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Farra C, Awwad J, Hamadeh L, Khoueiry P, Halawi Z, Yazbeck N, Daher R, Souaid M, Hamdar L, Yammine T, Yunis K. CFTR mutational screening by next-generation sequencing reveals novel variants and a high carrier rate in a Middle Eastern population. Ann Hum Genet 2021; 86:80-86. [PMID: 34888852 DOI: 10.1111/ahg.12450] [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: 04/29/2021] [Revised: 10/28/2021] [Accepted: 10/29/2021] [Indexed: 11/28/2022]
Abstract
Cystic fibrosis is the most common life-limiting autosomal recessive disease in western countries with an incidence of 1:2500 in United States and 1:1000 in some European countries. Similar incidences were noted for the Middle East with variations from 1 in 2560 to 1 in 15,876 according to the degree of consanguinity. This is a preliminary systematic study that aims to assess the incidence and carrier rate of cystic fibrosis in the Middle Eastern Lebanese population; known for a high frequency of consanguinity. One hundred thirteen DNA samples were collected from neonatal blood cards obtained from newborns to healthy unrelated families with no previous history of Cystic fibrosis. Screening for Cystic Fibrosis-causing pathogenic variants was performed using next generation sequencing, and 17 different single nucleotide variants were detected, including six pathogenic and likely pathogenic. 5.5%-7% newborns were found to be carriers of a variant strongly suggestive of pathogenicity and comparable to published literature worldwide. This pilot analysis highlights the challenging interpretation of CFTR variants in a country underrepresented by large ethnic population analyses, and stresses the importance of premarital screening programs for Cystic fibrosis.
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Affiliation(s)
- Chantal Farra
- Department of Pediatrics, American University of Beirut Medical Center, Beirut, Lebanon.,Medical Genetics Unit, Department of pathology and Laboratory Medicine, American University of Beirut Medical Center, Beirut, Lebanon.,Medical Genetics Unit, Saint Joseph University, Beirut, Lebanon
| | - Johnny Awwad
- Department of Obstetrics and Gynecology, American University of Beirut Medical Center, Beirut, Lebanon
| | - Lama Hamadeh
- Medical Genetics Unit, Department of pathology and Laboratory Medicine, American University of Beirut Medical Center, Beirut, Lebanon
| | - Pierre Khoueiry
- Department of Biochemistry and Molecular Genetics, American University of Beirut Medical Center, Beirut, Lebanon
| | - Zeina Halawi
- Medical Genetics Unit, Department of pathology and Laboratory Medicine, American University of Beirut Medical Center, Beirut, Lebanon
| | - Nadine Yazbeck
- Department of Pediatrics, American University of Beirut Medical Center, Beirut, Lebanon
| | - Rose Daher
- Medical Genetics Unit, Department of pathology and Laboratory Medicine, American University of Beirut Medical Center, Beirut, Lebanon
| | - Mirna Souaid
- Medical Genetics Unit, Department of pathology and Laboratory Medicine, American University of Beirut Medical Center, Beirut, Lebanon.,Medical Genetics Unit, Saint Joseph University, Beirut, Lebanon
| | - Layal Hamdar
- Department of Obstetrics and Gynecology, American University of Beirut Medical Center, Beirut, Lebanon
| | - Tony Yammine
- Medical Genetics Unit, Saint Joseph University, Beirut, Lebanon
| | - Khalid Yunis
- Department of Pediatrics, American University of Beirut Medical Center, Beirut, Lebanon
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Schulpis KH, Molou E, Manta-Vogli P, Dotsikas Y, Thodi G, Chatzidaki M, Loukas YL. Perinatal Reduced Blood Concentrations of Free Carnitine and Acylcarnitines in Infants with Cystic Fibrosis. Am J Perinatol 2021; 38:828-833. [PMID: 31891954 DOI: 10.1055/s-0039-3402723] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
OBJECTIVE Cystic fibrosis (CF) is a multisystemic inherited disease. The aim of this study was to determine free carnitine (FC) and acylcarnitine concentrations in CF newborns with various mutations of the CFTR gene perinatally. STUDY DESIGN FC/acylcarnitines were determined in dried blood spots via liquid chromatography-tandem mass spectrometry (LC-MS/MS) on the third day of life of full-term normal (n = 50) and CF (n = 28) newborns. For infants with elevated immunoreactive trypsinogen values, FC/acylcarnitines were quantified again 48 hours later, followed by mutational analysis of CFTR gene via Sanger sequencing. RESULTS Initial FC and sums of acylcarnitine concentrations were statistically significantly lower in CF patients than in controls and even lower 48 hours later. The mutations F508del and 621 + 1G > T were predominantly identified among CF patients. CONCLUSION Low FC and acylcarnitine concentrations were measured perinatally in CF patients, for all CFTR mutations detected. Carnitine supplementation of breastfeeding mothers could be beneficial.
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Affiliation(s)
| | - Elina Molou
- Laboratory of Prenatal and Neonatal Screening, Neoscreen Ltd., Athens, Greece
| | - Penelope Manta-Vogli
- Department of Clinical Nutrition and Dietetics, Aghia Sofia Children's Hospital, Athens, Greece
| | - Yannis Dotsikas
- Laboratory of Pharmaceutical Analysis, Department of Pharmacy, National and Kapodistrian University of Athens, Athens, Greece
| | - Georgia Thodi
- Laboratory of Prenatal and Neonatal Screening, Neoscreen Ltd., Athens, Greece
| | - Maria Chatzidaki
- Laboratory of Prenatal and Neonatal Screening, Neoscreen Ltd., Athens, Greece
| | - Yannis L Loukas
- Laboratory of Pharmaceutical Analysis, Department of Pharmacy, National and Kapodistrian University of Athens, Athens, Greece
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Next-Generation Sequencing for Molecular Diagnosis of Cystic Fibrosis in a Brazilian Cohort. DISEASE MARKERS 2021; 2021:9812074. [PMID: 33613790 PMCID: PMC7878085 DOI: 10.1155/2021/9812074] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Revised: 12/23/2020] [Accepted: 01/27/2021] [Indexed: 12/05/2022]
Abstract
Cystic fibrosis (CF), an autosomal recessive genetic disease, is recognized as one of the most prevalent diseases in Caucasian populations. Epidemiological data show that the incidence of CF varies between countries and ethnic groups in the same region. CF occurs due to pathogenic variants in the gene encoding cystic fibrosis transmembrane conductance regulator (CFTR), located on chromosome 7q31.2. To date, more than 2,000 variants have been registered in the CFTR database. The study of these variants leads to the diagnosis and the possibility of a specific treatment for each patient through precision medicine. In this study, complete screening of CFTR was performed through next-generation sequencing (NGS) to gain insight into the variants circulating in the population of Rio de Janeiro and to provide patient access to treatment through genotype-specific therapies. Samples from 93 patients with an inconclusive molecular diagnosis were subjected to full-length screening of CFTR using an Illumina NGS HiSeq platform. Among these patients, 46 had two pathogenic variants, whereas 12 had only one CFTR variant. Twenty-four variants were not part of our routine screening. Of these 24 variants, V938Gfs∗37 had not been described in the CF databases previously. This research achieved a molecular diagnosis of the patients with CF and identification of possible molecular candidates for genotype-specific treatments.
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Arslan AB, Zamani AG, Pekcan S, Yıldırım MS. A Novel Pathogenic Variant of the CFTR Gene in a Patient with Cystic Fibrosis Phenotype-c.4096A > T. J Pediatr Genet 2020; 9:40-43. [PMID: 31976142 DOI: 10.1055/s-0039-1694964] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Accepted: 07/11/2019] [Indexed: 10/26/2022]
Abstract
Cystic fibrosis is a chronic multisystemic disease originating from functional alterations in CFTR (cystic fibrosis transmembrane conductance regulator) protein. To date, more than 300 pathogenic variants have been described in the literature. However, the diagnosis of CF, which was thought to become easier after the CFTR gene was identified, became more complicated due to the enormous amount of variations. In this study, we present a patient whose clinical findings were consistent with cystic fibrosis (CF) and showed a homozygous missense change that is not previously reported in the CFTR gene as pathogenic. In the next-generation sequencing analysis, homozygous c.4096A > T single-nucleotide exchange (I1366F [p.Ile1366Phe], missense) was shown in both alleles of the patient' CFTR gene. According to our database analysis, this variant has not yet been previously reported (VarSome, ClinVar, MutationTaster, Ensembl, dbSNP, PubMed). We do consider the change as pathogenic since the patient's findings were compatible with CF and the data analysis was in favor of pathogenicity. The most recent consensus report published in 2017 emphasized the importance of CFTR gene analysis, and this study emphasizes the difficulties of associating CFTR gene variations with a clinical picture and constitutes a new data on the genotype-phenotype correlation of CFTR variants. Also, considering the frequency of CF (according to World Health Organization data, every 1 out of 2,000-3,000 infants is born with CF in European Union countries and every 1 out of 3,500 in the United States) as well as the increasing rate of molecular studies performed on CF patients worldwide, reporting novel variation has an additional value.
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Affiliation(s)
- Ahmet Burak Arslan
- Department of Medical Genetics, Meram Medical Faculty, Necmettin Erbakan University, Konya, Turkey
| | - Ayşe Gül Zamani
- Department of Medical Genetics, Meram Medical Faculty, Necmettin Erbakan University, Konya, Turkey
| | - Sevgi Pekcan
- Pediatric Pulmonology Division, Department of Pediatrics, Meram Medical Faculty, Necmettin Erbakan University, Konya, Turkey
| | - Mahmut Selman Yıldırım
- Department of Medical Genetics, Meram Medical Faculty, Necmettin Erbakan University, Konya, Turkey
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5
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Bell SC, Mall MA, Gutierrez H, Macek M, Madge S, Davies JC, Burgel PR, Tullis E, Castaños C, Castellani C, Byrnes CA, Cathcart F, Chotirmall SH, Cosgriff R, Eichler I, Fajac I, Goss CH, Drevinek P, Farrell PM, Gravelle AM, Havermans T, Mayer-Hamblett N, Kashirskaya N, Kerem E, Mathew JL, McKone EF, Naehrlich L, Nasr SZ, Oates GR, O'Neill C, Pypops U, Raraigh KS, Rowe SM, Southern KW, Sivam S, Stephenson AL, Zampoli M, Ratjen F. The future of cystic fibrosis care: a global perspective. THE LANCET. RESPIRATORY MEDICINE 2020; 8:65-124. [PMID: 31570318 PMCID: PMC8862661 DOI: 10.1016/s2213-2600(19)30337-6] [Citation(s) in RCA: 548] [Impact Index Per Article: 137.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Revised: 07/19/2019] [Accepted: 08/14/2019] [Indexed: 02/06/2023]
Abstract
The past six decades have seen remarkable improvements in health outcomes for people with cystic fibrosis, which was once a fatal disease of infants and young children. However, although life expectancy for people with cystic fibrosis has increased substantially, the disease continues to limit survival and quality of life, and results in a large burden of care for people with cystic fibrosis and their families. Furthermore, epidemiological studies in the past two decades have shown that cystic fibrosis occurs and is more frequent than was previously thought in populations of non-European descent, and the disease is now recognised in many regions of the world. The Lancet Respiratory Medicine Commission on the future of cystic fibrosis care was established at a time of great change in the clinical care of people with the disease, with a growing population of adult patients, widespread genetic testing supporting the diagnosis of cystic fibrosis, and the development of therapies targeting defects in the cystic fibrosis transmembrane conductance regulator (CFTR), which are likely to affect the natural trajectory of the disease. The aim of the Commission was to bring to the attention of patients, health-care professionals, researchers, funders, service providers, and policy makers the various challenges associated with the changing landscape of cystic fibrosis care and the opportunities available for progress, providing a blueprint for the future of cystic fibrosis care. The discovery of the CFTR gene in the late 1980s triggered a surge of basic research that enhanced understanding of the pathophysiology and the genotype-phenotype relationships of this clinically variable disease. Until recently, available treatments could only control symptoms and restrict the complications of cystic fibrosis, but advances in CFTR modulator therapies to address the basic defect of cystic fibrosis have been remarkable and the field is evolving rapidly. However, CFTR modulators approved for use to date are highly expensive, which has prompted questions about the affordability of new treatments and served to emphasise the considerable gap in health outcomes for patients with cystic fibrosis between high-income countries, and low-income and middle-income countries (LMICs). Advances in clinical care have been multifaceted and include earlier diagnosis through the implementation of newborn screening programmes, formalised airway clearance therapy, and reduced malnutrition through the use of effective pancreatic enzyme replacement and a high-energy, high-protein diet. Centre-based care has become the norm in high-income countries, allowing patients to benefit from the skills of expert members of multidisciplinary teams. Pharmacological interventions to address respiratory manifestations now include drugs that target airway mucus and airway surface liquid hydration, and antimicrobial therapies such as antibiotic eradication treatment in early-stage infections and protocols for maintenance therapy of chronic infections. Despite the recent breakthrough with CFTR modulators for cystic fibrosis, the development of novel mucolytic, anti-inflammatory, and anti-infective therapies is likely to remain important, especially for patients with more advanced stages of lung disease. As the median age of patients with cystic fibrosis increases, with a rapid increase in the population of adults living with the disease, complications of cystic fibrosis are becoming increasingly common. Steps need to be taken to ensure that enough highly qualified professionals are present in cystic fibrosis centres to meet the needs of ageing patients, and new technologies need to be adopted to support communication between patients and health-care providers. In considering the future of cystic fibrosis care, the Commission focused on five key areas, which are discussed in this report: the changing epidemiology of cystic fibrosis (section 1); future challenges of clinical care and its delivery (section 2); the building of cystic fibrosis care globally (section 3); novel therapeutics (section 4); and patient engagement (section 5). In panel 1, we summarise key messages of the Commission. The challenges faced by all stakeholders in building and developing cystic fibrosis care globally are substantial, but many opportunities exist for improved care and health outcomes for patients in countries with established cystic fibrosis care programmes, and in LMICs where integrated multidisciplinary care is not available and resources are lacking at present. A concerted effort is needed to ensure that all patients with cystic fibrosis have access to high-quality health care in the future.
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Affiliation(s)
- Scott C Bell
- Department of Thoracic Medicine, The Prince Charles Hospital, Brisbane, QLD, Australia; QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia.
| | - Marcus A Mall
- Charité - Universitätsmedizin Berlin, Berlin Institute of Health, Berlin, Germany; German Center for Lung Research, Berlin, Germany
| | | | - Milan Macek
- Department of Biology and Medical Genetics, Second Faculty of Medicine, Motol University Hospital, Charles University, Prague, Czech Republic
| | - Susan Madge
- Royal Brompton and Harefield NHS Foundation Trust, London, UK
| | - Jane C Davies
- Royal Brompton and Harefield NHS Foundation Trust, London, UK; National Heart and Lung Institute, Imperial College, London, UK
| | - Pierre-Régis Burgel
- Hôpital Cochin, Assistance Publique-Hôpitaux de Paris, Paris, France; Université Paris Descartes, Institut Cochin, Paris, France
| | - Elizabeth Tullis
- St Michael's Hospital, Toronto, ON, Canada; University of Toronto, Toronto, ON, Canada
| | - Claudio Castaños
- Hospital de Pediatria "Juan P Garrahan", Buenos Aires, Argentina
| | - Carlo Castellani
- Cystic Fibrosis Centre, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Catherine A Byrnes
- Starship Children's Hospital, Auckland, New Zealand; University of Auckland, Auckland, New Zealand
| | - Fiona Cathcart
- Royal Brompton and Harefield NHS Foundation Trust, London, UK
| | - Sanjay H Chotirmall
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore
| | | | | | - Isabelle Fajac
- Hôpital Cochin, Assistance Publique-Hôpitaux de Paris, Paris, France; Université Paris Descartes, Institut Cochin, Paris, France
| | | | - Pavel Drevinek
- Department of Medical Microbiology, Second Faculty of Medicine, Motol University Hospital, Charles University, Prague, Czech Republic
| | | | - Anna M Gravelle
- Cystic Fibrosis Clinic, British Columbia Children's Hospital, Vancouver, BC, Canada
| | - Trudy Havermans
- Cystic Fibrosis Centre, University Hospital Leuven, Leuven, Belgium
| | - Nicole Mayer-Hamblett
- University of Washington, Seattle, WA, USA; Seattle Children's Research Institute, Seattle, WA, USA
| | | | | | - Joseph L Mathew
- Post Graduate Institute of Medical Education and Research, Chandigarh, India
| | - Edward F McKone
- School of Medicine, St Vincent's University Hospital, Dublin, Ireland; University College Dublin School of Medicine, Dublin, Ireland
| | - Lutz Naehrlich
- Universities of Giessen and Marburg Lung Center, German Center of Lung Research, Justus-Liebig-University Giessen, Giessen, Germany
| | - Samya Z Nasr
- CS Mott Children's Hospital, Ann Arbor, MI, USA; University of Michigan, Ann Arbor, MI, USA
| | | | | | | | | | - Steven M Rowe
- University of Alabama at Birmingham, Birmingham, AL, USA
| | - Kevin W Southern
- Alder Hey Children's Hospital, Liverpool, UK; University of Liverpool, Liverpool, UK
| | - Sheila Sivam
- Royal Prince Alfred Hospital, Sydney, NSW, Australia; Woolcock Institute of Medical Research, Sydney, NSW, Australia
| | - Anne L Stephenson
- St Michael's Hospital, Toronto, ON, Canada; University of Toronto, Toronto, ON, Canada
| | - Marco Zampoli
- Division of Paediatric Pulmonology and MRC Unit for Child and Adolescent Health, University of Cape Town, Cape Town, South Africa; Red Cross War Memorial Children's Hospital, Cape Town, South Africa
| | - Felix Ratjen
- University of Toronto, Toronto, ON, Canada; Division of Respiratory Medicine, Department of Paediatrics, Translational Medicine Research Program, The Hospital for Sick Children, University of Toronto, Toronto, ON, Canada.
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Improved detection of CFTR variants by targeted next-generation sequencing in male infertility: a case series. Reprod Biomed Online 2019; 39:963-968. [DOI: 10.1016/j.rbmo.2019.08.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Revised: 07/11/2019] [Accepted: 08/20/2019] [Indexed: 11/18/2022]
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7
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Lucarelli M, Porcaro L, Biffignandi A, Costantino L, Giannone V, Alberti L, Bruno SM, Corbetta C, Torresani E, Colombo C, Seia M. A New Targeted CFTR Mutation Panel Based on Next-Generation Sequencing Technology. J Mol Diagn 2017; 19:788-800. [PMID: 28736296 DOI: 10.1016/j.jmoldx.2017.06.002] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2017] [Revised: 06/01/2017] [Accepted: 06/07/2017] [Indexed: 01/16/2023] Open
Abstract
Searching for mutations in the cystic fibrosis transmembrane conductance regulator gene (CFTR) is a key step in the diagnosis of and neonatal and carrier screening for cystic fibrosis (CF), and it has implications for prognosis and personalized therapy. The large number of mutations and genetic and phenotypic variability make this search a complex task. Herein, we developed, validated, and tested a laboratory assay for an extended search for mutations in CFTR using a next-generation sequencing-based method, with a panel of 188 CFTR mutations customized for the Italian population. Overall, 1426 dried blood spots from neonatal screening, 402 genomic DNA samples from various origins, and 1138 genomic DNA samples from patients with CF were analyzed. The assay showed excellent analytical and diagnostic operative characteristics. We identified and experimentally validated 159 (of 188) CFTR mutations. The assay achieved detection rates of 95.0% and 95.6% in two large-scale case series of CF patients from central and northern Italy, respectively. These detection rates are among the highest reported so far with a genetic test for CF based on a mutation panel. This assay appears to be well suited for diagnostics, neonatal and carrier screening, and assisted reproduction, and it represents a considerable advantage in CF genetic counseling.
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Affiliation(s)
- Marco Lucarelli
- Department of Cellular Biotechnologies and Hematology, Sapienza University, Rome, Italy; Pasteur Institute Cenci Bolognetti Foundation, Sapienza University, Rome, Italy.
| | - Luigi Porcaro
- Medical Genetics Laboratory, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Alice Biffignandi
- Medical Genetics Laboratory, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Lucy Costantino
- Medical Genetics Laboratory, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Valentina Giannone
- Medical Genetics Laboratory, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Luisella Alberti
- Newborn Screening Laboratory, ASST Fatebenefratelli Sacco-PO Ospedale dei Bambini "V. Buzzi", Milan, Italy
| | - Sabina Maria Bruno
- Department of Cellular Biotechnologies and Hematology, Sapienza University, Rome, Italy
| | - Carlo Corbetta
- Newborn Screening Laboratory, ASST Fatebenefratelli Sacco-PO Ospedale dei Bambini "V. Buzzi", Milan, Italy
| | - Erminio Torresani
- Unit of Microbiology, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Carla Colombo
- Cystic Fibrosis Centre, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, University of Milan, Milan, Italy
| | - Manuela Seia
- Medical Genetics Laboratory, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
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Abstract
PURPOSE OF REVIEW Expanded carrier screening, which detects carriers for a large number of autosomal recessive and X-linked diseases, is increasing in clinical utilization. A recent joint statement from multiple professional societies, in addition to a growing literature base, offers perspective on rationale, decision points, and reasonable methods of implementation. RECENT FINDINGS Current literature addresses three areas: pre- and posttest education, including optimal use of formal genetic counseling, and differing characteristics of laboratory tests. Surveys of obstetricians and genetics providers also offer insight into optimal practice methods. SUMMARY We review the carrier screening process in chronological sequence - pretest, test selection, and posttest results disclosure - and points to be considered, recommending possible practice protocols based on available literature and our combined laboratory and clinical practice experience.
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9
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Biswas B. Clinical Performance Evaluation of Molecular Diagnostic Tests. J Mol Diagn 2016; 18:803-812. [PMID: 27639547 DOI: 10.1016/j.jmoldx.2016.06.008] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2015] [Revised: 05/19/2016] [Accepted: 06/01/2016] [Indexed: 10/21/2022] Open
Abstract
Molecular diagnostic tests with application to clinical diagnostics involve studies in infectious diseases, inherited diseases, oncology, predisposition to disease, or the description of polymorphisms linked to disease states. General considerations in the design of evaluation of diagnostic test trials and statistical principles for reporting the results are discussed. A brief overview of the general statistical considerations related to the intent of use, test development versus validation, different types of biases, and issues with missing data are provided. Furthermore, issues related to commonly used but not necessarily correct methods to characterize the performance in the presence and absence of a clinical reference standard are discussed. These issues are broadly applicable to any molecular diagnostic test with a dichotomous result. This overview may help the clinical molecular diagnostic community to evaluate tests that provide a dichotomous result.
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Affiliation(s)
- Bipasa Biswas
- Center for Devices and Radiological Health, US Food and Drug Administration, Silver Spring, Maryland.
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10
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Pettitt D, Smith J, Meadows N, Arshad Z, Schuh A, DiGiusto D, Bountra C, Holländer G, Barker R, Brindley D. Regulatory barriers to the advancement of precision medicine. EXPERT REVIEW OF PRECISION MEDICINE AND DRUG DEVELOPMENT 2016. [DOI: 10.1080/23808993.2016.1176526] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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11
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Lefterova MI, Shen P, Odegaard JI, Fung E, Chiang T, Peng G, Davis RW, Wang W, Kharrazi M, Schrijver I, Scharfe C. Next-Generation Molecular Testing of Newborn Dried Blood Spots for Cystic Fibrosis. J Mol Diagn 2016; 18:267-82. [PMID: 26847993 DOI: 10.1016/j.jmoldx.2015.11.005] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2015] [Revised: 10/21/2015] [Accepted: 11/19/2015] [Indexed: 12/19/2022] Open
Abstract
Newborn screening for cystic fibrosis enables early detection and management of this debilitating genetic disease. Implementing comprehensive CFTR analysis using Sanger sequencing as a component of confirmatory testing of all screen-positive newborns has remained impractical due to relatively lengthy turnaround times and high cost. Here, we describe CFseq, a highly sensitive, specific, rapid (<3 days), and cost-effective assay for comprehensive CFTR gene analysis from dried blood spots, the common newborn screening specimen. The unique design of CFseq integrates optimized dried blood spot sample processing, a novel multiplex amplification method from as little as 1 ng of genomic DNA, and multiplex next-generation sequencing of 96 samples in a single run to detect all relevant CFTR mutation types. Sequence data analysis utilizes publicly available software supplemented by an expert-curated compendium of >2000 CFTR variants. Validation studies across 190 dried blood spots demonstrated 100% sensitivity and a positive predictive value of 100% for single-nucleotide variants and insertions and deletions and complete concordance across the polymorphic poly-TG and consecutive poly-T tracts. Additionally, we accurately detected both a known exon 2,3 deletion and a previously undetected exon 22,23 deletion. CFseq is thus able to replace all existing CFTR molecular assays with a single robust, definitive assay at significant cost and time savings and could be adapted to high-throughput screening of other inherited conditions.
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Affiliation(s)
- Martina I Lefterova
- Department of Pathology, Stanford University Medical Center, Stanford, California
| | - Peidong Shen
- Stanford Genome Technology Center, Stanford University, Palo Alto, California
| | - Justin I Odegaard
- Department of Pathology, Stanford University Medical Center, Stanford, California
| | - Eula Fung
- Department of Pathology, Stanford University Medical Center, Stanford, California
| | - Tsoyu Chiang
- Department of Pathology, Stanford University Medical Center, Stanford, California
| | - Gang Peng
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Ronald W Davis
- Stanford Genome Technology Center, Stanford University, Palo Alto, California
| | - Wenyi Wang
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Martin Kharrazi
- California Department of Public Health, Environmental Health Investigations Branch, Richmond, California
| | - Iris Schrijver
- Department of Pathology, Stanford University Medical Center, Stanford, California; Department of Pediatrics, Stanford University Medical Center, Stanford, California
| | - Curt Scharfe
- Department of Pathology, Stanford University Medical Center, Stanford, California; Stanford Genome Technology Center, Stanford University, Palo Alto, California.
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12
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Lauschke VM, Ingelman-Sundberg M. Precision Medicine and Rare Genetic Variants. Trends Pharmacol Sci 2016; 37:85-86. [DOI: 10.1016/j.tips.2015.10.006] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2015] [Accepted: 10/26/2015] [Indexed: 10/22/2022]
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13
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Hendrix MM, Foster SL, Cordovado SK. Newborn Screening Quality Assurance Program for CFTR Mutation Detection and Gene Sequencing to Identify Cystic Fibrosis. JOURNAL OF INBORN ERRORS OF METABOLISM AND SCREENING 2016; 4. [PMID: 28261631 PMCID: PMC5332130 DOI: 10.1177/2326409816661358] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
All newborn screening laboratories in the United States and many worldwide screen for cystic fibrosis. Most laboratories use a second-tier genotyping assay to identify a panel of mutations in the CF transmembrane regulator (CFTR) gene. Centers for Disease Control and Prevention’s Newborn Screening Quality Assurance Program houses a dried blood spot repository of samples containing CFTR mutations to assist newborn screening laboratories and ensure high-quality mutation detection in a high-throughput environment. Recently, CFTR mutation detection has increased in complexity with expanded genotyping panels and gene sequencing. To accommodate the growing quality assurance needs, the repository samples were characterized with several multiplex genotyping methods, Sanger sequencing, and 3 next-generation sequencing assays using a high-throughput, low-concentration DNA extraction method. The samples performed well in all of the assays, providing newborn screening laboratories with a resource for complex CFTR mutation detection and next-generation sequencing as they transition to new methods.
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