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Lennon NJ, Kottyan LC, Kachulis C, Abul-Husn NS, Arias J, Belbin G, Below JE, Berndt SI, Chung WK, Cimino JJ, Clayton EW, Connolly JJ, Crosslin DR, Dikilitas O, Velez Edwards DR, Feng Q, Fisher M, Freimuth RR, Ge T, Glessner JT, Gordon AS, Patterson C, Hakonarson H, Harden M, Harr M, Hirschhorn JN, Hoggart C, Hsu L, Irvin MR, Jarvik GP, Karlson EW, Khan A, Khera A, Kiryluk K, Kullo I, Larkin K, Limdi N, Linder JE, Loos RJF, Luo Y, Malolepsza E, Manolio TA, Martin LJ, McCarthy L, McNally EM, Meigs JB, Mersha TB, Mosley JD, Musick A, Namjou B, Pai N, Pesce LL, Peters U, Peterson JF, Prows CA, Puckelwartz MJ, Rehm HL, Roden DM, Rosenthal EA, Rowley R, Sawicki KT, Schaid DJ, Smit RAJ, Smith JL, Smoller JW, Thomas M, Tiwari H, Toledo DM, Vaitinadin NS, Veenstra D, Walunas TL, Wang Z, Wei WQ, Weng C, Wiesner GL, Yin X, Kenny EE. Selection, optimization and validation of ten chronic disease polygenic risk scores for clinical implementation in diverse US populations. Nat Med 2024; 30:480-487. [PMID: 38374346 PMCID: PMC10878968 DOI: 10.1038/s41591-024-02796-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Accepted: 01/02/2024] [Indexed: 02/21/2024]
Abstract
Polygenic risk scores (PRSs) have improved in predictive performance, but several challenges remain to be addressed before PRSs can be implemented in the clinic, including reduced predictive performance of PRSs in diverse populations, and the interpretation and communication of genetic results to both providers and patients. To address these challenges, the National Human Genome Research Institute-funded Electronic Medical Records and Genomics (eMERGE) Network has developed a framework and pipeline for return of a PRS-based genome-informed risk assessment to 25,000 diverse adults and children as part of a clinical study. From an initial list of 23 conditions, ten were selected for implementation based on PRS performance, medical actionability and potential clinical utility, including cardiometabolic diseases and cancer. Standardized metrics were considered in the selection process, with additional consideration given to strength of evidence in African and Hispanic populations. We then developed a pipeline for clinical PRS implementation (score transfer to a clinical laboratory, validation and verification of score performance), and used genetic ancestry to calibrate PRS mean and variance, utilizing genetically diverse data from 13,475 participants of the All of Us Research Program cohort to train and test model parameters. Finally, we created a framework for regulatory compliance and developed a PRS clinical report for return to providers and for inclusion in an additional genome-informed risk assessment. The initial experience from eMERGE can inform the approach needed to implement PRS-based testing in diverse clinical settings.
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Affiliation(s)
| | - Leah C Kottyan
- Cincinnati Children's Hospital Medical Center, University of Cincinnati, Cincinnati, OH, USA
| | | | | | - Josh Arias
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Gillian Belbin
- Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | - Sonja I Berndt
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | | | - James J Cimino
- University of Alabama at Birmingham, Birmingham, AL, USA
| | | | | | - David R Crosslin
- Tulane University, New Orleans, LA, USA
- University of Washington, Seattle, WA, USA
| | | | | | - QiPing Feng
- Vanderbilt University Medical Center, Nashville, TN, USA
| | | | | | - Tian Ge
- Mass General Brigham, Boston, MA, USA
| | | | | | | | | | - Maegan Harden
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Margaret Harr
- Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Joel N Hirschhorn
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Boston Children's Hospital, Boston, MA, USA
| | - Clive Hoggart
- Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Li Hsu
- Fred Hutchinson Cancer Center, Seattle, WA, USA
| | | | | | | | | | - Amit Khera
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | | | - Katie Larkin
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Nita Limdi
- University of Alabama at Birmingham, Birmingham, AL, USA
| | | | - Ruth J F Loos
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Yuan Luo
- Northwestern University, Evanston, IL, USA
| | | | - Teri A Manolio
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Lisa J Martin
- Cincinnati Children's Hospital Medical Center, University of Cincinnati, Cincinnati, OH, USA
| | - Li McCarthy
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | | | - Tesfaye B Mersha
- Cincinnati Children's Hospital Medical Center, University of Cincinnati, Cincinnati, OH, USA
| | | | | | - Bahram Namjou
- Cincinnati Children's Hospital Medical Center, University of Cincinnati, Cincinnati, OH, USA
| | - Nihal Pai
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | | | | | - Cynthia A Prows
- Cincinnati Children's Hospital Medical Center, University of Cincinnati, Cincinnati, OH, USA
| | | | - Heidi L Rehm
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Dan M Roden
- Vanderbilt University Medical Center, Nashville, TN, USA
| | | | - Robb Rowley
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | | | | | | | | | | | | | - Hemant Tiwari
- University of Alabama at Birmingham, Birmingham, AL, USA
| | | | | | | | | | - Zhe Wang
- Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Wei-Qi Wei
- Vanderbilt University Medical Center, Nashville, TN, USA
| | | | | | | | - Eimear E Kenny
- Icahn School of Medicine at Mount Sinai, New York, NY, USA
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Walton NA, Nagarajan R, Wang C, Sincan M, Freimuth RR, Everman DB, Walton DC, McGrath SP, Lemas DJ, Benos PV, Alekseyenko AV, Song Q, Gamsiz Uzun E, Taylor CO, Uzun A, Person TN, Rappoport N, Zhao Z, Williams MS. Enabling the clinical application of artificial intelligence in genomics: a perspective of the AMIA Genomics and Translational Bioinformatics Workgroup. J Am Med Inform Assoc 2024; 31:536-541. [PMID: 38037121 PMCID: PMC10797281 DOI: 10.1093/jamia/ocad211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2023] [Revised: 10/09/2023] [Accepted: 10/26/2023] [Indexed: 12/02/2023] Open
Abstract
OBJECTIVE Given the importance AI in genomics and its potential impact on human health, the American Medical Informatics Association-Genomics and Translational Biomedical Informatics (GenTBI) Workgroup developed this assessment of factors that can further enable the clinical application of AI in this space. PROCESS A list of relevant factors was developed through GenTBI workgroup discussions in multiple in-person and online meetings, along with review of pertinent publications. This list was then summarized and reviewed to achieve consensus among the group members. CONCLUSIONS Substantial informatics research and development are needed to fully realize the clinical potential of such technologies. The development of larger datasets is crucial to emulating the success AI is achieving in other domains. It is important that AI methods do not exacerbate existing socio-economic, racial, and ethnic disparities. Genomic data standards are critical to effectively scale such technologies across institutions. With so much uncertainty, complexity and novelty in genomics and medicine, and with an evolving regulatory environment, the current focus should be on using these technologies in an interface with clinicians that emphasizes the value each brings to clinical decision-making.
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Affiliation(s)
- Nephi A Walton
- Division of Medical Genetics, University of Utah School of Medicine, Salt Lake City, UT 84112 ,United States
| | - Radha Nagarajan
- Enterprise Information Services, Cedars-Sinai Medical Center, Los Angeles, CA 90025, United States
- Information Services Department, Children’s Hospital of Orange County, Orange, CA 92868, United States
| | - Chen Wang
- Division of Computational Biology, Department of Quantitative Health Sciences, Center for Individualized Medicine, Mayo Clinic, Rochester, MN 55905, United States
| | - Murat Sincan
- Flatiron Health, New York, NY 10013, United States
- Department of Internal Medicine, Sanford School of Medicine, University of South Dakota, Sioux Falls, SD 57107, United States
| | - Robert R Freimuth
- Department of Artificial Intelligence and Informatics, Center for Individualized Medicine, Mayo Clinic, Rochester, MN 55905, United States
| | - David B Everman
- EverMed Genetics and Genomics Consulting LLC, Greenville, SC 29607, United States
| | | | - Scott P McGrath
- CITRIS Health, CITRIS and Banatao Institute, University of California Berkeley, Berkeley, CA 94720, United States
| | - Dominick J Lemas
- Department of Health Outcomes and Biomedical Informatics, University of Florida, Gainesville, FL 32610, United States
| | - Panayiotis V Benos
- Department of Epidemiology, University of Florida, Gainesville, FL 32610, United States
| | - Alexander V Alekseyenko
- Department of Public Health Sciences, Biomedical Informatics Center, Medical University of South Carolina, Charleston, SC 29403, United States
| | - Qianqian Song
- Department of Health Outcomes and Biomedical Informatics, University of Florida, Gainesville, FL 32610, United States
| | - Ece Gamsiz Uzun
- Department of Pathology and Laboratory Medicine, Rhode Island Hospital and Lifespan Medical Center, Providence, RI 02915, United States
- Department of Pathology and Laboratory Medicine, Warren Alpert Medical School of Brown University, Providence, RI 02915, United States
| | - Casey Overby Taylor
- Departments of Medicine and Biomedical Engineering, Johns Hopkins School of Medicine, Baltimore, MD 21205, United States
| | - Alper Uzun
- Department of Pathology and Laboratory Medicine, Warren Alpert Medical School of Brown University, Providence, RI 02915, United States
- Legorreta Cancer Center, Brown University, Providence, RI 02915, United States
| | - Thomas Nate Person
- Department of Bioinformatics and Genomics, Huck Institutes of the Life Sciences, Penn State University, Bloomsburg, PA 16802, United States
| | - Nadav Rappoport
- Department of Software and Information Systems Engineering, Ben-Gurion University of the Negev, Beer Sheva 8410501, Israel
| | - Zhongming Zhao
- Center for Precision Health, McWilliams School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, United States
| | - Marc S Williams
- Department of Genomic Health, Geisinger, Danville, PA 17822, United States
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3
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Khalifa A, Freimuth RR. Representing NIH Genetic Test Registry Data in the FHIR Genomic Study Resource. Stud Health Technol Inform 2023; 305:398-401. [PMID: 37387049 DOI: 10.3233/shti230515] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/01/2023]
Abstract
The National Institute of Health (NIH) Genetic Testing Registry (GTR) provides a variety of information about genetic tests such as relevant methods, conditions, and performing laboratories. This study mapped a subset of GTR data to the newly developed HL7®-FHIR® Genomic Study resource. Using open-source tools, a web application was developed to implement data mapping and provides many GTR test records as Genomic Study resources. The developed system demonstrates the feasibility of using open-source tools and the FHIR Genomic Study resource to represent publicly available genetic testing information. This study validates the overall design of the Genomic Study resource and proposes two enhancements to support additional data elements.
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Affiliation(s)
- Aly Khalifa
- Department of Artificial Intelligence and Informatics, Mayo Clinic, Rochester, Minnesota
- Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota
| | - Robert R Freimuth
- Department of Artificial Intelligence and Informatics, Mayo Clinic, Rochester, Minnesota
- Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota
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4
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Linder JE, Allworth A, Bland HT, Caraballo PJ, Chisholm RL, Clayton EW, Crosslin DR, Dikilitas O, DiVietro A, Esplin ED, Forman S, Freimuth RR, Gordon AS, Green R, Harden MV, Holm IA, Jarvik GP, Karlson EW, Labrecque S, Lennon NJ, Limdi NA, Mittendorf KF, Murphy SN, Orlando L, Prows CA, Rasmussen LV, Rasmussen-Torvik L, Rowley R, Sawicki KT, Schmidlen T, Terek S, Veenstra D, Velez Edwards DR, Absher D, Abul-Husn NS, Alsip J, Bangash H, Beasley M, Below JE, Berner ES, Booth J, Chung WK, Cimino JJ, Connolly J, Davis P, Devine B, Fullerton SM, Guiducci C, Habrat ML, Hain H, Hakonarson H, Harr M, Haverfield E, Hernandez V, Hoell C, Horike-Pyne M, Hripcsak G, Irvin MR, Kachulis C, Karavite D, Kenny EE, Khan A, Kiryluk K, Korf B, Kottyan L, Kullo IJ, Larkin K, Liu C, Malolepsza E, Manolio TA, May T, McNally EM, Mentch F, Miller A, Mooney SD, Murali P, Mutai B, Muthu N, Namjou B, Perez EF, Puckelwartz MJ, Rakhra-Burris T, Roden DM, Rosenthal EA, Saadatagah S, Sabatello M, Schaid DJ, Schultz B, Seabolt L, Shaibi GQ, Sharp RR, Shirts B, Smith ME, Smoller JW, Sterling R, Suckiel SA, Thayer J, Tiwari HK, Trinidad SB, Walunas T, Wei WQ, Wells QS, Weng C, Wiesner GL, Wiley K, Peterson JF. Returning integrated genomic risk and clinical recommendations: The eMERGE study. Genet Med 2023; 25:100006. [PMID: 36621880 PMCID: PMC10085845 DOI: 10.1016/j.gim.2023.100006] [Citation(s) in RCA: 24] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 12/16/2022] [Accepted: 12/21/2022] [Indexed: 01/09/2023] Open
Abstract
PURPOSE Assessing the risk of common, complex diseases requires consideration of clinical risk factors as well as monogenic and polygenic risks, which in turn may be reflected in family history. Returning risks to individuals and providers may influence preventive care or use of prophylactic therapies for those individuals at high genetic risk. METHODS To enable integrated genetic risk assessment, the eMERGE (electronic MEdical Records and GEnomics) network is enrolling 25,000 diverse individuals in a prospective cohort study across 10 sites. The network developed methods to return cross-ancestry polygenic risk scores, monogenic risks, family history, and clinical risk assessments via a genome-informed risk assessment (GIRA) report and will assess uptake of care recommendations after return of results. RESULTS GIRAs include summary care recommendations for 11 conditions, education pages, and clinical laboratory reports. The return of high-risk GIRA to individuals and providers includes guidelines for care and lifestyle recommendations. Assembling the GIRA required infrastructure and workflows for ingesting and presenting content from multiple sources. Recruitment began in February 2022. CONCLUSION Return of a novel report for communicating monogenic, polygenic, and family history-based risk factors will inform the benefits of integrated genetic risk assessment for routine health care.
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Affiliation(s)
- Jodell E Linder
- Vanderbilt Institute for Clinical and Translational Research, Vanderbilt University Medical Center, Nashville, TN
| | - Aimee Allworth
- Division of Medical Genetics, Department of Medicine, University of Washington Medical Center, Seattle, WA
| | - Harris T Bland
- Department of Biomedical Informatics and Department of Medicine, Vanderbilt University Medical Center, Nashville, TN
| | - Pedro J Caraballo
- Department of Internal Medicine and Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN
| | - Rex L Chisholm
- Center for Genetic Medicine, Northwestern University, Chicago, IL
| | - Ellen Wright Clayton
- Center for Biomedical Ethics and Society, Vanderbilt University Medical Center, Nashville, TN
| | - David R Crosslin
- Division of Biomedical Informatics and Genomics, John W. Deming Department of Medicine, Tulane University School of Medicine, New Orleans, LA
| | - Ozan Dikilitas
- Mayo Clinician Investigator Training Program, Department of Internal Medicine and Department of Cardiovascular Medicine, Mayo Clinic, Rochester, MN
| | - Alanna DiVietro
- Vanderbilt Institute for Clinical and Translational Research, Vanderbilt University Medical Center, Nashville, TN
| | | | - Sophie Forman
- Vanderbilt Institute for Clinical and Translational Research, Vanderbilt University Medical Center, Nashville, TN
| | - Robert R Freimuth
- Department of Artificial Intelligence and Informatics, Mayo Clinic, Rochester, MN
| | - Adam S Gordon
- Department of Pharmacology, Feinberg School of Medicine, and Center for Genetic Medicine, Northwestern University, Chicago, IL
| | - Richard Green
- Department of Biomedical Informatics and Medical Education, University of Washington Medical Center, Seattle, WA
| | | | - Ingrid A Holm
- Division of Genetics and Genomics and Manton Center for Orphan Diseases Research, Boston Children's Hospital, Department of Pediatrics, Harvard Medical School, Boston, MA
| | - Gail P Jarvik
- Division of Medical Genetics, Department of Medicine and Department of Genome Science, University of Washington Medical Center, Seattle, WA
| | - Elizabeth W Karlson
- Division of Rheumatology, Inflammation and Immunity, Department of Medicine, Brigham and Women's Hospital, Boston, MA
| | - Sofia Labrecque
- Vanderbilt Institute for Clinical and Translational Research, Vanderbilt University Medical Center, Nashville, TN
| | | | - Nita A Limdi
- Department of Neurology, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL
| | - Kathleen F Mittendorf
- Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN
| | - Shawn N Murphy
- Department of Neurology, Massachusetts General Hospital, Boston, MA
| | - Lori Orlando
- Center for Applied Genomics and Precision Medicine, Duke University, Durham, NC
| | - Cynthia A Prows
- Divisions of Human Genetics and Patient Services, Cincinnati Children's Hospital Medical Center, Cincinnati, OH
| | - Luke V Rasmussen
- Department of Preventive Medicine, Northwestern University, Chicago, IL
| | | | - Robb Rowley
- Division of Genomic Medicine, National Human Genome Research Institute, Bethesda, MD
| | - Konrad Teodor Sawicki
- Department of Cardiology and Center for Genetic Medicine, Northwestern University, Chicago, IL
| | | | - Shannon Terek
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA
| | - David Veenstra
- School of Pharmacy, University of Washington, Seattle, WA
| | - Digna R Velez Edwards
- Division of Quantitative Science, Department of Obstetrics and Gynecology, Department of Biomedical Sciences, Vanderbilt University Medical Center, Nashville, TN
| | | | - Noura S Abul-Husn
- Institute for Genomic Health, Department of Medicine, Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY
| | | | - Hana Bangash
- Department of Cardiovascular Medicine, Mayo Clinic, Rochester, MN
| | - Mark Beasley
- Department of Biostatistics, School of Public Health, University of Alabama at Birmingham, Birmingham, AL
| | - Jennifer E Below
- Division of Genetic Medicine, Department of Medicine, Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN
| | - Eta S Berner
- Department of Health Services Administration, University of Alabama at Birmingham, Birmingham, AL
| | - James Booth
- Department of Emergency Medicine, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL
| | - Wendy K Chung
- Departments of Pediatrics and Medicine, Columbia University Irving Medical Center, Columbia University, New York, NY
| | - James J Cimino
- Division of General Internal Medicine and the Informatics Institute, Department of Medicine, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL
| | - John Connolly
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Patrick Davis
- Department of Biomedical Informatics and Medical Education, University of Washington Medical Center, Seattle, WA
| | - Beth Devine
- School of Pharmacy, University of Washington, Seattle, WA
| | - Stephanie M Fullerton
- Department of Bioethics and Humanities, University of Washington School of Medicine, Seattle, WA
| | | | - Melissa L Habrat
- Department of Biomedical Informatics and Medical Education, University of Washington Medical Center, Seattle, WA
| | - Heather Hain
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Hakon Hakonarson
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Margaret Harr
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA
| | | | | | - Christin Hoell
- Department of Obstetrics & Gynecology and Center for Genetic Medicine, Northwestern University, Chicago, IL
| | - Martha Horike-Pyne
- Division of Medical Genetics, Department of Medicine, University of Washington Medical Center, Seattle, WA
| | - George Hripcsak
- Department of Biomedical Informatics, Columbia University Irving Medical Center, Columbia University, New York, NY
| | - Marguerite R Irvin
- Department of Epidemiology, School of Public Health, University of Alabama at Birmingham, Birmingham, AL
| | | | - Dean Karavite
- Department of Biomedical and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Eimear E Kenny
- Institute for Genomic Health, Department of Medicine, Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Atlas Khan
- Division of Nephrology, Department of Medicine, Columbia University Irving Medical Center, New York, NY
| | - Krzysztof Kiryluk
- Division of Nephrology, Department of Medicine, Columbia University Irving Medical Center, New York, NY
| | - Bruce Korf
- Department of Genetics, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL
| | - Leah Kottyan
- The Center for Autoimmune Genomics and Etiology, Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH
| | - Iftikhar J Kullo
- Department of Cardiovascular Medicine, Mayo Clinic, Rochester, MN
| | - Katie Larkin
- Broad Institute of MIT and Harvard, Cambridge, MA
| | - Cong Liu
- Department of Biomedical Informatics, Columbia University Irving Medical Center, Columbia University, New York, NY
| | | | - Teri A Manolio
- Division of Genomic Medicine, National Human Genome Research Institute, Bethesda, MD
| | - Thomas May
- Elson S. Floyd College of Medicine, Washington State University, Vancouver, WA
| | | | - Frank Mentch
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Alexandra Miller
- Department of Cardiovascular Medicine, Mayo Clinic, Rochester, MN
| | - Sean D Mooney
- Department of Biomedical Informatics and Medical Education, University of Washington Medical Center, Seattle, WA
| | - Priyanka Murali
- Division of Medical Genetics, Department of Medicine, University of Washington Medical Center, Seattle, WA
| | - Brenda Mutai
- Division of Medical Genetics, Department of Medicine, University of Washington Medical Center, Seattle, WA
| | - Naveen Muthu
- Department of Biomedical and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Bahram Namjou
- The Center for Autoimmune Genomics and Etiology, Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH
| | - Emma F Perez
- Department of Medicine, Brigham and Women's Hospital, Mass General Brigham Personalized Medicine, Boston, MA
| | - Megan J Puckelwartz
- Department of Pharmacology, Feinberg School of Medicine, and Center for Genetic Medicine, Northwestern University, Chicago, IL
| | | | - Dan M Roden
- Departments of Medicine, Pharmacology, and Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN
| | - Elisabeth A Rosenthal
- Division of Medical Genetics, Department of Medicine, University of Washington Medical Center, Seattle, WA
| | | | - Maya Sabatello
- Division of Nephrology, Department of Medicine & Division of Ethics, Department of Medical Humanities and Ethics, Columbia University Irving Medical Center, New York, NY
| | - Dan J Schaid
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN
| | - Baergen Schultz
- Division of Genomic Medicine, National Human Genome Research Institute, Bethesda, MD
| | - Lynn Seabolt
- Vanderbilt Institute for Clinical and Translational Research, Vanderbilt University Medical Center, Nashville, TN
| | - Gabriel Q Shaibi
- Center for Health Promotion and Disease Prevention, Arizona State University, Phoenix, AZ
| | - Richard R Sharp
- Biomedical Ethics Program, Department of Quantitative Health Science, Mayo Clinic, Rochester, MN
| | - Brian Shirts
- Department of Laboratory Medicine & Pathology, University of Washington Medical Center, Seattle, WA
| | - Maureen E Smith
- Department of Cardiology and Center for Genetic Medicine, Northwestern University, Chicago, IL
| | - Jordan W Smoller
- Department of Psychiatry and Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA
| | - Rene Sterling
- Division of Genomics and Society, National Human Genome Research Institute, Bethesda, MD
| | - Sabrina A Suckiel
- The Institute for Genomic Health, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Jeritt Thayer
- Department of Biomedical and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Hemant K Tiwari
- Department of Biostatistics, School of Public Health, University of Alabama at Birmingham, Birmingham, AL
| | - Susan B Trinidad
- Department of Bioethics and Humanities, University of Washington School of Medicine, Seattle, WA
| | - Theresa Walunas
- Department of Medicine and Center for Health Information Partnerships, Northwestern University, Chicago, IL
| | - Wei-Qi Wei
- Department of Biomedical Informatics and Department of Medicine, Vanderbilt University Medical Center, Nashville, TN
| | - Quinn S Wells
- Division of Cardiovascular Medicine, Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN
| | - Chunhua Weng
- Department of Biomedical Informatics, Columbia University Irving Medical Center, Columbia University, New York, NY
| | - Georgia L Wiesner
- Division of Genetic Medicine, Department of Medicine, Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN
| | - Ken Wiley
- Division of Genomic Medicine, National Human Genome Research Institute, Bethesda, MD
| | - Josh F Peterson
- Center for Precision Medicine, Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN.
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5
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Goar W, Babb L, Chamala S, Cline M, Freimuth RR, Hart RK, Kuzma K, Lee J, Nelson T, Prlić A, Riehle K, Smith A, Stahl K, Yates AD, Rehm HL, Wagner AH. Development and application of a computable genotype model in the GA4GH Variation Representation Specification. Pac Symp Biocomput 2023; 28:383-394. [PMID: 36540993 PMCID: PMC9782714] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
As the diversity of genomic variation data increases with our growing understanding of the role of variation in health and disease, it is critical to develop standards for precise inter-system exchange of these data for research and clinical applications. The Global Alliance for Genomics and Health (GA4GH) Variation Representation Specification (VRS) meets this need through a technical terminology and information model for disambiguating and concisely representing variation concepts. Here we discuss the recent Genotype model in VRS, which may be used to represent the allelic composition of a genetic locus. We demonstrate the use of the Genotype model and the constituent Haplotype model for the precise and interoperable representation of pharmacogenomic diplotypes, HGVS variants, and VCF records using VRS and discuss how this can be leveraged to enable interoperable exchange and search operations between assayed variation and genomic knowledgebases.
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Affiliation(s)
- Wesley Goar
- Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, USA
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6
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Hui D, Xiao B, Dikilitas O, Freimuth RR, Irvin MR, Jarvik GP, Kottyan L, Kullo I, Limdi NA, Liu C, Luo Y, Namjou B, Puckelwartz MJ, Schaid D, Tiwari H, Wei WQ, Verma S, Kim D, Ritchie MD. Quantifying factors that affect polygenic risk score performance across diverse ancestries and age groups for body mass index. Pac Symp Biocomput 2023; 28:437-448. [PMID: 36540998 PMCID: PMC10018532] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Polygenic risk scores (PRS) have led to enthusiasm for precision medicine. However, it is well documented that PRS do not generalize across groups differing in ancestry or sample characteristics e.g., age. Quantifying performance of PRS across different groups of study participants, using genome-wide association study (GWAS) summary statistics from multiple ancestry groups and sample sizes, and using different linkage disequilibrium (LD) reference panels may clarify which factors are limiting PRS transferability. To evaluate these factors in the PRS generation process, we generated body mass index (BMI) PRS (PRSBMI) in the Electronic Medical Records and Genomics (eMERGE) network (N=75,661). Analyses were conducted in two ancestry groups (European and African) and three age ranges (adult, teenagers, and children). For PRSBMI calculations, we evaluated five LD reference panels and three sets of GWAS summary statistics of varying sample size and ancestry. PRSBMI performance increased for both African and European ancestry individuals using cross-ancestry GWAS summary statistics compared to European-only summary statistics (6.3% and 3.7% relative R2 increase, respectively, pAfrican=0.038, pEuropean=6.26x10-4). The effects of LD reference panels were more pronounced in African ancestry study datasets. PRSBMI performance degraded in children; R2 was less than half of teenagers or adults. The effect of GWAS summary statistics sample size was small when modeled with the other factors. Additionally, the potential of using a PRS generated for one trait to predict risk for comorbid diseases is not well understood especially in the context of cross-ancestry analyses - we explored clinical comorbidities from the electronic health record associated with PRSBMI and identified significant associations with type 2 diabetes and coronary atherosclerosis. In summary, this study quantifies the effects that ancestry, GWAS summary statistic sample size, and LD reference panel have on PRS performance, especially in cross-ancestry and age-specific analyses.
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Affiliation(s)
- Daniel Hui
- Graduate Program in Genomics and Computational Biology, University of Pennsylvania, Philadelphia, PA, USA
| | - Brenda Xiao
- Graduate Program in Genomics and Computational Biology, University of Pennsylvania, Philadelphia, PA, USA
| | - Ozan Dikilitas
- Department of Internal Medicine, Department of Cardiovascular Medicine, Clinician-Investigator Training Program, Mayo Clinic, Rochester MN
| | - Robert R. Freimuth
- Department of Artificial Intelligence and Informatics, Mayo Clinic, Rochester, MN, USA
| | - Marguerite R. Irvin
- Department of Epidemiology, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Gail P. Jarvik
- Departments of Medicine and Genome Sciences, University of Washington, Seattle WA, USA
| | - Leah Kottyan
- Center for Autoimmune Genomics and Etiology, Department of Pediatrics, University of Cincinnati, Cincinnati, OH, USA
| | - Iftikhar Kullo
- Division of Cardiovascular Diseases, Mayo Clinic, Rochester, MN 55905, USA
| | - Nita A. Limdi
- Department of Neurology & Epidemiology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Cong Liu
- Department of Biomedical Informatics, Columbia University, New York, NY, USA
| | - Yuan Luo
- Department of Preventive Medicine (Health and Biomedical Informatics), Northwestern University, Chicago, IL USA
| | - Bahram Namjou
- Department of Pediatrics, University of Cincinnati, Cincinnati, OH, USA
| | | | - Daniel Schaid
- Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, Rochester, MN 55905, USA
| | - Hemant Tiwari
- Department of Biostatistics, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Wei-Qi Wei
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Shefali Verma
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Dokyoon Kim
- Department of Biostatistics, Epidemiology and Informatics, Institute for Biomedical Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Marylyn D. Ritchie
- Department of Genetics, Institute for Biomedical Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
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7
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Zhao Y, Brush M, Wang C, Wagner AH, Liu H, Freimuth RR. Leveraging a pharmacogenomics knowledgebase to formulate a drug response phenotype terminology for genomic medicine. Bioinformatics 2022; 38:5279-5287. [PMID: 36222570 PMCID: PMC9710557 DOI: 10.1093/bioinformatics/btac646] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 05/31/2022] [Indexed: 12/24/2022] Open
Abstract
MOTIVATION Despite the increasing evidence of utility of genomic medicine in clinical practice, systematically integrating genomic medicine information and knowledge into clinical systems with a high-level of consistency, scalability and computability remains challenging. A comprehensive terminology is required for relevant concepts and the associated knowledge model for representing relationships. In this study, we leveraged PharmGKB, a comprehensive pharmacogenomics (PGx) knowledgebase, to formulate a terminology for drug response phenotypes that can represent relationships between genetic variants and treatments. We evaluated coverage of the terminology through manual review of a randomly selected subset of 200 sentences extracted from genetic reports that contained concepts for 'Genes and Gene Products' and 'Treatments'. RESULTS Results showed that our proposed drug response phenotype terminology could cover 96% of the drug response phenotypes in genetic reports. Among 18 653 sentences that contained both 'Genes and Gene Products' and 'Treatments', 3011 sentences were able to be mapped to a drug response phenotype in our proposed terminology, among which the most discussed drug response phenotypes were response (994), sensitivity (829) and survival (332). In addition, we were able to re-analyze genetic report context incorporating the proposed terminology and enrich our previously proposed PGx knowledge model to reveal relationships between genetic variants and treatments. In conclusion, we proposed a drug response phenotype terminology that enhanced structured knowledge representation of genomic medicine. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Yiqing Zhao
- Department of Artificial Intelligence and Informatics, Mayo Clinic, Rochester, MN 55905, USA
| | - Matthew Brush
- Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Chen Wang
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN 55905, USA
| | - Alex H Wagner
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children’s Hospital, Columbus, OH 43205, USA
- Department of Pediatrics, The Ohio State University College of Medicine, Columbus, OH 43210, USA
- Department of Biomedical Informatics, The Ohio State University College of Medicine, Columbus, OH 43210, USA
| | - Hongfang Liu
- Department of Artificial Intelligence and Informatics, Mayo Clinic, Rochester, MN 55905, USA
| | - Robert R Freimuth
- Department of Artificial Intelligence and Informatics, Mayo Clinic, Rochester, MN 55905, USA
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8
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Wiley K, Findley L, Goldrich M, Rakhra-Burris TK, Stevens A, Williams P, Bult CJ, Chisholm R, Deverka P, Ginsburg GS, Green ED, Jarvik G, Mensah GA, Ramos E, Relling MV, Roden DM, Rowley R, Alterovitz G, Aronson S, Bastarache L, Cimino JJ, Crowgey EL, Del Fiol G, Freimuth RR, Hoffman MA, Jeff J, Johnson K, Kawamoto K, Madhavan S, Mendonca EA, Ohno-Machado L, Pratap S, Taylor CO, Ritchie MD, Walton N, Weng C, Zayas-Cabán T, Manolio TA, Williams MS. A research agenda to support the development and implementation of genomics-based clinical informatics tools and resources. J Am Med Inform Assoc 2022; 29:1342-1349. [PMID: 35485600 PMCID: PMC9277642 DOI: 10.1093/jamia/ocac057] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 02/22/2022] [Accepted: 04/08/2022] [Indexed: 11/12/2022] Open
Abstract
OBJECTIVE The Genomic Medicine Working Group of the National Advisory Council for Human Genome Research virtually hosted its 13th genomic medicine meeting titled "Developing a Clinical Genomic Informatics Research Agenda". The meeting's goal was to articulate a research strategy to develop Genomics-based Clinical Informatics Tools and Resources (GCIT) to improve the detection, treatment, and reporting of genetic disorders in clinical settings. MATERIALS AND METHODS Experts from government agencies, the private sector, and academia in genomic medicine and clinical informatics were invited to address the meeting's goals. Invitees were also asked to complete a survey to assess important considerations needed to develop a genomic-based clinical informatics research strategy. RESULTS Outcomes from the meeting included identifying short-term research needs, such as designing and implementing standards-based interfaces between laboratory information systems and electronic health records, as well as long-term projects, such as identifying and addressing barriers related to the establishment and implementation of genomic data exchange systems that, in turn, the research community could help address. DISCUSSION Discussions centered on identifying gaps and barriers that impede the use of GCIT in genomic medicine. Emergent themes from the meeting included developing an implementation science framework, defining a value proposition for all stakeholders, fostering engagement with patients and partners to develop applications under patient control, promoting the use of relevant clinical workflows in research, and lowering related barriers to regulatory processes. Another key theme was recognizing pervasive biases in data and information systems, algorithms, access, value, and knowledge repositories and identifying ways to resolve them.
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Affiliation(s)
- Ken Wiley
- National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Laura Findley
- National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Madison Goldrich
- National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Tejinder K Rakhra-Burris
- Department of Medicine, Center for Applied Genomics & Precision Medicine, Duke University, Durham, North Carolina, USA
| | - Ana Stevens
- National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Pamela Williams
- Department of Medicine, Center for Applied Genomics & Precision Medicine, Duke University, Durham, North Carolina, USA
| | | | - Rex Chisholm
- Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
| | - Patricia Deverka
- Center for Translational and Policy Research in Precision Medicine, University of California at San Francisco, San Francisco, California, USA
| | - Geoffrey S Ginsburg
- All of Us Research Program, National Institutes of Health, Bethesda, Maryland, USA
| | - Eric D Green
- National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Gail Jarvik
- Division of Medical Genetics, University of Washington, Seattle, Washington, USA
| | - George A Mensah
- National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Erin Ramos
- National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Mary V Relling
- Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Dan M Roden
- Departments of Medicine, Pharmacology, and Biomedical Informatics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Robb Rowley
- National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Gil Alterovitz
- Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Samuel Aronson
- Mass General Brigham, Research Information Sciences and Computing, Somerville, Massachusetts, USA
| | - Lisa Bastarache
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - James J Cimino
- Heersink School of Medicine, University of Alabama at Birmingham, Alabama, USA
| | | | - Guilherme Del Fiol
- Department of Biomedical Informatics, University of Utah School of Medicine, Salt Lake City, Utah, USA
| | - Robert R Freimuth
- Department of Artificial Intelligence and Informatics, Mayo Clinic, Rochester, Minnesota, USA
| | - Mark A Hoffman
- School of Medicine, Children's Mercy Hospital Kansas City, University of Missouri Kansas City, Lees Summit, Missouri, USA
| | | | - Kevin Johnson
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Kensaku Kawamoto
- Department of Biomedical Informatics, University of Utah School of Medicine, Salt Lake City, Utah, USA
| | - Subha Madhavan
- Innovation Center for Biomedical Informatics, Georgetown University, Washington, District of Columbia, USA
| | - Eneida A Mendonca
- Regenstrief Institute, Inc., Indianapolis, Indiana, USA.,Department of Pediatrics, Department of Biostatistics and Health Data Sciences, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Lucila Ohno-Machado
- Department of Biomedical Informatics, University of California San Diego, La Jolla, California, USA
| | - Siddharth Pratap
- Bioinformatics Core, Meharry Medical College, Nashville, Tennessee, USA
| | | | - Marylyn D Ritchie
- Department of Genetics, Perelman School of Medicine, Institute for Biomedical Informatics, Penn Center for Precision Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Nephi Walton
- Intermountain Precision Genomics, Intermountain Healthcare, St George, Utah, USA
| | - Chunhua Weng
- Department of Biomedical Informatics, Columbia University, New York, New York, USA
| | - Teresa Zayas-Cabán
- National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA
| | - Teri A Manolio
- National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Marc S Williams
- Geisinger, Genomic Medicine Institute, Danville, Pennsylvania, USA
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9
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Cannon M, Kuzma K, Stevenson J, Liu J, O'Sullivan C, Chaudhari BP, Brush M, Freimuth RR, Nelson T, Baudis M, Griffith OL, Griffith M, Babb L, Cline MS, Liu X, Walsh B, Wagner AH. Abstract 1177: Introduction of the GA4GH Variation Representation Specification (VRS) and supporting tools for discovery and exchange of clinical genomic and cytogenomic knowledge in cancers. Cancer Res 2022. [DOI: 10.1158/1538-7445.am2022-1177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Precision oncology is the practice of interpreting the clinical significance of observed molecular changes in patient neoplasms, potentially impacting medical decision making and care. This process is labor-intensive and (among other challenges) involves accurately translating between variation representation conventions from one resource to the next. For example, differences in representations of Copy Number Variation (CNV) from genomic regions, cytogenomic bands, or gene features create challenges in knowledge matching due to lack of standards covering all of these modalities of observed variation.The Global Alliance for Genomics and Health (GA4GH; ga4gh.org) is an international collaborative of genomic data sharing initiatives (Driver Projects) developing genomic data sharing standards within a human rights framework. GA4GH recently published the Variation Representation Specification (VRS; pronounced “verse”), a standard for the computational representation of biomolecular variation. VRS is a terminology, schema, and associated conventions for creating uniquely identifiable and federatable representations of molecular variation. VRS has formal data classes well-suited to differentiating between variation on a single molecule (e.g. tandem duplications) from variation measured at a systemic level (e.g. genome-wide copy number variation). In addition to molecular sequence variation, VRS also supports variation on cytogenetic coordinate systems and genes, making it well-suited to representing variation associated with cancer biomarkers.We demonstrate the use of VRS to model reported gene-associated CNVs from the AACR Project GENIE cohort, to aid in the computational discovery of evidence from clinico-genomic knowledgebases with genomic or cytogenomic CNV representations. We highlight the use case of knowledge matching to the Atlas of Genetics and Cytogenetics in Oncology and Haematology (“the Atlas”; atlasgeneticsoncology.org), a cytogenetics resource historically driven by user website navigation. Using VRS search tools we developed for the Variant Interpretation for Cancer Consortium (VICC; cancervariants.org) GA4GH Driver Project, we found that 64% of GENIE samples with reported CNVs matched clinically relevant knowledge in the Atlas. This work was enabled by programmatic search tools leveraging standard VRS object structures, demonstrating how VRS enables collection of real-world evidence across more resources without manual interpretation or custom normalization methods. We conclude with a survey of open-source tools supporting this analysis as well as search of other clinico-genomic knowledgebases with VRS, including CIViC (civicdb.org), BRCA Exchange (brcaexchange.org), and the Molecular Oncology Almanac (moalmanac.org).
Citation Format: Matthew Cannon, Kori Kuzma, James Stevenson, Jiachen Liu, Colin O'Sullivan, Bimal P. Chaudhari, Matthew Brush, Robert R. Freimuth, Tristan Nelson, Michael Baudis, Obi L. Griffith, Malachi Griffith, Lawrence Babb, Melissa S. Cline, Xuelu Liu, Brian Walsh, Alex H. Wagner. Introduction of the GA4GH Variation Representation Specification (VRS) and supporting tools for discovery and exchange of clinical genomic and cytogenomic knowledge in cancers [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 1177.
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Affiliation(s)
| | - Kori Kuzma
- 1Nationwide Children's Hospital, Columbus, OH
| | | | | | | | | | | | | | | | | | | | | | | | | | - Xuelu Liu
- 2Dana-Farber Cancer Institute, Boston, MA
| | - Brian Walsh
- 10Oregon Health & Science University, Portland, OR
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10
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Wang L, Scherer SE, Bielinski SJ, Muzny DM, Jones LA, Black JL, Moyer AM, Giri J, Sharp RR, Matey ET, Wright JA, Oyen LJ, Nicholson WT, Wiepert M, Sullard T, Curry TB, Vitek CRR, McAllister TM, Sauver JL, Caraballo PJ, Lazaridis KN, Venner E, Qin X, Hu J, Kovar CL, Korchina V, Walker K, Doddapaneni H, Wu TJ, Raj R, Denson S, Liu W, Chandanavelli G, Zhang L, Wang Q, Kalra D, Karow MB, Harris KJ, Sicotte H, Peterson SE, Barthel AE, Moore BE, Skierka JM, Kluge ML, Kotzer KE, Kloke K, Vander Pol JM, Marker H, Sutton JA, Kekic A, Ebenhoh A, Bierle DM, Schuh MJ, Grilli C, Erickson S, Umbreit A, Ward L, Crosby S, Nelson EA, Levey S, Elliott M, Peters SG, Pereira N, Frye M, Shamoun F, Goetz MP, Kullo IJ, Wermers R, Anderson JA, Formea CM, El Melik RM, Zeuli JD, Herges JR, Krieger CA, Hoel RW, Taraba JL, Thomas SR, Absah I, Bernard ME, Fink SR, Gossard A, Grubbs PL, Jacobson TM, Takahashi P, Zehe SC, Buckles S, Bumgardner M, Gallagher C, Fee-Schroeder K, Nicholas NR, Powers ML, Ragab AK, Richardson DM, Stai A, Wilson J, Pacyna JE, Olson JE, Sutton EJ, Beck AT, Horrow C, Kalari KR, Larson NB, Liu H, Wang L, Lopes GS, Borah BJ, Freimuth RR, Zhu Y, Jacobson DJ, Hathcock MA, Armasu SM, McGree ME, Jiang R, Koep TH, Ross JL, Hilden M, Bosse K, Ramey B, Searcy I, Boerwinkle E, Gibbs RA, Weinshilboum RM. Implementation of preemptive DNA sequence-based pharmacogenomics testing across a large academic medical center: The Mayo-Baylor RIGHT 10K Study. Genet Med 2022; 24:1062-1072. [PMID: 35331649 PMCID: PMC9272414 DOI: 10.1016/j.gim.2022.01.022] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 01/25/2022] [Accepted: 01/26/2022] [Indexed: 12/12/2022] Open
Abstract
PURPOSE The Mayo-Baylor RIGHT 10K Study enabled preemptive, sequence-based pharmacogenomics (PGx)-driven drug prescribing practices in routine clinical care within a large cohort. We also generated the tools and resources necessary for clinical PGx implementation and identified challenges that need to be overcome. Furthermore, we measured the frequency of both common genetic variation for which clinical guidelines already exist and rare variation that could be detected by DNA sequencing, rather than genotyping. METHODS Targeted oligonucleotide-capture sequencing of 77 pharmacogenes was performed using DNA from 10,077 consented Mayo Clinic Biobank volunteers. The resulting predicted drug response-related phenotypes for 13 genes, including CYP2D6 and HLA, affecting 21 drug-gene pairs, were deposited preemptively in the Mayo electronic health record. RESULTS For the 13 pharmacogenes of interest, the genomes of 79% of participants carried clinically actionable variants in 3 or more genes, and DNA sequencing identified an average of 3.3 additional conservatively predicted deleterious variants that would not have been evident using genotyping. CONCLUSION Implementation of preemptive rather than reactive and sequence-based rather than genotype-based PGx prescribing revealed nearly universal patient applicability and required integrated institution-wide resources to fully realize individualized drug therapy and to show more efficient use of health care resources.
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Affiliation(s)
- Liewei Wang
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN,Division of Clinical Pharmacology, Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN
| | - Steven E. Scherer
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX
| | - Suzette J. Bielinski
- Division of Epidemiology, Department of Health Sciences Research, Mayo Clinic, Rochester, MN
| | - Donna M. Muzny
- Human Genome Sequencing Center Clinical Laboratory, Baylor College of Medicine, Houston, TX
| | - Leila A. Jones
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN
| | - John Logan Black
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN
| | - Ann M. Moyer
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN
| | - Jyothsna Giri
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN
| | | | | | | | | | - Wayne T. Nicholson
- Department of Anesthesiology and Perioperative Medicine, Mayo Clinic, Rochester, MN
| | - Mathieu Wiepert
- Department of Information Technology, Mayo Clinic, Rochester, MN
| | - Terri Sullard
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN
| | - Timothy B. Curry
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN,Department of Anesthesiology and Perioperative Medicine, Mayo Clinic, Rochester, MN
| | | | | | - Jennifer L. Sauver
- Division of Epidemiology, Department of Health Sciences Research, Mayo Clinic, Rochester, MN,Robert D. and Patricia E. Kern Center for the Science of Health Care Delivery, Mayo Clinic, Rochester, MN
| | - Pedro J. Caraballo
- Division of General Internal Medicine, Department of Internal Medicine, Mayo Clinic, Rochester, MN
| | - Konstantinos N. Lazaridis
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN,Division of Gastroenterology and Hepatology, Department of Internal Medicine, Mayo Clinic, Rochester, MN
| | - Eric Venner
- Human Genome Sequencing Center Clinical Laboratory, Baylor College of Medicine, Houston, TX
| | - Xiang Qin
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX
| | - Jianhong Hu
- Human Genome Sequencing Center Clinical Laboratory, Baylor College of Medicine, Houston, TX
| | - Christie L. Kovar
- Human Genome Sequencing Center Clinical Laboratory, Baylor College of Medicine, Houston, TX
| | - Viktoriya Korchina
- Human Genome Sequencing Center Clinical Laboratory, Baylor College of Medicine, Houston, TX
| | - Kimberly Walker
- Human Genome Sequencing Center Clinical Laboratory, Baylor College of Medicine, Houston, TX
| | | | - Tsung-Jung Wu
- Human Genome Sequencing Center Clinical Laboratory, Baylor College of Medicine, Houston, TX
| | - Ritika Raj
- Human Genome Sequencing Center Clinical Laboratory, Baylor College of Medicine, Houston, TX
| | - Shawn Denson
- Human Genome Sequencing Center Clinical Laboratory, Baylor College of Medicine, Houston, TX
| | - Wen Liu
- Human Genome Sequencing Center Clinical Laboratory, Baylor College of Medicine, Houston, TX
| | - Gauthami Chandanavelli
- Human Genome Sequencing Center Clinical Laboratory, Baylor College of Medicine, Houston, TX
| | - Lan Zhang
- Human Genome Sequencing Center Clinical Laboratory, Baylor College of Medicine, Houston, TX
| | - Qiaoyan Wang
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX
| | - Divya Kalra
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX
| | - Mary Beth Karow
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN
| | | | - Hugues Sicotte
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN
| | - Sandra E. Peterson
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN
| | - Amy E. Barthel
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN
| | - Brenda E. Moore
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN
| | | | - Michelle L. Kluge
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN
| | - Katrina E. Kotzer
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN
| | - Karen Kloke
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN
| | | | - Heather Marker
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN
| | - Joseph A. Sutton
- Department of Information Technology, Mayo Clinic, Rochester, MN
| | | | | | - Dennis M. Bierle
- Division of General Internal Medicine, Department of Internal Medicine, Mayo Clinic, Rochester, MN
| | | | | | | | - Audrey Umbreit
- Department of Pharmacy, Mayo Clinic Health System, Mankato, MN
| | - Leah Ward
- Department of Pharmacy, Mayo Clinic, Jacksonville, FL
| | - Sheena Crosby
- Department of Pharmacy, Mayo Clinic, Jacksonville, FL
| | | | - Sharon Levey
- Department of Clinical Genomics, Mayo Clinic, Scottsdale, AZ
| | - Michelle Elliott
- Division of Hematology, Department of Internal Medicine, Mayo Clinic, Rochester, MN
| | - Steve G. Peters
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, Mayo Clinic, Rochester, MN
| | - Naveen Pereira
- Department of Cardiovascular Medicine, Mayo Clinic, Rochester, MN
| | - Mark Frye
- Department of Psychiatry and Psychology, Mayo Clinic, Rochester, MN
| | - Fadi Shamoun
- Department of Cardiovascular Medicine Mayo Clinic, Phoenix, AZ
| | - Matthew P. Goetz
- Division of Medical Oncology, Department of Oncology, Mayo Clinic, Rochester, MN
| | | | - Robert Wermers
- Division of Endocrinology, Diabetes, Metabolism, and Nutrition, Department of Internal Medicine, Mayo Clinic, Rochester, MN
| | | | | | | | | | | | | | | | | | - Scott R. Thomas
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN
| | - Imad Absah
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Mayo Clinic, Rochester, MN
| | | | - Stephanie R. Fink
- Division of Community Internal Medicine, Department of Internal Medicine, Mayo Clinic, Rochester, MN
| | - Andrea Gossard
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Mayo Clinic, Rochester, MN
| | | | | | - Paul Takahashi
- Division of Community Internal Medicine, Department of Internal Medicine, Mayo Clinic, Rochester, MN
| | | | - Susan Buckles
- Department of Public Affairs, Mayo Clinic, Rochester, MN
| | | | | | | | | | - Melody L. Powers
- Biospecimens Accessioning and Processing Laboratory, Mayo Clinic, Rochester, MN
| | - Ahmed K. Ragab
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN
| | | | - Anthony Stai
- Department of Information Technology, Mayo Clinic, Rochester, MN
| | - Jaymi Wilson
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN
| | - Joel E. Pacyna
- Biomedical Ethics Research Program, Mayo Clinic, Rochester, MN
| | - Janet E. Olson
- Division of Epidemiology, Department of Health Sciences Research, Mayo Clinic, Rochester, MN,Biomedical Ethics Research Program, Mayo Clinic, Rochester, MN
| | - Erica J. Sutton
- Biomedical Ethics Research Program, Mayo Clinic, Rochester, MN
| | - Annika T. Beck
- Biomedical Ethics Research Program, Mayo Clinic, Rochester, MN
| | - Caroline Horrow
- Biomedical Ethics Research Program, Mayo Clinic, Rochester, MN
| | - Krishna R. Kalari
- Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, Rochester, MN
| | - Nicholas B. Larson
- Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, Rochester, MN
| | - Hongfang Liu
- Division of Digital Health Sciences, Department of Health Sciences Research, Mayo Clinic, Rochester, MN
| | - Liwei Wang
- Division of Digital Health Sciences, Department of Health Sciences Research, Mayo Clinic, Rochester, MN
| | - Guilherme S. Lopes
- Division of Epidemiology, Department of Health Sciences Research, Mayo Clinic, Rochester, MN,Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, Rochester, MN
| | - Bijan J. Borah
- Robert D. and Patricia E. Kern Center for the Science of Health Care Delivery, Mayo Clinic, Rochester, MN,Division of Health Care Policy and Research, Department of Health Sciences Research, Mayo Clinic, Rochester, MN
| | - Robert R. Freimuth
- Division of Digital Health Sciences, Department of Health Sciences Research, Mayo Clinic, Rochester, MN
| | - Ye Zhu
- Robert D. and Patricia E. Kern Center for the Science of Health Care Delivery, Mayo Clinic, Rochester, MN
| | - Debra J. Jacobson
- Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, Rochester, MN
| | - Matthew A. Hathcock
- Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, Rochester, MN
| | - Sebastian M. Armasu
- Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, Rochester, MN
| | - Michaela E. McGree
- Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, Rochester, MN
| | - Ruoxiang Jiang
- Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, Rochester, MN
| | | | | | | | | | | | | | - Eric Boerwinkle
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX,Human Genome Sequencing Center Clinical Laboratory, Baylor College of Medicine, Houston, TX,School of Public Health, University of Texas Health Science Center at Houston, Houston, TX
| | - Richard A. Gibbs
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX,Corresponding Authors (), ()
| | - Richard M. Weinshilboum
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN,Division of Clinical Pharmacology, Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN,Corresponding Authors (), ()
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11
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Yu J, Pacheco JA, Ghosh AS, Luo Y, Weng C, Shang N, Benoit B, Carrell DS, Carroll RJ, Dikilitas O, Freimuth RR, Gainer VS, Hakonarson H, Hripcsak G, Kullo IJ, Mentch F, Murphy SN, Peissig PL, Ramirez AH, Walton N, Wei WQ, Rasmussen LV. Under-specification as the source of ambiguity and vagueness in narrative phenotype algorithm definitions. BMC Med Inform Decis Mak 2022; 22:23. [PMID: 35090449 PMCID: PMC8796627 DOI: 10.1186/s12911-022-01759-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 12/22/2021] [Indexed: 11/29/2022] Open
Abstract
Introduction Currently, one of the commonly used methods for disseminating electronic health record (EHR)-based phenotype algorithms is providing a narrative description of the algorithm logic, often accompanied by flowcharts. A challenge with this mode of dissemination is the potential for under-specification in the algorithm definition, which leads to ambiguity and vagueness. Methods This study examines incidents of under-specification that occurred during the implementation of 34 narrative phenotyping algorithms in the electronic Medical Record and Genomics (eMERGE) network. We reviewed the online communication history between algorithm developers and implementers within the Phenotype Knowledge Base (PheKB) platform, where questions could be raised and answered regarding the intended implementation of a phenotype algorithm. Results We developed a taxonomy of under-specification categories via an iterative review process between two groups of annotators. Under-specifications that lead to ambiguity and vagueness were consistently found across narrative phenotype algorithms developed by all involved eMERGE sites. Discussion and conclusion Our findings highlight that under-specification is an impediment to the accuracy and efficiency of the implementation of current narrative phenotyping algorithms, and we propose approaches for mitigating these issues and improved methods for disseminating EHR phenotyping algorithms. Supplementary Information The online version contains supplementary material available at 10.1186/s12911-022-01759-z.
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12
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Wagner AH, Babb L, Alterovitz G, Baudis M, Brush M, Cameron DL, Cline M, Griffith M, Griffith OL, Hunt SE, Kreda D, Lee JM, Li S, Lopez J, Moyer E, Nelson T, Patel RY, Riehle K, Robinson PN, Rynearson S, Schuilenburg H, Tsukanov K, Walsh B, Konopko M, Rehm HL, Yates AD, Freimuth RR, Hart RK. The GA4GH Variation Representation Specification: A computational framework for variation representation and federated identification. Cell Genom 2021; 1. [PMID: 35311178 PMCID: PMC8929418 DOI: 10.1016/j.xgen.2021.100027] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Maximizing the personal, public, research, and clinical value of genomic information will require the reliable exchange of genetic variation data. We report here the Variation Representation Specification (VRS, pronounced "verse"), an extensible framework for the computable representation of variation that complements contemporary human-readable and flat file standards for genomic variation representation. VRS provides semantically precise representations of variation and leverages this design to enable federated identification of biomolecular variation with globally consistent and unique computed identifiers. The VRS framework includes a terminology and information model, machine-readable schema, data sharing conventions, and a reference implementation, each of which is intended to be broadly useful and freely available for community use. VRS was developed by a partnership among national information resource providers, public initiatives, and diagnostic testing laboratories under the auspices of the Global Alliance for Genomics and Health (GA4GH).
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Affiliation(s)
- Alex H. Wagner
- Department of Pediatrics, The Ohio State University College of Medicine, Columbus, OH 43210, USA
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children’s Hospital, Columbus, OH 43215, USA
- Corresponding author
| | - Lawrence Babb
- Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Corresponding author
| | - Gil Alterovitz
- Harvard Medical School, Boston, MA 02115, USA
- Department of Medicine, Brigham and Women’s Hospital, Boston, MA 02115, USA
| | - Michael Baudis
- University of Zurich and Swiss Institute of Bioinformatics, Zurich, Switzerland
| | - Matthew Brush
- Oregon Health & Science University, Portland, OR 97239, USA
| | - Daniel L. Cameron
- Bioinformatics Division, Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia
| | - Melissa Cline
- UC Santa Cruz Genomics Institute, Santa Cruz, CA 95060, USA
| | - Malachi Griffith
- Washington University School of Medicine, St. Louis, MO 63108, USA
| | - Obi L. Griffith
- Washington University School of Medicine, St. Louis, MO 63108, USA
| | - Sarah E. Hunt
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - David Kreda
- Department of Biomedical Informatics, Harvard Medical School, Boston MA 02115, USA
| | - Jennifer M. Lee
- Essex Management LLC and National Cancer Institute, Rockville, MD 20850, USA
| | - Stephanie Li
- The Global Alliance for Genomics and Health, Toronto, ON, Canada
| | | | - Eric Moyer
- National Center for Biotechnology Information, National Library of Medicine National Institutes of Health, Bethesda, MD 20894, USA
| | | | | | - Kevin Riehle
- Baylor College of Medicine, Houston, TX 77030, USA
| | | | - Shawn Rynearson
- Utah Center for Genetic Discovery, University of Utah, Salt Lake City, UT 84112, USA
| | - Helen Schuilenburg
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Kirill Tsukanov
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Brian Walsh
- Oregon Health & Science University, Portland, OR 97239, USA
| | - Melissa Konopko
- The Global Alliance for Genomics and Health, Toronto, ON, Canada
| | - Heidi L. Rehm
- Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Cambridge, MA 02142, USA
| | - Andrew D. Yates
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Robert R. Freimuth
- Center for Individualized Medicine, Department of Artificial Intelligence and Informatics, Mayo Clinic, Rochester, MN 55905, USA
| | - Reece K. Hart
- Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- MyOme, Inc., Menlo Park, CA 94070, USA
- Corresponding author
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13
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Rehm HL, Page AJ, Smith L, Adams JB, Alterovitz G, Babb LJ, Barkley MP, Baudis M, Beauvais MJ, Beck T, Beckmann JS, Beltran S, Bernick D, Bernier A, Bonfield JK, Boughtwood TF, Bourque G, Bowers SR, Brookes AJ, Brudno M, Brush MH, Bujold D, Burdett T, Buske OJ, Cabili MN, Cameron DL, Carroll RJ, Casas-Silva E, Chakravarty D, Chaudhari BP, Chen SH, Cherry JM, Chung J, Cline M, Clissold HL, Cook-Deegan RM, Courtot M, Cunningham F, Cupak M, Davies RM, Denisko D, Doerr MJ, Dolman LI, Dove ES, Dursi LJ, Dyke SO, Eddy JA, Eilbeck K, Ellrott KP, Fairley S, Fakhro KA, Firth HV, Fitzsimons MS, Fiume M, Flicek P, Fore IM, Freeberg MA, Freimuth RR, Fromont LA, Fuerth J, Gaff CL, Gan W, Ghanaim EM, Glazer D, Green RC, Griffith M, Griffith OL, Grossman RL, Groza T, Guidry Auvil JM, Guigó R, Gupta D, Haendel MA, Hamosh A, Hansen DP, Hart RK, Hartley DM, Haussler D, Hendricks-Sturrup RM, Ho CW, Hobb AE, Hoffman MM, Hofmann OM, Holub P, Hsu JS, Hubaux JP, Hunt SE, Husami A, Jacobsen JO, Jamuar SS, Janes EL, Jeanson F, Jené A, Johns AL, Joly Y, Jones SJ, Kanitz A, Kato K, Keane TM, Kekesi-Lafrance K, Kelleher J, Kerry G, Khor SS, Knoppers BM, Konopko MA, Kosaki K, Kuba M, Lawson J, Leinonen R, Li S, Lin MF, Linden M, Liu X, Liyanage IU, Lopez J, Lucassen AM, Lukowski M, Mann AL, Marshall J, Mattioni M, Metke-Jimenez A, Middleton A, Milne RJ, Molnár-Gábor F, Mulder N, Munoz-Torres MC, Nag R, Nakagawa H, Nasir J, Navarro A, Nelson TH, Niewielska A, Nisselle A, Niu J, Nyrönen TH, O’Connor BD, Oesterle S, Ogishima S, Ota Wang V, Paglione LA, Palumbo E, Parkinson HE, Philippakis AA, Pizarro AD, Prlic A, Rambla J, Rendon A, Rider RA, Robinson PN, Rodarmer KW, Rodriguez LL, Rubin AF, Rueda M, Rushton GA, Ryan RS, Saunders GI, Schuilenburg H, Schwede T, Scollen S, Senf A, Sheffield NC, Skantharajah N, Smith AV, Sofia HJ, Spalding D, Spurdle AB, Stark Z, Stein LD, Suematsu M, Tan P, Tedds JA, Thomson AA, Thorogood A, Tickle TL, Tokunaga K, Törnroos J, Torrents D, Upchurch S, Valencia A, Guimera RV, Vamathevan J, Varma S, Vears DF, Viner C, Voisin C, Wagner AH, Wallace SE, Walsh BP, Williams MS, Winkler EC, Wold BJ, Wood GM, Woolley JP, Yamasaki C, Yates AD, Yung CK, Zass LJ, Zaytseva K, Zhang J, Goodhand P, North K, Birney E. GA4GH: International policies and standards for data sharing across genomic research and healthcare. Cell Genom 2021; 1:100029. [PMID: 35072136 PMCID: PMC8774288 DOI: 10.1016/j.xgen.2021.100029] [Citation(s) in RCA: 64] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The Global Alliance for Genomics and Health (GA4GH) aims to accelerate biomedical advances by enabling the responsible sharing of clinical and genomic data through both harmonized data aggregation and federated approaches. The decreasing cost of genomic sequencing (along with other genome-wide molecular assays) and increasing evidence of its clinical utility will soon drive the generation of sequence data from tens of millions of humans, with increasing levels of diversity. In this perspective, we present the GA4GH strategies for addressing the major challenges of this data revolution. We describe the GA4GH organization, which is fueled by the development efforts of eight Work Streams and informed by the needs of 24 Driver Projects and other key stakeholders. We present the GA4GH suite of secure, interoperable technical standards and policy frameworks and review the current status of standards, their relevance to key domains of research and clinical care, and future plans of GA4GH. Broad international participation in building, adopting, and deploying GA4GH standards and frameworks will catalyze an unprecedented effort in data sharing that will be critical to advancing genomic medicine and ensuring that all populations can access its benefits.
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Affiliation(s)
- Heidi L. Rehm
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Massachusetts General Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Angela J.H. Page
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Global Alliance for Genomics and Health, Toronto, ON, Canada
| | - Lindsay Smith
- Global Alliance for Genomics and Health, Toronto, ON, Canada
- Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Jeremy B. Adams
- Global Alliance for Genomics and Health, Toronto, ON, Canada
- Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Gil Alterovitz
- Brigham and Women’s Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | | | | | - Michael Baudis
- University of Zurich, Zurich, Switzerland
- SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Michael J.S. Beauvais
- Global Alliance for Genomics and Health, Toronto, ON, Canada
- McGill University, Montreal, QC, Canada
| | - Tim Beck
- University of Leicester, Leicester, UK
| | | | - Sergi Beltran
- CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- Universitat de Barcelona, Barcelona, Spain
| | - David Bernick
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | | | - Tiffany F. Boughtwood
- Australian Genomics, Parkville, VIC, Australia
- Murdoch Children’s Research Institute, Parkville, VIC, Australia
| | - Guillaume Bourque
- McGill University, Montreal, QC, Canada
- Canadian Center for Computational Genomics, Montreal, QC, Canada
| | | | | | - Michael Brudno
- Canadian Center for Computational Genomics, Montreal, QC, Canada
- University of Toronto, Toronto, ON, Canada
- University Health Network, Toronto, ON, Canada
- Vector Institute, Toronto, ON, Canada
- Canadian Distributed Infrastructure for Genomics (CanDIG), Toronto, ON, Canada
| | | | - David Bujold
- McGill University, Montreal, QC, Canada
- Canadian Center for Computational Genomics, Montreal, QC, Canada
- Canadian Distributed Infrastructure for Genomics (CanDIG), Toronto, ON, Canada
| | - Tony Burdett
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
| | | | | | - Daniel L. Cameron
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- University of Melbourne, Melbourne, VIC, Australia
| | | | | | | | - Bimal P. Chaudhari
- Nationwide Children’s Hospital, Columbus, OH, USA
- The Ohio State University, Columbus, OH, USA
| | - Shu Hui Chen
- National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | | | - Justina Chung
- Global Alliance for Genomics and Health, Toronto, ON, Canada
- Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Melissa Cline
- UC Santa Cruz Genomics Institute, Santa Cruz, CA, USA
| | | | | | - Mélanie Courtot
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
| | - Fiona Cunningham
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
| | | | | | | | | | | | | | - L. Jonathan Dursi
- University Health Network, Toronto, ON, Canada
- Canadian Distributed Infrastructure for Genomics (CanDIG), Toronto, ON, Canada
| | | | | | | | | | - Susan Fairley
- Global Alliance for Genomics and Health, Toronto, ON, Canada
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
| | - Khalid A. Fakhro
- Sidra Medicine, Doha, Qatar
- Weill Cornell Medicine - Qatar, Doha, Qatar
| | - Helen V. Firth
- Wellcome Sanger Institute, Hinxton, UK
- Addenbrooke’s Hospital, Cambridge, UK
| | | | | | - Paul Flicek
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
| | - Ian M. Fore
- National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Mallory A. Freeberg
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
| | | | - Lauren A. Fromont
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | | | - Clara L. Gaff
- Australian Genomics, Parkville, VIC, Australia
- Murdoch Children’s Research Institute, Parkville, VIC, Australia
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- University of Melbourne, Melbourne, VIC, Australia
| | - Weiniu Gan
- National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Elena M. Ghanaim
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - David Glazer
- Verily Life Sciences, South San Francisco, CA, USA
| | - Robert C. Green
- Brigham and Women’s Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Malachi Griffith
- Washington University School of Medicine in St. Louis, St. Louis, MO, USA
| | - Obi L. Griffith
- Washington University School of Medicine in St. Louis, St. Louis, MO, USA
| | | | | | | | - Roderic Guigó
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Dipayan Gupta
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
| | | | - Ada Hamosh
- Johns Hopkins University, Baltimore, MD, USA
| | - David P. Hansen
- Australian Genomics, Parkville, VIC, Australia
- The Australian e-Health Research Centre, CSIRO, Herston, QLD, Australia
| | - Reece K. Hart
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Invitae, San Francisco, CA, USA
- MyOme, Inc, San Bruno, CA, USA
| | | | - David Haussler
- UC Santa Cruz Genomics Institute, Santa Cruz, CA, USA
- Howard Hughes Medical Institute, University of California, Santa Cruz, CA, USA
| | | | | | | | - Michael M. Hoffman
- University of Toronto, Toronto, ON, Canada
- University Health Network, Toronto, ON, Canada
- Vector Institute, Toronto, ON, Canada
| | - Oliver M. Hofmann
- University of Toronto, Toronto, ON, Canada
- University of Melbourne, Melbourne, VIC, Australia
| | - Petr Holub
- BBMRI-ERIC, Graz, Austria
- Masaryk University, Brno, Czech Republic
| | | | | | - Sarah E. Hunt
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
| | - Ammar Husami
- Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, USA
| | | | - Saumya S. Jamuar
- SingHealth Duke-NUS Genomic Medicine Centre, Singapore, Republic of Singapore
- SingHealth Duke-NUS Institute of Precision Medicine, Singapore, Republic of Singapore
| | - Elizabeth L. Janes
- Global Alliance for Genomics and Health, Toronto, ON, Canada
- University of Waterloo, Waterloo, ON, Canada
| | | | - Aina Jené
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Amber L. Johns
- Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
| | - Yann Joly
- McGill University, Montreal, QC, Canada
| | - Steven J.M. Jones
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada
| | - Alexander Kanitz
- SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
- University of Basel, Basel, Switzerland
| | | | - Thomas M. Keane
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
- University of Nottingham, Nottingham, UK
| | - Kristina Kekesi-Lafrance
- Global Alliance for Genomics and Health, Toronto, ON, Canada
- McGill University, Montreal, QC, Canada
| | | | - Giselle Kerry
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
| | - Seik-Soon Khor
- National Center for Global Health and Medicine Hospital, Tokyo, Japan
- University of Tokyo, Tokyo, Japan
| | | | | | | | | | | | - Rasko Leinonen
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
| | - Stephanie Li
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Global Alliance for Genomics and Health, Toronto, ON, Canada
| | | | - Mikael Linden
- CSC–IT Center for Science, Espoo, Finland
- ELIXIR Finland, Espoo, Finland
| | | | - Isuru Udara Liyanage
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
| | | | | | | | - Alice L. Mann
- Global Alliance for Genomics and Health, Toronto, ON, Canada
- Wellcome Sanger Institute, Hinxton, UK
| | | | | | | | - Anna Middleton
- Wellcome Connecting Science, Hinxton, UK
- University of Cambridge, Cambridge, UK
| | - Richard J. Milne
- Wellcome Connecting Science, Hinxton, UK
- University of Cambridge, Cambridge, UK
| | | | - Nicola Mulder
- H3ABioNet, Computational Biology Division, IDM, Faculty of Health Sciences, Cape Town, South Africa
| | | | - Rishi Nag
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
| | - Hidewaki Nakagawa
- Japan Agency for Medical Research & Development (AMED), Tokyo, Japan
- RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | | | - Arcadi Navarro
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Institute of Evolutionary Biology (UPF-CSIC), Universitat Pompeu Fabra (UPF), Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats, Barcelona, Spain
- Barcelonaβeta Brain Research Center (BBRC), Pasqual Maragall Foundation, Barcelona, Spain
| | | | - Ania Niewielska
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
| | - Amy Nisselle
- Murdoch Children’s Research Institute, Parkville, VIC, Australia
- University of Melbourne, Melbourne, VIC, Australia
- Human Genetics Society of Australasia Education, Ethics & Social Issues Committee, Alexandria, NSW, Australia
| | - Jeffrey Niu
- University Health Network, Toronto, ON, Canada
| | - Tommi H. Nyrönen
- CSC–IT Center for Science, Espoo, Finland
- ELIXIR Finland, Espoo, Finland
| | | | - Sabine Oesterle
- SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | | | - Vivian Ota Wang
- National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | | | - Emilio Palumbo
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Helen E. Parkinson
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
| | | | | | | | - Jordi Rambla
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | | | - Renee A. Rider
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Peter N. Robinson
- The Jackson Laboratory, Farmington, CT, USA
- University of Connecticut, Farmington, CT, USA
| | - Kurt W. Rodarmer
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | | | - Alan F. Rubin
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- University of Melbourne, Melbourne, VIC, Australia
| | - Manuel Rueda
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | | | | | | | - Helen Schuilenburg
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
| | - Torsten Schwede
- SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
- University of Basel, Basel, Switzerland
| | | | | | | | - Neerjah Skantharajah
- Global Alliance for Genomics and Health, Toronto, ON, Canada
- Ontario Institute for Cancer Research, Toronto, ON, Canada
| | | | - Heidi J. Sofia
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Dylan Spalding
- CSC–IT Center for Science, Espoo, Finland
- ELIXIR Finland, Espoo, Finland
| | | | - Zornitza Stark
- Australian Genomics, Parkville, VIC, Australia
- Murdoch Children’s Research Institute, Parkville, VIC, Australia
- University of Melbourne, Melbourne, VIC, Australia
| | - Lincoln D. Stein
- Ontario Institute for Cancer Research, Toronto, ON, Canada
- University of Toronto, Toronto, ON, Canada
| | | | - Patrick Tan
- SingHealth Duke-NUS Genomic Medicine Centre, Singapore, Republic of Singapore
- Precision Health Research Singapore, Singapore, Republic of Singapore
- Genome Institute of Singapore, Singapore, Republic of Singapore
| | | | - Alastair A. Thomson
- National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Adrian Thorogood
- McGill University, Montreal, QC, Canada
- University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | | | - Katsushi Tokunaga
- University of Tokyo, Tokyo, Japan
- National Center for Global Health and Medicine, Tokyo, Japan
| | - Juha Törnroos
- CSC–IT Center for Science, Espoo, Finland
- ELIXIR Finland, Espoo, Finland
| | - David Torrents
- Institució Catalana de Recerca i Estudis Avançats, Barcelona, Spain
- Barcelona Supercomputing Center, Barcelona, Spain
| | - Sean Upchurch
- California Institute of Technology, Pasadena, CA, USA
| | - Alfonso Valencia
- Institució Catalana de Recerca i Estudis Avançats, Barcelona, Spain
- Barcelona Supercomputing Center, Barcelona, Spain
| | | | - Jessica Vamathevan
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
| | - Susheel Varma
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
- Health Data Research UK, London, UK
| | - Danya F. Vears
- Murdoch Children’s Research Institute, Parkville, VIC, Australia
- University of Melbourne, Melbourne, VIC, Australia
- Human Genetics Society of Australasia Education, Ethics & Social Issues Committee, Alexandria, NSW, Australia
- Melbourne Law School, University of Melbourne, Parkville, VIC, Australia
| | - Coby Viner
- University of Toronto, Toronto, ON, Canada
- University Health Network, Toronto, ON, Canada
| | | | - Alex H. Wagner
- Nationwide Children’s Hospital, Columbus, OH, USA
- The Ohio State University, Columbus, OH, USA
| | | | | | | | - Eva C. Winkler
- Section of Translational Medical Ethics, University Hospital Heidelberg, Heidelberg, Germany
| | | | | | | | | | - Andrew D. Yates
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
| | - Christina K. Yung
- Ontario Institute for Cancer Research, Toronto, ON, Canada
- Indoc Research, Toronto, ON, Canada
| | - Lyndon J. Zass
- H3ABioNet, Computational Biology Division, IDM, Faculty of Health Sciences, Cape Town, South Africa
| | - Ksenia Zaytseva
- McGill University, Montreal, QC, Canada
- Canadian Centre for Computational Genomics, Montreal, QC, Canada
| | - Junjun Zhang
- Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Peter Goodhand
- Global Alliance for Genomics and Health, Toronto, ON, Canada
- Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Kathryn North
- Murdoch Children’s Research Institute, Parkville, VIC, Australia
- University of Toronto, Toronto, ON, Canada
- University of Melbourne, Melbourne, VIC, Australia
| | - Ewan Birney
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
- European Molecular Biology Laboratory, Heidelberg, Germany
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Wagner AH, Vlachos IS, Sonkin D, Terraf P, Kesserwan C, Sboner A, Coard T, Reich C, Ritter DI, Horak P, Zou YS, Tanska A, Berlin AM, Lu A, Cameron D, Williams HE, Lin WH, Toruner G, Danos A, Saliba J, Xu H, Xu X, Ryland G, Ceccarelli M, Zhang L, Rapisardo S, Rehder C, Liu X, Pallavajjala A, Park N, Satgunaseelan L, Lee K, Liu J, Griffith O, Freimuth RR, Stenzinger A, Baughn LB, Baudis M, Lee J, Li M, Roy A, Raca G. Abstract 449: A standard operating procedure for the curation of gene fusions. Cancer Res 2021. [DOI: 10.1158/1538-7445.am2021-449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Despite the well-established role of recurrent gene fusions as oncogenic drivers, current practices for characterizing and interpreting gene fusion events in clinical testing and in biomedical literature are inconsistent. From the conceptual definition of gene fusions to the salient elements that characterize these alterations, a lack of community-driven standards for the curation of gene fusions has resulted in a disparate landscape of fusion representations and supporting tools. Consequently, the evidence-based clinical evaluation of gene fusions requires extensive expert review for accurate interpretation of observed gene fusions with respect to putative evidence from biomedical literature. Furthermore, the lack of these standards inhibits the interoperability of tools, resources, and pipelines - impeding data sharing and downstream utility.To address these challenges, a cross-consortia initiative between the Variant Interpretation for Cancer Consortium and ClinGen was formed to develop a standard operating procedure (SOP) for the curation of gene fusions. The SOP is under development by an international and diverse set of experts in the representation, detection, and clinical interpretation of gene fusions. Participating stakeholders across academic, government, and industry sectors showcased challenges and solutions, and participated in community surveys and discussions to define and develop the SOP for this diverse class of alterations.An initial result of this effort was the precise molecular definition of genomic events and features constituting gene fusions. We distinguish these from similar but distinct classes of structural alterations through clinically-relevant examples. Next, we discuss our findings on community practices around the description and evaluation of gene fusions. We provide our recommendations for characterization and representation of gene fusions from these practices, and compare these recommendations to existing variant representation standards and formats (e.g. HGVS variant nomenclature). We also discuss the concurrent application of formats for standardized human- and machine-readable representations of gene fusion events.We conclude with discussion of the salient elements to enable rapid, scalable, and consistent evaluation of fusions curated from the biomedical literature. Recommendations are provided for the standardized capture of these elements to enable both intuitive and precise characterization of this diverse class of alterations in clinical reporting and literature. In summary, we provide a clinical-practice driven framework and nomenclature for gene fusions, including recommendations for human readability, computational precision, and data integrity within the SOP. This work is a substantial advancement towards standardized communication, investigation, and sharing of gene fusion data across clinical and research domains and specialties.
Citation Format: Alex H. Wagner, Ioannis S. Vlachos, Dmitriy Sonkin, Panieh Terraf, Chimene Kesserwan, Andrea Sboner, Thomas Coard, Christian Reich, Deborah I. Ritter, Peter Horak, Ying S. Zou, Anna Tanska, Aaron M. Berlin, Anna Lu, Daniel Cameron, Heather E. Williams, Wan-Hsin Lin, Gokce Toruner, Arpad Danos, Jason Saliba, Huiling Xu, Xinjie Xu, Georgina Ryland, Michele Ceccarelli, Liying Zhang, Sarah Rapisardo, Catherine Rehder, Xuelu Liu, Aparna Pallavajjala, Nicole Park, Laveniya Satgunaseelan, Kristy Lee, Jie Liu, Obi Griffith, Robert R. Freimuth, Albrecht Stenzinger, Linda B. Baughn, Michael Baudis, Jennifer Lee, Marilyn Li, Angshumoy Roy, Gordana Raca. A standard operating procedure for the curation of gene fusions [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 449.
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Affiliation(s)
| | | | | | - Panieh Terraf
- 4Memorial Sloan kettering Cancer Center, New York, NY
| | | | | | | | | | | | - Peter Horak
- 9NCT Heidelberg and DKFZ, Heidelberg, Germany
| | - Ying S. Zou
- 10The Johns Hopkins University School of Medicine, Baltimore, MD
| | - Anna Tanska
- 11Peter MacCallum Cancer Centre, Melbourne, Australia
| | | | - Anna Lu
- 13Frederick National Laboratory of Cancer Research, Frederick, MD
| | - Daniel Cameron
- 14Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
| | | | | | | | - Arpad Danos
- 18Washington University School of Medicine, St. Louis, MO
| | - Jason Saliba
- 18Washington University School of Medicine, St. Louis, MO
| | - Huiling Xu
- 11Peter MacCallum Cancer Centre, Melbourne, Australia
| | | | | | | | - Liying Zhang
- 21UCLA David Geffen School of Medicine, Los Angeles, CA
| | | | | | - Xuelu Liu
- 23Dana-Farber Cancer Institute, Boston, MA
| | | | - Nicole Park
- 24University Health Network, Toronto, Ontario, Canada
| | | | - Kristy Lee
- 1Nationwide Children's Hospital, Columbus, OH
| | - Jie Liu
- 26Cincinnati Children's Hospital Medical Center, Cincinnati, OH
| | - Obi Griffith
- 18Washington University School of Medicine, St. Louis, MO
| | | | | | | | | | | | - Marilyn Li
- 29Children's Hospital of Philadelphia, Philadelphia, PA
| | | | - Gordana Raca
- 30Keck School of Medicine of USC, Los Angeles, CA
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15
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Murugan M, Babb LJ, Overby Taylor C, Rasmussen LV, Freimuth RR, Venner E, Yan F, Yi V, Granite SJ, Zouk H, Aronson SJ, Power K, Fedotov A, Crosslin DR, Fasel D, Jarvik GP, Hakonarson H, Bangash H, Kullo IJ, Connolly JJ, Nestor JG, Caraballo PJ, Wei W, Wiley K, Rehm HL, Gibbs RA. Genomic considerations for FHIR®; eMERGE implementation lessons. J Biomed Inform 2021; 118:103795. [PMID: 33930535 PMCID: PMC8583906 DOI: 10.1016/j.jbi.2021.103795] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Revised: 04/06/2021] [Accepted: 04/25/2021] [Indexed: 01/17/2023]
Abstract
Structured representation of clinical genetic results is necessary for advancing precision medicine. The Electronic Medical Records and Genomics (eMERGE) Network's Phase III program initially used a commercially developed XML message format for standardized and structured representation of genetic results for electronic health record (EHR) integration. In a desire to move towards a standard representation, the network created a new standardized format based upon Health Level Seven Fast Healthcare Interoperability Resources (HL7® FHIR®), to represent clinical genomics results. These new standards improve the utility of HL7® FHIR® as an international healthcare interoperability standard for management of genetic data from patients. This work advances the establishment of standards that are being designed for broad adoption in the current health information technology landscape.
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Affiliation(s)
- Mullai Murugan
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA.
| | - Lawrence J Babb
- Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Casey Overby Taylor
- Departments of Medicine and Biomedical Engineering, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Luke V Rasmussen
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Robert R Freimuth
- Department of Digital Health Sciences, Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
| | - Eric Venner
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Fei Yan
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Victoria Yi
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Stephen J Granite
- Departments of Medicine and Biomedical Engineering, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Hana Zouk
- Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine, Cambridge, MA, USA; Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Samuel J Aronson
- Partners Personalized Medicine, Partners HealthCare, Cambridge, MA, USA
| | | | - Alex Fedotov
- Irving Institute for Clinical and Translational Research, Columbia University, New York, NY, USA
| | - David R Crosslin
- Department of Biomedical Informatics and Medical Education, University of Washington, Seattle, WA, USA
| | - David Fasel
- Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA
| | - Gail P Jarvik
- Department of Medicine (Medical Genetics) and Genome Sciences, University of Washington, Seattle, WA, USA
| | - Hakon Hakonarson
- Center for Applied Genomics, Children's Hospital of Philadelphia, PA, USA
| | - Hana Bangash
- Department of Cardiovascular Medicine, Mayo Clinic, Rochester, MN
| | - Iftikhar J Kullo
- Department of Cardiovascular Medicine, Mayo Clinic, Rochester, MN
| | - John J Connolly
- Center for Applied Genomics, Children's Hospital of Philadelphia, PA, USA
| | - Jordan G Nestor
- Department of Medicine, Division of Nephrology, Columbia University, New York, NY, USA
| | - Pedro J Caraballo
- Department of Medicine and Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | - WeiQi Wei
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Ken Wiley
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Heidi L Rehm
- Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Richard A Gibbs
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
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16
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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17
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Petersen C, Smith J, Freimuth RR, Goodman KW, Jackson GP, Kannry J, Liu H, Madhavan S, Sittig DF, Wright A. Recommendations for the safe, effective use of adaptive CDS in the US healthcare system: an AMIA position paper. J Am Med Inform Assoc 2021; 28:677-684. [PMID: 33447854 DOI: 10.1093/jamia/ocaa319] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 12/01/2020] [Indexed: 02/07/2023] Open
Abstract
The development and implementation of clinical decision support (CDS) that trains itself and adapts its algorithms based on new data-here referred to as Adaptive CDS-present unique challenges and considerations. Although Adaptive CDS represents an expected progression from earlier work, the activities needed to appropriately manage and support the establishment and evolution of Adaptive CDS require new, coordinated initiatives and oversight that do not currently exist. In this AMIA position paper, the authors describe current and emerging challenges to the safe use of Adaptive CDS and lay out recommendations for the effective management and monitoring of Adaptive CDS.
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Affiliation(s)
- Carolyn Petersen
- Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, Minnesota, USA
| | - Jeffery Smith
- The Office of the National Coordinator for Health Information Technology, Washington, DC, USA
| | - Robert R Freimuth
- Division of Digital Health Sciences, Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - Kenneth W Goodman
- Institute for Bioethics and Health Policy, University of Miami Miller School of Medicine, Miami, Florida, USA
| | - Gretchen Purcell Jackson
- IBM Watson Health, Cambridge, Massachusetts, USA.,Department of Pediatric Surgery, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Joseph Kannry
- Mount Sinai Health System, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Hongfang Liu
- Division of Digital Health Sciences, Mayo Clinic, Rochester, Minnesota, USA
| | - Subha Madhavan
- Department of Oncology, Georgetown Lombardi Comprehensive Cancer Center, Innovation Center for Biomedical Informatics, Georgetown University Medical Center, Washington, DC, USA
| | - Dean F Sittig
- School of Biomedical Informatics, The University of Texas Health Science Center at Houston, UT-Memorial Hermann Center for Healthcare Quality & Safety, Houston, Texas, USA
| | - Adam Wright
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
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18
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Wagner AH, Hart RK, Babb L, Freimuth RR, Coffman A, Liang Y, Pitel B, Roy A, Brush M, Lee J, Lu A, Coard T, Rao S, Ritter D, Walsh B, Mockus S, Horak P, King I, Sonkin D, Madhavan S, Raca G, Chakravarty D, Griffith M, Griffith OL. Abstract 1096: Harmonization standards from the Variant Interpretation for Cancer Consortium. Cancer Res 2020. [DOI: 10.1158/1538-7445.am2020-1096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
The use of clinical gene sequencing is now commonplace, and genome analysts and molecular pathologists are often tasked with the labor-intensive process of interpreting the clinical significance of large numbers of tumor variants. Numerous independent knowledgebases have been constructed to alleviate this manual burden, however these knowledgebases are non-interoperable. As a result, the analyst is left with a difficult tradeoff: for each knowledgebase used the analyst must understand the nuances particular to that resource and integrate its evidence accordingly when generating the clinical report, but for each knowledgebase omitted there is increased potential for missed findings of clinical significance.The Variant Interpretation for Cancer Consortium (VICC; cancervariants.org) was formed as a driver project of the Global Alliance for Genomics and Health (GA4GH; ga4gh.org) to address this concern. VICC members include representatives from several major somatic interpretation knowledgebases including CIViC, OncoKB, Jax-CKB, the Weill Cornell PMKB, the IRB-Barcelona Cancer Biomarkers Database, and others. Previously, the VICC built and reported on a harmonized meta-knowledgebase of 19,551 biomarker associations of harmonized variants, diseases, drugs, and evidence across the constituent resources.In that study, we analyzed the frequency with which the tumor samples from the AACR Project GENIE cohort would match to harmonized associations. Variant matches increased dramatically from 57% to 86% when broader matching to regions describing categorical variants were allowed. Unlike precise sequence variants with specified alternate alleles, categorical variants describe a collection of potential variants with a common feature, such as “V600” (non-valine alleles at the 600 residue), “Exon 20 mutations” (all non-silent mutations in exon 20), or “Gain-of-function” (hypermorphic alterations that activate or amplify gene activity). However, matching observed sequence variants to categorical variants is challenging, as the latter are typically only described as unstructured text. Here we describe the expressive and computational GA4GH Variation Representation specification (vr-spec.readthedocs.io), which we co-developed as members of the GA4GH Genomic Knowledge Standards work stream. This specification provides a schema for common, precise forms of variation (e.g. SNVs and Indels) and the method for computing identifiers from these objects. We highlight key aspects of the specification and our work to apply it to the characterization of categorical variation, showcasing the variant terminology and classification tools developed by the VICC to support this effort. These standards and tools are free, open-source, and extensible, overcoming barriers to standardized variant knowledge sharing and search.
Citation Format: Alex H. Wagner, Reece K. Hart, Larry Babb, Robert R. Freimuth, Adam Coffman, Yonghao Liang, Beth Pitel, Angshumoy Roy, Matthew Brush, Jennifer Lee, Anna Lu, Thomas Coard, Shruti Rao, Deborah Ritter, Brian Walsh, Susan Mockus, Peter Horak, Ian King, Dmitriy Sonkin, Subha Madhavan, Gordana Raca, Debyani Chakravarty, Malachi Griffith, Obi L. Griffith. Harmonization standards from the Variant Interpretation for Cancer Consortium [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 1096.
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Affiliation(s)
- Alex H. Wagner
- 1Washington University School of Medicine, Saint Louis, MO
| | | | | | | | - Adam Coffman
- 1Washington University School of Medicine, Saint Louis, MO
| | - Yonghao Liang
- 1Washington University School of Medicine, Saint Louis, MO
| | | | | | | | | | - Anna Lu
- 7National Cancer Institute, Bethesda, MD
| | | | | | | | - Brian Walsh
- 6Oregon Health and Science University, Portland, OR
| | - Susan Mockus
- 9The Jackson Laboratory for Genomic Medicine, Farmington, CT
| | - Peter Horak
- 10National Center for Tumor Diseases, Heidelberg, Germany
| | - Ian King
- 11University of Toronto, Toronto, Ontario, Canada
| | | | | | - Gordana Raca
- 12University of Southern California, Los Angeles, CA
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19
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Hoffman JM, Flynn AJ, Juskewitch JE, Freimuth RR. Biomedical Data Science and Informatics Challenges to Implementing Pharmacogenomics with Electronic Health Records. Annu Rev Biomed Data Sci 2020. [DOI: 10.1146/annurev-biodatasci-020320-093614] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Pharmacogenomic information must be incorporated into electronic health records (EHRs) with clinical decision support in order to fully realize its potential to improve drug therapy. Supported by various clinical knowledge resources, pharmacogenomic workflows have been implemented in several healthcare systems. Little standardization exists across these efforts, however, which limits scalability both within and across clinical sites. Limitations in information standards, knowledge management, and the capabilities of modern EHRs remain challenges for the widespread use of pharmacogenomics in the clinic, but ongoing efforts are addressing these challenges. Although much work remains to use pharmacogenomic information more effectively within clinical systems, the experiences of pioneering sites and lessons learned from those programs may be instructive for other clinical areas beyond genomics. We present a vision of what can be achieved as informatics and data science converge to enable further adoption of pharmacogenomics in the clinic.
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Affiliation(s)
- James M. Hoffman
- Department of Pharmaceutical Sciences and the Office of Quality and Patient Care, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
| | - Allen J. Flynn
- Department of Learning Health Sciences, Medical School, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Justin E. Juskewitch
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota 55905, USA
| | - Robert R. Freimuth
- Division of Digital Health Sciences, Department of Health Sciences Research, Center for Individualized Medicine, and Information and Knowledge Management, Mayo Clinic, Rochester, Minnesota 55905, USA
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20
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Hoell C, Wynn J, Rasmussen LV, Marsolo K, Aufox SA, Chung WK, Connolly JJ, Freimuth RR, Kochan D, Hakonarson H, Harr M, Holm IA, Kullo IJ, Lammers PE, Leppig KA, Leslie ND, Myers MF, Sharp RR, Smith ME, Prows CA. Participant choices for return of genomic results in the eMERGE Network. Genet Med 2020; 22:1821-1829. [PMID: 32669677 DOI: 10.1038/s41436-020-0905-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 06/29/2020] [Accepted: 06/30/2020] [Indexed: 12/18/2022] Open
Abstract
PURPOSE Secondary findings are typically offered in an all or none fashion when sequencing is used for clinical purposes. This study aims to describe the process of offering categorical and granular choices for results in a large research consortium. METHODS Within the third phase of the electronic MEdical Records and GEnomics (eMERGE) Network, several sites implemented studies that allowed participants to choose the type of results they wanted to receive from a multigene sequencing panel. Sites were surveyed to capture the details of the implementation protocols and results of these choices. RESULTS Across the ten eMERGE sites, 4664 participants including adolescents and adults were offered some type of choice. Categories of choices offered and methods for selecting categories varied. Most participants (94.5%) chose to learn all genetic results, while 5.5% chose subsets of results. Several sites allowed participants to change their choices at various time points, and 0.5% of participants made changes. CONCLUSION Offering choices that include learning some results is important and should be a dynamic process to allow for changes in scientific knowledge, participant age group, and individual preference.
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Affiliation(s)
- Christin Hoell
- Northwestern University, Feinberg School of Medicine, Chicago, IL, USA
| | - Julia Wynn
- Columbia University Irving Medical Center, New York, NY, USA
| | - Luke V Rasmussen
- Northwestern University, Feinberg School of Medicine, Chicago, IL, USA
| | - Keith Marsolo
- Department of Population Health Sciences, and Duke Clinical Research Institute, Duke University School of Medicine, Durham, NC, USA
| | - Sharon A Aufox
- Northwestern University, Feinberg School of Medicine, Chicago, IL, USA
| | - Wendy K Chung
- Columbia University Irving Medical Center, New York, NY, USA
| | - John J Connolly
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Robert R Freimuth
- Department of Health Sciences Research, Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
| | - David Kochan
- Department of Cardiovascular Medicine, Mayo Clinic, Rochester, MN, USA
| | - Hakon Hakonarson
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA, USA.,Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Margaret Harr
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Ingrid A Holm
- Division of Genetics and Genomics, and the Manton Center for Orphan Diseases Research, Boston Children's Hospital, Boston, MA, USA.,Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Iftikhar J Kullo
- Department of Cardiovascular Medicine, Mayo Clinic, Rochester, MN, USA
| | | | | | - Nancy D Leslie
- Division of Human Genetics, Cincinnati Children's Hospital, and University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Melanie F Myers
- Division of Human Genetics, Cincinnati Children's Hospital, and University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Richard R Sharp
- Biomedical Ethics Research Program, Mayo Clinic, Rochester, MN, USA
| | - Maureen E Smith
- Northwestern University, Feinberg School of Medicine, Chicago, IL, USA
| | - Cynthia A Prows
- Divisions of Human Genetics and Patient Services, Cincinnati Children's Hospital, Cincinnati, OH, USA.
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21
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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22
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McDonough CW, Breitenstein MK, Shahin M, Empey PE, Freimuth RR, Li L, Liebman M, Tuteja S. Translational Informatics Connects Real-World Information to Knowledge in an Increasingly Data-Driven World. Clin Pharmacol Ther 2020; 107:738-741. [PMID: 31837229 PMCID: PMC7678684 DOI: 10.1002/cpt.1719] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Accepted: 11/01/2019] [Indexed: 11/07/2022]
Affiliation(s)
| | | | | | | | | | - Lang Li
- Department of Biomedical Informatics, The Ohio State University, Columbus, OH
| | | | - Sony Tuteja
- University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
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23
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Wagner AH, Walsh B, Mayfield G, Tamborero D, Sonkin D, Krysiak K, Deu-Pons J, Duren RP, Gao J, McMurry J, Patterson S, Del Vecchio Fitz C, Pitel BA, Sezerman OU, Ellrott K, Warner JL, Rieke DT, Aittokallio T, Cerami E, Ritter DI, Schriml LM, Freimuth RR, Haendel M, Raca G, Madhavan S, Baudis M, Beckmann JS, Dienstmann R, Chakravarty D, Li XS, Mockus S, Elemento O, Schultz N, Lopez-Bigas N, Lawler M, Goecks J, Griffith M, Griffith OL, Margolin AA. A harmonized meta-knowledgebase of clinical interpretations of somatic genomic variants in cancer. Nat Genet 2020; 52:448-457. [PMID: 32246132 PMCID: PMC7127986 DOI: 10.1038/s41588-020-0603-8] [Citation(s) in RCA: 86] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Accepted: 02/26/2020] [Indexed: 12/19/2022]
Abstract
Precision oncology relies on accurate discovery and interpretation of genomic variants, enabling individualized diagnosis, prognosis and therapy selection. We found that six prominent somatic cancer variant knowledgebases were highly disparate in content, structure and supporting primary literature, impeding consensus when evaluating variants and their relevance in a clinical setting. We developed a framework for harmonizing variant interpretations to produce a meta-knowledgebase of 12,856 aggregate interpretations. We demonstrated large gains in overlap between resources across variants, diseases and drugs as a result of this harmonization. We subsequently demonstrated improved matching between a patient cohort and harmonized interpretations of potential clinical significance, observing an increase from an average of 33% per individual knowledgebase to 57% in aggregate. Our analyses illuminate the need for open, interoperable sharing of variant interpretation data. We also provide a freely available web interface (search.cancervariants.org) for exploring the harmonized interpretations from these six knowledgebases.
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Affiliation(s)
- Alex H Wagner
- Washington University School of Medicine, St. Louis, MO, USA
| | - Brian Walsh
- Oregon Health and Science University, Portland, OR, USA
| | | | - David Tamborero
- Pompeu Fabra University, Barcelona, Spain
- Karolinska Institute, Solna, Sweden
| | | | | | - Jordi Deu-Pons
- Institute for Research in Biomedicine, Barcelona, Spain
- Catalan Institution for Research and Advanced Studies, Barcelona, Spain
| | | | - Jianjiong Gao
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Julie McMurry
- Oregon Health and Science University, Portland, OR, USA
| | - Sara Patterson
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | | | | | | | - Kyle Ellrott
- Oregon Health and Science University, Portland, OR, USA
| | | | | | - Tero Aittokallio
- Institute for Molecular Medicine Finland, Helsinki, Finland
- University of Turku, Turku, Finland
| | | | - Deborah I Ritter
- Baylor College of Medicine, Houston, TX, USA
- Texas Children's Hospital, Houston, TX, USA
| | - Lynn M Schriml
- University of Maryland School of Medicine, Baltimore, MD, USA
| | | | - Melissa Haendel
- Oregon Health and Science University, Portland, OR, USA
- Linus Pauling Institute at Oregon State University, Corvallis, OR, USA
| | - Gordana Raca
- Children's Hospital Los Angeles, Los Angeles, CA, USA
- Keck School of Medicine of USC, Los Angeles, CA, USA
| | - Subha Madhavan
- Georgetown University Medical Center, Washington, DC, USA
| | | | | | | | | | | | - Susan Mockus
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | | | | | - Nuria Lopez-Bigas
- Pompeu Fabra University, Barcelona, Spain
- Institute for Research in Biomedicine, Barcelona, Spain
- Catalan Institution for Research and Advanced Studies, Barcelona, Spain
| | | | - Jeremy Goecks
- Oregon Health and Science University, Portland, OR, USA
| | | | - Obi L Griffith
- Washington University School of Medicine, St. Louis, MO, USA.
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24
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Bielinski SJ, St Sauver JL, Olson JE, Larson NB, Black JL, Scherer SE, Bernard ME, Boerwinkle E, Borah BJ, Caraballo PJ, Curry TB, Doddapaneni H, Formea CM, Freimuth RR, Gibbs RA, Giri J, Hathcock MA, Hu J, Jacobson DJ, Jones LA, Kalla S, Koep TH, Korchina V, Kovar CL, Lee S, Liu H, Matey ET, McGree ME, McAllister TM, Moyer AM, Muzny DM, Nicholson WT, Oyen LJ, Qin X, Raj R, Roger VL, Rohrer Vitek CR, Ross JL, Sharp RR, Takahashi PY, Venner E, Walker K, Wang L, Wang Q, Wright JA, Wu TJ, Wang L, Weinshilboum RM. Cohort Profile: The Right Drug, Right Dose, Right Time: Using Genomic Data to Individualize Treatment Protocol (RIGHT Protocol). Int J Epidemiol 2020; 49:23-24k. [PMID: 31378813 PMCID: PMC7124480 DOI: 10.1093/ije/dyz123] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/31/2019] [Indexed: 12/29/2022] Open
Affiliation(s)
- Suzette J Bielinski
- Division of Epidemiology, Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | - Jennifer L St Sauver
- Division of Epidemiology, Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
- Robert D and Patricia E Kern Center for the Science of Health Care Delivery, Mayo Clinic, Rochester, MN, USA
| | - Janet E Olson
- Division of Epidemiology, Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
| | - Nicholas B Larson
- Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | - John L Black
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Steven E Scherer
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | | | - Eric Boerwinkle
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, School of Public Health, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Bijan J Borah
- Robert D and Patricia E Kern Center for the Science of Health Care Delivery, Mayo Clinic, Rochester, MN, USA
- Division of Health Care Policy and Research, Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | - Pedro J Caraballo
- Division of General Internal Medicine, Department of Medicine, Mayo Clinic, Rochester, MN, USA
| | - Timothy B Curry
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
- Department of Anesthesia and Perioperative Medicine, Mayo Clinic, Rochester, MN, USA
| | | | | | - Robert R Freimuth
- Division of Digital Health Sciences, Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | - Richard A Gibbs
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Jyothsna Giri
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
| | - Matthew A Hathcock
- Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | - Jianhong Hu
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Debra J Jacobson
- Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | - Leila A Jones
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
| | - Sara Kalla
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | | | - Viktoriya Korchina
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Christie L Kovar
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Sandra Lee
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Hongfang Liu
- Division of Digital Health Sciences, Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | - Eric T Matey
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
- Department of Pharmacy, Mayo Clinic, Rochester, MN, USA
| | - Michaela E McGree
- Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | | | - Ann M Moyer
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Donna M Muzny
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Wayne T Nicholson
- Department of Anesthesia and Perioperative Medicine, Mayo Clinic, Rochester, MN, USA
| | - Lance J Oyen
- Department of Pharmacy, Mayo Clinic, Rochester, MN, USA
| | - Xiang Qin
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Ritika Raj
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Véronique L Roger
- Division of Epidemiology, Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
- Division of Cardiovascular Diseases, Department of Internal Medicine, Mayo Clinic, Rochester, MN, USA
| | | | | | - Richard R Sharp
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
- Division of Health Care Policy and Research, Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | - Paul Y Takahashi
- Division of Community Internal Medicine, Department of Medicine, Mayo Clinic, Rochester, MN, USA
| | - Eric Venner
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Kimberly Walker
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Liwei Wang
- Division of Digital Health Sciences, Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | - Qiaoyan Wang
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Jessica A Wright
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
- Department of Pharmacy, Mayo Clinic, Rochester, MN, USA
| | - Tsung-Jung Wu
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Liewei Wang
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
- Division of Clinical Pharmacology, Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, USA
| | - Richard M Weinshilboum
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
- Division of Clinical Pharmacology, Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, USA
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25
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Aronson S, Babb L, Ames D, Gibbs RA, Venner E, Connelly JJ, Marsolo K, Weng C, Williams MS, Hartzler AL, Liang WH, Ralston JD, Devine EB, Murphy S, Chute CG, Caraballo PJ, Kullo IJ, Freimuth RR, Rasmussen LV, Wehbe FH, Peterson JF, Robinson JR, Wiley K, Overby Taylor C. Empowering genomic medicine by establishing critical sequencing result data flows: the eMERGE example. J Am Med Inform Assoc 2019; 25:1375-1381. [PMID: 29860405 DOI: 10.1093/jamia/ocy051] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Accepted: 04/18/2018] [Indexed: 11/14/2022] Open
Abstract
The eMERGE Network is establishing methods for electronic transmittal of patient genetic test results from laboratories to healthcare providers across organizational boundaries. We surveyed the capabilities and needs of different network participants, established a common transfer format, and implemented transfer mechanisms based on this format. The interfaces we created are examples of the connectivity that must be instantiated before electronic genetic and genomic clinical decision support can be effectively built at the point of care. This work serves as a case example for both standards bodies and other organizations working to build the infrastructure required to provide better electronic clinical decision support for clinicians.
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Affiliation(s)
- Samuel Aronson
- Research Information Science and Computing, Partners HealthCare, Boston, Massachusetts, USA.,Partners Personalized Medicine, Partners HealthCare, Boston Massachusetts, USA
| | - Lawrence Babb
- Mitogen-GeneInsight, Sunquest Information Systems, Boston, Massachusetts, USA
| | - Darren Ames
- DNAnexus, Inc., Mountain View, California, USA
| | - Richard A Gibbs
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA
| | - Eric Venner
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA
| | - John J Connelly
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Keith Marsolo
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA.,Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
| | - Chunhua Weng
- Department of Biomedical Informatics, Columbia University, New York, New York, USA
| | - Marc S Williams
- Genomic Medicine Institute, Geisinger, Danville, Pennsylvania, USA
| | - Andrea L Hartzler
- Kaiser Permanente Washington Health Research Institute, Seattle, Washington, USA.,Department of Biomedical Informatics and Medical Education, University of Washington, Seattle, Washington, USA
| | - Wayne H Liang
- Informatics Institute, University of Alabama at Birmingham, Birmingham, Alabama, USA.,Department of Pediatrics, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - James D Ralston
- Kaiser Permanente Washington Health Research Institute, Seattle, Washington, USA.,Department of Biomedical Informatics and Medical Education, University of Washington, Seattle, Washington, USA
| | - Emily Beth Devine
- Department of Biomedical Informatics and Medical Education, University of Washington, Seattle, Washington, USA
| | - Shawn Murphy
- Research Information Science and Computing, Partners HealthCare, Boston, Massachusetts, USA
| | | | | | - Iftikhar J Kullo
- Department of Cardiovascular Diseases, Mayo Clinic, Rochester, Minnesota, USA
| | - Robert R Freimuth
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota, USA
| | - Luke V Rasmussen
- Department of Preventive Medicine, Division of Health and Biomedical Informatics, Northwestern University, Chicago, Illinois, USA
| | - Firas H Wehbe
- Department of Preventive Medicine, Division of Health and Biomedical Informatics, Northwestern University, Chicago, Illinois, USA
| | - Josh F Peterson
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Jamie R Robinson
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Ken Wiley
- National Human Genome Research Institute, Bethesda, Maryland, USA
| | - Casey Overby Taylor
- Genomic Medicine Institute, Geisinger, Danville, Pennsylvania, USA.,Department of Medicine, Johns Hopkins University, Baltimore, Maryland, USA
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26
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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] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 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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27
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Dolman L, Page A, Babb L, Freimuth RR, Arachchi H, Bizon C, Brush M, Fiume M, Haendel M, Hansen DP, Milosavljevic A, Patel RY, Pawliczek P, Yates AD, Rehm HL. ClinGen advancing genomic data-sharing standards as a GA4GH driver project. Hum Mutat 2019; 39:1686-1689. [PMID: 30311379 DOI: 10.1002/humu.23625] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Revised: 07/16/2018] [Accepted: 08/23/2018] [Indexed: 11/11/2022]
Abstract
The Clinical Genome Resource (ClinGen)'s work to develop a knowledge base to support the understanding of genes and variants for use in precision medicine and research depends on robust, broadly applicable, and adaptable technical standards for sharing data and information. To forward this goal, ClinGen has joined with the Global Alliance for Genomics and Health (GA4GH) to support the development of open, freely-available technical standards and regulatory frameworks for secure and responsible sharing of genomic and health-related data. In its capacity as one of the 15 inaugural GA4GH "Driver Projects," ClinGen is providing input on the key standards needs of the global genomics community, and has committed to participate on GA4GH Work Streams to support the development of: (1) a standard model for computer-readable variant representation; (2) a data model for linking variant data to annotations; (3) a specification to enable sharing of genomic variant knowledge and associated clinical interpretations; and (4) a set of best practices for use of phenotype and disease ontologies. ClinGen's participation as a GA4GH Driver Project will provide a robust environment to test drive emerging genomic knowledge sharing standards and prove their utility among the community, while accelerating the construction of the ClinGen evidence base.
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Affiliation(s)
- Lena Dolman
- Global Alliance for Genomics and Health Headquarters, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Angela Page
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | | | - Robert R Freimuth
- Department of Health Sciences Research, Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota
| | - Harindra Arachchi
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts.,Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Chris Bizon
- Renaissance Computing Institute, University of North Carolina, Chapel Hill, North Carolina
| | - Matthew Brush
- Oregon Clinical & Translational Research Institute, Oregon Health & Science University, Portland, Oregon
| | - Marc Fiume
- Global Alliance for Genomics and Health Headquarters, Ontario Institute for Cancer Research, Toronto, Ontario, Canada.,DNAstack, Toronto, Ontario, Canada
| | - Melissa Haendel
- Oregon Clinical & Translational Research Institute, Oregon Health & Science University, Portland, Oregon.,Linus Pauling Institute, Oregon State University, Corvallis, Oregon
| | - David P Hansen
- Australian e-Health Research Centre, CSIRO, UQ Health Sciences Building, Herston, Qld, Australia
| | | | - Ronak Y Patel
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Piotr Pawliczek
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Andrew D Yates
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Heidi L Rehm
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts.,Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts.,Center for Genomic Medicine, Massachusetts General Hospital, Boston, Massachusetts
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28
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Romano JD, Bernauer M, McGrath SP, Nagar SD, Freimuth RR. A Decade of Translational Bioinformatics: A Retrospective Analysis of "Year-in-Review" Presentations. AMIA Jt Summits Transl Sci Proc 2019; 2019:335-344. [PMID: 31258986 PMCID: PMC6568133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
For the past 11 years, the year-in-review (YIR) keynote presentation at the AMIA Informatics summit has been a perennial highlight. We hypothesized that the presented material from these keynotes could be used to assess both the recent trajectory of topics in informatics-especially translational bioinformatics (TBI)-as well as the scientific merit of the crowd-sourced process used to nominate, review, and select the papers presented at the YIR. We compare YIR articles to a background set of non-YIR articles from informatics journals using structured metadata and qualitative thematic analysis, paying specific attention to trends and popularity over time. These trends were inspected both internally (comparing the YIR sessions to each other) and externally (comparing them to the overall content of scientific literature for the same time period). In doing so, we identified some unexpected patterns that suggest important opportunities for TBI research in the future.
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29
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Pawliczek P, Patel RY, Ashmore LR, Jackson AR, Bizon C, Nelson T, Powell B, Freimuth RR, Strande N, Shah N, Paithankar S, Wright MW, Dwight S, Zhen J, Landrum M, McGarvey P, Babb L, Plon SE, Milosavljevic A. ClinGen Allele Registry links information about genetic variants. Hum Mutat 2018; 39:1690-1701. [PMID: 30311374 PMCID: PMC6519371 DOI: 10.1002/humu.23637] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Revised: 08/01/2018] [Accepted: 08/28/2018] [Indexed: 11/18/2022]
Abstract
Effective exchange of information about genetic variants is currently hampered by the lack of readily available globally unique variant identifiers that would enable aggregation of information from different sources. The ClinGen Allele Registry addresses this problem by providing (1) globally unique "canonical" variant identifiers (CAids) on demand, either individually or in large batches; (2) access to variant-identifying information in a searchable Registry; (3) links to allele-related records in many commonly used databases; and (4) services for adding links to information about registered variants in external sources. A core element of the Registry is a canonicalization service, implemented using in-memory sequence alignment-based index, which groups variant identifiers denoting the same nucleotide variant and assigns unique and dereferenceable CAids. More than 650 million distinct variants are currently registered, including those from gnomAD, ExAC, dbSNP, and ClinVar, including a small number of variants registered by Registry users. The Registry is accessible both via a web interface and programmatically via well-documented Hypertext Transfer Protocol (HTTP) Representational State Transfer Application Programming Interface (REST-APIs). For programmatic interoperability, the Registry content is accessible in the JavaScript Object Notation for Linked Data (JSON-LD) format. We present several use cases and demonstrate how the linked information may provide raw material for reasoning about variant's pathogenicity.
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Affiliation(s)
- Piotr Pawliczek
- Department of Molecular and Human GeneticsBaylor College of MedicineHoustonTexas
| | - Ronak Y. Patel
- Department of Molecular and Human GeneticsBaylor College of MedicineHoustonTexas
| | - Lillian R. Ashmore
- Department of Molecular and Human GeneticsBaylor College of MedicineHoustonTexas
| | - Andrew R. Jackson
- Department of Molecular and Human GeneticsBaylor College of MedicineHoustonTexas
| | - Chris Bizon
- Renaissance Computing InstituteUniversity of North CarolinaChapel HillNorth Carolina
| | - Tristan Nelson
- Geisinger's Autism and Developmental MedicineLewisburgPennsylvania
| | - Bradford Powell
- Department of GeneticsUniversity of North CarolinaChapel HillNorth Carolina
| | | | - Natasha Strande
- Department of GeneticsUniversity of North CarolinaChapel HillNorth Carolina
| | - Neethu Shah
- Department of Molecular and Human GeneticsBaylor College of MedicineHoustonTexas
| | - Sameer Paithankar
- Department of Molecular and Human GeneticsBaylor College of MedicineHoustonTexas
| | - Matt W. Wright
- Department of Biomedical Data SciencesStanford University School of MedicinePalo AltoCalifornia
| | - Selina Dwight
- Department of Biomedical Data SciencesStanford University School of MedicinePalo AltoCalifornia
| | - Jimmy Zhen
- Department of Biomedical Data SciencesStanford University School of MedicinePalo AltoCalifornia
| | - Melissa Landrum
- National Center for Biotechnology InformationNational Institutes of HealthBethesdaMaryland
| | - Peter McGarvey
- Innovation Center for Biomedical InformaticsGeorgetown University Medical CenterWashingtonDistrict of Columbia
| | - Larry Babb
- Sunquest Information Systems CompanyBostonMassachusetts
| | - Sharon E. Plon
- Department of Molecular and Human GeneticsBaylor College of MedicineHoustonTexas
- Department of PediatricsBaylor College of Medicine HoustonTexas
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30
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Crump JK, Del Fiol G, Williams MS, Freimuth RR. Prototype of a Standards-Based EHR and Genetic Test Reporting Tool Coupled with HL7-Compliant Infobuttons. AMIA Jt Summits Transl Sci Proc 2018; 2017:330-339. [PMID: 29888091 PMCID: PMC5961781] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Integration of genetic information is becoming increasingly important in clinical practice. However, genetic information is often ambiguous and difficult to understand, and clinicians have reported low-self-efficacy in integrating genetics into their care routine. The Health Level Seven (HL7) Infobutton standard helps to integrate online knowledge resources within Electronic Health Records (EHRs) and is required for EHR certification in the US. We implemented a prototype of a standards-based genetic reporting application coupled with infobuttons leveraging the Infobutton and Fast Healthcare Interoperability Resources (FHIR) Standards. Infobutton capabilities were provided by Open Infobutton, an open source package compliant with the HL7 Infobutton Standard. The resulting prototype demonstrates how standards-based reporting of genetic results, coupled with curated knowledge resources, can provide dynamic access to clinical knowledge on demand at the point of care. The proposed functionality can be enabled within any EHR system that has been certified through the US Meaningful Use program.
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Affiliation(s)
- Jacob K Crump
- Department of Biomedical Informatics, University of Utah, Salt Lake City, Utah
| | - Guilherme Del Fiol
- Department of Biomedical Informatics, University of Utah, Salt Lake City, Utah
| | - Marc S Williams
- Genomic Medicine Institute, Geisinger, Danville, Pennsylvania
| | - Robert R Freimuth
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota
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31
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Freimuth RR, Formea CM, Hoffman JM, Matey E, Peterson JF, Boyce RD. Implementing Genomic Clinical Decision Support for Drug-Based Precision Medicine. CPT Pharmacometrics Syst Pharmacol 2017; 6:153-155. [PMID: 28109071 PMCID: PMC5351408 DOI: 10.1002/psp4.12173] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 12/08/2016] [Revised: 01/16/2017] [Accepted: 01/17/2017] [Indexed: 11/07/2022]
Abstract
The explosive growth of patient-specific genomic information relevant to drug therapy will continue to be a defining characteristic of biomedical research. To implement drug-based personalized medicine (PM) for patients, clinicians need actionable information incorporated into electronic health records (EHRs). New clinical decision support (CDS) methods and informatics infrastructure are required in order to comprehensively integrate, interpret, deliver, and apply the full range of genomic data for each patient.
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Affiliation(s)
- R R Freimuth
- Department of Health Sciences Research, Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - C M Formea
- Department of Pharmacy, Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - J M Hoffman
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - E Matey
- Department of Pharmacy, Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - J F Peterson
- Department of Biomedical Informatics and Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - R D Boyce
- Department of Biomedical Informatics, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
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Luzum JA, Pakyz RE, Elsey AR, Haidar CE, Peterson JF, Whirl-Carrillo M, Handelman SK, Palmer K, Pulley JM, Beller M, Schildcrout JS, Field JR, Weitzel KW, Cooper-DeHoff RM, Cavallari LH, O’Donnell PH, Altman RB, Pereira N, Ratain MJ, Roden DM, Embi PJ, Sadee W, Klein TE, Johnson JA, Relling MV, Wang L, Weinshilboum RM, Shuldiner AR, Freimuth RR. The Pharmacogenomics Research Network Translational Pharmacogenetics Program: Outcomes and Metrics of Pharmacogenetic Implementations Across Diverse Healthcare Systems. Clin Pharmacol Ther 2017; 102:502-510. [PMID: 28090649 PMCID: PMC5511786 DOI: 10.1002/cpt.630] [Citation(s) in RCA: 102] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Accepted: 01/11/2017] [Indexed: 12/23/2022]
Abstract
Numerous pharmacogenetic clinical guidelines and recommendations have been published, but barriers have hindered the clinical implementation of pharmacogenetics. The Translational Pharmacogenetics Program (TPP) of the National Institutes of Health (NIH) Pharmacogenomics Research Network was established in 2011 to catalog and contribute to the development of pharmacogenetic implementations at eight US healthcare systems, with the goal to disseminate real-world solutions for the barriers to clinical pharmacogenetic implementation. The TPP collected and normalized pharmacogenetic implementation metrics through June 2015, including gene-drug pairs implemented, interpretations of alleles and diplotypes, numbers of tests performed and actionable results, and workflow diagrams. TPP participant institutions developed diverse solutions to overcome many barriers, but the use of Clinical Pharmacogenetics Implementation Consortium (CPIC) guidelines provided some consistency among the institutions. The TPP also collected some pharmacogenetic implementation outcomes (scientific, educational, financial, and informatics), which may inform healthcare systems seeking to implement their own pharmacogenetic testing programs.
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Affiliation(s)
- Jasmine A. Luzum
- Department of Clinical Pharmacy, College of Pharmacy, University of Michigan, Ann Arbor, MI, USA
- Center for Pharmacogenomics, College of Medicine, Ohio State University, Columbus, OH, USA
| | - Ruth E. Pakyz
- Program for Personalized and Genomic Medicine, School of Medicine, University of Maryland, Baltimore, MD, USA
| | - Amanda R. Elsey
- Department of Pharmacotherapy and Translational Research and Center for Pharmacogenomics, University of Florida, Gainesville, FL, USA
| | - Cyrine E. Haidar
- Department of Pharmaceutical Sciences, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
| | - Josh F. Peterson
- Department of Medicine, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
- Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | | | - Samuel K. Handelman
- Center for Pharmacogenomics, College of Medicine, Ohio State University, Columbus, OH, USA
| | - Kathleen Palmer
- Program for Personalized and Genomic Medicine, School of Medicine, University of Maryland, Baltimore, MD, USA
| | - Jill M. Pulley
- Vanderbilt Institute for Clinical and Translational Research, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Marc Beller
- Office of Research Informatics, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Jonathan S. Schildcrout
- Department of Statistics, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Julie R. Field
- Vanderbilt Institute for Clinical and Translational Research, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Kristin W. Weitzel
- Department of Pharmacotherapy and Translational Research and Center for Pharmacogenomics, University of Florida, Gainesville, FL, USA
| | - Rhonda M. Cooper-DeHoff
- Department of Pharmacotherapy and Translational Research and Center for Pharmacogenomics, University of Florida, Gainesville, FL, USA
| | - Larisa H. Cavallari
- Department of Pharmacotherapy and Translational Research and Center for Pharmacogenomics, University of Florida, Gainesville, FL, USA
| | - Peter H. O’Donnell
- Center for Personalized Therapeutics, University of Chicago, Chicago, IL, USA
| | - Russ B. Altman
- Stanford University School of Medicine, Palo Alto, California, USA
| | - Naveen Pereira
- Division of Cardiovascular Diseases, Mayo Clinic, Rochester, MN, USA
| | - Mark J. Ratain
- Center for Personalized Therapeutics, University of Chicago, Chicago, IL, USA
| | - Dan M. Roden
- Department of Medicine, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Peter J. Embi
- Department of Biomedical Informatics, Ohio State University, Columbus, OH, USA
| | - Wolfgang Sadee
- Center for Pharmacogenomics, College of Medicine, Ohio State University, Columbus, OH, USA
- Department of Cancer Biology and Genetics, College of Medicine, Ohio State University, Columbus, OH, USA
| | - Teri E. Klein
- Stanford University School of Medicine, Palo Alto, California, USA
| | - Julie A. Johnson
- Department of Pharmacotherapy and Translational Research and Center for Pharmacogenomics, University of Florida, Gainesville, FL, USA
| | - Mary V. Relling
- Department of Pharmaceutical Sciences, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
| | - Liewei Wang
- Department of Molecular Pharmacology & Experimental Therapeutics, Mayo Clinic, Rochester, MN, USA
| | - Richard M. Weinshilboum
- Department of Molecular Pharmacology & Experimental Therapeutics, Mayo Clinic, Rochester, MN, USA
| | - Alan R. Shuldiner
- Program for Personalized and Genomic Medicine, School of Medicine, University of Maryland, Baltimore, MD, USA
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Shellum JL, Freimuth RR, Peters SG, Nishimura RA, Chaudhry R, Demuth SJ, Knopp AL, Miksch TA, Milliner DS. Knowledge as a Service at the Point of Care. AMIA Annu Symp Proc 2017; 2016:1139-1148. [PMID: 28269911 PMCID: PMC5333226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
An electronic health record (EHR) can assist the delivery of high-quality patient care, in part by providing the capability for a broad range of clinical decision support, including contextual references (e.g., Infobuttons), alerts and reminders, order sets, and dashboards. All of these decision support tools are based on clinical knowledge; unfortunately, the mechanisms for managing rules, order sets, Infobuttons, and dashboards are often unrelated, making it difficult to coordinate the application of clinical knowledge to various components of the clinical workflow. Additional complexity is encountered when updating enterprise-wide knowledge bases and delivering the content through multiple modalities to different consumers. We present the experience of Mayo Clinic as a case study to examine the requirements and implementation challenges related to knowledge management across a large, multi-site medical center. The lessons learned through the development of our knowledge management and delivery platform will help inform the future development of interoperable knowledge resources.
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Affiliation(s)
- Jane L Shellum
- Office of Information and Knowledge Management, Mayo Clinic, Rochester, MN
| | - Robert R Freimuth
- Office of Information and Knowledge Management, Mayo Clinic, Rochester, MN
| | - Steve G Peters
- Office of Information and Knowledge Management, Mayo Clinic, Rochester, MN
| | - Rick A Nishimura
- Office of Information and Knowledge Management, Mayo Clinic, Rochester, MN
| | - Rajeev Chaudhry
- Office of Information and Knowledge Management, Mayo Clinic, Rochester, MN
| | - Steve J Demuth
- Office of Information and Knowledge Management, Mayo Clinic, Rochester, MN
| | - Amy L Knopp
- Office of Information and Knowledge Management, Mayo Clinic, Rochester, MN
| | - Timothy A Miksch
- Office of Information and Knowledge Management, Mayo Clinic, Rochester, MN
| | - Dawn S Milliner
- Office of Information and Knowledge Management, Mayo Clinic, Rochester, MN
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Caudle KE, Dunnenberger HM, Freimuth RR, Peterson JF, Burlison JD, Whirl-Carrillo M, Scott SA, Rehm HL, Williams MS, Klein TE, Relling MV, Hoffman JM. Standardizing terms for clinical pharmacogenetic test results: consensus terms from the Clinical Pharmacogenetics Implementation Consortium (CPIC). Genet Med 2017; 19:215-223. [PMID: 27441996 PMCID: PMC5253119 DOI: 10.1038/gim.2016.87] [Citation(s) in RCA: 303] [Impact Index Per Article: 43.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Accepted: 05/17/2016] [Indexed: 12/22/2022] Open
Abstract
INTRODUCTION Reporting and sharing pharmacogenetic test results across clinical laboratories and electronic health records is a crucial step toward the implementation of clinical pharmacogenetics, but allele function and phenotype terms are not standardized. Our goal was to develop terms that can be broadly applied to characterize pharmacogenetic allele function and inferred phenotypes. MATERIALS AND METHODS Terms currently used by genetic testing laboratories and in the literature were identified. The Clinical Pharmacogenetics Implementation Consortium (CPIC) used the Delphi method to obtain a consensus and agree on uniform terms among pharmacogenetic experts. RESULTS Experts with diverse involvement in at least one area of pharmacogenetics (clinicians, researchers, genetic testing laboratorians, pharmacogenetics implementers, and clinical informaticians; n = 58) participated. After completion of five surveys, a consensus (>70%) was reached with 90% of experts agreeing to the final sets of pharmacogenetic terms. DISCUSSION The proposed standardized pharmacogenetic terms will improve the understanding and interpretation of pharmacogenetic tests and reduce confusion by maintaining consistent nomenclature. These standard terms can also facilitate pharmacogenetic data sharing across diverse electronic health care record systems with clinical decision support.Genet Med 19 2, 215-223.
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Affiliation(s)
- Kelly E. Caudle
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Henry M. Dunnenberger
- Center for Molecular Medicine, NorthShore University HealthSystem, Evanston, Illinois, USA
| | - Robert R. Freimuth
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota, USA
| | - Josh F. Peterson
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Jonathan D. Burlison
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | | | - Stuart A. Scott
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Heidi L. Rehm
- Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA; The Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA
| | - Marc S. Williams
- Genomic Medicine Institute, Geisinger Health System, Danville, Pennsylvania, USA
| | - Teri E. Klein
- Department of Genetics, Stanford University, Stanford, California, USA
| | - Mary V. Relling
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - James M. Hoffman
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
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35
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Tenenbaum JD, Avillach P, Benham-Hutchins M, Breitenstein MK, Crowgey EL, Hoffman MA, Jiang X, Madhavan S, Mattison JE, Nagarajan R, Ray B, Shin D, Visweswaran S, Zhao Z, Freimuth RR. An informatics research agenda to support precision medicine: seven key areas. J Am Med Inform Assoc 2016; 23:791-5. [PMID: 27107452 PMCID: PMC4926738 DOI: 10.1093/jamia/ocv213] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Accepted: 12/24/2015] [Indexed: 01/22/2023] Open
Abstract
The recent announcement of the Precision Medicine Initiative by President Obama has brought precision medicine (PM) to the forefront for healthcare providers, researchers, regulators, innovators, and funders alike. As technologies continue to evolve and datasets grow in magnitude, a strong computational infrastructure will be essential to realize PM's vision of improved healthcare derived from personal data. In addition, informatics research and innovation affords a tremendous opportunity to drive the science underlying PM. The informatics community must lead the development of technologies and methodologies that will increase the discovery and application of biomedical knowledge through close collaboration between researchers, clinicians, and patients. This perspective highlights seven key areas that are in need of further informatics research and innovation to support the realization of PM.
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Affiliation(s)
- Jessica D Tenenbaum
- Department of Biostatistics and Bioinformatics, Duke University, Durham, NC, USA
| | - Paul Avillach
- Department of Biomedical Informatics, Harvard Medical School & Children's Hospital Informatics Program, Boston Children's Hospital, Boston, MA, USA
| | | | | | - Erin L Crowgey
- Center for Bioinformatics & Computational Biology, University of Delaware, Newark, DE, USA
| | - Mark A Hoffman
- Department of Biomedical & Health Informatics, University of Missouri - Kansas City, Children's Mercy Hospital, Kansas City, MO, USA
| | - Xia Jiang
- Department of Biomedical Informatics, University of Pittsburgh, Pittsburgh, PA, USA
| | - Subha Madhavan
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Innovation Center for Biomedical Informatics, Washington, DC, USA
| | - John E Mattison
- Exponential Medicine, Singularity University; Internal Medicine, System Solutions at Kaiser Permanente, Pasadena, CA, USA
| | | | - Bisakha Ray
- Center for Health Informatics and Bioinformatics, New York University School of Medicine, New York, NY, USA
| | - Dmitriy Shin
- Department of Pathology, MU Informatics Institute, University of Missouri, Columbia, MO, USA
| | - Shyam Visweswaran
- Department of Biomedical Informatics and the Intelligent Systems Program, University of Pittsburgh, Pittsburgh, PA, USA
| | - Zhongming Zhao
- Center for Precision Health, School of Biomedical Informatics, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Robert R Freimuth
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
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36
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Hoffman JM, Dunnenberger HM, Kevin Hicks J, Caudle KE, Whirl Carrillo M, Freimuth RR, Williams MS, Klein TE, Peterson JF. Developing knowledge resources to support precision medicine: principles from the Clinical Pharmacogenetics Implementation Consortium (CPIC). J Am Med Inform Assoc 2016; 23:796-801. [PMID: 27026620 DOI: 10.1093/jamia/ocw027] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Accepted: 01/13/2016] [Indexed: 11/13/2022] Open
Abstract
To move beyond a select few genes/drugs, the successful adoption of pharmacogenomics into routine clinical care requires a curated and machine-readable database of pharmacogenomic knowledge suitable for use in an electronic health record (EHR) with clinical decision support (CDS). Recognizing that EHR vendors do not yet provide a standard set of CDS functions for pharmacogenetics, the Clinical Pharmacogenetics Implementation Consortium (CPIC) Informatics Working Group is developing and systematically incorporating a set of EHR-agnostic implementation resources into all CPIC guidelines. These resources illustrate how to integrate pharmacogenomic test results in clinical information systems with CDS to facilitate the use of patient genomic data at the point of care. Based on our collective experience creating existing CPIC resources and implementing pharmacogenomics at our practice sites, we outline principles to define the key features of future knowledge bases and discuss the importance of these knowledge resources for pharmacogenomics and ultimately precision medicine.
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Affiliation(s)
- James M Hoffman
- Department of Pharmaceutical Sciences, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Henry M Dunnenberger
- Center for Molecular Medicine, NorthShore University HealthSystem, Evanston, IL, USA
| | - J Kevin Hicks
- Pharmacy Department and Genomic Medicine Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Kelly E Caudle
- Department of Pharmaceutical Sciences, St Jude Children's Research Hospital, Memphis, TN, USA
| | | | - Robert R Freimuth
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | - Marc S Williams
- Genomic Medicine Institute, Geisinger Health System, Danville, PA, USA
| | - Teri E Klein
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Josh F Peterson
- Departments of Medicine and Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, USA
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37
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Wiley LK, Tarczy-Hornoch P, Denny JC, Freimuth RR, Overby CL, Shah N, Martin RD, Sarkar IN. Harnessing next-generation informatics for personalizing medicine: a report from AMIA's 2014 Health Policy Invitational Meeting. J Am Med Inform Assoc 2016; 23:413-9. [PMID: 26911808 PMCID: PMC6457095 DOI: 10.1093/jamia/ocv111] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2015] [Revised: 06/22/2015] [Accepted: 06/24/2015] [Indexed: 11/13/2022] Open
Abstract
The American Medical Informatics Association convened the 2014 Health Policy Invitational Meeting to develop recommendations for updates to current policies and to establish an informatics research agenda for personalizing medicine. In particular, the meeting focused on discussing informatics challenges related to personalizing care through the integration of genomic or other high-volume biomolecular data with data from clinical systems to make health care more efficient and effective. This report summarizes the findings (n = 6) and recommendations (n = 15) from the policy meeting, which were clustered into 3 broad areas: (1) policies governing data access for research and personalization of care; (2) policy and research needs for evolving data interpretation and knowledge representation; and (3) policy and research needs to ensure data integrity and preservation. The meeting outcome underscored the need to address a number of important policy and technical considerations in order to realize the potential of personalized or precision medicine in actual clinical contexts.
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Affiliation(s)
- Laura K Wiley
- Department of Biomedical Informatics, Vanderbilt University, Nashville, Tennessee, USA
| | - Peter Tarczy-Hornoch
- Department of Biomedical Informatics and Medical Education, University of Washington, Seattle, Washington, USA
| | - Joshua C Denny
- Department of Biomedical Informatics, Vanderbilt University, Nashville, Tennessee, USA
| | - Robert R Freimuth
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota, USA
| | - Casey L Overby
- Program for Personalized and Genomic Medicine, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Nigam Shah
- Center for Biomedical Informatics Research, Stanford University, Stanford, California, USA
| | - Ross D Martin
- Chesapeake Regional Information System for our Patients (CRISP), Columbia, Maryland, USA
| | - Indra Neil Sarkar
- Center for Biomedical Informatics, Brown University, Providence, Rhode Island, USA
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Aziz A, Kawamoto K, Eilbeck K, Williams MS, Freimuth RR, Hoffman MA, Rasmussen LV, Overby CL, Shirts BH, Hoffman JM, Welch BM. The genomic CDS sandbox: An assessment among domain experts. J Biomed Inform 2016; 60:84-94. [PMID: 26778834 DOI: 10.1016/j.jbi.2015.12.019] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2015] [Revised: 12/11/2015] [Accepted: 12/29/2015] [Indexed: 01/17/2023]
Abstract
Genomics is a promising tool that is becoming more widely available to improve the care and treatment of individuals. While there is much assertion, genomics will most certainly require the use of clinical decision support (CDS) to be fully realized in the routine clinical setting. The National Human Genome Research Institute (NHGRI) of the National Institutes of Health recently convened an in-person, multi-day meeting on this topic. It was widely recognized that there is a need to promote the innovation and development of resources for genomic CDS such as a CDS sandbox. The purpose of this study was to evaluate a proposed approach for such a genomic CDS sandbox among domain experts and potential users. Survey results indicate a significant interest and desire for a genomic CDS sandbox environment among domain experts. These results will be used to guide the development of a genomic CDS sandbox.
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Affiliation(s)
- Ayesha Aziz
- Medical University of South Carolina, Charleston, SC, United States.
| | | | - Karen Eilbeck
- University of Utah, Salt Lake City, UT, United States.
| | | | | | | | | | | | | | - James M Hoffman
- St. Jude Children's Research Hospital, Memphis, TN, United States.
| | - Brandon M Welch
- Medical University of South Carolina, Charleston, SC, United States.
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Linan MK, Sottara D, Freimuth RR. Creating Shareable Clinical Decision Support Rules for a Pharmacogenomics Clinical Guideline Using Structured Knowledge Representation. AMIA Annu Symp Proc 2015; 2015:1985-1994. [PMID: 26958298 PMCID: PMC4765632] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Pharmacogenomics (PGx) guidelines contain drug-gene relationships, therapeutic and clinical recommendations from which clinical decision support (CDS) rules can be extracted, rendered and then delivered through clinical decision support systems (CDSS) to provide clinicians with just-in-time information at the point of care. Several tools exist that can be used to generate CDS rules that are based on computer interpretable guidelines (CIG), but none have been previously applied to the PGx domain. We utilized the Unified Modeling Language (UML), the Health Level 7 virtual medical record (HL7 vMR) model, and standard terminologies to represent the semantics and decision logic derived from a PGx guideline, which were then mapped to the Health eDecisions (HeD) schema. The modeling and extraction processes developed here demonstrate how structured knowledge representations can be used to support the creation of shareable CDS rules from PGx guidelines.
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Affiliation(s)
- Margaret K Linan
- Department of Biomedical Informatics, Arizona State University, Scottsdale, AZ
| | - Davide Sottara
- Department of Biomedical Informatics, Arizona State University, Scottsdale, AZ; Office of Information and Knowledge Management, Mayo Clinic, Rochester, MN
| | - Robert R Freimuth
- Office of Information and Knowledge Management, Mayo Clinic, Rochester, MN; Department of Health Sciences Research, Mayo Clinic, Rochester, MN
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40
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Samwald M, Blagec K, Hofer S, Freimuth RR. Analyzing the potential for incorrect haplotype calls with different pharmacogenomic assays in different populations: a simulation based on 1000 Genomes data. Pharmacogenomics 2015; 16:1713-21. [PMID: 26419264 DOI: 10.2217/pgs.15.108] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
AIM Many currently available pharmacogenomic assays and algorithms interrogate a set of 'tag' polymorphisms for inferring haplotypes. We wanted to test the accuracy of such haplotype inferences across different populations. MATERIALS & METHODS We simulated haplotype inferences made by existing pharmacogenomic assays for seven important pharmacogenes based on full genome data of 2504 persons in the 1000 Genomes dataset. RESULTS A sizable fraction of samples did not match any of the haplotypes in the star allele nomenclature systems. We found no clear population bias in the accuracy of results of simulated assays. CONCLUSION Haplotype nomenclatures and inference algorithms need to be improved to adequately capture pharmacogenomic diversity in human populations.
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Affiliation(s)
- Matthias Samwald
- Section for Medical Expert & Knowledge-Based Systems, Center for Medical Statistics, Informatics & Intelligent Systems, Medical University of Vienna, Spitalgasse 23, 1090 Vienna, Austria
| | - Kathrin Blagec
- Section for Medical Expert & Knowledge-Based Systems, Center for Medical Statistics, Informatics & Intelligent Systems, Medical University of Vienna, Spitalgasse 23, 1090 Vienna, Austria
| | - Sebastian Hofer
- Section for Medical Expert & Knowledge-Based Systems, Center for Medical Statistics, Informatics & Intelligent Systems, Medical University of Vienna, Spitalgasse 23, 1090 Vienna, Austria
| | - Robert R Freimuth
- Department of Health Sciences Research, Mayo Clinic, 200 First Street SW, Rochester, MN 55905, USA
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41
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Herr TM, Bielinski SJ, Bottinger E, Brautbar A, Brilliant M, Chute CG, Denny J, Freimuth RR, Hartzler A, Kannry J, Kohane IS, Kullo IJ, Lin S, Pathak J, Peissig P, Pulley J, Ralston J, Rasmussen L, Roden D, Tromp G, Williams MS, Starren J. A conceptual model for translating omic data into clinical action. J Pathol Inform 2015; 6:46. [PMID: 26430534 PMCID: PMC4584438 DOI: 10.4103/2153-3539.163985] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Accepted: 07/01/2015] [Indexed: 01/27/2023] Open
Abstract
Genomic, proteomic, epigenomic, and other “omic” data have the potential to enable precision medicine, also commonly referred to as personalized medicine. The volume and complexity of omic data are rapidly overwhelming human cognitive capacity, requiring innovative approaches to translate such data into patient care. Here, we outline a conceptual model for the application of omic data in the clinical context, called “the omic funnel.” This model parallels the classic “Data, Information, Knowledge, Wisdom pyramid” and adds context for how to move between each successive layer. Its goal is to allow informaticians, researchers, and clinicians to approach the problem of translating omic data from bench to bedside, by using discrete steps with clearly defined needs. Such an approach can facilitate the development of modular and interoperable software that can bring precision medicine into widespread practice.
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Affiliation(s)
- Timothy M Herr
- Department of Preventive Medicine, Division of Health and Biomedical Informatics, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Suzette J Bielinski
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota, USA
| | - Erwin Bottinger
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine, Mount Sinai, New York, USA
| | - Ariel Brautbar
- Division of Genetics and Endocrinology, Cook Children's Medical Center, Fort Worth, Texas, USA
| | - Murray Brilliant
- Center for Human Genetics, Marshfield Clinic Research Foundation, Marshfield, Wisconsin, USA
| | - Christopher G Chute
- Division of General Internal Medicine, Johns Hopkins University, Baltimore, Maryland, USA
| | - Joshua Denny
- Department of Biomedical Informatics, Vanderbilt University, Nashville, Tennessee, USA
| | - Robert R Freimuth
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota, USA
| | | | - Joseph Kannry
- Icahn School of Medicine, Mount Sinai, New York, USA
| | - Isaac S Kohane
- Center for Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, USA
| | - Iftikhar J Kullo
- Division of Cardiovascular Diseases, Mayo Clinic, Rochester, Minnesota, USA
| | - Simon Lin
- Nationwide Children's Hospital, Columbus, Ohio, USA
| | - Jyotishman Pathak
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota, USA
| | - Peggy Peissig
- Biomedical Informatics Research Center, Marshfield Clinic Research Foundation, Marshfield, Wisconsin, USA
| | - Jill Pulley
- Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - James Ralston
- Group Health Research Institute, Seattle, Washington, USA
| | - Luke Rasmussen
- Department of Preventive Medicine, Division of Health and Biomedical Informatics, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Dan Roden
- Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Gerard Tromp
- Weis Center for Research, Danville, Pennsylvania, USA
| | - Marc S Williams
- Genomic Medicine Institute, Geisinger Health System, Danville, Pennsylvania, USA
| | - Justin Starren
- Department of Preventive Medicine, Division of Health and Biomedical Informatics, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
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Shirts BH, Salama JS, Aronson SJ, Chung WK, Gray SW, Hindorff LA, Jarvik GP, Plon SE, Stoffel EM, Tarczy-Hornoch PZ, Van Allen EM, Weck KE, Chute CG, Freimuth RR, Grundmeier RW, Hartzler AL, Li R, Peissig PL, Peterson JF, Rasmussen LV, Starren JB, Williams MS, Overby CL. CSER and eMERGE: current and potential state of the display of genetic information in the electronic health record. J Am Med Inform Assoc 2015; 22:1231-42. [PMID: 26142422 DOI: 10.1093/jamia/ocv065] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2015] [Accepted: 05/12/2015] [Indexed: 11/13/2022] Open
Abstract
OBJECTIVE Clinicians' ability to use and interpret genetic information depends upon how those data are displayed in electronic health records (EHRs). There is a critical need to develop systems to effectively display genetic information in EHRs and augment clinical decision support (CDS). MATERIALS AND METHODS The National Institutes of Health (NIH)-sponsored Clinical Sequencing Exploratory Research and Electronic Medical Records & Genomics EHR Working Groups conducted a multiphase, iterative process involving working group discussions and 2 surveys in order to determine how genetic and genomic information are currently displayed in EHRs, envision optimal uses for different types of genetic or genomic information, and prioritize areas for EHR improvement. RESULTS There is substantial heterogeneity in how genetic information enters and is documented in EHR systems. Most institutions indicated that genetic information was displayed in multiple locations in their EHRs. Among surveyed institutions, genetic information enters the EHR through multiple laboratory sources and through clinician notes. For laboratory-based data, the source laboratory was the main determinant of the location of genetic information in the EHR. The highest priority recommendation was to address the need to implement CDS mechanisms and content for decision support for medically actionable genetic information. CONCLUSION Heterogeneity of genetic information flow and importance of source laboratory, rather than clinical content, as a determinant of information representation are major barriers to using genetic information optimally in patient care. Greater effort to develop interoperable systems to receive and consistently display genetic and/or genomic information and alert clinicians to genomic-dependent improvements to clinical care is recommended.
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Affiliation(s)
- Brian H Shirts
- Department of Laboratory Medicine, University of Washington, Seattle, WA, 98195, USA
| | - Joseph S Salama
- Department of Medicine, Division of Medical Genetics, University of Washington, Seattle, WA, USA
| | | | - Wendy K Chung
- Department of Pediatrics, Columbia University Medical Center, New York, NY, USA
| | - Stacy W Gray
- Department of Medicine, Harvard Medical School, Boston, MA, USA Dana-Farber Cancer Institute, Boston, MA, USA
| | - Lucia A Hindorff
- National Human Genome Research Institute, NIH, Rockville, MD, USA
| | - Gail P Jarvik
- Department of Medicine, Division of Medical Genetics, University of Washington, Seattle, WA, USA Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Sharon E Plon
- Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - Elena M Stoffel
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Peter Z Tarczy-Hornoch
- Department of Biomedical Informatics and Medical Education, University of Washington, Seattle, WA, USA
| | - Eliezer M Van Allen
- Dana-Farber Cancer Institute, Boston, MA, USA The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Karen E Weck
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Christopher G Chute
- Department of Health Sciences Research, Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, MN, USA
| | - Robert R Freimuth
- Department of Health Sciences Research, Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, MN, USA
| | - Robert W Grundmeier
- Department of Biomedical and Health Informatics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Andrea L Hartzler
- Group Health Research Institute, Group Health Cooperative, Seattle, WA, USA
| | - Rongling Li
- National Human Genome Research Institute, NIH, Rockville, MD, USA
| | - Peggy L Peissig
- Biomedical Informatics Research Center, Marshfield Clinic Research Foundation, Marshfield, WI, USA
| | - Josh F Peterson
- Department of Biomedical Informatics, Vanderbilt, Nashville, TN, USA
| | - Luke V Rasmussen
- Department of Preventive Medicine, Division of Health and Biomedical Informatics, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Justin B Starren
- Department of Preventive Medicine, Division of Health and Biomedical Informatics, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Marc S Williams
- Genome Medicine Institute, Geisinger Medical Center, Danville, PA, USA
| | - Casey L Overby
- Genome Medicine Institute, Geisinger Medical Center, Danville, PA, USA Department of Medicine, Program for Personalized and Genomic Medicine and Center for Health-Related Informatics and Bioimaging, University of Maryland School of Medicine, Baltimore, MD, USA
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43
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Samwald M, Miñarro Giménez JA, Boyce RD, Freimuth RR, Adlassnig KP, Dumontier M. Pharmacogenomic knowledge representation, reasoning and genome-based clinical decision support based on OWL 2 DL ontologies. BMC Med Inform Decis Mak 2015; 15:12. [PMID: 25880555 PMCID: PMC4340468 DOI: 10.1186/s12911-015-0130-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2014] [Accepted: 01/13/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Every year, hundreds of thousands of patients experience treatment failure or adverse drug reactions (ADRs), many of which could be prevented by pharmacogenomic testing. However, the primary knowledge needed for clinical pharmacogenomics is currently dispersed over disparate data structures and captured in unstructured or semi-structured formalizations. This is a source of potential ambiguity and complexity, making it difficult to create reliable information technology systems for enabling clinical pharmacogenomics. METHODS We developed Web Ontology Language (OWL) ontologies and automated reasoning methodologies to meet the following goals: 1) provide a simple and concise formalism for representing pharmacogenomic knowledge, 2) finde errors and insufficient definitions in pharmacogenomic knowledge bases, 3) automatically assign alleles and phenotypes to patients, 4) match patients to clinically appropriate pharmacogenomic guidelines and clinical decision support messages and 5) facilitate the detection of inconsistencies and overlaps between pharmacogenomic treatment guidelines from different sources. We evaluated different reasoning systems and test our approach with a large collection of publicly available genetic profiles. RESULTS Our methodology proved to be a novel and useful choice for representing, analyzing and using pharmacogenomic data. The Genomic Clinical Decision Support (Genomic CDS) ontology represents 336 SNPs with 707 variants; 665 haplotypes related to 43 genes; 22 rules related to drug-response phenotypes; and 308 clinical decision support rules. OWL reasoning identified CDS rules with overlapping target populations but differing treatment recommendations. Only a modest number of clinical decision support rules were triggered for a collection of 943 public genetic profiles. We found significant performance differences across available OWL reasoners. CONCLUSIONS The ontology-based framework we developed can be used to represent, organize and reason over the growing wealth of pharmacogenomic knowledge, as well as to identify errors, inconsistencies and insufficient definitions in source data sets or individual patient data. Our study highlights both advantages and potential practical issues with such an ontology-based approach.
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Affiliation(s)
- Matthias Samwald
- Center for Medical Statistics, Informatics, and Intelligent Systems, Medical University of Vienna, Spitalgasse 23, 1090, Vienna, Austria.
| | - Jose Antonio Miñarro Giménez
- Center for Medical Statistics, Informatics, and Intelligent Systems, Medical University of Vienna, Spitalgasse 23, 1090, Vienna, Austria.,Institute of Medical Informatics, Statistics, and Documentation; Medical University of Graz, Auenbruggerplatz 2, 8036, Graz, Austria
| | - Richard D Boyce
- Department of Biomedical Informatics, University of Pittsburgh, 5607 Baum Blvd, Suite 419, Pittsburgh, PA, 15206-3701, USA
| | - Robert R Freimuth
- Department of Health Sciences Research; Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA
| | - Klaus-Peter Adlassnig
- Center for Medical Statistics, Informatics, and Intelligent Systems, Medical University of Vienna, Spitalgasse 23, 1090, Vienna, Austria.,Medexter Healthcare GmbH, Borschkegasse 7/5, 1090, Vienna, Austria
| | - Michel Dumontier
- Stanford Center for Biomedical Informatics Research, Stanford University, 1265 Welch Road, Stanford, CA, 94305-5479, USA
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Caudle KE, Klein TE, Hoffman JM, Muller DJ, Whirl-Carrillo M, Gong L, McDonagh EM, Sangkuhl K, Thorn CF, Schwab M, Agundez JAG, Freimuth RR, Huser V, Lee MTM, Iwuchukwu OF, Crews KR, Scott SA, Wadelius M, Swen JJ, Tyndale RF, Stein CM, Roden D, Relling MV, Williams MS, Johnson SG. Incorporation of pharmacogenomics into routine clinical practice: the Clinical Pharmacogenetics Implementation Consortium (CPIC) guideline development process. Curr Drug Metab 2014; 15:209-17. [PMID: 24479687 PMCID: PMC3977533 DOI: 10.2174/1389200215666140130124910] [Citation(s) in RCA: 272] [Impact Index Per Article: 27.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2013] [Revised: 10/11/2013] [Accepted: 01/21/2014] [Indexed: 11/22/2022]
Abstract
The Clinical Pharmacogenetics Implementation Consortium (CPIC) publishes genotype-based drug guidelines to help
clinicians understand how available genetic test results could be used to optimize drug therapy. CPIC has focused initially on well-known
examples of pharmacogenomic associations that have been implemented in selected clinical settings, publishing nine to date. Each CPIC
guideline adheres to a standardized format and includes a standard system for grading levels of evidence linking genotypes to phenotypes
and assigning a level of strength to each prescribing recommendation. CPIC guidelines contain the necessary information to help
clinicians translate patient-specific diplotypes for each gene into clinical phenotypes or drug dosing groups. This paper reviews the
development process of the CPIC guidelines and compares this process to the Institute of Medicine’s Standards for Developing Trustworthy
Clinical Practice Guidelines.
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45
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Overby CL, Rasmussen LV, Hartzler A, Connolly JJ, Peterson JF, Hedberg RE, Freimuth RR, Shirts BH, Denny JC, Larson EB, Chute CG, Jarvik GP, Ralston JD, Shuldiner AR, Starren J, Kullo IJ, Tarczy-Hornoch P, Williams MS. A Template for Authoring and Adapting Genomic Medicine Content in the eMERGE Infobutton Project. AMIA Annu Symp Proc 2014; 2014:944-953. [PMID: 25954402 PMCID: PMC4419923] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The Electronic Medical Records and Genomics (eMERGE) Network is a national consortium that is developing methods and best practices for using the electronic health record (EHR) for genomic medicine and research. We conducted a multi-site survey of information resources to support integration of pharmacogenomics into clinical care. This work aimed to: (a) characterize the diversity of information resource implementation strategies among eMERGE institutions; (b) develop a master template containing content topics of important for genomic medicine (as identified by the DISCERN-Genetics tool); and (c) assess the coverage of content topics among information resources developed by eMERGE institutions. Given that a standard implementation does not exist and sites relied on a diversity of information resources, we identified a need for a national effort to efficiently produce sharable genomic medicine resources capable of being accessed from the EHR. We discuss future areas of work to prepare institutions to use infobuttons for distributing standardized genomic content.
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Affiliation(s)
- Casey L Overby
- Program for Personalized and Genomic Medicine and Department of Medicine, University of Maryland, Baltimore, MD ; Center for Health-related Informatics and Bioimaging, University of Maryland, Baltimore, MD
| | - Luke V Rasmussen
- Department of Preventive Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA
| | - Andrea Hartzler
- The Information School, The Children's Hospital of Philadelphia, Philadelphia, PA
| | - John J Connolly
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, PA
| | - Josh F Peterson
- Department of Biomedical Informatics, Vanderbilt University, Nashville, TN ; Department of Medicine, Vanderbilt University, Nashville, TN
| | - RoseMary E Hedberg
- Department of Preventive Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA
| | | | | | - Joshua C Denny
- Department of Biomedical Informatics, Vanderbilt University, Nashville, TN ; Department of Medicine, Vanderbilt University, Nashville, TN
| | | | | | - Gail P Jarvik
- Department of Medical Genetics, University of Washington, Seattle, WA
| | | | - Alan R Shuldiner
- Program for Personalized and Genomic Medicine and Department of Medicine, University of Maryland, Baltimore, MD
| | - Justin Starren
- Department of Preventive Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA ; Medical Social Sciences, Northwestern University, Chicago, IL
| | | | | | - Marc S Williams
- Genomic Medicine Institute, Geisinger Health System, Danville, PA
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Freimuth RR, Wix K, Zhu Q, Siska M, Chute CG. Evaluation of RxNorm for Medication Clinical Decision Support. AMIA Annu Symp Proc 2014; 2014:554-563. [PMID: 25954360 PMCID: PMC4419908] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
We evaluated the potential use of RxNorm to provide standardized representations of generic drug name and route of administration to facilitate management of drug lists for clinical decision support (CDS) rules. We found a clear representation of generic drug name but not route of administration. We identified several issues related to data quality, including erroneous or missing defined relationships, and the use of different concept hierarchies to represent the same drug. More importantly, we found extensive semantic precoordination of orthogonal concepts related to route and dose form, which would complicate the use of RxNorm for drug-based CDS. This study demonstrated that while RxNorm is a valuable resource for the standardization of medications used in clinical practice, additional work is required to enhance the terminology so that it can support expanded use cases, such as managing drug lists for CDS.
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Affiliation(s)
- Robert R Freimuth
- Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Rochester, MN ; Office of Information and Knowledge Management, Rochester, MN
| | - Kelly Wix
- Pharmacy Services Information Systems; Mayo Clinic, Rochester, MN
| | - Qian Zhu
- Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Rochester, MN
| | - Mark Siska
- Pharmacy Services Information Systems; Mayo Clinic, Rochester, MN
| | - Christopher G Chute
- Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Rochester, MN
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47
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Samwald M, Freimuth RR. Making data on essential pharmacogenes available for every patient everywhere: the Medicine Safety Code initiative. Pharmacogenomics 2014; 14:1529-31. [PMID: 24088121 DOI: 10.2217/pgs.13.121] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Affiliation(s)
- Matthias Samwald
- Section for Medical Expert & Knowledge-Based Systems, Center for Medical Statistics, Informatics & Intelligent Systems, Medical University of Vienna, Spitalgasse 23, A-1090 Vienna, Austria.
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48
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Freimuth RR, Zhu Q, Pathak J, Chute CG. Simplifying complex clinical element models to encourage adoption. AMIA Jt Summits Transl Sci Proc 2014; 2014:26-31. [PMID: 25954573 PMCID: PMC4419759] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Clinical Element Models (CEMs) were developed to provide a normalized form for the exchange of clinical data. The CEM specification is quite complex and specialized knowledge is required to understand and implement the models, which presents a significant barrier to investigators and study designers. To encourage the adoption of CEMs at the time of data collection and reduce the need for retrospective normalization efforts, we developed an approach that provides a simplified view of CEMs for non-experts while retaining the full semantic detail of the underlying logical models. This allows investigators to approach CEMs through generalized representations that are intended to be more intuitive than the native models, and it permits them to think conceptually about their data elements without worrying about details related to the CEM logical models and syntax. We demonstrate our approach using data elements from the Pharmacogenomics Research Network (PGRN).
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49
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Martin MA, Hoffman JM, Freimuth RR, Klein TE, Dong BJ, Pirmohamed M, Hicks JK, Wilkinson MR, Haas DW, Kroetz DL. Clinical Pharmacogenetics Implementation Consortium Guidelines for HLA-B Genotype and Abacavir Dosing: 2014 update. Clin Pharmacol Ther 2014; 95:499-500. [PMID: 24561393 DOI: 10.1038/clpt.2014.38] [Citation(s) in RCA: 90] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2013] [Accepted: 02/07/2014] [Indexed: 11/09/2022]
Abstract
The Clinical Pharmacogenetics Implementation Consortium (CPIC) Guidelines for HLA-B Genotype and Abacavir Dosing were originally published in April 2012. We reviewed recent literature and concluded that none of the evidence would change the therapeutic recommendations in the original guideline; therefore, the original publication remains clinically current. However, we have updated the Supplementary Material online and included additional resources for applying CPIC guidelines to the electronic health record. Up-to-date information can be found at PharmGKB (http://www.pharmgkb.org).
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Affiliation(s)
- M A Martin
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, California, USA
| | - J M Hoffman
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - R R Freimuth
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota, USA
| | - T E Klein
- Department of Genetics, Stanford University, Stanford, California, USA
| | - B J Dong
- Department of Clinical Pharmacy, University of California, San Francisco, San Francisco, California, USA
| | - M Pirmohamed
- Department of Pharmacology, University of Liverpool, Liverpool, UK
| | - J K Hicks
- Department of Pharmacy and Center for Personalized Healthcare, Cleveland Clinic, Cleveland, Ohio, USA
| | - M R Wilkinson
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - D W Haas
- Department of Medicine, Vanderbilt University, Nashville, Tennessee, USA
| | - D L Kroetz
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, California, USA
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50
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Bielinski SJ, Olson JE, Pathak J, Weinshilboum RM, Wang L, Lyke KJ, Ryu E, Targonski PV, Van Norstrand MD, Hathcock MA, Takahashi PY, McCormick JB, Johnson KJ, Maschke KJ, Rohrer Vitek CR, Ellingson MS, Wieben ED, Farrugia G, Morrisette JA, Kruckeberg KJ, Bruflat JK, Peterson LM, Blommel JH, Skierka JM, Ferber MJ, Black JL, Baudhuin LM, Klee EW, Ross JL, Veldhuizen TL, Schultz CG, Caraballo PJ, Freimuth RR, Chute CG, Kullo IJ. Preemptive genotyping for personalized medicine: design of the right drug, right dose, right time-using genomic data to individualize treatment protocol. Mayo Clin Proc 2014; 89:25-33. [PMID: 24388019 PMCID: PMC3932754 DOI: 10.1016/j.mayocp.2013.10.021] [Citation(s) in RCA: 222] [Impact Index Per Article: 22.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/13/2013] [Revised: 10/16/2013] [Accepted: 10/23/2013] [Indexed: 01/08/2023]
Abstract
OBJECTIVE To report the design and implementation of the Right Drug, Right Dose, Right Time-Using Genomic Data to Individualize Treatment protocol that was developed to test the concept that prescribers can deliver genome-guided therapy at the point of care by using preemptive pharmacogenomics (PGx) data and clinical decision support (CDS) integrated into the electronic medical record (EMR). PATIENTS AND METHODS We used a multivariate prediction model to identify patients with a high risk of initiating statin therapy within 3 years. The model was used to target a study cohort most likely to benefit from preemptive PGx testing among the Mayo Clinic Biobank participants, with a recruitment goal of 1000 patients. We used a Cox proportional hazards model with variables selected through the Lasso shrinkage method. An operational CDS model was adapted to implement PGx rules within the EMR. RESULTS The prediction model included age, sex, race, and 6 chronic diseases categorized by the Clinical Classifications Software for International Classification of Diseases, Ninth Revision codes (dyslipidemia, diabetes, peripheral atherosclerosis, disease of the blood-forming organs, coronary atherosclerosis and other heart diseases, and hypertension). Of the 2000 Biobank participants invited, 1013 (51%) provided blood samples, 256 (13%) declined participation, 555 (28%) did not respond, and 176 (9%) consented but did not provide a blood sample within the recruitment window (October 4, 2012, through March 20, 2013). Preemptive PGx testing included CYP2D6 genotyping and targeted sequencing of 84 PGx genes. Synchronous real-time CDS was integrated into the EMR and flagged potential patient-specific drug-gene interactions and provided therapeutic guidance. CONCLUSION This translational project provides an opportunity to begin to evaluate the impact of preemptive sequencing and EMR-driven genome-guided therapy. These interventions will improve understanding and implementation of genomic data in clinical practice.
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Affiliation(s)
| | - Janet E Olson
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN
| | | | - Richard M Weinshilboum
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN; Center for Individualized Medicine, Mayo Clinic, Rochester, MN
| | - Liewei Wang
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN
| | - Kelly J Lyke
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN
| | - Euijung Ryu
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN
| | - Paul V Targonski
- Division of Primary Care Internal Medicine, Mayo Clinic, Rochester, MN
| | | | | | - Paul Y Takahashi
- Division of Primary Care Internal Medicine, Mayo Clinic, Rochester, MN
| | - Jennifer B McCormick
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN; Center for Individualized Medicine, Mayo Clinic, Rochester, MN; Division of General Internal Medicine, Mayo Clinic, Rochester, MN
| | - Kiley J Johnson
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN
| | | | | | | | - Eric D Wieben
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN
| | - Gianrico Farrugia
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN; Division of Gastroenterology, Mayo Clinic, Rochester, MN
| | | | - Keri J Kruckeberg
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN
| | - Jamie K Bruflat
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN
| | - Lisa M Peterson
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN
| | - Joseph H Blommel
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN
| | - Jennifer M Skierka
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN
| | - Matthew J Ferber
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN
| | - John L Black
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN
| | - Linnea M Baudhuin
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN
| | - Eric W Klee
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN
| | - Jason L Ross
- Department of Information Technology, Mayo Clinic, Rochester, MN
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