak KM, Lenta R, Klotzle B, San J, Goldstein WM, Moturi S, Devers P, Woolworth J, Peters E, Elashoff B, Stoerker J, Wolff DJ, Friedman KJ, Highsmith WE, Lin E, Ong FS. Clinical investigational studies for validation of a next-generation sequencingin vitrodiagnostic device for cystic fibrosis testing. Expert Rev Mol Diagn 2014; 14:605-22. [DOI: 10.1586/14737159.2014.916618] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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39
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Affiliation(s)
- Shruti M Paranjape
- Eudowood Division of Pediatric Respiratory Sciences and The Johns Hopkins Cystic Fibrosis Center, The Johns Hopkins Medical Institutions, Baltimore, MD
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40
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Abstract
As a student I recall being told that half of what we would learn in medical school would be proven to be wrong. The challenges were to identify the incorrect half and, often more challenging, be willing to give up our entrenched ideas. Myths have been defined as traditional concepts or practice with no basis in fact. A misunderstanding is a mistaken approach or incomplete knowledge that can be resolved with better evidence, while firmly established misunderstandings can become dogma; a point of view put forth as authoritative without basis in fact. In this paper, I explore a number of myths, mistakes, and dogma related to cystic fibrosis disease and care. Many of these are myths that have long been vanquished and even forgotten, while others are controversial. In the future, many things taken as either fact or "clinical experience" today will be proven wrong. Let us examine these myths with an open mind and willingness to change our beliefs when justified.
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Affiliation(s)
- Bruce K Rubin
- Department of Pediatrics, Virginia Commonwealth University School of Medicine, Richmond, Virginia, U.S.A..
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41
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Zvereff VV, Faruki H, Edwards M, Friedman KJ. Cystic fibrosis carrier screening in a North American population. Genet Med 2013; 16:539-46. [DOI: 10.1038/gim.2013.188] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2013] [Accepted: 10/31/2013] [Indexed: 12/25/2022] Open
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Attitudes and opinions of pregnant women who are not offered cystic fibrosis carrier screening. Eur J Hum Genet 2013; 22:859-65. [PMID: 24253861 DOI: 10.1038/ejhg.2013.267] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2013] [Revised: 10/05/2013] [Accepted: 10/24/2013] [Indexed: 11/09/2022] Open
Abstract
Cystic fibrosis (CF) is the most common severe, autosomal recessive disease among Caucasians. A population-based CF carrier screening programme was implemented in Victoria, Australia, in 2006. Carrier screening for CF is currently only offered in the private health system. The aim of this study was to determine the attitudes and opinions of pregnant women in the public health system, towards screening for CF. Pregnant women were recruited in the antenatal clinics of two public hospitals, and invited to participate in the study. Results of this study were compared with previous studies where screening for CF carrier status was offered. Of the participants (n=158), the majority were aged 25-34 years old (66.1%) and were Caucasian (45.8%). Compared with those who were offered screening (reported in previous studies) participants in the current study were younger, had a lower level of education and a lower income. Knowledge was significantly lower in those who were not offered screening compared with those who were offered screening. The majority of participants believe CF carrier screening should be offered in the public health system (80.5%) and almost half would have liked to receive an offer of screening during their current pregnancy (49.7%). In order for the programme to be equitable, screening for CF carrier status needs to be offered in both the public and private health system and ideally should be at no cost to the user.
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Cooper DN, Krawczak M, Polychronakos C, Tyler-Smith C, Kehrer-Sawatzki H. Where genotype is not predictive of phenotype: towards an understanding of the molecular basis of reduced penetrance in human inherited disease. Hum Genet 2013; 132:1077-130. [PMID: 23820649 PMCID: PMC3778950 DOI: 10.1007/s00439-013-1331-2] [Citation(s) in RCA: 417] [Impact Index Per Article: 37.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2013] [Accepted: 06/15/2013] [Indexed: 02/06/2023]
Abstract
Some individuals with a particular disease-causing mutation or genotype fail to express most if not all features of the disease in question, a phenomenon that is known as 'reduced (or incomplete) penetrance'. Reduced penetrance is not uncommon; indeed, there are many known examples of 'disease-causing mutations' that fail to cause disease in at least a proportion of the individuals who carry them. Reduced penetrance may therefore explain not only why genetic diseases are occasionally transmitted through unaffected parents, but also why healthy individuals can harbour quite large numbers of potentially disadvantageous variants in their genomes without suffering any obvious ill effects. Reduced penetrance can be a function of the specific mutation(s) involved or of allele dosage. It may also result from differential allelic expression, copy number variation or the modulating influence of additional genetic variants in cis or in trans. The penetrance of some pathogenic genotypes is known to be age- and/or sex-dependent. Variable penetrance may also reflect the action of unlinked modifier genes, epigenetic changes or environmental factors. At least in some cases, complete penetrance appears to require the presence of one or more genetic variants at other loci. In this review, we summarize the evidence for reduced penetrance being a widespread phenomenon in human genetics and explore some of the molecular mechanisms that may help to explain this enigmatic characteristic of human inherited disease.
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Affiliation(s)
- David N. Cooper
- Institute of Medical Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff, CF14 4XN UK
| | - Michael Krawczak
- Institute of Medical Informatics and Statistics, Christian-Albrechts University, 24105 Kiel, Germany
| | | | - Chris Tyler-Smith
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA UK
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44
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Langfelder-Schwind E, Karczeski B, Strecker MN, Redman J, Sugarman EA, Zaleski C, Brown T, Keiles S, Powers A, Ghate S, Darrah R. Molecular testing for cystic fibrosis carrier status practice guidelines: recommendations of the National Society of Genetic Counselors. J Genet Couns 2013; 23:5-15. [PMID: 24014130 DOI: 10.1007/s10897-013-9636-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2013] [Accepted: 07/29/2013] [Indexed: 12/12/2022]
Abstract
PURPOSE To provide practice recommendations for genetic counselors whose clients are considering cystic fibrosis (CF) carrier testing or seeking information regarding CF molecular test results. The goals of these recommendations are to: 1) Provide updated information about the natural history, diagnosis, and treatment of CF and related conditions. 2) Supplement genetic counselors' knowledge and understanding of the available carrier screening and diagnostic testing options. 3) Describe the current state of genotype/phenotype correlations for CFTR mutations and an approach to interpreting both novel and previously described variants. 4) Provide a framework for genetic counselors to assist clients' decision-making regarding CF carrier testing, prenatal diagnosis, and pregnancy management. Disclaimer The practice guidelines of the National Society of Genetic Counselors (NSGC) are developed by members of the NSGC to assist genetic counselors and other health care providers in making decisions about appropriate management of genetic concerns; including access to and/or delivery of services. Each practice guideline focuses on a clinical or practice-based issue, and is the result of a review and analysis of current professional literature believed to be reliable. As such, information and recommendations within the NSGC practice guidelines reflect the current scientific and clinical knowledge at the time of publication, are only current as of their publication date, and are subject to change without notice as advances emerge.In addition, variations in practice, which take into account the needs of the individual patient and the resources and limitations unique to the institution or type of practice, may warrant approaches, treatments and/or procedures that differ from the recommendations outlined in this guideline. Therefore, these recommendations should not be construed as dictating an exclusive course of management, nor does the use of such recommendations guarantee a particular outcome. Genetic counseling practice guidelines are never intended to displace a health care provider's best medical judgment based on the clinical circumstances of a particular patient or patient population.Practice guidelines are published by NSGC for educational and informational purposes only, and NSGC does not "approve" or "endorse" any specific methods, practices, or sources of information.
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Haider BA, Olofin I, Wang M, Spiegelman D, Ezzati M, Fawzi WW. Anaemia, prenatal iron use, and risk of adverse pregnancy outcomes: systematic review and meta-analysis. BMJ 2013; 346:f3443. [PMID: 23794316 PMCID: PMC3689887 DOI: 10.1136/bmj.f3443] [Citation(s) in RCA: 434] [Impact Index Per Article: 39.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 05/20/2013] [Indexed: 01/16/2023]
Abstract
OBJECTIVES To summarise evidence on the associations of maternal anaemia and prenatal iron use with maternal haematological and adverse pregnancy outcomes; and to evaluate potential exposure-response relations of dose of iron, duration of use, and haemoglobin concentration in prenatal period with pregnancy outcomes. DESIGN Systematic review and meta-analysis DATA SOURCES Searches of PubMed and Embase for studies published up to May 2012 and references of review articles. STUDY SELECTION CRITERIA Randomised trials of prenatal iron use and prospective cohort studies of prenatal anaemia; cross sectional and case-control studies were excluded. RESULTS 48 randomised trials (17 793 women) and 44 cohort studies (1 851 682 women) were included. Iron use increased maternal mean haemoglobin concentration by 4.59 (95% confidence interval 3.72 to 5.46) g/L compared with controls and significantly reduced the risk of anaemia (relative risk 0.50, 0.42 to 0.59), iron deficiency (0.59, 0.46 to 0.79), iron deficiency anaemia (0.40, 0.26 to 0.60), and low birth weight (0.81, 0.71 to 0.93). The effect of iron on preterm birth was not significant (relative risk 0.84, 0.68 to 1.03). Analysis of cohort studies showed a significantly higher risk of low birth weight (adjusted odds ratio 1.29, 1.09 to 1.53) and preterm birth (1.21, 1.13 to 1.30) with anaemia in the first or second trimester. Exposure-response analysis indicated that for every 10 mg increase in iron dose/day, up to 66 mg/day, the relative risk of maternal anaemia was 0.88 (0.84 to 0.92) (P for linear trend<0.001). Birth weight increased by 15.1 (6.0 to 24.2) g (P for linear trend=0.005) and risk of low birth weight decreased by 3% (relative risk 0.97, 0.95 to 0.98) for every 10 mg increase in dose/day (P for linear trend<0.001). Duration of use was not significantly associated with the outcomes after adjustment for dose. Furthermore, for each 1 g/L increase in mean haemoglobin, birth weight increased by 14.0 (6.8 to 21.8) g (P for linear trend=0.002); however, mean haemoglobin was not associated with the risk of low birth weight and preterm birth. No evidence of a significant effect on duration of gestation, small for gestational age births, and birth length was noted. CONCLUSIONS Daily prenatal use of iron substantially improved birth weight in a linear dose-response fashion, probably leading to a reduction in risk of low birth weight. An improvement in prenatal mean haemoglobin concentration linearly increased birth weight.
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Affiliation(s)
- Batool A Haider
- Departments of Epidemiology and Nutrition, Harvard School of Public Health, 677 Huntington Avenue, Boston, MA 02115, USA.
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Hsu J, Avila PC, Kern RC, Hayes MG, Schleimer RP, Pinto JM. Genetics of chronic rhinosinusitis: state of the field and directions forward. J Allergy Clin Immunol 2013; 131:977-93, 993.e1-5. [PMID: 23540616 PMCID: PMC3715963 DOI: 10.1016/j.jaci.2013.01.028] [Citation(s) in RCA: 82] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2012] [Revised: 01/10/2013] [Accepted: 01/11/2013] [Indexed: 01/15/2023]
Abstract
The cause of chronic rhinosinusitis (CRS) remains unclear. Study of the genetic susceptibility to CRS might be a valuable strategy to understand the pathogenesis of this burdensome disorder. The purpose of this review is to critically evaluate the current literature regarding the genetics of CRS in a comprehensive fashion. The most promising findings from candidate gene studies include the cystic fibrosis transmembrane conductance regulator gene (CFTR), as well as genes involved in antigen presentation, innate and adaptive immune responses, tissue remodeling, and arachidonic acid metabolism. We also review the few hypothesis-independent genetic studies of CRS (ie, linkage analysis and pooling-based genome-wide association studies). Interpretation of the current literature is limited by challenges with study design, sparse replication, few functional correlates of associated polymorphisms, and inadequate examination of linkage disequilibrium or expression quantitative trait loci for reported associations. Given the relationship of CRS to other airway disorders with well-characterized genetic components (eg, asthma), study of the genetics of CRS deserves increased attention and investment, including the organization of large, detailed, and collaborative studies to advance knowledge of the mechanisms that underlie this disorder.
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Affiliation(s)
- Joy Hsu
- Division of Allergy-Immunology, Northwestern University Feinberg School of Medicine, Chicago, IL 60637, USA
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Fedick A, Su J, Jalas C, Northrop L, Devkota B, Ekstein J, Treff NR. High-throughput carrier screening using TaqMan allelic discrimination. PLoS One 2013; 8:e59722. [PMID: 23555759 PMCID: PMC3608587 DOI: 10.1371/journal.pone.0059722] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2012] [Accepted: 02/17/2013] [Indexed: 12/29/2022] Open
Abstract
Members of the Ashkenazi Jewish community are at an increased risk for inheritance of numerous genetic diseases such that carrier screening is medically recommended. This paper describes the development and evaluation of 30 TaqMan allelic discrimination qPCR assays for 29 mutations on 2 different high-throughput platforms. Four of these mutations are in the GBA gene and are successfully examined using short amplicons due to the qualitative nature of TaqMan allelic discrimination. Two systems were tested for their reliability (call rate) and consistency with previous diagnoses (diagnostic accuracy) indicating a call rate of 99.04% and a diagnostic accuracy of 100% (+/−0.00%) from one platform, and a call rate of 94.66% and a diagnostic accuracy of 93.35% (+/−0.29%) from a second for 9,216 genotypes. Results for mutations tested at the expected carrier frequency indicated a call rate of 97.87% and a diagnostic accuracy of 99.96% (+/−0.05%). This study demonstrated the ability of a high throughput qPCR methodology to accurately and reliably genotype 29 mutations in parallel. The universally applicable nature of this technology provides an opportunity to increase the number of mutations that can be screened simultaneously, and reduce the cost and turnaround time for accommodating newly identified and clinically relevant mutations.
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Affiliation(s)
- Anastasia Fedick
- Department of Microbiology and Molecular Genetics, University of Medicine and Dentistry of New Jersey-Robert Wood Johnson Medical School, Piscataway, New Jersey, United States of America.
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Yarlagadda S, Zhang W, Penmatsa H, Ren A, Arora K, Naren AP, Khan FAI, Donnellan CA, Srinivasan S, Stokes DC, Kappes JC. A young Hispanic with c.1646G>A mutation exhibits severe cystic fibrosis lung disease: is ivacaftor an option for therapy? Am J Respir Crit Care Med 2013; 186:694-6. [PMID: 23027855 DOI: 10.1164/ajrccm.186.7.694] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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An empirical estimate of carrier frequencies for 400+ causal Mendelian variants: results from an ethnically diverse clinical sample of 23,453 individuals. Genet Med 2012; 15:178-86. [PMID: 22975760 PMCID: PMC3908551 DOI: 10.1038/gim.2012.114] [Citation(s) in RCA: 179] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Purpose: Recent developments in genomics have led to expanded carrier screening panels capable of assessing hundreds of causal mutations for genetic disease. This new technology enables simultaneous measurement of carrier frequencies for many diseases. As the resultant rank-ordering of carrier frequencies impacts the design and prioritization of screening programs, the accuracy of this ranking is a public health concern. Methods: A total of 23,453 individuals from many obstetric, genetics, and infertility clinics were referred for routine recessive disease carrier screening. Multiplex carrier screening was performed and results were aggregated for this study. Results: Twenty-four percent of individuals were identified as carriers for at least one of 108 disorders, and 5.2% were carriers for multiple disorders. We report tabulations of carrier frequency by self-identified ethnicity and disease. Conclusion: To our knowledge, this study of a large, ethnically diverse clinical sample provides the most accurate measurements to date of carrier frequencies for hundreds of recessive alleles. The study also yields information on the clinical considerations associated with routine use of expanded panels and provides support for a pan-ethnic screening paradigm that minimizes the use of “racial” categories by the physician, as recommended by recent guidelines.
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