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Johnson D, Del Fiol G, Kawamoto K, Romagnoli KM, Sanders N, Isaacson G, Jenkins E, Williams MS. Genetically guided precision medicine clinical decision support tools: a systematic review. J Am Med Inform Assoc 2024; 31:1183-1194. [PMID: 38558013 PMCID: PMC11031215 DOI: 10.1093/jamia/ocae033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 02/06/2024] [Accepted: 02/26/2024] [Indexed: 04/04/2024] Open
Abstract
OBJECTIVES Patient care using genetics presents complex challenges. Clinical decision support (CDS) tools are a potential solution because they provide patient-specific risk assessments and/or recommendations at the point of care. This systematic review evaluated the literature on CDS systems which have been implemented to support genetically guided precision medicine (GPM). MATERIALS AND METHODS A comprehensive search was conducted in MEDLINE and Embase, encompassing January 1, 2011-March 14, 2023. The review included primary English peer-reviewed research articles studying humans, focused on the use of computers to guide clinical decision-making and delivering genetically guided, patient-specific assessments, and/or recommendations to healthcare providers and/or patients. RESULTS The search yielded 3832 unique articles. After screening, 41 articles were identified that met the inclusion criteria. Alerts and reminders were the most common form of CDS used. About 27 systems were integrated with the electronic health record; 2 of those used standards-based approaches for genomic data transfer. Three studies used a framework to analyze the implementation strategy. DISCUSSION Findings include limited use of standards-based approaches for genomic data transfer, system evaluations that do not employ formal frameworks, and inconsistencies in the methodologies used to assess genetic CDS systems and their impact on patient outcomes. CONCLUSION We recommend that future research on CDS system implementation for genetically GPM should focus on implementing more CDS systems, utilization of standards-based approaches, user-centered design, exploration of alternative forms of CDS interventions, and use of formal frameworks to systematically evaluate genetic CDS systems and their effects on patient care.
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Affiliation(s)
- Darren Johnson
- Department of Genomic Health, Geisinger Health Systems, Danville, PA 17822, United States
| | - Guilherme Del Fiol
- Department of Biomedical Informatics, University of Utah, Salt Lake City, UT 84108, United States
| | - Kensaku Kawamoto
- Department of Biomedical Informatics, University of Utah, Salt Lake City, UT 84108, United States
| | - Katrina M Romagnoli
- Department of Genomic Health, Geisinger Health Systems, Danville, PA 17822, United States
| | - Nathan Sanders
- School of Medicine, Geisinger Health Systems, Danville, PA 17822, United States
| | - Grace Isaacson
- Family Medicine, Penn Highlands Healthcare, DuBois, PA 16830, United States
| | - Elden Jenkins
- School of Medicine, Noorda College of Osteopathic Medicine, Provo, UT 84606, United States
| | - Marc S Williams
- Department of Genomic Health, Geisinger Health Systems, Danville, PA 17822, United States
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Kwon S, Safer J, Nguyen DT, Hoksza D, May P, Arbesfeld JA, Rubin AF, Campbell AJ, Burgin A, Iqbal S. Genomics 2 Proteins portal: A resource and discovery tool for linking genetic screening outputs to protein sequences and structures. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.02.573913. [PMID: 38260256 PMCID: PMC10802383 DOI: 10.1101/2024.01.02.573913] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Recent advances in AI-based methods have revolutionized the field of structural biology. Concomitantly, high-throughput sequencing and functional genomics technologies have enabled the detection and generation of variants at an unprecedented scale. However, efficient tools and resources are needed to link these two disparate data types - to "map" variants onto protein structures, to better understand how the variation causes disease and thereby design therapeutics. Here we present the Genomics 2 Proteins Portal (G2P; g2p.broadinstitute.org/): a human proteome-wide resource that maps 19,996,443 genetic variants onto 42,413 protein sequences and 77,923 structures, with a comprehensive set of structural and functional features. Additionally, the G2P portal generalizes the capability of linking genomics to proteins beyond databases by allowing users to interactively upload protein residue-wise annotations (variants, scores, etc.) as well as the protein structure to establish the connection. The portal serves as an easy-to-use discovery tool for researchers and scientists to hypothesize the structure-function relationship between natural or synthetic variations and their molecular phenotype.
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Morgan NV. Editorial: Case reports in cardiovascular genetics and systems medicine: 2022. Front Cardiovasc Med 2023; 10:1282147. [PMID: 37767370 PMCID: PMC10520268 DOI: 10.3389/fcvm.2023.1282147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Accepted: 09/04/2023] [Indexed: 09/29/2023] Open
Affiliation(s)
- Neil V. Morgan
- Institute of Cardiovascular Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom
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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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5
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Halim-Fikri H, Syed-Hassan SNRK, Wan-Juhari WK, Assyuhada MGSN, Hernaningsih Y, Yusoff NM, Merican AF, Zilfalil BA. Central resources of variant discovery and annotation and its role in precision medicine. ASIAN BIOMED 2022; 16:285-298. [PMID: 37551357 PMCID: PMC10392146 DOI: 10.2478/abm-2022-0032] [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] [Indexed: 08/09/2023]
Abstract
Rapid technological advancement in high-throughput genomics, microarray, and deep sequencing technologies has accelerated the possibility of more complex precision medicine research using large amounts of heterogeneous health-related data from patients, including genomic variants. Genomic variants can be identified and annotated based on the reference human genome either within the sequence as a whole or in a putative functional genomic element. The American College of Medical Genetics and Genomics (ACMG) and the Association for Molecular Pathology (AMP) mutually created standards and guidelines for the appraisal of proof to expand consistency and straightforwardness in clinical variation interpretations. Various efforts toward precision medicine have been facilitated by many national and international public databases that classify and annotate genomic variation. In the present study, several resources are highlighted with recognition and data spreading of clinically important genetic variations.
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Affiliation(s)
- Hashim Halim-Fikri
- Malaysian Node of the Human Variome Project, School of Medical Sciences, Universiti Sains Malaysia, Kelantan16150, Malaysia
| | | | - Wan-Khairunnisa Wan-Juhari
- Malaysian Node of the Human Variome Project, School of Medical Sciences, Universiti Sains Malaysia, Kelantan16150, Malaysia
- Human Genome Centre, School of Medical Sciences, Universiti Sains Malaysia, Kelantan16150, Malaysia
| | - Mat Ghani Siti Nor Assyuhada
- Malaysian Node of the Human Variome Project, School of Medical Sciences, Universiti Sains Malaysia, Kelantan16150, Malaysia
| | - Yetti Hernaningsih
- Department of Clinical Pathology, Faculty of Medicine Universitas Airlangga, Dr. Soetomo Academic General Hospital, Surabaya, Indonesia
| | - Narazah Mohd Yusoff
- Department of Clinical Pathology, Faculty of Medicine Universitas Airlangga, Dr. Soetomo Academic General Hospital, Surabaya, Indonesia
- Clinical Diagnostic Laboratory, Advanced Medical and Dental Institute, Universiti Sains Malaysia, Penang13200, Malaysia
| | - Amir Feisal Merican
- Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur50603, Malaysia
- Center of Research for Computational Sciences and Informatics in Biology, Bio Industry, Environment, Agriculture and Healthcare (CRYSTAL), University of Malaya, Kuala Lumpur50603, Malaysia
| | - Bin Alwi Zilfalil
- Malaysian Node of the Human Variome Project, School of Medical Sciences, Universiti Sains Malaysia, Kelantan16150, Malaysia
- Human Genome Centre, School of Medical Sciences, Universiti Sains Malaysia, Kelantan16150, Malaysia
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Abstract
Pharmacogenomics is increasingly important to guide objective, safe, and effective individualised prescribing. Personalised prescribing has revolutionised treatments in the past decade, allowing clinicians to maximise drug efficacy and minimise adverse effects based on a person’s genetic profile. Opioids, the gold standard for cancer pain relief, are among the commonest medications prescribed in palliative care practice. This narrative review examines the literature surrounding opioid pharmacogenomics and its applicability to the palliative care cancer population. There is currently limited intersection between the fields of palliative care and pharmacogenomics, but growing evidence presents a need to build linkages between the two disciplines. Pharmacogenomic evidence guiding opioid prescribing is currently available for codeine and tramadol, which relates to CYP2D6 gene variants. However, these medications are prescribed less commonly for pain in palliative care. Research is accelerating with other opioids, where oxycodone (CYP2D6) and methadone (CYP2B6, ABCB1) already have moderate evidence of an association in terms of drug metabolism and downstream analgesic response and side effects. OPRM1 and COMT are receiving increasing attention and have implications for all opioids, with changes in opioid dosage requirements observed but they have not yet been studied widely enough to be considered clinically actionable. Current evidence indicates that incorporation of pharmacogenomic testing into opioid prescribing practice should focus on the CYP2D6 gene and its actionable variants. Although opioid pharmacogenomic tests are not widely used in clinical practice, the progressively reducing costs and rapid turnover means greater accessibility and affordability to patients, and thus, clinicians will be increasingly asked to provide guidance in this area. The upsurge in pharmacogenomic research will likely discover more actionable gene variants to expand international guidelines to impact opioid prescribing. This rapidly expanding area requires consideration and monitoring by clinicians in order for key findings with clinical implications to be accessible, meaningfully interpretable and communicated.
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7
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DeVoe E, Oliver GR, Zenka R, Blackburn PR, Cousin MA, Boczek NJ, Kocher JPA, Urrutia R, Klee EW, Zimmermann MT. P 2T 2: Protein Panoramic annoTation Tool for the interpretation of protein coding genetic variants. JAMIA Open 2021; 4:ooab065. [PMID: 34377961 PMCID: PMC8346652 DOI: 10.1093/jamiaopen/ooab065] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 07/06/2021] [Accepted: 07/17/2021] [Indexed: 11/29/2022] Open
Abstract
MOTIVATION Genomic data are prevalent, leading to frequent encounters with uninterpreted variants or mutations with unknown mechanisms of effect. Researchers must manually aggregate data from multiple sources and across related proteins, mentally translating effects between the genome and proteome, to attempt to understand mechanisms. MATERIALS AND METHODS P2T2 presents diverse data and annotation types in a unified protein-centric view, facilitating the interpretation of coding variants and hypothesis generation. Information from primary sequence, domain, motif, and structural levels are presented and also organized into the first Paralog Annotation Analysis across the human proteome. RESULTS Our tool assists research efforts to interpret genomic variation by aggregating diverse, relevant, and proteome-wide information into a unified interactive web-based interface. Additionally, we provide a REST API enabling automated data queries, or repurposing data for other studies. CONCLUSION The unified protein-centric interface presented in P2T2 will help researchers interpret novel variants identified through next-generation sequencing. Code and server link available at github.com/GenomicInterpretation/p2t2.
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Affiliation(s)
- Elias DeVoe
- Clinical and Translational Sciences Institute, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, USA
| | - Gavin R Oliver
- Department of Health Science Research, Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, Minnesota, USA
- Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - Roman Zenka
- Department of Health Science Research, Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, Minnesota, USA
| | - Patrick R Blackburn
- Clinical and Translational Sciences Institute, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, USA
- Center for Individualized Medicine, Mayo Clinic, Jacksonville, Florida, USA
| | - Margot A Cousin
- Department of Health Science Research, Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, Minnesota, USA
- Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - Nicole J Boczek
- Department of Health Science Research, Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, Minnesota, USA
- Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - Jean-Pierre A Kocher
- Department of Health Science Research, Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, Minnesota, USA
- Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - Raul Urrutia
- Genomic Sciences and Precision Medicine Center, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, USA
- Department of Surgery, Medical College of Wisconsin, Milwaukee, Wisconsin, 53226, USA
| | - Eric W Klee
- Department of Health Science Research, Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, Minnesota, USA
- Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - Michael T Zimmermann
- Clinical and Translational Sciences Institute, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, USA
- Genomic Sciences and Precision Medicine Center, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, USA
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8
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Potilinski MC, Tate PS, Lorenc VE, Gallo JE. New insights into oxidative stress and immune mechanisms involved in age-related macular degeneration tackled by novel therapies. Neuropharmacology 2021; 188:108513. [PMID: 33662390 DOI: 10.1016/j.neuropharm.2021.108513] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Revised: 02/14/2021] [Accepted: 02/22/2021] [Indexed: 12/20/2022]
Abstract
The prevalence of age-related macular degeneration (AMD) has increased in the last years. Although anti-VEGF agents have improved the prognosis of exudative AMD, dry AMD has still devastating effects on elderly people vision. Oxidative stress and inflammation are mechanisms involved in AMD pathogenesis and its progression. Molecular pathways involving epidermal growth factor receptor (EGFR), bone morphogenetic protein (BMP4) and the nuclear erythroid related factor 2 (Nrf2) are behind oxidative stress in AMD due to their participation in antioxidant cellular pathways. As a consequence of the disbalance produced in the antioxidant mechanisms, there is an activation of innate and adaptative immune response with cell recruitment, changes in complement factors expression, and modification of cellular milieu. Different therapies are being studied to treat dry AMD based on the possible effects on antioxidant molecular pathways or their action on the immune response. There is a wide range of treatments presented in this review, from natural antioxidant compounds to cell and gene therapy, based on their mechanisms. Finally, we hypothesize that alpha-1-antitrypsin (AAT), an anti-inflammatory and immunomodulatory molecule that can also modulate antioxidant cellular defenses, could be a good candidate for testing in AMD. This article is part of the special ssue on 'The Quest for Disease-Modifying Therapies for Neurodegenerative Disorders'.
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Affiliation(s)
- María Constanza Potilinski
- Nanomedicine & Vision Lab, Instituto de Investigaciones en Medicina Translacional, Universidad Austral, CONICET, Pilar, Buenos Aires, Argentina
| | - Pablo S Tate
- Laboratorio de Enfermedades Neurodegenerativas, Instituto de Investigaciones en Medicina Translacional, Universidad Austral, CONICET, Pilar, Buenos Aires, Argentina
| | - Valeria E Lorenc
- Nanomedicine & Vision Lab, Instituto de Investigaciones en Medicina Translacional, Universidad Austral, CONICET, Pilar, Buenos Aires, Argentina
| | - Juan E Gallo
- Nanomedicine & Vision Lab, Instituto de Investigaciones en Medicina Translacional, Universidad Austral, CONICET, Pilar, Buenos Aires, Argentina; Departamento de Oftalmología, Hospital Universitario Austral, Pilar, Buenos Aires, Argentina.
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10
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Peterson JF, Roden DM, Orlando LA, Ramirez AH, Mensah GA, Williams MS. Building evidence and measuring clinical outcomes for genomic medicine. Lancet 2019; 394:604-610. [PMID: 31395443 PMCID: PMC6730663 DOI: 10.1016/s0140-6736(19)31278-4] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Revised: 04/08/2019] [Accepted: 05/16/2019] [Indexed: 12/13/2022]
Abstract
Human genomic sequencing has potential diagnostic, prognostic, and therapeutic value across a wide breadth of clinical disciplines. One barrier to widespread adoption is the paucity of evidence for improved outcomes in patients who do not already have an indication for more focused testing. In this Series paper, we review clinical outcome studies in genomic medicine and discuss the important features and key challenges to building evidence for next generation sequencing in the context of routine patient care.
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Affiliation(s)
- Josh F Peterson
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, USA; Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA.
| | - Dan M Roden
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, USA; Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA; Department of Pharmacology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Lori A Orlando
- Center for Applied Genomics and Precision Medicine, Duke University School of Medicine, Durham, NC, USA
| | - Andrea H Ramirez
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - George A Mensah
- Center for Translation Research and Implementation Science, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
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11
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Manolio TA, Rowley R, Williams MS, Roden D, Ginsburg GS, Bult C, Chisholm RL, Deverka PA, McLeod HL, Mensah GA, Relling MV, Rodriguez LL, Tamburro C, Green ED. Opportunities, resources, and techniques for implementing genomics in clinical care. Lancet 2019; 394:511-520. [PMID: 31395439 PMCID: PMC6699751 DOI: 10.1016/s0140-6736(19)31140-7] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Revised: 04/09/2019] [Accepted: 05/03/2019] [Indexed: 12/19/2022]
Abstract
Advances in technologies for assessing genomic variation and an increasing understanding of the effects of genomic variants on health and disease are driving the transition of genomics from the research laboratory into clinical care. Genomic medicine, or the use of an individual's genomic information as part of their clinical care, is increasingly gaining acceptance in routine practice, including in assessing disease risk in individuals and their families, diagnosing rare and undiagnosed diseases, and improving drug safety and efficacy. We describe the major types and measurement tools of genomic variation that are currently of clinical importance, review approaches to interpreting genomic sequence variants, identify publicly available tools and resources for genomic test interpretation, and discuss several key barriers in using genomic information in routine clinical practice.
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Affiliation(s)
- Teri A Manolio
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA.
| | - Robb Rowley
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | | | - Dan Roden
- Department of Medicine, Department of Pharmacology, and Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Geoffrey S Ginsburg
- Duke Center for Applied Genomic and Precision Medicine, Duke University, Durham, NC, USA
| | - Carol Bult
- The Jackson Laboratory for Mammalian Genetics, Bar Harbor, ME, USA
| | - Rex L Chisholm
- Center for Genetic Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | | | - Howard L McLeod
- DeBartolo Family Personalized Medicine Institute, Moffitt Cancer Center, Tampa, FL, USA
| | - George A Mensah
- Center for Translation Research and Implementation Science, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Mary V Relling
- Pharmaceutical Sciences Department, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Laura Lyman Rodriguez
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Cecelia Tamburro
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Eric D Green
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
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12
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Gornick MC, Ryan KA, Scherer AM, Roberts JS, De Vries RG, Uhlmann WR. Interpretations of the Term "Actionable" when Discussing Genetic Test Results: What you Mean Is Not What I Heard. J Genet Couns 2019; 28:334-342. [PMID: 30964581 PMCID: PMC10558004 DOI: 10.1007/s10897-018-0289-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Accepted: 08/02/2018] [Indexed: 12/11/2022]
Abstract
In genomic medicine, the familiarity and inexactness of the term "actionable" can lead to multiple interpretations and mistaken beliefs about realistic treatment options. As part of a larger study focusing on public attitudes toward policies for the return of secondary genomic results, we looked at how members of the lay public interpret the term "medically actionable" in the context of genetic testing. We also surveyed a convenience sample of oncologists as part of a separate study and asked them to define the term "medically actionable." After being provided with a definition of the term, 21 out of 60 (35%) layperson respondents wrote an additional action not specified in the provided definition (12 mentioned "cure" and 9 mentioned environment or behavioral change) and 17 (28%) indicated "something can be done" with no action specified. In contrast, 52 surveyed oncologists did not mention environment, behavioral change, or cure. Based on our findings, we propose that rather than using the term "actionable" alone, providers should also say "what they mean" to reduce miscommunication and confusion that could negatively impact medical decision-making. Lastly, to guide clinicians during patient- provider discussion about genetic test results, we provide examples of phrasing to facilitate clearer communication and understanding of the term "actionable."
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Affiliation(s)
- Michele C. Gornick
- Center for Bioethics and Social Sciences in Medicine, University of Michigan Medical School, Ann Arbor, MI
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI
| | - Kerry A. Ryan
- Center for Bioethics and Social Sciences in Medicine, University of Michigan Medical School, Ann Arbor, MI
| | - Aaron M. Scherer
- University of Iowa Carver College of Medicine, Department of Internal Medicine, Iowa City, IA
| | - J. Scott Roberts
- Center for Bioethics and Social Sciences in Medicine, University of Michigan Medical School, Ann Arbor, MI
- Department of Health Behavior & Health Education, School of Public Health, University of Michigan, Ann Arbor, MI
| | - Raymond G. De Vries
- Center for Bioethics and Social Sciences in Medicine, University of Michigan Medical School, Ann Arbor, MI
- Department of Learning Health Sciences, University of Michigan Medical School, Ann Arbor, MI
| | - Wendy R. Uhlmann
- Center for Bioethics and Social Sciences in Medicine, University of Michigan Medical School, Ann Arbor, MI
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI
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13
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Clayton EW, Halverson CM, Sathe NA, Malin BA. A systematic literature review of individuals' perspectives on privacy and genetic information in the United States. PLoS One 2018; 13:e0204417. [PMID: 30379944 PMCID: PMC6209148 DOI: 10.1371/journal.pone.0204417] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Accepted: 09/05/2018] [Indexed: 11/24/2022] Open
Abstract
Concerns about genetic privacy affect individuals' willingness to accept genetic testing in clinical care and to participate in genomics research. To learn what is already known about these views, we conducted a systematic review, which ultimately analyzed 53 studies involving the perspectives of 47,974 participants on real or hypothetical privacy issues related to human genetic data. Bibliographic databases included MEDLINE, Web of Knowledge, and Sociological Abstracts. Three investigators independently screened studies against predetermined criteria and assessed risk of bias. The picture of genetic privacy that emerges from this systematic literature review is complex and riddled with gaps. When asked specifically "are you worried about genetic privacy," the general public, patients, and professionals frequently said yes. In many cases, however, that question was posed poorly or only in the most general terms. While many participants expressed concern that genomic and medical information would be revealed to others, respondents frequently seemed to conflate privacy, confidentiality, control, and security. People varied widely in how much control they wanted over the use of data. They were more concerned about use by employers, insurers, and the government than they were about researchers and commercial entities. In addition, people are often willing to give up some privacy to obtain other goods. Importantly, little attention was paid to understanding the factors-sociocultural, relational, and media-that influence people's opinions and decisions. Future investigations should explore in greater depth which concerns about genetic privacy are most salient to people and the social forces and contexts that influence those perceptions. It is also critical to identify the social practices that will make the collection and use of these data more trustworthy for participants as well as to identify the circumstances that lead people to set aside worries and decide to participate in research.
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Affiliation(s)
- Ellen W. Clayton
- Center for Biomedical Ethics and Society, Vanderbilt University Medical Center, Nashville, TN, United States of America
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN, United States of America
- Center for Genetic Privacy & Identity in Community Settings, Vanderbilt University Medical Center, Nashville, TN, United States of America
| | - Colin M. Halverson
- Center for Biomedical Ethics and Society, Vanderbilt University Medical Center, Nashville, TN, United States of America
| | - Nila A. Sathe
- Vanderbilt Evidence-Based Practice Center, Institute for Medicine and Public Health, and Department of Health Policy, Vanderbilt University Medical Center, Nashville, TN, United States of America
| | - Bradley A. Malin
- Center for Genetic Privacy & Identity in Community Settings, Vanderbilt University Medical Center, Nashville, TN, United States of America
- Departments of Biomedical Informatics and Biostatistics, Vanderbilt University Medical Center, Nashville, TN, United States of America
- Department of Electrical Engineering and Computer Science, Vanderbilt University, Nashville, TN, United States of America
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Scheuner MT, Russell MM, Chanfreau-Coffinier C, Peredo J, Yano EM, Hamilton AB, Lerner B, Provenzale D, Knight SJ, Voils CI. Stakeholders' views on the value of outcomes from clinical genetic and genomic interventions. Genet Med 2018; 21:1371-1380. [PMID: 30377384 DOI: 10.1038/s41436-018-0344-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2018] [Accepted: 10/09/2018] [Indexed: 11/09/2022] Open
Abstract
PURPOSE Robust evidence about the value of clinical genomic interventions (CGIs), such as genetic/genomic testing or clinical genetic evaluation, is limited. We obtained stakeholders' perspectives on outcomes from CGIs to help inform their value. METHODS We used an adapted Delphi expert panel process. Two anonymous survey rounds assessed the value of 44 CGI outcomes and whether a third party should pay for them, with discussion in between rounds. RESULTS Sixty-six panelists responded to the first-round survey and 60 to the second. Policy-makers/payers gave the lowest ratings for value and researchers gave the highest. Patients/consumers had the most uncertainty about value and payment by a third party. Uncertainty about value was observed when evidence of proven health benefit was lacking, potential harms outweighed benefits for reproductive outcomes, and outcomes had only personal utility for individuals or family members. Agreement about outcomes for which a third party should not pay included prevention through surgery with unproven health benefits, establishing ancestry, parental consanguinity, and paternity. CONCLUSION Research is needed to understand factors contributing to uncertainty and stakeholder differences about the value of CGI outcomes. Reaching consensus will accelerate the creation of metrics to generate the evidence needed to inform value and guide policies that promote availability, uptake, and coverage of CGIs.
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Affiliation(s)
- Maren T Scheuner
- Department of Pediatrics, Division of Medical Genetics, University of California-San Francisco, San Francisco, CA, USA. .,San Francisco VA Healthcare System, San Francisco, CA, USA. .,VA HSR&D Center for the Study of Healthcare Innovation Implementation and Policy, Los Angeles, CA, USA.
| | - Marcia M Russell
- VA HSR&D Center for the Study of Healthcare Innovation Implementation and Policy, Los Angeles, CA, USA.,VA Greater Los Angeles Healthcare System, Los Angeles, CA, USA.,Department of Surgery, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Catherine Chanfreau-Coffinier
- VA HSR&D Center for the Study of Healthcare Innovation Implementation and Policy, Los Angeles, CA, USA.,VA Salt Lake City Healthcare System, Salt Lake City, UT, USA
| | - Jane Peredo
- VA Greater Los Angeles Healthcare System, Los Angeles, CA, USA
| | - Elizabeth M Yano
- VA HSR&D Center for the Study of Healthcare Innovation Implementation and Policy, Los Angeles, CA, USA.,Department of Health Policy & Management, UCLA Fielding School of Public Health, Los Angeles, CA, USA
| | - Alison B Hamilton
- VA HSR&D Center for the Study of Healthcare Innovation Implementation and Policy, Los Angeles, CA, USA.,Department of Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | | | - Dawn Provenzale
- VA Cooperative Studies Program Epidemiology Center, Durham, NC, USA.,Duke University School of Medicine, Durham, NC, USA
| | - Sara J Knight
- VA Salt Lake City Healthcare System, Salt Lake City, UT, USA.,Department of Medicine, Division of Epidemiology, University of Utah, Salt Lake City, UT, USA
| | - Corrine I Voils
- William S. Middleton Memorial Veterans Hospital, Madison, WI, USA.,Department of Surgery, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
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15
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Challenges of Identifying Clinically Actionable Genetic Variants for Precision Medicine. JOURNAL OF HEALTHCARE ENGINEERING 2018; 2016:3617572. [PMID: 27195526 PMCID: PMC4955563 DOI: 10.1155/2016/3617572] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/05/2015] [Accepted: 03/17/2016] [Indexed: 12/30/2022]
Abstract
Advances in genomic medicine have the potential to change the way we treat human disease, but translating these advances into reality for improving healthcare outcomes depends essentially on our ability to discover disease- and/or drug-associated clinically actionable genetic mutations. Integration and manipulation of diverse genomic data and comprehensive electronic health records (EHRs) on a big data infrastructure can provide an efficient and effective way to identify clinically actionable genetic variants for personalized treatments and reduce healthcare costs. We review bioinformatics processing of next-generation sequencing (NGS) data, bioinformatics infrastructures for implementing precision medicine, and bioinformatics approaches for identifying clinically actionable genetic variants using high-throughput NGS data and EHRs.
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16
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Crawford DC, Restrepo NA, Diggins KE, Farber-Eger E, Wells QS. Frequency and phenotype consequence of APOC3 rare variants in patients with very low triglyceride levels. BMC Med Genomics 2018; 11:66. [PMID: 30255797 PMCID: PMC6156840 DOI: 10.1186/s12920-018-0387-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Background High levels of triglycerides (TG ≥200 mg/dL) are an emerging risk factor for cardiovascular disease. Conversely, very low levels of TG are associated with decreased risk for cardiovascular disease. Precision medicine aims to capitalize on recent findings that rare variants such as APOC3 R19X (rs76353203) are associated with risk of disease, but it is unclear how population-based associations can be best translated in clinical settings at the individual-patient level. Methods To explore the potential usefulness of screening for genetic predictors of cardiovascular disease, we surveyed BioVU, the Vanderbilt University Medical Center’s biorepository linked to de-identified electronic health records (EHRs), for APOC3 19X mutations among adult European American patients (> 45 and > 55 years of age for men and women, respectively) with the lowest percentile of TG levels. The initial search identified 262 patients with the lowest TG levels in the biorepository; among these, 184 patients with sufficient DNA and the lowest TG levels were chosen for Illumina ExomeChip genotyping. Results A total of two patients were identified as heterozygotes of APOC3 R19X for a minor allele frequency (MAF) of 0.55% in this patient population. Both heterozygous patients had only a single mention of TG in the EHR (31 and 35 mg/dL, respectively), and one patient had evidence of previous cardiovascular disease. Conclusions In this patient population, we identified two patients who were carriers of the APOC3 19X null variant, but only one lacked evidence of disease in the EHR highlighting the challenges of inclusion of functional or previously associated genetic variation in clinical risk assessment. Electronic supplementary material The online version of this article (10.1186/s12920-018-0387-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Dana C Crawford
- Department of Population and Quantitative Health Sciences, Institute for Computational Biology, Case Western Reserve University, 2103 Cornell Road, Wolstein Research Building, Suite 2-527, Cleveland, OH, 44106, USA.
| | - Nicole A Restrepo
- Department of Population and Quantitative Health Sciences, Institute for Computational Biology, Case Western Reserve University, 2103 Cornell Road, Wolstein Research Building, Suite 2-527, Cleveland, OH, 44106, USA
| | - Kirsten E Diggins
- Cancer Biology, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Eric Farber-Eger
- Vanderbilt Institute for Clinical and Translational Research, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Quinn S Wells
- Departments of Medicine and Pharmacology, Vanderbilt University Medical Center, Nashville, TN, USA
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17
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Burbulis IE, Wierman MB, Wolpert M, Haakenson M, Lopes MB, Schiff D, Hicks J, Loe J, Ratan A, McConnell MJ. Improved molecular karyotyping in glioblastoma. Mutat Res 2018; 811:16-26. [PMID: 30055482 DOI: 10.1016/j.mrfmmm.2018.06.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Revised: 06/22/2018] [Accepted: 06/24/2018] [Indexed: 06/08/2023]
Abstract
Uneven replication creates artifacts during whole genome amplification (WGA) that confound molecular karyotype assignment in single cells. Here, we present an improved WGA recipe that increased coverage and detection of copy number variants (CNVs) in single cells. We examined serial resections of glioblastoma (GBM) tumor from the same patient and found low-abundance clones containing CNVs in clinically relevant loci that were not observable using bulk DNA sequencing. We discovered extensive genomic variability in this class of tumor and provide a practical approach for investigating somatic mosaicism.
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Affiliation(s)
- Ian E Burbulis
- Department of Biochemistry and Molecular Genetics, University of Virginia, School of Medicine, Charlottesville, VA, United States; Escuela de Medicina, Universidad San Sebastian, Puerto Montt, Chile
| | - Margaret B Wierman
- Department of Biochemistry and Molecular Genetics, University of Virginia, School of Medicine, Charlottesville, VA, United States
| | - Matt Wolpert
- Department of Biochemistry and Molecular Genetics, University of Virginia, School of Medicine, Charlottesville, VA, United States
| | - Mark Haakenson
- Department of Biochemistry and Molecular Genetics, University of Virginia, School of Medicine, Charlottesville, VA, United States
| | - Maria-Beatriz Lopes
- Department of Pathology, University of Virginia, School of Medicine, Charlottesville, VA, United States
| | - David Schiff
- Department of Neurology, University of Virginia, School of Medicine, Charlottesville, VA, United States
| | - James Hicks
- Michelson Center, University of Southern California, Los Angeles, CA, United States; Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, United States
| | - Justin Loe
- Full Genomes Corp, Inc., Rockville, MD, United States
| | - Aakrosh Ratan
- Department of Biochemistry and Molecular Genetics, University of Virginia, School of Medicine, Charlottesville, VA, United States; Center for Public Health Genomics, University of Virginia, School of Medicine, Charlottesville, VA, United States
| | - Michael J McConnell
- Department of Biochemistry and Molecular Genetics, University of Virginia, School of Medicine, Charlottesville, VA, United States; Department of Neuroscience, University of Virginia, School of Medicine, Charlottesville, VA, United States; Center for Public Health Genomics, University of Virginia, School of Medicine, Charlottesville, VA, United States; Center for Brain Immunology and Glia, University of Virginia, School of Medicine, Charlottesville, VA, United States.
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18
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Abstract
With the increased use of modern next generation sequencing technologies in routine molecular pathology practice, the proportion of cancer cases with a definite or probable hereditary background seems to be steadily increasing. Currently, it is assumed that ≥10% of all malignancies develop in the setting of germline predisposition. Diagnosis and recognition of cancer predisposition syndromes relies not rarely on distinctive histopathological features that proved to be highly valuable and reproducible in uncovering those diseases that would otherwise have gone undetected by clinicians as being hereditary in nature. This is especially true in case of new mutations without suspicious family history. Example of such entities are fumarate hydratase-deficient renal cell carcinoma (RCC), succinate dehydrogenase-deficient RCC, hereditary gastrointestinal stromal tumor syndromes and many other diseases. It is remarkable that many of these inherited cancer syndromes do present as unifocal disease with highly variable age of onset so that many of them are misinterpreted as sporadic on clinical grounds. Availability of specialized cancer screening programs and disease-specific follow-up schemes for several hereditary cancer syndromes encourages the recognition of such disorders, so that "at risk patients" can be enrolled in such programs for early detection and timely intervention/ treatment of these malignancies which are in the majority of cases aggressive. In several conditions, as in familial adenomatous polyposis coli (FAP), well established prophylactic surgical interventions may be adopted to prevent the disease manifestations, highlighting the importance of the timely recognition of these potentially life-limiting neoplasms. In this review, the clinicopathological, demographic and histological features that are considered highly suggestive of a hereditary basis of "a neoplasm under consideration" are highlighted and discussed briefly. The details of some of these entities are in addition dealt with in reviews devoted to them in this special issue.
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Affiliation(s)
- Abbas Agaimy
- Institute of Pathology, Friedrich-Alexander-University Erlangen-Nürnberg, University Hospital, Erlangen, Germany.
| | - Arndt Hartmann
- Institute of Pathology, Friedrich-Alexander-University Erlangen-Nürnberg, University Hospital, Erlangen, Germany
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19
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Marshall DA, Gonzalez JM, MacDonald KV, Johnson FR. Estimating Preferences for Complex Health Technologies: Lessons Learned and Implications for Personalized Medicine. VALUE IN HEALTH : THE JOURNAL OF THE INTERNATIONAL SOCIETY FOR PHARMACOECONOMICS AND OUTCOMES RESEARCH 2017; 20:32-39. [PMID: 28212966 PMCID: PMC5319756 DOI: 10.1016/j.jval.2016.08.737] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2016] [Accepted: 08/26/2016] [Indexed: 05/09/2023]
Abstract
We examine key study design challenges of using stated-preference methods to estimate the value of whole-genome sequencing (WGS) as a specific example of genomic testing. Assessing the value of WGS is complex because WGS provides multiple findings, some of which can be incidental in nature and unrelated to the specific health concerns that motivated the test. In addition, WGS results can include actionable findings (variants considered to be clinically useful and can be acted on), findings for which evidence for best clinical action is not available (variants considered clinically valid but do not meet as high of a standard for clinical usefulness), and findings of unknown significance. We consider three key challenges encountered in designing our national study on the value of WGS-layers of uncertainty, potential downstream consequences with endogenous aspects, and both positive and negative utility associated with testing information-and potential solutions as strategies to address these challenges. We conceptualized the decision to acquire WGS information as a series of sequential choices that are resolved separately. To determine the value of WGS information at the initial decision to undergo WGS, we used contingent valuation questions, and to elicit respondent preferences for reducing risks of health problems and the consequences of taking the steps to reduce these risks, we used a discrete-choice experiment. We conclude by considering the implications for evaluating the value of other complex health technologies that involve multiple forms of uncertainty.
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Affiliation(s)
- Deborah A Marshall
- Department of Community Health Sciences, University of Calgary, Calgary, Alberta, Canada.
| | | | - Karen V MacDonald
- Department of Community Health Sciences, University of Calgary, Calgary, Alberta, Canada
| | - F Reed Johnson
- Duke Clinical Research Institute, Duke University, Durham, NC, USA
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20
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The value of genetic testing: beyond clinical utility. Genet Med 2016; 19:763-771. [DOI: 10.1038/gim.2016.186] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2016] [Accepted: 10/06/2016] [Indexed: 12/26/2022] Open
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21
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Skinner D, Raspberry KA, King M. The nuanced negative: Meanings of a negative diagnostic result in clinical exome sequencing. SOCIOLOGY OF HEALTH & ILLNESS 2016; 38:1303-1317. [PMID: 27538589 PMCID: PMC5089912 DOI: 10.1111/1467-9566.12460] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Genomic sequencing technology is moving rapidly from the research setting into clinical medicine but significant technological and interpretive challenges remain. Exome sequencing (ES) in its recent clinical application provides a genetic diagnosis in about 25 per cent of cases (Berg 2014). While this diagnostic yield is substantial, it also indicates that in a majority of cases, patients are receiving negative results (i.e. no explanatory genetic variant found) from this technology. There are a number of uncertainties regarding the meaning of a negative result in the current context of ES. A negative result may be due to current technological limitations that hinder detection of disease-causing variants or to gaps in the knowledge base that prohibit accurate interpretation of their pathogenicity; or it may indicate that there is not a genetic etiology for the disorder. In this paper we examine the uncertainties and nuances of the negative result from genome sequencing and how both clinicians and patients make meaning of it as revealed in ethnographic observations of the clinic session where results are returned, and in interviews with patients. We find that clinicians and patients construct the meaning of a negative result in ways that are uncertain, contingent, and multivalent; but invested with optimism, promise, and potentiality.
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Affiliation(s)
- Debra Skinner
- FPG Child Development Institute, University of North Carolina at Chapel Hill, USA.
| | - Kelly A Raspberry
- FPG Child Development Institute, University of North Carolina at Chapel Hill, USA
| | - Martha King
- Department of Anthropology, University of North Carolina at Chapel Hill, USA
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22
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Manolio TA. Implementing genomics and pharmacogenomics in the clinic: The National Human Genome Research Institute's genomic medicine portfolio. Atherosclerosis 2016; 253:225-236. [PMID: 27612677 PMCID: PMC5064852 DOI: 10.1016/j.atherosclerosis.2016.08.034] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Revised: 08/19/2016] [Accepted: 08/23/2016] [Indexed: 01/08/2023]
Abstract
Increasing knowledge about the influence of genetic variation on human health and growing availability of reliable, cost-effective genetic testing have spurred the implementation of genomic medicine in the clinic. As defined by the National Human Genome Research Institute (NHGRI), genomic medicine uses an individual's genetic information in his or her clinical care, and has begun to be applied effectively in areas such as cancer genomics, pharmacogenomics, and rare and undiagnosed diseases. In 2011 NHGRI published its strategic vision for the future of genomic research, including an ambitious research agenda to facilitate and promote the implementation of genomic medicine. To realize this agenda, NHGRI is consulting and facilitating collaborations with the external research community through a series of "Genomic Medicine Meetings," under the guidance and leadership of the National Advisory Council on Human Genome Research. These meetings have identified and begun to address significant obstacles to implementation, such as lack of evidence of efficacy, limited availability of genomics expertise and testing, lack of standards, and difficulties in integrating genomic results into electronic medical records. The six research and dissemination initiatives comprising NHGRI's genomic research portfolio are designed to speed the evaluation and incorporation, where appropriate, of genomic technologies and findings into routine clinical care. Actual adoption of successful approaches in clinical care will depend upon the willingness, interest, and energy of professional societies, practitioners, patients, and payers to promote their responsible use and share their experiences in doing so.
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Affiliation(s)
- Teri A Manolio
- Division of Genomic Medicine, National Human Genome Research Institute, 5635 Fishers Lane, Room 4113, MSC 9305, Bethesda MD, USA.
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23
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Moreno Uribe LM, Miller SF. Genetics of the dentofacial variation in human malocclusion. Orthod Craniofac Res 2016; 18 Suppl 1:91-9. [PMID: 25865537 DOI: 10.1111/ocr.12083] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/14/2014] [Indexed: 01/12/2023]
Abstract
Malocclusions affect individuals worldwide, resulting in compromised function and esthetics. Understanding the etiological factors contributing to the variation in dentofacial morphology associated with malocclusions is the key to develop novel treatment approaches. Advances in dentofacial phenotyping, which is the comprehensive characterization of hard and soft tissue variation in the craniofacial complex, together with the acquisition of large-scale genomic data have started to unravel genetic mechanisms underlying facial variation. Knowledge on the genetics of human malocclusion is limited even though results attained thus far are encouraging, with promising opportunities for future research. This review summarizes the most common dentofacial variations associated with malocclusions and reviews the current knowledge of the roles of genes in the development of malocclusions. Lastly, this review will describe ways to advance malocclusion research, following examples from the expanding fields of phenomics and genomic medicine, which aim to better patient outcomes.
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Affiliation(s)
- L M Moreno Uribe
- Department of Orthodontics, College of Dentistry, University of Iowa, Iowa City, IA, USA; Dows Institute for Dental Research, College of Dentistry, University of Iowa, Iowa City, IA, USA
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24
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Manolio TA, Ward R, Ginsburg GS. Clinical implementation of genomic medicine: the importance of global collaboration. EXPERT REVIEW OF PRECISION MEDICINE AND DRUG DEVELOPMENT 2016. [DOI: 10.1080/23808993.2016.1192460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
- Teri A. Manolio
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Robyn Ward
- University of Queensland, Brisbane, QLD, Australia
| | - Geoffrey S. Ginsburg
- Center for Applied Genomics and Precision Medicine, Duke University, Durham, NC, USA
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25
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Marshall DA, Gonzalez JM, Johnson FR, MacDonald KV, Pugh A, Douglas MP, Phillips KA. What are people willing to pay for whole-genome sequencing information, and who decides what they receive? Genet Med 2016; 18:1295-1302. [PMID: 27253734 PMCID: PMC5133139 DOI: 10.1038/gim.2016.61] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2015] [Accepted: 03/30/2016] [Indexed: 01/31/2023] Open
Abstract
PURPOSE Whole genome sequencing (WGS) can be used as a powerful diagnostic tool which could also be used for screening but may generate anxiety, unnecessary testing and overtreatment. Current guidelines suggest reporting clinically actionable secondary findings when diagnostic testing is performed. We estimated preferences for receiving WGS results. METHODS A US nationally representative survey (n=410 adults) was used to rank preferences for who decides (expert panel, your doctor, you) which WGS results are reported. We estimated the value of information about variants with varying levels of clinical usefulness using willingness-to-pay contingent valuation questions. RESULTS 43% preferred to decide themselves what information is included in the WGS report. 38% (95% CI:33–43%) would not pay for actionable variants, and 3% (95% CI:1–5%) would pay more than $1000. 55% (95% CI:50–60%) would not pay for variants in which medical treatment is currently unclear, and 7% (95% CI:5–9%) would pay more than $400. CONCLUSION Most people prefer to decide what WGS results are reported. Despite valuing actionable information more, some respondents perceive that genetic information could negatively impact them. Preference heterogeneity for WGS information should be considered in the development of policies, particularly to integrate patient preferences with personalized medicine and shared decision making.
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Affiliation(s)
- Deborah A Marshall
- Department of Community Health Sciences, University of Calgary, Calgary, Alberta, Canada
| | | | - F Reed Johnson
- Duke Clinical Research Institute, Duke University, Durham, North Carolina, USA
| | - Karen V MacDonald
- Department of Community Health Sciences, University of Calgary, Calgary, Alberta, Canada
| | - Amy Pugh
- Research Triangle Institute, Research Triangle Park, North Carolina, USA
| | - Michael P Douglas
- Department of Clinical Pharmacy, Center for Translational and Policy Research on Personalized Medicine (TRANSPERS), University of California at San Francisco, San Francisco, California, USA
| | - Kathryn A Phillips
- UCSF Philip R. Lee Institute for Health Policy, University of California at San Francisco, San Francisco, California, USA.,UCSF Helen Diller Family Comprehensive Cancer Center, University of California at San Francisco, San Francisco, California, USA
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26
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Klinkenberg-Ramirez S, Neri PM, Volk LA, Samaha SJ, Newmark LP, Pollard S, Varugheese M, Baxter S, Aronson SJ, Rehm HL, Bates DW. Evaluation: A Qualitative Pilot Study of Novel Information Technology Infrastructure to Communicate Genetic Variant Updates. Appl Clin Inform 2016; 7:461-76. [PMID: 27437054 PMCID: PMC4941853 DOI: 10.4338/aci-2015-11-ra-0162] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2015] [Accepted: 03/21/2016] [Indexed: 01/24/2023] Open
Abstract
BACKGROUND Partners HealthCare Personalized Medicine developed GeneInsight Clinic (GIC), a tool designed to communicate updated variant information from laboratory geneticists to treating clinicians through automated alerts, categorized by level of variant interpretation change. OBJECTIVES The study aimed to evaluate feedback from the initial users of the GIC, including the advantages and challenges to receiving this variant information and using this technology at the point of care. METHODS Healthcare professionals from two clinics that ordered genetic testing for cardiomyopathy and related disorders were invited to participate in one-hour semi-structured interviews and/ or a one-hour focus group. Using a Grounded Theory approach, transcript concepts were coded and organized into themes. RESULTS Two genetic counselors and two physicians from two treatment clinics participated in individual interviews. Focus group participants included one genetic counselor and four physicians. Analysis resulted in 8 major themes related to structuring and communicating variant knowledge, GIC's impact on the clinic, and suggestions for improvements. The interview analysis identified longitudinal patient care, family data, and growth in genetic testing content as potential challenges to optimization of the GIC infrastructure. DISCUSSION Participants agreed that GIC implementation increased efficiency and effectiveness of the clinic through increased access to genetic variant information at the point of care. CONCLUSION Development of information technology (IT) infrastructure to aid in the organization and management of genetic variant knowledge will be critical as the genetic field moves towards whole exome and whole genome sequencing. Findings from this study could be applied to future development of IT support for genetic variant knowledge management that would serve to improve clinicians' ability to manage and care for patients.
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Affiliation(s)
| | - Pamela M. Neri
- Clinical and Quality Analysis, Partners HealthCare System, Wellesley, MA
| | - Lynn A. Volk
- Clinical and Quality Analysis, Partners HealthCare System, Wellesley, MA
| | - Sara J. Samaha
- Clinical and Quality Analysis, Partners HealthCare System, Wellesley, MA
| | - Lisa P. Newmark
- Clinical and Quality Analysis, Partners HealthCare System, Wellesley, MA
| | - Stephanie Pollard
- Clinical and Quality Analysis, Partners HealthCare System, Wellesley, MA
| | - Matthew Varugheese
- Information Systems, Partners HealthCare Personalized Medicine, Cambridge, MA
| | - Samantha Baxter
- Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine, Cambridge, MA
| | - Samuel J. Aronson
- Information Systems, Partners HealthCare Personalized Medicine, Cambridge, MA
| | - Heidi L. Rehm
- Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine, Cambridge, MA
- Harvard Medical School, Boston, MA
- Brigham and Women’s Hospital, Boston, MA
| | - David W. Bates
- Clinical and Quality Analysis, Partners HealthCare System, Wellesley, MA
- Harvard Medical School, Boston, MA
- Brigham and Women’s Hospital, Boston, MA
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27
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Hoffman JM, Dunnenberger HM, Kevin Hicks J, Caudle KE, Whirl Carrillo M, Freimuth RR, Williams MS, Klein TE, Peterson JF. Developing knowledge resources to support precision medicine: principles from the Clinical Pharmacogenetics Implementation Consortium (CPIC). J Am Med Inform Assoc 2016; 23:796-801. [PMID: 27026620 DOI: 10.1093/jamia/ocw027] [Citation(s) in RCA: 72] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Accepted: 01/13/2016] [Indexed: 11/13/2022] Open
Abstract
To move beyond a select few genes/drugs, the successful adoption of pharmacogenomics into routine clinical care requires a curated and machine-readable database of pharmacogenomic knowledge suitable for use in an electronic health record (EHR) with clinical decision support (CDS). Recognizing that EHR vendors do not yet provide a standard set of CDS functions for pharmacogenetics, the Clinical Pharmacogenetics Implementation Consortium (CPIC) Informatics Working Group is developing and systematically incorporating a set of EHR-agnostic implementation resources into all CPIC guidelines. These resources illustrate how to integrate pharmacogenomic test results in clinical information systems with CDS to facilitate the use of patient genomic data at the point of care. Based on our collective experience creating existing CPIC resources and implementing pharmacogenomics at our practice sites, we outline principles to define the key features of future knowledge bases and discuss the importance of these knowledge resources for pharmacogenomics and ultimately precision medicine.
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Affiliation(s)
- James M Hoffman
- Department of Pharmaceutical Sciences, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Henry M Dunnenberger
- Center for Molecular Medicine, NorthShore University HealthSystem, Evanston, IL, USA
| | - J Kevin Hicks
- Pharmacy Department and Genomic Medicine Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Kelly E Caudle
- Department of Pharmaceutical Sciences, St Jude Children's Research Hospital, Memphis, TN, USA
| | | | - Robert R Freimuth
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | - Marc S Williams
- Genomic Medicine Institute, Geisinger Health System, Danville, PA, USA
| | - Teri E Klein
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Josh F Peterson
- Departments of Medicine and Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, USA
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Yohe SL, Carter AB, Pfeifer JD, Crawford JM, Cushman-Vokoun A, Caughron S, Leonard DGB. Standards for Clinical Grade Genomic Databases. Arch Pathol Lab Med 2016; 139:1400-12. [PMID: 26516938 DOI: 10.5858/arpa.2014-0568-cp] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
CONTEXT Next-generation sequencing performed in a clinical environment must meet clinical standards, which requires reproducibility of all aspects of the testing. Clinical-grade genomic databases (CGGDs) are required to classify a variant and to assist in the professional interpretation of clinical next-generation sequencing. Applying quality laboratory standards to the reference databases used for sequence-variant interpretation presents a new challenge for validation and curation. OBJECTIVES To define CGGD and the categories of information contained in CGGDs and to frame recommendations for the structure and use of these databases in clinical patient care. DESIGN Members of the College of American Pathologists Personalized Health Care Committee reviewed the literature and existing state of genomic databases and developed a framework for guiding CGGD development in the future. RESULTS Clinical-grade genomic databases may provide different types of information. This work group defined 3 layers of information in CGGDs: clinical genomic variant repositories, genomic medical data repositories, and genomic medicine evidence databases. The layers are differentiated by the types of genomic and medical information contained and the utility in assisting with clinical interpretation of genomic variants. Clinical-grade genomic databases must meet specific standards regarding submission, curation, and retrieval of data, as well as the maintenance of privacy and security. CONCLUSION These organizing principles for CGGDs should serve as a foundation for future development of specific standards that support the use of such databases for patient care.
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Affiliation(s)
| | | | | | | | | | | | - Debra G B Leonard
- From the Department of Laboratory Medicine and Pathology, University of Minnesota Medical Center, Minneapolis (Dr Yohe); the Department of Pathology and Laboratory Medicine and the Department of Biomedical Informatics, Emory University, Atlanta, Georgia (Dr Carter); the Department of Pathology, Washington University School of Medicine, St. Louis, Missouri (Dr Pfeifer); the Department of Pathology and Laboratory Medicine, Hofstra North Shore-Long Island Jewish School of Medicine, Hempstead, New York (Dr Crawford); the Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha (Dr Cushman-Vokoun); the MAWD Pathology Group, North Kansas City, Missouri (Dr Caughron); and the Department of Pathology and Laboratory Medicine, University of Vermont College of Medicine, Burlington (Dr Leonard)
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Read T, Richmond PA, Dowell RD. A trans-acting Variant within the Transcription Factor RIM101 Interacts with Genetic Background to Determine its Regulatory Capacity. PLoS Genet 2016; 12:e1005746. [PMID: 26751950 PMCID: PMC4709078 DOI: 10.1371/journal.pgen.1005746] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2015] [Accepted: 11/25/2015] [Indexed: 11/19/2022] Open
Abstract
Most genetic variants associated with disease occur within regulatory regions of the genome, underscoring the importance of defining the mechanisms underlying differences in regulation of gene expression between individuals. We discovered a pair of co-regulated, divergently oriented transcripts, AQY2 and ncFRE6, that are expressed in one strain of Saccharomyces cerevisiae, ∑1278b, but not in another, S288c. By combining classical genetics techniques with high-throughput sequencing, we identified a trans-acting single nucleotide polymorphism within the transcription factor RIM101 that causes the background-dependent expression of both transcripts. Subsequent RNA-seq experiments revealed that RIM101 regulates many more targets in S288c than in ∑1278b and that deletion of RIM101 in both backgrounds abrogates the majority of differential expression between the strains. Strikingly, only three transcripts undergo a significant change in expression after swapping RIM101 alleles between backgrounds, implying that the differences in the RIM101 allele lead to a remarkably focused transcriptional response. However, hundreds of RIM101-dependent targets undergo a subtle but consistent shift in expression in the S288c RIM101-swapped strain, but not its ∑1278b counterpart. We conclude that ∑1278b may harbor a variant(s) that buffers against widespread transcriptional dysregulation upon introduction of a non-native RIM101 allele, emphasizing the importance of accounting for genetic background when assessing the impact of a regulatory variant.
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Affiliation(s)
- Timothy Read
- Department of Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, Boulder, Colorado, United States of America
| | - Phillip A. Richmond
- Department of Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, Boulder, Colorado, United States of America
- BioFrontiers Institute, University of Colorado, Boulder, Boulder, Colorado, United States of America
| | - Robin D. Dowell
- Department of Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, Boulder, Colorado, United States of America
- BioFrontiers Institute, University of Colorado, Boulder, Boulder, Colorado, United States of America
- * E-mail:
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Reliably Detecting Clinically Important Variants Requires Both Combined Variant Calls and Optimized Filtering Strategies. PLoS One 2015; 10:e0143199. [PMID: 26600436 PMCID: PMC4658170 DOI: 10.1371/journal.pone.0143199] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2015] [Accepted: 11/02/2015] [Indexed: 12/21/2022] Open
Abstract
A diversity of tools is available for identification of variants from genome sequence data. Given the current complexity of incorporating external software into a genome analysis infrastructure, a tendency exists to rely on the results from a single tool alone. The quality of the output variant calls is highly variable however, depending on factors such as sequence library quality as well as the choice of short-read aligner, variant caller, and variant caller filtering strategy. Here we present a two-part study first using the high quality ‘genome in a bottle’ reference set to demonstrate the significant impact the choice of aligner, variant caller, and variant caller filtering strategy has on overall variant call quality and further how certain variant callers outperform others with increased sample contamination, an important consideration when analyzing sequenced cancer samples. This analysis confirms previous work showing that combining variant calls of multiple tools results in the best quality resultant variant set, for either specificity or sensitivity, depending on whether the intersection or union, of all variant calls is used respectively. Second, we analyze a melanoma cell line derived from a control lymphocyte sample to determine whether software choices affect the detection of clinically important melanoma risk-factor variants finding that only one of the three such variants is unanimously detected under all conditions. Finally, we describe a cogent strategy for implementing a clinical variant detection pipeline; a strategy that requires careful software selection, variant caller filtering optimizing, and combined variant calls in order to effectively minimize false negative variants. While implementing such features represents an increase in complexity and computation the results offer indisputable improvements in data quality.
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31
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Christenhusz GM, Devriendt K, Van Esch H, Dierickx K. Ethical signposts for clinical geneticists in secondary variant and incidental finding disclosure discussions. MEDICINE, HEALTH CARE, AND PHILOSOPHY 2015; 18:361-370. [PMID: 25407129 DOI: 10.1007/s11019-014-9611-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
While ethical and empirical interest in so-called secondary variants and incidental findings in clinical genetics contexts is growing, critical reflection on the ethical foundations of the various recommendations proposed is thus far largely lacking. We examine and critique the ethical justifications of the three most prominent disclosure positions: briefly, the clinical geneticist decides, a joint decision, and the patient decides. Subsequently, instead of immediately developing a new disclosure option, we explore relevant foundational ethical values and norms, drawing on the normative and empirical ethical literature. Four ethical signposts are thereby developed to help guide disclosure discussions. These are: respectful sharing of the clinician's expertise; transparent communication; epistemic modesty; and respect for the embedded nature of the patient. We conclude by considering the most common current disclosure positions in the light of the four ethical signposts.
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Manolio TA, Abramowicz M, Al-Mulla F, Anderson W, Balling R, Berger AC, Bleyl S, Chakravarti A, Chantratita W, Chisholm RL, Dissanayake VHW, Dunn M, Dzau VJ, Han BG, Hubbard T, Kolbe A, Korf B, Kubo M, Lasko P, Leego E, Mahasirimongkol S, Majumdar PP, Matthijs G, McLeod HL, Metspalu A, Meulien P, Miyano S, Naparstek Y, O'Rourke PP, Patrinos GP, Rehm HL, Relling MV, Rennert G, Rodriguez LL, Roden DM, Shuldiner AR, Sinha S, Tan P, Ulfendahl M, Ward R, Williams MS, Wong JEL, Green ED, Ginsburg GS. Global implementation of genomic medicine: We are not alone. Sci Transl Med 2015; 7:290ps13. [PMID: 26041702 PMCID: PMC4898888 DOI: 10.1126/scitranslmed.aab0194] [Citation(s) in RCA: 112] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Around the world, innovative genomic-medicine programs capitalize on singular capabilities arising from local health care systems, cultural or political milieus, and unusual selected risk alleles or disease burdens. Such individual efforts might benefit from the sharing of approaches and lessons learned in other locales. The U.S. National Human Genome Research Institute and the National Academy of Medicine recently brought together 25 of these groups to compare projects, to examine the current state of implementation and desired near-term capabilities, and to identify opportunities for collaboration that promote the responsible practice of genomic medicine. Efforts to coalesce these groups around concrete but compelling signature projects should accelerate the responsible implementation of genomic medicine in efforts to improve clinical care worldwide.
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Affiliation(s)
- Teri A Manolio
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892-9305, USA.
| | | | - Fahd Al-Mulla
- Genatak-Global Med Clinic, Kuwait University, Kuwait 46300, Kuwait
| | - Warwick Anderson
- National Health and Medical Research Council, Canberra, ACT 2601, Australia
| | - Rudi Balling
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, L-4362 Luxembourg
| | - Adam C Berger
- Board on Health Sciences Policy, Institute of Medicine, Washington, DC 20001, USA
| | - Steven Bleyl
- Intermountain Healthcare, Salt Lake City, UT 84111, USA
| | - Aravinda Chakravarti
- McKusick-Nathans Institute of Genetic Medicine, John Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | | | - Rex L Chisholm
- Center for Genetic Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Vajira H W Dissanayake
- Human Genetics Unit, Faculty of Medicine, University of Colombo, Colombo 00800, Sri Lanka
| | - Michael Dunn
- Genetic and Molecular Sciences, The Wellcome Trust, London NW1 2BE, UK
| | - Victor J Dzau
- National Academy of Medicine, Washington, DC 20001, USA
| | - Bok-Ghee Han
- Center for Genome Science, Korea National Institute of Health, Chungcheongbuk-do 363-951 Korea
| | - Tim Hubbard
- Department of Medical and Molecular Genetics, King's College, London SE1 9RT, and Genomics England, London EC1M 6BQ, UK
| | - Anne Kolbe
- National Health Committee, Auckland 1050, New Zealand
| | - Bruce Korf
- Center for Genomic Science, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Michiaki Kubo
- Center for Integrative Medical Science (IMS), RIKEN, Yokohama 230-0045, Japan
| | - Paul Lasko
- Institute of Genetics, Canadian Institutes of Health Research, and McGill University, Montreal, Quebec, H3A 0G4 Canada
| | - Erkki Leego
- Estonian Genome Center, University of Tartu, Tartu 51010 Estonia
| | | | - Partha P Majumdar
- National Institute of Biomedical Genomics and Indian Statistical Institute, Kalyani 741251 India
| | - Gert Matthijs
- Center for Human Genetics, University of Leuven (KU Leuven), B-3000 Leuven, Belgium
| | - Howard L McLeod
- DeBartolo Family Personalized Medicine Institute, Moffitt Cancer Center, Tampa, FL 33612 USA
| | - Andres Metspalu
- Estonian Genome Center, University of Tartu, Tartu 51010 Estonia
| | | | - Satoru Miyano
- Institute of Medical Science, University of Tokyo, 108-8639 Tokyo, Japan
| | - Yaakov Naparstek
- Research and Academic Affairs, Hadassah Hebrew University Hospital, Jerusalem 91120, Israel
| | - P Pearl O'Rourke
- Office of Human Research Affairs, Partners HealthCare, Boston, MA 02199, USA
| | - George P Patrinos
- Department of Pharmacy, School of Health Sciences, University of Patras, Patras, 26504 Greece
| | - Heidi L Rehm
- Laboratory for Molecular Medicine, Partners Healthcare Systems, Boston, MA 02139, USA
| | - Mary V Relling
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Gad Rennert
- Carmel Medical Center Department of Community Medicine and Epidemiology, Clalit National Personalized Medicine Program, Haifa 34362, Israel
| | - Laura Lyman Rodriguez
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892-9305, USA
| | - Dan M Roden
- Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Alan R Shuldiner
- Program in Personalized and Genomic Medicine, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Sukdeb Sinha
- Department of Biotechnology, Ministry of Science and Technology, Govt., New Delhi 110 003 India
| | - Patrick Tan
- Duke-National University of Singapore Graduate Medical School, Singapore 169857, Singapore
| | | | - Robyn Ward
- University of Queensland, St. Lucia, QLD 4067 Australia
| | - Marc S Williams
- Genomic Medicine Institute, Geisinger Health System, Danville, PA 18510, USA
| | - John E L Wong
- National University of Singapore, Singapore 119228, Singapore
| | - Eric D Green
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892-9305, USA
| | - Geoffrey S Ginsburg
- Center for Applied Genomics and Precision Medicine, Duke University, Durham, NC 27710, USA.
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Katsanis SH, Minear MA, Vorderstrasse A, Yang N, Reeves JW, Rakhra-Burris T, Cook-Deegan R, Ginsburg GS, Simmons LA. Perspectives on genetic and genomic technologies in an academic medical center: the duke experience. J Pers Med 2015; 5:67-82. [PMID: 25854543 PMCID: PMC4493486 DOI: 10.3390/jpm5020067] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2015] [Revised: 03/16/2015] [Accepted: 04/02/2015] [Indexed: 12/18/2022] Open
Abstract
UNLABELLED In this age of personalized medicine, genetic and genomic testing is expected to become instrumental in health care delivery, but little is known about its actual implementation in clinical practice. METHODS We surveyed Duke faculty and healthcare providers to examine the extent of genetic and genomic testing adoption. We assessed providers' use of genetic and genomic testing options and indications in clinical practice, providers' awareness of pharmacogenetic applications, and providers' opinions on returning research-generated genetic test results to participants. Most clinician respondents currently use family history routinely in their clinical practice, but only 18 percent of clinicians use pharmacogenetics. Only two respondents correctly identified the number of drug package inserts with pharmacogenetic indications. We also found strong support for the return of genetic research results to participants. Our results demonstrate that while Duke healthcare providers are enthusiastic about genomic technologies, use of genomic tools outside of research has been limited. Respondents favor return of research-based genetic results to participants, but clinicians lack knowledge about pharmacogenetic applications. We identified challenges faced by this institution when implementing genetic and genomic testing into patient care that should inform a policy and education agenda to improve provider support and clinician-researcher partnerships.
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Affiliation(s)
- Sara Huston Katsanis
- Center for Applied Genomics and Precision Medicine, Duke University School of Medicine and Health System, Durham, NC 27708, USA.
- Duke Science and Society, Duke University, Durham, NC 27708, USA.
| | - Mollie A Minear
- Center for Applied Genomics and Precision Medicine, Duke University School of Medicine and Health System, Durham, NC 27708, USA.
- Duke Science and Society, Duke University, Durham, NC 27708, USA.
| | - Allison Vorderstrasse
- Center for Applied Genomics and Precision Medicine, Duke University School of Medicine and Health System, Durham, NC 27708, USA.
- Duke University School of Nursing, Durham, NC 27708, USA.
| | - Nancy Yang
- Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
| | | | - Tejinder Rakhra-Burris
- Center for Applied Genomics and Precision Medicine, Duke University School of Medicine and Health System, Durham, NC 27708, USA.
| | - Robert Cook-Deegan
- Center for Applied Genomics and Precision Medicine, Duke University School of Medicine and Health System, Durham, NC 27708, USA.
- Duke Science and Society, Duke University, Durham, NC 27708, USA.
- Sanford School of Public Policy, Duke University, Durham, NC 27708, USA.
| | - Geoffrey S Ginsburg
- Center for Applied Genomics and Precision Medicine, Duke University School of Medicine and Health System, Durham, NC 27708, USA.
| | - Leigh Ann Simmons
- Center for Applied Genomics and Precision Medicine, Duke University School of Medicine and Health System, Durham, NC 27708, USA.
- Duke University School of Nursing, Durham, NC 27708, USA.
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34
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Affiliation(s)
- Alfred L George
- From the Department of Pharmacology and Center for Pharmacogenomics, Northwestern University Feinberg School of Medicine, Chicago, IL.
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35
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Mooney SD. Progress towards the integration of pharmacogenomics in practice. Hum Genet 2014; 134:459-65. [PMID: 25238897 DOI: 10.1007/s00439-014-1484-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2014] [Accepted: 08/20/2014] [Indexed: 12/12/2022]
Abstract
Understanding the role genes and genetic variants play in clinical treatment response continues to be an active area of research with the goal of common clinical use. This goal has developed into today's industry of pharmacogenomics, where new drug-gene relationships are discovered and further characterized, published and then curated into national and international resources for use by researchers and clinicians. These efforts have given us insight into what a pharmacogenomic variant is, and how it differs from human disease variants and common polymorphisms. While publications continue to reveal pharmacogenomic relationships between genes and specific classes of drugs, many challenges remain toward the goal of widespread use clinically. First, the clinical guidelines for pharmacogenomic testing are still in their infancy. Second, sequencing technologies are changing rapidly making it somewhat unclear what genetic data will be available to the clinician at the time of care. Finally, what and when to return data to a patient is an area under constant debate. New innovations such as PheWAS approaches and whole genome sequencing studies are enabling a tsunami of new findings. In this review, pharmacogenomic variants, pharmacogenomic resources, interpretation clinical guidelines and challenges, such as WGS approaches, and the impact of pharmacogenomics on drug development and regulatory approval are reviewed.
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Affiliation(s)
- Sean D Mooney
- Buck Institute for Research on Aging, 8001 Redwood Blvd, Novato, CA, 94945, USA,
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36
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Angrist M, Jamal L. Living laboratory: whole-genome sequencing as a learning healthcare enterprise. Clin Genet 2014; 87:311-8. [PMID: 25045831 DOI: 10.1111/cge.12461] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2014] [Revised: 06/30/2014] [Accepted: 07/15/2014] [Indexed: 01/16/2023]
Abstract
With the proliferation of affordable large-scale human genomic data come profound and vexing questions about management of such data and their clinical uncertainty. These issues challenge the view that genomic research on human beings can (or should) be fully segregated from clinical genomics, either conceptually or practically. Here, we argue that the sharp distinction between clinical care and research is especially problematic in the context of large-scale genomic sequencing of people with suspected genetic conditions. Core goals of both enterprises (e.g. understanding genotype-phenotype relationships; generating an evidence base for genomic medicine) are more likely to be realized at a population scale if both those ordering and those undergoing sequencing for diagnostic reasons are routinely and longitudinally studied. Rather than relying on expensive and lengthy randomized clinical trials and meta-analyses, we propose leveraging nascent clinical-research hybrid frameworks into a broader, more permanent instantiation of exploratory medical sequencing. Such an investment could enlighten stakeholders about the real-life challenges posed by whole-genome sequencing, such as establishing the clinical actionability of genetic variants, returning 'off-target' results to families, developing effective service delivery models and monitoring long-term outcomes.
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Affiliation(s)
- M Angrist
- Science and Society, Social Science Research Institute and Sanford School of Public Policy, Duke University, Durham, NC, USA
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37
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Prows CA, Tran G, Blosser B. Whole exome or genome sequencing: nurses need to prepare families for the possibilities. J Adv Nurs 2014; 70:2736-45. [DOI: 10.1111/jan.12516] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/02/2014] [Indexed: 12/27/2022]
Affiliation(s)
- Cynthia A. Prows
- Division of Human Genetics; Department of Pediatrics; Department of Patient Services; Children's Hospital Medical Center; Cincinnati; Ohio USA
| | - Grace Tran
- The University of Texas MD Anderson Cancer Center; University of Cincinnati, Cincinnati Children's Hospital Medical Center; Ohio USA
| | - Beverly Blosser
- Division of Human Genetics; Cytogenetics Laboratory, Children's Hospital Medical Center, Cincinnati; Ohio USA
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38
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Evidence synthesis and guideline development in genomic medicine: current status and future prospects. Genet Med 2014; 17:63-7. [PMID: 24946156 DOI: 10.1038/gim.2014.69] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2014] [Accepted: 05/07/2014] [Indexed: 01/24/2023] Open
Abstract
PURPOSE With the accelerated implementation of genomic medicine, health-care providers will depend heavily on professional guidelines and recommendations. Because genomics affects many diseases across the life span, no single professional group covers the entirety of this rapidly developing field. METHODS To pursue a discussion of the minimal elements needed to develop evidence-based guidelines in genomics, the Centers for Disease Control and Prevention and the National Cancer Institute jointly held a workshop to engage representatives from 35 organizations with interest in genomics (13 of which make recommendations). The workshop explored methods used in evidence synthesis and guideline development and initiated a dialogue to compare these methods and to assess whether they are consistent with the Institute of Medicine report "Clinical Practice Guidelines We Can Trust." RESULTS The participating organizations that develop guidelines or recommendations all had policies to manage guideline development and group membership, and processes to address conflicts of interests. However, there was wide variation in the reliance on external reviews, regular updating of recommendations, and use of systematic reviews to assess the strength of scientific evidence. CONCLUSION Ongoing efforts are required to establish criteria for guideline development in genomic medicine as proposed by the Institute of Medicine.
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Manolio TA, Green ED. Leading the way to genomic medicine. AMERICAN JOURNAL OF MEDICAL GENETICS PART C-SEMINARS IN MEDICAL GENETICS 2014; 166C:1-7. [PMID: 24619573 DOI: 10.1002/ajmg.c.31384] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The National Human Genome Research Institute, in close collaboration with its research community, is pursuing an ambitious research agenda to facilitate and promote the implementation of genomics in clinical care. Since 2011, research programs utilizing next-generation sequencing in the management of cancer and other multigenic conditions, workup of undiagnosed conditions, and evaluation of disorders of the newborn period have been initiated, along with projects identifying clinically actionable variants and exploring the ethical and social implications of reporting these findings. Several genomic medicine symposia and other consultations have helped to shape these research initiatives and develop educational materials for physicians and others working to implement the use of genomic findings in clinical care. These efforts provide a valuable complement to the highly successful basic genomics research enterprise that has at last enabled the transition of genomics from the bench to the bedside.
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