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Dordunoo D, Limoges J, Chiu P, Puddester R, Carlsson L, Pike A. Genomics-informed nursing strategies and health equity: A scoping review protocol. PLoS One 2023; 18:e0295914. [PMID: 38100433 PMCID: PMC10723661 DOI: 10.1371/journal.pone.0295914] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Accepted: 11/29/2023] [Indexed: 12/17/2023] Open
Abstract
OBJECTIVE The objective of this scoping review is to map the available evidence on strategies that nurses can use to facilitate genomics-informed healthcare to address health disparities. INTRODUCTION Advancements in genomics over the last two decades have led to an increase in the delivery of genomics-informed health care. Although the integration of genomics into health care services continues to enhance patient outcomes, access to genomic technologies is not equitable, exacerbating existing health disparities amongst certain populations. As the largest portion of the health workforce, nurses play a critical role in the delivery of equitable genomics-informed care. However, little is known about how nurses can help address health disparities within the context of genomics-informed health care. A review of the literature will provide the necessary foundation to identify promising practices, policy, and knowledge gaps for further areas of inquiry. INCLUSION CRITERIA We will include papers that explore strategies that nurses can undertake to facilitate genomics-informed care to address health disparities. METHODS This review will be conducted using JBI methodology for scoping reviews. We will search electronic databases including MEDLINE (OVID), EMBASE, Cochrane Library, PsychInfo, and CINAHL for quantitative and qualitative studies, systematic reviews and grey literature. Theses, books, and unavailable full-text papers will be excluded. The search will be limited to papers from 2013 and beyond. Two reviewers will screen titles and abstracts followed by full-text and disagreements will be resolved by a third reviewer. We will use a data extraction tool using Microsoft Excel and analyse data using descriptive statistics and conventional content analysis. Findings will be presented in the form of evidence tables and a narrative summary. We will report findings using the Preferred Reporting Items for Systematic reviews and Meta-Analyses extension for Scoping Reviews (PRISMA-ScR). DISCUSSION Genomics will continue to transform all aspects of health care across the wellness continuum from prevention, assessment, diagnosis, management, treatment, and palliative care. The identification of nursing strategies to address health disparities will build the foundation for policy and practice to ensure that the integration of genomic technologies benefits everyone.
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Affiliation(s)
- Dzifa Dordunoo
- University of Victoria, School of Nursing, Director, Centre for Evidence informed Nursing and Health Care: JBI Centre of Excellence, Victoria, Canada
| | - Jacqueline Limoges
- Athabasca University, Chair, Ontario Cancer Research Ethics Board, Toronto, Canada
| | | | - Rebecca Puddester
- Memorial University of Newfoundland, Faculty of Nursing, St. John’s, Canada
| | | | - April Pike
- Memorial University of Newfoundland, Faculty of Nursing, St. John’s, Canada
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Fahim SM, Alexander CSW, Qian J, Ngorsuraches S, Hohmann NS, Lloyd KB, Reagan A, Hart L, McCormick N, Westrick SC. Current published evidence on barriers and proposed strategies for genetic testing implementation in health care settings: A scoping review. J Am Pharm Assoc (2003) 2023; 63:998-1016. [PMID: 37119989 DOI: 10.1016/j.japh.2023.04.022] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2022] [Revised: 04/20/2023] [Accepted: 04/22/2023] [Indexed: 05/01/2023]
Abstract
BACKGROUND The slow uptake of genetic testing in routine clinical practice warrants the attention of researchers and practitioners to find effective strategies to facilitate implementation. OBJECTIVES This study aimed to identify the barriers to and strategies for pharmacogenetic testing implementation in a health care setting from published literature. METHODS A scoping review was conducted in August 2021 with an expanded literature search using Ovid MEDLINE, Web of Science, International Pharmaceutical Abstract, and Google Scholar to identify studies reporting implementation of pharmacogenetic testing in a health care setting, from a health care system's perspective. Articles were screened using DistillerSR and findings were organized using the 5 major domains of Consolidated Framework for Implementation Research (CFIR). RESULTS A total of 3536 unique articles were retrieved from the above sources, with only 253 articles retained after title and abstract screening. Upon screening the full texts, 57 articles (representing 46 unique practice sites) were found matching the inclusion criteria. We found that most reported barriers and their associated strategies to the implementation of pharmacogenetic testing surrounded 2 CFIR domains: intervention characteristics and inner settings. Factors relating to cost and reimbursement were described as major barriers in the intervention characteristics. In the same domain, another major barrier was the lack of utility studies to provide evidence for genetic testing uptake. Technical hurdles, such as integrating genetic information to medical records, were identified as an inner settings barrier. Collaborations and lessons from early implementers could be useful strategies to overcome majority of the barriers across different health care settings. Strategies proposed by the included implementation studies to overcome these barriers are summarized and can be used as guidance in future. CONCLUSION Barriers and strategies identified in this scoping review can provide implementation guidance for practice sites that are interested in implementing genetic testing.
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Núñez-Samudio V, Arcos-Burgos M, Landires I. Rare diseases: democratising genetic testing in LMICs. Lancet 2023; 401:1339-1340. [PMID: 37087169 DOI: 10.1016/s0140-6736(23)00343-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 02/09/2023] [Indexed: 04/24/2023]
Affiliation(s)
- Virginia Núñez-Samudio
- Unidad de Genética y Salud Pública, Instituto de Ciencias Médicas, Las Tablas 0710-00043, Panama; Sistema Nacional de Investigación, Secretaría Nacional de Ciencia, Tecnología e Innovación, Ciudad del Saber, Clayton, Panama
| | | | - Iván Landires
- Unidad de Genética y Salud Pública, Instituto de Ciencias Médicas, Las Tablas 0710-00043, Panama; Sistema Nacional de Investigación, Secretaría Nacional de Ciencia, Tecnología e Innovación, Ciudad del Saber, Clayton, Panama; Consulta de Genética Médica, Hospital Joaquín Pablo Franco Sayas, Ministry of Health, Las Tablas, Panama.
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Dikilitas O, Sherafati A, Saadatagah S, Satterfield BA, Kochan DC, Anderson KC, Chung WK, Hebbring SJ, Salvati ZM, Sharp RR, Sturm AC, Gibbs RA, Rowley R, Venner E, Linder JE, Jones LK, Perez EF, Peterson JF, Jarvik GP, Rehm HL, Zouk H, Roden DM, Williams MS, Manolio TA, Kullo IJ. Familial Hypercholesterolemia in the Electronic Medical Records and Genomics Network: Prevalence, Penetrance, Cardiovascular Risk, and Outcomes After Return of Results. CIRCULATION. GENOMIC AND PRECISION MEDICINE 2023; 16:e003816. [PMID: 37071725 PMCID: PMC10113961 DOI: 10.1161/circgen.122.003816] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Accepted: 01/03/2023] [Indexed: 02/24/2023]
Abstract
BACKGROUND The implications of secondary findings detected in large-scale sequencing projects remain uncertain. We assessed prevalence and penetrance of pathogenic familial hypercholesterolemia (FH) variants, their association with coronary heart disease (CHD), and 1-year outcomes following return of results in phase III of the electronic medical records and genomics network. METHODS Adult participants (n=18 544) at 7 sites were enrolled in a prospective cohort study to assess the clinical impact of returning results from targeted sequencing of 68 actionable genes, including LDLR, APOB, and PCSK9. FH variant prevalence and penetrance (defined as low-density lipoprotein cholesterol >155 mg/dL) were estimated after excluding participants enrolled on the basis of hypercholesterolemia. Multivariable logistic regression was used to estimate the odds of CHD compared to age- and sex-matched controls without FH-associated variants. Process (eg, referral to a specialist or ordering new tests), intermediate (eg, new diagnosis of FH), and clinical (eg, treatment modification) outcomes within 1 year after return of results were ascertained by electronic health record review. RESULTS The prevalence of FH-associated pathogenic variants was 1 in 188 (69 of 13,019 unselected participants). Penetrance was 87.5%. The presence of an FH variant was associated with CHD (odds ratio, 3.02 [2.00-4.53]) and premature CHD (odds ratio, 3.68 [2.34-5.78]). At least 1 outcome occurred in 92% of participants; 44% received a new diagnosis of FH and 26% had treatment modified following return of results. CONCLUSIONS In a multisite cohort of electronic health record-linked biobanks, monogenic FH was prevalent, penetrant, and associated with presence of CHD. Nearly half of participants with an FH-associated variant received a new diagnosis of FH and a quarter had treatment modified after return of results. These results highlight the potential utility of sequencing electronic health record-linked biobanks to detect FH.
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Affiliation(s)
- Ozan Dikilitas
- Department of Internal Medicine (O.D.), Mayo Clinic, Rochester, MN
- Department of Cardiovascular Medicine (O.D., A.S., S.S., B.A.S., D.C.K., I.J.K.), Mayo Clinic, Rochester, MN
| | - Alborz Sherafati
- Department of Cardiovascular Medicine (O.D., A.S., S.S., B.A.S., D.C.K., I.J.K.), Mayo Clinic, Rochester, MN
| | - Seyedmohammad Saadatagah
- Department of Cardiovascular Medicine (O.D., A.S., S.S., B.A.S., D.C.K., I.J.K.), Mayo Clinic, Rochester, MN
| | - Benjamin A Satterfield
- Department of Cardiovascular Medicine (O.D., A.S., S.S., B.A.S., D.C.K., I.J.K.), Mayo Clinic, Rochester, MN
| | - David C Kochan
- Department of Cardiovascular Medicine (O.D., A.S., S.S., B.A.S., D.C.K., I.J.K.), Mayo Clinic, Rochester, MN
| | - Katherine C Anderson
- Department of Medicine (K.C.A., J.E.L., J.F.P.), Vanderbilt University Medical Center, Nashville, TN
| | - Wendy K Chung
- Departments of Pediatrics and Medicine, Columbia University Irving Medical Center, New York (W.K.C.)
| | | | - Zachary M Salvati
- Genomic Medicine Institute, Geisinger, Danville, PA (Z.M.S., A.C.S., L.K.J., M.S.W.)
| | - Richard R Sharp
- Biomedical Ethics Research Program (R.R.S.), Mayo Clinic, Rochester, MN
| | - Amy C Sturm
- Genomic Medicine Institute, Geisinger, Danville, PA (Z.M.S., A.C.S., L.K.J., M.S.W.)
| | - Richard A Gibbs
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX (R.A.G., E.V.)
| | - Robb Rowley
- National Human Genome Research Institute, Bethesda, MD (R.R., T.A.M.)
| | - Eric Venner
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX (R.A.G., E.V.)
| | - Jodell E Linder
- Department of Medicine (K.C.A., J.E.L., J.F.P.), Vanderbilt University Medical Center, Nashville, TN
| | - Laney K Jones
- Genomic Medicine Institute, Geisinger, Danville, PA (Z.M.S., A.C.S., L.K.J., M.S.W.)
| | - Emma F Perez
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA (E.F.P.)
| | - Josh F Peterson
- Department of Medicine (K.C.A., J.E.L., J.F.P.), Vanderbilt University Medical Center, Nashville, TN
| | - Gail P Jarvik
- Departments of Medicine (Medical Genetics) and Genome Sciences, University of Washington Medical Center, Seattle (G.P.J.)
| | - Heidi L Rehm
- Laboratory for Molecular Medicine, Partners Healthcare Personalized Medicine, Cambridge (H.L.R., H.Z.)
| | - Hana Zouk
- Laboratory for Molecular Medicine, Partners Healthcare Personalized Medicine, Cambridge (H.L.R., H.Z.)
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston (H.Z.)
| | - Dan M Roden
- Departments of Medicine, Pharmacology, and Biomedical Informatics (D.M.R.), Vanderbilt University Medical Center, Nashville, TN
| | - Marc S Williams
- Genomic Medicine Institute, Geisinger, Danville, PA (Z.M.S., A.C.S., L.K.J., M.S.W.)
| | - Teri A Manolio
- National Human Genome Research Institute, Bethesda, MD (R.R., T.A.M.)
| | - Iftikhar J Kullo
- Department of Cardiovascular Medicine (O.D., A.S., S.S., B.A.S., D.C.K., I.J.K.), Mayo Clinic, Rochester, MN
- Gonda Vascular Ctr (I.J.K.), Mayo Clinic, Rochester, MN
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van der Wouden CH, Guchelaar HJ, Swen JJ. Precision Medicine Using Pharmacogenomic Panel-Testing: Current Status and Future Perspectives. Clin Lab Med 2022; 42:587-602. [PMID: 36368784 DOI: 10.1016/j.cll.2022.09.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Cathelijne H van der Wouden
- Department of Clinical Pharmacy & Toxicology, Leiden University Medical Center, Albinusdreef 2, Leiden 2333ZA, The Netherlands; Leiden Network for Personalised Therapeutics, Leiden, The Netherlands
| | - Henk-Jan Guchelaar
- Department of Clinical Pharmacy & Toxicology, Leiden University Medical Center, Albinusdreef 2, Leiden 2333ZA, The Netherlands; Leiden Network for Personalised Therapeutics, Leiden, The Netherlands
| | - Jesse J Swen
- Department of Clinical Pharmacy & Toxicology, Leiden University Medical Center, Albinusdreef 2, Leiden 2333ZA, The Netherlands; Leiden Network for Personalised Therapeutics, Leiden, The Netherlands.
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McCormick CZ, Yu KD, Johns A, Campbell-Salome G, Hallquist MLG, Sturm AC, Buchanan AH. Investigating Psychological Impact after Receiving Genetic Risk Results-A Survey of Participants in a Population Genomic Screening Program. J Pers Med 2022; 12:jpm12121943. [PMID: 36556164 PMCID: PMC9781266 DOI: 10.3390/jpm12121943] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 11/17/2022] [Accepted: 11/19/2022] [Indexed: 11/24/2022] Open
Abstract
Genomic screening programs have potential to benefit individuals who may not be clinically ascertained, but little is known about the psychological impact of receiving genetic results in this setting. The current study sought to further the understanding of individuals’ psychological response to receiving an actionable genetic test result from genomic screening. Telephone surveys were conducted with patient-participants at 6 weeks and 6 months post genetic result disclosure between September 2019 and May 2021 and assessed emotional response to receiving results via the FACToR, PANAS, and decision regret scales. Overall, 354 (29.4%) study participants completed both surveys. Participants reported moderate positive emotions and low levels of negative emotions, uncertainty, privacy concern, and decision regret over time. There were significant decreases in negative emotions (p = 0.0004) and uncertainty (p = 0.0126) between time points on the FACToR scale. “Interested” was the highest scoring discrete emotion (T1 3.6, T2 3.3, scale 0−5) but was significantly lower at 6 months (<0.0001). Coupled with other benefits of genomic screening, these results of modest psychological impact waning over time adds support to clinical utility of population genomic screening programs. However, questions remain regarding how to elicit an emotional response that motivates behavior change without causing psychological harm.
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Affiliation(s)
| | | | - Alicia Johns
- Department of Population Health Sciences, Geisinger, Danville, PA 17822, USA
| | - Gemme Campbell-Salome
- Department of Genomic Health, Geisinger, Danville, PA 17822, USA
- Department of Population Health Sciences, Geisinger, Danville, PA 17822, USA
| | | | - Amy C. Sturm
- Department of Genomic Health, Geisinger, Danville, PA 17822, USA
- 23andMe, Sunnyvale, CA 94086, USA
| | - Adam H. Buchanan
- Department of Genomic Health, Geisinger, Danville, PA 17822, USA
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Husereau D, Steuten L, Muthu V, Thomas DM, Spinner DS, Ivany C, Mengel M, Sheffield B, Yip S, Jacobs P, Sullivan T. Effective and Efficient Delivery of Genome-Based Testing-What Conditions Are Necessary for Health System Readiness? Healthcare (Basel) 2022; 10:healthcare10102086. [PMID: 36292532 PMCID: PMC9602865 DOI: 10.3390/healthcare10102086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 10/09/2022] [Accepted: 10/12/2022] [Indexed: 01/09/2023] Open
Abstract
Health systems internationally must prepare for a future of genetic/genomic testing to inform healthcare decision-making while creating research opportunities. High functioning testing services will require additional considerations and health system conditions beyond traditional diagnostic testing. Based on a literature review of good practices, key informant interviews, and expert discussion, this article attempts to synthesize what conditions are necessary, and what good practice may look like. It is intended to aid policymakers and others designing future systems of genome-based care and care prevention. These conditions include creating communities of practice and healthcare system networks; resource planning; across-region informatics; having a clear entry/exit point for innovation; evaluative function(s); concentrated or coordinated service models; mechanisms for awareness and care navigation; integrating innovation and healthcare delivery functions; and revisiting approaches to financing, education and training, regulation, and data privacy and security. The list of conditions we propose was developed with an emphasis on describing conditions that would be applicable to any healthcare system, regardless of capacity, organizational structure, financing, population characteristics, standardization of care processes, or underlying culture.
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Affiliation(s)
- Don Husereau
- School of Epidemiology and Public Health, University of Ottawa, Ottawa, ON K1G 5Z3, Canada
- Correspondence: ; Tel.: +1-6132994379
| | - Lotte Steuten
- Office of Health Economics, London SE1 2HB, UK
- City Health Economics Centre (CHEC), City University of London, London EC1V 0HB, UK
| | - Vivek Muthu
- Marivek Healthcare Consulting, Epsom KT18 7PF, UK
| | - David M. Thomas
- Garvan Institute of Medical Research, Sydney, NSW 2010, Australia
- Omico, Sydney, NSW 2010, Australia
| | - Daryl S. Spinner
- Menarini Silicon Biosystems Inc., Huntingdon Valley, PA 19006, USA
| | - Craig Ivany
- Provincial Health Services Authority, Vancouver, BC V5Z 1G1, Canada
| | - Michael Mengel
- Department of Laboratory Medicine & Pathology, University of Alberta, Edmonton, AB T6G 2S2, Canada
| | | | - Stephen Yip
- Department of Pathology and Laboratory Medicine, Faculty of Medicine, University of British Columbia, Vancouver, BC V6T 1Z7, Canada
| | - Philip Jacobs
- Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB T6G 2R3, Canada
| | - Terrence Sullivan
- Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, ON M5T 3M6, Canada
- Gerald Bronfman Department of Oncology, McGill University, Montreal, QC H4A 3T2, Canada
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Sherafati A, Elsekaily O, Saadatagah S, Kochan DC, Lee C, Wiesner GL, Liu C, Dellefave-Castillo L, Namjou B, Perez EF, Salvati ZM, Connolly JJ, Hakonarson H, Williams MS, Jarvik GP, Chung WK, McNally EM, Manolio TA, Kullo IJ. Pathogenic variants in arteriopathy genes detected in a targeted sequencing study: Penetrance and 1-year outcomes after return of results. Genet Med 2022; 24:2123-2133. [PMID: 35943490 PMCID: PMC9837827 DOI: 10.1016/j.gim.2022.07.007] [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: 03/06/2022] [Revised: 07/04/2022] [Accepted: 07/04/2022] [Indexed: 01/18/2023] Open
Abstract
PURPOSE We estimated the penetrance of pathogenic/likely pathogenic (P/LP) variants in arteriopathy-related genes and assessed near-term outcomes following return of results. METHODS Participants (N = 24,520) in phase III of the Electronic Medical Records and Genomics network underwent targeted sequencing of 68 actionable genes, including 9 genes associated with arterial aneurysmal diseases. Penetrance was estimated on the basis of the presence of relevant clinical traits. Outcomes occurring within 1 year of return of results included new diagnoses, referral to a specialist, new tests ordered, surveillance initiated, and new medications started. RESULTS P/LP variants were present in 34 participants. The average penetrance across genes was 59%, ranging from 86% for FBN1 variants to 25% for SMAD3. Of 16 participants in whom results were returned, 1-year outcomes occurred in 63%. A new diagnosis was made in 44% of the participants, 56% were referred to a specialist, a new test was ordered in 44%, surveillance was initiated in 31%, and a new medication was started in 31%. CONCLUSION Penetrance of P/LP variants in arteriopathy-related genes, identified in a large, targeted sequencing study, was variable and overall lower than that reported in clinical cohorts. Meaningful outcomes within the first year were noted in 63% of participants who received results.
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Affiliation(s)
- Alborz Sherafati
- Department of Cardiovascular Medicine, Mayo Clinic, Rochester, MN
| | - Omar Elsekaily
- Department of Cardiovascular Medicine, Mayo Clinic, Rochester, MN
| | | | - David C Kochan
- Department of Cardiovascular Medicine, Mayo Clinic, Rochester, MN
| | - Christopher Lee
- Department of Cardiovascular Medicine, Mayo Clinic, Rochester, MN
| | - Georgia L Wiesner
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN
| | - Cong Liu
- Department of Biomedical Informatics, Columbia University Irving Medical Center, New York, NY
| | - Lisa Dellefave-Castillo
- Center for Genetic Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL
| | - Bahram Namjou
- Center for Autoimmune Genomics and Etiology (CAGE), Cincinnati Children's Hospital Medical Center, Cincinnati, OH
| | - Emma F Perez
- Department of Medicine, Brigham and Women's Hospital, Boston MA
| | | | - John J Connolly
- The Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Hakon Hakonarson
- The Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA; Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA; Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA; Division of Pulmonary Medicine, Children's Hospital of Philadelphia, Philadelphia, PA
| | | | - Gail P Jarvik
- Division of Medical Genetics, Department of Medicine, University of Washington Medical Center, Seattle, WA; Department of Genome Sciences, University of Washington Medical Center, Seattle, WA
| | - Wendy K Chung
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY; Department of Medicine, Columbia University Irving Medical Center, New York, NY
| | - Elizabeth M McNally
- Center for Genetic Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL
| | - Teri A Manolio
- Division of Genomic Medicine, National Human Genome Research Institute, Bethesda, MD
| | - Iftikhar J Kullo
- Department of Cardiovascular Medicine, Mayo Clinic, Rochester, MN; Gonda Vascular Center, Mayo Clinic, Rochester, MN.
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Linder JE, Bastarache L, Hughey JJ, Peterson JF. The Role of Electronic Health Records in Advancing Genomic Medicine. Annu Rev Genomics Hum Genet 2021; 22:219-238. [PMID: 34038146 PMCID: PMC9297710 DOI: 10.1146/annurev-genom-121120-125204] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Recent advances in genomic technology and widespread adoption of electronic health records (EHRs) have accelerated the development of genomic medicine, bringing promising research findings from genome science into clinical practice. Genomic and phenomic data, accrued across large populations through biobanks linked to EHRs, have enabled the study of genetic variation at a phenome-wide scale. Through new quantitative techniques, pleiotropy can be explored with phenome-wide association studies, the occurrence of common complex diseases can be predicted using the cumulative influence of many genetic variants (polygenic risk scores), and undiagnosed Mendelian syndromes can be identified using EHR-based phenotypic signatures (phenotype risk scores). In this review, we trace the role of EHRs from the development of genome-wide analytic techniques to translational efforts to test these new interventions to the clinic. Throughout, we describe the challenges that remain when combining EHRs with genetics to improve clinical care.
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Affiliation(s)
- Jodell E Linder
- Vanderbilt Institute for Clinical and Translational Research, Vanderbilt University Medical Center, Nashville, Tennessee 37203, USA;
| | - Lisa Bastarache
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, Tennessee 37203, USA; , ,
| | - Jacob J Hughey
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, Tennessee 37203, USA; , ,
| | - Josh F Peterson
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, Tennessee 37203, USA; , ,
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee 37203, USA
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Complex analysis of the personalized pharmacotherapy in the management of COVID-19 patients and suggestions for applications of predictive, preventive, and personalized medicine attitude. EPMA J 2021; 12:307-324. [PMID: 34306260 PMCID: PMC8283099 DOI: 10.1007/s13167-021-00247-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Accepted: 06/08/2021] [Indexed: 02/07/2023]
Abstract
Aims Coronavirus disease 2019 (COVID-19) is rapidly spreading worldwide. Drug therapy is one of the major treatments, but contradictory results of clinical trials have been reported among different individuals. Furthermore, comprehensive analysis of personalized pharmacotherapy is still lacking. In this study, analyses were performed on 47 well-characterized COVID-19 drugs used in the personalized treatment of COVID-19. Methods Clinical trials with published results of drugs use for COVID-19 treatment were collected to evaluate drug efficacy. Drug-to-Drug Interactions (DDIs) were summarized and classified. Functional variations in actionable pharmacogenes were collected and systematically analysed. “Gene Score” and “Drug Score” were defined and calculated to systematically analyse ethnicity-based genetic differences, which are important for the safer use of COVID-19 drugs. Results Our results indicated that four antiviral agents (ritonavir, darunavir, daclatasvir and sofosbuvir) and three immune regulators (budesonide, colchicine and prednisone) as well as heparin and enalapril could generate the highest number of DDIs with common concomitantly utilized drugs. Eight drugs (ritonavir, daclatasvir, sofosbuvir, ribavirin, interferon alpha-2b, chloroquine, hydroxychloroquine (HCQ) and ceftriaxone had actionable pharmacogenomics (PGx) biomarkers among all ethnic groups. Fourteen drugs (ritonavir, daclatasvir, prednisone, dexamethasone, ribavirin, HCQ, ceftriaxone, zinc, interferon beta-1a, remdesivir, levofloxacin, lopinavir, human immunoglobulin G and losartan) showed significantly different pharmacogenomic characteristics in relation to the ethnic origin of the patient. Conclusion We recommend that particularly for patients with comorbidities to avoid serious DDIs, the predictive, preventive, and personalized medicine (PPPM, 3 PM) strategies have to be applied for COVID-19 treatment, and genetic tests should be performed for drugs with actionable pharmacogenes, especially in some ethnic groups with a higher frequency of functional variations, as our analysis showed. We also suggest that drugs associated with higher ethnic genetic differences should be given priority in future pharmacogenetic studies for COVID-19 management. To facilitate translation of our results into clinical practice, an approach conform with PPPM/3 PM principles was suggested. In summary, the proposed PPPM/3 PM attitude should be obligatory considered for the overall COVID-19 management. Supplementary Information The online version contains supplementary material available at 10.1007/s13167-021-00247-0.
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Penetrance and outcomes at 1-year following return of actionable variants identified by genome sequencing. Genet Med 2021; 23:1192-1201. [PMID: 33824501 PMCID: PMC9839314 DOI: 10.1038/s41436-021-01142-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 02/26/2021] [Accepted: 03/01/2021] [Indexed: 01/17/2023] Open
Abstract
PURPOSE We estimated penetrance of actionable genetic variants and assessed near-term outcomes following return of results (RoR). METHODS Participants (n = 2,535) with hypercholesterolemia and/or colon polyps underwent targeted sequencing of 68 genes and 14 single-nucleotide variants. Penetrance was estimated based on presence of relevant traits in the electronic health record (EHR). Outcomes occurring within 1-year of RoR were ascertained by EHR review. Analyses were stratified by tier 1 and non-tier 1 disorders. RESULTS Actionable findings were present in 122 individuals and results were disclosed to 98. The average penetrance for tier 1 disorder variants (67%; n = 58 individuals) was higher than in non-tier 1 variants (46.5%; n = 58 individuals). After excluding 45 individuals (decedents, nonresponders, known genetic diagnoses, mosaicism), ≥1 outcomes were noted in 83% of 77 participants following RoR; 78% had a process outcome (referral to a specialist, new testing, surveillance initiated); 68% had an intermediate outcome (new test finding or diagnosis); 19% had a clinical outcome (therapy modified, risk reduction surgery). Risk reduction surgery occurred more often in participants with tier 1 than those with non-tier 1 variants. CONCLUSION Relevant phenotypic traits were observed in 57% whereas a clinical outcome occurred in 19% of participants with actionable genomic variants in the year following RoR.
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Murata T, Hozumi C, Hiroshima Y, Shimoya K, Hongo A, Inubushi S, Tanino H, Hoffman RM. Co-implantation of Tumor and Extensive Surrounding Tissue Improved the Establishment Rate of Surgical Specimens of Human-Patient Cancer in Nude Mice: Toward the Goal of Universal Individualized Cancer Therapy. In Vivo 2021; 34:3241-3245. [PMID: 33144429 DOI: 10.21873/invivo.12160] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2020] [Revised: 09/16/2020] [Accepted: 09/17/2020] [Indexed: 12/16/2022]
Abstract
BACKGROUND/AIM The discovery of the nude mouse model enabled the experimental growth of human-patient tumors. However, the low establishment rate of tumors in nude and other immunodeficient strains of mice has limited wide-spread clinical use. MATERIALS AND METHODS In order to increase the establishment rate of surgical specimens of patient tumors, we transplanted tumors to nude mice subcutaneously along with large amounts of surrounding tissue of the tumor. RESULTS The new transplantation method increased the establishment rate in nude mice to 66% compared to the old method of implanting the surgical tumor specimen with surrounding tissue removed (14%). High stage and presence of metastasis in the patient donor are positively correlated to tumor engraftment in nude mice. CONCLUSION The new method can potentially allow most cancer patients who undergo surgery or biopsy to have their own mouse model for drug-sensitivity testing.
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Affiliation(s)
- Takuya Murata
- Department of Obstetrics and Gynecology 2, Kawasaki Medical School, Okayama, Japan
| | | | - Yukihiko Hiroshima
- Department of Cancer Genome Medicine, Kanagawa Cancer Center Research Institute, Kanagawa, Japan
| | - Koichiro Shimoya
- Department of Obstetrics and Gynecology 1, Kawasaki Medical School, Kurashiki, Japan
| | - Atsushi Hongo
- Department of Obstetrics and Gynecology 2, Kawasaki Medical School, Okayama, Japan
| | - Sachiko Inubushi
- Breast Surgery, Department of Surgery, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Hirokazu Tanino
- Breast Surgery, Department of Surgery, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Robert M Hoffman
- AntiCancer Inc, San Diego, CA, U.S.A. .,Department of Surgery, University of California, San Diego, CA, U.S.A
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Fortin Ensign S, Hrachova M, Chang S, Mrugala MM. Assessing the utility and attitudes toward molecular testing in neuro-oncology: a survey of the Society for Neuro-Oncology members. Neurooncol Pract 2021; 8:310-316. [PMID: 34055378 PMCID: PMC8153811 DOI: 10.1093/nop/npab003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND Molecular testing (MT) is utilized in neuro-oncology with increasing frequency. The aim of this study was to determine clinical practice patterns to acquire this information, interpret and utilize MT for patient care, and identify unmet needs in the practical clinical application of MT. METHODS We conducted a voluntary online survey of providers within the Society for Neuro-Oncology (SNO) membership database between March and April 2019. RESULTS We received 152 responses out of 2022 SNO members (7.5% of membership). 88.8% of respondents routinely order MT for newly diagnosed gliomas. Of those who do not, testing is preferentially performed in younger patients or those with midline tumors. 82.8% use MT in recurrent gliomas. Other common indications included: metastatic tumors, meningioma, and medulloblastoma. Many providers utilize more than one resource (36.0%), most frequently using in-house (41.8%) over commercially available panels. 78.1% used the results for clinical decision-making, with BRAF, EGFR, ALK, and H3K27 mutations most commonly directing treatment decisions. Approximately, half (48.5%) of respondents have molecular tumor boards at their institutions. Respondents would like to see SNO-endorsed guidelines on MT, organized lists of targeted agents available for specific mutations, a database of targetable mutations and clinical trials, and more educational programs on MT. CONCLUSION This survey was marked by several limitations including response rate and interpretation of MT. Among respondents, there is routine use of MT in Neuro-Oncology, however, there remains a need for increased guidance for providers to effectively incorporate the expanding genomic data resulting from MT into daily Neuro-Oncology practice.
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Affiliation(s)
| | - Maya Hrachova
- Department of Neurology, University of California, Irvine Medical Center, Orange, California
| | - Susan Chang
- Division of Neuro-Oncology, Department of Neurosurgery, University of California San Francisco, San Francisco, California
| | - Maciej M Mrugala
- Department of Neurology, Mayo Clinic Cancer Center, Phoenix, Arizona
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Abstract
Genomic information is poised to play an increasing role in clinical care, extending beyond highly penetrant genetic conditions to less penetrant genotypes and common disorders. But with this shift, the question of clinical utility becomes a major challenge. A collaborative effort is necessary to determine the information needed to evaluate different uses of genomic information and then acquire that information. Another challenge must also be addressed if that process is to provide equitable benefits: the lack of diversity of genomic data. Current genomic knowledge comes primarily from populations of European descent, which poses the risk that most of the human population will be shortchanged when health benefits of genomics emerge. These two challenges have defined my career as a geneticist and have taught me that solutions must start with dialogue across disciplinary and social divides.
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Affiliation(s)
- Wylie Burke
- Department of Bioethics and Humanities, University of Washington, Seattle, Washington 98195, USA;
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The need for widely available genomic testing in rare eye diseases: an ERN-EYE position statement. Orphanet J Rare Dis 2021; 16:142. [PMID: 33743793 PMCID: PMC7980559 DOI: 10.1186/s13023-021-01756-x] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Accepted: 02/18/2021] [Indexed: 12/26/2022] Open
Abstract
Background Rare Eye Diseases (RED) are the leading cause of visual impairment and blindness for children and young adults in Europe. This heterogeneous group of conditions includes over 900 disorders ranging from relatively prevalent disorders such as retinitis pigmentosa to very rare entities such as developmental eye anomalies. A significant number of patients with RED have an underlying genetic etiology. One of the aims of the European Reference Network for Rare Eye Diseases (ERN–EYE) is to facilitate improvement in diagnosis of RED in European member states. Main body Technological advances have allowed genetic and genomic testing for RED. The outcome of genetic testing allows better understanding of the condition and allows reproductive and therapeutic options. The increase of the number of clinical trials for RED has provided urgency for genetic testing in RED. A survey of countries participating in ERN-EYE demonstrated that the majority are able to access some forms of genomic testing. However, there is significant variability, particularly regarding testing as part of clinical service. Some countries have a well-delineated rare disease pathway and have a national plan for rare diseases combined or not with a national plan for genomics in medicine. In other countries, there is a well-established organization of genetic centres that offer reimbursed genomic testing of RED and other rare diseases. Clinicians often rely upon research-funded laboratories or private companies. Notably, some member states rely on cross-border testing by way of an academic research project. Consequently, many clinicians are either unable to access testing or are confronted with long turnaround times. Overall, while the cost of sequencing has dropped, the cumulative cost of a genomic testing service for populations remains considerable. Importantly, the majority of countries reported healthcare budgets that limit testing. Short conclusion Despite technological advances, critical gaps in genomic testing remain in Europe, especially in smaller countries where no formal genomic testing pathways exist. Even within larger countries, the existing arrangements are insufficient to meet the demand and to ensure access. ERN-EYE promotes access to genetic testing in RED and emphasizes the clinical need and relevance of genetic testing in RED.
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DNA-based screening and population health: a points to consider statement for programs and sponsoring organizations from the American College of Medical Genetics and Genomics (ACMG). Genet Med 2021; 23:989-995. [PMID: 33727704 DOI: 10.1038/s41436-020-01082-w] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 12/14/2020] [Accepted: 12/17/2020] [Indexed: 02/06/2023] Open
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Generating evidence for precision medicine: considerations made by the Ubiquitous Pharmacogenomics Consortium when designing and operationalizing the PREPARE study. Pharmacogenet Genomics 2021; 30:131-144. [PMID: 32317559 PMCID: PMC7331826 DOI: 10.1097/fpc.0000000000000405] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
OBJECTIVES Pharmacogenetic panel-based testing represents a new model for precision medicine. A sufficiently powered prospective study assessing the (cost-)effectiveness of a panel-based pharmacogenomics approach to guide pharmacotherapy is lacking. Therefore, the Ubiquitous Pharmacogenomics Consortium initiated the PREemptive Pharmacogenomic testing for prevention of Adverse drug Reactions (PREPARE) study. Here, we provide an overview of considerations made to mitigate multiple methodological challenges that emerged during the design. METHODS An evaluation of considerations made when designing the PREPARE study across six domains: study aims and design, primary endpoint definition and collection of adverse drug events, inclusion and exclusion criteria, target population, pharmacogenomics intervention strategy, and statistical analyses. RESULTS Challenges and respective solutions included: (1) defining and operationalizing a composite primary endpoint enabling measurement of the anticipated effect, by including only severe, causal, and drug genotype-associated adverse drug reactions; (2) avoiding overrepresentation of frequently prescribed drugs within the patient sample while maintaining external validity, by capping drugs of enrolment; (3) designing the pharmacogenomics intervention strategy to be applicable across ethnicities and healthcare settings; and (4) designing a statistical analysis plan to avoid dilution of effect by initially excluding patients without a gene-drug interaction in a gatekeeping analysis. CONCLUSION Our design considerations will enable quantification of the collective clinical utility of a panel of pharmacogenomics-markers within one trial as a proof-of-concept for pharmacogenomics-guided pharmacotherapy across multiple actionable gene-drug interactions. These considerations may prove useful to other investigators aiming to generate evidence for precision medicine.
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18
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MobiDetails: online DNA variants interpretation. Eur J Hum Genet 2020; 29:356-360. [PMID: 33161418 DOI: 10.1038/s41431-020-00755-z] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 10/22/2020] [Indexed: 11/08/2022] Open
Abstract
MobiDetails is an expert tool, online application which gathers useful data for the interpretation of DNA variants in the context of molecular diagnosis. It brings together in a single tool many sources of data, such as population genetics, various kinds of predictors, Human Genome Variation Society (HGVS) nomenclatures, curated databases, and access to various annotations. Accurate interpretation of DNA variants is crucial and can impact the patient care or have familial outcomes (prenatal diagnosis). Its importance will increase in the coming years with the expansion of the personalized medicine. MobiDetails is specifically designed to help with this task. Exonic or intronic substitutions and small insertions/deletions related to more than 18,000 human genes are easily submitted and annotated in real-time. It is a responsive website that can be accessed using mobiles or tablets during medical staff meetings. MobiDetails is based on publicly available resources, does not include any specific data on patients or phenotypes, and is freely available for academic use at https://mobidetails.iurc.montp.inserm.fr/MD/ .
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Hsiao SJ, Sireci AN, Pendrick D, Freeman C, Fernandes H, Schwartz GK, Henick BS, Mansukhani MM, Roth KA, Carvajal RD, Oberg JA. Clinical Utilization, Utility, and Reimbursement for Expanded Genomic Panel Testing in Adult Oncology. JCO Precis Oncol 2020; 4:1038-1048. [DOI: 10.1200/po.20.00048] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
PURPOSE The routine use of large next-generation sequencing (NGS) pan-cancer panels is required to identify the increasing number of, but often uncommon, actionable alterations to guide therapy. Inconsistent coverage and variable payment is hindering NGS adoption into clinical practice. A review of test utilization, clinical utility, coverage, and reimbursement was conducted in a cohort of patients diagnosed with high-risk cancer who received pan-cancer panel testing as part of their clinical care. MATERIALS AND METHODS The Columbia Combined Cancer Panel (CCCP), a 467-gene panel designed to detect DNA variations in solid and liquid tumors, was performed in the Laboratory of Personalized Genomic Medicine at Columbia University Irving Medical Center. Utilization was characterized at test order. Results were reviewed by a molecular pathologist, followed by a multidisciplinary molecular tumor board where clinical utility was classified by consensus. Reimbursement was reviewed after payers provided final coverage decisions. RESULTS NGS was performed on 359 high-risk tumors from 349 patients. Reimbursement data were available for 246 cases. The most common reason providers ordered CCCP testing was for patients diagnosed with a treatment-resistant or recurrent tumor (n = 214; 61%). Findings were clinically impactful for 229 cases (64%). Molecular alterations that may inform future therapy in the event of progression or relapse were found in 42% of cases, and a targeted therapy was initiated in 23 cases (6.6%). The majority of tests were denied coverage by payers (n = 190; 77%). On average, insurers reimbursed 10.75% of the total NGS service charge. CONCLUSION CCCP testing identified clinically impactful alterations in 64% of cases. Limited coverage and low reimbursement remain barriers, and broader reimbursement policies are needed to adopt pan-cancer NGS testing that benefits patients into clinical practice.
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Affiliation(s)
- Susan J. Hsiao
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY
| | - Anthony N. Sireci
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY
| | - Danielle Pendrick
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY
| | - Christopher Freeman
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY
| | - Helen Fernandes
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY
| | - Gary K. Schwartz
- Division of Hematology and Oncology, Department of Medicine, Columbia University Irving Medical Center, New York, NY
| | - Brian S. Henick
- Division of Hematology and Oncology, Department of Medicine, Columbia University Irving Medical Center, New York, NY
| | - Mahesh M. Mansukhani
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY
| | - Kevin A. Roth
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY
| | - Richard D. Carvajal
- Division of Hematology and Oncology, Department of Medicine, Columbia University Irving Medical Center, New York, NY
| | - Jennifer A. Oberg
- Division of Hematology, Oncology, and Stem Cell Transplantation, Department of Pediatrics, Columbia University Irving Medical Center, New York, NY
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McDonald WS, Wagner JK, Deverka PA, Woods LA, Peterson JF, Williams MS. Genetic testing and employer-sponsored wellness programs: An overview of current vendors, products, and practices. Mol Genet Genomic Med 2020; 8:e1414. [PMID: 32715662 PMCID: PMC7549551 DOI: 10.1002/mgg3.1414] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 06/01/2020] [Accepted: 07/02/2020] [Indexed: 01/21/2023] Open
Abstract
BACKGROUND Employer-sponsored corporate wellness programs have spread despite limited evidence of effectiveness in improving health or reducing costs. Some programs have offered genetic testing as a benefit to employees, but little is known about this practice. METHODS In December 2019, we conducted a systematic Google search to identify vendors offering corporate wellness programs involving genetics. We performed qualitative content analysis of publicly available information about the vendors' products and practices disclosed on their websites. RESULTS Fifteen vendors were identified. Details regarding genetic testing offered within wellness programs were difficult to decipher from vendors' websites, including which specific products were included. No evidence was provided to support vendor claimed improvements in employer costs, employee health, and job performance. Only half offered health and genetic counseling services. Most vendors were ambiguous regarding data sharing. Disclaimer language was included in vendors' stated risks and limitations, ostensibly to avoid oversight and liability. CONCLUSION We found a lack of transparency among corporate wellness program vendors, underscoring challenges that stakeholders encounter when trying to assess (a) how such programs are using genetics, (b) the potential benefits of such applications, and (c) the adequacy of protections to ensure scientific evidence support any health claims and genetic nondiscrimination.
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Affiliation(s)
| | - Jennifer K. Wagner
- Center for Translational Bioethics & Health Care PolicyGeisingerDanvillePAUSA
| | | | - Laura A. Woods
- Vanderbilt Institute for Clinical and Translational ResearchVanderbilt University Medical CenterNashvilleTNUSA
| | - Josh F. Peterson
- Department of Biomedical Informatics and MedicineVanderbilt University Medical CenterNashvilleTNUSA
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21
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Zhong M, van der Walt A, Campagna MP, Stankovich J, Butzkueven H, Jokubaitis V. The Pharmacogenetics of Rituximab: Potential Implications for Anti-CD20 Therapies in Multiple Sclerosis. Neurotherapeutics 2020; 17:1768-1784. [PMID: 33058021 PMCID: PMC7851267 DOI: 10.1007/s13311-020-00950-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/09/2020] [Indexed: 12/13/2022] Open
Abstract
There are a broad range of disease-modifying therapies (DMTs) available in relapsing-remitting multiple sclerosis (RRMS), but limited biomarkers exist to personalise DMT choice. All DMTs, including monoclonal antibodies such as rituximab and ocrelizumab, are effective in preventing relapses and preserving neurological function in MS. However, each agent harbours its own risk of therapeutic failure or adverse events. Pharmacogenetics, the study of the effects of genetic variation on therapeutic response or adverse events, could improve the precision of DMT selection. Pharmacogenetic studies of rituximab in MS patients are lacking, but pharmacogenetic markers in other rituximab-treated autoimmune conditions have been identified. This review will outline the wider implications of pharmacogenetics and the mechanisms of anti-CD20 agents in MS. We explore the non-MS rituximab literature to characterise pharmacogenetic variants that could be of prognostic relevance in those receiving rituximab, ocrelizumab or other monoclonal antibodies for MS.
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Affiliation(s)
- Michael Zhong
- Department of Neuroscience, Central Clinical School, Monash University, Melbourne, Australia.
- Department of Neurology, Alfred Health, Level 6, Alfred Centre, 99 Commercial Road, Melbourne, Victoria, 3004, Australia.
| | - Anneke van der Walt
- Department of Neuroscience, Central Clinical School, Monash University, Melbourne, Australia
- Department of Neurology, Alfred Health, Level 6, Alfred Centre, 99 Commercial Road, Melbourne, Victoria, 3004, Australia
| | - Maria Pia Campagna
- Department of Neuroscience, Central Clinical School, Monash University, Melbourne, Australia
| | - Jim Stankovich
- Department of Neuroscience, Central Clinical School, Monash University, Melbourne, Australia
| | - Helmut Butzkueven
- Department of Neuroscience, Central Clinical School, Monash University, Melbourne, Australia
- Department of Neurology, Alfred Health, Level 6, Alfred Centre, 99 Commercial Road, Melbourne, Victoria, 3004, Australia
| | - Vilija Jokubaitis
- Department of Neuroscience, Central Clinical School, Monash University, Melbourne, Australia
- Department of Neurology, Alfred Health, Level 6, Alfred Centre, 99 Commercial Road, Melbourne, Victoria, 3004, Australia
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Ferreira-Gonzalez A. Plasma PIK3CA Mutation Testing in Advanced Breast Cancer Patients for Personalized Medicine: A Value Proposition. J Appl Lab Med 2020; 5:1076-1089. [PMID: 32901282 DOI: 10.1093/jalm/jfaa117] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Accepted: 06/24/2020] [Indexed: 12/15/2022]
Abstract
BACKGROUND Even though endocrine therapy is often initially successful in treating advanced breast cancer, most patients inevitably face disease progression. In advanced hormone receptor-positive (HR+) breast cancer, activation of the PI3K downstream pathway is a critical feature of the mechanism of endocrine resistance. A significant recent advance in treating HR+ advanced breast cancer has been the recent introduction of PI3K inhibitor (PI3Ki) for the treatment of patients with HR+, HER2-negative (HER2-) advanced or metastatic breast cancer that harbors PIK3CA mutations. A value proposition concept was applied to assess the potential benefits of cell-free tumor DNA (ctDNA) testing to identify patients who might respond to PI3Ki treatment. CONTENT By applying the framework of the value proposition to >35 publications, in addition to recommendations from professional organizations, it was evident that robust clinical evidence exists to support the role of ctDNA PIK3CA mutation evaluation in identifying patients with advanced breast cancer who could benefit from PI3Ki treatment. SUMMARY Detection of PIK3CA gene mutations in HR+HER2- advanced breast cancer patients allows for the identification of patients who might benefit from more effective personalized treatment with molecularly targeted drugs.
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A three-year follow-up study evaluating clinical utility of exome sequencing and diagnostic potential of reanalysis. NPJ Genom Med 2020; 5:37. [PMID: 32963807 PMCID: PMC7484757 DOI: 10.1038/s41525-020-00144-x] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Accepted: 08/14/2020] [Indexed: 01/05/2023] Open
Abstract
Exome sequencing (ES) has become one of the important diagnostic tools in clinical genetics with a reported diagnostic rate of 25–58%. Many studies have illustrated the diagnostic and immediate clinical impact of ES. However, up to 75% of individuals remain undiagnosed and there is scarce evidence supporting clinical utility beyond a follow-up period of >1 year. This is a 3-year follow-up analysis to our previous publication by Mak et al. (NPJ Genom. Med. 3:19, 2018), to evaluate the long-term clinical utility of ES and the diagnostic potential of exome reanalysis. The diagnostic yield of the initial study was 41% (43/104). Exome reanalysis in 46 undiagnosed individuals has achieved 12 new diagnoses. The additional yield compared with the initial analysis was at least 12% (increased from 41% to at least 53%). After a median follow-up period of 3.4 years, change in clinical management was observed in 72.2% of the individuals (26/36), leading to positive change in clinical outcome in four individuals (11%). There was a minimum healthcare cost saving of HKD$152,078 (USD$19,497; €17,282) annually for these four individuals. There were a total of six pregnancies from five families within the period. Prenatal diagnosis was performed in four pregnancies; one fetus was affected and resulted in termination. None of the parents underwent preimplantation genetic diagnosis. This 3-year follow-up study demonstrated the long-term clinical utility of ES at individual, familial and health system level, and the promising diagnostic potential of subsequent reanalysis. This highlights the benefits of implementing ES and regular reanalysis in the clinical setting.
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Secondary findings in inherited heart conditions: a genotype-first feasibility study to assess phenotype, behavioural and psychosocial outcomes. Eur J Hum Genet 2020; 28:1486-1496. [PMID: 32686758 PMCID: PMC7576165 DOI: 10.1038/s41431-020-0694-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 06/12/2020] [Accepted: 06/30/2020] [Indexed: 12/28/2022] Open
Abstract
Disclosing secondary findings (SF) from genome sequencing (GS) can alert carriers to disease risk. However, evidence around variant-disease association and consequences of disclosure for individuals and healthcare services is limited. We report on the feasibility of an approach to identification of SF in inherited cardiac conditions (ICC) genes in participants in a rare disease GS study, followed by targeted clinical evaluation. Qualitative methods were used to explore behavioural and psychosocial consequences of disclosure. ICC genes were analysed in genome sequence data from 7203 research participants; a two-stage approach was used to recruit genotype-blind variant carriers and matched controls. Cardiac-focused medical and family history collection and genetic counselling were followed by standard clinical tests, blinded to genotype. Pathogenic ICC variants were identified in 0.61% of individuals; 20 were eligible for the present study. Four variant carriers and seven non-carrier controls participated. One variant carrier had a family history of ICC and was clinically affected; a second was clinically unaffected and had no relevant family history. One variant, in two unrelated participants, was subsequently reclassified as being of uncertain significance. Analysis of qualitative data highlights participant satisfaction with approach, willingness to follow clinical recommendations, but variable outcomes of relatives’ engagement with healthcare services. In conclusion, when offered access to SF, many people choose not to pursue them. For others, disclosure of ICC SF in a specialist setting is valued and of likely clinical utility, and can be expected to identify individuals with, and without a phenotype.
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25
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Buchanan AH, Lester Kirchner H, Schwartz MLB, Kelly MA, Schmidlen T, Jones LK, Hallquist MLG, Rocha H, Betts M, Schwiter R, Butry L, Lazzeri AL, Frisbie LR, Rahm AK, Hao J, Willard HF, Martin CL, Ledbetter DH, Williams MS, Sturm AC. Clinical outcomes of a genomic screening program for actionable genetic conditions. Genet Med 2020; 22:1874-1882. [PMID: 32601386 PMCID: PMC7605431 DOI: 10.1038/s41436-020-0876-4] [Citation(s) in RCA: 71] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Revised: 06/12/2020] [Accepted: 06/12/2020] [Indexed: 01/07/2023] Open
Abstract
Purpose Three genetic conditions—hereditary breast and ovarian cancer syndrome, Lynch syndrome, and familial hypercholesterolemia—have tier 1 evidence for interventions that reduce morbidity and mortality, prompting proposals to screen unselected populations for these conditions. We examined the impact of genomic screening on risk management and early detection in an unselected population. Methods Observational study of electronic health records (EHR) among individuals in whom a pathogenic/likely pathogenic variant in a tier 1 gene was discovered through Geisinger’s MyCode project. EHR of all eligible participants was evaluated for a prior genetic diagnosis and, among participants without such a diagnosis, relevant personal/family history, postdisclosure clinical diagnoses, and postdisclosure risk management. Results Eighty-seven percent of participants (305/351) did not have a prior genetic diagnosis of their tier 1 result. Of these, 65% had EHR evidence of relevant personal and/or family history of disease. Of 255 individuals eligible to have risk management, 70% (n = 179) had a recommended risk management procedure after results disclosure. Thirteen percent of participants (41/305) received a relevant clinical diagnosis after results disclosure. Conclusion Genomic screening programs can identify previously unrecognized individuals at increased risk of cancer and heart disease and facilitate risk management and early cancer detection.
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Affiliation(s)
| | - H Lester Kirchner
- Department of Population Health Sciences, Geisinger, Danville, PA, USA
| | | | | | - Tara Schmidlen
- Genomic Medicine Institute, Geisinger, Danville, PA, USA
| | - Laney K Jones
- Genomic Medicine Institute, Geisinger, Danville, PA, USA
| | | | - Heather Rocha
- Genomic Medicine Institute, Geisinger, Danville, PA, USA
| | - Megan Betts
- Genomic Medicine Institute, Geisinger, Danville, PA, USA
| | | | - Loren Butry
- Genomic Medicine Institute, Geisinger, Danville, PA, USA
| | | | | | | | - Jing Hao
- Genomic Medicine Institute, Geisinger, Danville, PA, USA.,Department of Population Health Sciences, Geisinger, Danville, PA, USA
| | - Huntington F Willard
- Genomic Medicine Institute, Geisinger, Danville, PA, USA.,Genome Medical, Durham, NC, USA
| | - Christa L Martin
- Genomic Medicine Institute, Geisinger, Danville, PA, USA.,Autism and Developmental Medicine Institute, Geisinger, Lewisburg, PA, USA
| | - David H Ledbetter
- Genomic Medicine Institute, Geisinger, Danville, PA, USA.,Autism and Developmental Medicine Institute, Geisinger, Lewisburg, PA, USA
| | | | - Amy C Sturm
- Genomic Medicine Institute, Geisinger, Danville, PA, USA
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Damkier P. Obviously nine believers: Actionable germline genetic variants for pre-emptive pharmacogenetic testing. Basic Clin Pharmacol Toxicol 2020; 126:5-6. [PMID: 31597220 DOI: 10.1111/bcpt.13335] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Accepted: 09/25/2019] [Indexed: 01/19/2023]
Affiliation(s)
- Per Damkier
- Department of Clinical Biochemistry and Pharmacology, Odense University Hospital, Odense, Denmark.,Department of Clinical Research, University of Southern Denmark, Odense, Denmark
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27
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Scott RH, Fowler TA, Caulfield M. Genomic medicine: time for health-care transformation. Lancet 2019; 394:454-456. [PMID: 31395438 DOI: 10.1016/s0140-6736(19)31796-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Accepted: 07/31/2019] [Indexed: 11/26/2022]
Affiliation(s)
- Richard H Scott
- Genomics England, Queen Mary University of London, London, UK; Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Tom A Fowler
- Genomics England, Queen Mary University of London, London, UK; William Harvey Research Institute, Queen Mary University of London, London EC1M 6BQ, UK
| | - Mark Caulfield
- Genomics England, Queen Mary University of London, London, UK; William Harvey Research Institute, Queen Mary University of London, London EC1M 6BQ, UK.
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28
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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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