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Johnson D, Del Fiol G, Kawamoto K, Romagnoli KM, Sanders N, Isaacson G, Jenkins E, Williams MS. Genetically guided precision medicine clinical decision support tools: a systematic review. J Am Med Inform Assoc 2024; 31:1183-1194. [PMID: 38558013 PMCID: PMC11031215 DOI: 10.1093/jamia/ocae033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 02/06/2024] [Accepted: 02/26/2024] [Indexed: 04/04/2024] Open
Abstract
OBJECTIVES Patient care using genetics presents complex challenges. Clinical decision support (CDS) tools are a potential solution because they provide patient-specific risk assessments and/or recommendations at the point of care. This systematic review evaluated the literature on CDS systems which have been implemented to support genetically guided precision medicine (GPM). MATERIALS AND METHODS A comprehensive search was conducted in MEDLINE and Embase, encompassing January 1, 2011-March 14, 2023. The review included primary English peer-reviewed research articles studying humans, focused on the use of computers to guide clinical decision-making and delivering genetically guided, patient-specific assessments, and/or recommendations to healthcare providers and/or patients. RESULTS The search yielded 3832 unique articles. After screening, 41 articles were identified that met the inclusion criteria. Alerts and reminders were the most common form of CDS used. About 27 systems were integrated with the electronic health record; 2 of those used standards-based approaches for genomic data transfer. Three studies used a framework to analyze the implementation strategy. DISCUSSION Findings include limited use of standards-based approaches for genomic data transfer, system evaluations that do not employ formal frameworks, and inconsistencies in the methodologies used to assess genetic CDS systems and their impact on patient outcomes. CONCLUSION We recommend that future research on CDS system implementation for genetically GPM should focus on implementing more CDS systems, utilization of standards-based approaches, user-centered design, exploration of alternative forms of CDS interventions, and use of formal frameworks to systematically evaluate genetic CDS systems and their effects on patient care.
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Affiliation(s)
- Darren Johnson
- Department of Genomic Health, Geisinger Health Systems, Danville, PA 17822, United States
| | - Guilherme Del Fiol
- Department of Biomedical Informatics, University of Utah, Salt Lake City, UT 84108, United States
| | - Kensaku Kawamoto
- Department of Biomedical Informatics, University of Utah, Salt Lake City, UT 84108, United States
| | - Katrina M Romagnoli
- Department of Genomic Health, Geisinger Health Systems, Danville, PA 17822, United States
| | - Nathan Sanders
- School of Medicine, Geisinger Health Systems, Danville, PA 17822, United States
| | - Grace Isaacson
- Family Medicine, Penn Highlands Healthcare, DuBois, PA 16830, United States
| | - Elden Jenkins
- School of Medicine, Noorda College of Osteopathic Medicine, Provo, UT 84606, United States
| | - Marc S Williams
- Department of Genomic Health, Geisinger Health Systems, Danville, PA 17822, United States
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Dolin RH, Shenvi E, Alvarez C, Barrows RC, Boxwala A, Lee B, Nathanson BH, Kleyner Y, Hagemann R, Hongsermeier T, Kapusnik-Uner J, Lakdawala A, Shalaby J. PillHarmonics: An Orchestrated Pharmacogenetics Medication Clinical Decision Support Service. Appl Clin Inform 2024; 15:378-387. [PMID: 38388174 PMCID: PMC11098593 DOI: 10.1055/a-2274-6763] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Accepted: 02/07/2024] [Indexed: 02/24/2024] Open
Abstract
OBJECTIVES Pharmacogenetics (PGx) is increasingly important in individualizing therapeutic management plans, but is often implemented apart from other types of medication clinical decision support (CDS). The lack of integration of PGx into existing CDS may result in incomplete interaction information, which may pose patient safety concerns. We sought to develop a cloud-based orchestrated medication CDS service that integrates PGx with a broad set of drug screening alerts and evaluate it through a clinician utility study. METHODS We developed the PillHarmonics service for implementation per the CDS Hooks protocol, algorithmically integrating a wide range of drug interaction knowledge using cloud-based screening services from First Databank (drug-drug/allergy/condition), PharmGKB (drug-gene), and locally curated content (drug-renal/hepatic/race). We performed a user study, presenting 13 clinicians and pharmacists with a prototype of the system's usage in synthetic patient scenarios. We collected feedback via a standard questionnaire and structured interview. RESULTS Clinician assessment of PillHarmonics via the Technology Acceptance Model questionnaire shows significant evidence of perceived utility. Thematic analysis of structured interviews revealed that aggregated knowledge, concise actionable summaries, and information accessibility were highly valued, and that clinicians would use the service in their practice. CONCLUSION Medication safety and optimizing efficacy of therapy regimens remain significant issues. A comprehensive medication CDS system that leverages patient clinical and genomic data to perform a wide range of interaction checking and presents a concise and holistic view of medication knowledge back to the clinician is feasible and perceived as highly valuable for more informed decision-making. Such a system can potentially address many of the challenges identified with current medication-related CDS.
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Affiliation(s)
| | - Edna Shenvi
- Elimu Informatics, El Cerrito, California, United States
| | - Carla Alvarez
- Elimu Informatics, El Cerrito, California, United States
| | | | - Aziz Boxwala
- Elimu Informatics, El Cerrito, California, United States
| | - Benson Lee
- College of Pharmacy, Touro University California, Vallejo, California, United States
| | | | - Yelena Kleyner
- Elimu Informatics, El Cerrito, California, United States
| | - Rachel Hagemann
- Independent Contractor, San Francisco, California, United States
| | | | | | | | - James Shalaby
- Elimu Informatics, El Cerrito, California, United States
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3
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Dolin RH, Gupta R, Newsom K, Heale BS, Gothi S, Starostik P, Chamala S. Automated HL7v2 LRI informatics framework for streamlining genomics-EHR data integration. J Pathol Inform 2023; 14:100330. [PMID: 37719179 PMCID: PMC10504540 DOI: 10.1016/j.jpi.2023.100330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 07/08/2023] [Accepted: 08/09/2023] [Indexed: 09/19/2023] Open
Abstract
While VCF formatted files are the lingua franca of next-generation sequencing, most EHRs do not provide native VCF support. As a result, labs often must send non-structured PDF reports to the EHR. On the other hand, while FHIR adoption is growing, most EHRs support HL7 interoperability standards, particularly those based on the HL7 Version 2 (HL7v2) standard. The HL7 Version 2 genomics component of the HL7 Laboratory Results Interface (HL7v2 LRI) standard specifies a formalism for the structured communication of genomic data from lab to EHR. We previously described an open-source tool (vcf2fhir) that converts VCF files into HL7 FHIR format. In this report, we describe how the utility has been extended to output HL7v2 LRI data that contains both variants and variant annotations (e.g., predicted phenotypes and therapeutic implications). Using this HL7v2 converter, we implemented an automated pipeline for moving structured genomic data from the clinical laboratory to EHR. We developed an open source hl7v2GenomicsExtractor that converts genomic interpretation report files into a series of HL7v2 observations conformant to HL7v2 LRI. We further enhanced the converter to produce output conformant to Epic's genomic import specification and to support alternative input formats. An automated pipeline for pushing standards-based structured genomic data directly into the EHR was successfully implemented, where genetic variant data and the clinical annotations are now both available to be viewed in the EHR through Epic's genomics module. Issues encountered in the development and deployment of the HL7v2 converter primarily revolved around data variability issues, primarily lack of a standardized representation of data elements within various genomic interpretation report files. The technical implementation of a HL7v2 message transformation to feed genomic variant and clinical annotation data into an EHR has been successful. In addition to genetic variant data, the implementation described here releases the valuable asset of clinically relevant genomic annotations provided by labs from static PDFs to calculable, structured data in EHR systems.
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Affiliation(s)
| | - Rohan Gupta
- Elimu Informatics, Inc, Richmond, CA, USA
- Department of Computer Science, Shri Mata Vaishno Devi University, Katra, Jammu and Kashmir, India
| | - Kimberly Newsom
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, FL, USA
| | | | - Shailesh Gothi
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, FL, USA
| | - Petr Starostik
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, FL, USA
| | - Srikar Chamala
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, FL, USA
- Department of Pathology and Laboratory Medicine, Children’s Hospital Los Angeles, CA, USA
- Department of Pathology, University of Southern California, CA, USA
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4
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Dolin RH, Heale BSE, Alterovitz G, Gupta R, Aronson J, Boxwala A, Gothi SR, Haines D, Hermann A, Hongsermeier T, Husami A, Jones J, Naeymi-Rad F, Rapchak B, Ravishankar C, Shalaby J, Terry M, Xie N, Zhang P, Chamala S. Introducing HL7 FHIR Genomics Operations: a developer-friendly approach to genomics-EHR integration. J Am Med Inform Assoc 2022; 30:485-493. [PMID: 36548217 PMCID: PMC9933060 DOI: 10.1093/jamia/ocac246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 11/16/2022] [Accepted: 12/02/2022] [Indexed: 12/24/2022] Open
Abstract
OBJECTIVE Enabling clinicians to formulate individualized clinical management strategies from the sea of molecular data remains a fundamentally important but daunting task. Here, we describe efforts towards a new paradigm in genomics-electronic health record (HER) integration, using a standardized suite of FHIR Genomics Operations that encapsulates the complexity of molecular data so that precision medicine solution developers can focus on building applications. MATERIALS AND METHODS FHIR Genomics Operations essentially "wrap" a genomics data repository, presenting a uniform interface to applications. More importantly, operations encapsulate the complexity of data within a repository and normalize redundant data representations-particularly relevant in genomics, where a tremendous amount of raw data exists in often-complex non-FHIR formats. RESULTS Fifteen FHIR Genomics Operations have been developed, designed to support a wide range of clinical scenarios, such as variant discovery; clinical trial matching; hereditary condition and pharmacogenomic screening; and variant reanalysis. Operations are being matured through the HL7 balloting process, connectathons, pilots, and the HL7 FHIR Accelerator program. DISCUSSION Next-generation sequencing can identify thousands to millions of variants, whose clinical significance can change over time as our knowledge evolves. To manage such a large volume of dynamic and complex data, new models of genomics-EHR integration are needed. Qualitative observations to date suggest that freeing application developers from the need to understand the nuances of genomic data, and instead base applications on standardized APIs can not only accelerate integration but also dramatically expand the applications of Omic data in driving precision care at scale for all.
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Affiliation(s)
- Robert H Dolin
- Corresponding Author: Robert H. Dolin, MD, Elimu Informatics, 1709 Julian Ct, El Cerrito, CA 94530, USA;
| | | | - Gil Alterovitz
- Brigham and Women’s Hospital, Boston, Massachusetts, USA,Harvard/MIT Division of Health Sciences and Technology, Harvard Medical School, Boston, Massachusetts, USA
| | - Rohan Gupta
- Shri Mata Vaishno Devi University, Katra, Jammu and Kashmir, India
| | | | | | - Shaileshbhai R Gothi
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, Florida, USA
| | - David Haines
- Leap of Faith Technologies, Libertyville, Illinois, USA
| | - Arthur Hermann
- Department of Health IT Strategy & Policy, Kaiser Permanente, Pasadena, California, USA
| | | | - Ammar Husami
- Division of Human Genetics, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, USA,Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
| | - James Jones
- Computational Health Informatics Program, Boston Children’s Hospital, Boston, Massachusetts, USA
| | | | | | | | | | - May Terry
- MITRE Corporation, McLean, Virginia, USA
| | - Ning Xie
- Biomedical Cybernetics Laboratory, Department of Medicine, Brigham and Women’s Hospital, Boston, Massachusetts, USA
| | - Powell Zhang
- Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Srikar Chamala
- Keck School of Medicine, Department of Pathology, University of Southern California, Los Angeles, California, USA,Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, California, USA
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Sukasem C, Jantararoungtong T, Koomdee N. Pharmacogenomics research and its clinical implementation in Thailand: Lessons learned from the resource-limited settings. Drug Metab Pharmacokinet 2021; 39:100399. [PMID: 34098253 DOI: 10.1016/j.dmpk.2021.100399] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 03/31/2021] [Accepted: 04/07/2021] [Indexed: 02/07/2023]
Abstract
Several barriers present challenges to implementing pharmacogenomics into practice. This review will provide an overview of the current pharmacogenomics practices and research in Thailand, address the challenges and lessons learned from delivering clinical pharmacogenomic services in Thailand, emphasize the pharmacogenomics implementation issues that must be overcome, and identify current pharmacogenomic initiatives and plans to facilitate clinical implementation of pharmacogenomics in Thailand. Ever since the pharmacogenomics research began in 2004 in Thailand, a multitude of pharmacogenomics variants associated with drug responses have been identified in the Thai population, such as HLA-B∗15:02 for carbamazepine and oxcarbazepine, HLA-B∗58:01 for allopurinol, HLA-B∗13:01 for dapsone and cotrimoxazole, CYP2B6 variants for efavirenz, CYP2C9∗3 for phenytoin and warfarin, CYP3A5∗3 for tacrolimus, and UGT1A1∗6 and UGT1A1∗28 for irinotecan, etc. The future of pharmacogenomics guided therapy in clinical settings across Thailand appears promising because of the availability of evidence of clinical validity of the pharmacogenomics testing and support for reimbursement of pharmacogenomics testing.
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Affiliation(s)
- Chonlaphat Sukasem
- Division of Pharmacogenomics and Personalized Medicine, Department of Pathology, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, 10400, Thailand; Laboratory for Pharmacogenomics, Somdech Phra Debaratana Medical Center (SDMC), Ramathibodi Hospital, Bangkok, 10400, Thailand; Bumrungrad International Hospital, Thailand.
| | - Thawinee Jantararoungtong
- Division of Pharmacogenomics and Personalized Medicine, Department of Pathology, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, 10400, Thailand; Laboratory for Pharmacogenomics, Somdech Phra Debaratana Medical Center (SDMC), Ramathibodi Hospital, Bangkok, 10400, Thailand
| | - Napatrupron Koomdee
- Division of Pharmacogenomics and Personalized Medicine, Department of Pathology, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, 10400, Thailand; Laboratory for Pharmacogenomics, Somdech Phra Debaratana Medical Center (SDMC), Ramathibodi Hospital, Bangkok, 10400, Thailand
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Karimi S, Jiang X, Dolin RH, Kim M, Boxwala A. A secure system for genomics clinical decision support. J Biomed Inform 2020; 112:103602. [PMID: 33080397 PMCID: PMC8577277 DOI: 10.1016/j.jbi.2020.103602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2020] [Revised: 09/07/2020] [Accepted: 10/12/2020] [Indexed: 11/26/2022]
Abstract
We developed a prototype genomic archiving and communications system to securely store genome data and provide clinical decision support (CDS). This system operates on a client-server model. The client encrypts the data, and the server stores data and performs the computations necessary for CDS. Computations are directly performed on encrypted data, and the client decrypts results. The server cannot decrypt inputs or outputs, which provides strong guarantees of security. We have validated our system with three genomics-based CDS applications. The results demonstrate that it is possible to resolve a long-standing dilemma in genomic data privacy and accessibility, by using a principled cryptographical framework and a mathematical representation of genome data and CDS questions.
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Affiliation(s)
| | - Xiaoqian Jiang
- UT Health School of Biomedical Informatics, Houston, TX, United States
| | | | - Miran Kim
- UT Health School of Biomedical Informatics, Houston, TX, United States
| | - Aziz Boxwala
- Elimu Informatics Inc., Richmond, CA, United States
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7
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Kanungo S, Barr J, Crutchfield P, Fealko C, Soares N. Ethical Considerations on Pediatric Genetic Testing Results in Electronic Health Records. Appl Clin Inform 2020; 11:755-763. [PMID: 33176390 DOI: 10.1055/s-0040-1718753] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
Abstract
BACKGROUND Advances in technology and access to expanded genetic testing have resulted in more children and adolescents receiving genetic testing for diagnostic and prognostic purposes. With increased adoption of the electronic health record (EHR), genetic testing is increasingly resulted in the EHR. However, this leads to challenges in both storage and disclosure of genetic results, particularly when parental results are combined with child genetic results. PRIVACY AND ETHICAL CONSIDERATIONS Accidental disclosure and erroneous documentation of genetic results can occur due to the nature of their presentation in the EHR and documentation processes by clinicians. Genetic information is both sensitive and identifying, and requires a considered approach to both timing and extent of disclosure to families and access to clinicians. METHODS This article uses an interdisciplinary approach to explore ethical issues surrounding privacy, confidentiality of genetic data, and access to genetic results by health care providers and family members, and provides suggestions in a stakeholder format for best practices on this topic for clinicians and informaticians. Suggestions are made for clinicians on documenting and accessing genetic information in the EHR, and on collaborating with genetics specialists and disclosure of genetic results to families. Additional considerations for families including ethics around results of adolescents and special scenarios for blended families and foster minors are also provided. Finally, administrators and informaticians are provided best practices on both institutional processes and EHR architecture, including security and access control, with emphasis on the minimum necessary paradigm and parent/patient engagement and control of the use and disclosure of data. CONCLUSION The authors hope that these best practices energize specialty societies to craft practice guidelines on genetic information management in the EHR with interdisciplinary input that addresses all stakeholder needs.
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Affiliation(s)
- Shibani Kanungo
- Pediatric and Adolescent Medicine, Western Michigan University Homer Stryker M.D. School of Medicine, Kalamazoo, Michigan, United States
| | - Jayne Barr
- Internal Medicine-Pediatrics, MetroHealth, Cleveland, Ohio, United States
| | - Parker Crutchfield
- Medical Ethics, Humanities, and Law, Western Michigan University Homer Stryker M.D. School of Medicine, Kalamazoo, Michigan, United States
| | - Casey Fealko
- Pediatric and Adolescent Medicine, Western Michigan University Homer Stryker M.D. School of Medicine, Kalamazoo, Michigan, United States
| | - Neelkamal Soares
- Pediatric and Adolescent Medicine, Western Michigan University Homer Stryker M.D. School of Medicine, Kalamazoo, Michigan, United States
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