Defining the disease liability of variants in the cystic fibrosis transmembrane conductance regulator gene
Garry Cutting and colleagues report a comprehensive functional and clinical analysis of CFTR variants reported in cystic fibrosis. They determine that 128 of 160 CFTR variants with an allele frequency of >0.01% are causal for disease. Allelic heterogeneity in disease-causing genes presents a subs...
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| Published in | Nature genetics Vol. 45; no. 10; pp. 1160 - 1167 |
|---|---|
| Main Authors | , , , , , , , , , , , , , , , , , , , , |
| Format | Journal Article |
| Language | English |
| Published |
New York
Nature Publishing Group US
01.10.2013
Nature Publishing Group |
| Subjects | |
| Online Access | Get full text |
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| Abstract | Garry Cutting and colleagues report a comprehensive functional and clinical analysis of
CFTR
variants reported in cystic fibrosis. They determine that 128 of 160
CFTR
variants with an allele frequency of >0.01% are causal for disease.
Allelic heterogeneity in disease-causing genes presents a substantial challenge to the translation of genomic variation into clinical practice. Few of the almost 2,000 variants in the cystic fibrosis transmembrane conductance regulator gene
CFTR
have empirical evidence that they cause cystic fibrosis. To address this gap, we collected both genotype and phenotype data for 39,696 individuals with cystic fibrosis in registries and clinics in North America and Europe. In these individuals, 159
CFTR
variants had an allele frequency of ł0.01%. These variants were evaluated for both clinical severity and functional consequence, with 127 (80%) meeting both clinical and functional criteria consistent with disease. Assessment of disease penetrance in 2,188 fathers of individuals with cystic fibrosis enabled assignment of 12 of the remaining 32 variants as neutral, whereas the other 20 variants remained of indeterminate effect. This study illustrates that sourcing data directly from well-phenotyped subjects can address the gap in our ability to interpret clinically relevant genomic variation. |
|---|---|
| AbstractList | Allelic heterogeneity in disease-causing genes presents a substantial challenge to the translation of genomic variation into clinical practice. Few of the almost 2,000 variants in the cystic fibrosis transmembrane conductance regulator gene CFTR have empirical evidence that they cause cystic fibrosis. To address this gap, we collected both genotype and phenotype data for 39,696 individuals with cystic fibrosis in registries and clinics in North America and Europe. In these individuals, 159 CFTR variants had an allele frequency of ł0.01%. These variants were evaluated for both clinical severity and functional consequence, with 127 (80%) meeting both clinical and functional criteria consistent with disease. Assessment of disease penetrance in 2,188 fathers of individuals with cystic fibrosis enabled assignment of 12 of the remaining 32 variants as neutral, whereas the other 20 variants remained of indeterminate effect. This study illustrates that sourcing data directly from well-phenotyped subjects can address the gap in our ability to interpret clinically relevant genomic variation. Allelic heterogeneity in disease-causing genes presents a substantial challenge to the translation of genomic variation into clinical practice. Few of the almost 2,000 variants in the cystic fibrosis transmembrane conductance regulator gene CFTR have empirical evidence that they cause cystic fibrosis. To address this gap, we collected both genotype and phenotype data for 39,696 individuals with cystic fibrosis in registries and clinics in North America and Europe. In these individuals, 159 CFTR variants had an allele frequency of ≥ 0.01 %. These variants were evaluated for both clinical severity and functional consequence, with 127 (80%) meeting both clinical and functional criteria consistent with disease. Assessment of disease penetrance in 2,188 fathers of individuals with cystic fibrosis enabled assignment of 12 of the remaining 32 variants as neutral, whereas the other 20 variants remained of indeterminate effect. This study illustrates that sourcing data directly from well-phenotyped subjects can address the gap in our ability to interpret clinically relevant genomic variation. Allelic heterogeneity in disease-causing genes presents a substantial challenge to the translation of genomic variation into clinical practice. Few of the almost 2,000 variants in the cystic fibrosis transmembrane conductance regulator gene CFTR have empirical evidence that they cause cystic fibrosis. To address this gap, we collected both genotype and phenotype data for 39,696 individuals with cystic fibrosis in registries and clinics in North America and Europe. In these individuals, 159 CFTR variants had an allele frequency of 0.01%. These variants were evaluated for both clinical severity and functional consequence, with 127 (80%) meeting both clinical and functional criteria consistent with disease. Assessment of disease penetrance in 2,188 fathers of individuals with cystic fibrosis enabled assignment of 12 of the remaining 32 variants as neutral, whereas the other 20 variants remained of indeterminate effect. This study illustrates that sourcing data directly from well-phenotyped subjects can address the gap in our ability to interpret clinically relevant genomic variation. Garry Cutting and colleagues report a comprehensive functional and clinical analysis of CFTR variants reported in cystic fibrosis. They determine that 128 of 160 CFTR variants with an allele frequency of >0.01% are causal for disease. Allelic heterogeneity in disease-causing genes presents a substantial challenge to the translation of genomic variation into clinical practice. Few of the almost 2,000 variants in the cystic fibrosis transmembrane conductance regulator gene CFTR have empirical evidence that they cause cystic fibrosis. To address this gap, we collected both genotype and phenotype data for 39,696 individuals with cystic fibrosis in registries and clinics in North America and Europe. In these individuals, 159 CFTR variants had an allele frequency of ł0.01%. These variants were evaluated for both clinical severity and functional consequence, with 127 (80%) meeting both clinical and functional criteria consistent with disease. Assessment of disease penetrance in 2,188 fathers of individuals with cystic fibrosis enabled assignment of 12 of the remaining 32 variants as neutral, whereas the other 20 variants remained of indeterminate effect. This study illustrates that sourcing data directly from well-phenotyped subjects can address the gap in our ability to interpret clinically relevant genomic variation. Allelic heterogeneity in disease-causing genes presents a substantial challenge to the translation of genomic variation to clinical practice. Few of the almost 2,000 variants in the cystic fibrosis transmembrane conductance regulator ( CFTR ) gene have empirical evidence that they cause cystic fibrosis. To address this gap, we collected both genotype and phenotype data for 39,696 cystic fibrosis patients in registries and clinics in North America and Europe. Among these patients, 159 CFTR variants had an allele frequency of ≥0.01%. These variants were evaluated for both clinical severity and functional consequence with 127 (80%) meeting both clinical and functional criteria consistent with disease. Assessment of disease penetrance in 2,188 fathers of cystic fibrosis patients enabled assignment of 12 of the remaining 32 variants as neutral while the other 20 variants remained indeterminate. This study illustrates that sourcing data directly from well-phenotyped subjects can address the gap in our ability to interpret clinically-relevant genomic variation. Allelic heterogeneity in disease-causing genes presents a substantial challenge to the translation of genomic variation into clinical practice. Few of the almost 2,000 variants in the cystic fibrosis transmembrane conductance regulator gene CFTR have empirical evidence that they cause cystic fibrosis. To address this gap, we collected both genotype and phenotype data for 39,696 individuals with cystic fibrosis in registries and clinics in North America and Europe. In these individuals, 159 CFTR variants had an allele frequency of ≥0.01%. These variants were evaluated for both clinical severity and functional consequence, with 127 (80%) meeting both clinical and functional criteria consistent with disease. Assessment of disease penetrance in 2,188 fathers of individuals with cystic fibrosis enabled assignment of 12 of the remaining 32 variants as neutral, whereas the other 20 variants remained of indeterminate effect. This study illustrates that sourcing data directly from well-phenotyped subjects can address the gap in our ability to interpret clinically relevant genomic variation. [PUBLICATION ABSTRACT] Allelic heterogeneity in disease-causing genes presents a substantial challenge to the translation of genomic variation into clinical practice. Few of the almost 2,000 variants in the cystic fibrosis transmembrane conductance regulator gene CFTR have empirical evidence that they cause cystic fibrosis. To address this gap, we collected both genotype and phenotype data for 39,696 individuals with cystic fibrosis in registries and clinics in North America and Europe. In these individuals, 159 CFTR variants had an allele frequency of ł0.01%. These variants were evaluated for both clinical severity and functional consequence, with 127 (80%) meeting both clinical and functional criteria consistent with disease. Assessment of disease penetrance in 2,188 fathers of individuals with cystic fibrosis enabled assignment of 12 of the remaining 32 variants as neutral, whereas the other 20 variants remained of indeterminate effect. This study illustrates that sourcing data directly from well-phenotyped subjects can address the gap in our ability to interpret clinically relevant genomic variation.Allelic heterogeneity in disease-causing genes presents a substantial challenge to the translation of genomic variation into clinical practice. Few of the almost 2,000 variants in the cystic fibrosis transmembrane conductance regulator gene CFTR have empirical evidence that they cause cystic fibrosis. To address this gap, we collected both genotype and phenotype data for 39,696 individuals with cystic fibrosis in registries and clinics in North America and Europe. In these individuals, 159 CFTR variants had an allele frequency of ł0.01%. These variants were evaluated for both clinical severity and functional consequence, with 127 (80%) meeting both clinical and functional criteria consistent with disease. Assessment of disease penetrance in 2,188 fathers of individuals with cystic fibrosis enabled assignment of 12 of the remaining 32 variants as neutral, whereas the other 20 variants remained of indeterminate effect. This study illustrates that sourcing data directly from well-phenotyped subjects can address the gap in our ability to interpret clinically relevant genomic variation. |
| Audience | Academic |
| Author | Zielenski, Julian Patrinos, George P Van Goor, Fredrick Dorfman, Ruslan Castellani, Carlo Thomas, Philip J Penland, Christopher M Masica, David L Sharma, Neeraj Siklosi, Karen R Lewis, Michelle H Cutting, Garry R Karchin, Rachel Kaniecki, Kyle Yu, Haihui Rommens, Johanna M Corey, Mary Ramalho, Anabela S Sosnay, Patrick R Millen, Linda Amaral, Margarida D |
| AuthorAffiliation | 14 Dalla Lana School of Public Health, University of Toronto, ON, Canada 13 Program in Child Evaluative Health Sciences, The Hospital for Sick Children, Toronto, ON, Canada 15 Genetics and Public Policy Center, Berman Institute for Bioethics, Johns Hopkins University, Baltimore, MD 3 McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, MD 16 Department of Molecular Genetics, University of Toronto, ON, Canada 1 Department of Medicine, Johns Hopkins University, Baltimore, MD 5 Department of Genetics and Development, Columbia University College of Physicians and Surgeons, New York, NY 12 University of Patras, School of Health Sciences, Department of Pharmacy, University Campus, Patras, Greece 6 University of Lisboa, Faculty of Sciences, Centre for Biodiversity, Functional and Integrative Genomics (BioFIG), Lisboa, Portugal 2 Perdana University Graduate School of Medicine, Serdang, Malaysia 9 Geneyouin Inc., Maple, ON, Canada 19 Department of Pediatrics, Johns Hopkins |
| AuthorAffiliation_xml | – name: 1 Department of Medicine, Johns Hopkins University, Baltimore, MD – name: 10 Department of Biomedical Engineering, Institute for Computational Medicine, Johns Hopkins University, Baltimore, MD – name: 7 Department of Genetics, National Institute of Health, Lisboa, Portugal – name: 9 Geneyouin Inc., Maple, ON, Canada – name: 3 McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, MD – name: 17 Cystic Fibrosis Center, Azienda Ospedaliera Universitaria Integrata, Verona, Italy – name: 2 Perdana University Graduate School of Medicine, Serdang, Malaysia – name: 13 Program in Child Evaluative Health Sciences, The Hospital for Sick Children, Toronto, ON, Canada – name: 15 Genetics and Public Policy Center, Berman Institute for Bioethics, Johns Hopkins University, Baltimore, MD – name: 12 University of Patras, School of Health Sciences, Department of Pharmacy, University Campus, Patras, Greece – name: 14 Dalla Lana School of Public Health, University of Toronto, ON, Canada – name: 8 Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada – name: 4 Vertex Pharmaceuticals Incorporated, San Diego, CA – name: 5 Department of Genetics and Development, Columbia University College of Physicians and Surgeons, New York, NY – name: 6 University of Lisboa, Faculty of Sciences, Centre for Biodiversity, Functional and Integrative Genomics (BioFIG), Lisboa, Portugal – name: 19 Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, MD, USA – name: 18 Cystic Fibrosis Foundation, Bethesda, MD – name: 11 Department of Physiology, University of Texas Southwestern Medical Center, Dallas, TX, USA – name: 16 Department of Molecular Genetics, University of Toronto, ON, Canada |
| Author_xml | – sequence: 1 givenname: Patrick R surname: Sosnay fullname: Sosnay, Patrick R organization: Department of Medicine, Johns Hopkins University, Perdana University Graduate School of Medicine, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University – sequence: 2 givenname: Karen R surname: Siklosi fullname: Siklosi, Karen R organization: McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University – sequence: 3 givenname: Fredrick surname: Van Goor fullname: Van Goor, Fredrick organization: Vertex Pharmaceuticals, Inc – sequence: 4 givenname: Kyle surname: Kaniecki fullname: Kaniecki, Kyle organization: McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Department of Genetics and Development, Columbia University College of Physicians and Surgeons – sequence: 5 givenname: Haihui surname: Yu fullname: Yu, Haihui organization: Vertex Pharmaceuticals, Inc – sequence: 6 givenname: Neeraj surname: Sharma fullname: Sharma, Neeraj organization: McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University – sequence: 7 givenname: Anabela S surname: Ramalho fullname: Ramalho, Anabela S organization: Centre for Biodiversity, Functional and Integrative Genomics (BioFIG), Faculty of Sciences, University of Lisboa, Department of Genetics, National Institute of Health – sequence: 8 givenname: Margarida D surname: Amaral fullname: Amaral, Margarida D organization: Centre for Biodiversity, Functional and Integrative Genomics (BioFIG), Faculty of Sciences, University of Lisboa, Department of Genetics, National Institute of Health – sequence: 9 givenname: Ruslan surname: Dorfman fullname: Dorfman, Ruslan organization: Program in Genetics and Genome Biology, The Hospital for Sick Children, Geneyouin, Inc – sequence: 10 givenname: Julian surname: Zielenski fullname: Zielenski, Julian organization: Program in Genetics and Genome Biology, The Hospital for Sick Children – sequence: 11 givenname: David L surname: Masica fullname: Masica, David L organization: Department of Biomedical Engineering, Institute for Computational Medicine, Johns Hopkins University – sequence: 12 givenname: Rachel surname: Karchin fullname: Karchin, Rachel organization: Department of Biomedical Engineering, Institute for Computational Medicine, Johns Hopkins University – sequence: 13 givenname: Linda surname: Millen fullname: Millen, Linda organization: Department of Physiology, University of Texas Southwestern Medical Center – sequence: 14 givenname: Philip J surname: Thomas fullname: Thomas, Philip J organization: Department of Physiology, University of Texas Southwestern Medical Center – sequence: 15 givenname: George P surname: Patrinos fullname: Patrinos, George P organization: Department of Pharmacy, School of Health Sciences, University of Patras, University Campus – sequence: 16 givenname: Mary surname: Corey fullname: Corey, Mary organization: Program in Child Evaluative Health Sciences, The Hospital for Sick Children, Dalla Lana School of Public Health, University of Toronto – sequence: 17 givenname: Michelle H surname: Lewis fullname: Lewis, Michelle H organization: Genetics and Public Policy Center, Berman Institute for Bioethics, Johns Hopkins University – sequence: 18 givenname: Johanna M surname: Rommens fullname: Rommens, Johanna M organization: Program in Genetics and Genome Biology, The Hospital for Sick Children, Department of Molecular Genetics, University of Toronto – sequence: 19 givenname: Carlo surname: Castellani fullname: Castellani, Carlo organization: Cystic Fibrosis Center, Azienda Ospedaliera Universitaria Integrata – sequence: 20 givenname: Christopher M surname: Penland fullname: Penland, Christopher M organization: Cystic Fibrosis Foundation – sequence: 21 givenname: Garry R surname: Cutting fullname: Cutting, Garry R email: gcutting@jhmi.edu organization: McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Department of Pediatrics, Johns Hopkins University School of Medicine |
| BackLink | https://www.ncbi.nlm.nih.gov/pubmed/23974870$$D View this record in MEDLINE/PubMed |
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| Snippet | Garry Cutting and colleagues report a comprehensive functional and clinical analysis of
CFTR
variants reported in cystic fibrosis. They determine that 128 of... Allelic heterogeneity in disease-causing genes presents a substantial challenge to the translation of genomic variation into clinical practice. Few of the... Allelic heterogeneity in disease-causing genes presents a substantial challenge to the translation of genomic variation to clinical practice. Few of the almost... |
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| SubjectTerms | 631/208 692/699 Agriculture Algorithms Animal Genetics and Genomics Biomedicine Cancer Research Colleges & universities Cystic fibrosis Cystic Fibrosis - genetics Cystic Fibrosis Transmembrane Conductance Regulator - genetics Diagnosis Experiments Female Gene Frequency Gene Function Genetic aspects Genetic screening Genetic translation Genotype Genotype & phenotype Heterogeneity Human Genetics Humans Laboratories Liability Male Methods Phenotype |
| Title | Defining the disease liability of variants in the cystic fibrosis transmembrane conductance regulator gene |
| URI | https://link.springer.com/article/10.1038/ng.2745 https://www.ncbi.nlm.nih.gov/pubmed/23974870 https://www.proquest.com/docview/1450028864 https://www.proquest.com/docview/1437579588 https://www.proquest.com/docview/1664206425 https://pubmed.ncbi.nlm.nih.gov/PMC3874936 |
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