1
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Salinas DB, Ginsburg DK, Wee CP, Saeed MM, Brewington JJ. Gradual increase in sweat chloride concentration is associated with a higher risk of CRMS/CFSPID to CF reclassification. Pediatr Pulmonol 2023; 58:1074-1084. [PMID: 36582049 DOI: 10.1002/ppul.26296] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 12/10/2022] [Accepted: 12/23/2022] [Indexed: 12/31/2022]
Abstract
OBJECTIVES Universal implementation of cystic fibrosis (CF) newborn screening (NBS) has led to the diagnostic dilemma of infants with CF screen-positive, inconclusive diagnosis (CFSPID), with limited guidance regarding prognosis and standardized care. Rates of reclassification from CFSPID to CF vary and risk factors for reclassification are not well established. We investigated whether clinical characteristics are associated with the risk of reclassification from CFSPID to a CF diagnosis. METHODS Children with a positive CF NBS were recruited from two sites in California. Retrospective, longitudinal, and cross-sectional data were collected. A subset of subjects had nasal epithelial cells collected for CF transmembrane conductance regulator (CFTR) functional assessment. Multivariate logistic regression was used to assess the risk of reclassification. RESULTS A total of 112 children completed the study (CF = 53, CFSPID = 59). Phenotypic characteristics between groups showed differences in pancreatic insufficiency prevalence, immunoreactive trypsinogen (IRT) levels, and Pseudomonas aeruginosa (PSA) colonization. Spirometry measures were not different between groups. Nasal epithelial cells from 10 subjects showed 7%-30% of wild-type (WT)-CFTR (wtCFTR) function in those who reclassified and 27%-67% of wtCFTR function in those who retained the CFSPID designation. Modeling revealed that increasing sweat chloride concentration (sw[Cl- ]) and PSA colonization were independent risk factors for reclassification to CF. CONCLUSION Increasing sw[Cl- ] and a history of PSA colonization are associated with the risk of reclassification from CFSPID to CF in a population with high IRT and two CFTR variants. A close follow-up to monitor phenotypic changes remains critical in this population. The role of CFTR functional assays in this population requires further exploration.
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Affiliation(s)
- Danieli B Salinas
- Department of Pediatrics, Division of Pediatric Pulmonology, Children's Hospital Los Angeles, Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| | - Daniella K Ginsburg
- Department of Pediatrics, Division of Pediatric Pulmonology, Children's Hospital Los Angeles, Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| | - Choo Phei Wee
- Department of Population and Public Health Sciences, Keck School of Medicine, Southern California Clinical and Translational Science Institute (SC-CTSI), University of Southern California, Los Angeles, California, USA
| | - Muhammed M Saeed
- Division of Pediatric Pulmonology, Kaiser Permanente Los Angles Medical Center, Los Angeles, California, USA
| | - John J Brewington
- Department of Pediatrics, Division of Pulmonary Medicine, Cincinnati Children's Hospital Medical Center, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
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2
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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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3
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Chakraborty P, Potter BK, Hayeems RZ. Maximizing Benefits and Minimizing Harms: Diagnostic Uncertainty Arising From Newborn Screening. Pediatrics 2021; 148:183448. [PMID: 34814191 DOI: 10.1542/peds.2021-052822] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 09/21/2021] [Indexed: 11/24/2022] Open
Affiliation(s)
- Pranesh Chakraborty
- Department of Pediatrics, Children's Hospital of Eastern Ontario and University of Ottawa, Ottawa, Ontario, Canada.,Newborn Screening Ontario, Children's Hospital of Eastern Ontario, Ottawa, Ontario, Canada
| | - Beth K Potter
- Newborn Screening Ontario, Children's Hospital of Eastern Ontario, Ottawa, Ontario, Canada.,School of Epidemiology and Public Health, University of Ottawa, Ottawa, Ontario, Canada
| | - Robin Z Hayeems
- Program in Child Health Evaluative Sciences, Hospital for Sick Children Research Institute, Toronto, Ontario, Canada.,Institute for Health Policy, Management, and Evaluation, University of Toronto, Toronto, Ontario, Canada
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4
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Validation of a Custom Next-Generation Sequencing Assay for Cystic Fibrosis Newborn Screening. Int J Neonatal Screen 2021; 7:ijns7040073. [PMID: 34842611 PMCID: PMC8628990 DOI: 10.3390/ijns7040073] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 10/20/2021] [Accepted: 10/28/2021] [Indexed: 11/16/2022] Open
Abstract
Newborn screening (NBS) for Cystic Fibrosis (CF) is associated with improved outcomes. All US states screen for CF; however, CF NBS algorithms have high false positive (FP) rates. In New York State (NYS), the positive predictive value of CF NBS improved from 3.7% to 25.2% following the implementation of a three-tier IRT-DNA-SEQ approach using commercially available tests. Here we describe a modification of the NYS CF NBS algorithm via transition to a new custom next-generation sequencing (NGS) platform for more comprehensive cystic fibrosis transmembrane conductance regulator (CFTR) gene analysis. After full gene sequencing, a tiered strategy is used to first analyze only a specific panel of 338 clinically relevant CFTR variants (second-tier), followed by unblinding of all sequence variants and bioinformatic assessment of deletions/duplications in a subset of samples requiring third-tier analysis. We demonstrate the analytical and clinical validity of the assay and the feasibility of use in the NBS setting. The custom assay has streamlined our molecular workflow, increased throughput, and allows for bioinformatic customization of second-tier variant panel content. NBS aims to identify those infants with the highest disease risk. Technological molecular improvements can be applied to NBS algorithms to reduce the burden of FP referrals without loss of sensitivity.
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5
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The Cystic Fibrosis Foundation Patient Registry. Design and Methods of a National Observational Disease Registry. Ann Am Thorac Soc 2018; 13:1173-9. [PMID: 27078236 DOI: 10.1513/annalsats.201511-781oc] [Citation(s) in RCA: 244] [Impact Index Per Article: 40.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
RATIONALE The Cystic Fibrosis Foundation Patient Registry (CFFPR) is an ongoing patient registry study that collects longitudinal demographic, clinical, and treatment information about persons with cystic fibrosis (CF) in the United States. CF is a life-shortening genetic disorder that occurs in approximately 1 in 3,500 births in the United States. High-quality observational data is important for clinical research, quality improvement, and clinical management. OBJECTIVES To describe the data collection, patient population, and key limitations of the CFFPR. METHODS Inclusion criteria for the CFFPR include diagnosis with CF or a CFTR-associated disorder, care at an accredited care center program, and provision of informed consent. Data from clinic visits and hospitalizations are collected through a secure website. Loss to follow-up and generalizability were examined using several methods. The accuracy of CFFPR data was evaluated with an audit of 2012 CFFPR data compared to the medical record. MEASUREMENTS AND MAIN RESULTS Since 1986, the CFFPR contains the records of 48,463 individuals with CF. Participation among individuals seen at accredited care centers is high, and loss to follow-up is low. An audit of 2012 CFFPR data suggests that the CFFPR contains 95% of clinic visits and 90% of hospitalizations found in the medical record for these patients, and nearly all of the audited fields were highly accurate. CONCLUSIONS Registries such as the CFFPR are important tools for research, clinical care, and tracking incidence, mortality and population trends.
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6
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Sermet-Gaudelus I, Brouard J, Audrézet MP, Couderc Kohen L, Weiss L, Wizla N, Vrielynck S, LLerena K, Le Bourgeois M, Deneuville E, Remus N, Nguyen-Khoa T, Raynal C, Roussey M, Girodon E. Guidelines for the clinical management and follow-up of infants with inconclusive cystic fibrosis diagnosis through newborn screening. Arch Pediatr 2017; 24:e1-e14. [PMID: 29174009 DOI: 10.1016/j.arcped.2017.07.015] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2017] [Revised: 06/21/2017] [Accepted: 07/04/2017] [Indexed: 01/17/2023]
Abstract
Neonatal screening for cystic fibrosis (CF) can detect infants with elevated immunoreactive trypsinogen (IRT) levels and inconclusive sweat tests and/or CFTR DNA results. These cases of uncertain diagnosis are defined by (1) either the presence of at most one CF-associated cystic fibrosis transmembrane conductance regulator (CFTR) mutation with sweat chloride values between 30 and 59mmol/L or (2) two CFTR mutations with at least one of unknown pathogenic potential and a sweat chloride concentration below 60mmol/L. This encompasses various clinical situations whose progression cannot be predicted. In these cases, a sweat chloride test has to be repeated at 12 months, and if possible at 6 and 24 months of life along with extended CFTR sequencing to detect rare mutations. When the diagnosis is not definite, CFTR functional explorations may provide a better understanding of CFTR dysfunction. The initial evaluation of these infants must be conducted in dedicated CF reference centers and should include bacteriological sputum analysis, chest radiology, and fecal elastase assay. The primary care physicians in charge of these patients should be familiar with the current management of CF and should work in collaboration with CF centers. A follow-up should be performed in a CF reference center at 3, 6, and 12 months of life and every year thereafter. Any symptom indicative of CF requires immediate reevaluation of the diagnosis. These guidelines were established by the "neonatal screening and difficult diagnoses" working group of the French CF society. Their objective is to standardize the management of infants with unclear diagnosis.
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Affiliation(s)
- I Sermet-Gaudelus
- Cystic fibrosis center, Necker-Enfants-Malades hospital, 75015 Paris, France; Inserm U1151, 75993 Paris, France.
| | - J Brouard
- Cystic fibrosis reference center, hôpital de la Côte-de-Nacre, 14033 Caen, France
| | - M-P Audrézet
- Molecular genetic laboratory, CHRU de Brest, 29609 Brest, France
| | - L Couderc Kohen
- Cystic fibrosis reference center, Charles-Nicolle hospital, 76000 Rouen, France
| | - L Weiss
- Cystic fibrosis reference center, Hautepierre hospital, 67200 Strasbourg, France
| | - N Wizla
- Cystic fibrosis reference center, Jeanne-de-Flandres hospital, 59000 Lille, France
| | - S Vrielynck
- Cystic fibrosis reference center, child and mother hospital, 69677 Lyon, France
| | - K LLerena
- Cystic fibrosis center, university hospital, 38700 Grenoble, France
| | - M Le Bourgeois
- Cystic fibrosis center, Necker-Enfants-Malades hospital, 75015 Paris, France
| | - E Deneuville
- Cystic fibrosis center, CHU de Rennes, 35000 Rennes, France
| | - N Remus
- Cystic fibrosis center, Créteil intercommunal hospital, 94000 Créteil, France
| | - T Nguyen-Khoa
- Cystic fibrosis center, Necker-Enfants-Malades hospital, 75015 Paris, France
| | - C Raynal
- UMR 5535, molecular genetic institute, 34293 Montpellier, France
| | - M Roussey
- Association française pour le dépistage et la prévention des handicaps de l'Enfant, 75015 Paris, France
| | - E Girodon
- Inserm U1151, 75993 Paris, France; Molecular genetics laboratory, Cochin hospital, 75014 Paris, France
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7
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Munck A, Delmas D, Audrézet MP, Lemonnier L, Cheillan D, Roussey M. Optimization of the French cystic fibrosis newborn screening programme by a centralized tracking process. J Med Screen 2017; 25:6-12. [PMID: 28454512 PMCID: PMC5813881 DOI: 10.1177/0969141317692611] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Objectives To evaluate the French cystic fibrosis newborn screening algorithm, based on data tracked by a centralized monitoring process, from 2002 to 2014. The programme aimed to attain European Standards in terms of positive predictive value, sensitivity, the ratio of screen positive patients diagnosed with cystic fibrosis to infants who screen positive but with inconclusive diagnosis (CFSPID), and time to diagnosis. Methods Retrospective analysis of programme performance, compliance with the algorithm, and changes in screening strategy. Results Modifications in the flow chart protocol improved the positive predictive value to 0.31 while maintaining the sensitivity at 0.95. Among infants diagnosed with cystic fibrosis, or identified as CFSPID, sweat test results were obtained for 94%, and two mutations were identified after exhaustive screening for the gene, when applicable, in 99.6%. The rate of pending diagnosis was very low (0.5%). The ratio of infants with cystic fibrosis:CFSPID was 6.3:1. Age at initial visit at the CF centre was ≤ 35 days, respectively, in 53%/26%. Conclusion Performances were in agreement with European standards, but timeliness of initial visit needed improvement. Our data complement an accumulating body of evidence demonstrating that attention must be paid to such ethical considerations as limiting carrier detection and inconclusive diagnosis. Newborn screening programmes should have a rigorous centralized monitoring process to warrant adjustments for improving performance to attain consensus guidelines.
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Affiliation(s)
- Anne Munck
- 1 Association Française pour le Dépistage et la Prévention des Handicaps de l' Enfant (AFDPHE), Paris, France.,2 Hôpital Robert Debré Assistante publique-Hôpitaux de Paris, Université Paris 7, CF Centre, Paris, France
| | - Dominique Delmas
- 1 Association Française pour le Dépistage et la Prévention des Handicaps de l' Enfant (AFDPHE), Paris, France
| | - Marie-Pierre Audrézet
- 1 Association Française pour le Dépistage et la Prévention des Handicaps de l' Enfant (AFDPHE), Paris, France.,3 Laboratoire de Génétique Moléculaire, CHRU, Brest, France
| | | | - David Cheillan
- 1 Association Française pour le Dépistage et la Prévention des Handicaps de l' Enfant (AFDPHE), Paris, France.,5 Hospices Civils de Lyon, Service des Maladies héréditaires du Métabolisme et Dépistage néonatal, INSERM U 1060, Lyon, France
| | - Michel Roussey
- 1 Association Française pour le Dépistage et la Prévention des Handicaps de l' Enfant (AFDPHE), Paris, France
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8
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[Interstitial processes of the lungs in childhood]. DER PATHOLOGE 2017; 38:260-271. [PMID: 28349192 DOI: 10.1007/s00292-017-0280-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Interstitial processes in the lungs of children can be due to several underlying diseases. Knowledge of the child's age is important as genetic aberrations play a major role in diseases in the first 2 years, whereas immunological diseases are more common starting in kindergarden age. In general lung diseases are rare in children, which makes the diagnostics difficult and results in a delayed diagnosis. In addition, pediatric pulmonologists are often very reluctant to perform lung biopsies due to a lack of a specialized pathologist. In order to make a contribution to the diagnostics of pediatric pulmonary diseases, pathologists should be specialized in pulmonary pathology, have a good knowledge of genetic methods and fetal lung development, which includes the genetic factors involved in lung growth and differentiation. A close cooperation with the pediatric pulmonologist is necessary and each patient should be discussed jointly on an interstitial lung disease board to promote the quality of diagnostics. The pathologist should be aware that the developing lungs of children are not just a smaller form of adult lungs and often react very differently. In this article, we mainly focus on diffuse infiltration patterns, such as ground glass and reticulonodular infiltrations as described in high-resolution computed tomography (HRCT). Localized interstitial processes, which can sometimes be tumor-like and malformations are not dealt with; however, vascular malformations are included as these often manifest as diffuse interstitial infiltrations and must therefore be taken into consideration for the differential diagnostics.
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9
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Sermet-Gaudelus I, Brouard J, Audrézet MP, Couderc Kohen L, Weiss L, Wizla N, Vrielynck S, LLerena K, Le Bourgeois M, Deneuville E, Remus N, Nguyen-Khoa T, Raynal C, Roussey M, Girodon E. [Management of infants whose diagnosis is inconclusive at neonatal screening for cystic fibrosis]. Arch Pediatr 2017; 24:401-414. [PMID: 28258861 DOI: 10.1016/j.arcped.2017.01.019] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2016] [Revised: 01/24/2017] [Accepted: 01/24/2017] [Indexed: 10/20/2022]
Abstract
Neonatal screening for cystic fibrosis (CF) may detect infants with elevated immunoreactive trypsinogen (IRT) levels but with inconclusive sweat tests and/or DNA results. This includes cases associating (1) either the presence of at most one CF-causing mutation and sweat chloride values between 30 and 59mmol/L or (2) two CFTR mutations with at least one of unknown pathogenicity and a sweat chloride below 60mmol/L. This encompasses different clinical situations whose progression cannot be predicted. These cases require redoing the sweat test at 12 months and if possible at 6 and 24 months of life. This must be associated with extended genotyping. CFTR functional explorations can also help by investigating CFTR dysfunction. These infants must be initially evaluated in dedicated CF centers including bacteriological sputum analysis, chest radiology and fecal elastase dosage. A home practitioner must be informed of the specificity of follow-up. These infants will be reviewed in the CF center at 3, 6 and 12 months and every year. Any CF-related symptom requires reevaluation of the diagnosis. These guidelines were established by the "neonatal screening and difficult diagnoses" working group of the French CF Society. They aim to standardize management of infants with unclear diagnosis in French CF centers.
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Affiliation(s)
- I Sermet-Gaudelus
- Centre de ressources et de compétences en mucoviscidose, hôpital Necker-Enfants Malades, 149, rue de Sévres, 75015 Paris, France; Inserm U 1151, Paris, France.
| | - J Brouard
- Centre de ressources et de compétences en mucoviscidose, hôpital de la Côte-de-Nacre, 14033 Caen, France
| | - M-P Audrézet
- Laboratoire de génétique moléculaire, CHRU de Brest, 29609 Brest, France
| | - L Couderc Kohen
- Centre de ressources et de compétences en mucoviscidose, hôpital Charles-Nicolle, 76000 Rouen, France
| | - L Weiss
- Centre de ressources et de compétences en mucoviscidose, hôpital de Hautepierre, 67200 Strasbourg, France
| | - N Wizla
- Centre de ressources et de compétences en mucoviscidose, hôpital Jeanne-de-Flandres, 59000 Lille, France
| | - S Vrielynck
- Centre de ressources et de compétences en mucoviscidose, hôpital Mère-Enfant, 69677 Lyon, France
| | - K LLerena
- Centre de ressources et de compétences en mucoviscidose, CHU, 38700 Grenoble, France
| | - M Le Bourgeois
- Centre de ressources et de compétences en mucoviscidose, hôpital Necker-Enfants Malades, 149, rue de Sévres, 75015 Paris, France
| | - E Deneuville
- Centre de ressources et de compétences en mucoviscidose, CHU, 35000 Rennes, France
| | - N Remus
- Centre de ressources et de compétences en mucoviscidose, hôpital InterCommunal de Créteil, 94000 Créteil, France
| | - T Nguyen-Khoa
- Centre de ressources et de compétences en mucoviscidose, hôpital Necker-Enfants Malades, 149, rue de Sévres, 75015 Paris, France
| | - C Raynal
- Institut de génétique moléculaire, UMR 5535, 34293 Montpellier, France
| | - M Roussey
- Association française pour le dépistage et la prévention des handicaps de l'enfant, 75015 Paris, France
| | - E Girodon
- Laboratoire de génétique moléculaire, hôpital Cochin, 75014 Paris, France
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10
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Farrell PM, White TB, Howenstine MS, Munck A, Parad RB, Rosenfeld M, Sommerburg O, Accurso FJ, Davies JC, Rock MJ, Sanders DB, Wilschanski M, Sermet-Gaudelus I, Blau H, Gartner S, McColley SA. Diagnosis of Cystic Fibrosis in Screened Populations. J Pediatr 2017; 181S:S33-S44.e2. [PMID: 28129810 DOI: 10.1016/j.jpeds.2016.09.065] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
OBJECTIVE Cystic fibrosis (CF) can be difficult to diagnose, even when newborn screening (NBS) tests yield positive results. This challenge is exacerbated by the multitude of NBS protocols, misunderstandings about screening vs diagnostic tests, and the lack of guidelines for presumptive diagnoses. There is also confusion regarding the designation of age at diagnosis. STUDY DESIGN To improve diagnosis and achieve standardization in definitions worldwide, the CF Foundation convened a committee of 32 experts with a mission to develop clear and actionable consensus guidelines on diagnosis of CF with an emphasis on screened populations, especially the newborn population. A comprehensive literature review was performed with emphasis on relevant articles published during the past decade. RESULTS After reviewing the common screening protocols and outcome scenarios, 14 of 27 consensus statements were drafted that apply to screened populations. These were approved by 80% or more of the participants. CONCLUSIONS It is recommended that all diagnoses be established by demonstrating dysfunction of the CF transmembrane conductance regulator (CFTR) channel, initially with a sweat chloride test and, when needed, potentially with newer methods assessing membrane transport directly, such as intestinal current measurements. Even in babies with 2 CF-causing mutations detected via NBS, diagnosis must be confirmed by demonstrating CFTR dysfunction. The committee also recommends that the latest classifications identified in the Clinical and Functional Translation of CFTR project [http://www.cftr2.org/index.php] should be used to aid with CF diagnosis. Finally, to avoid delays in treatment, we provide guidelines for presumptive diagnoses and recommend how to determine the age of diagnosis.
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Affiliation(s)
- Philip M Farrell
- Departments of Pediatrics and Population Health Sciences, University of Wisconsin School of Medicine and Public Health, Madison, WI
| | | | - Michelle S Howenstine
- Section of Pediatric Pulmonology, Allergy, and Sleep Medicine, Indiana University School of Medicine, Riley Hospital for Children, Indianapolis, IN
| | - Anne Munck
- Centres de Ressources et de Compétences pour la Mucoviscidose, Hôpital Robert Debre, Paris, France
| | - Richard B Parad
- Department of Pediatric and Newborn Medicine, Harvard Medical School, Brigham and Women's Hospital, Boston, MA
| | - Margaret Rosenfeld
- Department of Pediatrics, Seattle Children's Research Institute, University of Washington School of Medicine, Seattle, WA
| | | | - Frank J Accurso
- Children's Hospital Colorado, University of Colorado School of Medicine, Aurora, CO
| | - Jane C Davies
- Pediatric Respirology and Experimental Medicine, Imperial College London and Pediatric Respiratory Medicine, Royal Brompton and Harefield National Health Service Foundation Trust, London, United Kingdom
| | - Michael J Rock
- Departments of Pediatrics and Population Health Sciences, University of Wisconsin School of Medicine and Public Health, Madison, WI
| | - Don B Sanders
- Department of Pediatrics, Section of Pediatric Pulmonology, Allergy and Sleep Medicine, Riley Hospital for Children, Indiana University School of Medicine, Indianapolis, IN
| | - Michael Wilschanski
- Pediatric Gastroenterology, Hadassah Hebrew University Medical Center, Jerusalem, Israel
| | - Isabelle Sermet-Gaudelus
- Institut Necker Enfants Malades/INSERM U1151, Hôpital Necker Enfants Malades, Centres de Ressources et de Compétences pour la Mucoviscidose, Paris, France
| | - Hannah Blau
- Sackler Faculty of Medicine, Graub Cystic Fibrosis Center, Pulmonary Institute Schneider Children's Medical Center of Israel, Petah Tikva, Tel Aviv University, Tel Aviv, Israel
| | | | - Susanna A McColley
- Ann and Robert H. Lurie Children's Hospital of Chicago, Northwestern University Feinberg School of Medicine, Chicago, IL
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11
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Ren CL, Borowitz DS, Gonska T, Howenstine MS, Levy H, Massie J, Milla C, Munck A, Southern KW. Cystic Fibrosis Transmembrane Conductance Regulator-Related Metabolic Syndrome and Cystic Fibrosis Screen Positive, Inconclusive Diagnosis. J Pediatr 2017; 181S:S45-S51.e1. [PMID: 28129812 DOI: 10.1016/j.jpeds.2016.09.066] [Citation(s) in RCA: 88] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
OBJECTIVE An unintended consequence of cystic fibrosis (CF) newborn screening (NBS) is the identification of infants with a positive NBS test but inconclusive diagnostic testing. These infants are classified as CF transmembrane conductance regulator-related metabolic syndrome (CRMS) in the US and CF screen positive, inconclusive diagnosis (CFSPID) in other countries. Diagnostic and management decisions of these infants are challenges for CF healthcare professionals and stressful situations for families. As CF NBS has become more widespread across the world, increased information about the epidemiology and outcomes of these infants is becoming available. These data were reviewed at the 2015 CF Foundation Diagnosis Consensus Conference, and a harmonized definition of CRMS and CFSPID was developed. STUDY DESIGN At the consensus conference, participants reviewed published and unpublished studies of CRMS/CFSPID and used a modified Delphi methodology to develop a harmonized approach to the definition of CRMS/CFSPID. RESULTS Several studies of CRMS/CFSPID from populations around the world have been published in the past year. Although the studies vary in the number of infants studied, study design, and outcome measures, there have been some consistent findings. CRMS/CFSPID occurs relatively frequently, with CF:CRMS that ranges from 3 to 5 cases of CF for every 1 case of CRMS/CFSPID in regions where gene sequencing is not used. The incidence varies by NBS protocol used, and in some regions more cases of CRMS/CFSPID are detected than cases of CF. The majority of individuals with CRMS/CFSPID do not develop CF disease or progress to a diagnosis of CF. However, between 10% and 20% of asymptomatic infants can develop clinical features concerning for CF, such as a respiratory culture positive for Pseudomonas aeruginosa. Most studies have only reported short-term outcomes in the first 1-3 years of life; the long-term outcomes of CRMS/CFSPID remain unknown. The European CF Society definition of CFSPID and the CF Foundation definition of CRMS differ only slightly, and the consensus conference was able to create a unified definition of CRMS/CFSPID. CONCLUSIONS CRMS/CFSPID is a relatively common outcome of CF NBS, and clinicians need to be prepared to counsel families whose NBS test falls into this classification. The vast majority of infants with CRMS/CFSPID will remain free from disease manifestations early in life. However, a small proportion may develop clinical features concerning for CF or demonstrate progression to a clinical phenotype compatible with a CF diagnosis, and their long-term outcomes are not known. A consistent international definition of CRMS/CFSPID will allow for better data collection for study of outcomes and result in improved patient care.
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Affiliation(s)
- Clement L Ren
- Section of Pediatric Pulmonology, Allergy, and Sleep Medicine, Indiana University School of Medicine, Riley Hospital for Children, Indianapolis, IN
| | - Drucy S Borowitz
- Clinical Pediatrics, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY
| | - Tanja Gonska
- Division of Gastroenterology, Hepatology, and Nutrition, and Physiology and Experimental Medicine, Research Institute, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Michelle S Howenstine
- Section of Pediatric Pulmonology, Allergy, and Sleep Medicine, Indiana University School of Medicine, Riley Hospital for Children, Indianapolis, IN
| | - Hara Levy
- Division of Pulmonary Medicine, Department of Pediatrics, Ann and Robert H. Lurie Children's Hospital of Chicago, Chicago, IL
| | - John Massie
- Department of Respiratory Medicine, Royal Children's Hospital. and Department of Pediatrics, University of Melbourne, Melbourne, Victoria, Australia
| | - Carlos Milla
- Center for Excellence in Pulmonary Biology, Stanford University, Palo Alto, CA
| | - Anne Munck
- Centres de Ressources et de Compétences pour la Mucoviscidose, Hôpital Robert Debre, Paris, France
| | - Kevin W Southern
- Department for Women's and Children's Health, University of Liverpool, Institute in the Park, Alder Hey Children's Hospital, Liverpool, United Kingdom
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Abstract
Cystic fibrosis (CF) is the most common autosomal-recessive disease in white persons. Significant advances in therapies and outcomes have occurred for people with CF over the past 30 years. Many of these improvements have come about through the concerted efforts of the CF Foundation and international CF societies; networks of CF care centers; and the worldwide community of care providers, researchers, and patients and families. There are still hurdles to overcome to continue to improve the quality of life, reduce CF complications, prolong survival, and ultimately cure CF. This article reviews the epidemiology of CF, including trends in incidence and prevalence, clinical characteristics, common complications, and survival.
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Affiliation(s)
- Don B. Sanders
- Department of Pediatrics, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin
| | - Aliza Fink
- Epidemiology, Cystic Fibrosis Foundation, Bethesda, Maryland
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14
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Sontag MK, Lee R, Wright D, Freedenberg D, Sagel SD. Improving the Sensitivity and Positive Predictive Value in a Cystic Fibrosis Newborn Screening Program Using a Repeat Immunoreactive Trypsinogen and Genetic Analysis. J Pediatr 2016; 175:150-158.e1. [PMID: 27131402 DOI: 10.1016/j.jpeds.2016.03.046] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/28/2015] [Revised: 02/16/2016] [Accepted: 03/16/2016] [Indexed: 12/20/2022]
Abstract
OBJECTIVE To evaluate the performance of a new cystic fibrosis (CF) newborn screening algorithm, comprised of immunoreactive trypsinogen (IRT) in first (24-48 hours of life) and second (7-14 days of life) dried blood spot plus DNA on second dried blood spot, over existing algorithms. STUDY DESIGN A retrospective review of the IRT/IRT/DNA algorithm implemented in Colorado, Wyoming, and Texas. RESULTS A total of 1 520 079 newborns were screened, 32 557 (2.1%) had abnormal first IRT; 8794 (0.54%) on second. Furthermore, 14 653 mutation analyses were performed; 1391 newborns were referred for diagnostic testing; 274 newborns were diagnosed; and 201/274 (73%) of newborns had 2 mutations on the newborn screening CFTR panel. Sensitivity was 96.2%, compared with sensitivity of 76.1% observed with IRT/IRT (105 ng/mL cut-offs, P < .0001). The ratio of newborns with CF to heterozygote carriers was 1:2.5, and newborns with CF to newborns with CFTR-related metabolic syndrome was 10.8:1. The overall positive predictive value was 20%. The median age of diagnosis was 28, 30, and 39.5 days in the 3 states. CONCLUSIONS IRT/IRT/DNA is more sensitive than IRT/IRT because of lower cut-offs (∼97 percentile or 60 ng/mL); higher cut-offs in IRT/IRT programs (>99 percentile, 105 ng/mL) would not achieve sufficient sensitivity. Carrier identification and identification of newborns with CFTR-related metabolic syndrome is less common in IRT/IRT/DNA compared with IRT/DNA. The time to diagnosis is nominally longer, but diagnosis can be achieved in the neonatal period and opportunities to further improve timeliness have been enacted. IRT/IRT/DNA algorithm should be considered by programs with 2 routine screens.
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Affiliation(s)
- Marci K Sontag
- Department of Epidemiology, Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, CO.
| | - Rachel Lee
- Laboratory Services Section, Texas Department of State Health Services, Austin, TX; Laboratory Services Division, Colorado Department of Public Health and Environment, Denver, CO
| | - Daniel Wright
- Laboratory Services Division, Colorado Department of Public Health and Environment, Denver, CO
| | - Debra Freedenberg
- Laboratory Services Section, Texas Department of State Health Services, Austin, TX
| | - Scott D Sagel
- Department of Pediatrics, Children's Hospital Colorado, University of Colorado School of Medicine, Aurora, CO
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15
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Abstract
The diagnosis of cystic fibrosis (CF) has evolved over the past decade as newborn screening has become universal in the United States and elsewhere. The heterogeneity of phenotypes associated with CF transmembrane conductance regulator (CFTR) dysfunction and mutations in the CFTR gene has become clearer, ranging from classic pancreatic-insufficient CF to manifestations in only 1 organ system to indeterminate diagnoses identified by newborn screening. The tools available for diagnosis have also expanded. This article reviews the newest diagnostic criteria for CF, newborn screening, prenatal screening and diagnosis, and indeterminate diagnoses in newborn-screened infants and symptomatic adults.
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16
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Salinas DB, Sosnay PR, Azen C, Young S, Raraigh KS, Keens TG, Kharrazi M. Benign and Deleterious Cystic Fibrosis Transmembrane Conductance Regulator Mutations Identified by Sequencing in Positive Cystic Fibrosis Newborn Screen Children from California. PLoS One 2016; 11:e0155624. [PMID: 27214204 PMCID: PMC4877015 DOI: 10.1371/journal.pone.0155624] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Accepted: 05/02/2016] [Indexed: 12/19/2022] Open
Abstract
Background Of the 2007 Cystic Fibrosis Transmembrane Conductance Regulator (CFTR) mutations, 202 have been assigned disease liability. California’s racially diverse population, along with CFTR sequencing as part of newborn screening model, provides the opportunity to examine the phenotypes of children with uncategorized mutations to help inform disease liability and penetrance. Methods We conducted a retrospective cohort study based on children screened from 2007 to 2011 and followed for two to six years. Newborns that screened positive were divided into three genotype groups: those with two CF-causing mutations (CF-C); those with one mutation of varying clinic consequence (VCC); and those with one mutation of unknown disease liability (Unknown). Sweat chloride tests, pancreatic sufficiency status, and Pseudomonas aeruginosa colonization were compared. Results Children with two CF-causing mutations had a classical CF phenotype, while 5% of VCC (4/78) and 11% of Unknown (27/244) met diagnostic criteria of CF. Children carrying Unknown mutations 2215insG with D836Y, and T1036N had early and classical CF phenotype, while others carrying 1525-42G>A, L320V, L967S, R170H, and 296+28A>G had a benign clinical presentation, suggesting that these are non-CF causing. Conclusions While most infants with VCC and Unknown CFTR mutations do not meet diagnostic criteria for CF, a small proportion do. These findings highlight the range of genotypes and phenotypes in the first few years of life following CF newborn screening when CFTR sequencing is performed.
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Affiliation(s)
- Danieli B. Salinas
- Department of Pediatrics, Division of Pediatric Pulmonology, Children’s Hospital Los Angeles, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
- * E-mail:
| | - Patrick R. Sosnay
- Department of Medicine, Division of Pulmonary and Critical Care Medicine and McKusick-Nathans Institute of Medical Genetics, Johns Hopkins University School of Medicine, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Colleen Azen
- Department of Biostatistics, Southern California Clinical and Translational Science Institute, Children’s Hospital Los Angeles, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
| | - Suzanne Young
- The Sequoia Foundation, La Jolla, California, United States of America
| | - Karen S. Raraigh
- McKusick-Nathans Institute of Medical Genetics, Johns Hopkins University School of Medicine, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Thomas G. Keens
- Department of Pediatrics, Division of Pediatric Pulmonology, Children’s Hospital Los Angeles, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
| | - Martin Kharrazi
- Division of Environmental and Occupational Disease Control, Environmental Health Investigations Branch, Environmental Epidemiology Section, California Department of Public Health, Richmond, California, United States of America
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17
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Pique L, Graham S, Pearl M, Kharrazi M, Schrijver I. Cystic fibrosis newborn screening programs: implications of the CFTR variant spectrum in nonwhite patients. Genet Med 2016; 19:36-44. [DOI: 10.1038/gim.2016.48] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2015] [Accepted: 03/08/2016] [Indexed: 11/10/2022] Open
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18
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Newborn screening for cystic fibrosis. THE LANCET RESPIRATORY MEDICINE 2016; 4:653-661. [PMID: 27053341 DOI: 10.1016/s2213-2600(16)00053-9] [Citation(s) in RCA: 100] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2015] [Revised: 01/23/2016] [Accepted: 01/28/2016] [Indexed: 01/16/2023]
Abstract
Since the late 1970s when the potential of the immunoreactive trypsinogen assay for early identification of infants with cystic fibrosis was first recognised, the performance of newborn blood spot screening (NBS) has been continually assessed and its use has gradually expanded. NBS for cystic fibrosis is a cost-effective strategy and, if standards of care are fully implemented and robust management pathways are in place, has a positive effect on clinical outcomes. In the past decade, NBS has undergone rapid expansion and an unprecedented number of infants with cystic fibrosis have access to early diagnosis and care. Cystic fibrosis NBS has now moved on from the development phase and is entering an era of consolidation. In the future, research should focus on the rationalisation and optimisation of existing programmes, with particular attention to bioethical implications such as unwanted detection of carriers and inconclusive diagnoses.
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19
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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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20
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Kay DM, Maloney B, Hamel R, Pearce M, DeMartino L, McMahon R, McGrath E, Krein L, Vogel B, Saavedra-Matiz CA, Caggana M, Tavakoli NP. Screening for cystic fibrosis in New York State: considerations for algorithm improvements. Eur J Pediatr 2016; 175:181-93. [PMID: 26293390 DOI: 10.1007/s00431-015-2616-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/28/2015] [Revised: 08/04/2015] [Accepted: 08/10/2015] [Indexed: 12/15/2022]
Abstract
UNLABELLED Newborn screening for cystic fibrosis (CF), a chronic progressive disease affecting mucus viscosity, has been beneficial in both improving life expectancy and the quality of life for individuals with CF. In New York State from 2007 to 2012 screening for CF involved measuring immunoreactive trypsinogen (IRT) levels in dried blood spots from newborns using the IMMUCHEM(™) Blood Spot Trypsin-MW ELISA kit. Any specimen in the top 5% IRT level underwent DNA analysis using the InPlex(®) CF Molecular Test. Of the 1.48 million newborns screened during the 6-year time period, 7631 babies were referred for follow-up. CF was confirmed in 251 cases, and 94 cases were diagnosed with CF transmembrane conductance regulated-related metabolic syndrome or possible CF. Nine reports of false negatives were made to the program. Variation in daily average IRT was observed depending on the season (4-6 ng/ml) and kit lot (<3 ng/ml), supporting the use of a floating cutoff. The screening method had a sensitivity of 96.5%, specificity of 99.6%, positive predictive value of 4.5%, and negative predictive value of 99.5%. CONCLUSION Considerations for CF screening algorithms should include IRT variations resulting from age at specimen collection, sex, race/ethnicity, season, and manufacturer kit lots. WHAT IS KNOWN Measuring IRT level in dried blood spots is the first-tier screen for CF. Current algorithms for CF screening lead to substantial false-positive referral rates. WHAT IS NEW IRT values were affected by age of infant when specimen is collected, race/ethnicity and sex of infant, and changes in seasons and manufacturer kit lots The prevalence of CF in NYS is 1 in 4200 with the highest prevalence in White infants (1 in 2600) and the lowest in Black infants (1 in 15,400).
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Affiliation(s)
- Denise M Kay
- Division of Genetics, Wadsworth Center, New York State Department of Health, David Axelrod Institute, 120, New Scotland Ave., Albany, NY, 12208, USA.
| | - Breanne Maloney
- Division of Genetics, Wadsworth Center, New York State Department of Health, David Axelrod Institute, 120, New Scotland Ave., Albany, NY, 12208, USA.
| | - Rhonda Hamel
- Division of Genetics, Wadsworth Center, New York State Department of Health, David Axelrod Institute, 120, New Scotland Ave., Albany, NY, 12208, USA.
| | - Melissa Pearce
- Division of Genetics, Wadsworth Center, New York State Department of Health, David Axelrod Institute, 120, New Scotland Ave., Albany, NY, 12208, USA.
| | - Lenore DeMartino
- Division of Genetics, Wadsworth Center, New York State Department of Health, David Axelrod Institute, 120, New Scotland Ave., Albany, NY, 12208, USA.
| | - Rebecca McMahon
- Division of Genetics, Wadsworth Center, New York State Department of Health, David Axelrod Institute, 120, New Scotland Ave., Albany, NY, 12208, USA.
| | - Emily McGrath
- Division of Genetics, Wadsworth Center, New York State Department of Health, David Axelrod Institute, 120, New Scotland Ave., Albany, NY, 12208, USA.
| | - Lea Krein
- Division of Genetics, Wadsworth Center, New York State Department of Health, David Axelrod Institute, 120, New Scotland Ave., Albany, NY, 12208, USA.
| | - Beth Vogel
- Division of Genetics, Wadsworth Center, New York State Department of Health, David Axelrod Institute, 120, New Scotland Ave., Albany, NY, 12208, USA.
| | - Carlos A Saavedra-Matiz
- Division of Genetics, Wadsworth Center, New York State Department of Health, David Axelrod Institute, 120, New Scotland Ave., Albany, NY, 12208, USA.
| | - Michele Caggana
- Division of Genetics, Wadsworth Center, New York State Department of Health, David Axelrod Institute, 120, New Scotland Ave., Albany, NY, 12208, USA.
| | - Norma P Tavakoli
- Division of Genetics, Wadsworth Center, New York State Department of Health, David Axelrod Institute, 120, New Scotland Ave., Albany, NY, 12208, USA. .,Department of Biomedical Sciences, School of Public Health, State University of New York, Albany, NY, USA.
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21
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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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22
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Damaged goods?: an empirical cohort study of blood specimens collected 12 to 23 hours after birth in newborn screening in California. Genet Med 2015; 18:259-64. [DOI: 10.1038/gim.2015.154] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2015] [Accepted: 09/14/2015] [Indexed: 11/08/2022] Open
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23
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Hughes EE, Stevens CF, Saavedra-Matiz CA, Tavakoli NP, Krein LM, Parker A, Zhang Z, Maloney B, Vogel B, DeCelie-Germana J, Kier C, Anbar RD, Berdella MN, Comber PG, Dozor AJ, Goetz DM, Guida L, Kattan M, Ting A, Voter KZ, van Roey P, Caggana M, Kay DM. Clinical Sensitivity of Cystic Fibrosis Mutation Panels in a Diverse Population. Hum Mutat 2015; 37:201-8. [PMID: 26538069 DOI: 10.1002/humu.22927] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2015] [Accepted: 10/20/2015] [Indexed: 12/11/2022]
Abstract
Infants are screened for cystic fibrosis (CF) in New York State (NYS) using an IRT-DNA algorithm. The purpose of this study was to validate and assess clinical validity of the US FDA-cleared Illumina MiSeqDx CF 139-Variant Assay (139-VA) in the diverse NYS CF population. The study included 439 infants with CF identified via newborn screening (NBS) from 2002 to 2012. All had been screened using the Abbott Molecular CF Genotyping Assay or the Hologic InPlex CF Molecular Test. All with CF and zero or one mutation were tested using the 139-VA. DNA extracted from dried blood spots was reliably and accurately genotyped using the 139-VA. Sixty-three additional mutations were identified. Clinical sensitivity of three panels ranged from 76.2% (23 mutations recommended for screening by ACMG/ACOG) to 79.7% (current NYS 39-mutation InPlex panel), up to 86.0% for the 139-VA. For all, sensitivity was highest in Whites and lowest in the Black population. Although the sample size was small, there was a nearly 20% increase in sensitivity for the Black CF population using the 139-VA (68.2%) over the ACMG/ACOG and InPlex panels (both 50.0%). Overall, the 139-VA is more sensitive than other commercially available panels, and could be considered for NBS, clinical, or research laboratories conducting CF screening.
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Affiliation(s)
- Erin E Hughes
- Division of Genetics, Wadsworth Center, New York State Department of Health, Albany, New York
| | - Colleen F Stevens
- Division of Genetics, Wadsworth Center, New York State Department of Health, Albany, New York
| | - Carlos A Saavedra-Matiz
- 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, School of Public Health, State University of New York, Albany, New York
| | - Lea M Krein
- Division of Genetics, Wadsworth Center, New York State Department of Health, Albany, New York
| | - April Parker
- Division of Genetics, Wadsworth Center, New York State Department of Health, Albany, New York
| | - Zhen Zhang
- Applied Genomics Technologies Core, Wadsworth Center, New York State Department of Health, Albany, New York
| | - Breanne Maloney
- Division of Genetics, Wadsworth Center, New York State Department of Health, Albany, New York
| | - Beth Vogel
- 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
| | - Ran D Anbar
- SUNY Upstate Medical University/Golisano Children's Hospital, Syracuse, New York
| | - Maria N Berdella
- The Cystic Fibrosis Center, Mount Sinai Beth Israel, New York, New York
| | | | - Allen J Dozor
- Maria Fareri Children's Hospital at Westchester Medical Center and New York Medical College, Valhalla, New York
| | | | - Louis Guida
- Good Samaritan Hospital, North Babylon, New York
| | - Meyer Kattan
- Columbia University Medical Center, New York, New York
| | - Andrew Ting
- Mount Sinai School of Medicine, New York, New York
| | - Karen Z Voter
- Strong Memorial Hospital, University of Rochester Medical Center, Rochester, New York
| | | | - Patrick van Roey
- Division of Genetics, Wadsworth Center, New York State Department of Health, Albany, New York.,Applied Genomics Technologies Core, 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
| | - Denise M Kay
- Division of Genetics, Wadsworth Center, New York State Department of Health, Albany, New York
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Dewulf J, Vermeulen F, Wanyama S, Thomas M, Proesmans M, Dupont L, De Boeck K. Treatment burden in patients with at least one class IV or V CFTR mutation. Pediatr Pulmonol 2015; 50:1230-6. [PMID: 26540286 DOI: 10.1002/ppul.23313] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/29/2015] [Revised: 08/04/2015] [Accepted: 08/28/2015] [Indexed: 12/27/2022]
Abstract
CFTR mutations are grouped according to disease-causing mechanism. Several studies demonstrated that patients having at least one mutation of class IV/V, present with a milder phenotype, but little is known about their relative treatment burden. We compared treatment burden between patients with two class I, II, or III mutations and patients with at least one mutation of class IV/V in the 2010 database of the Belgian CF Registry. We calculated a "Treatment Burden Index" (TBI) by assigning long term therapies to categories low, medium and high intensity, for differential weighing in the total score. There were 779 patients with two known class I/II/III mutations and 94 patients with at least one class IV/V mutation. Compared to class I/II/III, class IV/V patients had a lower median number of clinic visits (4 vs. 5; P < 0.001), a lower risk of hospitalization (24.7% vs. 50.8%; P < 0.001) and intravenous antibiotic treatment (23.5% vs. 46.0%; P < 0.001) and a lower median TBI (6 vs. 9; P < 0.001). These differences remained significant when only class IV/V patients with pancreatic insufficiency (n = 31) were considered. This study clearly demonstrates the significantly lower treatment burden in patients with CF and at least one class IV/V mutation compared to patients with two class I/II/III mutations and contributes to providing better individual counseling at time of diagnosis.
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Affiliation(s)
- Jonas Dewulf
- Department of Pediatrics, University Hospitals of Leuven, Belgium
| | | | - Simeon Wanyama
- Scientific Institute of Public Health, on behalf of the Belgian CF Registry, Brussels, Belgium
| | - Muriel Thomas
- Scientific Institute of Public Health, on behalf of the Belgian CF Registry, Brussels, Belgium
| | | | - Lieven Dupont
- Department of Pulmonology, University Hospitals of Leuven, Belgium
| | - Kris De Boeck
- Department of Pediatrics, University Hospitals of Leuven, Belgium
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Kopp BT, Nicholson L, Paul G, Tobias J, Ramanathan C, Hayes D. Geographic variations in cystic fibrosis: An analysis of the U.S. CF Foundation Registry. Pediatr Pulmonol 2015; 50:754-62. [PMID: 25825016 DOI: 10.1002/ppul.23185] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/23/2014] [Revised: 12/29/2014] [Accepted: 01/23/2015] [Indexed: 11/12/2022]
Abstract
BACKGROUND Emerging evidence suggests that the prevalence of pathogens common in cystic fibrosis (CF) may be unevenly distributed across the United States (U.S.). However, very little is known regarding the U.S. distribution of other CF modifiers such as medication usage and patient demographics. Therefore, we sought to determine if regional differences exist in the distribution of demographic variables and patient disease characteristics in the U.S. that may play a role in differential CF outcomes. METHODS Data were analyzed from the 30,896 subjects in the U.S. CF Foundation Patient Registry during the years 2007-2012, via geographical grouping of states based upon the Nationwide Inpatient Sample classification. RESULTS Significant differences in racial distribution were seen, including half of the total U.S. African-American CF population residing in the South. Both African-Americans and Hispanics had increased Medicaid usage (52.2%, 41.8%, respectively). Culture-reported pathogens were markedly different across the U.S., with the highest percentage of patients with Methicillin-resistant Staphylococcus aureus (41.9%), Pseudomonas aeruginosa (71.2%), and non-tuberculous mycobacterium (10.0%) in the South. The South region also had the lowest mean body mass index and forced expiratory volume in one second. Chronic medication usage such as inhaled tobramycin or macrolides followed P. aeruginosa distribution, while inhaled dornase alfa was most used in the West (84.7%). Co-morbid conditions varied, with the highest percentage of depressed subjects in the Midwest (18.3%). Mean regional mortality rates were not statistically different among regions, although highest in each age grouping of the South. CONCLUSIONS The U.S. has significant regional variations in CF demographics, insurance, pathogens, medication usage, and co-morbidities, without an overall impact on regional mortality. Regional variations in care practices should be studied further based on the findings.
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Affiliation(s)
- Benjamin T Kopp
- Section of Pulmonary Medicine, Nationwide Children's Hospital, Columbus, Ohio.,Center for Microbial Pathogenesis, The Research Institute at Nationwide Children's Hospital, Columbus, Ohio
| | - Lisa Nicholson
- Institute for Population Research, The Ohio State University, Columbus, Ohio
| | - Grace Paul
- Section of Pulmonary Medicine, Nationwide Children's Hospital, Columbus, Ohio
| | - Joseph Tobias
- Department of Anesthesiology & Pain Medicine, Nationwide Children's Hospital, Columbus, Ohio
| | - Chandar Ramanathan
- Section of Pulmonary Medicine, Nationwide Children's Hospital, Columbus, Ohio
| | - Don Hayes
- Section of Pulmonary Medicine, Nationwide Children's Hospital, Columbus, Ohio
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Levy H, Farrell PM. New challenges in the diagnosis and management of cystic fibrosis. J Pediatr 2015; 166:1337-41. [PMID: 26008169 PMCID: PMC4477509 DOI: 10.1016/j.jpeds.2015.03.042] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/04/2015] [Accepted: 03/19/2015] [Indexed: 01/03/2023]
Affiliation(s)
- Hara Levy
- Division of Pulmonary Medicine, Department of Pediatrics, Stanley Manne Research Institute, Northwestern University Feinberg School of Medicine, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois
| | - Philip M Farrell
- Departments of Pediatrics and Population Health Sciences, University of Wisconsin School of Medicine and Public Health, Clinical Sciences Center, Madison, Wisconsin
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Bhattacharjee A, Sokolsky T, Wyman SK, Reese MG, Puffenberger E, Strauss K, Morton H, Parad RB, Naylor EW. Development of DNA confirmatory and high-risk diagnostic testing for newborns using targeted next-generation DNA sequencing. Genet Med 2015; 17:337-47. [PMID: 25255367 DOI: 10.1038/gim.2014.117] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2014] [Accepted: 07/31/2014] [Indexed: 12/30/2022] Open
Abstract
PURPOSE Genetic testing is routinely used for second-tier confirmation of newborn sequencing results to rule out false positives and to confirm diagnoses in newborns undergoing inpatient and outpatient care. We developed a targeted next-generation sequencing panel coupled with a variant processing pipeline and demonstrated utility and performance benchmarks across multiple newborn disease presentations in a retrospective clinical study. METHODS The test utilizes an in silico gene filter that focuses directly on 126 genes related to newborn screening diseases and is applied to the exome or a next-generation sequencing panel called NBDx. NBDx targets the 126 genes and additional newborn-specific disorders. It integrates DNA isolation from minimally invasive biological specimens, targeted next-generation screening, and rapid characterization of genetic variation. RESULTS We report a rapid parallel processing of 8 to 20 cases within 105 hours with high coverage on our NBDx panel. Analytical sensitivity of 99.8% was observed across known mutation hotspots. Concordance calls with or without clinical summaries were 94% and 75%, respectively. CONCLUSION Rapid, automated targeted next-generation sequencing and analysis are practical in newborns for second-tier confirmation and neonatal intensive care unit diagnoses, laying a foundation for future primary DNA-based molecular screening of additional disorders and improving existing molecular testing options for newborns.
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Affiliation(s)
| | | | | | | | | | - Kevin Strauss
- Clinic for Special Children, Strasburg, Pennsylvania, USA
| | - Holmes Morton
- Clinic for Special Children, Strasburg, Pennsylvania, USA
| | - Richard B Parad
- Department of Pediatric Newborn Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Edwin W Naylor
- 1] Parabase Genomics, Boston, Massachusetts, USA [2] Division of Genetics, Department of Pediatrics, Medical University of South Carolina, Charleston, South Carolina, USA
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Audrézet MP, Munck A, Scotet V, Claustres M, Roussey M, Delmas D, Férec C, Desgeorges M. Comprehensive CFTR gene analysis of the French cystic fibrosis screened newborn cohort: implications for diagnosis, genetic counseling, and mutation-specific therapy. Genet Med 2014; 17:108-16. [DOI: 10.1038/gim.2014.113] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2014] [Accepted: 05/06/2014] [Indexed: 11/09/2022] Open
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