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Capalbo A, de Wert G, Henneman L, Kakourou G, Mcheik S, Peterlin B, van El C, Vassena R, Vermeulen N, Viville S, Forzano F. An ESHG-ESHRE survey on the current practice of expanded carrier screening in medically assisted reproduction. Hum Reprod 2024:deae131. [PMID: 38872341 DOI: 10.1093/humrep/deae131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 05/21/2024] [Indexed: 06/15/2024] Open
Abstract
STUDY QUESTION What is the current practice and views on (expanded) carrier screening ((E)CS) among healthcare professionals in medically assisted reproductive (MAR) practices in Europe? SUMMARY ANSWER The findings show a limited support for ECS with less than half of the respondents affiliated to centres offering ECS, and substantial variation in practice between centres in Europe. WHAT IS KNOWN ALREADY The availability of next-generation sequencing, which enables testing for large groups of genes simultaneously, has facilitated the introduction and expansion of ECS strategies, currently offered particularly in the private sector in the context of assisted reproduction. STUDY DESIGN, SIZE, DURATION A cross-sectional survey evaluating practice and current views among professionals working in MAR practice in different European countries was designed using the online SurveyMonkey tool. The web-based questionnaire included questions on general information regarding the current practice of (E)CS in MAR and questions on what is offered, to whom the test is offered, and how it is offered. It consisted mostly of multiple-choice questions with comment boxes, but also included open questions on the respondents' attitudes/concerns relevant to (E)CS practice, and room to upload requested files (e.g. guidelines and gene panels). In total, 338 responses were collected from 8 February 2022 to 11 April 2022. PARTICIPANTS/MATERIALS, SETTING, METHODS The online survey was launched with an invitation email from the ESHRE central office (n = 4889 emails delivered) and the European Society of Human Genetics (ESHG) central office (n = 1790 emails delivered) sent to the ESHRE and ESHG members, and by social media posts. The survey was addressed to European MAR centres or gamete banks and to centres located in non-European countries participating in the European IVF-monitoring Consortium. Two reminder emails were sent. After exclusion of 39 incomplete responses received (e.g. only background information), 299 respondents from 40 different countries were included for analyses. MAIN RESULTS AND THE ROLE OF CHANCE Overall, 42.5% (127/299) of respondents were affiliated to centres offering ECS. The perceived responsibility to enable prospective parents to make informed reproductive decisions and preventing suffering/burden for parents were the main reasons to offer ECS. A single ECS panel is offered by nearly 45% (39/87 received answers) of the centres offering ECS, 25.3% (22/87) of those centres offer a selection of ECS panels, and 29.9% (26/87) offer whole exome sequencing and a large in silico panel. Different ranges of panel sizes and conditions were included in the ECS panel(s) offered. Most of the respondents (81.8%; 72/88 received answers) indicated that the panels they offer are universal and target the entire population. Pathogenic variants (89.7%; 70/78 received answers), and to a lesser extent, likely pathogenic variants (64.1%%; 50/78 received answers), were included in the ECS report for individuals and couples undergoing MAR with their own gametes. According to 87.9% (80/91 received answers) of the respondents, patients have to pay to undergo an ECS test. Most respondents (76.2%; 61/80 received answers) reported that counselling is provided before and after the ECS test. Preimplantation genetic testing, the use of donor gametes, and prenatal diagnostic testing were the three main reproductive options discussed with identified carrier couples. The main reason, according to the respondents, for not offering ECS in their centre, was the lack of professional recommendations supporting ECS (52.5%; 73/139 received answers) and the high cost for couples or reimbursement not being available (49.6%; 69/139). The challenges and moral dilemmas encountered by the respondents revolved mainly around the content of the offer, including the variants classification and the heterogeneity of the panels, the counselling, and the cost of the test. LIMITATIONS, REASONS FOR CAUTION Although the total number of respondents was acceptable, the completion rate of the survey was suboptimal. In addition, the heterogeneity of answers to open-ended questions and the ambiguity of some of the answers, along with incomplete responses, posed a challenge in interpreting survey results. It is also plausible that some questions were not easily understood by the respondents. For this reason, response and non-response bias are acknowledged as further limitations of the survey. WIDER IMPLICATIONS OF THE FINDINGS The results of this survey could aid in identifying potential challenges or areas for improvement in the current practice of ECS in the MAR field and contribute to the discussion on how to address them. The results underline the need to stimulate a more knowledge-based debate on the complexity and the pros and cons of a possible implementation of ECS in MAR. STUDY FUNDING/COMPETING INTEREST(S) All costs relating to the development process were covered from European Society of Human Reproduction and Embryology and European Society of Human Genetics funds. There was no external funding of the development process or manuscript production. A.C. is full-time employee of Juno Genetics. L.H. declared receiving a research grant during the past 36 months from the Netherlands Organisation for Health Research and Development. She has also participated in a Health Council report of the Netherlands on preconception carrier screening and collaborated with the VSOP Dutch Genetic Alliance (patient umbrella organization on rare and genetic disorders). L.H. and C.v.E. are affiliated with Amsterdam University Medical Centre, a hospital that offers ECS in a non-commercial setting. R.V. received honoraria for presentations from Merck Academy and is unpaid board member of the executive committee of the Spanish Fertility Society. The other authors had nothing to disclose. TRIAL REGISTRATION NUMBER N/A.
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Affiliation(s)
- Antonio Capalbo
- Department of Reproductive Genetics, Juno Genetics, Rome, Italy
- Unit of Medical Genetics, Centre for Advanced Studies and Technology (CAST), "G. d'Annunzio" University of Chieti-Pescara, Chieti, Italy
| | - Guido de Wert
- Department of Health, Ethics and Society, Faculty of Health, Medicine and Life Sciences, Maastricht University, Maastricht, The Netherlands
- Department of Health, Ethics and Society, CAPHRI Care and Public Health Research Institute, Maastricht University, Maastricht, The Netherlands
- GROW School for Oncology and Reproduction, Maastricht University, Maastricht, The Netherlands
| | - Lidewij Henneman
- Department of Human Genetics and Amsterdam Reproduction and Development Research Institute, Amsterdam UMC, Location Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Georgia Kakourou
- Laboratory of Medical Genetics, Choremio Research Laboratory, National and Kapodistrian University of Athens, "Agia Sophia" Children's Hospital, Athens, Greece
| | | | - Borut Peterlin
- Clinical Institute of Genomic Medicine, University Medical Centre Ljubljana, Ljubljana, Slovenia
| | - Carla van El
- Department of Human Genetics, Amsterdam Public Health Research Institute, Amsterdam UMC, Location Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | | | | | - Stéphane Viville
- Department of Developmental Biology, Institute of Genetics and Molecular and Cellular Biology, University of Strasbourg, Strasbourg, France
- Department of Functional Genomics and Cancer, CNRS UMR 7104-INSERM U1258 Illkrich-Graffenstaden France
- Laboratory of Genetic Diagnostic, Genetics of Infertility Unit (UF3472), Strasbourg University Hospital, Strasbourg, France
| | - Francesca Forzano
- Department of Clinical Genetics, Guy's and St Thomas NHS Foundation Trust, London, UK
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Murugan M, Yuan B, Venner E, Ballantyne CM, Robinson KM, Coons JC, Wang L, Empey PE, Gibbs RA. Empowering personalized pharmacogenomics with generative AI solutions. J Am Med Inform Assoc 2024; 31:1356-1366. [PMID: 38447590 PMCID: PMC11105140 DOI: 10.1093/jamia/ocae039] [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: 12/29/2023] [Revised: 02/06/2024] [Accepted: 02/19/2024] [Indexed: 03/08/2024] Open
Abstract
OBJECTIVE This study evaluates an AI assistant developed using OpenAI's GPT-4 for interpreting pharmacogenomic (PGx) testing results, aiming to improve decision-making and knowledge sharing in clinical genetics and to enhance patient care with equitable access. MATERIALS AND METHODS The AI assistant employs retrieval-augmented generation (RAG), which combines retrieval and generative techniques, by harnessing a knowledge base (KB) that comprises data from the Clinical Pharmacogenetics Implementation Consortium (CPIC). It uses context-aware GPT-4 to generate tailored responses to user queries from this KB, further refined through prompt engineering and guardrails. RESULTS Evaluated against a specialized PGx question catalog, the AI assistant showed high efficacy in addressing user queries. Compared with OpenAI's ChatGPT 3.5, it demonstrated better performance, especially in provider-specific queries requiring specialized data and citations. Key areas for improvement include enhancing accuracy, relevancy, and representative language in responses. DISCUSSION The integration of context-aware GPT-4 with RAG significantly enhanced the AI assistant's utility. RAG's ability to incorporate domain-specific CPIC data, including recent literature, proved beneficial. Challenges persist, such as the need for specialized genetic/PGx models to improve accuracy and relevancy and addressing ethical, regulatory, and safety concerns. CONCLUSION This study underscores generative AI's potential for transforming healthcare provider support and patient accessibility to complex pharmacogenomic information. While careful implementation of large language models like GPT-4 is necessary, it is clear that they can substantially improve understanding of pharmacogenomic data. With further development, these tools could augment healthcare expertise, provider productivity, and the delivery of equitable, patient-centered healthcare services.
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Affiliation(s)
- Mullai Murugan
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, United States
| | - Bo Yuan
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, United States
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, United States
| | - Eric Venner
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, United States
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, United States
| | - Christie M Ballantyne
- Sections of Cardiology and Cardiovascular Research, Department of Medicine, Baylor College of Medicine, Houston, TX, United States
| | | | - James C Coons
- School of Pharmacy, University of Pittsburgh, Pittsburgh, PA, United States
- Department of Pharmacy, UPMC Presbyterian-Shadyside Hospital, Pittsburgh, PA, United States
| | - Liwen Wang
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, United States
| | - Philip E Empey
- School of Pharmacy, University of Pittsburgh, Pittsburgh, PA, United States
- Institute for Precision Medicine, UPMC/University of Pittsburgh, Pittsburgh, PA, United States
| | - Richard A Gibbs
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, United States
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, United States
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3
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Zeng S, Qing Q, Xu W, Yu S, Zheng M, Tan H, Peng J, Huang J. Personalized anesthesia and precision medicine: a comprehensive review of genetic factors, artificial intelligence, and patient-specific factors. Front Med (Lausanne) 2024; 11:1365524. [PMID: 38784235 PMCID: PMC11111965 DOI: 10.3389/fmed.2024.1365524] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Accepted: 04/22/2024] [Indexed: 05/25/2024] Open
Abstract
Precision medicine, characterized by the personalized integration of a patient's genetic blueprint and clinical history, represents a dynamic paradigm in healthcare evolution. The emerging field of personalized anesthesia is at the intersection of genetics and anesthesiology, where anesthetic care will be tailored to an individual's genetic make-up, comorbidities and patient-specific factors. Genomics and biomarkers can provide more accurate anesthetic protocols, while artificial intelligence can simplify anesthetic procedures and reduce anesthetic risks, and real-time monitoring tools can improve perioperative safety and efficacy. The aim of this paper is to present and summarize the applications of these related fields in anesthesiology by reviewing them, exploring the potential of advanced technologies in the implementation and development of personalized anesthesia, realizing the future integration of new technologies into clinical practice, and promoting multidisciplinary collaboration between anesthesiology and disciplines such as genomics and artificial intelligence.
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Affiliation(s)
- Shiyue Zeng
- Zhuzhou Clinical College, Jishou University, Jishou, China
| | - Qi Qing
- Zhuzhou Clinical College, Jishou University, Jishou, China
| | - Wei Xu
- Department of Anesthesiology, Zhuzhou Central Hospital, Zhuzhou, China
| | - Simeng Yu
- Zhuzhou Clinical College, Jishou University, Jishou, China
| | - Mingzhi Zheng
- Department of Anesthesiology, Zhuzhou Central Hospital, Zhuzhou, China
| | - Hongpei Tan
- Department of Radiology, Third Xiangya Hospital, Central South University, Changsha, China
| | - Junmin Peng
- Department of Anesthesiology, Zhuzhou Central Hospital, Zhuzhou, China
| | - Jing Huang
- Department of Anesthesiology, Zhuzhou Central Hospital, Zhuzhou, China
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Hogg CJ. Translating genomic advances into biodiversity conservation. Nat Rev Genet 2024; 25:362-373. [PMID: 38012268 DOI: 10.1038/s41576-023-00671-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/12/2023] [Indexed: 11/29/2023]
Abstract
A key action of the new Global Biodiversity Framework is the maintenance of genetic diversity in all species to safeguard their adaptive potential. To achieve this goal, a translational mindset, which aims to convert results of basic research into direct practical benefits, needs to be applied to biodiversity conservation. Despite much discussion on the value of genomics to conservation, a disconnect between those generating genomic resources and those applying it to biodiversity management remains. As global efforts to generate reference genomes for non-model species increase, investment into practical biodiversity applications is critically important. Applications such as understanding population and multispecies diversity and longitudinal monitoring need support alongside education for policymakers on integrating the data into evidence-based decisions. Without such investment, the opportunity to revolutionize global biodiversity conservation using genomics will not be fully realized.
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Affiliation(s)
- Carolyn J Hogg
- School of Life & Environmental Sciences, The University of Sydney, Sydney, NSW, Australia.
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5
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Bastaki K, Velayutham D, Irfan A, Adnan M, Mohammed S, Mbarek H, Qoronfleh MW, Jithesh PV. Forging the path to precision medicine in Qatar: a public health perspective on pharmacogenomics initiatives. Front Public Health 2024; 12:1364221. [PMID: 38550311 PMCID: PMC10977610 DOI: 10.3389/fpubh.2024.1364221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2024] [Accepted: 02/20/2024] [Indexed: 04/02/2024] Open
Abstract
Pharmacogenomics (PGx) is an important component of precision medicine that promises tailored treatment approaches based on an individual's genetic information. Exploring the initiatives in research that help to integrate PGx test into clinical setting, identifying the potential barriers and challenges as well as planning the future directions, are all important for fruitful PGx implementation in any population. Qatar serves as an exemplar case study for the Middle East, having a small native population compared to a diverse immigrant population, advanced healthcare system, national genome program, and several educational initiatives on PGx and precision medicine. This paper attempts to outline the current state of PGx research and implementation in Qatar within the global context, emphasizing ongoing initiatives and educational efforts. The inclusion of PGx in university curricula and healthcare provider training, alongside precision medicine conferences, showcase Qatar's commitment to advancing this field. However, challenges persist, including the requirement for population specific implementation strategies, complex genetic data interpretation, lack of standardization, and limited awareness. The review suggests policy development for future directions in continued research investment, conducting clinical trials for the feasibility of PGx implementation, ethical considerations, technological advancements, and global collaborations to overcome these barriers.
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Affiliation(s)
- Kholoud Bastaki
- Clinical and Pharmacy Practice Department, College of Pharmacy, QU Health, Qatar University, Doha, Qatar
| | - Dinesh Velayutham
- College of Health & Life Sciences, Hamad Bin Khalifa University, Education City, Doha, Qatar
| | - Areeba Irfan
- College of Health & Life Sciences, Hamad Bin Khalifa University, Education City, Doha, Qatar
| | - Mohd Adnan
- College of Health & Life Sciences, Hamad Bin Khalifa University, Education City, Doha, Qatar
| | - Sawsan Mohammed
- College of Medicine, Pre-Clinical Education Department, QU Health, Qatar University, Doha, Qatar
| | | | - M. Waild Qoronfleh
- Q3 Research Institute (QRI), Research & Policy Division, Ann Arbor, MI, United States
| | - Puthen Veettil Jithesh
- College of Health & Life Sciences, Hamad Bin Khalifa University, Education City, Doha, Qatar
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6
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Zhou Y, Lauschke VM. Next-generation sequencing in pharmacogenomics - fit for clinical decision support? Expert Rev Clin Pharmacol 2024; 17:213-223. [PMID: 38247431 DOI: 10.1080/17512433.2024.2307418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 01/16/2024] [Indexed: 01/23/2024]
Abstract
INTRODUCTION The technological advances of sequencing methods during the past 20 years have fuelled the generation of large amounts of sequencing data that comprise common variations, as well as millions of rare and personal variants that would not be identified by conventional genotyping. While comprehensive sequencing is technically feasible, its clinical utility for guiding personalized treatment decisions remains controversial. AREAS COVERED We discuss the opportunities and challenges of comprehensive sequencing compared to targeted genotyping for pharmacogenomic applications. Current pharmacogenomic sequencing panels are heterogeneous and clinical actionability of the included genes is not a major focus. We provide a current overview and critical discussion of how current studies utilize sequencing data either retrospectively from biobanks, databases or repurposed diagnostic sequencing, or prospectively using pharmacogenomic sequencing. EXPERT OPINION While sequencing-based pharmacogenomics has provided important insights into genetic variations underlying the safety and efficacy of a multitude pharmacological treatments, important hurdles for the clinical implementation of pharmacogenomic sequencing remain. We identify gaps in the interpretation of pharmacogenetic variants, technical challenges pertaining to complex loci and variant phasing, as well as unclear cost-effectiveness and incomplete reimbursement. It is critical to address these challenges in order to realize the promising prospects of pharmacogenomic sequencing.
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Affiliation(s)
- Yitian Zhou
- Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden
| | - Volker M Lauschke
- Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden
- Dr Margarete Fischer-Bosch Institute of Clinical Pharmacology, Stuttgart, Germany
- University of Tübingen, Tübingen, Germany
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7
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Patil R, Ashraf F, Dayeh SA, Prakash SK. Genomic Medicine Guidance: A Point-of-Care App for Heritable Thoracic Aortic Diseases. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.12.22.23299696. [PMID: 38234729 PMCID: PMC10793513 DOI: 10.1101/2023.12.22.23299696] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2024]
Abstract
Genetic testing can determine familial and personal risks for heritable thoracic aortic aneurysms and dissections (TAD). The 2022 ACC/AHA guidelines for TAD recommend management decisions based on the specific gene mutation. However, many clinicians lack sufficient comfort or insight to integrate genetic information into clinical practice. We therefore developed the Genomic Medicine Guidance (GMG) app, an interactive point-of care tool to inform clinicians and patients about TAD diagnosis, treatment, and surveillance. GMG is a REDCap-based app that combines publicly available genetic data and clinical recommendations based on the TAD guidelines into one translational education tool. TAD genetic information in GMG was sourced from the Montalcino Aortic Consortium, a worldwide collaboration of TAD centers of excellence, and the NIH genetic repositories ClinVar and ClinGen. The app streamlines data on the 13 most frequently mutated TAD genes with 2,286 unique pathogenic mutations that cause TAD so that users receive comprehensive recommendations for diagnostic testing, imaging, surveillance, medical therapy, preventative surgical repair, as well as guidance for exercise safety and management during pregnancy. The app output can be displayed in a clinician view or exported as an informative pamphlet in a patient-friendly format. The overall goal of the GMG app is to make genomic medicine more accessible to clinicians and patients, while serving as a unifying platform for research. We anticipate that these features will be catalysts for collaborative projects that aim to understand the spectrum of genetic variants that contribute to TAD.
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Affiliation(s)
- Rohan Patil
- Department of Internal Medicine, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, Texas, USA
| | - Fatima Ashraf
- McWilliams School of Bioinformatics, University of Texas Health Science Center at Houston, Houston, Texas, USA
| | - Samer Abu Dayeh
- Department of Internal Medicine, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, Texas, USA
| | - Siddharth K. Prakash
- Department of Internal Medicine, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, Texas, USA
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8
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Shue SA, Rowe E, Bell LA, Damush T, DeLong A, Gowan T, Skaar T, Haggstrom D. Pharmacogenomics implementation across multiple clinic settings: a qualitative evaluation. Pharmacogenomics 2023; 24:881-893. [PMID: 37975236 DOI: 10.2217/pgs-2023-0179] [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] [Indexed: 11/19/2023] Open
Abstract
Aim: To advance clinical adoption and implementation of pharmacogenomics (PGx) testing, barriers and facilitators to these efforts must be understood. This study identified and examined barriers and facilitators to active implementation of a PGx program across multiple clinic settings in an academic healthcare system. Materials & methods: 28 contributors to the PGx implementation (e.g., clinical providers, informatics specialists) completed an interview to elicit their perceptions of the implementation. Results: Qualitative analysis identified several barriers and facilitators that spanned different stages of the implementation process. Specifically, unclear test payment mechanisms, decision support tool development, rigid workflows and provider education were noted as barriers to the PGx implementation. A multidisciplinary implementation team and leadership support emerged as key facilitators. Furthermore, participants also suggested strategies to overcome or maintain these factors. Conclusion: Assessing real-world implementation perceptions and suggested strategies from a range of implementation contributors facilitates a more comprehensive framework and best-practice guidelines for PGx implementation.
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Affiliation(s)
- Sarah A Shue
- VA HSR&D Center for Health Information & Communication, Roudebush VA Medical Center, Indianapolis, IN 46202, USA
| | - Elizabeth Rowe
- Division of Clinical Pharmacology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Lauren A Bell
- Division of Clinical Pharmacology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Teresa Damush
- VA HSR&D Center for Health Information & Communication, Roudebush VA Medical Center, Indianapolis, IN 46202, USA
- Division of General Internal Medicine & Geriatrics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
- Center for Health Services Research, Regenstrief Institute, Indianapolis, IN 46202, USA
| | - Alexis DeLong
- Center for Health Services Research, Regenstrief Institute, Indianapolis, IN 46202, USA
| | - Tayler Gowan
- Center for Health Services Research, Regenstrief Institute, Indianapolis, IN 46202, USA
| | - Todd Skaar
- Division of Clinical Pharmacology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - David Haggstrom
- VA HSR&D Center for Health Information & Communication, Roudebush VA Medical Center, Indianapolis, IN 46202, USA
- Division of General Internal Medicine & Geriatrics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
- Center for Health Services Research, Regenstrief Institute, Indianapolis, IN 46202, USA
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Owolabi P, Adam Y, Adebiyi E. Personalizing medicine in Africa: current state, progress and challenges. Front Genet 2023; 14:1233338. [PMID: 37795248 PMCID: PMC10546210 DOI: 10.3389/fgene.2023.1233338] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 09/11/2023] [Indexed: 10/06/2023] Open
Abstract
Personalized medicine has been identified as a powerful tool for addressing the myriad of health issues facing different health systems globally. Although recent studies have expanded our understanding of how different factors such as genetics and the environment play significant roles in affecting the health of individuals, there are still several other issues affecting their translation into personalizing health interventions globally. Since African populations have demonstrated huge genetic diversity, there is a significant need to apply the concepts of personalized medicine to overcome various African-specific health challenges. Thus, we review the current state, progress, and challenges facing the adoption of personalized medicine in Africa with a view to providing insights to critical stakeholders on the right approach to deploy.
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Affiliation(s)
- Paul Owolabi
- Covenant Applied Informatics and Communication, Africa Centre of Excellence (CApIC-ACE), Covenant University, Ota, Ogun State, Nigeria
- Department of Computer and Information Science, Covenant University, Ota, Ogun State, Nigeria
| | - Yagoub Adam
- Covenant University Bioinformatics Research (CUBRe), Covenant University, Ota, Ogun State, Nigeria
| | - Ezekiel Adebiyi
- Covenant Applied Informatics and Communication, Africa Centre of Excellence (CApIC-ACE), Covenant University, Ota, Ogun State, Nigeria
- Department of Computer and Information Science, Covenant University, Ota, Ogun State, Nigeria
- Covenant University Bioinformatics Research (CUBRe), Covenant University, Ota, Ogun State, Nigeria
- Applied Bioinformatics Division, German Cancer Research Center (DKFZ), Heidelberg, Germany
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10
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Spiekerkoetter U, Bick D, Scott R, Hopkins H, Krones T, Gross ES, Bonham JR. Genomic newborn screening: Are we entering a new era of screening? J Inherit Metab Dis 2023; 46:778-795. [PMID: 37403863 DOI: 10.1002/jimd.12650] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 06/01/2023] [Accepted: 06/13/2023] [Indexed: 07/06/2023]
Abstract
Population newborn screening (NBS) for phenylketonuria began in the United States in 1963. In the 1990s electrospray ionization mass spectrometry permitted an array of pathognomonic metabolites to be identified simultaneously, enabling up to 60 disorders to be recognized with a single test. In response, differing approaches to the assessment of the harms and benefits of screening have resulted in variable screening panels worldwide. Thirty years on and another screening revolution has emerged with the potential for first line genomic testing extending the range of screening conditions recognized after birth to many hundreds. At the annual SSIEM conference in 2022 in Freiburg, Germany, an interactive plenary discussion on genomic screening strategies and their challenges and opportunities was conducted. The Genomics England Research project proposes the use of Whole Genome Sequencing to offer extended NBS to 100 000 babies for defined conditions with a clear benefit for the child. The European Organization for Rare Diseases seeks to include "actionable" conditions considering also other types of benefits. Hopkins Van Mil, a private UK research institute, determined the views of citizens and revealed as a precondition that families are provided with adequate information, qualified support, and that autonomy and data are protected. From an ethical standpoint, the benefits ascribed to screening and early treatment need to be considered in relation to asymptomatic, phenotypically mild or late-onset presentations, where presymptomatic treatment may not be required. The different perspectives and arguments demonstrate the unique burden of responsibility on those proposing new and far-reaching developments in NBS programs and the need to carefully consider both harms and benefits.
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Affiliation(s)
- Ute Spiekerkoetter
- Department of Pediatrics, Adolescent Medicine and Neonatology, Faculty of Medicine, University Children's Hospital, Freiburg, Germany
| | | | | | | | - Tanja Krones
- URPP Human Reproduction Reloaded - H2R and Institute of Biomedical Ethics and History of Medicine, University Hospital/University of Zurich, Zurich, Switzerland
| | | | - James R Bonham
- International Society of Neonatal Screening, Maarssen, The Netherlands
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Felker SA, Lawlor JMJ, Hiatt SM, Thompson ML, Latner DR, Finnila CR, Bowling KM, Bonnstetter ZT, Bonini KE, Kelly NR, Kelley WV, Hurst ACE, Rashid S, Kelly MA, Nakouzi G, Hendon LG, Bebin EM, Kenny EE, Cooper GM. Poison exon annotations improve the yield of clinically relevant variants in genomic diagnostic testing. Genet Med 2023; 25:100884. [PMID: 37161864 PMCID: PMC10524927 DOI: 10.1016/j.gim.2023.100884] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 05/01/2023] [Accepted: 05/03/2023] [Indexed: 05/11/2023] Open
Abstract
PURPOSE Neurodevelopmental disorders (NDDs) often result from rare genetic variation, but genomic testing yield for NDDs remains below 50%, suggesting that clinically relevant variants may be missed by standard analyses. Here, we analyze "poison exons" (PEs), which are evolutionarily conserved alternative exons often absent from standard gene annotations. Variants that alter PE inclusion can lead to loss of function and may be highly penetrant contributors to disease. METHODS We curated published RNA sequencing data from developing mouse cortex to define 1937 conserved PE regions potentially relevant to NDDs, and we analyzed variants found by genome sequencing in multiple NDD cohorts. RESULTS Across 2999 probands, we found 6 novel clinically relevant variants in PE regions. Five of these variants are in genes that are part of the sodium voltage-gated channel alpha subunit family (SCN1A, SCN2A, and SCN8A), which is associated with epilepsies. One variant is in SNRPB, associated with cerebrocostomandibular syndrome. These variants have moderate to high computational impact assessments, are absent from population variant databases, and in genes with gene-phenotype associations consistent with each probands reported features. CONCLUSION With a very minimal increase in variant analysis burden (average of 0.77 variants per proband), annotation of PEs can improve diagnostic yield for NDDs and likely other congenital conditions.
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Affiliation(s)
| | | | - Susan M Hiatt
- HudsonAlpha Institute for Biotechnology, Huntsville, AL
| | | | | | | | | | | | - Katherine E Bonini
- Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Nicole R Kelly
- Division of Pediatric Genetic Medicine, Department of Pediatrics, Children's Hospital at Montefiore/Montefiore Medical Center/Albert Einstein College of Medicine, Bronx, NY
| | | | | | | | | | | | | | - E Martina Bebin
- Department of Neurology, University of Alabama at Birmingham, Birmingham, AL
| | - Eimear E Kenny
- Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY; Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY
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Padmanabhan S, du Toit C, Dominiczak AF. Cardiovascular precision medicine - A pharmacogenomic perspective. CAMBRIDGE PRISMS. PRECISION MEDICINE 2023; 1:e28. [PMID: 38550953 PMCID: PMC10953758 DOI: 10.1017/pcm.2023.17] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 05/24/2023] [Accepted: 06/12/2023] [Indexed: 05/16/2024]
Abstract
Precision medicine envisages the integration of an individual's clinical and biological features obtained from laboratory tests, imaging, high-throughput omics and health records, to drive a personalised approach to diagnosis and treatment with a higher chance of success. As only up to half of patients respond to medication prescribed following the current one-size-fits-all treatment strategy, the need for a more personalised approach is evident. One of the routes to transforming healthcare through precision medicine is pharmacogenomics (PGx). Around 95% of the population is estimated to carry one or more actionable pharmacogenetic variants and over 75% of adults over 50 years old are on a prescription with a known PGx association. Whilst there are compelling examples of pharmacogenomic implementation in clinical practice, the case for cardiovascular PGx is still evolving. In this review, we shall summarise the current status of PGx in cardiovascular diseases and look at the key enablers and barriers to PGx implementation in clinical practice.
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Affiliation(s)
- Sandosh Padmanabhan
- BHF Glasgow Cardiovascular Research Centre, School of Cardiovascular and Metabolic Health, University of Glasgow, Glasgow, UK
| | - Clea du Toit
- BHF Glasgow Cardiovascular Research Centre, School of Cardiovascular and Metabolic Health, University of Glasgow, Glasgow, UK
| | - Anna F. Dominiczak
- BHF Glasgow Cardiovascular Research Centre, School of Cardiovascular and Metabolic Health, University of Glasgow, Glasgow, UK
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Salma M, Alaterre E, Moreaux J, Soler E. Var∣Decrypt: a novel and user-friendly tool to explore and prioritize variants in whole-exome sequencing data. Epigenetics Chromatin 2023; 16:23. [PMID: 37312221 DOI: 10.1186/s13072-023-00497-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 05/23/2023] [Indexed: 06/15/2023] Open
Abstract
BACKGROUND High-throughput sequencing (HTS) offers unprecedented opportunities for the discovery of causative gene variants in multiple human disorders including cancers, and has revolutionized clinical diagnostics. However, despite more than a decade of use of HTS-based assays, extracting relevant functional information from whole-exome sequencing (WES) data remains challenging, especially for non-specialists lacking in-depth bioinformatic skills. RESULTS To address this limitation, we developed Var∣Decrypt, a web-based tool designed to greatly facilitate WES data browsing and analysis. Var∣Decrypt offers a wide range of gene and variant filtering possibilities, clustering and enrichment tools, providing an efficient way to derive patient-specific functional information and to prioritize gene variants for functional analyses. We applied Var∣Decrypt on WES datasets of 10 acute erythroid leukemia patients, a rare and aggressive form of leukemia, and recovered known disease oncogenes in addition to novel putative drivers. We additionally validated the performance of Var∣Decrypt using an independent dataset of ~ 90 multiple myeloma WES, recapitulating the identified deregulated genes and pathways, showing the general applicability and versatility of Var∣Decrypt for WES analysis. CONCLUSION Despite years of use of WES in human health for diagnosis and discovery of disease drivers, WES data analysis still remains a complex task requiring advanced bioinformatic skills. In that context, there is a need for user-friendly all-in-one dedicated tools for data analysis, to allow biologists and clinicians to extract relevant biological information from patient datasets. Here, we provide Var∣Decrypt (trial version accessible here: https://vardecrypt.com/app/vardecrypt ), a simple and intuitive Rshiny application created to fill this gap. Source code and detailed user tutorial are available at https://gitlab.com/mohammadsalma/vardecrypt .
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Affiliation(s)
- Mohammad Salma
- Institut de Génétique Moléculaire de Montpellier, Univ Montpellier, CNRS, Montpellier, France.
- Laboratory of Excellence GR-Ex, Université de Paris, Paris, France.
| | - Elina Alaterre
- Institute of Human Genetics, UMR 9002 CNRS-UM, Montpellier, France
| | - Jérôme Moreaux
- Department of Biological Hematology, CHU Montpellier, Montpellier, France
- Institute of Human Genetics, UMR 9002 CNRS-UM, Montpellier, France
- Institut Universitaire de France (IUF), Paris, France
| | - Eric Soler
- Institut de Génétique Moléculaire de Montpellier, Univ Montpellier, CNRS, Montpellier, France.
- Laboratory of Excellence GR-Ex, Université de Paris, Paris, France.
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Ellis SD, Brooks JV, Birken SA, Morrow E, Hilbig ZS, Wulff-Burchfield E, Kinney AY, Ellerbeck EF. Determinants of targeted cancer therapy use in community oncology practice: a qualitative study using the Theoretical Domains Framework and Rummler-Brache process mapping. Implement Sci Commun 2023; 4:66. [PMID: 37308981 PMCID: PMC10259814 DOI: 10.1186/s43058-023-00441-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Accepted: 05/25/2023] [Indexed: 06/14/2023] Open
Abstract
BACKGROUND Precision medicine holds enormous potential to improve outcomes for cancer patients, offering improved rates of cancer control and quality of life. Not all patients who could benefit from targeted cancer therapy receive it, and some who may not benefit do receive targeted therapy. We sought to comprehensively identify determinants of targeted therapy use among community oncology programs, where most cancer patients receive their care. METHODS Guided by the Theoretical Domains Framework, we conducted semi-structured interviews with 24 community cancer care providers and mapped targeted therapy delivery across 11 cancer care delivery teams using a Rummler-Brache diagram. Transcripts were coded to the framework using template analysis, and inductive coding was used to identify key behaviors. Coding was revised until a consensus was reached. RESULTS Intention to deliver precision medicine was high across all participants interviewed, who also reported untenable knowledge demands. We identified distinctly different teams, processes, and determinants for (1) genomic test ordering and (2) delivery of targeted therapies. A key determinant of molecular testing was role alignment. The dominant expectation for oncologists to order and interpret genomic tests is at odds with their role as treatment decision-makers' and pathologists' typical role to stage tumors. Programs in which pathologists considered genomic test ordering as part of their staging responsibilities reported high and timely testing rates. Determinants of treatment delivery were contingent on resources and ability to offset delivery costs, which low- volume programs could not do. Rural programs faced additional treatment delivery challenges. CONCLUSIONS We identified novel determinants of targeted therapy delivery that potentially could be addressed through role re-alignment. Standardized, pathology-initiated genomic testing may prove fruitful in ensuring patients eligible for targeted therapy are identified, even if the care they need cannot be delivered at small and rural sites which may have distinct challenges in treatment delivery. Incorporating behavior specification and Rummler-Brache process mapping with determinant analysis may extend its usefulness beyond the identification of the need for contextual adaptation.
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Affiliation(s)
- Shellie D. Ellis
- University of Kansas School of Medicine, 3901 Rainbow Blvd., Kansas City, KS 66610 USA
| | - Joanna Veazey Brooks
- University of Kansas School of Medicine, 3901 Rainbow Blvd., Kansas City, KS 66610 USA
| | - Sarah A. Birken
- Wake Forest University School of Medicine, 525 Vine Street, Winston-Salem, NC 27101 USA
| | - Emily Morrow
- Kansas City Kansas Community College, 7250 State Ave., Kansas City, KS 66112 USA
| | - Zachary S. Hilbig
- University of Kansas School of Medicine, 3901 Rainbow Blvd., Kansas City, KS 66610 USA
| | | | - Anita Y. Kinney
- Rutgers Cancer Institute of New Jersey, Rutgers University, 195 Little Albany St., New Brunswick, NJ 08901 USA
| | - Edward F. Ellerbeck
- University of Kansas School of Medicine, 3901 Rainbow Blvd., Kansas City, KS 66610 USA
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15
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Felker SA, Lawlor JMJ, Hiatt SM, Thompson ML, Latner DR, Finnila CR, Bowling KM, Bonnstetter ZT, Bonini KE, Kelly NR, Kelley WV, Hurst ACE, Kelly MA, Nakouzi G, Hendon LG, Bebin EM, Kenny EE, Cooper GM. Poison exon annotations improve the yield of clinically relevant variants in genomic diagnostic testing. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.12.523654. [PMID: 36711854 PMCID: PMC9882217 DOI: 10.1101/2023.01.12.523654] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Purpose Neurodevelopmental disorders (NDDs) often result from rare genetic variation, but genomic testing yield for NDDs remains around 50%, suggesting some clinically relevant rare variants may be missed by standard analyses. Here we analyze "poison exons" (PEs) which, while often absent from standard gene annotations, are alternative exons whose inclusion results in a premature termination codon. Variants that alter PE inclusion can lead to loss-of-function and may be highly penetrant contributors to disease. Methods We curated published RNA-seq data from developing mouse cortex to define 1,937 PE regions conserved between humans and mice and potentially relevant to NDDs. We then analyzed variants found by genome sequencing in multiple NDD cohorts. Results Across 2,999 probands, we found six clinically relevant variants in PE regions that were previously overlooked. Five of these variants are in genes that are part of the sodium voltage-gated channel alpha subunit family ( SCN1A, SCN2A , and SCN8A ), associated with epilepsies. One variant is in SNRPB , associated with Cerebrocostomandibular Syndrome. These variants have moderate to high computational impact assessments, are absent from population variant databases, and were observed in probands with features consistent with those reported for the associated gene. Conclusion With only a minimal increase in variant analysis burden (most probands had zero or one candidate PE variants in a known NDD gene, with an average of 0.77 per proband), annotation of PEs can improve diagnostic yield for NDDs and likely other congenital conditions.
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Affiliation(s)
| | - James MJ Lawlor
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA 35806
| | - Susan M Hiatt
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA 35806
| | | | - Donald R Latner
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA 35806
| | | | - Kevin M Bowling
- Washington University School of Medicine, Saint Louis, MO, USA 63110
| | | | - Katherine E Bonini
- Institute for Genomic Health, Icahn School of Medicine at Mount Sinai. New York, NY, USA 10029
| | - Nicole R Kelly
- Department of Pediatrics, Division of Pediatric Genetic Medicine, Children’s Hospital at Montefiore/Montefiore Medical Center/Albert Einstein College of Medicine, Bronx, NY, USA 10467
| | - Whitley V Kelley
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA 35806
| | - Anna CE Hurst
- University of Alabama in Birmingham, Birmingham, AL, USA 35294
| | | | | | - Laura G Hendon
- University of Mississippi Medical Center, Jackson, MS, 39216
| | - E Martina Bebin
- Department of Neurology, University of Alabama at Birmingham, Birmingham, AL, USA 35294
| | - Eimear E Kenny
- Institute for Genomic Health, Icahn School of Medicine at Mount Sinai. New York, NY, USA 10029,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA 10029,Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA 10029
| | - Gregory M Cooper
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA 35806
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Haga SB, Chung WK, Cubano LA, Curry TB, Empey PE, Ginsburg GS, Mangold K, Miyake CY, Prakash SK, Ramsey LB, Rowley R, Rohrer Vitek CR, Skaar TC, Wynn J, Manolio TA. Development of Competency-based Online Genomic Medicine Training (COGENT). Per Med 2023; 20:55-64. [PMID: 36416152 PMCID: PMC10291206 DOI: 10.2217/pme-2022-0101] [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: 09/02/2022] [Accepted: 10/17/2022] [Indexed: 11/25/2022]
Abstract
The fields of genetics and genomics have greatly expanded across medicine through the development of new technologies that have revealed genetic contributions to a wide array of traits and diseases. Thus, the development of widely available educational resources for all healthcare providers is essential to ensure the timely and appropriate utilization of genetics and genomics patient care. In 2020, the National Human Genome Research Institute released a call for new proposals to develop accessible, sustainable online education for health providers. This paper describes the efforts of the six teams awarded to reach the goal of providing genetic and genomic training modules that are broadly available for busy clinicians.
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Affiliation(s)
- Susanne B Haga
- Department of Medicine, Duke University School of Medicine, Program in Precision Medicine, 101 Science Drive, Durham, NC 27708, USA
| | - Wendy K Chung
- Department of Pediatrics, Columbia University Irving Medical Center, 1150 St. Nicholas Avenue, Room 620 New York, NY 10032, USA
- Department of Medicine, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Luis A Cubano
- National Human Genome Research Institute, Division of Genomic Medicine, 6700B Rockledge Dr, Suite 3100, Bethesda, MD 20892-6908, USA
| | - Timothy B Curry
- Center for Individualized Medicine, College of Medicine, Mayo Clinic, Rochester, MN 55905, USA
- Department of Anesthesia & Perioperative Medicine, Mayo Clinic, Rochester, MN 55905, USA
| | - Philip E Empey
- Department of Pharmacy & Therapeutics, Pharmacogenomics Center of Excellence, University of Pittsburgh School of Pharmacy, 9064 Salk Hall, 3501 Terrace Street, Pittsburgh, PA 15261, USA
| | - Geoffrey S Ginsburg
- National Institutes of Health, All of Us Research Program, Bethesda, MD 20892, USA
| | - Kara Mangold
- Center for Individualized Medicine, College of Medicine, Mayo Clinic, Rochester, MN 55905, USA
| | - Christina Y Miyake
- Department of Pediatrics, Texas Children’s Hospital, 6651 Main Street, Suite E1960.22, Houston, TX 77030, USA
- Department of Molecular Physiology & Biophysics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Siddharth K Prakash
- Department of Internal Medicine, Division of Medical Genetics, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Laura B Ramsey
- Divisions of Clinical Pharmacology & Research in Patient Services, Cincinnati Children’s Hospital Medical Center, Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
| | - Robb Rowley
- National Human Genome Research Institute, Division of Genomic Medicine, 6700B Rockledge Dr, Suite 3100, Bethesda, MD 20892-6908, USA
| | - Carolyn R Rohrer Vitek
- Center for Individualized Medicine, College of Medicine, Mayo Clinic, Rochester, MN 55905, USA
| | - Todd C Skaar
- Department of Medicine, Division of Clinical Pharmacology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Julia Wynn
- Department of Pediatrics, Columbia University Irving Medical Center, 1150 St. Nicholas Avenue, Room 620 New York, NY 10032, USA
| | - Teri A Manolio
- National Human Genome Research Institute, Division of Genomic Medicine, 6700B Rockledge Dr, Suite 3100, Bethesda, MD 20892-6908, USA
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Boyer MS, Widmer D, Cohidon C, Desvergne B, Cornuz J, Guessous I, Cerqui D. Representations of personalised medicine in family medicine: a qualitative analysis. BMC PRIMARY CARE 2022; 23:37. [PMID: 35232380 PMCID: PMC8889694 DOI: 10.1186/s12875-022-01650-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Accepted: 02/18/2022] [Indexed: 11/24/2022]
Abstract
Background The promise of personalised medicine (PM) to transform healthcare has sparked great enthusiasm in the last years. Yet, its lack of consensus around the nature and scope of the concept has ended in terminological confusion amongst the users in primary care. We aimed to investigate the perceptions of doctors and their patients in response to this evolving concept. This present article focuses on the general understanding of personalised medicine, underlining the confusion over the concept. Methods Semi-structured comprehensive interviews were conducted with 10 general practitioners (GPs) and 10 of their patients. The purposive sampling took into account the doctor’s age, sex, and place of practice (rural/urban); each doctor recruited one patient of the same age and sex. Each interview began with the same open-ended question about the participant’s knowledge of the topic, after which a working definition was provided to continue the discussion. Using the grounded theory method, the analysis consisted of open coding, axial coding and selective coding. Results From our present analysis focusing on the general understanding of PM, three main themes representing the concept emerged. The first two representations being “centred on the person as a whole” and “focused on alternative and complementary methods”, in which the therapeutic relationship was stated as key. The third theme “medicine open to innovation” involved the few participants who had a good understanding of the concept and could associate personalised medicine with genomics. For those who value therapeutic relationship, the risks of accepting innovation could result in “fast-food” medicine and interpersonal barriers. Discussion PM is predominantly unfamiliar in family medicine. It is misinterpreted as a holistic or integrative type of medicine. This semantic confusion probably lies in the choice of the label “personalised” or from the lack of a uniform definition for the term.
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Carrasco E, López-Fernández A, Codina-Sola M, Valenzuela I, Cueto-González AM, Villacampa G, Navarro V, Torres-Esquius S, Palau D, Cruellas M, Torres M, Perez-Dueñas B, Abulí A, Diez O, Sábado-Álvarez C, García-Arumí E, Tizzano EF, Moreno L, Balmaña J. Clinical and psychological implications of secondary and incidental findings in cancer susceptibility genes after exome sequencing in patients with rare disorders. J Med Genet 2022:jmg-2022-108929. [DOI: 10.1136/jmg-2022-108929] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Accepted: 11/11/2022] [Indexed: 12/03/2022]
Abstract
Background/ObjectivesExome sequencing may identify pathogenic variants unrelated with the purpose of the analysis. We investigated the frequency of secondary and incidental findings (SF/IF) in cancer susceptibility genes (CSG), their clinical actionability and the psychological impact in individuals with an SF/IF (cases) compared with individuals tested due to their cancer history (controls).MethodsThis study analysed 533 exomes ordered for non-cancer conditions. Medical records were reviewed for clinical actionability of SF/IF. Psychological impact was analysed using the Multidimensional Impact of Cancer Risk Assessment (MICRA) scale and compared between cases and controls with a propensity score weighting method.ResultsThe frequency of SF/IF in CSG was 2.1% (95% CI 1.1% to 3.8%): threeBRCA2, threePMS2, twoSDHB, and one each inBRCA1,MLH1andRAD51C. Among the relatives, 18 were carriers. Twenty enrolled for surveillance, and a neoplasm was diagnosed in 20%: three paragangliomas and one breast cancer. Cases presented higher MICRA mean scores than controls (21.3 vs 16.2 in MICRA total score, 6.3 vs 4.2 in the distress subscale, and 8.3 vs 6.6 in the uncertainty subscale; all p<0.001).ConclusionSF/IF in CSG were identified in 2.1% of patients. Despite a numerically higher psychological impact, the identification of SF/IF allowed early detection and cancer prevention in families without cancer history.
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Smith J, Braithwaite J, O'Brien TA, Smith S, Tyrrell VJ, Mould EVA, Long JC, Rapport F. The Voices of Stakeholders Involved in Precision Medicine: The Co-Design and Evaluation of Qualitative Indicators of Intervention Acceptability, Fidelity and Context in PRecISion Medicine for Children With Cancer in Australia. QUALITATIVE HEALTH RESEARCH 2022; 32:1865-1880. [PMID: 36066496 DOI: 10.1177/10497323221120501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
We report a novel approach of amalgamating implementation outcomes of acceptability and fidelity alongside context as a new way of qualitatively evaluating implementation outcomes and context of a precision medicine intervention. A rapid qualitative online proforma was co-designed with stakeholders and sent to a purposive sample of healthcare professionals involved in an early-phase clinical trial intervention. Data were analysed using Framework Analysis. A total of 24 out of 68 proformas were returned. Although some participants raised concerns about drug medication access issues, the main intervention was well accepted and understood across professional groups. Comprehension was enhanced through exposure to specialist multidisciplinary meeting arrangements. In conclusion, a rapid data collection tool and framework are now available to assess readily measurable, qualitative indicators of acceptability, fidelity of receipt and contextual fit within the dynamic precision medicine context.
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Affiliation(s)
- James Smith
- Centre for Healthcare Resilience and Implementation Science, 208044Australian Institute of Health Innovation, Macquarie University, Sydney, NSW, Australia
| | - Jeffrey Braithwaite
- Centre for Healthcare Resilience and Implementation Science, 208044Australian Institute of Health Innovation, Macquarie University, Sydney, NSW, Australia
| | - Tracey A O'Brien
- Faculty of Medicine, School of Women's and Children's Health, 7800University of New South Wales, Sydney, NSW, Australia
- Kids Cancer Centre, Sydney Children's Hospital, Randwick, NSW, Australia
| | - Stephanie Smith
- School of Population Health, 1649Curtin University, Perth, WA, Australia
- School of Nursing and Midwifery, Edith Cowan University, Perth, WA, Australia
- Perth Children's Hospital, Nedlands, WA, Australia
| | - Vanessa J Tyrrell
- Children's Cancer Institute, 188680Lowy Cancer Research Centre, University of New South Wales, Randwick, NSW, Australia
| | - Emily V A Mould
- Children's Cancer Institute, 188680Lowy Cancer Research Centre, University of New South Wales, Randwick, NSW, Australia
| | - Janet C Long
- Centre for Healthcare Resilience and Implementation Science, 208044Australian Institute of Health Innovation, Macquarie University, Sydney, NSW, Australia
| | - Frances Rapport
- Centre for Healthcare Resilience and Implementation Science, 208044Australian Institute of Health Innovation, Macquarie University, Sydney, NSW, Australia
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Inaam ul haq M, Li Q, Hou J, Iftekhar A. Detecting the research structure and topic trends of social media using static and dynamic probabilistic topic models. ASLIB J INFORM MANAG 2022. [DOI: 10.1108/ajim-02-2022-0091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
PurposeA huge volume of published research articles is available on social media which evolves because of the rapid scientific advances and this paper aims to investigate the research structure of social media.Design/methodology/approachThis study employs an integrated topic modeling and text mining-based approach on 30381 Scopus index titles, abstracts, and keywords published between 2006 and 2021. It combines analytical analysis of top-cited reviews with topic modeling as means of semantic validation. The output sequences of the dynamic model are further analyzed using the statistical techniques that facilitate the extraction of topic clusters, communities, and potential inter-topic research directions.FindingsThis paper brings into vision the research structure of social media in terms of topics, temporal topic evolutions, topic trends, emerging, fading, and consistent topics of this domain. It also traces various shifts in topic themes. The hot research topics are the application of the machine or deep learning towards social media in general, alcohol consumption in different regions and its impact, Social engagement and media platforms. Moreover, the consistent topics in both models include food management in disaster, health study of diverse age groups, and emerging topics include drug violence, analysis of social media news for misinformation, and problems of Internet addiction.Originality/valueThis study extends the existing topic modeling-based studies that analyze the social media literature from a specific disciplinary viewpoint. It focuses on semantic validations of topic-modeling output and correlations among the topics and also provides a two-stage cluster analysis of the topics.
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Sahu M, Gupta R, Ambasta RK, Kumar P. Artificial intelligence and machine learning in precision medicine: A paradigm shift in big data analysis. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2022; 190:57-100. [PMID: 36008002 DOI: 10.1016/bs.pmbts.2022.03.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
The integration of artificial intelligence in precision medicine has revolutionized healthcare delivery. Precision medicine identifies the phenotype of particular patients with less-common responses to treatment. Recent studies have demonstrated that translational research exploring the convergence between artificial intelligence and precision medicine will help solve the most difficult challenges facing precision medicine. Here, we discuss different aspects of artificial intelligence in precision medicine that improve healthcare delivery. First, we discuss how artificial intelligence changes the landscape of precision medicine and the evolution of artificial intelligence in precision medicine. Second, we highlight the synergies between artificial intelligence and precision medicine and promises of artificial intelligence and precision medicine in healthcare delivery. Third, we briefly explain the promise of big data analytics and the integration of nanomaterials in precision medicine. Last, we highlight the challenges and opportunities of artificial intelligence in precision medicine.
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Affiliation(s)
- Mehar Sahu
- Molecular Neuroscience and Functional Genomics Laboratory, Delhi Technological University (Formerly Delhi College of Engineering), Shahbad Daulatpur, Delhi, India
| | - Rohan Gupta
- Molecular Neuroscience and Functional Genomics Laboratory, Delhi Technological University (Formerly Delhi College of Engineering), Shahbad Daulatpur, Delhi, India
| | - Rashmi K Ambasta
- Molecular Neuroscience and Functional Genomics Laboratory, Delhi Technological University (Formerly Delhi College of Engineering), Shahbad Daulatpur, Delhi, India
| | - Pravir Kumar
- Molecular Neuroscience and Functional Genomics Laboratory, Delhi Technological University (Formerly Delhi College of Engineering), Shahbad Daulatpur, Delhi, India.
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22
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Carroll JC, Liddy C, Afkham A, Keely E, Goh ES, Graham GE, Permaul JA, Allanson J, Heisey R, Makuwaza T, Manca DP, O'Brien MA, Grunfeld E. Use of eConsult to enhance genetics service delivery in primary care: A multimethod study. Genet Med 2022; 24:2034-2041. [PMID: 35947109 DOI: 10.1016/j.gim.2022.07.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 06/30/2022] [Accepted: 07/01/2022] [Indexed: 10/15/2022] Open
Abstract
PURPOSE Electronic consultation (eConsult) is a freely-available secure online platform connecting primary care providers (PCPs) to geneticists. Our purpose was to determine whether eConsult is effective in improving genetics service delivery in primary care. METHODS PCP questionnaires regarding eConsult's utility, geneticists' tracking form assessments of eConsult type and appropriateness, and geneticists' interviews on implementing eConsult were carried out. RESULTS In 2 regions of Ontario, Canada, from January 2019 to June 2020, there were 305 genetics eConsults. For 169 (55%), PCPs indicated receiving good advice for a new course of action; for 110 (36%), referral was now avoided; and for 261 (86%), eConsult was perceived valuable for patient management. Of the 131 geneticist-completed tracking forms, cancer questions were most common (68, 52%). For 63 (48%), geneticists disagreed/strongly disagreed PCPs should know the answer to the referral question. From the interview data, it was observed that geneticists described eConsult positively and suggested how it might improve access and efficiencies if integrated into genetic service delivery. Dealing with eConsults virtually could reduce waitlists, and suggesting appropriate investigations for PCPs could improve efficiencies. CONCLUSION eConsult offers a potential solution for receiving timely genetics advice and avoiding unnecessary patient referrals, however, greater effect on access and wait times will need systematic integration into PCP and geneticist practice.
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Affiliation(s)
- June C Carroll
- Ray D. Wolfe Department of Family Medicine, Mount Sinai Hospital, Sinai Health, Toronto, Ontario, Canada; Department of Family & Community Medicine, University of Toronto, Ontario, Canada.
| | - Clare Liddy
- C.T. Lamont Primary Health Care Research Centre, Bruyere Research Institute, Ottawa, Ontario, Canada; Department of Family Medicine, University of Ottawa, Ontario, Canada; Ontario eConsult Centre of Excellence, The Ottawa Hospital, Ottawa, Ontario, Canada
| | - Amir Afkham
- Ontario Health East, Ottawa, Ontario, Canada
| | - Erin Keely
- Ontario eConsult Centre of Excellence, The Ottawa Hospital, Ottawa, Ontario, Canada; Division of Endocrinology & Metabolism, The Ottawa Hospital, Ottawa, Ontario, Canada; Department of Medicine, University of Ottawa, Ontario, Canada
| | - Elaine S Goh
- Laboratory Medicine and Genetics and Institute for Better Health, Trillium Health Partners, Mississauga, Ontario, Canada; Department of Laboratory Medicine & Pathobiology, University of Toronto, Ontario, Canada
| | - Gail E Graham
- Department of Pediatrics, University of Ottawa, Ontario, Canada; Department of Genetics, Children's Hospital of Eastern Ontario, Ottawa, Ontario, Canada
| | - Joanne A Permaul
- Ray D. Wolfe Department of Family Medicine, Mount Sinai Hospital, Sinai Health, Toronto, Ontario, Canada
| | - Judith Allanson
- Department of Pediatrics, University of Ottawa, Ontario, Canada; Department of Genetics, Children's Hospital of Eastern Ontario, Ottawa, Ontario, Canada
| | - Ruth Heisey
- Department of Family & Community Medicine, University of Toronto, Ontario, Canada; Department of Family and Community Medicine, Women's College Hospital, Toronto, Ontario, Canada
| | - Tutsirai Makuwaza
- Ray D. Wolfe Department of Family Medicine, Mount Sinai Hospital, Sinai Health, Toronto, Ontario, Canada
| | - Donna P Manca
- Department of Family Medicine, Faculty of Medicine & Dentistry, University of Alberta, Edmonton, Alberta, Canada
| | - Mary Ann O'Brien
- Department of Family & Community Medicine, University of Toronto, Ontario, Canada
| | - Eva Grunfeld
- Department of Family & Community Medicine, University of Toronto, Ontario, Canada; Ontario Institute for Cancer Research, Toronto, Ontario, Canada
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23
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Wood GM, van Boom S, Recourt K, Houwink EJF. FHH Quick App Review: How Can a Quality Review Process Assist Primary Care Providers in Choosing a Family Health History App for Patient Care? Genes (Basel) 2022; 13:genes13081407. [PMID: 36011320 PMCID: PMC9407515 DOI: 10.3390/genes13081407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 07/27/2022] [Accepted: 08/03/2022] [Indexed: 11/16/2022] Open
Abstract
Family health history (FHH) is a data type serving risk assessment, diagnosis, research, and preventive health. Despite technological leaps in genomic variant detection, FHH remains the most accessible, least expensive, and most practical assessment tool for assessing risks attributable to genetic inheritance. The purpose of this manuscript is to outline a process to assist primary care professionals in choosing FHH digital tools for patient care based on the new ISO/TS 82304-2 Technical Specification (TS), which is a recently developed method to determine eHealth app quality. With a focus on eHealth in primary care, we applied the quality label concept to FHH, and how a primary care physician can quickly review the quality and reliability of an FHH app. Based on our review of the ISO TS’s 81 questions, we compiled a list of 25 questions that are recommended to be more succinct as an initial review. We call this process the FHH Quick App Review. Our ‘informative-only’ 25 questions do not produce a quality score, but a guide to complete an initial review of FHH apps. Most of the questions are straight from the ISO TS, some are modified or de novo. We believe the 25 questions are not only relevant to FHH app reviews but could also serve to aid app development and clinical implementation.
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Affiliation(s)
| | | | - Kasper Recourt
- Department of Public Health and Primary Care (PHEG), Leiden University Medical Centre, 2333 ZA Leiden, The Netherlands
- National eHealth Living Lab (NELL), 2333 ZD Leiden, The Netherlands
| | - Elisa J. F. Houwink
- Department of Public Health and Primary Care (PHEG), Leiden University Medical Centre, 2333 ZA Leiden, The Netherlands
- National eHealth Living Lab (NELL), 2333 ZD Leiden, The Netherlands
- Correspondence:
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24
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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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25
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Mordenti M, Capicchioni V, Corsini S, Locatelli M, Abelli E, Banchelli F, Boarini M, Sangiorgi L. Preanalytical DNA assessment for downstream applications: How to optimize the management of human biospecimens to support molecular diagnosis-An experimental study. J Clin Lab Anal 2022; 36:e24531. [PMID: 35666551 PMCID: PMC9279999 DOI: 10.1002/jcla.24531] [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: 02/11/2022] [Revised: 05/17/2022] [Accepted: 05/18/2022] [Indexed: 11/09/2022] Open
Abstract
Background The development of next‐generation sequencing approaches has accelerated the diagnostic process, although at present, there is a lack of a clear consensus on efficient management of human samples for downstream applications. This study aims to investigate timeframe (in terms of short preservation), temperature, and additional preservation procedures (i.e., freeze and thaw cycles) for human biospecimens to implement the reliability and reproducibility of molecular investigations. Methods Overall, 45 whole peripheral bloods, 22 peripheral blood mononuclear cells samples, 15 saliva, and 15 buccal swab biospecimens (through the extracted DNA) were investigated, assessing yield, integrity, amplifiability, and sizing accuracy via the most common molecular techniques. Results Based on the overall evaluation criteria, the results indicate that DNA extracted from all samples, shortly preserved, have suitable quality and reliable reproducibility to be used in diagnostic activities and biomedical research, even if DNA from peripheral blood mononuclear cells is more affected by the experimental conditions. Conclusion Our findings confirm the reliability of peripheral blood samples in almost all the experimental conditions. Saliva and buccal swabs are efficient almost as well, while peripheral blood mononuclear cells, albeit remain a primary source of DNA for molecular screenings, represent a less efficient source.
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Affiliation(s)
- Marina Mordenti
- Department of Rare Skeletal Disorders, IRCCS Istituto Ortopedico Rizzoli, Bologna, Italy
| | - Valentina Capicchioni
- Department of Rare Skeletal Disorders, IRCCS Istituto Ortopedico Rizzoli, Bologna, Italy.,Ministry of Education, San Marino, Repubic of San Marino
| | - Serena Corsini
- Department of Rare Skeletal Disorders, IRCCS Istituto Ortopedico Rizzoli, Bologna, Italy
| | - Manuela Locatelli
- Department of Rare Skeletal Disorders, IRCCS Istituto Ortopedico Rizzoli, Bologna, Italy
| | - Elisabetta Abelli
- Department of Rare Skeletal Disorders, IRCCS Istituto Ortopedico Rizzoli, Bologna, Italy
| | - Federico Banchelli
- Department of Rare Skeletal Disorders, IRCCS Istituto Ortopedico Rizzoli, Bologna, Italy
| | - Manila Boarini
- Department of Rare Skeletal Disorders, IRCCS Istituto Ortopedico Rizzoli, Bologna, Italy
| | - Luca Sangiorgi
- Department of Rare Skeletal Disorders, IRCCS Istituto Ortopedico Rizzoli, Bologna, Italy
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26
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Best S, Vidic N, An K, Collins F, White SM. A systematic review of geographical inequities for accessing clinical genomic and genetic services for non-cancer related rare disease. Eur J Hum Genet 2022; 30:645-652. [PMID: 35046503 DOI: 10.1038/s41431-021-01022-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 11/28/2021] [Accepted: 12/02/2021] [Indexed: 11/09/2022] Open
Abstract
Place plays a significant role in our health. As genetic/genomic services evolve and are increasingly seen as mainstream, especially within the field of rare disease, it is important to ensure that where one lives does not impede access to genetic/genomic services. Our aim was to identify barriers and enablers of geographical equity in accessing clinical genomic or genetic services. We undertook a systematic review searching for articles relating to geographical access to genetic/genomic services for rare disease. Searching the databases Medline, EMBASE and PubMed returned 1803 papers. Screening led to the inclusion of 20 articles for data extraction. Using inductive thematic analysis, we identified four themes (i) Current service model design, (ii) Logistical issues facing clinicians and communities, (iii) Workforce capacity and capability and iv) Rural culture and consumer beliefs. Several themes were common to both rural and urban communities. However, many themes were exacerbated for rural populations due to a lack of clinician access to/relationships with genetic specialist staff, the need to provide more generalist services and a lack of genetic/genomic knowledge and skill. Additional barriers included long standing systemic service designs that are not fit for purpose due to historically ad hoc approaches to delivery of care. There were calls for needs assessments to clarify community needs. Enablers of geographically equitable care included the uptake of new innovative models of care and a call to raise both community and clinician knowledge and awareness to demystify the clinical offer from genetics/genomics services.
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Affiliation(s)
- Stephanie Best
- Australian Institute of Health Innovation, Macquarie University, Sydney, NSW, Australia. .,Australian Genomics, Murdoch Children's Research Institute, Melbourne, VIC, Australia.
| | - Nada Vidic
- Australian Genomics, Murdoch Children's Research Institute, Melbourne, VIC, Australia.,School of Women's and Children's Health, University of New South Wales, Sydney, NSW, Australia
| | - Kim An
- Department of Paediatrics, University of Melbourne, Melbourne, VIC, Australia
| | - Felicity Collins
- Clinical Genetics Service, Institute of Precision Medicine and Bioinformatics, Royal Prince Alfred Hospital, Sydney, NSW, Australia.,Divisions of Genomic Medicine, Paediatrics and Child Health, University of Sydney, Sydney, NSW, Australia
| | - Susan M White
- Australian Genomics, Murdoch Children's Research Institute, Melbourne, VIC, Australia.,Department of Paediatrics, University of Melbourne, Melbourne, VIC, Australia.,Victorian Clinical Genetics Services, Melbourne, VIC, Australia
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27
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Madden JA, Brothers KK, Williams JL, Myers MF, Leppig KA, Clayton EW, Wiesner GL, Holm IA. Impact of returning unsolicited genomic results to nongenetic health care providers in the eMERGE III Network. Genet Med 2022; 24:1297-1305. [PMID: 35341654 PMCID: PMC9940614 DOI: 10.1016/j.gim.2022.02.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 02/22/2022] [Accepted: 02/28/2022] [Indexed: 10/18/2022] Open
Abstract
PURPOSE As genomic sequencing becomes more common, medically actionable secondary findings will increasingly be returned to health care providers (HCPs), who will be faced with managing the resulting patient care. These findings are generally unsolicited, ie, unrelated to the sequencing indication and/or ordered by another clinician. METHODS To understand the impact of receiving unsolicited results, we interviewed HCPs who received genomic results for patients enrolled in the Electronic Medical Records and Genomics (eMERGE) Phase III Network, which returned results on >100 actionable genes to eMERGE participants and HCPs. RESULTS In total, 16 HCPs across 3 eMERGE sites were interviewed about their experience of receiving a positive (likely pathogenic or pathogenic), negative, or variant of uncertain significance result for a patient enrolled in eMERGE Phase III and about managing their patient on the basis of the result. Although unsolicited, HCPs felt responsible for managing the patient's resulting medical care. HCPs indicated that clinical utility depended on the actionability of results, and whereas comfort levels varied, confidence was improved by the availability of subspecialist consults. HCPs were concerned about patient anxiety, insurability, and missing an actionable result in the electronic health record. CONCLUSION Our findings help inform best practices for return of unsolicited genomic screening findings in the future.
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Affiliation(s)
- Jill A. Madden
- Division of Genetics & Genomics and the Manton Center for Orphan Disease Research, Boston Children’s Hospital, Boston, MA
| | - Kyle K. Brothers
- Department of Pediatrics, School of Medicine, University of Louisville, Louisville, KY
| | | | - Melanie F. Myers
- Department of Pediatrics, Cincinnati Children’s Hospital Medical Center, and College of Medicine, University of Cincinnati, Cincinnati, OH
| | | | - Ellen Wright Clayton
- Center for Biomedical Ethics and Society and Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN
| | - Georgia L. Wiesner
- Division of Genetic Medicine, Department of Medicine, and Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN
| | - Ingrid A. Holm
- Division of Genetics & Genomics and the Manton Center for Orphan Disease Research, Boston Children’s Hospital, Boston, MA,Department of Pediatrics, Harvard Medical School, Boston, MA,Correspondence and requests for materials should be addressed to Ingrid A. Holm, Division of Genetics and Genomics and the Manton Center for Orphan Disease Research, Boston Children’s Hospital, Boston, MA.
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28
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de Olazarra AS, Cortade DL, Wang SX. From saliva to SNP: non-invasive, point-of-care genotyping for precision medicine applications using recombinase polymerase amplification and giant magnetoresistive nanosensors. LAB ON A CHIP 2022; 22:2131-2144. [PMID: 35537344 PMCID: PMC9156572 DOI: 10.1039/d2lc00233g] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Genetic testing is considered a cornerstone of the precision medicine paradigm. Genotyping of single nucleotide polymorphisms (SNPs) has been shown to provide insights into several important issues, including therapy selection and drug responsiveness. However, a scarcity of widely deployable and cost-effective genotyping tools has limited the integration of precision medicine into routine clinical practice. The objective of our work was to develop a portable, cost-effective, and automated platform that performs SNP genotyping at the point-of-care (POC). Using recombinase polymerase amplification (RPA) and giant magnetoresistive (GMR) nanosensors, we present a highly automated and multiplexed point-of-care platform that utilizes direct saliva for the qualitative genotyping of four SNPs (rs4633, rs4680, rs4818, rs6269) along the catechol-O-methyltransferase gene (COMT), which is associated with the modulation of pain sensitivity and perioperative opioid use. Using this approach, we successfully amplify, detect, and genotype all four of the SNPs, demonstrating 100% accordance between the experimental results obtained using the automated RPA and GMR genotyping assay and the results obtained using a COMT PCR genotyping assay that was formerly validated using pyrosequencing. This automated, portable, and multiplexed RPA and GMR assay shows great promise as a solution for SNP genotyping at the POC and reinforces the broad applications of magnetic nanotechnology in biomedicine.
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Affiliation(s)
| | - Dana Lee Cortade
- Department of Materials Science and Engineering, Stanford University, Stanford, CA 94305, USA
| | - Shan X Wang
- Department of Electrical Engineering, Stanford University, Stanford, CA 94305, USA.
- Department of Materials Science and Engineering, Stanford University, Stanford, CA 94305, USA
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29
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Human Leukocyte Antigen (HLA) System: Genetics and Association with Bacterial and Viral Infections. J Immunol Res 2022; 2022:9710376. [PMID: 35664353 PMCID: PMC9162874 DOI: 10.1155/2022/9710376] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 05/08/2022] [Indexed: 12/19/2022] Open
Abstract
The human leukocyte antigen (HLA) system is one of the most crucial host factors influencing disease progression in bacterial and viral infections. This review provides the basic concepts of the structure and function of HLA molecules in humans. Here, we highlight the main findings on the associations between HLA class I and class II alleles and susceptibility to important infectious diseases such as tuberculosis, leprosy, melioidosis, Staphylococcus aureus infection, human immunodeficiency virus infection, coronavirus disease 2019, hepatitis B, and hepatitis C in populations worldwide. Finally, we discuss challenges in HLA typing to predict disease outcomes in clinical implementation. Evaluation of the impact of HLA variants on the outcome of bacterial and viral infections would improve the understanding of pathogenesis and identify those at risk from infectious diseases in distinct populations and may improve the individual treatment.
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30
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Feng YCA, Stanaway IB, Connolly JJ, Denny JC, Luo Y, Weng C, Wei WQ, Weiss ST, Karlson EW, Smoller JW. Psychiatric manifestations of rare variation in medically actionable genes: a PheWAS approach. BMC Genomics 2022; 23:385. [PMID: 35590255 PMCID: PMC9121574 DOI: 10.1186/s12864-022-08600-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Accepted: 04/22/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND As genomic sequencing moves closer to clinical implementation, there has been an increasing acceptance of returning incidental findings to research participants and patients for mutations in highly penetrant, medically actionable genes. A curated list of genes has been recommended by the American College of Medical Genetics and Genomics (ACMG) for return of incidental findings. However, the pleiotropic effects of these genes are not fully known. Such effects could complicate genetic counseling when returning incidental findings. In particular, there has been no systematic evaluation of psychiatric manifestations associated with rare variation in these genes. RESULTS Here, we leveraged a targeted sequence panel and real-world electronic health records from the eMERGE network to assess the burden of rare variation in the ACMG-56 genes and two psychiatric-associated genes (CACNA1C and TCF4) across common mental health conditions in 15,181 individuals of European descent. As a positive control, we showed that this approach replicated the established association between rare mutations in LDLR and hypercholesterolemia with no visible inflation from population stratification. However, we did not identify any genes significantly enriched with rare deleterious variants that confer risk for common psychiatric disorders after correction for multiple testing. Suggestive associations were observed between depression and rare coding variation in PTEN (P = 1.5 × 10-4), LDLR (P = 3.6 × 10-4), and CACNA1S (P = 5.8 × 10-4). We also observed nominal associations between rare variants in KCNQ1 and substance use disorders (P = 2.4 × 10-4), and APOB and tobacco use disorder (P = 1.1 × 10-3). CONCLUSIONS Our results do not support an association between psychiatric disorders and incidental findings in medically actionable gene mutations, but power was limited with the available sample sizes. Given the phenotypic and genetic complexity of psychiatric phenotypes, future work will require a much larger sequencing dataset to determine whether incidental findings in these genes have implications for risk of psychopathology.
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Affiliation(s)
- Yen-Chen A Feng
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA. .,Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA, USA. .,Institute of Epidemiology and Preventive Medicine, National Taiwan University, Taipei, Taiwan. .,Master of Public Health Program, National Taiwan University, Taipei, Taiwan.
| | - Ian B Stanaway
- Division of Nephrology, School of Medicine, Kidney Research Institute, University of Washington, Seattle, WA, USA
| | - John J Connolly
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Joshua C Denny
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, USA.,Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA.,All of Us Research Program, National Institutes of Health, Besthesda, MD, USA
| | - Yuan Luo
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Chunhua Weng
- Department of Biomedical Informatics, Columbia University Irving Medical Center, New York, NY, USA
| | - Wei-Qi Wei
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Scott T Weiss
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA.,Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Elizabeth W Karlson
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA.,Division of Rheumatology, Inflammation and Immunity, Brigham and Women's Hospital, Boston, MA, USA
| | - Jordan W Smoller
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA. .,Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA, USA. .,Center for Precision Psychiatry, Massachusetts General Hospital, Boston, MA, USA.
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31
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Silva P, Dahlke DV, Smith ML, Charles W, Gomez J, Ory MG, Ramos KS. An Idealized Clinicogenomic Registry to Engage Underrepresented Populations Using Innovative Technology. J Pers Med 2022; 12:jpm12050713. [PMID: 35629136 PMCID: PMC9144063 DOI: 10.3390/jpm12050713] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 04/18/2022] [Accepted: 04/26/2022] [Indexed: 11/26/2022] Open
Abstract
Current best practices in tumor registries provide a glimpse into a limited time frame over the natural history of disease, usually a narrow window around diagnosis and biopsy. This creates challenges meeting public health and healthcare reimbursement policies that increasingly require robust documentation of long-term clinical trajectories, quality of life, and health economics outcomes. These challenges are amplified for underrepresented minority (URM) and other disadvantaged populations, who tend to view the institution of clinical research with skepticism. Participation gaps leave such populations underrepresented in clinical research and, importantly, in policy decisions about treatment choices and reimbursement, thus further augmenting health, social, and economic disparities. Cloud computing, mobile computing, digital ledgers, tokenization, and artificial intelligence technologies are powerful tools that promise to enhance longitudinal patient engagement across the natural history of disease. These tools also promise to enhance engagement by giving participants agency over their data and addressing a major impediment to research participation. This will only occur if these tools are available for use with all patients. Distributed ledger technologies (specifically blockchain) converge these tools and offer a significant element of trust that can be used to engage URM populations more substantively in clinical research. This is a crucial step toward linking composite cohorts for training and optimization of the artificial intelligence tools for enhancing public health in the future. The parameters of an idealized clinical genomic registry are presented.
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Affiliation(s)
- Patrick Silva
- Health Science Center, Texas A&M University, 8441 Riverside Pkwy, Bryan, TX 77807, USA; (J.G.); (K.S.R.)
- Correspondence: ; Tel.: +1-979-436-9055
| | - Deborah Vollmer Dahlke
- School of Public Health, Texas A&M Health Science Center, 212 Adriance Lab Rd., College Station, TX 77843, USA; (D.V.D.); (M.L.S.); (M.G.O.)
| | - Matthew Lee Smith
- School of Public Health, Texas A&M Health Science Center, 212 Adriance Lab Rd., College Station, TX 77843, USA; (D.V.D.); (M.L.S.); (M.G.O.)
| | - Wendy Charles
- BurstIQ, 9635 Maroon Circle, #310, Englewood, CO 80112, USA;
| | - Jorge Gomez
- Health Science Center, Texas A&M University, 8441 Riverside Pkwy, Bryan, TX 77807, USA; (J.G.); (K.S.R.)
| | - Marcia G. Ory
- School of Public Health, Texas A&M Health Science Center, 212 Adriance Lab Rd., College Station, TX 77843, USA; (D.V.D.); (M.L.S.); (M.G.O.)
| | - Kenneth S. Ramos
- Health Science Center, Texas A&M University, 8441 Riverside Pkwy, Bryan, TX 77807, USA; (J.G.); (K.S.R.)
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Brown HL, Sherburn IA, Gaff C, Taylor N, Best S. Structured approaches to implementation of clinical genomics: A scoping review. Genet Med 2022; 24:1415-1424. [PMID: 35442192 DOI: 10.1016/j.gim.2022.03.017] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 03/18/2022] [Accepted: 03/18/2022] [Indexed: 12/23/2022] Open
Abstract
PURPOSE This study aimed to assess the extent to which structured approaches to implementation of clinical genomics, proposed or adapted, are informed by evidence. METHODS A systematic approach was used to identify peer-reviewed articles and gray literature to report on 4 research questions: 1. What structured approaches have been proposed to support implementation? 2. To what extent are the structured approaches informed by evidence? 3. How have structured approaches been deployed in the genomic setting? 4. What are the intended outcomes of the structured approaches? RESULTS A total of 30 unique structured approaches to implementation were reported across 23 peer-reviewed publications and 11 gray literature articles. Most approaches were process models, applied in the preadoption implementation phase, focusing on a "service" outcome. Key findings included a lack of implementation science theory informing the development/implementation of newly designed structured approaches in the genomic setting and a lack of measures to assess implementation effectiveness. CONCLUSION This scoping review identified a significant number of structured approaches developed to inform the implementation of genomic medicine into clinical practice, with limited use of implementation science to support the process. We recommend the use of existing implementation science theory and the expertise of implementation scientists to inform the design of genomic programs being implemented into clinical care.
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Affiliation(s)
- Helen L Brown
- Faculty of Health, Deakin University, Melbourne, Victoria, Australia.
| | - Isabella A Sherburn
- Australian Genomics, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Clara Gaff
- Melbourne Genomics Health Alliance, Walter and Eliza Hall Institute, Melbourne, Victoria, Australia; Department of Paediatrics, Melbourne Medical School, The University of Melbourne, Melbourne, Victoria, Australia
| | - Natalie Taylor
- School of Population Health, Faculty of Medicine, University of New South Wales, Sydney, New South Wales, Australia
| | - Stephanie Best
- Australian Genomics, Murdoch Children's Research Institute, Melbourne, Victoria, Australia; Australian Institute of Health Innovation (AIHI), Macquarie University, Sydney, New South Wales, Australia
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Bos W, Bunnik EM. Informed consent practices for exome sequencing: An interview study with clinical geneticists in the Netherlands. Mol Genet Genomic Med 2022; 10:e1882. [PMID: 35150093 PMCID: PMC8922961 DOI: 10.1002/mgg3.1882] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 12/21/2021] [Accepted: 01/14/2022] [Indexed: 11/07/2022] Open
Abstract
BACKGROUND Genomic sequencing is being used more frequently in the clinic, not only by clinical geneticists, but also by other specialists ("mainstreaming"). The use of genomic sequencing gives rise to challenges regarding informed consent, as it can yield more, and more complex results. METHODS This study maps the informed consent process for exome sequencing in the Netherlands by means of semistructured interviews with 14 clinical geneticists. Interviewees were asked about their strategies for informing patients about exome sequencing and supporting patients in their decision making, about what they think of as essential information elements, about the challenges they experience, and about their preferences for future policy and practice. RESULTS Clinical geneticists typically discuss the following topics: the nature and aim of the test, the possible results (including unsolicited or incidental findings and Variants of Uncertain Significance) of the test and the consequences of those results for the patient and their family members. Some clinical geneticists use a layered approach to informed consent, meaning that they give short and concise information at first, and provide more detailed information depending on the situation or the needs of the patient. CONCLUSION During pre-test counseling for genomic sequencing, clinical geneticists use various strategies to enhance patient understanding and personalization of the informed consent process. Going forward, layering information may be part of a solution to ethical challenges of informed consent, also in mainstream settings.
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Affiliation(s)
- Wendy Bos
- Department of Medical Ethics, Philosophy and History of MedicineErasmus MC, University Medical Centre RotterdamRotterdamthe Netherlands
| | - Eline M. Bunnik
- Department of Medical Ethics, Philosophy and History of MedicineErasmus MC, University Medical Centre RotterdamRotterdamthe Netherlands
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Lee AJ, Hui AC, Walker AD, Peshkin BN, Swain SM, Smith DM. Evaluation of a longitudinal pharmacogenomics education on pharmacist knowledge in a multicampus healthcare system. Pharmacogenomics 2022; 23:173-182. [PMID: 35042388 DOI: 10.2217/pgs-2021-0129] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Aim: To evaluate the effect of pharmacogenomics (PGx) education for pharmacists. Materials & Methods: Three-part weekly webinar series occurred in 2021. Pharmacists were assessed on their PGx knowledge at baseline and after each webinar. The primary end point was a change in the percent of correct responses between the baseline and week 1 assessment. Secondary end points included change in knowledge at weeks 4-8 and change in self-efficacy. Results: In total, 19 of 58 participants were eligible for the primary analysis, which showed an average improvement of 37% (p < 0.0001). Knowledge remained consistent between week 1 and weeks 4-8. Average self-efficacy increased (p < 0.0001) and was maintained at weeks 4-8. Conclusion: The PGx webinar series resulted in a lasting improvement in PGx knowledge and self-efficacy.
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Affiliation(s)
- Andrew J Lee
- Department of Pharmacy, MedStar Union Memorial Hospital, Baltimore, MD 21218, USA
| | - Adrian C Hui
- Department of Pharmacy, MedStar Union Memorial Hospital, Baltimore, MD 21218, USA
| | | | - Beth N Peshkin
- Georgetown University Medical Center, Washington, DC 20057, USA
| | - Sandra M Swain
- MedStar Health, Columbia, MD 21044, USA.,Georgetown University Medical Center, Washington, DC 20057, USA
| | - D Max Smith
- MedStar Health, Columbia, MD 21044, USA.,Georgetown University Medical Center, Washington, DC 20057, USA
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Hernandez S, Fairchild K, Pemberton M, Dahmer J, Zhang W, Palchuk MB, Topaloglu U. Applying FHIR Genomics for Research - From Sequencing to Database. AMIA ... ANNUAL SYMPOSIUM PROCEEDINGS. AMIA SYMPOSIUM 2022; 2022:236-243. [PMID: 35854733 PMCID: PMC9285172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 04/16/2023]
Abstract
The availability of next-generation sequencing (NGS) technologies and their continually declining costs have resulted in the accumulation of large genomic data sets. NGS results have traditionally been delivered in PDF format, and in some cases, structured data, e.g., XML or JSON formats, are also made available, but there is a lack of uniformity around the profiling of external vendor testing platforms. Atrium Health Wake Forest Baptist and TriNetX have harmonized and mapped genomic data to FHIR Genomic standards and imported it into the TriNetX database through a data pipeline. This process is translatable to other sequencing platforms and to other institutions. The addition of genotypic data to the TriNetX database to the reservoir of phenotypic data will promote enhanced industry trial recruitment, (ii) comprehensive intra-institutional genomic benchmarking/quality improvement, and eventually (iii) sweeping inter-institutional genomic research and treatment paradigm shifts.
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Affiliation(s)
| | - Karen Fairchild
- TriNetX, LLC, Cambridge, MA
- HL7 Clinical Genomics Working Group, Ann Arbor, MI
| | - Mark Pemberton
- Information Technology Services, Atrium Health Wake Forest Baptist, Winston-Salem, NC
| | | | - Wei Zhang
- Wake Forest School of Medicine, Winston-Salem, NC
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Hajek C, Hutchinson AM, Galbraith LN, Green RC, Murray MF, Petry N, Preys CL, Zawatsky CLB, Zoltick ES, Christensen KD. Improved provider preparedness through an 8-part genetics and genomic education program. Genet Med 2022; 24:214-224. [PMID: 34906462 PMCID: PMC9121992 DOI: 10.1016/j.gim.2021.08.008] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 06/25/2021] [Accepted: 08/13/2021] [Indexed: 01/03/2023] Open
Abstract
PURPOSE Large-scale genetics education appropriate for general practice providers is a growing priority. We describe the content and impact of a mandatory system-wide program implemented at Sanford Health. METHODS The Imagenetics Initiative at Sanford Health developed a 2-year genetics education program with quarterly web-based modules that were mandatory for all physicians and advanced practice providers. Scores of 0 to 5 were calculated for each module on the basis of the number of objectives that the participants reported as fulfilled. In addition, the participants completed surveys before starting and after finishing the education program, which included a 7-item measure scored 7 to 28 on the perceived preparedness to practice genetics. RESULTS Between 2252 and 2822 Sanford Health employees completed each of the 8 quarterly education modules. The ratings were highest for the module about using genomics to improve patient management (mean score = 4.3) and lowest for the module about different types of genetic tests and specialists. The mean perceived preparedness scores increased from 15.7 at pre-education to 19.1 at post-education (P < .001). CONCLUSION Web-based genetics education was highly effective in increasing health care providers' confidence about using genetics. Both comfort with personal knowledge and confidence regarding access to the system's genomic medicine experts increased significantly. The results demonstrate how scalable approaches can improve provider preparedness.
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Affiliation(s)
- Catherine Hajek
- Sanford Health Imagenetics, Sioux Falls, SD; Sanford School of Medicine, University of South Dakota, Sioux Falls, SD.
| | | | - Lauren N Galbraith
- Department of Population Medicine, Center for Healthcare Research in Pediatrics (CHERP), Harvard Pilgrim Health Care Institute, Boston, MA
| | - Robert C Green
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA; Broad Institute of MIT and Harvard, Cambridge, MA; Department of Medicine, Harvard Medical School, Boston, MA; Ariadne Labs, Boston, MA
| | | | - Natasha Petry
- Sanford Health Imagenetics, Fargo, ND; Department of Pharmacy Practice, School of Pharmacy, North Dakota State University, Fargo, ND
| | - Charlene L Preys
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA; MGH Institute of Health Professions, Boston, MA
| | - Carrie L B Zawatsky
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA; Ariadne Labs, Boston, MA
| | - Emilie S Zoltick
- Department of Population Medicine, Center for Healthcare Research in Pediatrics (CHERP), Harvard Pilgrim Health Care Institute, Boston, MA
| | - Kurt D Christensen
- Department of Population Medicine, Center for Healthcare Research in Pediatrics (CHERP), Harvard Pilgrim Health Care Institute, Boston, MA; Broad Institute of MIT and Harvard, Cambridge, MA; Department of Population Medicine, Harvard Medical School, Boston, MA
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Lessons learned from unsolicited findings in clinical exome sequencing of 16,482 individuals. Eur J Hum Genet 2021; 30:170-177. [PMID: 34697415 PMCID: PMC8821629 DOI: 10.1038/s41431-021-00964-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2021] [Revised: 08/02/2021] [Accepted: 09/09/2021] [Indexed: 12/31/2022] Open
Abstract
Unsolicited findings (UFs) are uncovered unintentionally and predispose to a disease unrelated to the clinical question. The frequency and nature of UFs uncovered in clinical practice remain largely unexplored. We here evaluated UFs identified during a 5-year period in which 16,482 index patients received clinical whole-exome sequencing (WES). UFs were identified in 0.58% (95/16,482) of index patients, indicating that the overall frequency of UFs in clinical WES is low. Fewer UFs were identified using restricted disease-gene panels (0.03%) than when using whole-exome/Mendeliome analysis (1.03%). The UF was disclosed to 86 of 95 individuals, for reasons of medical actionability. Only 61% of these UFs reside in a gene that is listed on the “ACMG59”-list, representing a list of 59 genes for which the American College of Medical Genetics recommends UF disclosure. The remaining 39% were grouped into four categories: disorders similar to “ACMG59”-listed disorders (25%); disorders for which disease manifestation could be influenced (7%); UFs providing reproductive options (2%); and UFs with pharmacogenetic implications (5%). Hence, our experience shows that UFs predisposing to medically actionable disorders affect a broader range of genes than listed on the “ACMG59”, advocating that a pre-defined gene list is too restrictive, and that UFs may require ad hoc evaluation of medical actionability. While both the identification and disclosure of UFs depend on local policy, our lessons learned provide general essential insight into the nature and odds of UFs in clinical exome sequencing.
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Eric V, Yi V, Murdock D, Kalla SE, Wu TJ, Sabo A, Li S, Meng Q, Tian X, Murugan M, Cohen M, Kovar C, Wei WQ, Chung WK, Weng C, Wiesner GL, Jarvik GP, Muzny D, Gibbs RA. Neptune: an environment for the delivery of genomic medicine. Genet Med 2021; 23:1838-1846. [PMID: 34257418 PMCID: PMC8487966 DOI: 10.1038/s41436-021-01230-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Accepted: 05/13/2021] [Indexed: 11/08/2022] Open
Abstract
PURPOSE Genomic medicine holds great promise for improving health care, but integrating searchable and actionable genetic data into electronic health records (EHRs) remains a challenge. Here we describe Neptune, a system for managing the interaction between a clinical laboratory and an EHR system during the clinical reporting process. METHODS We developed Neptune and applied it to two clinical sequencing projects that required report customization, variant reanalysis, and EHR integration. RESULTS Neptune has been applied for the generation and delivery of over 15,000 clinical genomic reports. This work spans two clinical tests based on targeted gene panels that contain 68 and 153 genes respectively. These projects demanded customizable clinical reports that contained a variety of genetic data types including single-nucleotide variants (SNVs), copy-number variants (CNVs), pharmacogenomics, and polygenic risk scores. Two variant reanalysis activities were also supported, highlighting this important workflow. CONCLUSION Methods are needed for delivering structured genetic data to EHRs. This need extends beyond developing data formats to providing infrastructure that manages the reporting process itself. Neptune was successfully applied on two high-throughput clinical sequencing projects to build and deliver clinical reports to EHR systems. The software is open source and available at https://gitlab.com/bcm-hgsc/neptune .
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Affiliation(s)
- Venner Eric
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA.
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.
| | - Victoria Yi
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - David Murdock
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Sara E Kalla
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Tsung-Jung Wu
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Aniko Sabo
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Shoudong Li
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Qingchang Meng
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Xia Tian
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Mullai Murugan
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Michelle Cohen
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Christie Kovar
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Wei-Qi Wei
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Wendy K Chung
- Departments of Pediatrics and Medicine, Columbia University, New York, NY, USA
| | - Chunhua Weng
- Department of Biomedical Informatics, Columbia University, New York, New York, NY, USA
| | - Georgia L Wiesner
- Division of Genetic Medicine, Department of Internal Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Gail P Jarvik
- Department of Medicine (Medical Genetics), University of Washington School of Medicine, Seattle, WA, USA
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Donna Muzny
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 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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Staunton C, Kösters M, Pramstaller PP, Mascalzoni D. Return of research results (RoRR) to the healthy CHRIS cohort: designing a policy with the participants. J Community Genet 2021; 12:577-592. [PMID: 34241790 PMCID: PMC8554916 DOI: 10.1007/s12687-021-00536-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Accepted: 06/06/2021] [Indexed: 11/30/2022] Open
Abstract
Legal, financial and organizational challenges and the absence of coherent international guidelines and legal frameworks still discourage many genetic studies to share individual research results with their participants. Studies and institutions deciding to return genetic results will need to design their own study-specific return policy after due consideration of the ethical responsibilities. The Cooperative Health Research in South Tyrol (CHRIS) study, a healthy cohort study, did not foresee the return of individual genomic results during its baseline phase. However, as it was expected that the follow-up phase would generate an increasing amount of reliable genetic results, an update of the return of research results (RoRR) policy became necessary. To inform this revision, an empirical study using mixed methods was developed to investigate the views of CHRIS research participants (20), local general practitioners (3) and the local genetic counselling service (1). During the interviews, three different examples of potential genetic results with a very diverse potential impact on participants were presented: breast cancer, Parkinson disease and Huntington disease. The CHRIS participants also completed a short questionnaire, collecting personal information and asking for a self-evaluation of their knowledge about genetics. This study made it clear that research participants want to make autonomous decisions on the disclosure or non-disclosure of their results. While the motivations for participants' decisions were very diverse, we were able to identify several common criteria that had a strong influence on their choices. Providing information on these factors is crucial to enable participants to make truly informed decisions.
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Affiliation(s)
- Ciara Staunton
- Institute for Biomedicine, Eurac Research, Affiliated Institute of the University of Lübeck, Via Galvani 31, 39100, Bolzano, Italy
- School of Law, Middlesex University, Room WG35, The Burroughs, Hendon, London, NW4 4BT, UK
| | - Maria Kösters
- Institute for Biomedicine, Eurac Research, Affiliated Institute of the University of Lübeck, Via Galvani 31, 39100, Bolzano, Italy
| | - Peter P Pramstaller
- Institute for Biomedicine, Eurac Research, Affiliated Institute of the University of Lübeck, Via Galvani 31, 39100, Bolzano, Italy
- Department of Neurology, Central Hospital, 39100, Bolzano, Italy
| | - Deborah Mascalzoni
- Institute for Biomedicine, Eurac Research, Affiliated Institute of the University of Lübeck, Via Galvani 31, 39100, Bolzano, Italy.
- Department of Public Health and Caring Science, Uppsala University, CRB, P.O. Box 256, 751 05, Uppsala, Sweden.
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Haidar CE, Petry N, Oxencis C, Douglas JS, Hoffman JM. ASHP Statement on the Pharmacist's Role in Clinical Pharmacogenomics. Am J Health Syst Pharm 2021; 79:704-707. [PMID: 34487145 DOI: 10.1093/ajhp/zxab339] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Affiliation(s)
| | - Natasha Petry
- North Dakota State University, Sanford Health, Fargo, ND, USA
| | | | - Janine S Douglas
- The University of Texas MD Anderson Cancer Center, Houston, TX, USA
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Linder JE, Bastarache L, Hughey JJ, Peterson JF. The Role of Electronic Health Records in Advancing Genomic Medicine. Annu Rev Genomics Hum Genet 2021; 22:219-238. [PMID: 34038146 PMCID: PMC9297710 DOI: 10.1146/annurev-genom-121120-125204] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Recent advances in genomic technology and widespread adoption of electronic health records (EHRs) have accelerated the development of genomic medicine, bringing promising research findings from genome science into clinical practice. Genomic and phenomic data, accrued across large populations through biobanks linked to EHRs, have enabled the study of genetic variation at a phenome-wide scale. Through new quantitative techniques, pleiotropy can be explored with phenome-wide association studies, the occurrence of common complex diseases can be predicted using the cumulative influence of many genetic variants (polygenic risk scores), and undiagnosed Mendelian syndromes can be identified using EHR-based phenotypic signatures (phenotype risk scores). In this review, we trace the role of EHRs from the development of genome-wide analytic techniques to translational efforts to test these new interventions to the clinic. Throughout, we describe the challenges that remain when combining EHRs with genetics to improve clinical care.
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Affiliation(s)
- Jodell E Linder
- Vanderbilt Institute for Clinical and Translational Research, Vanderbilt University Medical Center, Nashville, Tennessee 37203, USA;
| | - Lisa Bastarache
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, Tennessee 37203, USA; , ,
| | - Jacob J Hughey
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, Tennessee 37203, USA; , ,
| | - Josh F Peterson
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, Tennessee 37203, USA; , ,
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee 37203, USA
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Nair SV, Madhulaxmi, Thomas G, Ankathil R. Next-Generation Sequencing in Cancer. J Maxillofac Oral Surg 2021; 20:340-344. [PMID: 34408360 DOI: 10.1007/s12663-020-01462-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Accepted: 09/28/2020] [Indexed: 11/28/2022] Open
Abstract
Objective In this article, we provide a gestalt idea about NGS technologies and their applications in cancer research and molecular diagnosis. Background Next-generation sequencing (NGS) advancements like DNA sequencing and RNA sequencing allow uncovering of genomic, transcriptomic, and epigenomic scenes of individual malignant growths. An assortment of genomic abnormalities can be screened at the same time, for example common and uncommon variations, auxiliary variations like insertions and deletions, copy-number variation, and fusion transcripts. Conclusion NGS innovations together with bioinformatics investigation, which extend our insight, are progressively used to analyze multiple genes in a cost-effective way and have been applied in examining clinical cancer samples and offering NGS-based molecular diagnosis. Application NGS is progressively significant as a device for the diagnosis of cancers.
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Affiliation(s)
- S Vinod Nair
- Department of Oral and Maxillofacial Surgery, P.M.S Dental College, Vattapara, Trivandrum, India
| | - Madhulaxmi
- Department of Oral and Maxillofacial Surgery, Saveetha Dental College, Chennai, India
| | - Gigi Thomas
- Community Medicine, Regional Cancer Centre, Trivandrum, India
| | - Ravindran Ankathil
- Human Genome Centre, School of Medical Sciences, Health Campus, Universiti Sains Malaysia, George Town, Malaysia
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Carroll JC, Morrison S, Miller FA, Wilson BJ, Permaul JA, Allanson J. Anticipating the primary care role in genomic medicine: expectations of genetics health professionals. J Community Genet 2021; 12:559-568. [PMID: 34379295 DOI: 10.1007/s12687-021-00544-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Accepted: 07/27/2021] [Indexed: 02/06/2023] Open
Abstract
Our purpose was to explore genetics health professionals' (GHPs) expectations of primary care providers' (PCPs) role in genomic medicine now and in the future. Focus groups/interviews were conducted with GHPs in Ontario, Canada. Recordings were transcribed and analysed using qualitative descriptive analysis. Five focus groups (6 clinical geneticists, 24 genetic counselors, 1 nurse, 4 laboratory staff, 3 genetics program administrators) and 3 interviews (nurses) were conducted. GHPs described a key role for PCPs in genomic medicine that could be enhanced if GHPs and PCPs worked together more effectively, making better use of GHPs as a scarce specialist resource, improving PCP knowledge and awareness of genomics, and increasing GHPs' understanding of primary care practice and how to provide PCPs meaningful education and support. Health system change is needed to facilitate the GHP/PCP relationship and improve care. This might include: PCPs ordering more genetic tests independently or with GHP guidance prior to GHP consultations, genomic expertise in primary care clinics or GHPs being accessible through buddy systems or virtually through telemedicine or electronic consultation, and developing educational materials and electronic decision support for PCPs. Our findings highlight need for change in delivering genomic medicine, which requires building the relationship between GHPs and PCPs, and creating new service delivery models to meet future needs.
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Affiliation(s)
- June C Carroll
- Department of Family and Community Medicine, Sinai Health, University of Toronto, Toronto, Canada.
| | | | - Fiona A Miller
- Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, Canada
| | - Brenda J Wilson
- Division of Community Health and Humanities, Faculty of Medicine, Memorial University of Newfoundland, St. John's, Canada
| | - Joanne A Permaul
- Ray D. Wolfe Department of Family Medicine, Sinai Health, Toronto, ON, Canada
| | - Judith Allanson
- Department of Genetics, Children's Hospital of Eastern Ontario, Ottawa, Canada.,Department of Pediatrics, University of Ottawa, Ottawa, Canada
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Wendrich K, Krabbenborg L. The use of molecular biomarker tests: an interview study with healthcare providers about a molecular biomarker test for prostate cancer. Per Med 2021; 18:471-482. [PMID: 34353117 DOI: 10.2217/pme-2020-0156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Aim: Investigate why healthcare providers are not always willing to use molecular biomarker tests, even though they promise to personalize disease diagnosis and treatment. Materials & methods: We interviewed 20 Dutch urological healthcare providers to ascertain why they used or did not use SelectMDx, a biomarker test for prostate cancer. Results: Whether and how it was used differed from the developers' expectations, because users and nonusers disagreed about its perceived advantages; the scientific and clinical evidence; the advantages of MRI; and the value of PCA3 testing. Financial issues and the absence of SelectMDx in professional guidelines and hospital care pathways also hampered its use. Conclusion: Eliciting users' and nonusers' views is important to better understand how biomarker tests can be embedded in clinical practice.
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Affiliation(s)
- Karine Wendrich
- Institute for Science in Society, Radboud University, Nijmegen, The Netherlands
| | - Lotte Krabbenborg
- Institute for Science in Society, Radboud University, Nijmegen, The Netherlands
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García-Foncillas J, Argente J, Bujanda L, Cardona V, Casanova B, Fernández-Montes A, Horcajadas JA, Iñiguez A, Ortiz A, Pablos JL, Pérez Gómez MV. Milestones of Precision Medicine: An Innovative, Multidisciplinary Overview. Mol Diagn Ther 2021; 25:563-576. [PMID: 34331269 DOI: 10.1007/s40291-021-00544-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/04/2021] [Indexed: 12/11/2022]
Abstract
Although the concept of precision medicine, in which healthcare is tailored to the molecular and clinical characteristics of each individual, is not new, its implementation in clinical practice has been heterogenous. In some medical specialties, precision medicine has gone from being just a promise to a reality that achieves better patient outcomes. This is a fact if we consider, for example, the great advances made in the genetic diagnosis and subsequent treatment of countless hereditary diseases, such as cystic fibrosis, which have improved the life expectancy of many of the affected children. In the field of oncology, the development of targeted therapies has prolonged the survival of patients with breast, lung, colorectal, melanoma, and hematological malignancies. In other disciplines, clinical milestones are perhaps less well known, but no less important. The current challenge is to expand and generalize the use of technologies that are central to precision medicine, such as massively parallel sequencing, to improve the management (prevention and treatment) of complex conditions such as cardiovascular, kidney, or autoimmune diseases. This process requires investment in specialized expertise, multidisciplinary collaboration, and the nationwide organization of genetic laboratories for diagnosis of specific diseases.
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Affiliation(s)
- Jesús García-Foncillas
- Department of Oncology, Oncohealth Institute, Fundacion Jimenez Diaz University Hospital, Autonomous University, Madrid, Spain. .,Medical Oncology Department, University Hospital Fundación Jiménez Díaz-Universidad Autonoma de Madrid, Madrid, Spain.
| | - Jesús Argente
- Department of Endocrinology, Instituto de Salud Carlos III, IMDEA Institute, Hospital Infantil Universitario Niño Jesús, Spanish PUBERE Registry, CIBER of Obesity and Nutrition (CIBEROBN), Universidad Autónoma de Madrid, Madrid, Spain.,Department of Pediatrics, Instituto de Salud Carlos III, IMDEA Institute, Hospital Infantil Universitario Niño Jesús, Spanish PUBERE Registry, CIBER of Obesity and Nutrition (CIBEROBN), Universidad Autónoma de Madrid, Madrid, Spain
| | - Luis Bujanda
- Department of Gastroenterology, Hospital Donostia/Instituto Biodonostia, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Universidad del País Vasco (UPV/EHU), San Sebastian, Spain
| | - Victoria Cardona
- Allergy Section, Department of Internal Medicine, Hospital Vall d'Hebron, Barcelona, Spain.,ARADyAL Research Network, Barcelona, Spain
| | - Bonaventura Casanova
- Neuroimmunology Unit, La Fe University and Polytechnic Hospital, Valencia, Spain.,Department of Medicine, Faculty of Medicine, University of Valencia, Valencia, Spain
| | - Ana Fernández-Montes
- Medical Oncology, Complejo Hospitalario Universitario de Ourense, Ourense, Spain
| | | | - Andrés Iñiguez
- Department of Cardiology, Hospital Álvaro Cunqueiro-Complejo Hospitalario Universitario, Vigo, Spain
| | - Alberto Ortiz
- Department of Nephrology and Hypertension, IIS-Fundación Jiménez Díaz-UAM, Madrid, Spain
| | - José L Pablos
- Grupo de Enfermedades Inflamatorias y Autoinmunes, Instituto de Investigación Hospital 12 de Octubre, Madrid, Spain.,Servicio de Reumatología, Hospital 12 de Octubre, Universidad Complutense de Madrid, Madrid, Spain
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46
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Best S, Long JC, Gaff C, Braithwaite J, Taylor N. Organizational perspectives on implementing complex health interventions: clinical genomics in Australia. J Health Organ Manag 2021; ahead-of-print. [PMID: 34283896 DOI: 10.1108/jhom-12-2020-0495] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
PURPOSE Clinical genomics is a complex, innovative medical speciality requiring clinical and organizational engagement to fulfil the clinical reward promised to date. Focus thus far has been on gene discovery and clinicians' perspectives. The purpose of this study was to use implementation science theory to identify organizational barriers and enablers to implementation of clinical genomics along an organizations' implementation journey from Preadoption through to Adoption and Implementation. DESIGN/METHODOLOGY/APPROACH We used a deductive qualitative approach study design drawing on implementation science theory - (1) Translation Science to Population Impact Framework, to inform semi structured interviews with organizational decision-makers collaborating with Australian and Melbourne Genomics, alongside and (2) Theoretical Domains Framework (TDF), to guide data analysis. FINDINGS We identified evolving organizational barriers across the implementation journey from Preadoption to Implementation. Initially the organizational focus is on understanding the value of clinical genomics (TDF code: belief about consequences) and setting the scene (TDF code: goals) before organizational (TDF codes: knowledge and belief about consequences) and clinician (TDF codes: belief about capability and intentions) willingness to adopt is apparent. Once at the stage of Implementation, leadership and clarity in organizational priorities (TDF codes: intentions, professional identity and emotion) that include clinical genomics are essential prerequisites to implementing clinical genomics in practice. Intuitive enablers were identified (e.g. 'providing multiple opportunities for people to come on board) and mapped hypothetically to barriers. ORIGINALITY/VALUE Attention to date has centred on the barriers facing clinicians when introducing clinical genomics into practice. This paper uses a combination of implementation science theories to begin to unravel the organizational perspectives of implementing this complex health intervention.
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Affiliation(s)
- Stephanie Best
- Australian Institute of Health Innovation, Macquarie University, North Ryde, Australia.,Australian Genomics, Murdoch Childrens Research Institute, Parkville, Australia
| | - Janet C Long
- Australian Institute of Health Innovation, Macquarie University, North Ryde, Australia
| | - Clara Gaff
- Melbourne Genomics Health Alliance, Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia.,The University of Melbourne, Melbourne, Australia
| | - Jeffrey Braithwaite
- Australian Institute of Health Innovation, Macquarie University, North Ryde, Australia
| | - Natalie Taylor
- Cancer Council New South Wales, Woolloomooloo, Australia.,The University of Sydney, Sydney, Australia
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Haga SB, Mills R, Moaddeb J, Liu Y, Voora D. Delivery of Pharmacogenetic Testing with or without Medication Therapy Management in a Community Pharmacy Setting. PHARMACOGENOMICS & PERSONALIZED MEDICINE 2021; 14:785-796. [PMID: 34276225 PMCID: PMC8277445 DOI: 10.2147/pgpm.s314961] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Accepted: 06/16/2021] [Indexed: 11/23/2022]
Abstract
Objective The delivery of pharmacogenetic (PGx) testing has primarily been through clinical and hospital settings. We conducted a study to explore the feasibility of delivering PGx testing through community pharmacies, a less-studied setting. Methods We conducted a cluster randomized trial of community pharmacies in North Carolina through two approaches: the provision of PGx testing alone or PGx testing with medication therapy management (MTM). Results A total of 150 patient participants were enrolled at 17 pharmacies and reported high satisfaction with their testing experience. Participants in the PGx plus MTM arm were more likely to recall a higher number of results (p=0.04) and more likely to clearly understand their choices for prevention or early detection of side effects (p=0.01). A medication or dose change based on the PGx results was made for 8.7% of participants. Conclusion Limited differences were observed in the provision of PGx testing as a standalone test or combined with MTM. A limited number of treatment changes were made based on PGx test results. Patient acceptance of PGx testing offered through the community pharmacy was very high, but the addition of MTM did not impact patient-reported perceptions about PGx testing or medication adherence.
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Affiliation(s)
- Susanne B Haga
- Center for Applied Genomics & Precision Medicine, Duke University School of Medicine, Durham, NC, 27708, USA
| | - Rachel Mills
- Center for Applied Genomics & Precision Medicine, Duke University School of Medicine, Durham, NC, 27708, USA
| | - Jivan Moaddeb
- Center for Applied Genomics & Precision Medicine, Duke University School of Medicine, Durham, NC, 27708, USA
| | - Yiling Liu
- Center for Applied Genomics & Precision Medicine, Duke University School of Medicine, Durham, NC, 27708, USA
| | - Deepak Voora
- Center for Applied Genomics & Precision Medicine, Duke University School of Medicine, Durham, NC, 27708, USA
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48
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Cordier T, Alonso‐Sáez L, Apothéloz‐Perret‐Gentil L, Aylagas E, Bohan DA, Bouchez A, Chariton A, Creer S, Frühe L, Keck F, Keeley N, Laroche O, Leese F, Pochon X, Stoeck T, Pawlowski J, Lanzén A. Ecosystems monitoring powered by environmental genomics: A review of current strategies with an implementation roadmap. Mol Ecol 2021; 30:2937-2958. [PMID: 32416615 PMCID: PMC8358956 DOI: 10.1111/mec.15472] [Citation(s) in RCA: 76] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 04/25/2020] [Accepted: 05/06/2020] [Indexed: 01/02/2023]
Abstract
A decade after environmental scientists integrated high-throughput sequencing technologies in their toolbox, the genomics-based monitoring of anthropogenic impacts on the biodiversity and functioning of ecosystems is yet to be implemented by regulatory frameworks. Despite the broadly acknowledged potential of environmental genomics to this end, technical limitations and conceptual issues still stand in the way of its broad application by end-users. In addition, the multiplicity of potential implementation strategies may contribute to a perception that the routine application of this methodology is premature or "in development", hence restraining regulators from binding these tools into legal frameworks. Here, we review recent implementations of environmental genomics-based methods, applied to the biomonitoring of ecosystems. By taking a general overview, without narrowing our perspective to particular habitats or groups of organisms, this paper aims to compare, review and discuss the strengths and limitations of four general implementation strategies of environmental genomics for monitoring: (a) Taxonomy-based analyses focused on identification of known bioindicators or described taxa; (b) De novo bioindicator analyses; (c) Structural community metrics including inferred ecological networks; and (d) Functional community metrics (metagenomics or metatranscriptomics). We emphasise the utility of the three latter strategies to integrate meiofauna and microorganisms that are not traditionally utilised in biomonitoring because of difficult taxonomic identification. Finally, we propose a roadmap for the implementation of environmental genomics into routine monitoring programmes that leverage recent analytical advancements, while pointing out current limitations and future research needs.
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Affiliation(s)
- Tristan Cordier
- Department of Genetics and EvolutionScience IIIUniversity of GenevaGenevaSwitzerland
| | - Laura Alonso‐Sáez
- AZTIMarine ResearchBasque Research and Technology Alliance (BRTA)Spain
| | | | - Eva Aylagas
- Red Sea Research Center (RSRC)Biological and Environmental Sciences and Engineering (BESE)King Abdullah University of Science and Technology (KAUST)ThuwalSaudi Arabia
| | - David A. Bohan
- AgroécologieINRAEUniversity of BourgogneUniversity Bourgogne Franche‐ComtéDijonFrance
| | | | - Anthony Chariton
- Department of Biological SciencesMacquarie UniversitySydneyNSWAustralia
| | - Simon Creer
- School of Natural SciencesBangor UniversityGwyneddUK
| | - Larissa Frühe
- Department of EcologyTechnische Universität KaiserslauternKaiserslauternGermany
| | | | - Nigel Keeley
- Benthic Resources and Processes GroupInstitute of Marine ResearchTromsøNorway
| | - Olivier Laroche
- Benthic Resources and Processes GroupInstitute of Marine ResearchTromsøNorway
| | - Florian Leese
- Aquatic Ecosystem ResearchFaculty of BiologyUniversity of Duisburg‐EssenEssenGermany
- Centre for Water and Environmental Research (ZWU)University of Duisburg‐EssenEssenGermany
| | - Xavier Pochon
- Coastal & Freshwater GroupCawthron InstituteNelsonNew Zealand
- Institute of Marine ScienceUniversity of AucklandWarkworthNew Zealand
| | - Thorsten Stoeck
- Department of EcologyTechnische Universität KaiserslauternKaiserslauternGermany
| | - Jan Pawlowski
- Department of Genetics and EvolutionScience IIIUniversity of GenevaGenevaSwitzerland
- ID‐Gene EcodiagnosticsGenevaSwitzerland
- Institute of OceanologyPolish Academy of SciencesSopotPoland
| | - Anders Lanzén
- AZTIMarine ResearchBasque Research and Technology Alliance (BRTA)Spain
- Basque Foundation for ScienceIKERBASQUEBilbaoSpain
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Abstract
ELSI (Ethical, Legal, and Social Issues) is a widely used acronym in the bioethics literature that encompasses a broad range of research examining the various impacts of science and technology on society. In Canada, GE3LS (Genetics, Ethical, Economic, Environmental, Legal, Social issues) is the term used to describe ELSI studies in the context of genetics and genomics research. It is intentionally more expansive in that GE3LS explicitly brings economic and environmental issues under its purview. ELSI/GE3LS research is increasingly relevant in recent years as there has been a greater emphasis on "translational research" that moves genomic discoveries from the bench to the clinic. The purpose of this chapter is to outline a range of ELSI-related work that might be conducted as part of a large scale genetics or genomics research project, and to provide some practical insights on how a scientific research team might incorporate a strong and effective ELSI program within its broader research mandate. We begin by describing the historical context of ELSI research and the development of GE3LS research in the Canadian context. We then illustrate how some ELSI research might unfold by outlining a variety of GE3LS research questions or content domains and the methodologies that might be employed in studying them. We conclude with some practical suggestions about how to build an effective ELSI/GE3LS team and focus within a broader scientific research program.
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50
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Gardner B, Doose M, Sanchez JI, Freedman AN, de Moor JS. Distribution of Genomic Testing Resources by Oncology Practice and Rurality: A Nationally Representative Study. JCO Precis Oncol 2021; 5:PO.21.00109. [PMID: 34568717 PMCID: PMC8457818 DOI: 10.1200/po.21.00109] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 05/04/2021] [Accepted: 05/11/2021] [Indexed: 12/11/2022] Open
Abstract
PURPOSE Oncologists are increasingly using molecular profiling to inform personalized patient treatment decisions. Despite its promising utility, the integration of genomic testing into diverse clinical health care settings across geographic settings has been understudied. METHODS We used data from the National Survey of Precision Medicine in Cancer Treatment, a nationally representative sample of practicing US oncologists, to assess the availability of six genomic testing resources, including on-site pathology, contracts with outside laboratories, on-site genetic counselors, internal policies or protocols for using genomic and biomarker testing, electronic medical record alerts, and genomic or molecular tumor boards. We used multivariate logistic regression models to examine differences in the availability of each genomic testing resource by practice type and rurality while adjusting for payer mix and patient volume. RESULTS A larger proportion of multispecialty group and academic practices had genomic testing resources available compared with solo and nonacademic practices. Electronic medical record alerts were the least available resource, whereas contracts with outside laboratories were the most available resource. Compared with urban practices, there were significantly fewer practices located in rural areas that had on-site pathology, on-site genetic counselors, protocols for genomic tests, and molecular tumor boards. CONCLUSION Genomic testing resources varied by practice type and geography among a nationally representative sample of practicing oncologists. This variation has important implications for the development of interventions and policies to support the more equitable delivery of precision oncology to patients with cancer.
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Affiliation(s)
- Brittany Gardner
- Division of Cancer Control and Population Sciences, National Cancer Institute, Rockville, MD
| | - Michelle Doose
- Healthcare Delivery Research Program, Division of Cancer Control and Population Sciences, National Cancer Institute, Rockville, MD
| | - Janeth I. Sanchez
- Healthcare Delivery Research Program, Division of Cancer Control and Population Sciences, National Cancer Institute, Rockville, MD
| | - Andrew N. Freedman
- Epidemiology and Genomics Research Program, Division of Cancer Control and Population Sciences, National Cancer Institute, Rockville, MD
| | - Janet S. de Moor
- Healthcare Delivery Research Program, Division of Cancer Control and Population Sciences, National Cancer Institute, Rockville, MD
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