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Blagec K, Swen JJ, Koopmann R, Cheung KC, Crommentuijn-van Rhenen M, Holsappel I, Konta L, Ott S, Steinberger D, Xu H, Cecchin E, Dolžan V, Dávila-Fajardo CL, Patrinos GP, Sunder-Plassmann G, Turner RM, Pirmohamed M, Guchelaar HJ, Samwald M. Pharmacogenomics decision support in the U-PGx project: Results and advice from clinical implementation across seven European countries. PLoS One 2022; 17:e0268534. [PMID: 35675343 PMCID: PMC9176797 DOI: 10.1371/journal.pone.0268534] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Accepted: 04/26/2022] [Indexed: 12/18/2022] Open
Abstract
Background The clinical implementation of pharmacogenomics (PGx) could be one of the first milestones towards realizing personalized medicine in routine care. However, its widespread adoption requires the availability of suitable clinical decision support (CDS) systems, which is often impeded by the fragmentation or absence of adequate health IT infrastructures. We report results of CDS implementation in the large-scale European research project Ubiquitous Pharmacogenomics (U-PGx), in which PGx CDS was rolled out and evaluated across more than 15 clinical sites in the Netherlands, Spain, Slovenia, Italy, Greece, United Kingdom and Austria, covering a wide variety of healthcare settings. Methods We evaluated the CDS implementation process through qualitative and quantitative process indicators. Quantitative indicators included statistics on generated PGx reports, median time from sampled upload until report delivery and statistics on report retrievals via the mobile-based CDS tool. Adoption of different CDS tools, uptake and usability were further investigated through a user survey among healthcare providers. Results of a risk assessment conducted prior to the implementation process were retrospectively analyzed and compared to actual encountered difficulties and their impact. Results As of March 2021, personalized PGx reports were produced from 6884 genotyped samples with a median delivery time of twenty minutes. Out of 131 invited healthcare providers, 65 completed the questionnaire (response rate: 49.6%). Overall satisfaction rates with the different CDS tools varied between 63.6% and 85.2% per tool. Delays in implementation were caused by challenges including institutional factors and complexities in the development of required tools and reference data resources, such as genotype-phenotype mappings. Conclusions We demonstrated the feasibility of implementing a standardized PGx decision support solution in a multinational, multi-language and multi-center setting. Remaining challenges for future wide-scale roll-out include the harmonization of existing PGx information in guidelines and drug labels, the need for strategies to lower the barrier of PGx CDS adoption for healthcare institutions and providers, and easier compliance with regulatory and legal frameworks.
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Affiliation(s)
- Kathrin Blagec
- Institute of Artificial Intelligence, Center for Medical Statistics, Informatics, and Intelligent Systems, Medical University of Vienna, Vienna, Austria
| | - Jesse J Swen
- Department of Clinical Pharmacy & Toxicology, Leiden University Medical Center, Leiden, The Netherlands
| | - Rudolf Koopmann
- Diagnosticum Center for Human Genetics, Frankfurt am Main, Germany.,Institute for Human Genetics, Justus Liebig University, Giessen, Germany
| | - Ka-Chun Cheung
- Medicines Information Centre, Royal Dutch Pharmacists Association (KNMP), The Hague, The Netherlands
| | | | - Inge Holsappel
- Medicines Information Centre, Royal Dutch Pharmacists Association (KNMP), The Hague, The Netherlands
| | - Lidija Konta
- Diagnosticum Center for Human Genetics, Frankfurt am Main, Germany
| | - Simon Ott
- Institute of Artificial Intelligence, Center for Medical Statistics, Informatics, and Intelligent Systems, Medical University of Vienna, Vienna, Austria
| | - Daniela Steinberger
- Diagnosticum Center for Human Genetics, Frankfurt am Main, Germany.,Institute for Human Genetics, Justus Liebig University, Giessen, Germany
| | - Hong Xu
- Institute of Artificial Intelligence, Center for Medical Statistics, Informatics, and Intelligent Systems, Medical University of Vienna, Vienna, Austria
| | - Erika Cecchin
- Experimental and Clinical Pharmacology Unit, Centro di Riferimento Oncologico di Aviano (CRO) IRCCS, Aviano, Italy
| | - Vita Dolžan
- Faculty of Medicine, Institute of Biochemistry and Molecular Genetics, Pharmacogenetics Laboratory, University of Ljubljana, Ljubljana, Slovenia
| | - Cristina Lucía Dávila-Fajardo
- Clinical Pharmacy Department, Hospital Universitario Virgen de las Nieves, Instituto de Investigación Biosanitaria Granada (Ibs.Granada), Granada, Spain
| | - George P Patrinos
- Department of Pharmacy, Laboratory of Pharmacogenomics and Individualized Therapy, University of Patras School of Health Sciences, Patras, Greece
| | - Gere Sunder-Plassmann
- Division of Nephrology and Dialysis, Department of Internal Medicine III, Medical University of Vienna, Vienna, Austria
| | - Richard M Turner
- The Wolfson Centre for Personalised Medicine, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Munir Pirmohamed
- Department of Molecular and Clinical Pharmacology, Royal Liverpool University Hospital and University of Liverpool, Liverpool, United Kingdom
| | - Henk-Jan Guchelaar
- Department of Clinical Pharmacy & Toxicology, Leiden University Medical Center, Leiden, The Netherlands
| | - Matthias Samwald
- Institute of Artificial Intelligence, Center for Medical Statistics, Informatics, and Intelligent Systems, Medical University of Vienna, Vienna, Austria
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Watkins M, Rynearson S, Henrie A, Eilbeck K. Implementing the VMC Specification to Reduce Ambiguity in Genomic Variant Representation. AMIA ... ANNUAL SYMPOSIUM PROCEEDINGS. AMIA SYMPOSIUM 2020; 2019:1226-1235. [PMID: 32308920 PMCID: PMC7153148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Current methods used for representing biological sequence variants allow flexibility, which has created redundancy within variant archives and discordance among variant representation tools. While research methodologies have been able to adapt to this ambiguity, strict clinical standards make it difficult to use this data in what would otherwise be useful clinical interventions. We implemented a specification developed by the GA4GH Variant Modeling Collaboration (VMC), which details a new approach to unambiguous representation of variants at the allelic level, as a haplotype, or as a genotype. Our implementation, called the VMC Test Suite (http://vcfclin.org), offers web tools to generate and insert VMC identifiers into a VCF file and to generate a VMC bundle JSON representation of a VCF file or HGVS expression. A command line tool with similar functionality is also introduced. These tools facilitate use of this standard-an important step toward reliable querying of variants and their associated annotations.
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Affiliation(s)
- Michael Watkins
- Biomedical Informatics, 421 Wakara Way, University of Utah, Salt Lake City, Utah 84108
| | - Shawn Rynearson
- Biomedical Informatics, 421 Wakara Way, University of Utah, Salt Lake City, Utah 84108
| | - Alex Henrie
- Biomedical Informatics, 421 Wakara Way, University of Utah, Salt Lake City, Utah 84108
| | - Karen Eilbeck
- Biomedical Informatics, 421 Wakara Way, University of Utah, Salt Lake City, Utah 84108
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3
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Nguyen KA, Patel H, Haggstrom DA, Zillich AJ, Imperiale TF, Russ AL. Utilizing a user-centered approach to develop and assess pharmacogenomic clinical decision support for thiopurine methyltransferase. BMC Med Inform Decis Mak 2019; 19:194. [PMID: 31623616 PMCID: PMC6798472 DOI: 10.1186/s12911-019-0919-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Accepted: 09/20/2019] [Indexed: 11/10/2022] Open
Abstract
Background A pharmacogenomic clinical decision support tool (PGx-CDS) for thiopurine medications can help physicians incorporate pharmacogenomic results into prescribing decisions by providing up-to-date, real-time decision support. However, the PGx-CDS user interface may introduce errors and promote alert fatigue. The objective of this study was to develop and evaluate a prototype of a PGx-CDS user interface for thiopurine medications with user-centered design methods. Methods This study had two phases: In phase I, we conducted qualitative interviews to assess providers’ information needs. Interview transcripts were analyzed through a combination of inductive and deductive qualitative analysis to develop design requirements for a PGx-CDS user interface. Using these requirements, we developed a user interface prototype and evaluated its usability (phase II). Results In total, 14 providers participated: 10 were interviewed in phase I, and seven providers completed usability testing in phase II (3 providers participated in both phases). Most (90%) participants were interested in PGx-CDS systems to help improve medication efficacy and patient safety. Interviews yielded 11 themes sorted into two main categories: 1) health care providers’ views on PGx-CDS and 2) important design features for PGx-CDS. We organized these findings into guidance for PGx-CDS content and display. Usability testing of the PGx-CDS prototype showed high provider satisfaction. Conclusion This is one of the first studies to utilize a user-centered design approach to develop and assess a PGx-CDS interface prototype for Thiopurine Methyltransferase (TPMT). This study provides guidance for the development of a PGx-CDS, and particularly for biomarkers such as TPMT.
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Affiliation(s)
- Khoa A Nguyen
- Department of Pharmacotherapy and Translational Research, University of Florida, College of Pharmacy, 1225 Center Drive, Gainesville, FL, 32610, USA. .,Center for Health Services Research, Regenstrief Institute Inc., 1101 W 10th St, Indianapolis, IN, USA. .,Center for Health Information and Communication, Department of Veterans Affairs (VA), Veterans Health Administration, Health Services Research and Development Service (CIN 13-416), Richard L. Roudebush VA Medical Center, 1481 W 10th St, Indianapolis, IN, 46202, USA. .,Department of Pharmacy Practice, College of Pharmacy, Purdue University, 640 Eskenazi Avenue, Indianapolis, IN, USA.
| | - Himalaya Patel
- Center for Health Information and Communication, Department of Veterans Affairs (VA), Veterans Health Administration, Health Services Research and Development Service (CIN 13-416), Richard L. Roudebush VA Medical Center, 1481 W 10th St, Indianapolis, IN, 46202, USA
| | - David A Haggstrom
- Center for Health Services Research, Regenstrief Institute Inc., 1101 W 10th St, Indianapolis, IN, USA.,Center for Health Information and Communication, Department of Veterans Affairs (VA), Veterans Health Administration, Health Services Research and Development Service (CIN 13-416), Richard L. Roudebush VA Medical Center, 1481 W 10th St, Indianapolis, IN, 46202, USA.,Department of Medicine, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Alan J Zillich
- Department of Pharmacy Practice, College of Pharmacy, Purdue University, 640 Eskenazi Avenue, Indianapolis, IN, USA
| | - Thomas F Imperiale
- Center for Health Services Research, Regenstrief Institute Inc., 1101 W 10th St, Indianapolis, IN, USA.,Center for Health Information and Communication, Department of Veterans Affairs (VA), Veterans Health Administration, Health Services Research and Development Service (CIN 13-416), Richard L. Roudebush VA Medical Center, 1481 W 10th St, Indianapolis, IN, 46202, USA.,Department of Medicine, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Alissa L Russ
- Center for Health Information and Communication, Department of Veterans Affairs (VA), Veterans Health Administration, Health Services Research and Development Service (CIN 13-416), Richard L. Roudebush VA Medical Center, 1481 W 10th St, Indianapolis, IN, 46202, USA.,Department of Pharmacy Practice, College of Pharmacy, Purdue University, 640 Eskenazi Avenue, Indianapolis, IN, USA
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Perera-Bel J, Hutter B, Heining C, Bleckmann A, Fröhlich M, Fröhling S, Glimm H, Brors B, Beißbarth T. From somatic variants towards precision oncology: Evidence-driven reporting of treatment options in molecular tumor boards. Genome Med 2018; 10:18. [PMID: 29544535 PMCID: PMC5856211 DOI: 10.1186/s13073-018-0529-2] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Accepted: 02/28/2018] [Indexed: 01/11/2023] Open
Abstract
Background A comprehensive understanding of cancer has been furthered with technological improvements and decreasing costs of next-generation sequencing (NGS). However, the complexity of interpreting genomic data is hindering the implementation of high-throughput technologies in the clinical context: increasing evidence on gene–drug interactions complicates the task of assigning clinical significance to genomic variants. Methods Here we present a method that automatically matches patient-specific genomic alterations to treatment options. The method relies entirely on public knowledge of somatic variants with predictive evidence on drug response. The output report is aimed at supporting clinicians in the task of finding the clinical meaning of genomic variants. We applied the method to 1) The Cancer Genome Atlas (TCGA) and Genomics Evidence Neoplasia Information Exchange (GENIE) cohorts and 2) 11 patients from the NCT MASTER trial whose treatment discussions included information on their genomic profiles. Results Our reporting strategy showed a substantial number of patients with actionable variants in the analyses of TCGA and GENIE samples. Notably, it was able to reproduce experts’ treatment suggestions in a retrospective study of 11 patients from the NCT MASTER trial. Our results establish a proof of concept for comprehensive, evidence-based reports as a supporting tool for discussing treatment options in tumor boards. Conclusions We believe that a standardized method to report actionable somatic variants will smooth the incorporation of NGS in the clinical context. We anticipate that tools like the one we present here will become essential in summarizing for clinicians the growing evidence in the field of precision medicine. The R code of the presented method is provided in Additional file 6 and available at https://github.com/jperera-bel/MTB-Report. Electronic supplementary material The online version of this article (10.1186/s13073-018-0529-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Júlia Perera-Bel
- Department of Medical Statistics, University Medical Center Göttingen, 37073, Göttingen, Germany
| | - Barbara Hutter
- Division Applied Bioinformatics, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT), 69120, Heidelberg, Germany
| | - Christoph Heining
- Division Translational Oncology, National Center for Tumor Diseases (NCT) and German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
| | - Annalen Bleckmann
- Department of Medical Statistics, University Medical Center Göttingen, 37073, Göttingen, Germany.,Department of Hematology and Medical Oncology, University Medical Center Göttingen, 37075, Göttingen, Germany
| | - Martina Fröhlich
- Division Applied Bioinformatics, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT), 69120, Heidelberg, Germany
| | - Stefan Fröhling
- Division Translational Oncology, National Center for Tumor Diseases (NCT) and German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany.,German Cancer Consortium (DKTK), 69120, Heidelberg, Germany
| | - Hanno Glimm
- German Cancer Consortium (DKTK), 69120, Heidelberg, Germany.,Department of Translational Medical Oncology, NCT-Dresden, University Hospital, Carl Gustav Carus, Technische Universität Dresden, 01307 Dresden and DKFZ, Heidelberg, 69120, Germany
| | - Benedikt Brors
- Division Applied Bioinformatics, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT), 69120, Heidelberg, Germany
| | - Tim Beißbarth
- Department of Medical Statistics, University Medical Center Göttingen, 37073, Göttingen, Germany.
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5
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Al Kawam A, Sen A, Datta A, Dickey N. Understanding the Bioinformatics Challenges of Integrating Genomics into Healthcare. IEEE J Biomed Health Inform 2017; 22:1672-1683. [PMID: 29990071 DOI: 10.1109/jbhi.2017.2778263] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Genomic data is paving the way towards personalized healthcare. By unveiling genetic disease-contributing factors, genomic data can aid in the detection, diagnosis, and treatment of a wide range of complex diseases. Integrating genomic data into healthcare is riddled with a wide range of challenges spanning social, ethical, legal, educational, economic, and technical aspects. Bioinformatics is a core integration aspect presenting an overwhelming number of unaddressed challenges. In this paper we tackle the fundamental bioinformatics integration concerns including: genomic data generation, storage, representation, and utilization in conjunction with clinical data. We divide the bioinformatics challenges into a series of seven intertwined integration aspects spanning the areas of informatics, knowledge management, and communication. For each aspect, we provide a detailed discussion of the current research directions, outstanding challenges, and possible resolutions. This paper seeks to help narrow the gap between the genomic applications, which are being predominantly utilized in research settings, and the clinical adoption of these applications.
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6
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Johnson A, Khotskaya YB, Brusco L, Zeng J, Holla V, Bailey AM, Litzenburger BC, Sanchez N, Shufean MA, Piha-Paul S, Subbiah V, Hong D, Routbort M, Broaddus R, Mills Shaw KR, Mills GB, Mendelsohn J, Meric-Bernstam F. Clinical Use of Precision Oncology Decision Support. JCO Precis Oncol 2017; 2017. [PMID: 30320296 DOI: 10.1200/po.17.00036] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
PURPOSE Precision oncology is hindered by the lack of decision support for determining the functional and therapeutic significance of genomic alterations in tumors and relevant clinically available options. To bridge this knowledge gap, we established a Precision Oncology Decision Support (PODS) team that provides annotations at the alteration-level and subsequently determined if clinical decision-making was influenced. METHODS Genomic alterations were annotated to determine actionability based on a variant's known or potential functional and/or therapeutic significance. The medical records of a subset of patients annotated in 2015 were manually reviewed to assess trial enrollment. A web-based survey was implemented to capture the reasons why genotype-matched therapies were not pursued. RESULTS PODS processed 1,669 requests for annotation of 4,084 alterations (2,254 unique) across 49 tumor types for 1,197 patients. 2,444 annotations for 669 patients included an actionable variant call: 32.5% actionable, 9.4% potentially, 29.7% unknown, 28.4% non-actionable. 66% of patients had at least one actionable/potentially actionable alteration. 20.6% (110/535) patients annotated enrolled on a genotype-matched trial. Trial enrolment was significantly higher for patients with actionable/potentially actionable alterations (92/333, 27.6%) than those with unknown (16/136, 11.8%) and non-actionable (2/66, 3%) alterations (p=0.00004). Actionable alterations in PTEN, PIK3CA, and ERBB2 most frequently led to enrollment on genotype-matched trials. Clinicians cited a variety of reasons why patients with actionable alterations did not enroll on trials. CONCLUSION Over half of alterations annotated were of unknown significance or non-actionable. Physicians were more likely to enroll a patient on a genotype-matched trial when an annotation supported actionability. Future studies are needed to demonstrate the impact of decision support on trial enrollment and oncologic outcomes.
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Affiliation(s)
- Amber Johnson
- Sheikh Khalifa Bin Zayed Al Nahyan Institute for Personalized Cancer Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Yekaterina B Khotskaya
- Sheikh Khalifa Bin Zayed Al Nahyan Institute for Personalized Cancer Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Lauren Brusco
- Sheikh Khalifa Bin Zayed Al Nahyan Institute for Personalized Cancer Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jia Zeng
- Sheikh Khalifa Bin Zayed Al Nahyan Institute for Personalized Cancer Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Vijaykumar Holla
- Sheikh Khalifa Bin Zayed Al Nahyan Institute for Personalized Cancer Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Ann M Bailey
- Sheikh Khalifa Bin Zayed Al Nahyan Institute for Personalized Cancer Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Beate C Litzenburger
- Sheikh Khalifa Bin Zayed Al Nahyan Institute for Personalized Cancer Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Nora Sanchez
- Sheikh Khalifa Bin Zayed Al Nahyan Institute for Personalized Cancer Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Md Abu Shufean
- Sheikh Khalifa Bin Zayed Al Nahyan Institute for Personalized Cancer Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Sarina Piha-Paul
- Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Vivek Subbiah
- Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - David Hong
- Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Mark Routbort
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Russell Broaddus
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Kenna R Mills Shaw
- Sheikh Khalifa Bin Zayed Al Nahyan Institute for Personalized Cancer Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Gordon B Mills
- Sheikh Khalifa Bin Zayed Al Nahyan Institute for Personalized Cancer Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.,Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - John Mendelsohn
- Sheikh Khalifa Bin Zayed Al Nahyan Institute for Personalized Cancer Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.,Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Funda Meric-Bernstam
- Sheikh Khalifa Bin Zayed Al Nahyan Institute for Personalized Cancer Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.,Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.,Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
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Khelifi M, Tarczy-Hornoch P, Devine EB, Pratt W. Design Recommendations for Pharmacogenomics Clinical Decision Support Systems. AMIA JOINT SUMMITS ON TRANSLATIONAL SCIENCE PROCEEDINGS. AMIA JOINT SUMMITS ON TRANSLATIONAL SCIENCE 2017; 2017:237-246. [PMID: 28815136 PMCID: PMC5543362] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
The use of pharmacogenomics (PGx) in clinical practice still faces challenges to fully adopt genetic information in targeting drug therapy. To incorporate genetics into clinical practice, many support the use of Pharmacogenomics Clinical Decision Support Systems (PGx-CDS) for medication prescriptions. This support was fueled by new guidelines to incorporate genetics for optimizing drug dosage and reducing adverse events. In addition, the complexity of PGx led to exploring CDS outside the paradigm of the basic CDS tools embedded in commercial electronic health records. Therefore, designing the right CDS is key to unleashing the full potential of pharmacogenomics and making it a part of clinicians' daily workflow. In this work, we 1) identify challenges and barriers of the implementation of PGx-CDS in clinical settings, 2) develop a new design approach to CDS with functional characteristics that can improve the adoption of pharmacogenomics guidelines and thus patient safety, and 3) create design guidelines and recommendations for such PGx-CDS tools.
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Banjar H, Adelson D, Brown F, Chaudhri N. Intelligent Techniques Using Molecular Data Analysis in Leukaemia: An Opportunity for Personalized Medicine Support System. BIOMED RESEARCH INTERNATIONAL 2017; 2017:3587309. [PMID: 28812013 PMCID: PMC5547708 DOI: 10.1155/2017/3587309] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Revised: 06/12/2017] [Accepted: 06/15/2017] [Indexed: 12/05/2022]
Abstract
The use of intelligent techniques in medicine has brought a ray of hope in terms of treating leukaemia patients. Personalized treatment uses patient's genetic profile to select a mode of treatment. This process makes use of molecular technology and machine learning, to determine the most suitable approach to treating a leukaemia patient. Until now, no reviews have been published from a computational perspective concerning the development of personalized medicine intelligent techniques for leukaemia patients using molecular data analysis. This review studies the published empirical research on personalized medicine in leukaemia and synthesizes findings across studies related to intelligence techniques in leukaemia, with specific attention to particular categories of these studies to help identify opportunities for further research into personalized medicine support systems in chronic myeloid leukaemia. A systematic search was carried out to identify studies using intelligence techniques in leukaemia and to categorize these studies based on leukaemia type and also the task, data source, and purpose of the studies. Most studies used molecular data analysis for personalized medicine, but future advancement for leukaemia patients requires molecular models that use advanced machine-learning methods to automate decision-making in treatment management to deliver supportive medical information to the patient in clinical practice.
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Affiliation(s)
- Haneen Banjar
- School of Computer Science, University of Adelaide, Adelaide, SA, Australia
- Department of Computer Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - David Adelson
- School of Molecular and Biomedical Science, University of Adelaide, Adelaide, SA, Australia
| | - Fred Brown
- School of Computer Science, University of Adelaide, Adelaide, SA, Australia
| | - Naeem Chaudhri
- Oncology Centre, Section of Hematology, HSCT, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
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Disclosing Genetic Risk for Coronary Heart Disease: Attitudes Toward Personal Information in Health Records. Am J Prev Med 2017; 52:499-506. [PMID: 28062272 PMCID: PMC5362329 DOI: 10.1016/j.amepre.2016.11.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/27/2016] [Revised: 08/30/2016] [Accepted: 11/04/2016] [Indexed: 01/25/2023]
Abstract
INTRODUCTION Incorporating genetic risk information in electronic health records (EHRs) will facilitate implementation of genomic medicine in clinical practice. However, little is known about patients' attitudes toward incorporation of genetic risk information as a component of personal health information in EHRs. This study investigated whether disclosure of a genetic risk score (GRS) for coronary heart disease influences attitudes toward incorporation of personal health information including genetic risk in EHRs. METHODS Participants aged 45-65 years with intermediate 10-year coronary heart disease risk were randomized to receive a conventional risk score (CRS) alone or with a GRS from a genetic counselor, followed by shared decision making with a physician using the same standard presentation and information templates for all study participants. The CRS and GRS were then incorporated into the EHR and made accessible to both patients and physicians. Baseline and post-disclosure surveys were completed to assess whether attitudes differed by GRS disclosure. Data were collected from 2013 to 2015 and analyzed in 2015-2016. RESULTS GRS and CRS participants reported similar positive attitudes toward incorporation of genetic risk information in the EHR. Compared with CRS participants, participants with high GRS were more concerned about the confidentiality of genetic risk information (OR=3.67, 95% CI=1.29, 12.32, p=0.01). Post-disclosure, frequency of patient portal access was associated with positive attitudes. CONCLUSIONS Participants in this study of coronary heart disease risk disclosure overall had positive attitudes toward incorporation of genetic risk information in EHRs, although those who received genetic risk information had concerns about confidentiality.
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10
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Nadkarni GN, Horowitz CR. Genomics in CKD: Is This the Path Forward? Adv Chronic Kidney Dis 2016; 23:120-4. [PMID: 26979150 DOI: 10.1053/j.ackd.2016.01.017] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2016] [Accepted: 01/26/2016] [Indexed: 01/13/2023]
Abstract
Recent advances in genomics and sequencing technology have led to a better understanding of genetic risk in CKD. Genetics could account in part for racial differences in treatment response for medications including antihypertensives and immunosuppressive medications due to its correlation with ancestry. However, there is still a substantial lag between generation of this knowledge and its adoption in routine clinical care. This review summarizes the recent advances in genomics and CKD, discusses potential reasons for its underutilization, and highlights potential avenues for application of genomic information to improve clinical care and outcomes in this particularly vulnerable population.
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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] [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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12
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Dougherty MJ, Wicklund C, Johansen Taber KA. Challenges and Opportunities for Genomics Education: Insights from an Institute of Medicine Roundtable Activity. THE JOURNAL OF CONTINUING EDUCATION IN THE HEALTH PROFESSIONS 2016; 36:82-85. [PMID: 26954250 DOI: 10.1097/ceh.0000000000000019] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Despite the growing availability of genomic tools for clinical care, many health care providers experience gaps in genomics knowledge and skills that serve as impediments to widespread and appropriate integration of genomics into routine care. A workshop recently held by the Institute of Medicine (IOM) Roundtable on Translating Genomics-Based Research for Health explored 1) the barriers that result in a perception among health care providers that the need for genomics education is not urgent and 2) the drivers that may spur a change in that attitude. This commentary promotes continuing and graduate education-informed by an awareness of barriers, drivers, and best practices-as the most effective approaches for preparing the workforce for genomic medicine and ultimately improving patient care, and argues that the time for education is now.
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Affiliation(s)
- Michael J Dougherty
- Dr. Dougherty: Director of Education, American Society of Human Genetics, Bethesda, MD and Adjoint Associate Professor, Department of Pediatrics, University of Colorado School of Medicine, Aurora, CO. Ms. Wicklund: Director, Graduate Program in Genetic Counseling, Feinberg School of Medicine, Northwestern University, Chicago, IL. Dr. Johansen Taber: Director of Personalized Medicine, American Medical Association, Chicago, IL
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13
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Efron PA, Mohr AM, Moore FA, Moldawer LL. The future of murine sepsis and trauma research models. J Leukoc Biol 2015; 98:945-52. [PMID: 26034205 PMCID: PMC4661039 DOI: 10.1189/jlb.5mr0315-127r] [Citation(s) in RCA: 82] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2015] [Revised: 04/24/2015] [Accepted: 05/06/2015] [Indexed: 12/23/2022] Open
Abstract
Recent comparisons of the murine and human transcriptome in health and disease have called into question the appropriateness of the use of murine models for human sepsis and trauma research. More specifically, researchers have debated the suitability of mouse models of severe inflammation that is intended for eventual translation to human patients. This mini-review outlines this recent research, as well as specifically defines the arguments for and against murine models of sepsis and trauma research based on these transcriptional studies. In addition, we review newer advancements in murine models of infection and injury and define what we envision as an evolving but viable future for murine studies of sepsis and trauma.
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Affiliation(s)
- Philip A Efron
- Department of Surgery, University of Florida College of Medicine, Gainesville, Florida, USA
| | - Alicia M Mohr
- Department of Surgery, University of Florida College of Medicine, Gainesville, Florida, USA
| | - Frederick A Moore
- Department of Surgery, University of Florida College of Medicine, Gainesville, Florida, USA
| | - Lyle L Moldawer
- Department of Surgery, University of Florida College of Medicine, Gainesville, Florida, USA
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14
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Mathias B, Lipori G, Moldawer LL, Efron PA. Integrating "big data" into surgical practice. Surgery 2015; 159:371-4. [PMID: 26603852 DOI: 10.1016/j.surg.2015.08.043] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2015] [Accepted: 08/12/2015] [Indexed: 12/19/2022]
Abstract
'Big data' is the next frontier of medicine. We now have the ability to generate and analyze large quantities of healthcare data. Although interpreting and integrating this information into clinical practice poses many challenges, the potential benefits of personalized medicine are seemingly without limit.
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Affiliation(s)
- Brittany Mathias
- Department of Surgery, University of Florida College of Medicine, Gainesville, FL
| | - Gigi Lipori
- University of Florida Health and Shands Hospital, Gainesville, FL
| | - Lyle L Moldawer
- Department of Surgery, University of Florida College of Medicine, Gainesville, FL
| | - Philip A Efron
- Department of Surgery, University of Florida College of Medicine, Gainesville, FL.
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15
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Johnson A, Zeng J, Bailey AM, Holla V, Litzenburger B, Lara-Guerra H, Mills GB, Mendelsohn J, Shaw KR, Meric-Bernstam F. The right drugs at the right time for the right patient: the MD Anderson precision oncology decision support platform. Drug Discov Today 2015; 20:1433-8. [PMID: 26148707 DOI: 10.1016/j.drudis.2015.05.013] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2015] [Revised: 05/08/2015] [Accepted: 05/27/2015] [Indexed: 02/07/2023]
Abstract
The development of resources for clinical interpretation of cancer-associated genetic alterations has significantly lagged behind the technical developments enabling their detection in a time- and cost-efficient manner. The lack of scientific and informatics decision support for oncologists can lead to no action being taken or suboptimal therapeutic choices being made, which could affect the clinical outcome of a patient as well as convoluting research findings from clinical trials. In this article, we describe the precision oncology decision support (PODS) platform developed within The Sheikh Khalifa Bin Zayed Al Nahyan Institute for Personalized Cancer Therapy (IPCT) at MD Anderson Cancer Center; the platform aims to bridge the gap between molecular alteration detection and identification of appropriate treatments.
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Affiliation(s)
- Amber Johnson
- Sheikh Khalifa Al Nahyan Ben Zayed Institute for Personalized Cancer Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Jia Zeng
- Sheikh Khalifa Al Nahyan Ben Zayed Institute for Personalized Cancer Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Ann M Bailey
- Sheikh Khalifa Al Nahyan Ben Zayed Institute for Personalized Cancer Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Vijaykumar Holla
- Sheikh Khalifa Al Nahyan Ben Zayed Institute for Personalized Cancer Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Beate Litzenburger
- Sheikh Khalifa Al Nahyan Ben Zayed Institute for Personalized Cancer Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Humberto Lara-Guerra
- Sheikh Khalifa Al Nahyan Ben Zayed Institute for Personalized Cancer Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Gordon B Mills
- Sheikh Khalifa Al Nahyan Ben Zayed Institute for Personalized Cancer Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - John Mendelsohn
- Sheikh Khalifa Al Nahyan Ben Zayed Institute for Personalized Cancer Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Kenna R Shaw
- Sheikh Khalifa Al Nahyan Ben Zayed Institute for Personalized Cancer Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Funda Meric-Bernstam
- Sheikh Khalifa Al Nahyan Ben Zayed Institute for Personalized Cancer Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
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16
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Welch BM, Rodriguez Loya S, Eilbeck K, Kawamoto K. A proposed clinical decision support architecture capable of supporting whole genome sequence information. J Pers Med 2015; 4:176-99. [PMID: 25411644 PMCID: PMC4234046 DOI: 10.3390/jpm4020176] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Whole genome sequence (WGS) information may soon be widely available to help clinicians personalize the care and treatment of patients. However, considerable barriers exist, which may hinder the effective utilization of WGS information in a routine clinical care setting. Clinical decision support (CDS) offers a potential solution to overcome such barriers and to facilitate the effective use of WGS information in the clinic. However, genomic information is complex and will require significant considerations when developing CDS capabilities. As such, this manuscript lays out a conceptual framework for a CDS architecture designed to deliver WGS-guided CDS within the clinical workflow. To handle the complexity and breadth of WGS information, the proposed CDS framework leverages service-oriented capabilities and orchestrates the interaction of several independently-managed components. These independently-managed components include the genome variant knowledge base, the genome database, the CDS knowledge base, a CDS controller and the electronic health record (EHR). A key design feature is that genome data can be stored separately from the EHR. This paper describes in detail: (1) each component of the architecture; (2) the interaction of the components; and (3) how the architecture attempts to overcome the challenges associated with WGS information. We believe that service-oriented CDS capabilities will be essential to using WGS information for personalized medicine.
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Affiliation(s)
- Brandon M. Welch
- Program in Personalized Health Care, University of Utah, 15 North 2030 East, EIHG Room 2110, Salt Lake City, UT 84112, USA
- Department of Biomedical Informatics, University of Utah, 26 South 2000 East, Room 5775 HSEB, Salt Lake City, UT 84112, USA; E-Mails: (K.E.); (K.K.)
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +1-585-455-0461
| | - Salvador Rodriguez Loya
- School of Engineering and Informatics, University of Sussex, Shawcross Building, Room Gc4, Falmer, Brighton, East Sussex, BN1 9QT, UK; E-Mail:
| | - Karen Eilbeck
- Department of Biomedical Informatics, University of Utah, 26 South 2000 East, Room 5775 HSEB, Salt Lake City, UT 84112, USA; E-Mails: (K.E.); (K.K.)
| | - Kensaku Kawamoto
- Department of Biomedical Informatics, University of Utah, 26 South 2000 East, Room 5775 HSEB, Salt Lake City, UT 84112, USA; E-Mails: (K.E.); (K.K.)
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Dunnenberger HM, Crews KR, Hoffman JM, Caudle KE, Broeckel U, Howard SC, Hunkler RJ, Klein TE, Evans WE, Relling MV. Preemptive clinical pharmacogenetics implementation: current programs in five US medical centers. Annu Rev Pharmacol Toxicol 2014; 55:89-106. [PMID: 25292429 DOI: 10.1146/annurev-pharmtox-010814-124835] [Citation(s) in RCA: 331] [Impact Index Per Article: 33.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Although the field of pharmacogenetics has existed for decades, practioners have been slow to implement pharmacogenetic testing in clinical care. Numerous publications describe the barriers to clinical implementation of pharmacogenetics. Recently, several freely available resources have been developed to help address these barriers. In this review, we discuss current programs that use preemptive genotyping to optimize the pharmacotherapy of patients. Array-based preemptive testing includes a large number of relevant pharmacogenes that impact multiple high-risk drugs. Using a preemptive approach allows genotyping results to be available prior to any prescribing decision so that genomic variation may be considered as an inherent patient characteristic in the planning of therapy. This review describes the common elements among programs that have implemented preemptive genotyping and highlights key processes for implementation, including clinical decision support.
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