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Hayeems RZ, Hoang N, Chenier S, Stavropoulos DJ, Pu S, Weksberg R, Shuman C. Capturing the clinical utility of genomic testing: medical recommendations following pediatric microarray. Eur J Hum Genet 2014; 23:1135-41. [PMID: 25491637 PMCID: PMC4538218 DOI: 10.1038/ejhg.2014.260] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2014] [Revised: 10/01/2014] [Accepted: 10/21/2014] [Indexed: 01/08/2023] Open
Abstract
Interpretation of pediatric chromosome microarray (CMA) results presents diagnostic and medical management challenges. Understanding management practices triggered by CMA will inform clinical utility and resource planning. Using a retrospective cohort design, we extracted clinical and management-related data from the records of 752 children with congenital anomalies and/or developmental delay who underwent CMA in an academic pediatric genetics clinic (2009–2011). Frequency distributions and relative rates (RR) of post-CMA medical recommendations in children with reportable and benign CMA results were calculated. Medical recommendations were provided for 79.6% of children with reportable results and 62.0% of children with benign results. Overall, recommendations included specialist consultation (40.8%), imaging (32.5%), laboratory investigations (17.2%), surveillance (4.6%), and family investigations (4.9%). Clinically significant variants and variants of uncertain clinical significance were associated with higher and slightly higher rates of management recommendations, respectively, compared with benign/no variants (RR=1.34; 95% CI (1.22–1.47); RR=1.23; 95% CI (1.09–1.38)). Recommendation rates for clinically significant versus uncertain results depended upon how uncertainty was classified (RRbroad=1.09; 95% CI (0.99–1.2); RRnarrow=1.12; 95% CI (1.02–1.24)). Recommendation rates also varied by the child's age and provider type. In conclusion, medical recommendations follow CMA for the majority of children. Compared with benign CMA results, clinically significant CMA variants are a significant driver of pediatric medical recommendations. Variants of uncertain clinical significance drive recommendations, but to a lesser extent. As a broadening range of specialists will need to respond to CMA results, targeted capacity building is warranted.
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Affiliation(s)
- Robin Z Hayeems
- 1] Program in Child Health Evaluative, Research Institute, The Hospital for Sick Children, Toronto, ON, Canada [2] Institute of Health Policy Management and Evaluation, The University of Toronto, Toronto, ON, Canada
| | - Ny Hoang
- 1] Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, ON, Canada [2] Program in Genetics and Genome Biology, Research Institute, The Hospital for Sick Children, Toronto, ON, Canada
| | - Sebastien Chenier
- Centre Hospitalier Universitaire de Sherbrooke, Sherbrooke, QC, Canada
| | - Dimitri J Stavropoulos
- Department of Paediatric Laboratory Medicine, The Hospital for Sick Children and The University of Toronto, Toronto, ON, Canada
| | - Shuye Pu
- Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada
| | - Rosanna Weksberg
- 1] Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, ON, Canada [2] Program in Genetics and Genome Biology, Research Institute, The Hospital for Sick Children, Toronto, ON, Canada [3] Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada [4] Institute of Medical Sciences, University of Toronto, Toronto, ON, Canada
| | - Cheryl Shuman
- 1] Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, ON, Canada [2] Program in Genetics and Genome Biology, Research Institute, The Hospital for Sick Children, Toronto, ON, Canada [3] Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
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302
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Blue-Smith J. Data collaboration will lead precision medicine. GENOMICS DATA 2014; 2:49. [PMID: 26484069 PMCID: PMC4536052 DOI: 10.1016/j.gdata.2014.04.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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303
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Osier MV. A board game for undergraduate genetics vocabulary and concept review: the pathway shuffle. JOURNAL OF MICROBIOLOGY & BIOLOGY EDUCATION 2014; 15:328-9. [PMID: 25574310 PMCID: PMC4278515 DOI: 10.1128/jmbe.v15i2.794] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
A board game for the review of fundamental genetics concepts is presented. The game is easily prepared and dropped into a classroom setting. Printable materials are available as article supplements. Preliminary results of field testing are discussed, demonstrating a meaningful improvement in student success.
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Affiliation(s)
- Michael V. Osier
- Corresponding author. Mailing address: Rochester Institute of Technology, 85 Lomb Memorial Drive, Rochester, NY 14623. Phone: 585-475-4392. E-mail:
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304
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Reporting genomic secondary findings: ACMG members weigh in. Genet Med 2014; 17:27-35. [PMID: 25394173 DOI: 10.1038/gim.2014.165] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2014] [Accepted: 10/14/2014] [Indexed: 12/17/2022] Open
Abstract
PURPOSE The aim of this study was to survey American College of Medical Genetics and Genomics members about secondary findings from clinical genome-scale sequencing. METHODS A Web-based survey was mailed to 1,687 members of the American College of Medical Genetics and Genomics. Exploratory factor analysis identified underlying factors assessed by survey items. Linear regression assessed associations between factor scores and respondent characteristics. RESULTS The response rate was 29%. Four factors explained 51% of the survey variance: best practices, patient preferences, guidance, and informed consent. Most agreed with "best practice" items describing seeking and reporting of secondary findings as consistent with medical standards, having sufficient evidence, and, for adults, the benefits generally outweighing potential harms. There was lack of agreement regarding benefits versus harms for children and impact on health-care resources. The majority agreed that patient preferences should be considered, including ability to opt out, and that informed consent was feasible and critical. Characteristics significantly associated with factor scores included country of residence, sequencing experience, and years in practice. CONCLUSION The American College of Medical Genetics and Genomics should update a list of genes to be assessed when clinical genome-scale sequencing is performed. Informed consent is necessary, and reporting of secondary findings should be optional. Research on implementation of secondary findings reporting is needed.
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305
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Affiliation(s)
- George P Patrinos
- Department of Pharmacy, School of Health Sciences, University of Patras, Patras, Greece
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306
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Tsai ACH, Liu X. Toward Best Practice in Using Molecular Diagnosis to Guide Medical Management, Are We There Yet? NORTH AMERICAN JOURNAL OF MEDICINE & SCIENCE 2014; 7:199-200. [PMID: 26191339 PMCID: PMC4505911] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Molecular genetics testing has made several huge breakthroughs in the past two decades and many molecular technologies have been applied to our daily medical progress. However, the clinical utility has not reach a consensus by the medical and genetic peers as well as third party payers. The predictive value and clinical applications are variable from one condition to the other. Numerous questions remain including technology deficits, data interpretation and unpredicted phenotypes in complex disorders. In this commentary, the authors reviewed the historical perspective of genetic testing and summarized the current technical deficit, clinical dilemma and suggested a few critical threshold to overcome before the implementation of useful genetic information in standard health care can become a reality.
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Affiliation(s)
- Anne Chun-Hui Tsai
- Department of Molecular and Medical Genetics and Pediatrics, Oregon Health & Science University, OR
| | - Xuezhong Liu
- Department of Otolaryngology and Dr. John T. Macdonald Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL
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307
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Patterson K. Dan Roden. Circ Res 2014; 115:693-5. [DOI: 10.1161/circresaha.113.303267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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308
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McGowan ML, Settersten RA, Juengst ET, Fishman JR. Integrating genomics into clinical oncology: ethical and social challenges from proponents of personalized medicine. Urol Oncol 2014; 32:187-92. [PMID: 24445286 DOI: 10.1016/j.urolonc.2013.10.009] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2013] [Revised: 10/09/2013] [Accepted: 10/11/2013] [Indexed: 11/16/2022]
Abstract
INTRODUCTION The use of molecular tools to individualize health care, predict appropriate therapies, and prevent adverse health outcomes has gained significant traction in the field of oncology under the banner of "personalized medicine" (PM). Enthusiasm for PM in oncology has been fueled by success stories of targeted treatments for a variety of cancers based on their molecular profiles. Though these are clear indications of optimism for PM, little is known about the ethical and social implications of personalized approaches in clinical oncology. OBJECTIVE The objective of this study is to assess how a range of stakeholders engaged in promoting, monitoring, and providing PM understand the challenges of integrating genomic testing and targeted therapies into clinical oncology. METHODS AND MATERIALS The study involved the analysis of in-depth interviews with 117 stakeholders whose experiences and perspectives on PM span a wide variety of institutional and professional settings. RESULTS Despite their considerable enthusiasm for this shift, promoters, monitors, and providers of PM identified 4 domains that provoke heightened ethical and social concerns: (1) informed consent for cancer genomic testing, (2) privacy, confidentiality, and disclosure of genomic test results, (3) access to genomic testing and targeted therapies in oncology, and (4) the costs of scaling up pharmacogenomic testing and targeted cancer therapies. CONCLUSIONS These specific concerns are not unique to oncology, or even genomics. However, those most invested in the success of PM view oncologists' responses to these challenges as precedent setting because oncology is farther along the path of clinical integration of genomic technologies than other fields of medicine. This study illustrates that the rapid emergence of PM approaches in clinical oncology provides a crucial lens for identifying and managing potential frictions and pitfalls that emerge as health care paradigms shift in these directions.
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Affiliation(s)
- Michelle L McGowan
- Department of Bioethics, Case Western Reserve University School of Medicine, Cleveland, OH.
| | - Richard A Settersten
- College of Public Health and Human Sciences, Oregon State University, Corvallis, OR
| | - Eric T Juengst
- Center for Bioethics, Department of Social Medicine, University of North Carolina, Chapel Hill, NC
| | - Jennifer R Fishman
- Biomedical Ethics Unit, Department of Social Studies of Medicine, McGill University, Montreal, Quebec, Canada
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309
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Snyder SR, Mitropoulou C, Patrinos GP, Williams MS. Economic Evaluation of Pharmacogenomics: A Value-Based Approach to Pragmatic Decision Making in the Face of Complexity. Public Health Genomics 2014; 17:256-64. [DOI: 10.1159/000366177] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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310
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Hendershot CS. Pharmacogenetic approaches in the treatment of alcohol use disorders: addressing clinical utility and implementation thresholds. Addict Sci Clin Pract 2014; 9:20. [PMID: 25217046 PMCID: PMC4165632 DOI: 10.1186/1940-0640-9-20] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2014] [Accepted: 09/11/2014] [Indexed: 12/22/2022] Open
Abstract
Despite advances in characterizing genetic influences on addiction liability and treatment response, clinical applications of these efforts have been slow to evolve. Although challenges to clinical translation remain, stakeholders already face decisions about evidentiary thresholds for the uptake of pharmacogenetic tests in practice. There is optimism about potential pharmacogenetic applications for the treatment of alcohol use disorders, with particular interest in the OPRM1 A118G polymorphism as a moderator of naltrexone response. Findings from human and animal studies suggest preliminary evidence for the clinical validity of this association; on this basis, arguments for clinical implementation can be made in accordance with existing frameworks for the uptake of genomic applications. However, generating evidence-based guidelines requires evaluating the clinical utility of pharmacogenetic tests. This goal will remain challenging, largely due to minimal data to inform clinical utility estimates. The pace of genomic discovery highlights the need for clinical utility and implementation research to inform future translation efforts. Near-term implementation of promising pharmacogenetic tests can help expedite this goal, generating an evidence base to enable efficient translation as additional gene-drug associations are discovered.
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Affiliation(s)
- Christian S Hendershot
- Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Ontario, Canada.
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311
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Cooper DN, Brand A, Dolzan V, Fortina P, Innocenti F, Michael Lee MT, Macek M, Al-Mulla F, Prainsack B, Squassina A, Vayena E, Vozikis A, Williams MS, Patrinos GP. Bridging genomics research between developed and developing countries: the Genomic Medicine Alliance. Per Med 2014; 11:615-623. [PMID: 29764053 DOI: 10.2217/pme.14.59] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The Genomic Medicine Alliance is a global academic research network that aims to establish and strengthen collaborative ties between the various genomic medicine stakeholders. Its focus lies on the translation of scientific research findings into clinical practice. It brings together experts from disciplines including genome informatics, pharmacogenomics, public health genomics, ethics in genomics and health economics, and it is supervised by a 14-member International Scientific Advisory Committee comprising internationally renowned scientists. The Alliance's official journal, Public Health Genomics, offers members a highly respected publication forum for their original research findings. In the short-to-medium term, the Genomic Medicine Alliance hopes to harmonize research activities between developed and developing countries and to organize educational activities in the field of genomic medicine.
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Affiliation(s)
- David N Cooper
- Institute of Medical Genetics, School of Medicine, Cardiff University, Cardiff, UK
| | - Angela Brand
- University of Maastricht, Institute of Public Health Genomics, Maastricht, The Netherlands
| | - Vita Dolzan
- University of Ljubljana, School of Medicine, Ljubljana, Slovenia
| | - Paolo Fortina
- Thomas Jefferson University, Kimmel Cancer Center, Philadelphia, PA, USA
| | - Federico Innocenti
- Institute of Pharmacogenomics & Individualized Therapy, University of North Carolina, Chapel Hill, NC, USA
| | - Ming Ta Michael Lee
- Laboratory for International Alliance on Genomic Research, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Milan Macek
- Charles University Prague & Faculty Hospital Motol, Institute of Biology & Medical Genetics, Prague, Czech Republic
| | - Fahd Al-Mulla
- University of Kuwait, Molecular Pathology Unit, Safat, Kuwait
| | - Barbara Prainsack
- King's College London, Department of Social Science, Health & Medicine, London, UK
| | - Alessio Squassina
- University of Cagliari, School of Medicine, Department of Biomedical Sciences, Cagliari, Italy
| | - Effy Vayena
- University of Zurich, Institute of Biomedical Ethics, Zurich, Switzerland
| | | | - Marc S Williams
- Geisinger Health System, Genomic Medicine Institute, Danville, PA, USA
| | - George P Patrinos
- University of Patras, School of Health Sciences, Department of Pharmacy, University Campus, Rion, GR-26504, Patras, Greece
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312
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Affiliation(s)
- Laurie A. Demmer
- Department of Pediatrics, Carolinas Medical Center, Charlotte, North Carolina 28232;
| | - Darrel J. Waggoner
- Department of Human Genetics and Pediatrics, University of Chicago, Chicago, Illinois 60637;
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313
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Kraus C, Rau TT, Lux P, Erlenbach-Wünsch K, Löhr S, Krumbiegel M, Thiel CT, Stöhr R, Agaimy A, Croner RS, Stürzl M, Hohenberger W, Hartmann A, Reis A. Comprehensive screening for mutations associated with colorectal cancer in unselected cases reveals penetrant and nonpenetrant mutations. Int J Cancer 2014; 136:E559-68. [PMID: 25142776 DOI: 10.1002/ijc.29149] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2014] [Revised: 07/17/2014] [Accepted: 07/25/2014] [Indexed: 12/14/2022]
Abstract
Germline mutation testing in patients with colorectal cancer (CRC) is offered only to a subset of patients with a clinical presentation or tumor histology suggestive of familial CRC syndromes, probably underestimating familial CRC predisposition. The aim of our study was to determine whether unbiased screening of newly diagnosed CRC cases with next generation sequencing (NGS) increases the overall detection rate of germline mutations. We analyzed 152 consecutive CRC patients for germline mutations in 18 CRC-associated genes using NGS. All patients were also evaluated for Bethesda criteria and all tumors were investigated for microsatellite instability, immunohistochemistry for mismatch repair proteins and the BRAF*V600E somatic mutation. NGS based sequencing identified 27 variants in 9 genes in 23 out of 152 patients studied (18%). Three of them were already reported as pathogenic and 12 were class 3 germline variants with an uncertain prediction of pathogenicity. Only 1 of these patients fulfilled Bethesda criteria and had a microsatellite instable tumor and an MLH1 germline mutation. The others would have been missed with current approaches: 2 with a MSH6 premature termination mutation and 12 uncertain, potentially pathogenic class 3 variants in APC, MLH1, MSH2, MSH6, MSH3 and MLH3. The higher NGS mutation detection rate compared with current testing strategies based on clinicopathological criteria is probably due to the large genetic heterogeneity and overlapping clinical presentation of the various CRC syndromes. It can also identify apparently nonpenetrant germline mutations complicating the clinical management of the patients and their families.
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Affiliation(s)
- Cornelia Kraus
- Institute of Human Genetics, University Hospital Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
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314
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SanGiovanni JP, Chew EY. Clinical applications of age-related macular degeneration genetics. Cold Spring Harb Perspect Med 2014; 4:cshperspect.a017228. [PMID: 25125423 DOI: 10.1101/cshperspect.a017228] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Understanding genetic causes of age-related macular degeneration (AMD) will eventually yield effective discoveries and improvements in predictive/prognostic methods. These include, but are not limited to, reliable disease prediction (screening for increased discrimination of clinical risk), differential classification of AMD subtypes with biomarkers (development of risk-linked molecular taxonomies), selection of optimal preventive and therapeutic interventions (guided by a biologically meaningful understanding of treatment response), and drug dosing. In this review, we discuss clinical applications informed by key findings in AMD genetics, and provide commentary on leveraging extant and forthcoming evidence to improve AMD risk prediction, AMD classification, and knowledge on the genetic basis of drug activity and toxicity. Advances in translating AMD genetics findings for AMD risk prediction require development of a genetics-based causality for AMD incidence and progression. Molecular subtyping of AMD phenotypes requires a set of dynamic biomarkers presenting prognostic value; although these have yet to be identified, the formation of multidisciplinary teams and their participation in large-scale consortia may yield promising results. Drugs targeting complement and vascular endothelial growth factor (VEGF) systems are under evaluation, and forthcoming work on rare variants and noncoding DNA in AMD pathogenesis will likely reveal biochemical pathways enriched with AMD-associated genetic variants. Pharmacologic targets in these pathways may inform a rational and effective therapeutic approach to preventing and treating this sight-threatening disease.
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Affiliation(s)
- John Paul SanGiovanni
- National Eye Institute, Clinical Trials Branch, Division of Epidemiology and Clinical Applications, National Eye Institute, National Institutes of Health, Bethesda, Maryland 20892
| | - Emily Y Chew
- National Eye Institute, Clinical Trials Branch, Division of Epidemiology and Clinical Applications, National Eye Institute, National Institutes of Health, Bethesda, Maryland 20892
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315
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316
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Savage SK, Ziniel SI, Stoler J, Margulies DM, Holm IA, Brownstein CA. An assessment of clinician and researcher needs for support in the era of genomic medicine. Per Med 2014; 11:569-579. [PMID: 29758800 DOI: 10.2217/pme.14.48] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
AIM To assess clinicians' and researchers' past, current and anticipated future use of next-generation sequencing (NGS) and anticipated needs for support. Materials & methods: A web-based survey was conducted at Boston Children's Hospital. RESULTS Many clinicians anticipate that they will use exome/genome sequencing (44.8%) and/or candidate gene panels (50%) within the next year. Researcher respondents anticipate the need for exome/genome sequencing (48.0%) and candidate gene panels (31.8%). Few respondents (13.6%) said that they felt 'Completely Ready' or 'Pretty Much Ready' to incorporate NGS into their clinical practice or research. CONCLUSION Researchers and clinicians anticipate increased utilization of NGS. Respondents indicated varying degrees of need for a diverse list of support services, ranking interpretation and clinical correlation support as the most needed services.
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Affiliation(s)
- Sarah K Savage
- Division of Genetics & Genomics, Boston Children's Hospital, Boston, MA 02115, USA
| | - Sonja I Ziniel
- Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA.,Division of Adolescent/Young Adult Medicine, Boston Children's Hospital, Boston, MA 02115, USA.,Center for Patient Safety & Quality Research, Program for Patient Safety and Quality, Boston Children's Hospital, Boston, MA 02115, USA
| | - Joan Stoler
- Division of Genetics & Genomics, Boston Children's Hospital, Boston, MA 02115, USA.,Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - David M Margulies
- Division of Genetics & Genomics, Boston Children's Hospital, Boston, MA 02115, USA.,Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA.,Division for Developmental Medicine, Boston Children's Hospital, Boston, MA 02115, USA.,Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA
| | - Ingrid A Holm
- Division of Genetics & Genomics, Boston Children's Hospital, Boston, MA 02115, USA.,Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA.,Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA 02115, USA
| | - Catherine A Brownstein
- Division of Genetics & Genomics, Boston Children's Hospital, Boston, MA 02115, USA.,Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA.,Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA 02115, USA
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317
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Johansen Taber KA, Dickinson BD. Pharmacogenomic knowledge gaps and educational resource needs among physicians in selected specialties. PHARMACOGENOMICS & PERSONALIZED MEDICINE 2014; 7:145-62. [PMID: 25045280 PMCID: PMC4100727 DOI: 10.2147/pgpm.s63715] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
BACKGROUND The use of pharmacogenomic testing in the clinical setting has the potential to improve the safety and effectiveness of drug therapy, yet studies have revealed that physicians lack knowledge about the topic of pharmacogenomics, and are not prepared to implement it in the clinical setting. This study further explores the pharmacogenomic knowledge deficit and educational resource needs among physicians. MATERIALS AND METHODS Surveys of primary care physicians, cardiologists, and psychiatrists were conducted. RESULTS Few physicians reported familiarity with the topic of pharmacogenomics, but more reported confidence in their knowledge about the influence of genetics on drug therapy. Only a small minority had undergone formal training in pharmacogenomics, and a majority reported being unsure what type of pharmacogenomic tests were appropriate to order for the clinical situation. Respondents indicated that an ideal pharmacogenomic educational resource should be electronic and include such components as how to interpret pharmacogenomic test results, recommendations for prescribing, population subgroups most likely to be affected, and contact information for laboratories offering pharmacogenomic testing. CONCLUSION Physicians continue to demonstrate pharmacogenomic knowledge gaps, and are unsure about how to use pharmacogenomic testing in clinical practice. Educational resources that are clinically oriented and easily accessible are preferred by physicians, and may best support appropriate clinical implementation of pharmacogenomics.
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Affiliation(s)
| | - Barry D Dickinson
- Department of Science and Biotechnology, American Medical Association, Chicago, IL, USA
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318
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The business of genomic testing: a survey of early adopters. Genet Med 2014; 16:954-61. [PMID: 25010053 PMCID: PMC4262758 DOI: 10.1038/gim.2014.60] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2014] [Accepted: 04/24/2014] [Indexed: 12/16/2022] Open
Abstract
PURPOSE The practice of "genomic" (or "personalized") medicine requires the availability of appropriate diagnostic testing. Our study objective was to identify the reasons for health systems to bring next-generation sequencing into their clinical laboratories and to understand the process by which such decisions were made. Such information may be of value to other health systems seeking to provide next-generation sequencing testing to their patient populations. METHODS A standardized open-ended interview was conducted with the laboratory medical directors and/or department of pathology chairs of 13 different academic institutions in 10 different states. RESULTS Genomic testing for cancer dominated the institutional decision making, with three primary reasons: more effective delivery of cancer care, the perceived need for institutional leadership in the field of genomics, and the premise that genomics will eventually be cost-effective. Barriers to implementation included implementation cost; the time and effort needed to maintain this newer testing; challenges in interpreting genetic variants; establishing the bioinformatics infrastructure; and curating data from medical, ethical, and legal standpoints. Ultimate success depended on alignment with institutional strengths and priorities and working closely with institutional clinical programs. CONCLUSION These early adopters uniformly viewed genomic analysis as an imperative for developing their expertise in the implementation and practice of genomic medicine.
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319
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Comparative effectiveness of next generation genomic sequencing for disease diagnosis: design of a randomized controlled trial in patients with colorectal cancer/polyposis syndromes. Contemp Clin Trials 2014; 39:1-8. [PMID: 24997220 DOI: 10.1016/j.cct.2014.06.016] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2014] [Revised: 06/24/2014] [Accepted: 06/25/2014] [Indexed: 11/22/2022]
Abstract
Whole exome and whole genome sequencing are applications of next generation sequencing transforming clinical care, but there is little evidence whether these tests improve patient outcomes or if they are cost effective compared to current standard of care. These gaps in knowledge can be addressed by comparative effectiveness and patient-centered outcomes research. We designed a randomized controlled trial that incorporates these research methods to evaluate whole exome sequencing compared to usual care in patients being evaluated for hereditary colorectal cancer and polyposis syndromes. Approximately 220 patients will be randomized and followed for 12 months after return of genomic findings. Patients will receive findings associated with colorectal cancer in a first return of results visit, and findings not associated with colorectal cancer (incidental findings) during a second return of results visit. The primary outcome is efficacy to detect mutations associated with these syndromes; secondary outcomes include psychosocial impact, cost-effectiveness and comparative costs. The secondary outcomes will be obtained via surveys before and after each return visit. The expected challenges in conducting this randomized controlled trial include the relatively low prevalence of genetic disease, difficult interpretation of some genetic variants, and uncertainty about which incidental findings should be returned to patients. The approaches utilized in this study may help guide other investigators in clinical genomics to identify useful outcome measures and strategies to address comparative effectiveness questions about the clinical implementation of genomic sequencing in clinical care.
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320
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Abstract
Developments in genomics continue to increase the number of disorders for which genetic testing is available, whether in the primary healthcare system, through direct-to-consumer testing, or as part of expanded newborn screening panels. This paper reviews a robust literature on public attitudes toward genetics and genetic testing. In general, attitudes are positive about genetic research and new genomic technologies, with majorities indicating an interest in genetic testing. However, complex beliefs comprise the public's thinking about genetics. Attitudes are driven by beliefs about the type of genetic research, the personal and clinical utility of tests, and the area of genetics in which testing is applied. Limitations of current research are noted and suggestions made for future research.
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Affiliation(s)
- Holly Etchegary
- Clinical Epidemiology, Division of Medicine, Faculty of Medicine, Memorial University, Room H1407, Level 1, Health Sciences Centre, 300 Prince Phillip Drive, St John's, NL A1B 3V6, Canada
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321
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The Rapidly Emerging Role for Whole Exome Sequencing in Clinical Genetics. CURRENT GENETIC MEDICINE REPORTS 2014. [DOI: 10.1007/s40142-014-0044-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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322
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Freudenberg-Hua Y, Freudenberg J, Vacic V, Abhyankar A, Emde AK, Ben-Avraham D, Barzilai N, Oschwald D, Christen E, Koppel J, Greenwald B, Darnell RB, Germer S, Atzmon G, Davies P. Disease variants in genomes of 44 centenarians. Mol Genet Genomic Med 2014; 2:438-50. [PMID: 25333069 PMCID: PMC4190879 DOI: 10.1002/mgg3.86] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2014] [Revised: 04/29/2014] [Accepted: 04/29/2014] [Indexed: 12/14/2022] Open
Abstract
To identify previously reported disease mutations that are compatible with extraordinary longevity, we screened the coding regions of the genomes of 44 Ashkenazi Jewish centenarians. Individual genome sequences were generated with 30× coverage on the Illumina HiSeq 2000 and single-nucleotide variants were called with the genome analysis toolkit (GATK). We identified 130 coding variants that were annotated as “pathogenic” or “likely pathogenic” based on the ClinVar database and that are infrequent in the general population. These variants were previously reported to cause a wide range of degenerative, neoplastic, and cardiac diseases with autosomal dominant, autosomal recessive, and X-linked inheritance. Several of these variants are located in genes that harbor actionable incidental findings, according to the recommendations of the American College of Medical Genetics. In addition, we found risk variants for late-onset neurodegenerative diseases, such as the APOE ε4 allele that was even present in a homozygous state in one centenarian who did not develop Alzheimer's disease. Our data demonstrate that the incidental finding of certain reported disease variants in an individual genome may not preclude an extraordinarily long life. When the observed variants are encountered in the context of clinical sequencing, it is thus important to exercise caution in justifying clinical decisions. In genome sequences of 44 Ashkenazi centenarians, we identified many coding variants that were annotated as “pathogenic” or “likely pathogenic” based on the ClinVar database. Our data demonstrate that the incidental finding of certain reported disease variants in an individual genome may not preclude an extraordinarily long life. When the observed variants are encountered in the context of clinical sequencing, it is thus important to exercise caution in justifying clinical decisions.
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Affiliation(s)
- Yun Freudenberg-Hua
- The Litwin-Zucker Research Center for the Study of Alzheimer's Disease and Memory Disorders, The Feinstein Institute for Medical Research, North Shore-LIJ Manhasset, New York, 11030 ; Division of Geriatric Psychiatry, Zucker Hillside Hospital, North Shore-LIJ Glen Oaks, New York, 11040
| | - Jan Freudenberg
- Robert S. Boas Center for Genomics and Human Genetics, The Feinstein Institute for Medical Research, North Shore-LIJ Manhasset, New York, 11030
| | - Vladimir Vacic
- New York Genome Center 101 Avenue of the Americas, New York, New York, 10013
| | - Avinash Abhyankar
- New York Genome Center 101 Avenue of the Americas, New York, New York, 10013
| | - Anne-Katrin Emde
- New York Genome Center 101 Avenue of the Americas, New York, New York, 10013
| | - Danny Ben-Avraham
- Institute for Aging Research Departments of Medicine and Genetics, Albert Einstein College of Medicine 1300 Morris Park Avenue, Bronx, New York, 10461
| | - Nir Barzilai
- Institute for Aging Research Departments of Medicine and Genetics, Albert Einstein College of Medicine 1300 Morris Park Avenue, Bronx, New York, 10461
| | - Dayna Oschwald
- New York Genome Center 101 Avenue of the Americas, New York, New York, 10013
| | - Erika Christen
- The Litwin-Zucker Research Center for the Study of Alzheimer's Disease and Memory Disorders, The Feinstein Institute for Medical Research, North Shore-LIJ Manhasset, New York, 11030
| | - Jeremy Koppel
- The Litwin-Zucker Research Center for the Study of Alzheimer's Disease and Memory Disorders, The Feinstein Institute for Medical Research, North Shore-LIJ Manhasset, New York, 11030 ; Division of Geriatric Psychiatry, Zucker Hillside Hospital, North Shore-LIJ Glen Oaks, New York, 11040
| | - Blaine Greenwald
- Division of Geriatric Psychiatry, Zucker Hillside Hospital, North Shore-LIJ Glen Oaks, New York, 11040
| | - Robert B Darnell
- New York Genome Center 101 Avenue of the Americas, New York, New York, 10013 ; Department of Molecular Neuro-Oncology, Howard Hughes Medical Institute, The Rockefeller University 1230 York Avenue, New York, New York, 10065
| | - Soren Germer
- New York Genome Center 101 Avenue of the Americas, New York, New York, 10013
| | - Gil Atzmon
- Institute for Aging Research Departments of Medicine and Genetics, Albert Einstein College of Medicine 1300 Morris Park Avenue, Bronx, New York, 10461
| | - Peter Davies
- The Litwin-Zucker Research Center for the Study of Alzheimer's Disease and Memory Disorders, The Feinstein Institute for Medical Research, North Shore-LIJ Manhasset, New York, 11030
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323
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Rigter T, Henneman L, Broerse JEW, Shepherd M, Blanco I, Kristoffersson U, Cornel MC. Developing a framework for implementation of genetic services: learning from examples of testing for monogenic forms of common diseases. J Community Genet 2014; 5:337-47. [PMID: 24895224 DOI: 10.1007/s12687-014-0189-x] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2014] [Accepted: 05/14/2014] [Indexed: 01/28/2023] Open
Abstract
Genetics in health care is shifting, and responsibilities of genetic and nongenetic specialists are changing, requiring new guidance on how to adapt health care to advances in genetic services. This paper explores facilitators and barriers in the process of implementation of innovations in genetic health care. Furthermore, lessons learnt for optimizing development of new genetic services are summarized. Barriers and facilitators in transition processes were identified using mixed methods, including an online open-ended questionnaire among professionals and an international expert meeting. A multi-case study approach was used to explore recent experiences with innovations in genetic services in different phases of implementation. Barriers encountered in transitions in genetic service provision include the following: lack of genetic knowledge and skills among nongenetic health care providers, resistance to new divisions of responsibilities, and a need for more close collaboration and communication between geneticists and nongeneticists. Facilitating factors include the following: statutory registration of genetic specialists, availability of essential staff and equipment, and existence of registries and guidelines. Other challenges are experienced in the establishment of the appropriate legal and financial structures. A set of points to consider for genetic innovation processes is proposed, addressing, e.g., transition management and cooperation and communication strategies.
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Affiliation(s)
- Tessel Rigter
- Department of Clinical Genetics, EMGO Institute for Health and Care Research, VU University Medical Center (BS7, D450), PO Box 7057, 1007, Amsterdam, The Netherlands
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324
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Raghavan S, Vassy JL. Do physicians think genomic medicine will be useful for patient care? Per Med 2014; 11:424-433. [PMID: 26161114 DOI: 10.2217/pme.14.25] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Significant technological improvements over the last decade have led to a vast expansion in the understanding of the genomic architecture of human disease. However, the use of genomic information, so-called genomic medicine, in routine clinical care, has been slow in comparison to the growth in genomic discovery. The uptake of genomic technology into clinical practice will depend on physicians' perspectives of its utility in patient care. We review recent literature addressing physician attitudes regarding the usefulness and limitations of genomic testing. We conclude by proposing research areas to better understand the role physicians will play in the uptake of genomic information into clinical medicine.
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Affiliation(s)
- Sridharan Raghavan
- General Medicine Division, Department of Medicine, Massachusetts General Hospital, 50 Staniford Street, 9th Floor, Boston, MA 02114, USA ; Fellowship in General Medicine & Primary Care, Harvard Medical School, Boston, MA, USA
| | - Jason L Vassy
- Section of General Internal Medicine, VA Boston Healthcare System, 150 South Huntington Avenue, 152-G, Boston, MA 02130, USA ; Division of General Medicine & Primary Care, Department of Medicine, Brigham & Women's Hospital, Boston, MA, USA ; Department of Medicine, Harvard Medical School, Boston, MA, USA
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325
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Solomon BD. Obstacles and opportunities for the future of genomic medicine. Mol Genet Genomic Med 2014; 2:205-9. [PMID: 24936509 PMCID: PMC4049360 DOI: 10.1002/mgg3.78] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2014] [Accepted: 03/25/2014] [Indexed: 12/15/2022] Open
Affiliation(s)
- Benjamin D Solomon
- Division of Medical Genomics, Inova Translational Medicine Institute, Inova Health System Falls Church, Virginia ; Department of Pediatrics, Inova Children's Hospital, Inova Health System Falls Church, Virginia
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326
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Berkman BE, Hull SC, Eckstein L. The unintended implications of blurring the line between research and clinical care in a genomic age. Per Med 2014; 11:285-295. [PMID: 25506378 DOI: 10.2217/pme.14.3] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
While the development of next-generation sequencing technology has had a paradigm-changing impact on biomedical research, there is likely to be a gap between discovery of therapeutic benefits in research and actual adoption of the new technology into clinical practice. This gap can create pressure on the research enterprise to provide individualized care more typical of the clinic setting because it is uniquely accessible in research. This blurring of the line between research and clinical care is understandable, and perhaps even inevitable. But even if the gap is only transitory, such a blurring can have lasting implications, both by expanding obligations imposed on researchers, but also by challenging long-held ethical views. We explore this idea, focusing on how the dissolving distinction between research and clinical care has influenced the vigorous debate around how researchers should manage genetic findings (sometimes separated into primary and incidental or secondary findings) resulting from research.
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Affiliation(s)
- Benjamin E Berkman
- Office of the Clinical Director, National Human Genome Research Institute, Bethesda, MD, USA ; Department of Bioethics, Clinical Center, NIH, Bethesda, MD, USA
| | - Sara Chandros Hull
- Office of the Clinical Director, National Human Genome Research Institute, Bethesda, MD, USA ; Department of Bioethics, Clinical Center, NIH, Bethesda, MD, USA
| | - Lisa Eckstein
- Department of Bioethics, Clinical Center, NIH, Bethesda, MD, USA ; Faculty of Law, University of Tasmania, Australia
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327
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Hull SC, Berkman BE. Grappling with genomic incidental findings in the clinical realm. Chest 2014; 145:226-230. [PMID: 24493507 DOI: 10.1378/chest.13-1976] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
We have learned a remarkable amount in recent decades about genomics and its potential contributions to human health and medical practice. However, genomic sequencing technology, which is starting to become incorporated into clinical care, also raises ethical challenges. In particular, there has been significant debate about the appropriate management of genomic incidental findings (GIFs), which we define as pathogenic or likely pathogenic test results that are not apparently relevant to the diagnostic indications for which the tests were ordered. Although there is an emerging consensus that clinicians will have at least some obligation to disclose GIFs to patients, the scope of that obligation is unclear. This commentary identifies nuanced issues that clinicians will likely face in the foreseeable future regarding their emerging obligations to disclose clinically actionable GIFs. Will clinicians be expected to look actively for GIFs? Should GIFs for adult-onset disorders be disclosed to children? What obligations will clinicians have to disclose GIFs to family members of deceased patients? What role should informed consent play? There is value to exploring the range of views on these questions at this time, before genomic sequencing has fully matured as a technology, so that clinicians can anticipate how they will respond to the discovery of GIFs once sequencing becomes a more routine part of clinical care. Genomics is ultimately going to play an important role in the practice of pulmonary medicine, and it is important for pulmonologists and other subspecialists to be well informed about what to expect.
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Affiliation(s)
- Sara Chandros Hull
- Office of the Clinical Director, National Human Genome Research Institute.
| | - Benjamin E Berkman
- Office of the Clinical Director, National Human Genome Research Institute; Department of Bioethics, Clinical Center, National Institutes of Health, Bethesda, MD
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328
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Personalised medicine, disease prevention, and the inverse care law: more harm than benefit? Eur J Epidemiol 2014; 29:383-90. [PMID: 24729105 DOI: 10.1007/s10654-014-9898-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2013] [Accepted: 04/02/2014] [Indexed: 01/11/2023]
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329
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Calzone KA, Jenkins J, Culp S, Caskey S, Badzek L. Introducing a New Competency Into Nursing Practice. JOURNAL OF NURSING REGULATION 2014; 5:40-47. [PMID: 25343056 PMCID: PMC4204730 DOI: 10.1016/s2155-8256(15)30098-3] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
As science advances, new competencies must be integrated into nursing practice to ensure the provision of safe, responsible, and accountable care. This article utilizes a model for integrating a new complex competency into nursing practice, using genomics as the exemplar competency. Nurses working at 23 Magnet® Recognition Program hospitals participated in a 1-year new competency integration effort.The aim of the study was to evaluate nursing workforce attitudes, receptivity, confidence, competency, knowledge, and practices regarding genomics. Results were analyzed using descriptive statistical techniques. Respondents were 7,798 licensed registered nurses. The majority (89%) said it was very or somewhat important for nurses to become more educated in the genetics of common diseases. Overall, the respondents felt genomics was important, but a genomic nursing competency deficit affecting all nurses regardless of academic preparation or role was observed. The study findings provide essential information to help guide the integration of a new competency into nursing practice.
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Affiliation(s)
- Kathleen A Calzone
- Kathleen A. Calzone, PhD, RN, APNG, FAAN, is a senior nurse specialist, research, National Institutes of Health, National Cancer Institute, Center for Cancer Research, Genetics Branch. Jean Jenkins, PhD, RN, FAAN, is a clinical advisor, National Institutes of Health, National Human Genome Research Institute, Genomic Healthcare Branch. Stacey Culp, PhD, is a research assistant professor, West Virginia University School of Nursing, Morgantown. Sarah Caskey, MS, is a project manager, West Virginia University School of Nursing. Laurie Badzek, LLM, JD, MS, RN, FAAN, is a professor and senior author, West Virginia University School of Nursing
| | - Jean Jenkins
- Kathleen A. Calzone, PhD, RN, APNG, FAAN, is a senior nurse specialist, research, National Institutes of Health, National Cancer Institute, Center for Cancer Research, Genetics Branch. Jean Jenkins, PhD, RN, FAAN, is a clinical advisor, National Institutes of Health, National Human Genome Research Institute, Genomic Healthcare Branch. Stacey Culp, PhD, is a research assistant professor, West Virginia University School of Nursing, Morgantown. Sarah Caskey, MS, is a project manager, West Virginia University School of Nursing. Laurie Badzek, LLM, JD, MS, RN, FAAN, is a professor and senior author, West Virginia University School of Nursing
| | - Stacey Culp
- Kathleen A. Calzone, PhD, RN, APNG, FAAN, is a senior nurse specialist, research, National Institutes of Health, National Cancer Institute, Center for Cancer Research, Genetics Branch. Jean Jenkins, PhD, RN, FAAN, is a clinical advisor, National Institutes of Health, National Human Genome Research Institute, Genomic Healthcare Branch. Stacey Culp, PhD, is a research assistant professor, West Virginia University School of Nursing, Morgantown. Sarah Caskey, MS, is a project manager, West Virginia University School of Nursing. Laurie Badzek, LLM, JD, MS, RN, FAAN, is a professor and senior author, West Virginia University School of Nursing
| | - Sarah Caskey
- Kathleen A. Calzone, PhD, RN, APNG, FAAN, is a senior nurse specialist, research, National Institutes of Health, National Cancer Institute, Center for Cancer Research, Genetics Branch. Jean Jenkins, PhD, RN, FAAN, is a clinical advisor, National Institutes of Health, National Human Genome Research Institute, Genomic Healthcare Branch. Stacey Culp, PhD, is a research assistant professor, West Virginia University School of Nursing, Morgantown. Sarah Caskey, MS, is a project manager, West Virginia University School of Nursing. Laurie Badzek, LLM, JD, MS, RN, FAAN, is a professor and senior author, West Virginia University School of Nursing
| | - Laurie Badzek
- Kathleen A. Calzone, PhD, RN, APNG, FAAN, is a senior nurse specialist, research, National Institutes of Health, National Cancer Institute, Center for Cancer Research, Genetics Branch. Jean Jenkins, PhD, RN, FAAN, is a clinical advisor, National Institutes of Health, National Human Genome Research Institute, Genomic Healthcare Branch. Stacey Culp, PhD, is a research assistant professor, West Virginia University School of Nursing, Morgantown. Sarah Caskey, MS, is a project manager, West Virginia University School of Nursing. Laurie Badzek, LLM, JD, MS, RN, FAAN, is a professor and senior author, West Virginia University School of Nursing
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330
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Kullo IJ, Haddad R, Prows CA, Holm I, Sanderson SC, Garrison NA, Sharp RR, Smith ME, Kuivaniemi H, Bottinger EP, Connolly JJ, Keating BJ, McCarty CA, Williams MS, Jarvik GP. Return of results in the genomic medicine projects of the eMERGE network. Front Genet 2014; 5:50. [PMID: 24723935 PMCID: PMC3972474 DOI: 10.3389/fgene.2014.00050] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2013] [Accepted: 02/18/2014] [Indexed: 01/13/2023] Open
Abstract
The electronic Medical Records and Genomics (eMERGE) (Phase I) network was established in 2007 to further genomic discovery using biorepositories linked to the electronic health record (EHR). In Phase II, which began in 2011, genomic discovery efforts continue and in addition the network is investigating best practices for implementing genomic medicine, in particular, the return of genomic results in the EHR for use by physicians at point-of-care. To develop strategies for addressing the challenges of implementing genomic medicine in the clinical setting, the eMERGE network is conducting studies that return clinically-relevant genomic results to research participants and their health care providers. These genomic medicine pilot studies include returning individual genetic variants associated with disease susceptibility or drug response, as well as genetic risk scores for common “complex” disorders. Additionally, as part of a network-wide pharmacogenomics-related project, targeted resequencing of 84 pharmacogenes is being performed and select genotypes of pharmacogenetic relevance are being placed in the EHR to guide individualized drug therapy. Individual sites within the eMERGE network are exploring mechanisms to address incidental findings generated by resequencing of the 84 pharmacogenes. In this paper, we describe studies being conducted within the eMERGE network to develop best practices for integrating genomic findings into the EHR, and the challenges associated with such work.
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Affiliation(s)
- Iftikhar J Kullo
- Division of Cardiovascular Diseases, Mayo Clinic Rochester, MN, USA
| | - Ra'ad Haddad
- Division of Cardiovascular Diseases, Mayo Clinic Rochester, MN, USA
| | - Cynthia A Prows
- Cincinnati Children's Hospital Medical Center Cincinnati, OH, USA
| | | | - Saskia C Sanderson
- Department of Genetics and Genomic Sciences, Charles R. Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai New York, NY, USA
| | - Nanibaa' A Garrison
- Center for Biomedical Ethics and Society, Department of Pediatrics, Vanderbilt University School of Medicine Nashville, TN, USA
| | | | - Maureen E Smith
- Feinberg School of Medicine, Northwestern University Chicago, IL, USA
| | - Helena Kuivaniemi
- The Sigfried and Janet Weis Center for Research, Geisinger Health System Danville, PA, USA
| | - Erwin P Bottinger
- Department of Genetics and Genomic Sciences, Charles R. Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai New York, NY, USA
| | - John J Connolly
- Center for Applied Genomics, Abramson Research Center, The Children's Hospital of Philadelphia Philadelphia, PA, USA
| | - Brendan J Keating
- Center for Applied Genomics, Abramson Research Center, The Children's Hospital of Philadelphia Philadelphia, PA, USA
| | | | - Marc S Williams
- Genomic Medicine Institute, Geisinger Health System Danville, PA, USA
| | - Gail P Jarvik
- Departments of Medicine (Medical Genetics) and Genome Sciences, University of Washington Seattle, WA, USA
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331
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Ramos EM, Din-Lovinescu C, Berg JS, Brooks LD, Duncanson A, Dunn M, Good P, Hubbard TJP, Jarvik GP, O'Donnell C, Sherry ST, Aronson N, Biesecker LG, Blumberg B, Calonge N, Colhoun HM, Epstein RS, Flicek P, Gordon ES, Green ED, Green RC, Hurles M, Kawamoto K, Knaus W, Ledbetter DH, Levy HP, Lyon E, Maglott D, McLeod HL, Rahman N, Randhawa G, Wicklund C, Manolio TA, Chisholm RL, Williams MS. Characterizing genetic variants for clinical action. AMERICAN JOURNAL OF MEDICAL GENETICS PART C-SEMINARS IN MEDICAL GENETICS 2014; 166C:93-104. [PMID: 24634402 DOI: 10.1002/ajmg.c.31386] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Genome-wide association studies, DNA sequencing studies, and other genomic studies are finding an increasing number of genetic variants associated with clinical phenotypes that may be useful in developing diagnostic, preventive, and treatment strategies for individual patients. However, few variants have been integrated into routine clinical practice. The reasons for this are several, but two of the most significant are limited evidence about the clinical implications of the variants and a lack of a comprehensive knowledge base that captures genetic variants, their phenotypic associations, and other pertinent phenotypic information that is openly accessible to clinical groups attempting to interpret sequencing data. As the field of medicine begins to incorporate genome-scale analysis into clinical care, approaches need to be developed for collecting and characterizing data on the clinical implications of variants, developing consensus on their actionability, and making this information available for clinical use. The National Human Genome Research Institute (NHGRI) and the Wellcome Trust thus convened a workshop to consider the processes and resources needed to: (1) identify clinically valid genetic variants; (2) decide whether they are actionable and what the action should be; and (3) provide this information for clinical use. This commentary outlines the key discussion points and recommendations from the workshop.
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332
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Wade JE, Ledbetter DH, Williams MS. Implementation of genomic medicine in a health care delivery system: a value proposition? AMERICAN JOURNAL OF MEDICAL GENETICS PART C-SEMINARS IN MEDICAL GENETICS 2014; 166C:112-6. [PMID: 24619641 DOI: 10.1002/ajmg.c.31392] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
The United States health care system is undergoing significant change and is seeking innovations in care delivery and reimbursement models that will lead to improved value for patients, providers, payers, and employers. Genomic medicine has the potential to be a disruptive innovation that if implemented intelligently can improve value. The article presents the perspective of the leaders of a large integrated healthcare delivery system regarding the decision to invest in implementation of genomic medicine.
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333
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Manolio TA, Green ED. Leading the way to genomic medicine. AMERICAN JOURNAL OF MEDICAL GENETICS PART C-SEMINARS IN MEDICAL GENETICS 2014; 166C:1-7. [PMID: 24619573 DOI: 10.1002/ajmg.c.31384] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The National Human Genome Research Institute, in close collaboration with its research community, is pursuing an ambitious research agenda to facilitate and promote the implementation of genomics in clinical care. Since 2011, research programs utilizing next-generation sequencing in the management of cancer and other multigenic conditions, workup of undiagnosed conditions, and evaluation of disorders of the newborn period have been initiated, along with projects identifying clinically actionable variants and exploring the ethical and social implications of reporting these findings. Several genomic medicine symposia and other consultations have helped to shape these research initiatives and develop educational materials for physicians and others working to implement the use of genomic findings in clinical care. These efforts provide a valuable complement to the highly successful basic genomics research enterprise that has at last enabled the transition of genomics from the bench to the bedside.
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334
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Shuldiner AR, Palmer K, Pakyz RE, Alestock TD, Maloney KA, O'Neill C, Bhatty S, Schub J, Overby CL, Horenstein RB, Pollin TI, Kelemen MD, Beitelshees AL, Robinson SW, Blitzer MG, McArdle PF, Brown L, Jeng LJB, Zhao RY, Ambulos N, Vesely MR. Implementation of pharmacogenetics: the University of Maryland Personalized Anti-platelet Pharmacogenetics Program. AMERICAN JOURNAL OF MEDICAL GENETICS PART C-SEMINARS IN MEDICAL GENETICS 2014; 166C:76-84. [PMID: 24616408 DOI: 10.1002/ajmg.c.31396] [Citation(s) in RCA: 73] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Despite a substantial evidence base, implementation of pharmacogenetics into routine patient care has been slow due to a number of non-trivial practical barriers. We implemented a Personalized Anti-platelet Pharmacogenetics Program (PAP3) for cardiac catheterization patients at the University of Maryland Medical Center and the Baltimore Veterans Administration Medical Center Patients' are offered CYP2C19 genetic testing, which is performed in our Clinical Laboratory Improvement Amendment (CLIA)-certified Translational Genomics Laboratory. Results are returned within 5 hr along with clinical decision support that includes interpretation of results and prescribing recommendations for anti-platelet therapy based on the Clinical Pharmacogenetics Implementation Consortium guidelines. Now with a working template for PAP3, implementation of other drug-gene pairs is in process. Lessons learned as described in this article may prove useful to other medical centers as they implement pharmacogenetics into patient care, a critical step in the pathway to personalized and genomic medicine.
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335
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Lazaridis KN, McAllister TM, Babovic-Vuksanovic D, Beck SA, Borad MJ, Bryce AH, Chanan-Khan AA, Ferber MJ, Fonseca R, Johnson KJ, Klee EW, Lindor NM, McCormick JB, McWilliams RR, Parker AS, Riegert-Johnson DL, Rohrer Vitek CR, Schahl KA, Schultz C, Stewart K, Then GC, Wieben ED, Farrugia G. Implementing individualized medicine into the medical practice. AMERICAN JOURNAL OF MEDICAL GENETICS PART C-SEMINARS IN MEDICAL GENETICS 2014; 166C:15-23. [PMID: 24616301 DOI: 10.1002/ajmg.c.31387] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
There is increasing recognition that genomic medicine as part of individualized medicine has a defined role in patient care. Rapid advances in technology and decreasing cost combine to bring genomic medicine closer to the clinical practice. There is also growing evidence that genomic-based medicine can advance patient outcomes, tailor therapy and decrease side effects. However the challenges to integrate genomics into the workflow involved in patient care remain vast, stalling assimilation of genomic medicine into mainstream medical practice. In this review we describe the approach taken by one institution to further individualize medicine by offering, executing and interpreting whole exome sequencing on a clinical basis through an enterprise-wide, standalone individualized medicine clinic. We present our experience designing and executing such an individualized medicine clinic, sharing lessons learned and describing early implementation outcomes.
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336
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Kassahn KS, Scott HS, Caramins MC. Integrating massively parallel sequencing into diagnostic workflows and managing the annotation and clinical interpretation challenge. Hum Mutat 2014; 35:413-23. [PMID: 24510514 DOI: 10.1002/humu.22525] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2013] [Accepted: 01/30/2014] [Indexed: 11/07/2022]
Abstract
Massively parallel sequencing has become a powerful tool for the clinical management of patients with applications in diagnosis, guidance of treatment, prediction of drug response, and carrier screening. A considerable challenge for the clinical implementation of these technologies is the management of the vast amount of sequence data generated, in particular the annotation and clinical interpretation of genomic variants. Here, we describe annotation steps that can be automated and common strategies employed for variant prioritization. The definition of best practice standards for variant annotation and prioritization is still ongoing; at present, there is limited consensus regarding an optimal clinical sequencing pipeline. We provide considerations to help define these. For the first time, clinical genetics and genomics is not limited by our ability to sequence, but our ability to clinically interpret and use genomic information in health management. We argue that the development of standardized variant annotation and interpretation approaches and software tools implementing these warrants further support. As we gain a better understanding of the significance of genomic variation through research, patients will be able to benefit from the full scope that these technologies offer.
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Affiliation(s)
- Karin S Kassahn
- Genetic and Molecular Pathology, SA Pathology, Women's and Children's Hospital, North Adelaide, South Australia, 5006, Australia; School of Molecular and Biomedical Science, University of Adelaide, Adelaide, South Australia, 5000, Australia
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Phillips KA, Ann Sakowski J, Trosman J, Douglas MP, Liang SY, Neumann P. The economic value of personalized medicine tests: what we know and what we need to know. Genet Med 2014; 16:251-7. [PMID: 24232413 PMCID: PMC3949119 DOI: 10.1038/gim.2013.122] [Citation(s) in RCA: 74] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2013] [Accepted: 07/09/2013] [Indexed: 11/09/2022] Open
Abstract
PURPOSE There is uncertainty about when personalized medicine tests provide economic value. We assessed evidence on the economic value of personalized medicine tests and gaps in the evidence base. METHODS We created a unique evidence base by linking data on published cost-utility analyses from the Tufts Cost-Effectiveness Analysis Registry with data measuring test characteristics and reflecting where value analyses may be most needed: (i) tests currently available or in advanced development, (ii) tests for drugs with Food and Drug Administration labels with genetic information, (iii) tests with demonstrated or likely clinical utility, (iv) tests for conditions with high mortality, and (v) tests for conditions with high expenditures. RESULTS We identified 59 cost-utility analyses studies that examined personalized medicine tests (1998-2011). A majority (72%) of the cost/quality-adjusted life year ratios indicate that testing provides better health although at higher cost, with almost half of the ratios falling below $50,000 per quality-adjusted life year gained. One-fifth of the results indicate that tests may save money. CONCLUSION Many personalized medicine tests have been found to be relatively cost-effective, although fewer have been found to be cost saving, and many available or emerging medicine tests have not been evaluated. More evidence on value will be needed to inform decision making and assessment of genomic priorities.
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Affiliation(s)
- Kathryn A Phillips
- 1] Department of Clinical Pharmacy, University of California, San Francisco, San Francisco, California, USA [2] UCSF Philip R. Lee Institute for Health Policy, San Francisco, California, USA [3] UCSF Helen Diller Family Comprehensive Cancer Center, San Francisco, California, USA [4] UCSF Institute for Human Genetics, Center for Business Models in Healthcare, Chicago, Illinois, USA
| | - Julie Ann Sakowski
- Department of Clinical Pharmacy, University of California, San Francisco, San Francisco, California, USA
| | - Julia Trosman
- 1] Department of Clinical Pharmacy, University of California, San Francisco, San Francisco, California, USA [2] UCSF Institute for Human Genetics, Center for Business Models in Healthcare, Chicago, Illinois, USA
| | - Michael P Douglas
- 1] Department of Clinical Pharmacy, University of California, San Francisco, San Francisco, California, USA [2] McKing Consulting Corporation, Fairfax, Virginia, USA
| | - Su-Ying Liang
- 1] Department of Clinical Pharmacy, University of California, San Francisco, San Francisco, California, USA [2] Palo Alto Medical Foundation Research Institute, Palo Alto, California, USA
| | - Peter Neumann
- Center for Evaluation of Value and Risk in Health, Institute for Clinical Research and Health Policy Studies, Tufts Medical Center, Boston, Massachusetts, USA
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Sivendran S, Chang R, Pham L, Phelps RG, Harcharik ST, Hall LD, Bernardo SG, Moskalenko MM, Sivendran M, Fu Y, de Moll EH, Pan M, Moon JY, Arora S, Cohain A, DiFeo A, Ferringer TC, Tismenetsky M, Tsui CL, Friedlander PA, Parides MK, Banchereau J, Chaussabel D, Lebwohl MG, Wolchok JD, Bhardwaj N, Burakoff SJ, Oh WK, Palucka K, Merad M, Schadt EE, Saenger YM. Dissection of immune gene networks in primary melanoma tumors critical for antitumor surveillance of patients with stage II-III resectable disease. J Invest Dermatol 2014; 134:2202-2211. [PMID: 24522433 DOI: 10.1038/jid.2014.85] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2013] [Revised: 01/14/2014] [Accepted: 01/15/2014] [Indexed: 01/18/2023]
Abstract
Patients with resected stage II-III cutaneous melanomas remain at high risk for metastasis and death. Biomarker development has been limited by the challenge of isolating high-quality RNA for transcriptome-wide profiling from formalin-fixed and paraffin-embedded (FFPE) primary tumor specimens. Using NanoString technology, RNA from 40 stage II-III FFPE primary melanomas was analyzed and a 53-immune-gene panel predictive of non-progression (area under the curve (AUC)=0.920) was defined. The signature predicted disease-specific survival (DSS P<0.001) and recurrence-free survival (RFS P<0.001). CD2, the most differentially expressed gene in the training set, also predicted non-progression (P<0.001). Using publicly available microarray data from 46 primary human melanomas (GSE15605), a coexpression module enriched for the 53-gene panel was then identified using unbiased methods. A Bayesian network of signaling pathways based on this data identified driver genes. Finally, the proposed 53-gene panel was confirmed in an independent test population of 48 patients (AUC=0.787). The gene signature was an independent predictor of non-progression (P<0.001), RFS (P<0.001), and DSS (P=0.024) in the test population. The identified driver genes are potential therapeutic targets, and the 53-gene panel should be tested for clinical application using a larger data set annotated on the basis of prospectively gathered data.
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Affiliation(s)
- Shanthi Sivendran
- Division of Hematology and Oncology, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA; Hematology/Oncology Medical Specialists, Lancaster General Health, Lancaster, Pennsylvania, USA
| | - Rui Chang
- Department of Genetics and Genomic Science, Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, New York, USA.
| | - Lisa Pham
- Department of Genetics and Genomic Science, Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Robert G Phelps
- Department of Dermatology, Tisch Cancer Center, Icahn School of Medicine at Mount Sinai, New York, New York, USA; Department of Pathology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Sara T Harcharik
- Department of Dermatology, Tisch Cancer Center, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Lawrence D Hall
- Department of Dermatology, Geisinger Health Systems, Dermatology Woodbine Danville, Danville, Pennsylvania, USA
| | - Sebastian G Bernardo
- Department of Dermatology, Tisch Cancer Center, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Marina M Moskalenko
- Division of Hematology and Oncology, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Meera Sivendran
- Department of Dermatology, Geisinger Health Systems, Dermatology Woodbine Danville, Danville, Pennsylvania, USA
| | - Yichun Fu
- Division of Hematology and Oncology, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Ellen H de Moll
- Division of Hematology and Oncology, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Michael Pan
- Division of Hematology and Oncology, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Jee Young Moon
- Department of Genetics and Genomic Science, Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Sonali Arora
- Department of Genetics and Genomic Science, Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Ariella Cohain
- Department of Genetics and Genomic Science, Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Analisa DiFeo
- Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, Ohio, USA
| | - Tammie C Ferringer
- Department of Pathology, Geisinger Health Systems, Danville, Pennsylvania, USA
| | - Mikhail Tismenetsky
- Department of Pathology, Icahn School of Medicine at Mount Sinai, New York, New York, USA; Department of Pathology, Englewood Hospital and Medical Center, Englewood, New Jersey, USA
| | - Cindy L Tsui
- Department of Dermatology, Tisch Cancer Center, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Philip A Friedlander
- Division of Hematology and Oncology, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Michael K Parides
- Center for Biostatistics, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Jacques Banchereau
- Department of Clinical Immunology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Damien Chaussabel
- Benaroya Research Institute at Virginia Mason, Seattle, Washington, USA
| | - Mark G Lebwohl
- Department of Dermatology, Tisch Cancer Center, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Jedd D Wolchok
- Ludwig Center for Cancer Immunotherapy, Memorial Sloan-Kettering Cancer Center, New York, New York, USA
| | - Nina Bhardwaj
- Division of Hematology and Oncology, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA; Department of Pathology, New York University, New York, New York, USA; Department of Dermatology, New York University, New York, New York, USA
| | - Steven J Burakoff
- Division of Hematology and Oncology, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - William K Oh
- Division of Hematology and Oncology, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Karolina Palucka
- Division of Hematology and Oncology, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA; Baylor Institute for Immunology Research, Dallas, Texas, USA
| | - Miriam Merad
- Division of Hematology and Oncology, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA; Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Eric E Schadt
- Department of Genetics and Genomic Science, Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Yvonne M Saenger
- Division of Hematology and Oncology, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA; Department of Dermatology, Tisch Cancer Center, Icahn School of Medicine at Mount Sinai, New York, New York, USA.
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339
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Delivery of clinical genetic consultative services in the Veterans Health Administration. Genet Med 2014; 16:609-19. [PMID: 24503778 DOI: 10.1038/gim.2013.202] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2013] [Accepted: 12/04/2013] [Indexed: 12/20/2022] Open
Abstract
OBJECTIVE To characterize the delivery of genetic consultative services for adults, we examined the prevalence and organizational determinants of genetic consult availability and the organization of these services in the Veterans Health Administration. METHODS We conducted a Web-based survey of Veterans Health Administration clinical leaders. We summarized facility characteristics using descriptive statistics. Multivariate logistic regression assessed associations between organizational characteristics and consult availability. RESULTS We received 353 survey responses from key informants representing 141 Veterans Affairs Medical Centers. Clinicians could obtain genetic consults at 110 (78%) Veterans Affairs Medical Centers. Cancer genetic and neurogenetic consults were most common. Academic affiliation (odds ratio = 3.0; 95% confidence interval: 1.1-8.6) and provider education about genetics (odds ratio = 2.9; 95% confidence interval: 1.1-7.8) were significantly associated with consult availability. The traditional model of multidisciplinary specialty clinics or coordinated services between geneticists and other providers was most prevalent, although variability in the organization of these services was described, with consults available on-site, at another Veterans Affairs Medical Center, via telegenetics, or at non-Veterans Health Administration facilities. The emerging model of nongeneticists integrating genetics into their practices was also reported, with considerable variability by specialty. CONCLUSION Both traditional and emerging models for genetic consultation are available in the Veterans Health Administration; however, there is variability in service organization that could influence quality of care.
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340
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Affiliation(s)
- Corinne D Engelman
- Department of Population Health Sciences, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin
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341
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Wagner JK, Mozersky JT, Pyeritz RE. "Use it or lose it" as an alternative approach to protect genetic privacy in personalized medicine. Urol Oncol 2014; 32:198-201. [PMID: 24445287 PMCID: PMC3970576 DOI: 10.1016/j.urolonc.2013.09.016] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2013] [Revised: 09/10/2013] [Accepted: 09/13/2013] [Indexed: 01/13/2023]
Affiliation(s)
- Jennifer K. Wagner
- University of Pennsylvania, Center for the Integration of Genetic Healthcare Technologies (CIGHT), 1112 Penn Tower, 399 S. 34 St., Philadelphia, PA 19104, 215-614-0689 (phone), 215-615-5315 (fax)
| | - Jessica T. Mozersky
- University of Pennsylvania, Center for the Integration of Genetic Healthcare Technologies (CIGHT), 1112 Penn Tower, 399 S. 34 St., Philadelphia, PA 19104, 215-614-0209 (phone), 215-615-5315 (fax)
| | - Reed E. Pyeritz
- University of Pennsylvania, Center for the Integration of Genetic Healthcare Technologies (CIGHT), 11-133 Smilow Center for Translational Research, 3400 Civic Center Blvd., PA 19104, 215-614-0933 (phone), 215-573-8606 (fax)
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342
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Horizon scanning for translational genomic research beyond bench to bedside. Genet Med 2014; 16:535-8. [PMID: 24406461 PMCID: PMC4079725 DOI: 10.1038/gim.2013.184] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2013] [Accepted: 10/25/2013] [Indexed: 12/16/2022] Open
Abstract
The dizzying pace of genomic discoveries is leading to an increasing number of clinical applications. However, very little translational research is ongoing beyond Bench to Bedside to assess validity, utility, implementation and outcomes of such applications. Here we report cross sectional results of ongoing horizon scanning of translational genomic research conducted between May 16, 2012 and May 15, 2013. Based on a weekly, systematic query of PubMed, we created a curated set of 505 beyond bench-to-bedside research publications, including 312 original research articles, 123 systematic and other reviews, 38 clinical guidelines, policies and recommendations, and 32 papers describing tools, decision support and educational materials. Most papers (62%) addressed a specific genomic test or other health application; almost half of these (n=180) were related to cancer. We estimate that these publications account for 0.5% of reported human genomics and genetics research during the same time. These data provide baseline information to track the evolving knowledge base and gaps in genomic medicine. Continuous horizon scanning is crucial for an evidence-based translation of genomic discoveries into improved health care and disease prevention.
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343
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Gene-environment interactions in severe intraventricular hemorrhage of preterm neonates. Pediatr Res 2014; 75:241-50. [PMID: 24192699 PMCID: PMC3946468 DOI: 10.1038/pr.2013.195] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/11/2013] [Accepted: 08/06/2013] [Indexed: 12/20/2022]
Abstract
Intraventricular hemorrhage (IVH) of the preterm neonate is a complex developmental disorder, with contributions from both the environment and the genome. IVH, or hemorrhage into the germinal matrix of the developing brain with secondary periventricular infarction, occurs in that critical period of time before the 32nd to 33rd wk postconception and has been attributed to changes in cerebral blood flow to the immature germinal matrix microvasculature. Emerging data suggest that genes subserving coagulation, inflammatory, and vascular pathways and their interactions with environmental triggers may influence both the incidence and severity of cerebral injury and are the subject of this review. Polymorphisms in the Factor V Leiden gene are associated with the atypical timing of IVH, suggesting an as yet unknown environmental trigger. The methylenetetrahydrofolate reductase (MTHFR) variants render neonates more vulnerable to cerebral injury in the presence of perinatal hypoxia. The present study demonstrates that the MTHFR 677C>T polymorphism and low 5-min Apgar score additively increase the risk of IVH. Finally, review of published preclinical data suggests the stressors of delivery result in hemorrhage in the presence of mutations in collagen 4A1, a major structural protein of the developing cerebral vasculature. Maternal genetics and fetal environment may also play a role.
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344
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Henderson GE, Wolf SM, Kuczynski KJ, Joffe S, Sharp RR, Parsons DW, Knoppers BM, Yu JH, Appelbaum PS. The challenge of informed consent and return of results in translational genomics: empirical analysis and recommendations. THE JOURNAL OF LAW, MEDICINE & ETHICS : A JOURNAL OF THE AMERICAN SOCIETY OF LAW, MEDICINE & ETHICS 2014; 42:344-55. [PMID: 25264092 PMCID: PMC4262925 DOI: 10.1111/jlme.12151] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
As exome and genome sequencing move into clinical application, questions surround how to elicit consent and handle potential return of individual genomic results. This study analyzes nine consent forms used in NIH-funded sequencing studies. Content analysis reveals considerable heterogeneity, including in defining results that may be returned, identifying potential benefits and risks of return, protecting privacy, addressing placement of results in the medical record, and data-sharing. In response to lack of consensus, we offer recommendations.
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Affiliation(s)
- Gail E Henderson
- Professor and the Chair of Social Medicine in the School of Medicine and an Adjunct Professor of Sociology at the University of North Carolina at Chapel Hill
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345
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Autoimmune liver disease, autoimmunity and liver transplantation. J Hepatol 2014; 60:210-23. [PMID: 24084655 DOI: 10.1016/j.jhep.2013.09.020] [Citation(s) in RCA: 142] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/25/2013] [Revised: 08/13/2013] [Accepted: 09/22/2013] [Indexed: 02/08/2023]
Abstract
Primary biliary cirrhosis (PBC), primary sclerosing cholangitis (PSC) and autoimmune hepatitis (AIH) represent the three major autoimmune liver diseases (AILD). PBC, PSC, and AIH are all complex disorders in that they result from the effects of multiple genes in combination with as yet unidentified environmental factors. Recent genome-wide association studies have identified numerous risk loci for PBC and PSC that host genes involved in innate or acquired immune responses. These loci may provide a clue as to the immune-based pathogenesis of AILD. Moreover, many significant risk loci for PBC and PSC are also risk loci for other autoimmune disorders, such type I diabetes, multiple sclerosis and rheumatoid arthritis, suggesting a shared genetic basis and possibly similar molecular pathways for diverse autoimmune conditions. There is no curative treatment for all three disorders, and a significant number of patients eventually progress to end-stage liver disease requiring liver transplantation (LT). LT in this context has a favourable overall outcome with current patient and graft survival exceeding 80% at 5years. Indications are as for other chronic liver disease although recent data suggest that while lethargy improves after transplantation, the effect is modest and variable so lethargy alone is not an indication. In contrast, pruritus rapidly responds. Cholangiocarcinoma, except under rigorous selection criteria, excludes LT because of the high risk of recurrence. All three conditions may recur after transplantation and are associated with a greater risk of both acute cellular and chronic ductopenic rejection. It is possible that a crosstalk between alloimmune and autoimmune response perpetuate each other. An immunological response toward self- or allo-antigens is well recognised after LT in patients transplanted for non-autoimmune indications and sometimes termed "de novo autoimmune hepatitis". Whether this is part of the spectrum of rejection or an autoimmune process is not clear. In this manuscript, we review novel findings about disease processes and mechanisms that lead to autoimmunity in the liver and their possible involvement in the immune response vs. the graft after LT.
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346
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Ormond KE, Cho MK. Translating personalized medicine using new genetic technologies in clinical practice: the ethical issues. Per Med 2014; 11:211-222. [PMID: 25221608 PMCID: PMC4160120 DOI: 10.2217/pme.13.104] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The integration of new genetic technologies into clinical practice holds great promise for the personalization of medical care, particularly the use of large-scale DNA sequencing for genome-wide genetic testing. However, these technologies also yield unprecedented amounts of information whose clinical implications are not fully understood, and we are still developing technical standards for measuring sequence accuracy. These technical and clinical challenges raise ethical issues that are similar to but qualitatively different from those that we are accustomed to dealing with for traditional medical genetics. The sheer amount of information afforded by genome sequencing requires rethinking of how to implement core ethical principles including, but not limited to: informed consent, privacy and data ownership and sharing, technology regulation, issues of access, particularly as new technology is integrated into clinical practice, and issues of potential stigma and impact on perceptions of disability. In this article, we will review the issues of informed consent, privacy, data ownership and technology regulation as they relate to the emerging field of personalized medicine and genomics.
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Affiliation(s)
- Kelly E Ormond
- Department of Genetics, Mail Stop-5208, Stanford University, Stanford, CA 94305-5208, USA
- Stanford Center for Biomedical Ethics, 1215 Welch Road, Modular A, Stanford, CA 94305-5417, USA
| | - Mildred K Cho
- Stanford Center for Biomedical Ethics, 1215 Welch Road, Modular A, Stanford, CA 94305-5417, USA
- Department of Pediatrics, 300 Pasteur Drive, Stanford, CA 94305-5208, USA
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Daneshjou R, Zappala Z, Kukurba K, Boyle SM, Ormond KE, Klein TE, Snyder M, Bustamante CD, Altman RB, Montgomery SB. PATH-SCAN: a reporting tool for identifying clinically actionable variants. PACIFIC SYMPOSIUM ON BIOCOMPUTING. PACIFIC SYMPOSIUM ON BIOCOMPUTING 2014:229-240. [PMID: 24297550 PMCID: PMC4008882] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
The American College of Medical Genetics and Genomics (ACMG) recently released guidelines regarding the reporting of incidental findings in sequencing data. Given the availability of Direct to Consumer (DTC) genetic testing and the falling cost of whole exome and genome sequencing, individuals will increasingly have the opportunity to analyze their own genomic data. We have developed a web-based tool, PATH-SCAN, which annotates individual genomes and exomes for ClinVar designated pathogenic variants found within the genes from the ACMG guidelines. Because mutations in these genes predispose individuals to conditions with actionable outcomes, our tool will allow individuals or researchers to identify potential risk variants in order to consult physicians or genetic counselors for further evaluation. Moreover, our tool allows individuals to anonymously submit their pathogenic burden, so that we can crowd source the collection of quantitative information regarding the frequency of these variants. We tested our tool on 1092 publicly available genomes from the 1000 Genomes project, 163 genomes from the Personal Genome Project, and 15 genomes from a clinical genome sequencing research project. Excluding the most commonly seen variant in 1000 Genomes, about 20% of all genomes analyzed had a ClinVar designated pathogenic variant that required further evaluation.
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Affiliation(s)
- Roxana Daneshjou
- Department of Genetics, Stanford University, Stanford, CA 94061, United States
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348
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Roden DM. Personalized medicine to treat arrhythmias. Curr Opin Pharmacol 2013; 15:61-7. [PMID: 24721655 DOI: 10.1016/j.coph.2013.11.013] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2013] [Revised: 11/27/2013] [Accepted: 11/28/2013] [Indexed: 11/26/2022]
Abstract
The efficacy of antiarrhythmic drug therapy is incomplete, with responses ranging from efficacy to no effect to severe adverse effects, including paradoxical drug-induced arrhythmia. Most antiarrhythmic drugs were developed at a time when the mechanisms underlying arrhythmias were not well understood. In the last decade, a range of experimental approaches have advanced our understanding of the molecular and genomic contributors to the generation of an arrhythmia-prone heart, and this information is directly informing targeted therapy with existing drugs or the development of new ones. The development of inexpensive whole genome sequencing holds the promise of identifying patients susceptible to arrhythmias in a presymptomatic phase, and thus implementing preventive therapies.
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Affiliation(s)
- Dan M Roden
- Vanderbilt University School of Medicine, Nashville, USA.
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349
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Cardiovascular Pharmacogenomics: Expectations and Practical Benefits. Clin Pharmacol Ther 2013; 95:281-93. [DOI: 10.1038/clpt.2013.234] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2013] [Accepted: 12/03/2013] [Indexed: 11/08/2022]
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350
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Goldspiel BR, Flegel WA, DiPatrizio G, Sissung T, Adams SD, Penzak SR, Biesecker LG, Fleisher TA, Patel JJ, Herion D, Figg WD, Lertora JJL, McKeeby JW. Integrating pharmacogenetic information and clinical decision support into the electronic health record. J Am Med Inform Assoc 2013; 21:522-8. [PMID: 24302286 DOI: 10.1136/amiajnl-2013-001873] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Pharmacogenetics (PG) examines gene variations for drug disposition, response, or toxicity. At the National Institutes of Health Clinical Center (NIH CC), a multidepartment Pharmacogenetics Testing Implementation Committee (PGTIC) was established to develop clinical decision support (CDS) algorithms for abacavir, carbamazepine, and allopurinol, medications for which human leukocyte antigen (HLA) variants predict severe hypersensitivity reactions. Providing PG CDS in the electronic health record (EHR) during order entry could prevent adverse drug events. Medical Logic Module (MLM) programming was used to implement PG CDS in our EHR. The MLM checks to see if an HLA sequence-based gene test is ordered. A message regarding test status (result present, absent, pending, or test not ordered) is displayed on the order form, and the MLM determines if the prescriber can place the order, place it but require an over-ride reason, or be blocked from placing the order. Since implementation, more than 725 medication orders have been placed for over 230 patients by 154 different prescribers for the three drugs included in our PG program. Prescribers commonly used an over-ride reason when placing the order mainly because patients had been receiving the drug without reaction before implementation of the CDS program. Successful incorporation of PG CDS into the NIH CC EHR required a coordinated, interdisciplinary effort to ensure smooth activation and a positive effect on patient care. Prescribers have adapted to using the CDS and have ordered PG testing as a direct result of the implementation.
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Affiliation(s)
- Barry R Goldspiel
- Pharmacy Department, National Institutes of Health Clinical Center, Bethesda, Maryland, USA
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