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Clayton EW, Smith ME, Anderson KC, Chung WK, Connolly JJ, Fullerton SM, McGowan ML, Peterson JF, Prows CA, Sabatello M, Holm IA. Studying the impact of translational genomic research: Lessons from eMERGE. Am J Hum Genet 2023; 110:1021-1033. [PMID: 37343562 PMCID: PMC10357472 DOI: 10.1016/j.ajhg.2023.05.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 05/22/2023] [Accepted: 05/23/2023] [Indexed: 06/23/2023] Open
Abstract
Two major goals of the Electronic Medical Record and Genomics (eMERGE) Network are to learn how best to return research results to patient/participants and the clinicians who care for them and also to assess the impact of placing these results in clinical care. Yet since its inception, the Network has confronted a host of challenges in achieving these goals, many of which had ethical, legal, or social implications (ELSIs) that required consideration. Here, we share impediments we encountered in recruiting participants, returning results, and assessing their impact, all of which affected our ability to achieve the goals of eMERGE, as well as the steps we took to attempt to address these obstacles. We divide the domains in which we experienced challenges into four broad categories: (1) study design, including recruitment of more diverse groups; (2) consent; (3) returning results to participants and their health care providers (HCPs); and (4) assessment of follow-up care of participants and measuring the impact of research on participants and their families. Since most phases of eMERGE have included children as well as adults, we also address the particular ELSI posed by including pediatric populations in this research. We make specific suggestions for improving translational genomic research to ensure that future projects can effectively return results and assess their impact on patient/participants and providers if the goals of genomic-informed medicine are to be achieved.
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Affiliation(s)
- Ellen Wright Clayton
- Center for Biomedical Ethics and Society, Departments of Pediatrics and Health Policy, Vanderbilt University Medical Center, Nashville, TN 37203, USA.
| | - Maureen E Smith
- Department of Medicine, Center for Genetic Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Katherine C Anderson
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Wendy K Chung
- Departments of Pediatrics and Medicine, Columbia University, New York, NY 10032, USA
| | - John J Connolly
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Stephanie M Fullerton
- Department of Bioethics & Humanities, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Michelle L McGowan
- Biomedical Ethics Research Program, Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN 55905, USA; Department of Women's, Gender, and Sexuality Studies, University of Cincinnati, Cincinnati, OH 45221, USA
| | - Josh F Peterson
- Center for Precision Medicine, Department of Biomedical Informatics, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37203, USA
| | - Cynthia A Prows
- Divisions of Human Genetics and Patient Services, Cincinnati Children's Hospital, Cincinnati, OH 45229, USA
| | - Maya Sabatello
- Center for Precision Medicine & Genomics, Department of Medicine, and Division of Ethics, Department of Medical Humanities & Ethics Columbia University Vagelos College of Physicians and Surgeons, NY, NY 10032, USA
| | - Ingrid A Holm
- Division of Genetics and Genomics, Boston Children's Hospital; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
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Romagnoli KM, Kulchak Rahm A, Jonas MC, Schwiter R, Klinger T, Ladd I, Salvati Z, DiNucci A, Blasi PR, Sheridan L, Scrol A, Henrikson NB. Human-Centered Design Study to Inform Traceback Cascade Genetic Testing Programs at Three Integrated Health Systems. Public Health Genomics 2023; 26:45-57. [PMID: 36871550 PMCID: PMC10475143 DOI: 10.1159/000529852] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Accepted: 02/20/2023] [Indexed: 03/06/2023] Open
Abstract
INTRODUCTION A traceback genetic testing program for ovarian cancer has the potential to identify individuals with hereditary breast and ovarian cancer and their relatives. Successful implementation depends on understanding and addressing the experiences, barriers, and preferences of the people served. METHODS We conducted a remote, human-centered design research study of people with ovarian, fallopian tube, or peritoneal cancer (probands) and people with a family history of ovarian cancer (relatives) at three integrated health systems between May and September 2021. Participants completed activities to elicit their preferences about ovarian cancer genetic testing messaging and to design their ideal experience receiving an invitation to participate in genetic testing. Interview data were analyzed using a rapid thematic analysis approach. RESULTS We interviewed 70 participants and identified five preferred experiences for a traceback program. Participants strongly prefer discussing genetic testing with their doctor but are comfortable discussing with other clinicians. The most highly preferred experience for both probands and relatives was to discuss with a knowledgeable clinician who could answer questions, followed by directed (sent directly to specific people) or passive (shared in a public area) communication. Repeated contact was acceptable for reminders. CONCLUSION Participants were open to receiving information about traceback genetic testing and recognized its value. Participants preferred discussing genetic testing with a trusted clinician. Directed communication was preferable to passive communication. Other valued information included how genetic tests help their family and the cost of genetic testing. These findings are informing traceback cascade genetic testing programs at all three sites.
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Affiliation(s)
- Katrina M Romagnoli
- Department of Health System Sciences, Geisinger Health System, Danville, Pennsylvania, USA
| | - Alanna Kulchak Rahm
- Department of Genomic Health, Geisinger Health System, Danville, Pennsylvania, USA
| | - Mary Cabell Jonas
- Mid-Atlantic Permanente Research Institute, Kaiser Permanente, Rockville, Maryland, USA
| | - Rachel Schwiter
- Department of Genomic Health, Geisinger Health System, Danville, Pennsylvania, USA
| | - Tracey Klinger
- Department of Genomic Health, Geisinger Health System, Danville, Pennsylvania, USA,
| | - Ilene Ladd
- Department of Genomic Health, Geisinger Health System, Danville, Pennsylvania, USA
| | - Zachary Salvati
- Department of Genomic Health, Geisinger Health System, Danville, Pennsylvania, USA
| | - Anna DiNucci
- Mid-Atlantic Permanente Research Institute, Kaiser Permanente, Rockville, Maryland, USA
| | - Paula Rae Blasi
- Kaiser Permanente Washington Health Research Institute, Kaiser Permanente, Seattle, Washington, USA
| | - Leigh Sheridan
- Kaiser Permanente Washington Health Research Institute, Kaiser Permanente, Seattle, Washington, USA
| | - Aaron Scrol
- Kaiser Permanente Washington Health Research Institute, Kaiser Permanente, Seattle, Washington, USA
| | - Nora B Henrikson
- Kaiser Permanente Washington Health Research Institute, Kaiser Permanente, Seattle, Washington, USA
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Santos Simarro F. Advances in clinical genetics and its current challenges. An Pediatr (Barc) 2022; 97:281.e1-281.e5. [PMID: 36115780 DOI: 10.1016/j.anpede.2022.08.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Accepted: 08/30/2022] [Indexed: 11/27/2022] Open
Abstract
The great advances in the development of genomic technologies and their incorporation into routine clinical practice is bringing about a change in which an individual's genetic information is becoming increasingly relevant to their medical care. This is known as genomic medicine. Its implementation is not without barriers, including difficulties in the assessment and interpretation of genomic data, deficient training of professionals and patients in this field, unequal access to units with expertise, and a lack of professional profiles and infrastructures necessary for the incorporation of genomic technologies into routine clinical practice. This article reviews the advances and challenges of genomic medicine.
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Affiliation(s)
- Fernando Santos Simarro
- Unidad de Diagnóstico Molecular y Genética Clínica, Hospital Universitario Son Espases, Palma de Mallorca, Spain.
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Santos Simarro F. Avances en genética clínica y sus retos actuales. An Pediatr (Barc) 2022. [DOI: 10.1016/j.anpedi.2022.08.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022] Open
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Rasmussen LV, Connolly JJ, Del Fiol G, Freimuth RR, Pet DB, Peterson JF, Shirts BH, Starren JB, Williams MS, Walton N, Taylor CO. Infobuttons for Genomic Medicine: Requirements and Barriers. Appl Clin Inform 2021; 12:383-390. [PMID: 33979874 DOI: 10.1055/s-0041-1729164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Abstract
OBJECTIVES The study aimed to understand potential barriers to the adoption of health information technology projects that are released as free and open source software (FOSS). METHODS We conducted a survey of research consortia participants engaged in genomic medicine implementation to assess perceived institutional barriers to the adoption of three systems: ClinGen electronic health record (EHR) Toolkit, DocUBuild, and MyResults.org. The survey included eight barriers from the Consolidated Framework for Implementation Research (CFIR), with additional barriers identified from a qualitative analysis of open-ended responses. RESULTS We analyzed responses from 24 research consortia participants from 18 institutions. In total, 14 categories of perceived barriers were evaluated, which were consistent with other observed barriers to FOSS adoption. The most frequent perceived barriers included lack of adaptability of the system, lack of institutional priority to implement, lack of trialability, lack of advantage of alternative systems, and complexity. CONCLUSION In addition to understanding potential barriers, we recommend some strategies to address them (where possible), including considerations for genomic medicine. Overall, FOSS developers need to ensure systems are easy to trial and implement and need to clearly articulate benefits of their systems, especially when alternatives exist. Institutional champions will remain a critical component to prioritizing genomic medicine projects.
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Affiliation(s)
- Luke V Rasmussen
- Department of Preventive Medicine, Northwestern University, Chicago, Illinois, United Sates
| | - John J Connolly
- The Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, United Sates
| | - Guilherme Del Fiol
- Department of Biomedical Informatics, University of Utah, Salt Lake City, Utah, United Sates
| | - Robert R Freimuth
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota, United Sates
| | - Douglas B Pet
- Department of Neurology, University of California San Francisco, San Francisco, California, United Sates
| | - Josh F Peterson
- Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, Tennessee, United Sates
| | - Brian H Shirts
- Department of Laboratory Medicine, University of Washington, Seattle, Washington, United Sates
| | - Justin B Starren
- Department of Preventive Medicine, Northwestern University, Chicago, Illinois, United Sates
| | - Marc S Williams
- Genomic Medicine Institute, Geisinger, Danville, Pennsylvania, United Sates
| | - Nephi Walton
- Genomic Medicine Institute, Geisinger, Danville, Pennsylvania, United Sates.,Intermountain Precision Genomics, Intermountain Healthcare, St George, Utah, United Sates
| | - Casey Overby Taylor
- Genomic Medicine Institute, Geisinger, Danville, Pennsylvania, United Sates.,Department of Medicine and Biomedical Engineering, Johns Hopkins School of Medicine, Baltimore, Maryland, United Sates
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Şık AS, Aydınoğlu AU, Aydın Son Y. Assessing the readiness of Turkish health information systems for integrating genetic/genomic patient data: System architecture and available terminologies, legislative, and protection of personal data. Health Policy 2020; 125:203-212. [PMID: 33342546 DOI: 10.1016/j.healthpol.2020.12.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Revised: 11/29/2020] [Accepted: 12/05/2020] [Indexed: 02/08/2023]
Abstract
Advances in genetic/genomic research and translational studies drive the progress on molecular diagnosis, personalised treatment, and monitoring. Healthcare professionals and governments are encouraged to set administrative regulations and implement structured and interoperable representation to utilise the genetic/genomic data, which will support precision medicine approaches through Health Information Systems (HIS). Clear regulations and careful legislation are also crucial for the security and privacy of genetic/genomic test data. In this article, we present a review of the National Health Information System of Turkey (NHIS-T) about interoperable health data representation for genetic tests. We discuss the content of rules and regulations related to genetic/genomic testing and structured data representation in Turkey. A brief comparison of the Turkish "Law on the Protection of Personal Data" (LPPD) in genetic/genomic data privacy with its counterparts is presented. The final discussion about the shortcomings of Turkey is transferable to health information systems worldwide. Constructing a national reference database and IT infrastructure to enable data integration and exchange between genomic data, metadata, and health records will improve genetics studies' utility and outcomes. The critical success factors behind integration are establishing broadly accepted terminologies and government guidance. The governments should set clear a transparent policy defining the legal and ethical framework, workforce training, clinical decision-support tools, public engagement, and education concurrently.
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Affiliation(s)
- Ayhan Serkan Şık
- Department of Medical Informatics, Middle East Technical University, METU Informatics Institute, Universiteler Mahallesi, Dumlupinar Bulvari, No:1, 06800, Ankara, Turkey; Department of Management Information Systems, Ankara Medipol University, Faculty of Economics, Administrative and Social Sciences, Haci Bayram Mahallesi, Talatpasa Bulvari, No:2, Ankara, Turkey.
| | - Arsev Umur Aydınoğlu
- Department of Science and Technology Policy Studies, Middle East Technical University, Universiteler Mahallesi, Dumlupinar Bulvari, No:1, MM Building 3rd Floor No: 320, 06800, Ankara, Turkey.
| | - Yeşim Aydın Son
- Department of Medical Informatics, Middle East Technical University, METU Informatics Institute, Universiteler Mahallesi, Dumlupinar Bulvari, No:1, 06800, Ankara, Turkey.
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Garcia SJ, Zayas-Cabán T, Freimuth RR. Sync for Genes: Making Clinical Genomics Available for Precision Medicine at the Point-of-Care. Appl Clin Inform 2020; 11:295-302. [PMID: 32323283 DOI: 10.1055/s-0040-1708051] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Making genomic data available at the point-of-care and for research is critical for the success of the Precision Medicine Initiative (PMI), a research initiative which seeks to change health care by "tak(ing) into account individual differences in people's genes, environments, and lifestyles." The Office of the National Coordinator for Health Information Technology (ONC) led Sync for Genes, a program to develop standards that make genomic data available when and where it matters most. This article discusses lessons learned from recent Sync for Genes activities. OBJECTIVES The goals of Sync for Genes were to (1) demonstrate exchange of genomic data using health data standards, (2) provide feedback for refinement of health data standards, and (3) synthesize project experiences to support the integration of genomic data at the point-of-care and for research. METHODS Four organizations participated in a program to test the Health Level Seven International (HL7®) Fast Healthcare Interoperability Resources (FHIR®) standard, which supports sharing genomic data. ONC provided access to subject matter experts, resources, tools, and technical guidance to support testing activities. Three of the four organizations participated in HL7 FHIR Connectathons to test FHIR's ability to exchange genomic diagnostic reports. RESULTS The organizations successfully demonstrated exchange of genomic diagnostic reports using FHIR. The feedback and artifacts that resulted from these activities were shared with HL7 and made publicly available. Four areas were identified as important considerations for similar projects: (1) FHIR proficiency, (2) developer support, (3) project scope, and (4) bridging health information technology and genomic expertise. CONCLUSION Precision medicine is a rapidly evolving field, and there is opportunity to continue maturing health data standards for the exchange of necessary genomic data, increasing the likelihood that the standard supports the needs of users.
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Affiliation(s)
- Stephanie J Garcia
- Office of the National Coordinator for Health Information Technology, Washington, District of Columbia, United States
| | - Teresa Zayas-Cabán
- Office of the National Coordinator for Health Information Technology, Washington, District of Columbia, United States
| | - Robert R Freimuth
- Division of Digital Health Sciences, Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota, United States
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Johnson KB, Clayton EW, Starren J, Peterson J. The Implementation Chasm Hindering Genome-informed Health Care. THE JOURNAL OF LAW, MEDICINE & ETHICS : A JOURNAL OF THE AMERICAN SOCIETY OF LAW, MEDICINE & ETHICS 2020; 48:119-125. [PMID: 32342791 PMCID: PMC7395963 DOI: 10.1177/1073110520916999] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The promises of precision medicine are often heralded in the medical and lay literature, but routine integration of genomics in clinical practice is still limited. While the "last mile' infrastructure to bring genomics to the bedside has been demonstrated in some healthcare settings, a number of challenges remain - both in the receptivity of today's health system and in its technical and educational readiness to respond to this evolution in care. To improve the impact of genomics on health and disease management, we will need to integrate both new knowledge and new care processes into existing workflows. This change will be onerous and time-consuming, but hopefully valuable to the provision of high quality, economically feasible care worldwide.
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Affiliation(s)
- Kevin B Johnson
- Kevin B. Johnson, M.D., M.S., is Cornelius Vanderbilt Professor and Chair of Biomedical Informatics, with a joint appointment in the Department of Pediatrics at Vanderbilt University Medical Center. He received his M.D. from Johns Hopkins Hospital in Baltimore and his M.S. in Medical Informatics from Stanford University in 1992. Ellen Wright Clayton, M.D., J.D., is the Craig-Weaver Professor of Pediatrics, Professor of Health Policy in the Center for Biomedical Ethics and Society at Vanderbilt University Medical Center, and Professor of Law at Vanderbilt University. She has been studying the ethical, legal, and social implications of genetics research and its translation to the clinic for many years. She is currently a PI of LawSeq as well as GetPreCiSe, a Center of Excellence in ELSI Research focused on genetic privacy and identity, and has been an investigator in the eMERGE Network since its inception. Justin Starren, M.D., M.S., Ph.D., is Professor of Preventive Medicine and Medical Social Sciences and Chief of the Division of Health and Biomedical Informatics at the Northwestern University Feinberg School of Medicine. He received his M.D. and M.S. in Immunogenetics from Washington University in St. Louis in 1987, and his Ph.D. in Biomedical Informatics from Columbia University in 1997. Josh Peterson, M.D., M.P.H., is an Associate Professor of Biomedical Informatics and Medicine at Vanderbilt University Medical Center. He received his M.D. from Vanderbilt University in 1997 and his M.P.H. from Harvard University School of Public Health in 2002
| | - Ellen Wright Clayton
- Kevin B. Johnson, M.D., M.S., is Cornelius Vanderbilt Professor and Chair of Biomedical Informatics, with a joint appointment in the Department of Pediatrics at Vanderbilt University Medical Center. He received his M.D. from Johns Hopkins Hospital in Baltimore and his M.S. in Medical Informatics from Stanford University in 1992. Ellen Wright Clayton, M.D., J.D., is the Craig-Weaver Professor of Pediatrics, Professor of Health Policy in the Center for Biomedical Ethics and Society at Vanderbilt University Medical Center, and Professor of Law at Vanderbilt University. She has been studying the ethical, legal, and social implications of genetics research and its translation to the clinic for many years. She is currently a PI of LawSeq as well as GetPreCiSe, a Center of Excellence in ELSI Research focused on genetic privacy and identity, and has been an investigator in the eMERGE Network since its inception. Justin Starren, M.D., M.S., Ph.D., is Professor of Preventive Medicine and Medical Social Sciences and Chief of the Division of Health and Biomedical Informatics at the Northwestern University Feinberg School of Medicine. He received his M.D. and M.S. in Immunogenetics from Washington University in St. Louis in 1987, and his Ph.D. in Biomedical Informatics from Columbia University in 1997. Josh Peterson, M.D., M.P.H., is an Associate Professor of Biomedical Informatics and Medicine at Vanderbilt University Medical Center. He received his M.D. from Vanderbilt University in 1997 and his M.P.H. from Harvard University School of Public Health in 2002
| | - Justin Starren
- Kevin B. Johnson, M.D., M.S., is Cornelius Vanderbilt Professor and Chair of Biomedical Informatics, with a joint appointment in the Department of Pediatrics at Vanderbilt University Medical Center. He received his M.D. from Johns Hopkins Hospital in Baltimore and his M.S. in Medical Informatics from Stanford University in 1992. Ellen Wright Clayton, M.D., J.D., is the Craig-Weaver Professor of Pediatrics, Professor of Health Policy in the Center for Biomedical Ethics and Society at Vanderbilt University Medical Center, and Professor of Law at Vanderbilt University. She has been studying the ethical, legal, and social implications of genetics research and its translation to the clinic for many years. She is currently a PI of LawSeq as well as GetPreCiSe, a Center of Excellence in ELSI Research focused on genetic privacy and identity, and has been an investigator in the eMERGE Network since its inception. Justin Starren, M.D., M.S., Ph.D., is Professor of Preventive Medicine and Medical Social Sciences and Chief of the Division of Health and Biomedical Informatics at the Northwestern University Feinberg School of Medicine. He received his M.D. and M.S. in Immunogenetics from Washington University in St. Louis in 1987, and his Ph.D. in Biomedical Informatics from Columbia University in 1997. Josh Peterson, M.D., M.P.H., is an Associate Professor of Biomedical Informatics and Medicine at Vanderbilt University Medical Center. He received his M.D. from Vanderbilt University in 1997 and his M.P.H. from Harvard University School of Public Health in 2002
| | - Josh Peterson
- Kevin B. Johnson, M.D., M.S., is Cornelius Vanderbilt Professor and Chair of Biomedical Informatics, with a joint appointment in the Department of Pediatrics at Vanderbilt University Medical Center. He received his M.D. from Johns Hopkins Hospital in Baltimore and his M.S. in Medical Informatics from Stanford University in 1992. Ellen Wright Clayton, M.D., J.D., is the Craig-Weaver Professor of Pediatrics, Professor of Health Policy in the Center for Biomedical Ethics and Society at Vanderbilt University Medical Center, and Professor of Law at Vanderbilt University. She has been studying the ethical, legal, and social implications of genetics research and its translation to the clinic for many years. She is currently a PI of LawSeq as well as GetPreCiSe, a Center of Excellence in ELSI Research focused on genetic privacy and identity, and has been an investigator in the eMERGE Network since its inception. Justin Starren, M.D., M.S., Ph.D., is Professor of Preventive Medicine and Medical Social Sciences and Chief of the Division of Health and Biomedical Informatics at the Northwestern University Feinberg School of Medicine. He received his M.D. and M.S. in Immunogenetics from Washington University in St. Louis in 1987, and his Ph.D. in Biomedical Informatics from Columbia University in 1997. Josh Peterson, M.D., M.P.H., is an Associate Professor of Biomedical Informatics and Medicine at Vanderbilt University Medical Center. He received his M.D. from Vanderbilt University in 1997 and his M.P.H. from Harvard University School of Public Health in 2002
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Coriolan S, Arikawe N, Moscati A, Zhou L, Dym S, Donmez S, Garba A, Falbaum S, Loewy Z, Lull M, Saad M, Shtaynberg J, Obeng AO. Pharmacy students' attitudes and perceptions toward pharmacogenomics education. Am J Health Syst Pharm 2020; 76:836-845. [PMID: 31415690 DOI: 10.1093/ajhp/zxz060] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
PURPOSE To evaluate final-year pharmacy students' perceptions toward pharmacogenomics education, their attitudes on its clinical relevance, and their readiness to use such knowledge in practice. METHODS A 19-question survey was developed and modified from prior studies and was pretested on a small group of pharmacogenomics faculty and pharmacy students. The final survey was administered to 978 final-year pharmacy students in 8 school/colleges of pharmacy in New York and New Jersey between January and May 2017. The survey targeted 3 main themes: perceptions toward pharmacogenomics education, attitudes toward the clinical relevance of this education, and the students' readiness to use knowledge of pharmacogenomics in practice. RESULTS With a 35% response rate, the majority (81%) of the 339 student participants believed that pharmacogenomics was a useful clinical tool for pharmacists, yet only 40% felt that it had been a relevant part of their training. Almost half (46%) received only 1-3 lectures on pharmacogenomics and the majority were not ready to use it in practice. Survey results pointed toward practice-based trainings such as pharmacogenomics rotations as the most helpful in preparing students for practice. CONCLUSIONS Final-year student pharmacists reported varying exposure to pharmacogenomics content in their pharmacy training and had positive attitudes toward the clinical relevance of the discipline, yet they expressed low confidence in their readiness to use this information in practice.
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Affiliation(s)
- Shanice Coriolan
- Candidate 2019, Albany College of Pharmacy and Health Sciences, Albany, NY
| | - Nimota Arikawe
- Candidate 2020, Albany College of Pharmacy and Health Sciences, Albany, NY
| | - Arden Moscati
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Lisheng Zhou
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Stephanie Dym
- Touro College of Pharmacy, Touro College, New York, NY
| | - Seda Donmez
- Wegmans School of Pharmacy, St. John Fisher College, Rochester, NY
| | - Adinoyi Garba
- D'Youville College School of Pharmacy, D'Youville College, Buffalo, NY
| | - Sasha Falbaum
- Fairleigh Dickinson College School of Pharmacy, Fairleigh Dickinson University, Teaneck, NJ
| | - Zvi Loewy
- Touro College of Pharmacy, Touro College, New York, NY
| | - Melinda Lull
- Wegmans School of Pharmacy, St. John Fisher College, Rochester, NY
| | - Maha Saad
- College of Pharmacy and Health Sciences, St. Johns University, Jamaica, NY
| | - Jane Shtaynberg
- Department of Experiential Education, LIU Brooklyn Arnold & Marie Schwartz College of Pharmacy, Brooklyn, NY
| | - Aniwaa Owusu Obeng
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY
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Afzal M, Hussain M, Malik KM, Lee S. Impact of Automatic Query Generation and Quality Recognition Using Deep Learning to Curate Evidence From Biomedical Literature: Empirical Study. JMIR Med Inform 2019; 7:e13430. [PMID: 31815673 PMCID: PMC6928703 DOI: 10.2196/13430] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Revised: 08/07/2019] [Accepted: 09/26/2019] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND The quality of health care is continuously improving and is expected to improve further because of the advancement of machine learning and knowledge-based techniques along with innovation and availability of wearable sensors. With these advancements, health care professionals are now becoming more interested and involved in seeking scientific research evidence from external sources for decision making relevant to medical diagnosis, treatments, and prognosis. Not much work has been done to develop methods for unobtrusive and seamless curation of data from the biomedical literature. OBJECTIVE This study aimed to design a framework that can enable bringing quality publications intelligently to the users' desk to assist medical practitioners in answering clinical questions and fulfilling their informational needs. METHODS The proposed framework consists of methods for efficient biomedical literature curation, including the automatic construction of a well-built question, the recognition of evidence quality by proposing extended quality recognition model (E-QRM), and the ranking and summarization of the extracted evidence. RESULTS Unlike previous works, the proposed framework systematically integrates the echelons of biomedical literature curation by including methods for searching queries, content quality assessments, and ranking and summarization. Using an ensemble approach, our high-impact classifier E-QRM obtained significantly improved accuracy than the existing quality recognition model (1723/1894, 90.97% vs 1462/1894, 77.21%). CONCLUSIONS Our proposed methods and evaluation demonstrate the validity and rigorousness of the results, which can be used in different applications, including evidence-based medicine, precision medicine, and medical education.
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Affiliation(s)
- Muhammad Afzal
- Department of Software, Sejong University, Seoul, Republic of Korea.,Department of Computer Science and Engineering, Oakland University, Rochester, MI, United States
| | - Maqbool Hussain
- Department of Software, Sejong University, Seoul, Republic of Korea
| | - Khalid Mahmood Malik
- Department of Computer Science and Engineering, Oakland University, Rochester, MI, United States
| | - Sungyoung Lee
- Department of Computer Science and Engineering, Kyung Hee University, Yongin, Republic of Korea
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Williams MS, Taylor CO, Walton NA, Goehringer SR, Aronson S, Freimuth RR, Rasmussen LV, Hall ES, Prows CA, Chung WK, Fedotov A, Nestor J, Weng C, Rowley RK, Wiesner GL, Jarvik GP, Del Fiol G. Genomic Information for Clinicians in the Electronic Health Record: Lessons Learned From the Clinical Genome Resource Project and the Electronic Medical Records and Genomics Network. Front Genet 2019; 10:1059. [PMID: 31737042 PMCID: PMC6830110 DOI: 10.3389/fgene.2019.01059] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Accepted: 10/03/2019] [Indexed: 01/05/2023] Open
Abstract
Genomic knowledge is being translated into clinical care. To fully realize the value, it is critical to place credible information in the hands of clinicians in time to support clinical decision making. The electronic health record is an essential component of clinician workflow. Utilizing the electronic health record to present information to support the use of genomic medicine in clinical care to improve outcomes represents a tremendous opportunity. However, there are numerous barriers that prevent the effective use of the electronic health record for this purpose. The electronic health record working groups of the Electronic Medical Records and Genomics (eMERGE) Network and the Clinical Genome Resource (ClinGen) project, along with other groups, have been defining these barriers, to allow the development of solutions that can be tested using implementation pilots. In this paper, we present “lessons learned” from these efforts to inform future efforts leading to the development of effective and sustainable solutions that will support the realization of genomic medicine.
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Affiliation(s)
- Marc S Williams
- Genomic Medicine Institute, Geisinger, Danville, PA, United States
| | - Casey Overby Taylor
- Genomic Medicine Institute, Geisinger, Danville, PA, United States.,Department of Medicine, Johns Hopkins University, Baltimore, MD, United States
| | - Nephi A Walton
- Genomic Medicine Institute, Geisinger, Danville, PA, United States
| | | | | | - Robert R Freimuth
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN, United States
| | - Luke V Rasmussen
- Department of Preventive Medicine, Northwestern University, Chicago, IL, United States
| | - Eric S Hall
- Department of Pediatrics, University of Cincinnati College of Medicine, and Cincinnati Children's Hospital Medical Center, Cincinnati, OH, United States
| | - Cynthia A Prows
- Divisions of Human Genetics and Patient Services, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, United States
| | - Wendy K Chung
- Departments of Pediatrics and Medicine, Columbia University, New York, NY, United States
| | - Alexander Fedotov
- Irving Institute for Clinical and Translational Research, Columbia University, New York, NY, United States
| | - Jordan Nestor
- Department of Medicine, Division of Nephrology, Columbia University, New York, NY, United States
| | - Chunhua Weng
- Department of Biomedical Informatics, Columbia University, New York, NY, United States
| | - Robb K Rowley
- National Human Genome Research Institute, Bethesda, MD, United States
| | - Georgia L Wiesner
- Division of Genetic Medicine, Department of Internal Medicine, Vanderbilt University Medical Center, Nashville, TN, United States
| | - Gail P Jarvik
- Departments of Medicine (Medical Genetics) and Genome Sciences, University of Washington, Seattle, WA, United States
| | - Guilherme Del Fiol
- Department of Biomedical Informatics, University of Utah, Salt Lake City, UT, United States
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12
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Ayatollahi H, Hosseini SF, Hemmat M. Integrating Genetic Data into Electronic Health Records: Medical Geneticists' Perspectives. Healthc Inform Res 2019; 25:289-296. [PMID: 31777672 PMCID: PMC6859263 DOI: 10.4258/hir.2019.25.4.289] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2019] [Revised: 10/28/2019] [Accepted: 10/28/2019] [Indexed: 01/04/2023] Open
Abstract
OBJECTIVES Genetic disorders are the main causes of many other diseases. Integrating genetic data into Electronic Health Records (EHRs) can facilitate the management of genetic information and care of patients in clinical practices. The aim of this study was to identify the main requirements for integrating genetic data into the EHR system from the medical geneticists' perspectives. METHODS The research was completed in 2018 and consisted of two phases. In the first phase, the main requirements for integrating genetic data into the EHR system were identified by reviewing the literature. In the second phase, a 5-point Likert scale questionnaire was developed based on the literature review and the results derived from the first phase. Then, the Delphi method was applied to reach a consensus about the integration requirements. RESULTS The findings of the first phase showed that data elements, including patients' and healthcare providers' personal data, clinical and genetic data, technical infrastructure, security issues and functional requirements, should be taken into account before data integration. In the second phase, a consensus was reached for most of the items (mean ≥3.75). The items with a mean value of less than 2.5 did not achieve a consensus and were removed from the final list. CONCLUSIONS The integration of genetic data into the EHRs can provide a ground for increasing accuracy and precision in the diagnosis and treatment of genetic disorders. Such integration requires adequate investments to identify users' requirements as well as technical and non-technical issues.
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Affiliation(s)
- Haleh Ayatollahi
- Health Management and Economics Research Center, Iran University of Medical Sciences, Tehran, Iran
- School of Health Management and Information Sciences, Iran University of Medical Sciences, Tehran, Iran
| | - Seyedeh Fatemeh Hosseini
- School of Health Management and Information Sciences, Iran University of Medical Sciences, Tehran, Iran
| | - Morteza Hemmat
- Social Determinants of Health Research Center, Saveh University of Medical Sciences, Saveh, Iran
- Student Research Committee, Saveh University of Medical Sciences, Saveh, Iran
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13
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Manolio TA, Rowley R, Williams MS, Roden D, Ginsburg GS, Bult C, Chisholm RL, Deverka PA, McLeod HL, Mensah GA, Relling MV, Rodriguez LL, Tamburro C, Green ED. Opportunities, resources, and techniques for implementing genomics in clinical care. Lancet 2019; 394:511-520. [PMID: 31395439 PMCID: PMC6699751 DOI: 10.1016/s0140-6736(19)31140-7] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Revised: 04/09/2019] [Accepted: 05/03/2019] [Indexed: 12/19/2022]
Abstract
Advances in technologies for assessing genomic variation and an increasing understanding of the effects of genomic variants on health and disease are driving the transition of genomics from the research laboratory into clinical care. Genomic medicine, or the use of an individual's genomic information as part of their clinical care, is increasingly gaining acceptance in routine practice, including in assessing disease risk in individuals and their families, diagnosing rare and undiagnosed diseases, and improving drug safety and efficacy. We describe the major types and measurement tools of genomic variation that are currently of clinical importance, review approaches to interpreting genomic sequence variants, identify publicly available tools and resources for genomic test interpretation, and discuss several key barriers in using genomic information in routine clinical practice.
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Affiliation(s)
- Teri A Manolio
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA.
| | - Robb Rowley
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | | | - Dan Roden
- Department of Medicine, Department of Pharmacology, and Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Geoffrey S Ginsburg
- Duke Center for Applied Genomic and Precision Medicine, Duke University, Durham, NC, USA
| | - Carol Bult
- The Jackson Laboratory for Mammalian Genetics, Bar Harbor, ME, USA
| | - Rex L Chisholm
- Center for Genetic Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | | | - Howard L McLeod
- DeBartolo Family Personalized Medicine Institute, Moffitt Cancer Center, Tampa, FL, USA
| | - George A Mensah
- Center for Translation Research and Implementation Science, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Mary V Relling
- Pharmaceutical Sciences Department, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Laura Lyman Rodriguez
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Cecelia Tamburro
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Eric D Green
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
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14
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Stark Z, Dolman L, Manolio TA, Ozenberger B, Hill SL, Caulfied MJ, Levy Y, Glazer D, Wilson J, Lawler M, Boughtwood T, Braithwaite J, Goodhand P, Birney E, North KN. Integrating Genomics into Healthcare: A Global Responsibility. Am J Hum Genet 2019; 104:13-20. [PMID: 30609404 PMCID: PMC6323624 DOI: 10.1016/j.ajhg.2018.11.014] [Citation(s) in RCA: 212] [Impact Index Per Article: 42.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Accepted: 11/20/2018] [Indexed: 01/09/2023] Open
Abstract
Genomic sequencing is rapidly transitioning into clinical practice, and implementation into healthcare systems has been supported by substantial government investment, totaling over US$4 billion, in at least 14 countries. These national genomic-medicine initiatives are driving transformative change under real-life conditions while simultaneously addressing barriers to implementation and gathering evidence for wider adoption. We review the diversity of approaches and current progress made by national genomic-medicine initiatives in the UK, France, Australia, and US and provide a roadmap for sharing strategies, standards, and data internationally to accelerate implementation.
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Affiliation(s)
- Zornitza Stark
- Australian Genomics Health Alliance, Melbourne VIC 3052, Australia; Murdoch Children's Research Institute, Melbourne VIC 3052, Australia; Department of Paediatrics, University of Melbourne, Melbourne VIC 3052, Australia
| | - Lena Dolman
- Global Alliance for Genomics and Health, 661 University Avenue, Suite 510, Toronto, ON M5G 0A3, Canada; Ontario Institute for Cancer Research, 661 University Avenue, Suite 510, Toronto, ON M5G 0A3, Canada
| | - Teri A Manolio
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892-2152, USA
| | - Brad Ozenberger
- All of Us Research Program, National Institutes of Health, Bethesda, MD 20892-2152, USA
| | - Sue L Hill
- National Health Service England, Skipton House, 80 London Road, London SE1 6LH, UK
| | - Mark J Caulfied
- Genomics England, Queen Mary University of London, Dawson Hall, London EC1M 6BQ, UK
| | - Yves Levy
- INSERM (French National Institute for Health and Medical Research), 75654 Paris Cedex 13, France
| | - David Glazer
- Verily Life Sciences, 269 East Grand Avenue, South San Francisco, CA 94080, USA
| | - Julia Wilson
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Mark Lawler
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, 97 Lisburn Road, Belfast BT9 7AE, UK
| | - Tiffany Boughtwood
- Australian Genomics Health Alliance, Melbourne VIC 3052, Australia; Murdoch Children's Research Institute, Melbourne VIC 3052, Australia
| | - Jeffrey Braithwaite
- Australian Genomics Health Alliance, Melbourne VIC 3052, Australia; Australian Institute of Health Innovation, Macquarie University, 75 Talavera Road, Sydney, NSW 2113, Australia
| | - Peter Goodhand
- Global Alliance for Genomics and Health, 661 University Avenue, Suite 510, Toronto, ON M5G 0A3, Canada; Ontario Institute for Cancer Research, 661 University Avenue, Suite 510, Toronto, ON M5G 0A3, Canada
| | - Ewan Birney
- Global Alliance for Genomics and Health, 661 University Avenue, Suite 510, Toronto, ON M5G 0A3, Canada; European Molecular Biology Laboratory-European Bioinformatics Institute, Hinxton, Cambridge CB10 1SD, UK
| | - Kathryn N North
- Australian Genomics Health Alliance, Melbourne VIC 3052, Australia; Murdoch Children's Research Institute, Melbourne VIC 3052, Australia; Department of Paediatrics, University of Melbourne, Melbourne VIC 3052, Australia; Global Alliance for Genomics and Health, 661 University Avenue, Suite 510, Toronto, ON M5G 0A3, Canada.
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15
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OpenEHR modeling for genomics in clinical practice. Int J Med Inform 2018; 120:147-156. [PMID: 30409340 DOI: 10.1016/j.ijmedinf.2018.10.007] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Revised: 04/18/2018] [Accepted: 10/15/2018] [Indexed: 12/13/2022]
Abstract
PURPOSE The increasing usage of high throughput sequencing in personalized medicine brings new challenges to the realm of healthcare informatics. Patient records need to accommodate data of unprecedented size and complexity as well as keep track of their production process. In this work we present a solution for integrating genomic data into electronic health records via openEHR archetypes. METHODS We use the popular Variant Call Format as the base format to represent genetic test results within openEHR. We evaluate existing openEHR archetypes to determine what can be extended or specialized and what needs to be developed ex novo. RESULTS Eleven new archetypes have been developed, while an existing one has been specialized to represent genomic data. We show their applicability to rare genetic diseases and compare our approach to HL7 FHIR. CONCLUSION The proposed model allows to represent genetic test results in health records in a structured format. It supports different levels of abstraction, allowing both automated processing and clinical decision support. It is extensible via external references, allowing to keep track of data provenance and adapt to future domain changes.
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16
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Physician-Reported Benefits and Barriers to Clinical Implementation of Genomic Medicine: A Multi-Site IGNITE-Network Survey. J Pers Med 2018; 8:jpm8030024. [PMID: 30042363 PMCID: PMC6163471 DOI: 10.3390/jpm8030024] [Citation(s) in RCA: 82] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Revised: 07/12/2018] [Accepted: 07/18/2018] [Indexed: 12/23/2022] Open
Abstract
Genetic medicine is one of the key components of personalized medicine, but adoption in clinical practice is still limited. To understand potential barriers and provider attitudes, we surveyed 285 physicians from five Implementing GeNomics In pracTicE (IGNITE) sites about their perceptions as to the clinical utility of genetic data as well as their preparedness to integrate it into practice. These responses were also analyzed in comparison to the type of study occurring at the physicians' institution (pharmacogenetics versus disease genetics). The majority believed that genetic testing is clinically useful; however, only a third believed that they had obtained adequate training to care for genetically "high-risk" patients. Physicians involved in pharmacogenetics initiatives were more favorable towards genetic testing applications; they found it to be clinically useful and felt more prepared and confident in their abilities to adopt it into their practice in comparison to those participating in disease genetics initiatives. These results suggest that investigators should explore which attributes of clinical pharmacogenetics (such as the use of simplified genetics-guided recommendations) can be implemented to improve attitudes and preparedness to implement disease genetics in care. Most physicians felt unprepared to use genetic information in their practice; accordingly, major steps should be taken to develop effective clinical tools and training strategies for physicians.
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17
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Caudle KE, Keeling NJ, Klein TE, Whirl-Carrillo M, Pratt VM, Hoffman JM. Standardization can accelerate the adoption of pharmacogenomics: current status and the path forward. Pharmacogenomics 2018; 19:847-860. [PMID: 29914287 DOI: 10.2217/pgs-2018-0028] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Successfully implementing pharmacogenomics into routine clinical practice requires an efficient process to order genetic tests and report the results to clinicians and patients. Lack of standardized approaches and terminology in clinical laboratory processes, ordering of the test and reporting of test results all impede this workflow. Expert groups such as the Association for Molecular Pathology and the Clinical Pharmacogenetics Implementation Consortium have published recommendations for standardizing laboratory genetic testing, reporting and terminology. Other resources such as PharmGKB, ClinVar, ClinGen and PharmVar have established databases of nomenclature for pharmacogenetic alleles and variants. Opportunities remain to develop new standards and further disseminate existing standards which will accelerate the implementation of pharmacogenomics.
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Affiliation(s)
- Kelly E Caudle
- Department of Pharmaceutical Sciences, St Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Nicholas J Keeling
- Department of Pharmaceutical Sciences, St Jude Children's Research Hospital, Memphis, TN 38105, USA.,Department of Pharmacy Administration, University of Mississippi School of Pharmacy, Oxford, MS 38655, USA
| | - Teri E Klein
- Department of Biomedical Data Science, Stanford University, Stanford, CA 94305, USA
| | | | - Victoria M Pratt
- Department of Medical & Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - James M Hoffman
- Department of Pharmaceutical Sciences, St Jude Children's Research Hospital, Memphis, TN 38105, USA.,Office of Quality & Patient Care, St Jude Children's Research Hospital, Memphis, TN 38105, USA
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18
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Fritsche LG, Gruber SB, Wu Z, Schmidt EM, Zawistowski M, Moser SE, Blanc VM, Brummett CM, Kheterpal S, Abecasis GR, Mukherjee B. Association of Polygenic Risk Scores for Multiple Cancers in a Phenome-wide Study: Results from The Michigan Genomics Initiative. Am J Hum Genet 2018; 102:1048-1061. [PMID: 29779563 DOI: 10.1016/j.ajhg.2018.04.001] [Citation(s) in RCA: 113] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2017] [Accepted: 03/26/2018] [Indexed: 12/11/2022] Open
Abstract
Health systems are stewards of patient electronic health record (EHR) data with extraordinarily rich depth and breadth, reflecting thousands of diagnoses and exposures. Measures of genomic variation integrated with EHRs offer a potential strategy to accurately stratify patients for risk profiling and discover new relationships between diagnoses and genomes. The objective of this study was to evaluate whether polygenic risk scores (PRS) for common cancers are associated with multiple phenotypes in a phenome-wide association study (PheWAS) conducted in 28,260 unrelated, genotyped patients of recent European ancestry who consented to participate in the Michigan Genomics Initiative, a longitudinal biorepository effort within Michigan Medicine. PRS for 12 cancer traits were calculated using summary statistics from the NHGRI-EBI catalog. A total of 1,711 synthetic case-control studies was used for PheWAS analyses. There were 13,490 (47.7%) patients with at least one cancer diagnosis in this study sample. PRS exhibited strong association for several cancer traits they were designed for, including female breast cancer, prostate cancer, melanoma, basal cell carcinoma, squamous cell carcinoma, and thyroid cancer. Phenome-wide significant associations were observed between PRS and many non-cancer diagnoses. To differentiate PRS associations driven by the primary trait from associations arising through shared genetic risk profiles, the idea of "exclusion PRS PheWAS" was introduced. Further analysis of temporal order of the diagnoses improved our understanding of these secondary associations. This comprehensive PheWAS used PRS instead of a single variant.
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Affiliation(s)
- Lars G Fritsche
- Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI 48109, USA; Center for Statistical Genetics, University of Michigan School of Public Health, Ann Arbor, MI 48109, USA; K.G. Jebsen Center for Genetic Epidemiology, Department of Public Health and Nursing, Norwegian University of Science and Technology, 7491 Trondheim, Sør-Trøndelag, Norway
| | - Stephen B Gruber
- USC Norris Comprehensive Cancer Center, Los Angeles, CA 90033, USA
| | - Zhenke Wu
- Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI 48109, USA; Michigan Institute for Data Science, University of Michigan, Ann Arbor, MI 48109, USA
| | - Ellen M Schmidt
- Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI 48109, USA
| | - Matthew Zawistowski
- Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI 48109, USA; Center for Statistical Genetics, University of Michigan School of Public Health, Ann Arbor, MI 48109, USA
| | - Stephanie E Moser
- Division of Pain Medicine, Department of Anesthesiology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Victoria M Blanc
- Central Biorepository, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Chad M Brummett
- Division of Pain Medicine, Department of Anesthesiology, University of Michigan Medical School, Ann Arbor, MI 48109, USA; Institute for Healthcare Policy and Innovation, University of Michigan, Ann Arbor, MI 48109, USA
| | - Sachin Kheterpal
- Division of Pain Medicine, Department of Anesthesiology, University of Michigan Medical School, Ann Arbor, MI 48109, USA; Institute for Healthcare Policy and Innovation, University of Michigan, Ann Arbor, MI 48109, USA
| | - Gonçalo R Abecasis
- Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI 48109, USA; Center for Statistical Genetics, University of Michigan School of Public Health, Ann Arbor, MI 48109, USA
| | - Bhramar Mukherjee
- Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI 48109, USA; Center for Statistical Genetics, University of Michigan School of Public Health, Ann Arbor, MI 48109, USA; Michigan Institute for Data Science, University of Michigan, Ann Arbor, MI 48109, USA; Department of Epidemiology, University of Michigan School of Public Health, Ann Arbor, MI 48109, USA; University of Michigan Comprehensive Cancer Center, University of Michigan, Ann Arbor, MI 48109, USA.
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19
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Mukherjee C, Sweet KM, Luzum JA, Abdel-Rasoul M, Christman MF, Kitzmiller JP. Clinical pharmacogenomics: patient perspectives of pharmacogenomic testing and the incidence of actionable test results in a chronic disease cohort. Per Med 2017; 14:383-388. [PMID: 29181084 DOI: 10.2217/pme-2017-0022] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2017] [Accepted: 07/04/2017] [Indexed: 02/06/2023]
Abstract
Aim This study aimed to examine pharmacogenomic test results and patient perspectives at an academic cardiovascular medicine clinic. Patients & methods Test results for three common cardiovascular drug-gene tests (warfarin-CYP2C9-VKORC1, clopidogrel-CYP2C19 and simvastatin-SLCO1B1) of 208 patients in the Ohio State University-Coriell Personalized Medicine Collaborative were examined to determine the incidence of potentially actionable test results. A post-hoc, anonymous, patient survey was also conducted. Results Potentially actionable test results for at least one of the three drug-gene tests were determined in 170 (82%) patients. Survey responses (n = 134) suggested that patients generally considered their test results to be important (median of 7.5 on a 10-point scale of importance) and were interested (median of 7.3 on a 10-point scale of interest) in a Clinical Pharmacogenomic Service. Conclusion Attitudes toward pharmacogenomic testing were generally favorable, and potentially actionable test results were not uncommon in this cardiovascular medicine cohort.
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Affiliation(s)
- Chandrama Mukherjee
- Department of Biological Chemistry & Pharmacology, Ohio State University, Columbus, OH 43210, USA.,Department of Biological Chemistry & Pharmacology, Ohio State University, Columbus, OH 43210, USA
| | - Kevin M Sweet
- Division of Human Genetics, Ohio State University, Columbus, OH 43210, USA.,Division of Human Genetics, Ohio State University, Columbus, OH 43210, USA
| | - Jasmine A Luzum
- Department of Clinical Pharmacy, College of Pharmacy, University of Michigan, Ann Arbor, MI 48109, USA.,Department of Clinical Pharmacy, College of Pharmacy, University of Michigan, Ann Arbor, MI 48109, USA
| | - Mahmoud Abdel-Rasoul
- Center for Biostatistics, College of Medicine, Ohio State University, 1800 Cannon Drive Columbus, OH 43210, USA.,Center for Biostatistics, College of Medicine, Ohio State University, 1800 Cannon Drive Columbus, OH 43210, USA
| | - Michael F Christman
- Coriell Institute for Medical Research, Camden, NJ 08103, USA.,Coriell Institute for Medical Research, Camden, NJ 08103, USA
| | - Joseph P Kitzmiller
- Department of Biological Chemistry & Pharmacology, Ohio State University, Columbus, OH 43210, USA.,Center for Pharmacogenomics, College of Medicine, Ohio State University, 5086 Graves Hall, 333 West 10th Avenue Columbus, OH 43210, USA.,Department of Biological Chemistry & Pharmacology, Ohio State University, Columbus, OH 43210, USA.,Center for Pharmacogenomics, College of Medicine, Ohio State University, 5086 Graves Hall, 333 West 10th Avenue Columbus, OH 43210, USA
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20
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Yohe S, Thyagarajan B. Review of Clinical Next-Generation Sequencing. Arch Pathol Lab Med 2017; 141:1544-1557. [PMID: 28782984 DOI: 10.5858/arpa.2016-0501-ra] [Citation(s) in RCA: 195] [Impact Index Per Article: 27.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
CONTEXT - Next-generation sequencing (NGS) is a technology being used by many laboratories to test for inherited disorders and tumor mutations. This technology is new for many practicing pathologists, who may not be familiar with the uses, methodology, and limitations of NGS. OBJECTIVE - To familiarize pathologists with several aspects of NGS, including current and expanding uses; methodology including wet bench aspects, bioinformatics, and interpretation; validation and proficiency; limitations; and issues related to the integration of NGS data into patient care. DATA SOURCES - The review is based on peer-reviewed literature and personal experience using NGS in a clinical setting at a major academic center. CONCLUSIONS - The clinical applications of NGS will increase as the technology, bioinformatics, and resources evolve to address the limitations and improve quality of results. The challenge for clinical laboratories is to ensure testing is clinically relevant, cost-effective, and can be integrated into clinical care.
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Affiliation(s)
- Sophia Yohe
- From the Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis
| | - Bharat Thyagarajan
- From the Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis
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21
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Rohrer Vitek CR, Abul-Husn NS, Connolly JJ, Hartzler AL, Kitchner T, Peterson JF, Rasmussen LV, Smith ME, Stallings S, Williams MS, Wolf WA, Prows CA. Healthcare provider education to support integration of pharmacogenomics in practice: the eMERGE Network experience. Pharmacogenomics 2017; 18:1013-1025. [PMID: 28639489 PMCID: PMC5941709 DOI: 10.2217/pgs-2017-0038] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Accepted: 05/07/2017] [Indexed: 12/30/2022] Open
Abstract
Ten organizations within the Electronic Medical Records and Genomics Network developed programs to implement pharmacogenomic sequencing and clinical decision support into clinical settings. Recognizing the importance of informed prescribers, a variety of strategies were used to incorporate provider education to support implementation. Education experiences with pharmacogenomics are described within the context of each organization's prior involvement, including the scope and scale of implementation specific to their Electronic Medical Records and Genomics projects. We describe common and distinct education strategies, provide exemplars and share challenges. Lessons learned inform future perspectives. Future pharmacogenomics clinical implementation initiatives need to include funding toward implementing provider education and evaluating outcomes.
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Affiliation(s)
| | - Noura S Abul-Husn
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - John J Connolly
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Andrea L Hartzler
- Department of Biomedical Informatics and Medical Education, University of Washington, Seattle, WA, 98195, USA
| | - Terrie Kitchner
- Center for Human Genetics, Marshfield Clinic Research Institute, Marshfield, WI, 54449, USA
| | - Josh F Peterson
- Department of Biomedical Informatics & Medicine, Vanderbilt University Medical Center, Nashville, TN, 37203, USA
| | - Luke V Rasmussen
- Department of Preventive Medicine, Division of Health & Biomedical Informatics, Northwestern University, Feinberg School of Medicine, Chicago, IL, 60611, USA
| | - Maureen E Smith
- Department of Medicine, Division of Cardiology, Northwestern University, Feinberg School of Medicine, Chicago, IL, 60611, USA
| | | | - Marc S Williams
- Genomic Medicine Institute, Geisinger Health System, Danville, PA, 17822, USA
| | - Wendy A Wolf
- Department of Pediatrics, Harvard Medical School, Division of Genetics & Genomics, Boston Children's Hospital, Boston, MA, 02115, USA
| | - Cynthia A Prows
- Departments of Pediatrics and Patient Services, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229-3039, USA
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