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Velasco de la Fuente D, Cherix N, Fasel D, Dubray J, Orsinger J, Siravo U, Tran Y. Control upgrade for the TCV coils power supplies. Fusion Engineering and Design 2023. [DOI: 10.1016/j.fusengdes.2023.113539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
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2
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Singhal P, Veturi Y, Dudek SM, Lucas A, Frase A, van Steen K, Schrodi SJ, Fasel D, Weng C, Pendergrass R, Schaid DJ, Kullo IJ, Dikilitas O, Sleiman PMA, Hakonarson H, Moore JH, Williams SM, Ritchie MD, Verma SS. Evidence of epistasis in regions of long-range linkage disequilibrium across five complex diseases in the UK Biobank and eMERGE datasets. Am J Hum Genet 2023; 110:575-591. [PMID: 37028392 PMCID: PMC10119154 DOI: 10.1016/j.ajhg.2023.03.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 03/07/2023] [Indexed: 04/09/2023] Open
Abstract
Leveraging linkage disequilibrium (LD) patterns as representative of population substructure enables the discovery of additive association signals in genome-wide association studies (GWASs). Standard GWASs are well-powered to interrogate additive models; however, new approaches are required for invesigating other modes of inheritance such as dominance and epistasis. Epistasis, or non-additive interaction between genes, exists across the genome but often goes undetected because of a lack of statistical power. Furthermore, the adoption of LD pruning as customary in standard GWASs excludes detection of sites that are in LD but might underlie the genetic architecture of complex traits. We hypothesize that uncovering long-range interactions between loci with strong LD due to epistatic selection can elucidate genetic mechanisms underlying common diseases. To investigate this hypothesis, we tested for associations between 23 common diseases and 5,625,845 epistatic SNP-SNP pairs (determined by Ohta's D statistics) in long-range LD (>0.25 cM). Across five disease phenotypes, we identified one significant and four near-significant associations that replicated in two large genotype-phenotype datasets (UK Biobank and eMERGE). The genes that were most likely involved in the replicated associations were (1) members of highly conserved gene families with complex roles in multiple pathways, (2) essential genes, and/or (3) genes that were associated in the literature with complex traits that display variable expressivity. These results support the highly pleiotropic and conserved nature of variants in long-range LD under epistatic selection. Our work supports the hypothesis that epistatic interactions regulate diverse clinical mechanisms and might especially be driving factors in conditions with a wide range of phenotypic outcomes.
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Affiliation(s)
- Pankhuri Singhal
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Yogasudha Veturi
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Scott M Dudek
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Anastasia Lucas
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Alex Frase
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Kristel van Steen
- Department of Human Genetics, Katholieke Universiteit Leuven, ON4 Herestraat 49, 3000 Leuven, Belgium
| | - Steven J Schrodi
- Laboratory of Genetics, School of Medicine and Public Health, University of Wisconsin, Madison, WI 53706, USA
| | - David Fasel
- Columbia University, New York, NY 10027, USA
| | | | | | | | | | | | | | - Hakon Hakonarson
- Children's Hospital of Pennsylvania, Philadelphia, PA 19104, USA
| | - Jason H Moore
- Department of Computational Biomedicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Scott M Williams
- Department of Genetics and Genome Sciences, School of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Marylyn D Ritchie
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
| | - Shefali S Verma
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
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3
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Wynn J, Milo Rasouly H, Vasquez-Loarte T, Saami AM, Weiss R, Ziniel SI, Appelbaum PS, Wright Clayton E, Christensen KD, Fasel D, Green RC, Hain HS, Harr M, Hoell C, Kullo IJ, Leppig KA, Myers MF, Pacyna JE, Perez EF, Prows CA, Kulchak Rahm A, Campbell-Salome G, Sharp RR, Smith ME, Wiesner GL, Williams JL, Blout Zawatsky CL, Gharavi AG, Chung WK, Holm IA. Do research participants share genomic screening results with family members? J Genet Couns 2021; 31:447-458. [PMID: 34665896 DOI: 10.1002/jgc4.1511] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2021] [Revised: 08/30/2021] [Accepted: 09/04/2021] [Indexed: 01/25/2023]
Abstract
The public health impact of genomic screening can be enhanced by cascade testing. However, cascade testing depends on communication of results to family members. While the barriers and facilitators of family communication have been researched following clinical genetic testing, the factors impacting the dissemination of genomic screening results are unknown. Using the pragmatic Electronic Medical Records and Genomics Network-3 (eMERGE-3) study, we explored the reported sharing practices of participants who underwent genomic screening across the United States. Six eMERGE-3 sites returned genomic screening results for mostly dominant medically actionable disorders and surveyed adult participants regarding communication of results with first-degree relatives. Across the sites, 279 participants completed a 1-month and/or 6-month post-results survey. By 6 months, only 34% of the 156 respondents shared their results with all first-degree relatives and 4% did not share with any. Over a third (39%) first-degree relatives were not notified of the results. Half (53%) of participants who received their results from a genetics provider shared them with all first-degree relatives compared with 11% of participants who received their results from a non-genetics provider. The most frequent reasons for sharing were a feeling of obligation (72%) and that the information could help family members make medical decisions (72%). The most common reasons indicated for not sharing were that the family members were too young (38%), or they were not in contact (25%) or not close to them (25%). These data indicate that the professional returning the results may impact sharing patterns, suggesting that there is a need to continue to educate healthcare providers regarding approaches to facilitate sharing of genetic results within families. Finally, these data suggest that interventions to increase sharing may be universally effective regardless of the origin of the genetic result.
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Affiliation(s)
- Julia Wynn
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY, USA
| | - Hila Milo Rasouly
- Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA
| | - Tania Vasquez-Loarte
- Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA
| | - Akilan M Saami
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY, USA.,Department of Epidemiology, Columbia University Mailman School of Public Health, New York, NY, USA
| | - Robyn Weiss
- Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA
| | - Sonja I Ziniel
- Department of Pediatrics, School of Medicine, University of Colorado, Aurora, CO, USA
| | - Paul S Appelbaum
- Department of Psychiatry, Center for Research on Ethical, Legal & Social Implications of Psychiatric, Neurologic & Behavior Genetics, Columbia University Irving Medical Center, New York, NY, USA
| | - Ellen Wright Clayton
- Center for Biomedical Ethics and Society and Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Kurt D Christensen
- Department of Population Medicine, Precision Medicine Translational Research (PROMoTeR) Center, Harvard Pilgrim Health Care Institute, Boston, MA, USA.,Department of Population Medicine, Harvard Medical School, Boston, MA, USA
| | - David Fasel
- Department of Biomedical Informatics, Columbia University Irving Medical Center, New York, NY, USA
| | - Robert C Green
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Heather S Hain
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Margaret Harr
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Christin Hoell
- Center for Genetic Medicine, Northwestern University, Chicago, IL, USA
| | - Iftikhar J Kullo
- Department of Cardiovascular Medicine, Mayo Clinic, Rochester, MN, USA
| | - Kathleen A Leppig
- Genetic Services and Kaiser Permanente Washington Health Research Institute, Kaiser Permanente of Washington, Seattle, WA, USA
| | - Melanie F Myers
- Divisions of Human Genetics and Patient Services, Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Joel E Pacyna
- Biomedical Ethics Program, Mayo Clinic, Rochester, MN, USA
| | - Emma F Perez
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Cynthia A Prows
- Divisions of Human Genetics and Patient Services, Children's Hospital Medical Center, Cincinnati, OH, USA
| | | | | | | | - Maureen E Smith
- Center for Genetic Medicine, Northwestern University, Chicago, IL, USA
| | - Georgia L Wiesner
- Division of Genetic Medicine, Department of Medicine, and Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | | | | | - Ali G Gharavi
- Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA
| | - Wendy K Chung
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY, USA.,Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA
| | - Ingrid A Holm
- Division of Genetics and Genomics and the Manton Center for Orphan Diseases Research, Boston Children's Hospital, Boston, MA, USA.,Department of Pediatrics, Harvard Medical School, Boston, MA, USA
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4
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Liu C, Zeinomar N, Chung WK, Kiryluk K, Gharavi AG, Hripcsak G, Crew KD, Shang N, Khan A, Fasel D, Manolio TA, Jarvik GP, Rowley R, Justice AE, Rahm AK, Fullerton SM, Smoller JW, Larson EB, Crane PK, Dikilitas O, Wiesner GL, Bick AG, Terry MB, Weng C. Generalizability of Polygenic Risk Scores for Breast Cancer Among Women With European, African, and Latinx Ancestry. JAMA Netw Open 2021; 4:e2119084. [PMID: 34347061 PMCID: PMC8339934 DOI: 10.1001/jamanetworkopen.2021.19084] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
IMPORTANCE Multiple polygenic risk scores (PRSs) for breast cancer have been developed from large research consortia; however, their generalizability to diverse clinical settings is unknown. OBJECTIVE To examine the performance of previously developed breast cancer PRSs in a clinical setting for women of European, African, and Latinx ancestry. DESIGN, SETTING, AND PARTICIPANTS This cohort study using the Electronic Medical Records and Genomics (eMERGE) network data set included 39 591 women from 9 contributing medical centers in the US that had electronic medical records (EMR) linked to genotype data. Breast cancer cases and controls were identified through a validated EMR phenotyping algorithm. MAIN OUTCOMES AND MEASURES Multivariable logistic regression was used to assess the association between breast cancer risk and 7 previously developed PRSs, adjusting for age, study site, breast cancer family history, and first 3 ancestry informative principal components. RESULTS This study included 39 591 women: 33 594 with European, 3801 with African, and 2196 with Latinx ancestry. The mean (SD) age at breast cancer diagnosis was 60.7 (13.0), 58.8 (12.5), and 60.1 (13.0) years for women with European, African, and Latinx ancestry, respectively. PRSs derived from women with European ancestry were associated with breast cancer risk in women with European ancestry (highest odds ratio [OR] per 1-SD increase, 1.46; 95% CI, 1.41-1.51), women with Latinx ancestry (highest OR, 1.31; 95% CI, 1.09-1.58), and women with African ancestry (OR, 1.19; 95% CI, 1.05-1.35). For women with European ancestry, this association with breast cancer risk was largest in the extremes of the PRS distribution, with ORs ranging from 2.19 (95% CI, 1.84-2.53) to 2.48 (95% CI, 1.89-3.25) for the 3 different PRSs examined for those in the highest 1% of the PRS compared with those in the middle quantile. Among women with Latinx and African ancestries at the extremes of the PRS distribution, there were no statistically significant associations. CONCLUSIONS AND RELEVANCE This cohort study found that PRS models derived from women with European ancestry for breast cancer risk generalized well for women with European, Latinx, and African ancestries across different clinical settings, although the effect sizes for women with African ancestry were smaller, likely because of differences in risk allele frequencies and linkage disequilibrium patterns. These results highlight the need to improve representation of diverse population groups, particularly women with African ancestry, in genomic research cohorts.
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Affiliation(s)
- Cong Liu
- Department of Biomedical Informatics, Columbia University Irving Medical Center, New York, New York
| | - Nur Zeinomar
- Department of Epidemiology, Columbia University Irving Medical Center, New York, New York
- Division of Medical Oncology, Rutgers Cancer Institute of New Jersey, Robert Wood Johnson Medical School, New Brunswick, New Jersey
| | - Wendy K. Chung
- Department of Pediatrics, Columbia University Irving Medical Center, New York, New York
| | - Krzysztof Kiryluk
- Department of Medicine, Columbia University Irving Medical Center, New York, New York
| | - Ali G. Gharavi
- Department of Medicine, Columbia University Irving Medical Center, New York, New York
| | - George Hripcsak
- Department of Biomedical Informatics, Columbia University Irving Medical Center, New York, New York
| | - Katherine D. Crew
- Department of Medicine, Columbia University Irving Medical Center, New York, New York
| | - Ning Shang
- Department of Biomedical Informatics, Columbia University Irving Medical Center, New York, New York
| | - Atlas Khan
- Department of Medicine, Columbia University Irving Medical Center, New York, New York
| | - David Fasel
- Department of Biomedical Informatics, Columbia University Irving Medical Center, New York, New York
| | - Teri A. Manolio
- National Human Genome Research Institute, Bethesda, Maryland
| | - Gail P. Jarvik
- Department of Medicine, University of Washington, Seattle
| | - Robb Rowley
- National Human Genome Research Institute, Bethesda, Maryland
| | - Ann E. Justice
- Department of Population Health Sciences, Geisinger, Danville, Pennsylvania
| | - Alanna K. Rahm
- Genomic Medicine Institute, Geisinger, Danville, Pennsylvania
| | | | - Jordan W. Smoller
- Psychiatric and Neurodevelopmental Genetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, Massachusetts
| | - Eric B. Larson
- Kaiser Permanente Washington Health Research Institute, Seattle, Washington
| | - Paul K. Crane
- Department of Medicine, University of Washington, Seattle
| | - Ozan Dikilitas
- Department of Cardiovascular Medicine, Mayo Clinic, Rochester, Minnesota
| | - Georgia L. Wiesner
- Department of Medicine, Division of Genetic Medicine, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Alexander G. Bick
- Department of Medicine, Division of Genetic Medicine, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Mary Beth Terry
- Department of Epidemiology, Columbia University Irving Medical Center, New York, New York
| | - Chunhua Weng
- Department of Biomedical Informatics, Columbia University Irving Medical Center, New York, New York
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5
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Murugan M, Babb LJ, Overby Taylor C, Rasmussen LV, Freimuth RR, Venner E, Yan F, Yi V, Granite SJ, Zouk H, Aronson SJ, Power K, Fedotov A, Crosslin DR, Fasel D, Jarvik GP, Hakonarson H, Bangash H, Kullo IJ, Connolly JJ, Nestor JG, Caraballo PJ, Wei W, Wiley K, Rehm HL, Gibbs RA. Genomic considerations for FHIR®; eMERGE implementation lessons. J Biomed Inform 2021; 118:103795. [PMID: 33930535 PMCID: PMC8583906 DOI: 10.1016/j.jbi.2021.103795] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Revised: 04/06/2021] [Accepted: 04/25/2021] [Indexed: 01/17/2023]
Abstract
Structured representation of clinical genetic results is necessary for advancing precision medicine. The Electronic Medical Records and Genomics (eMERGE) Network's Phase III program initially used a commercially developed XML message format for standardized and structured representation of genetic results for electronic health record (EHR) integration. In a desire to move towards a standard representation, the network created a new standardized format based upon Health Level Seven Fast Healthcare Interoperability Resources (HL7® FHIR®), to represent clinical genomics results. These new standards improve the utility of HL7® FHIR® as an international healthcare interoperability standard for management of genetic data from patients. This work advances the establishment of standards that are being designed for broad adoption in the current health information technology landscape.
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Affiliation(s)
- Mullai Murugan
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA.
| | - Lawrence J Babb
- Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Casey Overby Taylor
- Departments of Medicine and Biomedical Engineering, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Luke V Rasmussen
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Robert R Freimuth
- Department of Digital Health Sciences, Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
| | - Eric Venner
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Fei Yan
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Victoria Yi
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Stephen J Granite
- Departments of Medicine and Biomedical Engineering, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Hana Zouk
- Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine, Cambridge, MA, USA; Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Samuel J Aronson
- Partners Personalized Medicine, Partners HealthCare, Cambridge, MA, USA
| | | | - Alex Fedotov
- Irving Institute for Clinical and Translational Research, Columbia University, New York, NY, USA
| | - David R Crosslin
- Department of Biomedical Informatics and Medical Education, University of Washington, Seattle, WA, USA
| | - David Fasel
- Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA
| | - Gail P Jarvik
- Department of Medicine (Medical Genetics) and Genome Sciences, University of Washington, Seattle, WA, USA
| | - Hakon Hakonarson
- Center for Applied Genomics, Children's Hospital of Philadelphia, PA, USA
| | - Hana Bangash
- Department of Cardiovascular Medicine, Mayo Clinic, Rochester, MN
| | - Iftikhar J Kullo
- Department of Cardiovascular Medicine, Mayo Clinic, Rochester, MN
| | - John J Connolly
- Center for Applied Genomics, Children's Hospital of Philadelphia, PA, USA
| | - Jordan G Nestor
- Department of Medicine, Division of Nephrology, Columbia University, New York, NY, USA
| | - Pedro J Caraballo
- Department of Medicine and Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | - WeiQi Wei
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Ken Wiley
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Heidi L Rehm
- Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Richard A Gibbs
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
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6
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Shang N, Khan A, Polubriaginof F, Zanoni F, Mehl K, Fasel D, Drawz PE, Carrol RJ, Denny JC, Hathcock MA, Arruda-Olson AM, Peissig PL, Dart RA, Brilliant MH, Larson EB, Carrell DS, Pendergrass S, Verma SS, Ritchie MD, Benoit B, Gainer VS, Karlson EW, Gordon AS, Jarvik GP, Stanaway IB, Crosslin DR, Mohan S, Ionita-Laza I, Tatonetti NP, Gharavi AG, Hripcsak G, Weng C, Kiryluk K. Medical records-based chronic kidney disease phenotype for clinical care and "big data" observational and genetic studies. NPJ Digit Med 2021; 4:70. [PMID: 33850243 PMCID: PMC8044136 DOI: 10.1038/s41746-021-00428-1] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Accepted: 02/25/2021] [Indexed: 12/19/2022] Open
Abstract
Chronic Kidney Disease (CKD) represents a slowly progressive disorder that is typically silent until late stages, but early intervention can significantly delay its progression. We designed a portable and scalable electronic CKD phenotype to facilitate early disease recognition and empower large-scale observational and genetic studies of kidney traits. The algorithm uses a combination of rule-based and machine-learning methods to automatically place patients on the staging grid of albuminuria by glomerular filtration rate ("A-by-G" grid). We manually validated the algorithm by 451 chart reviews across three medical systems, demonstrating overall positive predictive value of 95% for CKD cases and 97% for healthy controls. Independent case-control validation using 2350 patient records demonstrated diagnostic specificity of 97% and sensitivity of 87%. Application of the phenotype to 1.3 million patients demonstrated that over 80% of CKD cases are undetected using ICD codes alone. We also demonstrated several large-scale applications of the phenotype, including identifying stage-specific kidney disease comorbidities, in silico estimation of kidney trait heritability in thousands of pedigrees reconstructed from medical records, and biobank-based multicenter genome-wide and phenome-wide association studies.
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Affiliation(s)
- Ning Shang
- Department of Biomedical Informatics, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY, USA
| | - Atlas Khan
- Division of Nephrology, Department of Medicine, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY, USA
| | - Fernanda Polubriaginof
- Department of Biomedical Informatics, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY, USA
| | - Francesca Zanoni
- Division of Nephrology, Department of Medicine, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY, USA
| | - Karla Mehl
- Division of Nephrology, Department of Medicine, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY, USA
| | - David Fasel
- Department of Biomedical Informatics, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY, USA
| | - Paul E Drawz
- Department of Medicine, University of Minnesota, Minnesota, MN, USA
| | - Robert J Carrol
- Department of Biomedical Informatics, Vanderbilt University, Nashville, TN, USA
| | - Joshua C Denny
- Department of Biomedical Informatics, Vanderbilt University, Nashville, TN, USA
- Departments of Medicine, Vanderbilt University, Nashville, TN, USA
| | | | | | | | - Richard A Dart
- Marshfield Clinic Research Institute, Marshfield, WI, USA
| | | | - Eric B Larson
- Kaiser Permanente Washington Health Research Institute, Seattle, WA, USA
| | - David S Carrell
- Kaiser Permanente Washington Health Research Institute, Seattle, WA, USA
| | | | | | | | | | | | | | - Adam S Gordon
- Center for Genetic Medicine, Northwestern University, Chicago, IL, USA
| | - Gail P Jarvik
- Departments of Medicine (Medical Genetics) and Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Ian B Stanaway
- Departments of Medicine (Medical Genetics) and Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - David R Crosslin
- Departments of Medicine (Medical Genetics) and Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
- Department of Biomedical Informatics and Medical Education, University of Washington, Seattle, WA, USA
| | - Sumit Mohan
- Division of Nephrology, Department of Medicine, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY, USA
| | - Iuliana Ionita-Laza
- Department of Biostatistics, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Nicholas P Tatonetti
- Department of Biomedical Informatics, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY, USA
| | - Ali G Gharavi
- Division of Nephrology, Department of Medicine, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY, USA
| | - George Hripcsak
- Department of Biomedical Informatics, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY, USA
| | - Chunhua Weng
- Department of Biomedical Informatics, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY, USA
| | - Krzysztof Kiryluk
- Division of Nephrology, Department of Medicine, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY, USA.
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7
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Nestor JG, Fedotov A, Fasel D, Marasa M, Milo-Rasouly H, Wynn J, Chung WK, Gharavi A, Hripcsak G, Bakken S, Sengupta S, Weng C. An electronic health record (EHR) log analysis shows limited clinician engagement with unsolicited genetic test results. JAMIA Open 2021; 4:ooab014. [PMID: 33709066 PMCID: PMC7935499 DOI: 10.1093/jamiaopen/ooab014] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 01/21/2021] [Accepted: 02/12/2021] [Indexed: 11/14/2022] Open
Abstract
How clinicians utilize medically actionable genomic information, displayed in the electronic health record (EHR), in medical decision-making remains unknown. Participating sites of the Electronic Medical Records and Genomics (eMERGE) Network have invested resources into EHR integration efforts to enable the display of genetic testing data across heterogeneous EHR systems. To assess clinicians’ engagement with unsolicited EHR-integrated genetic test results of eMERGE participants within a large tertiary care academic medical center, we analyzed automatically generated EHR access log data. We found that clinicians viewed only 1% of all the eMERGE genetic test results integrated in the EHR. Using a cluster analysis, we also identified different user traits associated with varying degrees of engagement with the EHR-integrated genomic data. These data contribute important empirical knowledge about clinicians limited and brief engagements with unsolicited EHR-integrated genetic test results of eMERGE participants. Appreciation for user-specific roles provide additional context for why certain users were more or less engaged with the unsolicited results. This study highlights opportunities to use EHR log data as a performance metric to more precisely inform ongoing EHR-integration efforts and decisions about the allocation of informatics resources in genomic research.
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Affiliation(s)
- Jordan G Nestor
- Department of Medicine, Division of Nephrology, Columbia University, New York, New York, USA
| | - Alexander Fedotov
- The Irving Institute for Clinical and Translational Research, Columbia University, New York, New York, USA
| | - David Fasel
- Department of Medicine, Center for Precision Medicine and Genomics, Columbia University, New York, New York, USA
| | - Maddalena Marasa
- Department of Medicine, Division of Nephrology, Columbia University, New York, New York, USA.,Department of Medicine, Center for Precision Medicine and Genomics, Columbia University, New York, New York, USA
| | - Hila Milo-Rasouly
- Department of Medicine, Division of Nephrology, Columbia University, New York, New York, USA.,Department of Medicine, Center for Precision Medicine and Genomics, Columbia University, New York, New York, USA
| | - Julia Wynn
- Department of Pediatrics, Columbia University, New York, New York, USA
| | - Wendy K Chung
- Departments of Pediatric and Medicine, Columbia University, New York, New York, USA
| | - Ali Gharavi
- Department of Medicine, Division of Nephrology, Columbia University, New York, New York, USA.,Department of Medicine, Center for Precision Medicine and Genomics, Columbia University, New York, New York, USA
| | - George Hripcsak
- Department of Biomedical Informatics, Columbia University, New York, New York, USA
| | - Suzanne Bakken
- Department of Biomedical Informatics, Columbia University, New York, New York, USA
| | - Soumitra Sengupta
- Department of Biomedical Informatics, Columbia University, New York, New York, USA
| | - Chunhua Weng
- Department of Biomedical Informatics, Columbia University, New York, New York, USA
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8
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Palmer MR, Kim DS, Crosslin DR, Stanaway IB, Rosenthal EA, Carrell DS, Cronkite DJ, Gordon A, Du X, Li YK, Williams MS, Weng C, Feng Q, Li R, Pendergrass SA, Hakonarson H, Fasel D, Sohn S, Sleiman P, Handelman SK, Speliotes E, Kullo IJ, Larson EB, Jarvik GP. Loci identified by a genome-wide association study of carotid artery stenosis in the eMERGE network. Genet Epidemiol 2020; 45:4-15. [PMID: 32964493 PMCID: PMC7891640 DOI: 10.1002/gepi.22360] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 07/29/2020] [Accepted: 08/11/2020] [Indexed: 12/21/2022]
Abstract
Carotid artery atherosclerotic disease (CAAD) is a risk factor for stroke. We used a genome-wide association (GWAS) approach to discover genetic variants associated with CAAD in participants in the electronic Medical Records and Genomics (eMERGE) Network. We identified adult CAAD cases with unilateral or bilateral carotid artery stenosis and controls without evidence of stenosis from electronic health records at eight eMERGE sites. We performed GWAS with a model adjusting for age, sex, study site, and genetic principal components of ancestry. In eMERGE we found 1793 CAAD cases and 17,958 controls. Two loci reached genome-wide significance, on chr6 in LPA (rs10455872, odds ratio [OR] (95% confidence interval [CI]) = 1.50 (1.30-1.73), p = 2.1 × 10-8 ) and on chr7, an intergenic single nucleotide variant (SNV; rs6952610, OR (95% CI) = 1.25 (1.16-1.36), p = 4.3 × 10-8 ). The chr7 association remained significant in the presence of the LPA SNV as a covariate. The LPA SNV was also associated with coronary heart disease (CHD; 4199 cases and 11,679 controls) in this study (OR (95% CI) = 1.27 (1.13-1.43), p = 5 × 10-5 ) but the chr7 SNV was not (OR (95% CI) = 1.03 (0.97-1.09), p = .37). Both variants replicated in UK Biobank. Elevated lipoprotein(a) concentrations ([Lp(a)]) and LPA variants associated with elevated [Lp(a)] have previously been associated with CAAD and CHD, including rs10455872. With electronic health record phenotypes in eMERGE and UKB, we replicated a previously known association and identified a novel locus associated with CAAD.
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Affiliation(s)
- Melody R Palmer
- Division of Medical Genetics, School of Medicine, University of Washington, Seattle, Washington, USA
| | - Daniel S Kim
- Department of Biostatistics, Center for Statistical Genetics, University of Michigan, Ann Arbor, Michigan, USA
| | - David R Crosslin
- Department of Biomedical Informatics and Medical Education, School of Medicine, University of Washington, Seattle, Washington, USA
| | - Ian B Stanaway
- Department of Biomedical Informatics and Medical Education, School of Medicine, University of Washington, Seattle, Washington, USA
| | - Elisabeth A Rosenthal
- Division of Medical Genetics, School of Medicine, University of Washington, Seattle, Washington, USA
| | - David S Carrell
- Kaiser Permanente Washington Health Research Institute, Seattle, Washington, USA
| | - David J Cronkite
- Kaiser Permanente Washington Health Research Institute, Seattle, Washington, USA
| | - Adam Gordon
- Center for Genetic Medicine, Northwestern University, Chicago, Illinois, USA
| | - Xiaomeng Du
- Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Yatong K Li
- Department of Biostatistics, Center for Statistical Genetics, University of Michigan, Ann Arbor, Michigan, USA
| | - Marc S Williams
- Genomic Medicine Institute, Geisinger, Danville, Pennsylvania, USA
| | - Chunhua Weng
- Department of Biomedical Informatics, Columbia University, New York, New York, USA
| | - Qiping Feng
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Rongling Li
- Division of Genomic Medicine, National Human Genome Research Institute, Bethesda, Maryland, USA
| | | | - Hakon Hakonarson
- Department of Pediatrics, The Center for Applied Genomics, Children's Hospital of Philadelphia, The Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - David Fasel
- Department of Biomedical Informatics, Columbia University, New York, New York, USA
| | | | - Patrick Sleiman
- Department of Pediatrics, The Children's Hospital of Philadelphia, The Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Samuel K Handelman
- Division of Gastroenterology, Department of Internal Medicine and Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, USA
| | - Elizabeth Speliotes
- Division of Gastroenterology, Department of Internal Medicine and Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, USA
| | - Iftikhar J Kullo
- Department of Cardiovascular Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - Eric B Larson
- Kaiser Permanente Washington Health Research Institute, Seattle, Washington, USA
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- The electronic Medical Records and GEnomics Network, NHGRI, NIH, Bethesda, Maryland, USA
| | - Gail P Jarvik
- Division of Medical Genetics, School of Medicine, University of Washington, Seattle, Washington, USA
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Li Y, Groopman EE, D'Agati V, Prakash S, Zhang J, Mizerska-Wasiak M, Caliskan Y, Fasel D, Karnib HH, Bono L, Omran SA, Sabban EA, Kiryluk K, Caridi G, Ghiggeri GM, Sanna-Cherchi S, Scolari F, Gharavi AG. Type IV Collagen Mutations in Familial IgA Nephropathy. Kidney Int Rep 2020; 5:1075-1078. [PMID: 32647767 PMCID: PMC7335950 DOI: 10.1016/j.ekir.2020.04.011] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2020] [Revised: 03/23/2020] [Accepted: 04/10/2020] [Indexed: 01/15/2023] Open
Affiliation(s)
- Yifu Li
- Divsion of Nephrology, Columbia University, New York, New York, USA
| | - Emily E Groopman
- Divsion of Nephrology, Columbia University, New York, New York, USA
| | - Vivette D'Agati
- Division of Renal Pathology, Columbia University, New York, New York, USA
| | - Sindhuri Prakash
- Divsion of Nephrology, Columbia University, New York, New York, USA
| | - Junying Zhang
- Divsion of Nephrology, Columbia University, New York, New York, USA
| | | | - Yasar Caliskan
- Division of Nephrology, Istanbul University, Istanbul, Turkey
| | - David Fasel
- Divsion of Nephrology, Columbia University, New York, New York, USA
| | - Hussein H Karnib
- Department of Medicine, American University of Beirut, Beirut, Lebanon
| | - Luisa Bono
- Nephrology Dialysis with Renal Transplant Department, Civico and Di Cristina Hospital, Palermo, Italy
| | - Sadek Al Omran
- King Faisal Specialist Hospital & Research Center (KFSHRC), Riyadh, Saudi Arabia
| | - Essam Al Sabban
- King Faisal Specialist Hospital & Research Center (KFSHRC), Riyadh, Saudi Arabia
| | | | - Gianluca Caridi
- Department of Nephrology and Transplantation, Istituto G. Gaslini Istituto di Ricovero e Cura a Carattere Scientifico, Genoa, Italy
| | - Gian Marco Ghiggeri
- Department of Nephrology and Transplantation, Istituto G. Gaslini Istituto di Ricovero e Cura a Carattere Scientifico, Genoa, Italy
| | | | - Francesco Scolari
- Department of Medical and Surgical Specialties, Radiological Sciences and Public Health, University of Brescia, Brescia, Italy
| | - Ali G Gharavi
- Divsion of Nephrology, Columbia University, New York, New York, USA
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10
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Salem JE, Shoemaker MB, Bastarache L, Shaffer CM, Glazer AM, Kroncke B, Wells QS, Shi M, Straub P, Jarvik GP, Larson EB, Velez Edwards DR, Edwards TL, Davis LK, Hakonarson H, Weng C, Fasel D, Knollmann BC, Wang TJ, Denny JC, Ellinor PT, Roden DM, Mosley JD. Association of Thyroid Function Genetic Predictors With Atrial Fibrillation: A Phenome-Wide Association Study and Inverse-Variance Weighted Average Meta-analysis. JAMA Cardiol 2020; 4:136-143. [PMID: 30673079 DOI: 10.1001/jamacardio.2018.4615] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Importance Thyroid hormone levels are tightly regulated through feedback inhibition by thyrotropin, produced by the pituitary gland. Hyperthyroidism is overwhelmingly due to thyroid disorders and is well recognized to contribute to a wide spectrum of cardiovascular morbidity, particularly the increasingly common arrhythmia atrial fibrillation (AF). Objective To determine the association between genetically determined thyrotropin levels and AF. Design, Setting, and Participants This phenome-wide association study scanned 1318 phenotypes associated with a polygenic predictor of thyrotropin levels identified by a previously published genome-wide association study that included participants of European ancestry. North American individuals of European ancestry with longitudinal electronic health records were analyzed from May 2008 to November 2016. Analysis began March 2018. Main Outcomes and Measures Clinical diagnoses associated with a polygenic predictor of thyrotropin levels. Exposures Genetically determined thyrotropin levels. Results Of 37 154 individuals, 19 330 (52%) were men. The thyrotropin polygenic predictor was positively associated with hypothyroidism (odds ratio [OR], 1.10; 95% CI, 1.07-1.14; P = 5 × 10-11) and inversely associated with diagnoses related to hyperthyroidism (OR, 0.64; 95% CI, 0.54-0.74; P = 2 × 10-8 for toxic multinodular goiter). Among nonthyroid associations, the top association was AF/flutter (OR, 0.93; 95% CI, 0.9-0.95; P = 9 × 10-7). When the analyses were repeated excluding 9801 individuals with any diagnoses of a thyroid-related disease, the AF association persisted (OR, 0.91; 95% CI, 0.88-0.95; P = 2.9 × 10-6). To replicate this association, we conducted an inverse-variance weighted average meta-analysis using AF single-nucleotide variant weights from a genome-wide association study of 17 931 AF cases and 115 142 controls. As in the discovery analyses, each SD increase in predicted thyrotropin was associated with a decreased risk of AF (OR, 0.86; 95% CI, 0.79-0.93; P = 4.7 × 10-4). In a set of AF cases (n = 745) and controls (n = 1680) older than 55 years, directly measured thyrotropin levels that fell within the normal range were inversely associated with AF risk (OR, 0.91; 95% CI, 0.83-0.99; P = .04). Conclusions and Relevance This study suggests a role for genetically determined variation in thyroid function within a physiologically accepted normal range as a risk factor for AF. The clinical decision to treat subclinical thyroid disease should incorporate the risk for AF as antithyroid medications to treat hyperthyroidism may reduce AF risk and thyroid hormone replacement for hypothyroidism may increase AF risk.
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Affiliation(s)
- Joe-Elie Salem
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee.,Sorbonne Université, Institut National de la Santé et de la Recherche Médicale (INSERM) CIC Paris-Est, AP-HP, Institute of Cardio metabolism and Nutrition (ICAN), Pitié-Salpêtrière Hospital, Department of Pharmacology, Paris, France.,Department of Pharmacology, Vanderbilt University Medical Center, Nashville, Tennessee
| | - M Benjamin Shoemaker
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Lisa Bastarache
- Biomedical Informatics, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Christian M Shaffer
- Department of Pharmacology, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Andrew M Glazer
- Department of Pharmacology, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Brett Kroncke
- Department of Pharmacology, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Quinn S Wells
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Mingjian Shi
- Biomedical Informatics, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Peter Straub
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Gail P Jarvik
- Department of Medicine (Medical Genetics), University of Washington, Seattle.,Department Genome Sciences, University of Washington, Seattle
| | - Eric B Larson
- Department of Medicine (Medical Genetics), University of Washington, Seattle.,Kaiser Permanente Washington Health Research Institute, Seattle
| | - Digna R Velez Edwards
- Department of Obstetrics and Gynecology, Vanderbilt University Medical Center, Nashville, Tennessee.,Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Todd L Edwards
- Biomedical Informatics, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Lea K Davis
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Hakon Hakonarson
- Divisions of Human Genetics and Pulmonary Medicine, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Chunhua Weng
- Department of Biomedical Informatics, Columbia University, New York
| | - David Fasel
- Department of Biomedical Informatics, Columbia University, New York
| | - Bjorn C Knollmann
- Department of Pharmacology, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Thomas J Wang
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Joshua C Denny
- Biomedical Informatics, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Patrick T Ellinor
- Cardiovascular Research Center, Massachusetts General Hospital, Boston.,The Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | - Dan M Roden
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee.,Department of Pharmacology, Vanderbilt University Medical Center, Nashville, Tennessee.,Biomedical Informatics, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Jonathan D Mosley
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee.,Biomedical Informatics, Vanderbilt University Medical Center, Nashville, Tennessee
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11
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Zouk H, Venner E, Lennon NJ, Muzny DM, Abrams D, Adunyah S, Albertson-Junkans L, Ames DC, Appelbaum P, Aronson S, Aufox S, Babb LJ, Balasubramanian A, Bangash H, Basford M, Bastarache L, Baxter S, Behr M, Benoit B, Bhoj E, Bielinski SJ, Bland HT, Blout C, Borthwick K, Bottinger EP, Bowser M, Brand H, Brilliant M, Brodeur W, Caraballo P, Carrell D, Carroll A, Almoguera B, Castillo L, Castro V, Chandanavelli G, Chiang T, Chisholm RL, Christensen KD, Chung W, Chute CG, City B, Cobb BL, Connolly JJ, Crane P, Crew K, Crosslin D, De Andrade M, De la Cruz J, Denson S, Denny J, DeSmet T, Dikilitas O, Friedrich C, Fullerton SM, Funke B, Gabriel S, Gainer V, Gharavi A, Glazer AM, Glessner JT, Goehringer J, Gordon AS, Graham C, Green RC, Gundelach JH, Dayal J, Hain HS, Hakonarson H, Harden MV, Harley J, Harr M, Hartzler A, Hayes MG, Hebbring S, Henrikson N, Hershey A, Hoell C, Holm I, Howell KM, Hripcsak G, Hu J, Jarvik GP, Jayaseelan JC, Jiang Y, Joo YY, Jose S, Josyula NS, Justice AE, Kalla SE, Kalra D, Karlson E, Kelly MA, Keating BJ, Kenny EE, Key D, Kiryluk K, Kitchner T, Klanderman B, Klee E, Kochan DC, Korchina V, Kottyan L, Kovar C, Kudalkar E, Kullo IJ, Lammers P, Larson EB, Lebo MS, Leduc M, Lee MT(M, Leppig KA, Leslie ND, Li R, Liang WH, Lin CF, Linder J, Lindor NM, Lingren T, Linneman JG, Liu C, Liu W, Liu X, Lynch J, Lyon H, Macbeth A, Mahadeshwar H, Mahanta L, Malin B, Manolio T, Marasa M, Marsolo K, Dinsmore MJ, Dodge S, Hynes ED, Dunlea P, Edwards TL, Eng CM, Fasel D, Fedotov A, Feng Q, Fleharty M, Foster A, Freimuth R, McGowan ML, McNally E, Meldrim J, Mentch F, Mosley J, Mukherjee S, Mullen TE, Muniz J, Murdock DR, Murphy S, Murugan M, Myers MF, Namjou B, Ni Y, Obeng AO, Onofrio RC, Taylor CO, Person TN, Peterson JF, Petukhova L, Pisieczko CJ, Pratap S, Prows CA, Puckelwartz MJ, Rahm AK, Raj R, Ralston JD, Ramaprasan A, Ramirez A, Rasmussen L, Rasmussen-Torvik L, Rasouly HM, Raychaudhuri S, Ritchie MD, Rives C, Riza B, Roden D, Rosenthal EA, Santani A, Schaid D, Scherer S, Scott S, Scrol A, Sengupta S, Shang N, Sharma H, Sharp RR, Singh R, Sleiman PM, Slowik K, Smith JC, Smith ME, Smoller JW, Sohn S, Stanaway IB, Starren J, Stroud M, Su J, Tolwinski K, Van Driest SL, Vargas SM, Varugheese M, Veenstra D, Verbitsky M, Vicente G, Wagner M, Walker K, Walunas T, Wang L, Wang Q, Wei WQ, Weiss ST, Wiesner GL, Wells Q, Weng C, White PS, Wiley KL, Williams JL, Williams MS, Wilson MW, Witkowski L, Woods LA, Woolf B, Wu TJ, Wynn J, Yang Y, Yi V, Zhang G, Zhang L, Rehm HL, Gibbs RA. Harmonizing Clinical Sequencing and Interpretation for the eMERGE III Network. Am J Hum Genet 2019; 105:588-605. [PMID: 31447099 PMCID: PMC6731372 DOI: 10.1016/j.ajhg.2019.07.018] [Citation(s) in RCA: 77] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Accepted: 07/26/2019] [Indexed: 12/25/2022] Open
Abstract
The advancement of precision medicine requires new methods to coordinate and deliver genetic data from heterogeneous sources to physicians and patients. The eMERGE III Network enrolled >25,000 participants from biobank and prospective cohorts of predominantly healthy individuals for clinical genetic testing to determine clinically actionable findings. The network developed protocols linking together the 11 participant collection sites and 2 clinical genetic testing laboratories. DNA capture panels targeting 109 genes were used for testing of DNA and sample collection, data generation, interpretation, reporting, delivery, and storage were each harmonized. A compliant and secure network enabled ongoing review and reconciliation of clinical interpretations, while maintaining communication and data sharing between clinicians and investigators. A total of 202 individuals had positive diagnostic findings relevant to the indication for testing and 1,294 had additional/secondary findings of medical significance deemed to be returnable, establishing data return rates for other testing endeavors. This study accomplished integration of structured genomic results into multiple electronic health record (EHR) systems, setting the stage for clinical decision support to enable genomic medicine. Further, the established processes enable different sequencing sites to harmonize technical and interpretive aspects of sequencing tests, a critical achievement toward global standardization of genomic testing. The eMERGE protocols and tools are available for widespread dissemination.
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12
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Siravo U, Alberti S, Dubray J, Fasel D, Perez A. Electrical integration of two 1MW/2s dual-frequency gyrotrons into the EC-system of the TCV tokamak. Fusion Engineering and Design 2019. [DOI: 10.1016/j.fusengdes.2019.02.117] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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13
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Bin W, Bruschi A, Fanale F, Francesca M, Lucca F, Albajar F, Alberti S, Carannante G, Cavinato M, Chelis I, Dell'Era F, Fasel D, Gantenbein G, Goodman T, Granucci G, Hogge JP, Ikeda R, Ioannidis Z, Legrand F, Mellera V, Minelli D, Nardone A, Pagonakis I, Rispoli N, Rzesnicki T, Sanchez F, Spinicchia N, Takahashi K, Tigelis I, Viganò F. Tests and developments of a long-pulse high-power 170 GHz absorbing matched load. Fusion Engineering and Design 2019. [DOI: 10.1016/j.fusengdes.2018.11.019] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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14
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Rasouly HM, Wynn J, Marasa M, Reingold R, Chatterjee D, Kapoor S, Piva S, Kil BH, Mu X, Alvarez M, Nestor J, Mehl K, Revah-Politi A, Lippa N, Ernst ME, Bier L, Espinal A, Haser B, Sinha A, Halim I, Fasel D, Cuneo N, Thompson JJ, Verbitsky M, Cohn EG, Goldman J, Marder K, Klitzman RL, Orjuela MA, So YS, Fedotov A, Crew KD, Kiryluk K, Appelbaum PS, Weng C, Siegel K, Gharavi AG, Chung WK. Correction: Evaluation of the cost and effectiveness of diverse recruitment methods for a genetic screening study. Genet Med 2019; 21:2407. [PMID: 31040387 DOI: 10.1038/s41436-019-0528-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
The original version of this Article contained an error in the undergraduate degree awarded to the author Ian Halim, which was incorrectly given as BS. This has now been corrected to BA in both the PDF and HTML versions of the Article.
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Affiliation(s)
- Hila Milo Rasouly
- Department of Medicine, Columbia University Medical Center, New York, NY, USA
| | - Julia Wynn
- Department of Pediatrics, Columbia University Medical Center, New York, NY, USA
| | - Maddalena Marasa
- Department of Medicine, Columbia University Medical Center, New York, NY, USA
| | - Rachel Reingold
- Department of Medicine, Columbia University Medical Center, New York, NY, USA
| | | | - Sheena Kapoor
- Department of Medicine, Columbia University Medical Center, New York, NY, USA
| | - Stacy Piva
- Department of Medicine, Columbia University Medical Center, New York, NY, USA
| | - Byum Hee Kil
- Department of Medicine, Columbia University Medical Center, New York, NY, USA
| | - Xueru Mu
- Department of Medicine, Columbia University Medical Center, New York, NY, USA
| | - Maria Alvarez
- Department of Medicine, Columbia University Medical Center, New York, NY, USA
| | - Jordan Nestor
- Department of Medicine, Columbia University Medical Center, New York, NY, USA
| | - Karla Mehl
- Department of Medicine, Columbia University Medical Center, New York, NY, USA
| | - Anya Revah-Politi
- Institute for Genomic Medicine, Columbia University Medical Center, New York, NY, USA
| | - Natalie Lippa
- Institute for Genomic Medicine, Columbia University Medical Center, New York, NY, USA
| | - Michelle E Ernst
- Institute for Genomic Medicine, Columbia University Medical Center, New York, NY, USA
| | - Louise Bier
- Institute for Genomic Medicine, Columbia University Medical Center, New York, NY, USA
| | - Aileen Espinal
- Department of Pediatrics, Columbia University Medical Center, New York, NY, USA
| | - Bianca Haser
- Department of Pediatrics, Columbia University Medical Center, New York, NY, USA
| | - Anoushka Sinha
- College of Physician & Surgeons, Columbia University, New York, NY, USA
| | - Ian Halim
- College of Physician & Surgeons, Columbia University, New York, NY, USA
| | - David Fasel
- Department of Biomedical Informatics, Columbia University Irving Medical Center, New York, NY, USA
| | - Nicole Cuneo
- Department of Medicine, Columbia University Medical Center, New York, NY, USA
| | | | - Miguel Verbitsky
- Department of Medicine, Columbia University Medical Center, New York, NY, USA
| | - Elizabeth G Cohn
- Department of Neurology, Aging & Dementia, Columbia University Medical Center, New York, NY, USA
| | - Jill Goldman
- Department of Neurology, Aging & Dementia, Columbia University Medical Center, New York, NY, USA
| | - Karen Marder
- Department of Neurology, Aging & Dementia, Columbia University Medical Center, New York, NY, USA
| | - Robert L Klitzman
- Department of Psychiatry, Columbia University Medical Center, New York, NY, USA
| | - Manuela A Orjuela
- Department of Pediatrics, Columbia University Medical Center, New York, NY, USA.,Department of Epidemiology, Columbia University Medical Center, New York, NY, USA
| | - Yat S So
- Department of Biomedical Informatics, Columbia University Irving Medical Center, New York, NY, USA
| | - Alex Fedotov
- Irving Institute of Clinical and Translational Research, Columbia University Medical Center, New York, NY, USA
| | - Katherine D Crew
- Department of Medicine, Columbia University Medical Center, New York, NY, USA
| | - Krzysztof Kiryluk
- Department of Medicine, Columbia University Medical Center, New York, NY, USA
| | - Paul S Appelbaum
- Department of Psychiatry, Columbia University Medical Center, New York, NY, USA
| | - Chunhua Weng
- Department of Biomedical Informatics, Columbia University Irving Medical Center, New York, NY, USA
| | - Karolynn Siegel
- Department of Sociomedical Sciences, Columbia University Mailman School of Public Health, New York, NY, USA
| | - Ali G Gharavi
- Department of Medicine, Columbia University Medical Center, New York, NY, USA
| | - Wendy K Chung
- Department of Medicine, Columbia University Medical Center, New York, NY, USA. .,Department of Pediatrics, Columbia University Medical Center, New York, NY, USA.
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15
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Zhang X, Veturi Y, Verma S, Bone W, Verma A, Lucas A, Hebbring S, Denny JC, Stanaway IB, Jarvik GP, Crosslin D, Larson EB, Rasmussen-Torvik L, Pendergrass SA, Smoller JW, Hakonarson H, Sleiman P, Weng C, Fasel D, Wei WQ, Kullo I, Schaid D, Chung WK, Ritchie MD. Detecting potential pleiotropy across cardiovascular and neurological diseases using univariate, bivariate, and multivariate methods on 43,870 individuals from the eMERGE network. Pac Symp Biocomput 2019; 24:272-283. [PMID: 30864329 PMCID: PMC6457436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
The link between cardiovascular diseases and neurological disorders has been widely observed in the aging population. Disease prevention and treatment rely on understanding the potential genetic nexus of multiple diseases in these categories. In this study, we were interested in detecting pleiotropy, or the phenomenon in which a genetic variant influences more than one phenotype. Marker-phenotype association approaches can be grouped into univariate, bivariate, and multivariate categories based on the number of phenotypes considered at one time. Here we applied one statistical method per category followed by an eQTL colocalization analysis to identify potential pleiotropic variants that contribute to the link between cardiovascular and neurological diseases. We performed our analyses on ~530,000 common SNPs coupled with 65 electronic health record (EHR)-based phenotypes in 43,870 unrelated European adults from the Electronic Medical Records and Genomics (eMERGE) network. There were 31 variants identified by all three methods that showed significant associations across late onset cardiac- and neurologic- diseases. We further investigated functional implications of gene expression on the detected "lead SNPs" via colocalization analysis, providing a deeper understanding of the discovered associations. In summary, we present the framework and landscape for detecting potential pleiotropy using univariate, bivariate, multivariate, and colocalization methods. Further exploration of these potentially pleiotropic genetic variants will work toward understanding disease causing mechanisms across cardiovascular and neurological diseases and may assist in considering disease prevention as well as drug repositioning in future research.
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Affiliation(s)
- Xinyuan Zhang
- Genomics and Computational Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA*Authors contributed equally to this work
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Salem M, Reichlin T, Fasel D, Leuppi-Taegtmeyer A. Torsade de pointes and systemic azole antifungal agents: Analysis of global spontaneous safety reports. Glob Cardiol Sci Pract 2017; 2017:11. [PMID: 29644223 PMCID: PMC5871400 DOI: 10.21542/gcsp.2017.11] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Background: Literature about torsade de pointes induced by azole antifungal agents is scarce, despite the well-known association. Furthermore, little is known about the latency time between commencing an azole antifungal agent and developing torsade de pointes. The objectives of the present study were therefore to identify all cases of torsade de pointes associated with systemic azole antifungal use reported to the WHO monitoring centre (Uppsala, Sweden) and to determine the latency times between commencing the azole and developing torsade de pointes. Methods: Investigator-driven, retrospective, descriptive analysis of post-marketing pharmacovigilance data regarding systemic azole antifungal agents and the development of torsade de pointes reported to the WHO monitoring centre 1995-2015. Results: 191 cases were reported as follows: fluconazole 130, itraconazole 22, ketoconazole 5, posaconazole 1, voriconazole 33. More than half of all cases involved concomitant suspected or interacting drugs. The median latency times between starting the azole and developing torsade de pointes ranged from 1 (posaconazole) - 9.5 days (itraconazole), range <1-250). Conclusions: Clinicians should be aware of these features of azole-associated torsade de pointes, avoid interacting drugs if at all possible and monitor at-risk patients.
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Affiliation(s)
- M Salem
- Department of Clinical Pharmacology and Toxicology, University & University Hospital Basel, Switzerland
| | - T Reichlin
- Department of Cardiology, University Hospital Basel, Switzerland
| | - D Fasel
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Basel, Switzerland
| | - A Leuppi-Taegtmeyer
- Department of Clinical Pharmacology and Toxicology, University & University Hospital Basel, Switzerland
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Hogge JP, Goodman TP, Alberti S, Albajar F, Avramides KA, Benin P, Bethuys S, Bin W, Bonicelli T, Bruschi A, Cirant S, Droz E, Dumbrajs O, Fasel D, Gandini F, Gantenbein G, Illy S, Jawla S, Jin J, Kern S, Lavanchy P, LiÉvin C, MarlÉtaz B, Marmillod P, Perez A, Piosczyk B, Pagonakis I, Porte L, Rzesnickl T, Siravo U, Thumm M, Tran MQ. First Experimental Results from the European Union 2-MW Coaxial Cavity ITER Gyrotron Prototype. Fusion Science and Technology 2017. [DOI: 10.13182/fst09-a4072] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- J.-P. Hogge
- aCRPP, EURATOM–Confédération Suisse, EPFL, CH-1015 Lausanne, Switzerland
| | - T. P. Goodman
- aCRPP, EURATOM–Confédération Suisse, EPFL, CH-1015 Lausanne, Switzerland
| | - S. Alberti
- aCRPP, EURATOM–Confédération Suisse, EPFL, CH-1015 Lausanne, Switzerland
| | - F. Albajar
- bEFDA Close Support Unit, Boltzmannstrasse 2, D-85748 Garching, Germany
| | - K. A. Avramides
- cSchool of Electrical and Computer Engineering, National Technical University of Athens Association EURATOM-Hellenic Republic, 9 Iroon Polytechniou st. GR-15772 Athens, Greece
| | - P. Benin
- dThales Electron Devices (TED), 2 Rue de Latécoère, F-78141 Vélizy-Villacoublay, France
| | - S. Bethuys
- dThales Electron Devices (TED), 2 Rue de Latécoère, F-78141 Vélizy-Villacoublay, France
| | - W. Bin
- eIstituto di Fisica del Plasma, Association EURATOM–ENEA-CNR, 20125 Milano, Italy
| | - T. Bonicelli
- bEFDA Close Support Unit, Boltzmannstrasse 2, D-85748 Garching, Germany
| | - A. Bruschi
- eIstituto di Fisica del Plasma, Association EURATOM–ENEA-CNR, 20125 Milano, Italy
| | - S. Cirant
- eIstituto di Fisica del Plasma, Association EURATOM–ENEA-CNR, 20125 Milano, Italy
| | - E. Droz
- aCRPP, EURATOM–Confédération Suisse, EPFL, CH-1015 Lausanne, Switzerland
| | - O. Dumbrajs
- fInstitute of Solid State Physics, University of Latvia, Kengaragastr. 8, LV-1063, Riga Latvia and Helsinki University of Technology, Association EURATOM-TEKES, FIN-02150 Espoo, Finland
| | - D. Fasel
- aCRPP, EURATOM–Confédération Suisse, EPFL, CH-1015 Lausanne, Switzerland
| | - F. Gandini
- eIstituto di Fisica del Plasma, Association EURATOM–ENEA-CNR, 20125 Milano, Italy
| | - G. Gantenbein
- gForschungszentrum Karlsruhe, IHM, EURATOM-FZK, D-76021 Karlsruhe, Germany
| | - S. Illy
- gForschungszentrum Karlsruhe, IHM, EURATOM-FZK, D-76021 Karlsruhe, Germany
| | - S. Jawla
- aCRPP, EURATOM–Confédération Suisse, EPFL, CH-1015 Lausanne, Switzerland
| | - J. Jin
- gForschungszentrum Karlsruhe, IHM, EURATOM-FZK, D-76021 Karlsruhe, Germany
| | - S. Kern
- gForschungszentrum Karlsruhe, IHM, EURATOM-FZK, D-76021 Karlsruhe, Germany
| | - P. Lavanchy
- aCRPP, EURATOM–Confédération Suisse, EPFL, CH-1015 Lausanne, Switzerland
| | - C. LiÉvin
- dThales Electron Devices (TED), 2 Rue de Latécoère, F-78141 Vélizy-Villacoublay, France
| | - B. MarlÉtaz
- aCRPP, EURATOM–Confédération Suisse, EPFL, CH-1015 Lausanne, Switzerland
| | - P. Marmillod
- aCRPP, EURATOM–Confédération Suisse, EPFL, CH-1015 Lausanne, Switzerland
| | - A. Perez
- aCRPP, EURATOM–Confédération Suisse, EPFL, CH-1015 Lausanne, Switzerland
| | - B. Piosczyk
- gForschungszentrum Karlsruhe, IHM, EURATOM-FZK, D-76021 Karlsruhe, Germany
| | - I. Pagonakis
- aCRPP, EURATOM–Confédération Suisse, EPFL, CH-1015 Lausanne, Switzerland
| | - L. Porte
- aCRPP, EURATOM–Confédération Suisse, EPFL, CH-1015 Lausanne, Switzerland
| | - T. Rzesnickl
- gForschungszentrum Karlsruhe, IHM, EURATOM-FZK, D-76021 Karlsruhe, Germany
| | - U. Siravo
- aCRPP, EURATOM–Confédération Suisse, EPFL, CH-1015 Lausanne, Switzerland
| | - M. Thumm
- hForschungszentrum Karlsruhe, IHM, EURATOM-FZK, D-76021 Karlsruhe, Germany and Universitaet Karlsruhe Institut fuer Hoechstfrequenztechnik und Elektronik, D-76131 Karlsruhe, Germany
| | - M. Q. Tran
- aCRPP, EURATOM–Confédération Suisse, EPFL, CH-1015 Lausanne, Switzerland
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Fasel D, Bonicelli T, Henderson MA, Tran MQ. Electrical Powering Concept for ITER Electron Cyclotron Radio-Frequency Sources. Fusion Science and Technology 2017. [DOI: 10.13182/fst08-a1669] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- D. Fasel
- Centre de Recherches en Physique des Plasmas CH-1015 Lausanne, Switzerland
| | - T. Bonicelli
- EFDA-CSU, Max Planck Institut Boltzmannstr. 2, D-85748 Garching, Germany
| | - M. A. Henderson
- Centre de Recherches en Physique des Plasmas CH-1015 Lausanne, Switzerland
| | - M. Q. Tran
- Centre de Recherches en Physique des Plasmas CH-1015 Lausanne, Switzerland
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19
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Albajar F, Aiello G, Alberti S, Arnold F, Avramidis K, Bader M, Batista R, Bertizzolo R, Bonicelli T, Braunmueller F, Brescan C, Bruschi A, von Burg B, Camino K, Carannante G, Casarin V, Castillo A, Cauvard F, Cavalieri C, Cavinato M, Chavan R, Chelis J, Cismondi F, Combescure D, Darbos C, Farina D, Fasel D, Figini L, Gagliardi M, Gandini F, Gantenbein G, Gassmann T, Gessner R, Goodman T, Gracia V, Grossetti G, Heemskerk C, Henderson M, Hermann V, Hogge J, Illy S, Ioannidis Z, Jelonnek J, Jin J, Kasparek W, Koning J, Krause A, Landis J, Latsas G, Li F, Mazzocchi F, Meier A, Moro A, Nousiainen R, Purohit D, Nowak S, Omori T, van Oosterhout J, Pacheco J, Pagonakis I, Platania P, Poli E, Preis A, Ronden D, Rozier Y, Rzesnicki T, Saibene G, Sanchez F, Sartori F, Sauter O, Scherer T, Schlatter C, Schreck S, Serikov A, Siravo U, Sozzi C, Spaeh P, Spichiger A, Strauss D, Takahashi K, Thumm M, Tigelis I, Vaccaro A, Vomvoridis J, Tran M, Weinhorst B. Status of Europe’s contribution to the ITER EC system. EPJ Web of Conferences 2015. [DOI: 10.1051/epjconf/20158704004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Le H, Felici F, Paley J, Duval B, Moret JM, Coda S, Sauter O, Fasel D, Marmillod P. Distributed digital real-time control system for TCV tokamak. Fusion Engineering and Design 2014. [DOI: 10.1016/j.fusengdes.2013.11.001] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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21
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Fasel D, Albajar F, Bonicelli T, Perez A, Rinaldi L, Siravo U, Sita L, Taddia G. 5MW CW supply system for the ITER gyrotrons Test Facility. Fusion Engineering and Design 2011. [DOI: 10.1016/j.fusengdes.2011.02.017] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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22
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Mossdorf E, Marzolini C, Fasel D, Mello Fayet A, Blum C, Donath M, Battegay M. [Drug-drug interactions with HIV treatments]. Praxis (Bern 1994) 2011; 100:1193-1196. [PMID: 21938715 DOI: 10.1024/1661-8157/a000673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
We develop a differential diagnosis and diagnostic approach to a possible drug-drug interaction between a cART based on boosted atazanavir and newly given drugs. History taking should not only encompass prescribed but also over-the-counter medication. Exchange of information between attending physicians as to therapeutic changes, documented side effects and adherence, therapeutic drug monitoring of cART and evaluation by pharmacologist in complex situations are the diagnostic tools at hand.
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Affiliation(s)
- E Mossdorf
- Klinik für Infektiologie und Spitalhygiene, Universitätsspital Basel.
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23
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Darbos C, Henderson M, Albajar F, Bigelow T, Bonicelli T, Chavan R, Denisov G, Fasel D, Heidinger R, Hogge J, Kobayashi N, Piosczyk B, Rao S, Rasmussen D, Saibene G, Sakamoto K, Takahashi K, Thumm M. Progress in design and integration of the ITER Electron Cyclotron H&CD system. Fusion Engineering and Design 2009. [DOI: 10.1016/j.fusengdes.2009.02.007] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Henderson M, Alberti S, Benin P, Bonicelli T, Chavan R, Campbell D, Cirant S, Dammertz G, Dormicchi O, Dumbrajs O, Fasel D, Goodman T, Heidinger R, Hogge JP, Kasparek W, Lievin C, Piosczyk B, Poli E, Ramponi G, Saibene G, Sauter O, Serikov A, Taddia G, Thumm M, Tran M, Verhoeven A, Zohm H. EU developments of the ITER ECRH system. Fusion Engineering and Design 2007. [DOI: 10.1016/j.fusengdes.2007.01.029] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Dammertz G, Alberti S, Fasel D, Giguet E, Koppenburg K, Kuntze M, Legrand F, Leonhardt W, Lievin C, Müller G, Neffe G, Piosczyk B, Schmid M, Sterk A, Thumm M, Tran M, Verhoeven A. Power modulation capabilities of the 140 GHz/1 MW gyrotron for the stellarator Wendelstein 7-X. Fusion Engineering and Design 2003. [DOI: 10.1016/s0920-3796(03)00085-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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26
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Fasel D, Alberti S, Bonicelli T, Cleasen R, Goodman T, Hogge J, Perez A, Santinelli M, Sterk A, Tran M, Verhoeven T. Design study of a test stand for ITER gyrotron. Fusion Engineering and Design 2003. [DOI: 10.1016/s0920-3796(03)00123-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Fasel D, Lucı́a C, Ganuza D, Doyharzabal I. 30 kV/10 mA solid state anode modulator for gyrotron plasma heating: design issues and results. Fusion Engineering and Design 2001. [DOI: 10.1016/s0920-3796(01)00273-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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28
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Sauter O, Henderson MA, Hofmann F, Goodman T, Alberti S, Angioni C, Appert K, Behn R, Blanchard P, Bosshard P, Chavan R, Coda S, Duval BP, Fasel D, Favre A, Furno I, Gorgerat P, Hogge J, Isoz P, Joye B, Lavanchy P, Lister JB, Llobet X, Magnin J, Mandrin P, Manini A. Steady-state fully noninductive current driven by electron cyclotron waves in a magnetically confined plasma. Phys Rev Lett 2000; 84:3322-3325. [PMID: 11019080 DOI: 10.1103/physrevlett.84.3322] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/1999] [Indexed: 05/23/2023]
Abstract
A steady-state, fully noninductive plasma current has been sustained for the first time in a tokamak using electron cyclotron current drive only. In this discharge, 123 kA of current have been sustained for the entire gyrotron pulse duration of 2 s. Careful distribution across the plasma minor radius of the power deposited from three 0. 5-MW gyrotrons was essential for reaching steady-state conditions. With central current drive, up to 153 kA of current have been fully replaced transiently for 100 ms. The noninductive scenario is confirmed by the ability to recharge the Ohmic transformer. The dependence of the current drive efficiency on the minor radius is also demonstrated.
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Affiliation(s)
- O Sauter
- Centre de Recherches en Physique des Plasmas, Association Euratom-Confederation Suisse, EPFL, 1015 Lausanne, Switzerland
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