1
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Genome screening, reporting, and genetic counseling for healthy populations. Hum Genet 2023; 142:181-192. [PMID: 36331656 PMCID: PMC9638226 DOI: 10.1007/s00439-022-02480-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 08/16/2022] [Indexed: 11/06/2022]
Abstract
Rapid advancements of genome sequencing (GS) technologies have enhanced our understanding of the relationship between genes and human disease. To incorporate genomic information into the practice of medicine, new processes for the analysis, reporting, and communication of GS data are needed. Blood samples were collected from adults with a PCR-confirmed SARS-CoV-2 (COVID-19) diagnosis (target N = 1500). GS was performed. Data were filtered and analyzed using custom pipelines and gene panels. We developed unique patient-facing materials, including an online intake survey, group counseling presentation, and consultation letters in addition to a comprehensive GS report. The final report includes results generated from GS data: (1) monogenic disease risks; (2) carrier status; (3) pharmacogenomic variants; (4) polygenic risk scores for common conditions; (5) HLA genotype; (6) genetic ancestry; (7) blood group; and, (8) COVID-19 viral lineage. Participants complete pre-test genetic counseling and confirm preferences for secondary findings before receiving results. Counseling and referrals are initiated for clinically significant findings. We developed a genetic counseling, reporting, and return of results framework that integrates GS information across multiple areas of human health, presenting possibilities for the clinical application of comprehensive GS data in healthy individuals.
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2
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Handra J, Guimond C, Jordan I, Lenahan B, Ohs K, Beauchesne R, Adam S, Friedman JM, Birch P. A personalized genomic results e-booklet, co-designed and pilot-tested by families. PEC INNOVATION 2022; 1:100039. [PMID: 37213729 PMCID: PMC10194288 DOI: 10.1016/j.pecinn.2022.100039] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 03/19/2022] [Accepted: 04/12/2022] [Indexed: 05/23/2023]
Abstract
Objective To develop and evaluate a personalizable genomic results e-booklet that helps families understand their genomic testing results and navigate available resources. Methods The need for the Genomics Results e-Booklet was identified by families, after which this tool was developed by a team of clinical researchers and three parent-advisors. We customized the genomic results e-booklet for 50 families participating in a genomic sequencing research study. We conducted an assessment using a 19-question survey and semi-structured interviews to elicit feedback and iteratively improve the tool. Results 25 users provided feedback via questionnaires and seven respondents were interviewed. Genomic Results e-Booklet recipients responded favorably: 96% of participants stated that it helped them remember information shared during their results appointment, 80% said it had or would help them communicate their results with other healthcare providers, 68% felt that it helped to identify and guide their next steps, and 72% anticipated that the e-booklet would have future utility. Conclusion The Genomic Results e-Booklet is a patient and family-oriented resource that complements post-test genetic counselling. Innovation Compared to traditional laboratory reports and clinical letters, the Genomics Results e-Booklet is patient-conceived and patient-centered, and allows clinicians to efficiently personalize content and prioritize patient understanding and support.
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Affiliation(s)
- Julia Handra
- Department of Medical Genetics, Faculty of Medicine, University of British Columbia, C201 - 4500 Oak Street, Vancouver, BC V6H 3N1, Canada
- BC Children's Hospital Research Institute, 938 W 28th Ave, Vancouver, BC V5Z 4H4, Canada
- Corresponding author.
| | - Colleen Guimond
- Department of Medical Genetics, Faculty of Medicine, University of British Columbia, C201 - 4500 Oak Street, Vancouver, BC V6H 3N1, Canada
- BC Children's Hospital Research Institute, 938 W 28th Ave, Vancouver, BC V5Z 4H4, Canada
| | | | | | - Kelsey Ohs
- Parent Research Advisor, British Columbia, Canada
| | - Rhea Beauchesne
- Department of Medical Genetics, Faculty of Medicine, University of British Columbia, C201 - 4500 Oak Street, Vancouver, BC V6H 3N1, Canada
- BC Children's Hospital Research Institute, 938 W 28th Ave, Vancouver, BC V5Z 4H4, Canada
| | - Shelin Adam
- Department of Medical Genetics, Faculty of Medicine, University of British Columbia, C201 - 4500 Oak Street, Vancouver, BC V6H 3N1, Canada
- BC Children's Hospital Research Institute, 938 W 28th Ave, Vancouver, BC V5Z 4H4, Canada
| | - Jan M. Friedman
- Department of Medical Genetics, Faculty of Medicine, University of British Columbia, C201 - 4500 Oak Street, Vancouver, BC V6H 3N1, Canada
- BC Children's Hospital Research Institute, 938 W 28th Ave, Vancouver, BC V5Z 4H4, Canada
| | - Patricia Birch
- Department of Medical Genetics, Faculty of Medicine, University of British Columbia, C201 - 4500 Oak Street, Vancouver, BC V6H 3N1, Canada
- BC Children's Hospital Research Institute, 938 W 28th Ave, Vancouver, BC V5Z 4H4, Canada
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3
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Recchia G, Lawrence AC, Freeman AL. Investigating the presentation of uncertainty in an icon array: A randomized trial. PEC INNOVATION 2022; 1:None. [PMID: 36518604 PMCID: PMC9731905 DOI: 10.1016/j.pecinn.2021.100003] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 10/20/2021] [Accepted: 10/26/2021] [Indexed: 06/17/2023]
Abstract
BACKGROUND Clinicians are often advised to use pictographs to communicate risk, but whether they offer benefits when communicating risk imprecision (e.g., 65%-79%) is unknown. PURPOSE To test whether any of three approaches to visualizing imprecision would more effectively communicate breast and ovarian cancer risk for BRCA1 pathogenic variant carriers. METHODS 1,300 UK residents were presented with a genetic report with information about BRCA1-related risks, with random assignment to one of four formats: no visualization (text alone), or a pictograph using shaded icons, a gradient, or arrows marking range endpoints. We also tested pictographs in two layouts. Analysis of variance (ANOVA) and regression was employed. RESULTS There was no effect of format. Participants shown pictographs vs. text alone had better uptake of breast cancer risk messages (p < .05, η 2 = 0.003). Pictographs facilitated memory for the specific amount of risk (p < 0.001, η 2 = 0.019), as did the tabular layout. Individuals not having completed upper secondary education may benefit most. CONCLUSIONS We found weak evidence in favor of using simple pictographs with ranges to communicate BRCA risk (versus text alone), and of the tabular layout. INNOVATION Testing different ways of communicating imprecision within pictographs is a novel and promising line of research.
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Affiliation(s)
- Gabriel Recchia
- Corresponding author at: Centre for Mathematical Sciences, Wilberforce Rd, Cambridge CB3 0WA, UK.
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4
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Charron M, Kaiser B, Dauge A, Gallois H, Lapointe J, Dorval M, Nabi H, Joly Y. Integrating hereditary breast and ovarian cancer genetic counselling and testing into mainstream clinical practice: Legal and ethical challenges. Crit Rev Oncol Hematol 2022; 178:103797. [PMID: 36031172 DOI: 10.1016/j.critrevonc.2022.103797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 07/07/2022] [Accepted: 08/21/2022] [Indexed: 11/30/2022] Open
Abstract
Health professionals not specialized in genetics are expected to take an increasing role in genetic services delivery. This article aims to identify legal and ethical challenges related to a collaborative oncogenetics service model, where non-genetic health professionals provide genetic services to patients. Through a scoping literature review, we identified issues to the provision of hereditary breast and ovarian cancer, or other hereditary adult cancers, genetic testing under this model. Concerns that arose in the literature were informed consent, lack of adherence to best practice guidelines, lack of education of non-genetic health professionals on the provision of genetic services, psychological impacts of genetic testing, continuity of care, the complexity of genetic test results, confidentiality, risks of medical mismanagement, and the associated medical responsibility liabilities. Despite these challenges, there is a growing consensus towards the feasibility of cancer genetic testing being undertaken by non-genetic healthcare professionals in a collaborative oncogenetics service model.
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Affiliation(s)
- Marilou Charron
- Centre of Genomics and Policy (CGP), McGill University, Montreal, Québec, Canada.
| | - Beatrice Kaiser
- Centre of Genomics and Policy (CGP), McGill University, Montreal, Québec, Canada
| | - Aurélie Dauge
- Centre of Genomics and Policy (CGP), McGill University, Montreal, Québec, Canada
| | - Hortense Gallois
- Centre of Genomics and Policy (CGP), McGill University, Montreal, Québec, Canada
| | - Julie Lapointe
- Oncology Division, CHU de Québec - Université Laval Research Center, Québec, Canada
| | - Michel Dorval
- Faculty of Pharmacy, Université Laval, Researcher Oncology Division, CHU de Québec - Université Laval Research Center, Canada
| | - Hermann Nabi
- Faculty of Medicine, Université Laval, Researcher Oncology Division, CHU de Québec - Université Laval Research Center, Canada
| | - Yann Joly
- Centre of Genomics and Policy (CGP), McGill University, Montreal, Québec, Canada
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5
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Sam J, Reble E, Kodida R, Shaw A, Clausen M, Salazar MG, Shickh S, Mighton C, Carroll JC, Armel SR, Aronson M, Capo-Chichi JM, Cohn I, Eisen A, Elser C, Graham T, Ott K, Panchal S, Piccinin C, Schrader KA, Kim RH, Lerner-Ellis J, Bombard Y. A comprehensive genomic reporting structure for communicating all clinically significant primary and secondary findings. Hum Genet 2022; 141:1875-1885. [PMID: 35739291 DOI: 10.1007/s00439-022-02466-5] [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: 03/28/2022] [Accepted: 06/05/2022] [Indexed: 11/25/2022]
Abstract
Genomic sequencing (GS) can reveal secondary findings (SFs), findings unrelated to the reason for testing, that can be overwhelming to both patients and providers. An effective approach for communicating all clinically significant primary and secondary GS results is needed to effectively manage this large volume of results. The aim of this study was to develop a comprehensive approach to communicate all clinically significant primary and SF results. A genomic test report with accompanying patient and provider letters were developed in three phases: review of current clinical reporting practices, consulting with genetic and non-genetics experts, and iterative refinement through circulation to key stakeholders. The genomic test report and consultation letters present a myriad of clinically relevant GS results in distinct, tabulated sections, including primary (cancer) and secondary findings, with in-depth details of each finding generated from exome sequencing. They provide detailed variant and disease information, personal and familial risk assessments, clinical management details, and additional resources to help support providers and patients with implementing healthcare recommendations related to their GS results. The report and consultation letters represent a comprehensive approach to communicate all clinically significant SFs to patients and providers, facilitating clinical management of GS results.
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Affiliation(s)
- Jordan Sam
- Genomics Health Services Research Program, Li Ka Shing Knowledge Institute, St. Michael's Hospital, Unity Health Toronto, 30 Bond Street, Toronto, ON, M5B 1W8, Canada
| | - Emma Reble
- Genomics Health Services Research Program, Li Ka Shing Knowledge Institute, St. Michael's Hospital, Unity Health Toronto, 30 Bond Street, Toronto, ON, M5B 1W8, Canada
| | - Rita Kodida
- Genomics Health Services Research Program, Li Ka Shing Knowledge Institute, St. Michael's Hospital, Unity Health Toronto, 30 Bond Street, Toronto, ON, M5B 1W8, Canada
| | - Angela Shaw
- Genomics Health Services Research Program, Li Ka Shing Knowledge Institute, St. Michael's Hospital, Unity Health Toronto, 30 Bond Street, Toronto, ON, M5B 1W8, Canada
| | - Marc Clausen
- Genomics Health Services Research Program, Li Ka Shing Knowledge Institute, St. Michael's Hospital, Unity Health Toronto, 30 Bond Street, Toronto, ON, M5B 1W8, Canada
| | - Mariana Gutierrez Salazar
- Genomics Health Services Research Program, Li Ka Shing Knowledge Institute, St. Michael's Hospital, Unity Health Toronto, 30 Bond Street, Toronto, ON, M5B 1W8, Canada
| | - Salma Shickh
- Genomics Health Services Research Program, Li Ka Shing Knowledge Institute, St. Michael's Hospital, Unity Health Toronto, 30 Bond Street, Toronto, ON, M5B 1W8, Canada
- University of Toronto, Toronto, ON, Canada
| | - Chloe Mighton
- Genomics Health Services Research Program, Li Ka Shing Knowledge Institute, St. Michael's Hospital, Unity Health Toronto, 30 Bond Street, Toronto, ON, M5B 1W8, Canada
- University of Toronto, Toronto, ON, Canada
| | - June C Carroll
- University of Toronto, Toronto, ON, Canada
- Mount Sinai Hospital, Sinai Health, Toronto, ON, Canada
| | - Susan Randall Armel
- University of Toronto, Toronto, ON, Canada
- Princess Margaret Cancer Centre, Toronto, ON, Canada
| | | | | | - Iris Cohn
- The Hospital for Sick Children, Toronto, ON, Canada
| | - Andrea Eisen
- Sunnybrook Health Sciences Centre, Toronto, ON, Canada
| | - Christine Elser
- University of Toronto, Toronto, ON, Canada
- Mount Sinai Hospital, Sinai Health, Toronto, ON, Canada
| | - Tracy Graham
- University of Toronto, Toronto, ON, Canada
- Sunnybrook Health Sciences Centre, Toronto, ON, Canada
| | - Karen Ott
- Sunnybrook Health Sciences Centre, Toronto, ON, Canada
| | - Seema Panchal
- Mount Sinai Hospital, Sinai Health, Toronto, ON, Canada
| | | | | | - Raymond H Kim
- University of Toronto, Toronto, ON, Canada
- Mount Sinai Hospital, Sinai Health, Toronto, ON, Canada
- University Health Network, Toronto, ON, Canada
- The Hospital for Sick Children, Toronto, ON, Canada
| | - Jordan Lerner-Ellis
- University of Toronto, Toronto, ON, Canada.
- Mount Sinai Hospital, Sinai Health, Toronto, ON, Canada.
- Department of Pathology and Laboratory Medicine, Mount Sinai Hospital, Sinai Health, 600 University Avenue, Toronto, ON, M5G 1X5, Canada.
- Lunenfeld-Tanenbaum Research Institute, Sinai Health, Toronto, ON, Canada.
| | - Yvonne Bombard
- Genomics Health Services Research Program, Li Ka Shing Knowledge Institute, St. Michael's Hospital, Unity Health Toronto, 30 Bond Street, Toronto, ON, M5B 1W8, Canada.
- University of Toronto, Toronto, ON, Canada.
- Ontario Institute for Cancer Research, Toronto, ON, Canada.
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6
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Christensen KD, Schonman EF, Robinson JO, Roberts JS, Diamond PM, Lee KB, Green RC, McGuire AL. Behavioral and psychological impact of genome sequencing: a pilot randomized trial of primary care and cardiology patients. NPJ Genom Med 2021; 6:72. [PMID: 34429410 PMCID: PMC8384838 DOI: 10.1038/s41525-021-00236-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Accepted: 07/30/2021] [Indexed: 12/20/2022] Open
Abstract
Many expect genome sequencing (GS) to become routine in patient care and preventive medicine, but uncertainties remain about its ability to motivate participants to improve health behaviors and the psychological impact of disclosing results. In a pilot trial with exploratory analyses, we randomized 100 apparently healthy, primary-care participants and 100 cardiology participants to receive a review of their family histories of disease, either alone or in addition to GS analyses. GS results included polygenic risk information for eight cardiometabolic conditions. Overall, no differences were observed between the percentage of participants in the GS and control arms, who reported changes to health behaviors such as diet and exercise at 6 months post disclosure (48% vs. 36%, respectively, p = 0.104). In the GS arm, however, the odds of reporting a behavior change increased by 52% per high-risk polygenic prediction (p = 0.032). Mean anxiety and depression scores for GS and control arms had confidence intervals within equivalence margins of ±1.5. Mediation analyses suggested an indirect impact of GS on health behaviors by causing positive psychological responses (p ≤ 0.001). Findings suggest that GS did not distress participants. Future research on GS in more diverse populations is needed to confirm that it does not raise risks for psychological harms and to confirm the ability of polygenic risk predictions to motivate preventive behaviors.
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Affiliation(s)
- Kurt D Christensen
- PRecisiOn Medicine Translational Research (PROMoTeR) Center, Department of Population Medicine, Harvard Pilgrim Health Care Institute, Boston, MA, USA. .,Department of Population Medicine, Harvard Medical School, Boston, MA, USA. .,Broad Institute of Harvard and MIT, Cambridge, MA, USA.
| | - Erica F Schonman
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Jill O Robinson
- Center for Medical Ethics and Health Policy at Baylor College of Medicine, Houston, TX, USA
| | - J Scott Roberts
- Department of Health Behavior and Health Education, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Pamela M Diamond
- Center for Health Promotion and Prevention Research, University of Texas Houston School of Public Health, Houston, TX, USA
| | - Kaitlyn B Lee
- Center for Medical Ethics and Health Policy at Baylor College of Medicine, Houston, TX, USA
| | - Robert C Green
- Broad Institute of Harvard and MIT, Cambridge, MA, USA.,Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA.,Partners Personalized Medicine, Boston, MA, USA.,Department of Medicine, Harvard Medical School, Boston, MA, USA.,Ariadne Labs, Boston, MA, USA
| | - Amy L McGuire
- Center for Medical Ethics and Health Policy at Baylor College of Medicine, Houston, TX, USA
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7
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Chan PA, Lewis KL, Biesecker BB, Erby LH, Fasaye GA, Epps S, Biesecker LG, Turbitt E. Preferences for and acceptability of receiving pharmacogenomic results by mail: A focus group study with a primarily African-American cohort. J Genet Couns 2021; 30:1582-1590. [PMID: 33876469 DOI: 10.1002/jgc4.1424] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2020] [Revised: 03/18/2021] [Accepted: 03/20/2021] [Indexed: 01/12/2023]
Abstract
Although genetic counseling is traditionally done through in-person, one-on-one visits, workforce shortages call for efficient result return mechanisms. Studies have shown that telephone and in-person return of cancer genetic results are equivalent for patient outcomes. Few studies have been conducted with other modes, result types or racially diverse participants. This study explored participants' perspectives on receiving pharmacogenomic results by mail. Two experienced moderators facilitated six focus groups with 49 individuals who self-identified primarily as African-American and consented to participate in a genome sequencing cohort study. Participants were given a hypothetical pharmacogenomic result report (positive for c.521T>C in SLCO1B1). An accompanying letter explained that the result was associated with statin intolerance along with a recommendation to share it with one's doctor and immediate relatives. Participants reacted to the idea of receiving this type of result by mail, discussing whether the letter's information was sufficient and what they predicted they would do with the result. Two researchers coded the focus group transcripts and identified themes. Many participants thought that it was appropriate to receive the result through the mail, but some suggested a phone call alerting the recipient to the letter. Others emphasized that although a letter was acceptable for disclosing pharmacogenomic results, it would be insufficient for what they perceived as life-threatening results. Most participants found the content sufficient. Some participants suggested resources about statin intolerance and warning signs be added. Most claimed they would share the result with their doctor, yet few participants offered they would share the result with their relatives. This exploratory study advances the evidence that African-American research participants are receptive to return of certain genetic results by approaches that do not involve direct contact with a genetic counselor and intend to share results with providers. ClinSeq: A Large-Scale Medical Sequencing Clinical Research Pilot Study (NCT00410241).
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Affiliation(s)
- Priscilla A Chan
- Medical Genomics and Metabolic Genetics Branch, National Human Genome Research Institute, Bethesda, MD, USA
| | - Katie L Lewis
- Medical Genomics and Metabolic Genetics Branch, National Human Genome Research Institute, Bethesda, MD, USA
| | | | - Lori H Erby
- Medical Genomics and Metabolic Genetics Branch, National Human Genome Research Institute, Bethesda, MD, USA
| | | | - Sandra Epps
- Medical Genomics and Metabolic Genetics Branch, National Human Genome Research Institute, Bethesda, MD, USA
| | - Leslie G Biesecker
- Medical Genomics and Metabolic Genetics Branch, National Human Genome Research Institute, Bethesda, MD, USA
| | - Erin Turbitt
- University of Technology Sydney, Sydney, Australia
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8
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Maxwell MD, Hsu R, Islam R, Robinson JO, Pereira S, Gardner CL, Green RC, De Castro M. Educating military primary health-care providers in genomic medicine: lessons learned from the MilSeq Project. Genet Med 2020; 22:1710-1717. [PMID: 32647274 DOI: 10.1038/s41436-020-0865-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Revised: 05/31/2020] [Accepted: 06/02/2020] [Indexed: 11/09/2022] Open
Abstract
PURPOSE With few trained genetics professionals, the Military Health System is ill-equipped to manage the rapid expansion of genomic medicine. The MilSeq Project introduces an alternative service delivery model (ASDM) in which primary health-care providers (HCPs) provide post-test counseling (PTC) to healthy Airmen who have undergone exome sequencing. We describe HCP performance after a prerequisite educational intervention (EI). METHODS After a brief EI and pre-/posteducation surveys, HCPs were eligible to provide PTC with a genetic counselor available for consult. PTC was recorded, transcribed, and reviewed. Opportunities for improvement were organized into four error adjustment categories: (1) knowledge limitation, (2) minor, (3) moderate, and (4) critical. Thematic analysis was also performed. RESULTS Pre-/posteducation survey responses revealed statistically significant improvements in all domains. Minor error adjustments were most represented (n = 93), followed by knowledge limitation (n = 39) and moderate (n = 19). No critical errors were identified, and 17 transcripts required no adjustment. Thematic analysis revealed four themes that would benefit from more focused education: (1) family-centered care, (2) conveying risk, (3) disease knowledge, and (4) assay knowledge. CONCLUSION HCPs demonstrated competence in basic PTC after a brief EI. This ASDM may be a viable interim response to the shortage of genetics professionals in some systems.
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Affiliation(s)
- Megan D Maxwell
- University Health System, San Antonio, TX, USA. .,University of Texas Health Science Center, San Antonio, TX, USA. .,Lackland Air Force Base, San Antonio, TX, USA. .,Brigham and Women's Hospital, Boston, MA, USA. .,Harvard Medical School, Boston, MA, USA.
| | - Rebecca Hsu
- Baylor College of Medicine, Houston, TX, USA
| | | | | | | | - Cubby L Gardner
- US Army Medical Research and Development Command, Fort Detrick, MD, USA
| | - Robert C Green
- Brigham and Women's Hospital, Boston, MA, USA.,Harvard Medical School, Boston, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | - Mauricio De Castro
- Air Force Medical Genetics Center, Keesler Air Force Base, Biloxi, MS, USA
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9
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Lee IH, Negron JA, Hernandez-Ferrer C, Alvarez WJ, Mandl KD, Kong SW. The Clinical Genome and Ancestry Report: An interactive web application for prioritizing clinically implicated variants from genome sequencing data with ancestry composition. Hum Mutat 2020; 41:387-396. [PMID: 31691385 PMCID: PMC7180092 DOI: 10.1002/humu.23942] [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: 08/05/2019] [Revised: 10/24/2019] [Accepted: 11/01/2019] [Indexed: 11/08/2022]
Abstract
Genome sequencing is positioned as a routine clinical work-up for diverse clinical conditions. A commonly used approach to highlight candidate variants with potential clinical implication is to search over locus- and gene-centric knowledge databases. Most web-based applications allow a federated query across diverse databases for a single variant; however, sifting through a large number of genomic variants with combination of filtering criteria is a substantial challenge. Here we describe the Clinical Genome and Ancestry Report (CGAR), an interactive web application developed to follow clinical interpretation workflows by organizing variants into seven categories: (1) reported disease-associated variants, (2) rare- and high-impact variants in putative disease-associated genes, (3) secondary findings that the American College of Medical Genetics and Genomics recommends reporting back to patients, (4) actionable pharmacogenomic variants, (5) focused reports for candidate genes, (6) de novo variant candidates for trio analysis, and (7) germline and somatic variants implicated in cancer risk, diagnosis, treatment and prognosis. For each variant, a comprehensive list of external links to variant-centric and phenotype databases are provided. Furthermore, genotype-derived ancestral composition is used to highlight allele frequencies from a matched population since some disease-associated variants show a wide variation between populations. CGAR is an open-source software and is available at https://tom.tch.harvard.edu/apps/cgar/.
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Affiliation(s)
- In-Hee Lee
- Computational Health Informatics Program, Boston Children’s Hospital, Boston, MA 02115
| | - Jose A. Negron
- Computational Health Informatics Program, Boston Children’s Hospital, Boston, MA 02115
| | | | | | - Kenneth D. Mandl
- Computational Health Informatics Program, Boston Children’s Hospital, Boston, MA 02115
- Department of Pediatrics, Harvard Medical School, Boston, MA 02115
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115
| | - Sek Won Kong
- Computational Health Informatics Program, Boston Children’s Hospital, Boston, MA 02115
- Department of Pediatrics, Harvard Medical School, Boston, MA 02115
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10
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Clinical application of genomic high-throughput data: Infrastructural, ethical, legal and psychosocial aspects. Eur Neuropsychopharmacol 2020; 31:1-15. [PMID: 31866110 DOI: 10.1016/j.euroneuro.2019.09.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Revised: 11/03/2018] [Accepted: 09/20/2019] [Indexed: 12/28/2022]
Abstract
Genomic high-throughput technologies (GHTT) such as next-generation sequencing represent a fast and cost-effective tool toward a more comprehensive understanding of the molecular background of complex diseases. However, technological advances contrast with insufficient application in clinical practice. Thus, patients, physicians, and other professionals are faced with tough challenges that forestall the efficient and effective implementation. With the increasing application of genetic testing, it is of paramount importance that physicians and other professionals in healthcare recognize the restrictions and potential of GHTT, in order to understand and interpret the complex data in the context of health and disease. At the same time, the growing volume and complexity of data is forever increasing the need for sustainable infrastructure and state-of-the-art tools for efficient data management, including their analysis and integration. The large pool of sensitive information remains difficult to interpret and fundamental questions spanning from billing to legal, social, and ethical issues have still not been resolved. Here we summarize and discuss these obstacles in an interdisciplinary context and suggest ways to overcome them. Continuous discussion with clinicians, data managers, biostatisticians, systems medicine experts, ethicists, legal scholars, and patients illuminates the strengths, weakness, and current practices in the pipeline from biomaterial to sequencing and data management. This discussion also highlights the new, cross-disciplinary working collaborations to realize the wide-ranging challenges in clinical genomics including the exceptional demands placed on the staff preparing and presenting the data, as well as the question as to how to report the data and results to patients.
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11
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Recchia G, Chiappi A, Chandratillake G, Raymond L, Freeman ALJ. Creating genetic reports that are understood by nonspecialists: a case study. Genet Med 2019; 22:353-361. [PMID: 31506646 PMCID: PMC7000324 DOI: 10.1038/s41436-019-0649-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Accepted: 08/22/2019] [Indexed: 11/09/2022] Open
Abstract
PURPOSE Guidelines recommend that genetic reports should be clear to nonspecialists, including patients. We investigated the feasibility of creating reports for cystic fibrosis carrier testing through a rapid user-centered design process that built on a previously developed generic template. We evaluated the new reports' communication efficacy and effects on comprehension against comparable reports used in current clinical practice. METHODS Thirty participants took part in three rounds of interviews. Usability problems were identified and rectified in each round. One hundred ninety-three participants took part in an evaluation of the resulting reports measuring subjective comprehension, risk probability comprehension, perceived communication efficacy, and other factors, as compared with standard reports. RESULTS Participants viewing the user-centered reports rated them as clearer, easier to understand, and more effective at communicating key information than standard reports. Both groups ended up with equivalent knowledge of risk probabilities, although we observed differences in how those probabilities were perceived. CONCLUSION Our findings demonstrate that by starting with a patient-friendly generic report template and modifying it for specific scenarios with a rapid user-centered design process, reports can be produced that are more effective at communicating key information. The resulting reports are now being implemented into clinical care.
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Affiliation(s)
- Gabriel Recchia
- Winton Centre for Risk and Evidence Communication, University of Cambridge, Cambridge, UK.
| | - Antonia Chiappi
- Institute of Continuing Education, University of Cambridge, Cambridge, UK
| | - Gemma Chandratillake
- Institute of Continuing Education, University of Cambridge, Cambridge, UK.,East of England NHS Genomic Medicine Centre, London, UK
| | - Lucy Raymond
- East of England NHS Genomic Medicine Centre, London, UK.,Department of Medical Genetics, University of Cambridge, Cambridge, UK.,NIHR Bioresource-Rare Disease, London, UK
| | - Alexandra L J Freeman
- Winton Centre for Risk and Evidence Communication, University of Cambridge, Cambridge, UK
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12
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Implementation of genomics in medical practice to deliver precision medicine for an Asian population. NPJ Genom Med 2019; 4:12. [PMID: 31231544 PMCID: PMC6555782 DOI: 10.1038/s41525-019-0085-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Accepted: 05/15/2019] [Indexed: 01/06/2023] Open
Abstract
Whilst the underlying principles of precision medicine are comparable across the globe, genomic references, health practices, costs and discrimination policies differ in Asian settings compared to the reported initiatives involving European-derived populations. We have addressed these variables by developing an evolving reference base of genomic and phenotypic data and a framework to return medically significant variants to consenting research participants applicable for the Asian context. Targeting 10,000 participants, over 2000 Singaporeans, with no known pre-existing health conditions, have consented to an extensive clinical health screen, family health history collection, genome sequencing and ongoing follow-up. Genomic variants in a subset of genes associated with Mendelian disorders and drug responses are analysed using an in-house bioinformatics pipeline. A multidisciplinary team reviews the classification of variants and a research report is generated. Medically significant variants are returned to consenting participants through a bespoke return-of-result genomics clinic. Variant validation and subsequent clinical referral are advised as appropriate. The design and implementation of this flexible learning framework enables a cohort of detailed phenotyping and genotyping of healthy Singaporeans to be established and the frequency of disease-causing variants in this population to be determined. Our findings will contribute to international precision medicine initiatives, bridging gaps with ethnic-specific data and insights from this understudied population.
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13
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Davis KW, Hamby Erby L, Fiallos K, Martin M, Wassman ER. A comparison of genomic laboratory reports and observations that may enhance their clinical utility for providers and patients. Mol Genet Genomic Med 2019; 7:e00551. [PMID: 31115190 PMCID: PMC6625363 DOI: 10.1002/mgg3.551] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Revised: 11/19/2018] [Accepted: 12/02/2018] [Indexed: 12/28/2022] Open
Abstract
Purpose To assess clinical chromosomal microarray (CMA) genomic testing reports for the following: (a) usage of reporting elements consistent with 2011 ACMG guidelines and other elements identified in the primary literature, (b) information quality, and (c) readability. Methods We retrospectively analyzed genomic testing reports from 2011 to 2016 provided to, or by our laboratory to aid in clinical detection and interpretation of copy number variants. Analysis was restricted to the following sections: interpretation, recommendations, limitations, and citations. Analysis included descriptive characteristics, reporting elements, reading difficulty using the Simple Measure of Gobbledygook (SMOG), and quality ratings using a subset of questions adapted from the DISCERN‐Genetics questionnaire. Results The analysis included 44 unique reports from 26 laboratories comprising four groups: specialty laboratories (SL; N = 9), reference laboratories (RL; N = 12), hospital laboratories (HL; N = 10), and university‐based laboratories (UL; N = 13). There were 23 abnormal/pathogenic reports and 21 of uncertain/unknown significance. Nine laboratories did not include one or more pieces of information based on ACMG guidelines; only one of ten laboratories reported condition‐specific management/treatment information when available and relevant. Average quality ratings and readability scores were not significantly different between laboratory types or result classification. Conclusions Reporting practices for most report elements varied widely; however, readability and quality did not differ significantly between laboratory types. Management and treatment information, even for well‐known conditions, are rarely included. Effectively communicating test results may be improved if certain reporting elements are incorporated. Recommendations to improve laboratory reports are provided.
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Affiliation(s)
| | - Lori Hamby Erby
- National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland
| | - Katie Fiallos
- Sidney Kimmel Cancer Center, Johns Hopkins School of Medicine, Baltimore, Maryland
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14
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Personal genomic screening: How best to facilitate preparedness of future clients. Eur J Med Genet 2019; 62:397-404. [DOI: 10.1016/j.ejmg.2019.05.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2018] [Revised: 02/23/2019] [Accepted: 05/06/2019] [Indexed: 12/24/2022]
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15
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Suwinski P, Ong C, Ling MHT, Poh YM, Khan AM, Ong HS. Advancing Personalized Medicine Through the Application of Whole Exome Sequencing and Big Data Analytics. Front Genet 2019; 10:49. [PMID: 30809243 PMCID: PMC6379253 DOI: 10.3389/fgene.2019.00049] [Citation(s) in RCA: 103] [Impact Index Per Article: 20.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Accepted: 01/21/2019] [Indexed: 12/11/2022] Open
Abstract
There is a growing attention toward personalized medicine. This is led by a fundamental shift from the ‘one size fits all’ paradigm for treatment of patients with conditions or predisposition to diseases, to one that embraces novel approaches, such as tailored target therapies, to achieve the best possible outcomes. Driven by these, several national and international genome projects have been initiated to reap the benefits of personalized medicine. Exome and targeted sequencing provide a balance between cost and benefit, in contrast to whole genome sequencing (WGS). Whole exome sequencing (WES) targets approximately 3% of the whole genome, which is the basis for protein-coding genes. Nonetheless, it has the characteristics of big data in large deployment. Herein, the application of WES and its relevance in advancing personalized medicine is reviewed. WES is mapped to Big Data “10 Vs” and the resulting challenges discussed. Application of existing biological databases and bioinformatics tools to address the bottleneck in data processing and analysis are presented, including the need for new generation big data analytics for the multi-omics challenges of personalized medicine. This includes the incorporation of artificial intelligence (AI) in the clinical utility landscape of genomic information, and future consideration to create a new frontier toward advancing the field of personalized medicine.
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Affiliation(s)
- Pawel Suwinski
- Malaysian Genomics Resource Centre Berhad, Kuala Lumpur, Malaysia
| | - ChuangKee Ong
- Centre for Bioinformatics, School of Data Sciences, Perdana University, Serdang, Malaysia.,Centre of Genomics Research, Precision Medicine and Genomics, AstraZeneca UK Limited, London, United Kingdom
| | - Maurice H T Ling
- Centre for Bioinformatics, School of Data Sciences, Perdana University, Serdang, Malaysia
| | - Yang Ming Poh
- Centre for Bioinformatics, School of Data Sciences, Perdana University, Serdang, Malaysia
| | - Asif M Khan
- Centre for Bioinformatics, School of Data Sciences, Perdana University, Serdang, Malaysia.,Graduate School of Medicine, Perdana University, Serdang, Malaysia
| | - Hui San Ong
- Centre for Bioinformatics, School of Data Sciences, Perdana University, Serdang, Malaysia
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16
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Sharma V, Fong A, Beckman RA, Rao S, Boca SM, McGarvey PB, Ratwani RM, Madhavan S. Eye-Tracking Study to Enhance Usability of Molecular Diagnostics Reports in Cancer Precision Medicine. JCO Precis Oncol 2018; 2:1-11. [PMID: 35135129 DOI: 10.1200/po.17.00296] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
PURPOSE We conducted usability studies on commercially available molecular diagnostic (MDX) test reports to identify strengths and weaknesses in content and form that drive clinical decision making. Given routine genomic testing in cancer medicine, oncologists must interpret MDX reports as well as evidence concerning clinical utility of biomarkers accurately for treatment or trial selection. This work aims to evaluate effectiveness of MDX reports in facilitating cancer treatment planning. METHODS Fourteen clinicians at an academic tertiary care medical facility, with a wide range of experience in oncology and in the use of molecular testing, participated in this study. Three commercially available, widely used, Clinical Laboratory Improvement Amendments (CLIA)-certified, College of American Pathologists (CAP)-accredited test reports (labeled Laboratories A, B, and C) were used. Eye tracking, surveys, and think-aloud protocols were used to collect usability data for these MDX reports focusing on ease of comprehension and actionability. RESULTS Clinicians found two primary areas in molecular diagnostic reports most useful for patient care: therapy options with benefit or lack of benefit to patients, including enrolling clinical trials; and pathogenic tumor molecular anomalies detected. Therapeutic implications and therapy classes such as US Food and Drug Administration-approved off-label, on-label, clinical trials were critical for decision making. However, all reports had usability and comprehension issues in these areas and could be improved. CONCLUSION Focused usability studies can help drive our understanding of the clinical workflow for use of molecular diagnostic tests in cancer care. This in turn can have major effects on quality of care, outcomes, costs, and patient satisfaction. This study demonstrates the use of specific usability techniques (eye tracking and think-aloud protocols) to help clinical laboratories improve MDX report design in a precision oncology treatment setting.
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Affiliation(s)
- Vishakha Sharma
- Vishakha Sharma, Robert A. Beckman, Shruti Rao, Simina M. Boca, Peter B. McGarvey, and Subha Madhavan, Georgetown University; Vishakha Sharma, Robert A. Beckman, Simina M. Boca, and Subha Madhavan, Georgetown University Medical Center; Allan Fong and Raj M. Ratwani, National Center for Human Factors in Healthcare, MedStar Health; and Raj M. Ratwani, Georgetown University School of Medicine, Washington, DC
| | - Allan Fong
- Vishakha Sharma, Robert A. Beckman, Shruti Rao, Simina M. Boca, Peter B. McGarvey, and Subha Madhavan, Georgetown University; Vishakha Sharma, Robert A. Beckman, Simina M. Boca, and Subha Madhavan, Georgetown University Medical Center; Allan Fong and Raj M. Ratwani, National Center for Human Factors in Healthcare, MedStar Health; and Raj M. Ratwani, Georgetown University School of Medicine, Washington, DC
| | - Robert A Beckman
- Vishakha Sharma, Robert A. Beckman, Shruti Rao, Simina M. Boca, Peter B. McGarvey, and Subha Madhavan, Georgetown University; Vishakha Sharma, Robert A. Beckman, Simina M. Boca, and Subha Madhavan, Georgetown University Medical Center; Allan Fong and Raj M. Ratwani, National Center for Human Factors in Healthcare, MedStar Health; and Raj M. Ratwani, Georgetown University School of Medicine, Washington, DC
| | - Shruti Rao
- Vishakha Sharma, Robert A. Beckman, Shruti Rao, Simina M. Boca, Peter B. McGarvey, and Subha Madhavan, Georgetown University; Vishakha Sharma, Robert A. Beckman, Simina M. Boca, and Subha Madhavan, Georgetown University Medical Center; Allan Fong and Raj M. Ratwani, National Center for Human Factors in Healthcare, MedStar Health; and Raj M. Ratwani, Georgetown University School of Medicine, Washington, DC
| | - Simina M Boca
- Vishakha Sharma, Robert A. Beckman, Shruti Rao, Simina M. Boca, Peter B. McGarvey, and Subha Madhavan, Georgetown University; Vishakha Sharma, Robert A. Beckman, Simina M. Boca, and Subha Madhavan, Georgetown University Medical Center; Allan Fong and Raj M. Ratwani, National Center for Human Factors in Healthcare, MedStar Health; and Raj M. Ratwani, Georgetown University School of Medicine, Washington, DC
| | - Peter B McGarvey
- Vishakha Sharma, Robert A. Beckman, Shruti Rao, Simina M. Boca, Peter B. McGarvey, and Subha Madhavan, Georgetown University; Vishakha Sharma, Robert A. Beckman, Simina M. Boca, and Subha Madhavan, Georgetown University Medical Center; Allan Fong and Raj M. Ratwani, National Center for Human Factors in Healthcare, MedStar Health; and Raj M. Ratwani, Georgetown University School of Medicine, Washington, DC
| | - Raj M Ratwani
- Vishakha Sharma, Robert A. Beckman, Shruti Rao, Simina M. Boca, Peter B. McGarvey, and Subha Madhavan, Georgetown University; Vishakha Sharma, Robert A. Beckman, Simina M. Boca, and Subha Madhavan, Georgetown University Medical Center; Allan Fong and Raj M. Ratwani, National Center for Human Factors in Healthcare, MedStar Health; and Raj M. Ratwani, Georgetown University School of Medicine, Washington, DC
| | - Subha Madhavan
- Vishakha Sharma, Robert A. Beckman, Shruti Rao, Simina M. Boca, Peter B. McGarvey, and Subha Madhavan, Georgetown University; Vishakha Sharma, Robert A. Beckman, Simina M. Boca, and Subha Madhavan, Georgetown University Medical Center; Allan Fong and Raj M. Ratwani, National Center for Human Factors in Healthcare, MedStar Health; and Raj M. Ratwani, Georgetown University School of Medicine, Washington, DC
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Christensen KD, Phillips KA, Green RC, Dukhovny D. Cost Analyses of Genomic Sequencing: Lessons Learned from the MedSeq Project. VALUE IN HEALTH : THE JOURNAL OF THE INTERNATIONAL SOCIETY FOR PHARMACOECONOMICS AND OUTCOMES RESEARCH 2018; 21:1054-1061. [PMID: 30224109 PMCID: PMC6444358 DOI: 10.1016/j.jval.2018.06.013] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Accepted: 06/11/2018] [Indexed: 05/17/2023]
Abstract
OBJECTIVE To summarize lessons learned while analyzing the costs of integrating whole genome sequencing into the care of cardiology and primary care patients in the MedSeq Project by conducting the first randomized controlled trial of whole genome sequencing in general and specialty medicine. METHODS Case study that describes key methodological and data challenges that were encountered or are likely to emerge in future work, describes the pros and cons of approaches considered by the study team, and summarizes the solutions that were implemented. RESULTS Major methodological challenges included defining whole genome sequencing, structuring an appropriate comparator, measuring downstream costs, and examining clinical outcomes. Discussions about solutions addressed conceptual and practical issues that arose because of definitions and analyses around the cost of genomic sequencing in trial-based studies. CONCLUSIONS The MedSeq Project provides an instructive example of how to conduct a cost analysis of whole genome sequencing that feasibly incorporates best practices while being sensitive to the varied applications and diversity of results it may produce. Findings provide guidance for researchers to consider when conducting or analyzing economic analyses of whole genome sequencing and other next-generation sequencing tests, particularly regarding costs.
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Affiliation(s)
- Kurt D Christensen
- Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.
| | - Kathryn A Phillips
- Department of Clinical Pharmacy, Center for Translational and Policy Research on Personalized Medicine (TRANSPERS), University of California San Francisco, San Francisco, CA, USA; Philip R. Lee Institute for Health Policy and Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - Robert C Green
- Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA; Partners HealthCare Personalized Medicine, Boston, MA, USA
| | - Dmitry Dukhovny
- Department of Pediatrics, Oregon Health & Science University, Portland, OR, USA
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18
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Song C, Duzkale H, Shen J. Reporting of Clinical Genome Sequencing Results. CURRENT PROTOCOLS IN HUMAN GENETICS 2018; 98:e61. [PMID: 29979828 DOI: 10.1002/cphg.61] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
High-throughput sequencing and high-performance computing technologies have become powerful tools in clinical genetic diagnosis of hereditary disorders and genetic screening of healthy individuals to provide information for the diagnosis, treatment, and prevention of diseases or impairment and assessment of health. For patients with undiagnosed disorders, including many rare disorders, the whole-genome sequencing (WGS) test may end the diagnostic odyssey, ultimately guiding clinical care for them and their families. A clinical WGS test relies on high-quality genome-sequencing data as well as sophisticated data-interpretation approaches. Results are returned to the ordering physician in a concise report featuring an overall test result and in-depth phenotype-driven interpretation of the known or plausible genetic explanation of test indications. Patients have the option to decide whether the report should include secondary and incidental findings. Protocols and templates for reporting clinical WGS results and supplementary information are described in this article. © 2018 by John Wiley & Sons, Inc.
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Affiliation(s)
- Cui Song
- Department of Endocrinology and Genetic Metabolic Diseases, Children's Hospital of Chongqing Medical University, Chongqing, China.,Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Hatice Duzkale
- Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - Jun Shen
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
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19
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Automated typing of red blood cell and platelet antigens: a whole-genome sequencing study. Lancet Haematol 2018; 5:e241-e251. [PMID: 29780001 PMCID: PMC6438177 DOI: 10.1016/s2352-3026(18)30053-x] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Revised: 04/11/2018] [Accepted: 04/12/2018] [Indexed: 01/05/2023]
Abstract
BACKGROUND There are more than 300 known red blood cell (RBC) antigens and 33 platelet antigens that differ between individuals. Sensitisation to antigens is a serious complication that can occur in prenatal medicine and after blood transfusion, particularly for patients who require multiple transfusions. Although pre-transfusion compatibility testing largely relies on serological methods, reagents are not available for many antigens. Methods based on single-nucleotide polymorphism (SNP) arrays have been used, but typing for ABO and Rh-the most important blood groups-cannot be done with SNP typing alone. We aimed to develop a novel method based on whole-genome sequencing to identify RBC and platelet antigens. METHODS This whole-genome sequencing study is a subanalysis of data from patients in the whole-genome sequencing arm of the MedSeq Project randomised controlled trial (NCT01736566) with no measured patient outcomes. We created a database of molecular changes in RBC and platelet antigens and developed an automated antigen-typing algorithm based on whole-genome sequencing (bloodTyper). This algorithm was iteratively improved to address cis-trans haplotype ambiguities and homologous gene alignments. Whole-genome sequencing data from 110 MedSeq participants (30 × depth) were used to initially validate bloodTyper through comparison with conventional serology and SNP methods for typing of 38 RBC antigens in 12 blood-group systems and 22 human platelet antigens. bloodTyper was further validated with whole-genome sequencing data from 200 INTERVAL trial participants (15 × depth) with serological comparisons. FINDINGS We iteratively improved bloodTyper by comparing its typing results with conventional serological and SNP typing in three rounds of testing. The initial whole-genome sequencing typing algorithm was 99·5% concordant across the first 20 MedSeq genomes. Addressing discordances led to development of an improved algorithm that was 99·8% concordant for the remaining 90 MedSeq genomes. Additional modifications led to the final algorithm, which was 99·2% concordant across 200 INTERVAL genomes (or 99·9% after adjustment for the lower depth of coverage). INTERPRETATION By enabling more precise antigen-matching of patients with blood donors, antigen typing based on whole-genome sequencing provides a novel approach to improve transfusion outcomes with the potential to transform the practice of transfusion medicine. FUNDING National Human Genome Research Institute, Doris Duke Charitable Foundation, National Health Service Blood and Transplant, National Institute for Health Research, and Wellcome Trust.
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20
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Vassy JL, Davis JK, Kirby C, Richardson IJ, Green RC, McGuire AL, Ubel PA. How Primary Care Providers Talk to Patients about Genome Sequencing Results: Risk, Rationale, and Recommendation. J Gen Intern Med 2018; 33:877-885. [PMID: 29374360 PMCID: PMC5975138 DOI: 10.1007/s11606-017-4295-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Revised: 11/14/2017] [Accepted: 12/20/2017] [Indexed: 01/28/2023]
Abstract
BACKGROUND Genomics will play an increasingly prominent role in clinical medicine. OBJECTIVE To describe how primary care physicians (PCPs) discuss and make clinical recommendations about genome sequencing results. DESIGN Qualitative analysis. PARTICIPANTS PCPs and their generally healthy patients undergoing genome sequencing. APPROACH Patients received clinical genome reports that included four categories of results: monogenic disease risk variants (if present), carrier status, five pharmacogenetics results, and polygenic risk estimates for eight cardiometabolic traits. Patients' office visits with their PCPs were audio-recorded, and summative content analysis was used to describe how PCPs discussed genomic results. KEY RESULTS For each genomic result discussed in 48 PCP-patient visits, we identified a "take-home" message (recommendation), categorized as continuing current management, further treatment, further evaluation, behavior change, remembering for future care, or sharing with family members. We analyzed how PCPs came to each recommendation by identifying 1) how they described the risk or importance of the given result and 2) the rationale they gave for translating that risk into a specific recommendation. Quantitative analysis showed that continuing current management was the most commonly coded recommendation across results overall (492/749, 66%) and for each individual result type except monogenic disease risk results. Pharmacogenetics was the most common result type to prompt a recommendation to remember for future care (94/119, 79%); carrier status was the most common type prompting a recommendation to share with family members (45/54, 83%); and polygenic results were the most common type prompting a behavior change recommendation (55/58, 95%). One-fifth of recommendation codes associated with monogenic results were for further evaluation (6/24, 25%). Rationales for these recommendations included patient context, family context, and scientific/clinical limitations of sequencing. CONCLUSIONS PCPs distinguish substantive differences among categories of genome sequencing results and use clinical judgment to justify continuing current management in generally healthy patients with genomic results.
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Affiliation(s)
- Jason L Vassy
- Section of General Internal Medicine, VA Boston Healthcare System, Boston, MA, USA.
- Division of General Internal Medicine and Primary Care, Brigham and Women's Hospital, Boston, MA, USA.
- Department of Medicine, Harvard Medical School, Boston, MA, USA.
| | - J Kelly Davis
- Margolis Center for Health Policy, Duke University, Durham, NC, USA
| | - Christine Kirby
- Margolis Center for Health Policy, Duke University, Durham, NC, USA
| | - Ian J Richardson
- Division of General Internal Medicine and Primary Care, Brigham and Women's Hospital, Boston, MA, USA
| | - Robert C Green
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Division of Genetics, Brigham and Women's Hospital, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Amy L McGuire
- Center for Medical Ethics and Health Policy, Baylor College of Medicine, Houston, TX, USA
| | - Peter A Ubel
- Margolis Center for Health Policy, Duke University, Durham, NC, USA
- Fuqua School of Business, Sanford School of Public Policy, School of Medicine, Duke University, Durham, NC, USA
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21
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Cirino AL, Lakdawala NK, McDonough B, Conner L, Adler D, Weinfeld M, O'Gara P, Rehm HL, Machini K, Lebo M, Blout C, Green RC, MacRae CA, Seidman CE, Ho CY. A Comparison of Whole Genome Sequencing to Multigene Panel Testing in Hypertrophic Cardiomyopathy Patients. ACTA ACUST UNITED AC 2018; 10:CIRCGENETICS.117.001768. [PMID: 29030401 DOI: 10.1161/circgenetics.117.001768] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Accepted: 08/31/2017] [Indexed: 12/11/2022]
Abstract
BACKGROUND As DNA sequencing costs decline, genetic testing options have expanded. Whole exome sequencing and whole genome sequencing (WGS) are entering clinical use, posing questions about their incremental value compared with disease-specific multigene panels that have been the cornerstone of genetic testing. METHODS AND RESULTS Forty-one patients with hypertrophic cardiomyopathy who had undergone targeted hypertrophic cardiomyopathy genetic testing (either multigene panel or familial variant test) were recruited into the MedSeq Project, a clinical trial of WGS. Results from panel genetic testing and WGS were compared. In 20 of 41 participants, panel genetic testing identified variants classified as pathogenic, likely pathogenic, or uncertain significance. WGS identified 19 of these 20 variants, but the variant detection algorithm missed a pathogenic 18 bp duplication in myosin binding protein C (MYBPC3) because of low coverage. In 3 individuals, WGS identified variants in genes implicated in cardiomyopathy but not included in prior panel testing: a pathogenic protein tyrosine phosphatase, non-receptor type 11 (PTPN11) variant and variants of uncertain significance in integrin-linked kinase (ILK) and filamin-C (FLNC). WGS also identified 84 secondary findings (mean=2 per person, range=0-6), which mostly defined carrier status for recessive conditions. CONCLUSIONS WGS detected nearly all variants identified on panel testing, provided 1 new diagnostic finding, and allowed interrogation of posited disease genes. Several variants of uncertain clinical use and numerous secondary genetic findings were also identified. Whereas panel testing and WGS provided similar diagnostic yield, WGS offers the advantage of reanalysis over time to incorporate advances in knowledge, but requires expertise in genomic interpretation to appropriately incorporate WGS into clinical care. CLINICAL TRIAL REGISTRATION URL: https://clinicaltrials.gov. Unique identifier: NCT01736566.
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Affiliation(s)
- Allison L Cirino
- From the Cardiovascular Division (A.L.C., N.K.L., B.M., D.A., M.W., P.O., C.A.M., C.E.S., C.Y.H.), Department of Pathology (H.L.R.), and Division of Genetics (C.B., R.C.G., C.A.M.), Brigham and Women's Hospital, Boston, MA; Harvard Medical School, Boston, MA (N.K.L., B.M., D.A., M.W., P.O., H.L.R., R.C.G., C.A.M., C.E.S., C.Y.H.); Albany Medical College, NY (L.C.); Broad Institute of Harvard and MIT, Cambridge, MA (H.L.R., R.C.G., C.A.M.); Laboratory for Molecular Medicine (H.L.R., K.M., M.L.), Leadership Team (R.C.G.), Partners HealthCare Personalized Medicine, Cambridge, MA; and Howard Hughes Medical Institute, Chevy Chase, MD (C.E.S.)
| | - Neal K Lakdawala
- From the Cardiovascular Division (A.L.C., N.K.L., B.M., D.A., M.W., P.O., C.A.M., C.E.S., C.Y.H.), Department of Pathology (H.L.R.), and Division of Genetics (C.B., R.C.G., C.A.M.), Brigham and Women's Hospital, Boston, MA; Harvard Medical School, Boston, MA (N.K.L., B.M., D.A., M.W., P.O., H.L.R., R.C.G., C.A.M., C.E.S., C.Y.H.); Albany Medical College, NY (L.C.); Broad Institute of Harvard and MIT, Cambridge, MA (H.L.R., R.C.G., C.A.M.); Laboratory for Molecular Medicine (H.L.R., K.M., M.L.), Leadership Team (R.C.G.), Partners HealthCare Personalized Medicine, Cambridge, MA; and Howard Hughes Medical Institute, Chevy Chase, MD (C.E.S.)
| | - Barbara McDonough
- From the Cardiovascular Division (A.L.C., N.K.L., B.M., D.A., M.W., P.O., C.A.M., C.E.S., C.Y.H.), Department of Pathology (H.L.R.), and Division of Genetics (C.B., R.C.G., C.A.M.), Brigham and Women's Hospital, Boston, MA; Harvard Medical School, Boston, MA (N.K.L., B.M., D.A., M.W., P.O., H.L.R., R.C.G., C.A.M., C.E.S., C.Y.H.); Albany Medical College, NY (L.C.); Broad Institute of Harvard and MIT, Cambridge, MA (H.L.R., R.C.G., C.A.M.); Laboratory for Molecular Medicine (H.L.R., K.M., M.L.), Leadership Team (R.C.G.), Partners HealthCare Personalized Medicine, Cambridge, MA; and Howard Hughes Medical Institute, Chevy Chase, MD (C.E.S.)
| | - Lauren Conner
- From the Cardiovascular Division (A.L.C., N.K.L., B.M., D.A., M.W., P.O., C.A.M., C.E.S., C.Y.H.), Department of Pathology (H.L.R.), and Division of Genetics (C.B., R.C.G., C.A.M.), Brigham and Women's Hospital, Boston, MA; Harvard Medical School, Boston, MA (N.K.L., B.M., D.A., M.W., P.O., H.L.R., R.C.G., C.A.M., C.E.S., C.Y.H.); Albany Medical College, NY (L.C.); Broad Institute of Harvard and MIT, Cambridge, MA (H.L.R., R.C.G., C.A.M.); Laboratory for Molecular Medicine (H.L.R., K.M., M.L.), Leadership Team (R.C.G.), Partners HealthCare Personalized Medicine, Cambridge, MA; and Howard Hughes Medical Institute, Chevy Chase, MD (C.E.S.)
| | - Dale Adler
- From the Cardiovascular Division (A.L.C., N.K.L., B.M., D.A., M.W., P.O., C.A.M., C.E.S., C.Y.H.), Department of Pathology (H.L.R.), and Division of Genetics (C.B., R.C.G., C.A.M.), Brigham and Women's Hospital, Boston, MA; Harvard Medical School, Boston, MA (N.K.L., B.M., D.A., M.W., P.O., H.L.R., R.C.G., C.A.M., C.E.S., C.Y.H.); Albany Medical College, NY (L.C.); Broad Institute of Harvard and MIT, Cambridge, MA (H.L.R., R.C.G., C.A.M.); Laboratory for Molecular Medicine (H.L.R., K.M., M.L.), Leadership Team (R.C.G.), Partners HealthCare Personalized Medicine, Cambridge, MA; and Howard Hughes Medical Institute, Chevy Chase, MD (C.E.S.)
| | - Mark Weinfeld
- From the Cardiovascular Division (A.L.C., N.K.L., B.M., D.A., M.W., P.O., C.A.M., C.E.S., C.Y.H.), Department of Pathology (H.L.R.), and Division of Genetics (C.B., R.C.G., C.A.M.), Brigham and Women's Hospital, Boston, MA; Harvard Medical School, Boston, MA (N.K.L., B.M., D.A., M.W., P.O., H.L.R., R.C.G., C.A.M., C.E.S., C.Y.H.); Albany Medical College, NY (L.C.); Broad Institute of Harvard and MIT, Cambridge, MA (H.L.R., R.C.G., C.A.M.); Laboratory for Molecular Medicine (H.L.R., K.M., M.L.), Leadership Team (R.C.G.), Partners HealthCare Personalized Medicine, Cambridge, MA; and Howard Hughes Medical Institute, Chevy Chase, MD (C.E.S.)
| | - Patrick O'Gara
- From the Cardiovascular Division (A.L.C., N.K.L., B.M., D.A., M.W., P.O., C.A.M., C.E.S., C.Y.H.), Department of Pathology (H.L.R.), and Division of Genetics (C.B., R.C.G., C.A.M.), Brigham and Women's Hospital, Boston, MA; Harvard Medical School, Boston, MA (N.K.L., B.M., D.A., M.W., P.O., H.L.R., R.C.G., C.A.M., C.E.S., C.Y.H.); Albany Medical College, NY (L.C.); Broad Institute of Harvard and MIT, Cambridge, MA (H.L.R., R.C.G., C.A.M.); Laboratory for Molecular Medicine (H.L.R., K.M., M.L.), Leadership Team (R.C.G.), Partners HealthCare Personalized Medicine, Cambridge, MA; and Howard Hughes Medical Institute, Chevy Chase, MD (C.E.S.)
| | - Heidi L Rehm
- From the Cardiovascular Division (A.L.C., N.K.L., B.M., D.A., M.W., P.O., C.A.M., C.E.S., C.Y.H.), Department of Pathology (H.L.R.), and Division of Genetics (C.B., R.C.G., C.A.M.), Brigham and Women's Hospital, Boston, MA; Harvard Medical School, Boston, MA (N.K.L., B.M., D.A., M.W., P.O., H.L.R., R.C.G., C.A.M., C.E.S., C.Y.H.); Albany Medical College, NY (L.C.); Broad Institute of Harvard and MIT, Cambridge, MA (H.L.R., R.C.G., C.A.M.); Laboratory for Molecular Medicine (H.L.R., K.M., M.L.), Leadership Team (R.C.G.), Partners HealthCare Personalized Medicine, Cambridge, MA; and Howard Hughes Medical Institute, Chevy Chase, MD (C.E.S.)
| | - Kalotina Machini
- From the Cardiovascular Division (A.L.C., N.K.L., B.M., D.A., M.W., P.O., C.A.M., C.E.S., C.Y.H.), Department of Pathology (H.L.R.), and Division of Genetics (C.B., R.C.G., C.A.M.), Brigham and Women's Hospital, Boston, MA; Harvard Medical School, Boston, MA (N.K.L., B.M., D.A., M.W., P.O., H.L.R., R.C.G., C.A.M., C.E.S., C.Y.H.); Albany Medical College, NY (L.C.); Broad Institute of Harvard and MIT, Cambridge, MA (H.L.R., R.C.G., C.A.M.); Laboratory for Molecular Medicine (H.L.R., K.M., M.L.), Leadership Team (R.C.G.), Partners HealthCare Personalized Medicine, Cambridge, MA; and Howard Hughes Medical Institute, Chevy Chase, MD (C.E.S.)
| | - Matthew Lebo
- From the Cardiovascular Division (A.L.C., N.K.L., B.M., D.A., M.W., P.O., C.A.M., C.E.S., C.Y.H.), Department of Pathology (H.L.R.), and Division of Genetics (C.B., R.C.G., C.A.M.), Brigham and Women's Hospital, Boston, MA; Harvard Medical School, Boston, MA (N.K.L., B.M., D.A., M.W., P.O., H.L.R., R.C.G., C.A.M., C.E.S., C.Y.H.); Albany Medical College, NY (L.C.); Broad Institute of Harvard and MIT, Cambridge, MA (H.L.R., R.C.G., C.A.M.); Laboratory for Molecular Medicine (H.L.R., K.M., M.L.), Leadership Team (R.C.G.), Partners HealthCare Personalized Medicine, Cambridge, MA; and Howard Hughes Medical Institute, Chevy Chase, MD (C.E.S.)
| | - Carrie Blout
- From the Cardiovascular Division (A.L.C., N.K.L., B.M., D.A., M.W., P.O., C.A.M., C.E.S., C.Y.H.), Department of Pathology (H.L.R.), and Division of Genetics (C.B., R.C.G., C.A.M.), Brigham and Women's Hospital, Boston, MA; Harvard Medical School, Boston, MA (N.K.L., B.M., D.A., M.W., P.O., H.L.R., R.C.G., C.A.M., C.E.S., C.Y.H.); Albany Medical College, NY (L.C.); Broad Institute of Harvard and MIT, Cambridge, MA (H.L.R., R.C.G., C.A.M.); Laboratory for Molecular Medicine (H.L.R., K.M., M.L.), Leadership Team (R.C.G.), Partners HealthCare Personalized Medicine, Cambridge, MA; and Howard Hughes Medical Institute, Chevy Chase, MD (C.E.S.)
| | - Robert C Green
- From the Cardiovascular Division (A.L.C., N.K.L., B.M., D.A., M.W., P.O., C.A.M., C.E.S., C.Y.H.), Department of Pathology (H.L.R.), and Division of Genetics (C.B., R.C.G., C.A.M.), Brigham and Women's Hospital, Boston, MA; Harvard Medical School, Boston, MA (N.K.L., B.M., D.A., M.W., P.O., H.L.R., R.C.G., C.A.M., C.E.S., C.Y.H.); Albany Medical College, NY (L.C.); Broad Institute of Harvard and MIT, Cambridge, MA (H.L.R., R.C.G., C.A.M.); Laboratory for Molecular Medicine (H.L.R., K.M., M.L.), Leadership Team (R.C.G.), Partners HealthCare Personalized Medicine, Cambridge, MA; and Howard Hughes Medical Institute, Chevy Chase, MD (C.E.S.)
| | - Calum A MacRae
- From the Cardiovascular Division (A.L.C., N.K.L., B.M., D.A., M.W., P.O., C.A.M., C.E.S., C.Y.H.), Department of Pathology (H.L.R.), and Division of Genetics (C.B., R.C.G., C.A.M.), Brigham and Women's Hospital, Boston, MA; Harvard Medical School, Boston, MA (N.K.L., B.M., D.A., M.W., P.O., H.L.R., R.C.G., C.A.M., C.E.S., C.Y.H.); Albany Medical College, NY (L.C.); Broad Institute of Harvard and MIT, Cambridge, MA (H.L.R., R.C.G., C.A.M.); Laboratory for Molecular Medicine (H.L.R., K.M., M.L.), Leadership Team (R.C.G.), Partners HealthCare Personalized Medicine, Cambridge, MA; and Howard Hughes Medical Institute, Chevy Chase, MD (C.E.S.)
| | - Christine E Seidman
- From the Cardiovascular Division (A.L.C., N.K.L., B.M., D.A., M.W., P.O., C.A.M., C.E.S., C.Y.H.), Department of Pathology (H.L.R.), and Division of Genetics (C.B., R.C.G., C.A.M.), Brigham and Women's Hospital, Boston, MA; Harvard Medical School, Boston, MA (N.K.L., B.M., D.A., M.W., P.O., H.L.R., R.C.G., C.A.M., C.E.S., C.Y.H.); Albany Medical College, NY (L.C.); Broad Institute of Harvard and MIT, Cambridge, MA (H.L.R., R.C.G., C.A.M.); Laboratory for Molecular Medicine (H.L.R., K.M., M.L.), Leadership Team (R.C.G.), Partners HealthCare Personalized Medicine, Cambridge, MA; and Howard Hughes Medical Institute, Chevy Chase, MD (C.E.S.)
| | - Carolyn Y Ho
- From the Cardiovascular Division (A.L.C., N.K.L., B.M., D.A., M.W., P.O., C.A.M., C.E.S., C.Y.H.), Department of Pathology (H.L.R.), and Division of Genetics (C.B., R.C.G., C.A.M.), Brigham and Women's Hospital, Boston, MA; Harvard Medical School, Boston, MA (N.K.L., B.M., D.A., M.W., P.O., H.L.R., R.C.G., C.A.M., C.E.S., C.Y.H.); Albany Medical College, NY (L.C.); Broad Institute of Harvard and MIT, Cambridge, MA (H.L.R., R.C.G., C.A.M.); Laboratory for Molecular Medicine (H.L.R., K.M., M.L.), Leadership Team (R.C.G.), Partners HealthCare Personalized Medicine, Cambridge, MA; and Howard Hughes Medical Institute, Chevy Chase, MD (C.E.S.).
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22
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Christensen KD, Vassy JL, Phillips KA, Blout CL, Azzariti DR, Lu CY, Robinson JO, Lee K, Douglas MP, Yeh JM, Machini K, Stout NK, Rehm HL, McGuire AL, Green RC, Dukhovny D. Short-term costs of integrating whole-genome sequencing into primary care and cardiology settings: a pilot randomized trial. Genet Med 2018; 20:1544-1553. [PMID: 29565423 PMCID: PMC6151171 DOI: 10.1038/gim.2018.35] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Accepted: 01/30/2018] [Indexed: 12/26/2022] Open
Abstract
Purpose Great uncertainty exists about the costs associated with whole genome sequencing (WGS). Methods One hundred cardiology patients with cardiomyopathy diagnoses, and 100 ostensibly healthy primary care patients were randomized to receive a family history report alone or with a WGS report. Cardiology patients also reviewed prior genetic test results. WGS costs were estimated by tracking resource use and staff time. Downstream costs were estimated by identifying services in administrative data, medical records, and patient surveys for 6 months. Results The incremental cost per patient of WGS testing was $5,098 in cardiology settings and $5,073 in primary care settings compared to family history alone. Mean six month downstream costs did not differ statistically between the control and WGS arms in either setting (cardiology: difference = −$1,560, 95%CI −$7,558 to $3,866, p=0.36; primary care: difference = $681, 95%CI −$884 to $2,171, p=0.70). Scenario analyses showed the cost reduction of omitting or limiting the types of secondary findings was less than $69 and $182 per patient in cardiology and primary care, respectively. Conclusion Short-term costs of WGS were driven by the costs of sequencing and interpretation rather than downstream healthcare. Disclosing additional types of secondary findings has a limited cost impact following disclosure.
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Affiliation(s)
- Kurt D Christensen
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA. .,Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA.
| | - Jason L Vassy
- Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA.,Division of General Internal Medicine and Primary Care, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA.,Section of General Internal Medicine, VA Boston Healthcare System, Boston, Massachusetts, USA
| | - Kathryn A Phillips
- Department of Clinical Pharmacy, Center for Translational and Policy Research on Personalized Medicine (TRANSPERS), University of California San Francisco, San Francisco, California, USA.,Philip R. Lee Institute for Health Policy and Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California, USA
| | - Carrie L Blout
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Danielle R Azzariti
- Partners HealthCare Laboratory for Molecular Medicine, Cambridge, Massachusetts, USA
| | - Christine Y Lu
- Department of Population Medicine, Harvard Pilgrim Health Care Institute, Boston, Massachusetts, USA.,Department of Population Medicine, Harvard Medical School, Boston, Massachusetts, USA
| | - Jill O Robinson
- Center for Medical Ethics and Health Policy, Baylor College of Medicine, Houston, Texas, USA
| | - Kaitlyn Lee
- Center for Medical Ethics and Health Policy, Baylor College of Medicine, Houston, Texas, USA
| | - Michael P Douglas
- Department of Clinical Pharmacy, Center for Translational and Policy Research on Personalized Medicine (TRANSPERS), University of California San Francisco, San Francisco, California, USA
| | - Jennifer M Yeh
- Department of Pediatrics, Harvard Medical School, Boston, Massachusetts, USA.,Division of General Pediatrics, Boston Children's Hospital, Boston, Massachusetts, USA
| | - Kalotina Machini
- Partners HealthCare Laboratory for Molecular Medicine, Cambridge, Massachusetts, USA.,Department of Pathology, Harvard Medical School, Boston, Massachusetts, USA.,Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Natasha K Stout
- Department of Population Medicine, Harvard Pilgrim Health Care Institute, Boston, Massachusetts, USA.,Department of Population Medicine, Harvard Medical School, Boston, Massachusetts, USA
| | - Heidi L Rehm
- Partners HealthCare Laboratory for Molecular Medicine, Cambridge, Massachusetts, USA.,Department of Pathology, Harvard Medical School, Boston, Massachusetts, USA.,Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts, USA.,Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Amy L McGuire
- Center for Medical Ethics and Health Policy, Baylor College of Medicine, Houston, Texas, USA
| | - Robert C Green
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA.,Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA.,Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.,Partners HealthCare Personalized Medicine, Boston, Massachusetts, USA
| | - Dmitry Dukhovny
- Department of Pediatrics, Oregon Health & Science University, Portland, Oregon, USA
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23
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Ronquillo JG, Weng C, Lester WT. Assessing the readiness of precision medicine interoperabilty: An exploratory study of the National Institutes of Health genetic testing registry. JOURNAL OF INNOVATION IN HEALTH INFORMATICS 2017; 24:918. [PMID: 29334348 PMCID: PMC5891224 DOI: 10.14236/jhi.v24i4.918] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Accepted: 08/29/2017] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Precision medicine involves three major innovations currently taking place in healthcare: electronic health records, genomics, and big data. A major challenge for healthcare providers, however, is understanding the readiness for practical application of initiatives like precision medicine. OBJECTIVE To better understand the current state and challenges of precision medicine interoperability using a national genetic testing registry as a starting point, placed in the context of established interoperability formats. METHODS We performed an exploratory analysis of the National Institutes of Health Genetic Testing Registry. Relevant standards included Health Level Seven International Version 3 Implementation Guide for Family History, the Human Genome Organization Gene Nomenclature Committee (HGNC) database, and Systematized Nomenclature of Medicine - Clinical Terms (SNOMED CT). We analyzed the distribution of genetic testing laboratories, genetic test characteristics, and standardized genome/clinical code mappings, stratified by laboratory setting. RESULTS There were a total of 25472 genetic tests from 240 laboratories testing for approximately 3632 distinct genes. Most tests focused on diagnosis, mutation confirmation, and/or risk assessment of germline mutations that could be passed to offspring. Genes were successfully mapped to all HGNC identifiers, but less than half of tests mapped to SNOMED CT codes, highlighting significant gaps when linking genetic tests to standardized clinical codes that explain the medical motivations behind test ordering. Conclusion: While precision medicine could potentially transform healthcare, successful practical and clinical application will first require the comprehensive and responsible adoption of interoperable standards, terminologies, and formats across all aspects of the precision medicine pipeline.
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24
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Cirino AL, Lakdawala NK, McDonough B, Conner L, Adler D, Weinfeld M, O'Gara P, Rehm HL, Machini K, Lebo M, Blout C, Green RC, MacRae CA, Seidman CE, Ho CY. A Comparison of Whole Genome Sequencing to Multigene Panel Testing in Hypertrophic Cardiomyopathy Patients. CIRCULATION. CARDIOVASCULAR GENETICS 2017. [PMID: 29030401 DOI: 10.1161/circgenetics.117.001768.] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
BACKGROUND As DNA sequencing costs decline, genetic testing options have expanded. Whole exome sequencing and whole genome sequencing (WGS) are entering clinical use, posing questions about their incremental value compared with disease-specific multigene panels that have been the cornerstone of genetic testing. METHODS AND RESULTS Forty-one patients with hypertrophic cardiomyopathy who had undergone targeted hypertrophic cardiomyopathy genetic testing (either multigene panel or familial variant test) were recruited into the MedSeq Project, a clinical trial of WGS. Results from panel genetic testing and WGS were compared. In 20 of 41 participants, panel genetic testing identified variants classified as pathogenic, likely pathogenic, or uncertain significance. WGS identified 19 of these 20 variants, but the variant detection algorithm missed a pathogenic 18 bp duplication in myosin binding protein C (MYBPC3) because of low coverage. In 3 individuals, WGS identified variants in genes implicated in cardiomyopathy but not included in prior panel testing: a pathogenic protein tyrosine phosphatase, non-receptor type 11 (PTPN11) variant and variants of uncertain significance in integrin-linked kinase (ILK) and filamin-C (FLNC). WGS also identified 84 secondary findings (mean=2 per person, range=0-6), which mostly defined carrier status for recessive conditions. CONCLUSIONS WGS detected nearly all variants identified on panel testing, provided 1 new diagnostic finding, and allowed interrogation of posited disease genes. Several variants of uncertain clinical use and numerous secondary genetic findings were also identified. Whereas panel testing and WGS provided similar diagnostic yield, WGS offers the advantage of reanalysis over time to incorporate advances in knowledge, but requires expertise in genomic interpretation to appropriately incorporate WGS into clinical care. CLINICAL TRIAL REGISTRATION URL: https://clinicaltrials.gov. Unique identifier: NCT01736566.
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Affiliation(s)
- Allison L Cirino
- From the Cardiovascular Division (A.L.C., N.K.L., B.M., D.A., M.W., P.O., C.A.M., C.E.S., C.Y.H.), Department of Pathology (H.L.R.), and Division of Genetics (C.B., R.C.G., C.A.M.), Brigham and Women's Hospital, Boston, MA; Harvard Medical School, Boston, MA (N.K.L., B.M., D.A., M.W., P.O., H.L.R., R.C.G., C.A.M., C.E.S., C.Y.H.); Albany Medical College, NY (L.C.); Broad Institute of Harvard and MIT, Cambridge, MA (H.L.R., R.C.G., C.A.M.); Laboratory for Molecular Medicine (H.L.R., K.M., M.L.), Leadership Team (R.C.G.), Partners HealthCare Personalized Medicine, Cambridge, MA; and Howard Hughes Medical Institute, Chevy Chase, MD (C.E.S.)
| | - Neal K Lakdawala
- From the Cardiovascular Division (A.L.C., N.K.L., B.M., D.A., M.W., P.O., C.A.M., C.E.S., C.Y.H.), Department of Pathology (H.L.R.), and Division of Genetics (C.B., R.C.G., C.A.M.), Brigham and Women's Hospital, Boston, MA; Harvard Medical School, Boston, MA (N.K.L., B.M., D.A., M.W., P.O., H.L.R., R.C.G., C.A.M., C.E.S., C.Y.H.); Albany Medical College, NY (L.C.); Broad Institute of Harvard and MIT, Cambridge, MA (H.L.R., R.C.G., C.A.M.); Laboratory for Molecular Medicine (H.L.R., K.M., M.L.), Leadership Team (R.C.G.), Partners HealthCare Personalized Medicine, Cambridge, MA; and Howard Hughes Medical Institute, Chevy Chase, MD (C.E.S.)
| | - Barbara McDonough
- From the Cardiovascular Division (A.L.C., N.K.L., B.M., D.A., M.W., P.O., C.A.M., C.E.S., C.Y.H.), Department of Pathology (H.L.R.), and Division of Genetics (C.B., R.C.G., C.A.M.), Brigham and Women's Hospital, Boston, MA; Harvard Medical School, Boston, MA (N.K.L., B.M., D.A., M.W., P.O., H.L.R., R.C.G., C.A.M., C.E.S., C.Y.H.); Albany Medical College, NY (L.C.); Broad Institute of Harvard and MIT, Cambridge, MA (H.L.R., R.C.G., C.A.M.); Laboratory for Molecular Medicine (H.L.R., K.M., M.L.), Leadership Team (R.C.G.), Partners HealthCare Personalized Medicine, Cambridge, MA; and Howard Hughes Medical Institute, Chevy Chase, MD (C.E.S.)
| | - Lauren Conner
- From the Cardiovascular Division (A.L.C., N.K.L., B.M., D.A., M.W., P.O., C.A.M., C.E.S., C.Y.H.), Department of Pathology (H.L.R.), and Division of Genetics (C.B., R.C.G., C.A.M.), Brigham and Women's Hospital, Boston, MA; Harvard Medical School, Boston, MA (N.K.L., B.M., D.A., M.W., P.O., H.L.R., R.C.G., C.A.M., C.E.S., C.Y.H.); Albany Medical College, NY (L.C.); Broad Institute of Harvard and MIT, Cambridge, MA (H.L.R., R.C.G., C.A.M.); Laboratory for Molecular Medicine (H.L.R., K.M., M.L.), Leadership Team (R.C.G.), Partners HealthCare Personalized Medicine, Cambridge, MA; and Howard Hughes Medical Institute, Chevy Chase, MD (C.E.S.)
| | - Dale Adler
- From the Cardiovascular Division (A.L.C., N.K.L., B.M., D.A., M.W., P.O., C.A.M., C.E.S., C.Y.H.), Department of Pathology (H.L.R.), and Division of Genetics (C.B., R.C.G., C.A.M.), Brigham and Women's Hospital, Boston, MA; Harvard Medical School, Boston, MA (N.K.L., B.M., D.A., M.W., P.O., H.L.R., R.C.G., C.A.M., C.E.S., C.Y.H.); Albany Medical College, NY (L.C.); Broad Institute of Harvard and MIT, Cambridge, MA (H.L.R., R.C.G., C.A.M.); Laboratory for Molecular Medicine (H.L.R., K.M., M.L.), Leadership Team (R.C.G.), Partners HealthCare Personalized Medicine, Cambridge, MA; and Howard Hughes Medical Institute, Chevy Chase, MD (C.E.S.)
| | - Mark Weinfeld
- From the Cardiovascular Division (A.L.C., N.K.L., B.M., D.A., M.W., P.O., C.A.M., C.E.S., C.Y.H.), Department of Pathology (H.L.R.), and Division of Genetics (C.B., R.C.G., C.A.M.), Brigham and Women's Hospital, Boston, MA; Harvard Medical School, Boston, MA (N.K.L., B.M., D.A., M.W., P.O., H.L.R., R.C.G., C.A.M., C.E.S., C.Y.H.); Albany Medical College, NY (L.C.); Broad Institute of Harvard and MIT, Cambridge, MA (H.L.R., R.C.G., C.A.M.); Laboratory for Molecular Medicine (H.L.R., K.M., M.L.), Leadership Team (R.C.G.), Partners HealthCare Personalized Medicine, Cambridge, MA; and Howard Hughes Medical Institute, Chevy Chase, MD (C.E.S.)
| | - Patrick O'Gara
- From the Cardiovascular Division (A.L.C., N.K.L., B.M., D.A., M.W., P.O., C.A.M., C.E.S., C.Y.H.), Department of Pathology (H.L.R.), and Division of Genetics (C.B., R.C.G., C.A.M.), Brigham and Women's Hospital, Boston, MA; Harvard Medical School, Boston, MA (N.K.L., B.M., D.A., M.W., P.O., H.L.R., R.C.G., C.A.M., C.E.S., C.Y.H.); Albany Medical College, NY (L.C.); Broad Institute of Harvard and MIT, Cambridge, MA (H.L.R., R.C.G., C.A.M.); Laboratory for Molecular Medicine (H.L.R., K.M., M.L.), Leadership Team (R.C.G.), Partners HealthCare Personalized Medicine, Cambridge, MA; and Howard Hughes Medical Institute, Chevy Chase, MD (C.E.S.)
| | - Heidi L Rehm
- From the Cardiovascular Division (A.L.C., N.K.L., B.M., D.A., M.W., P.O., C.A.M., C.E.S., C.Y.H.), Department of Pathology (H.L.R.), and Division of Genetics (C.B., R.C.G., C.A.M.), Brigham and Women's Hospital, Boston, MA; Harvard Medical School, Boston, MA (N.K.L., B.M., D.A., M.W., P.O., H.L.R., R.C.G., C.A.M., C.E.S., C.Y.H.); Albany Medical College, NY (L.C.); Broad Institute of Harvard and MIT, Cambridge, MA (H.L.R., R.C.G., C.A.M.); Laboratory for Molecular Medicine (H.L.R., K.M., M.L.), Leadership Team (R.C.G.), Partners HealthCare Personalized Medicine, Cambridge, MA; and Howard Hughes Medical Institute, Chevy Chase, MD (C.E.S.)
| | - Kalotina Machini
- From the Cardiovascular Division (A.L.C., N.K.L., B.M., D.A., M.W., P.O., C.A.M., C.E.S., C.Y.H.), Department of Pathology (H.L.R.), and Division of Genetics (C.B., R.C.G., C.A.M.), Brigham and Women's Hospital, Boston, MA; Harvard Medical School, Boston, MA (N.K.L., B.M., D.A., M.W., P.O., H.L.R., R.C.G., C.A.M., C.E.S., C.Y.H.); Albany Medical College, NY (L.C.); Broad Institute of Harvard and MIT, Cambridge, MA (H.L.R., R.C.G., C.A.M.); Laboratory for Molecular Medicine (H.L.R., K.M., M.L.), Leadership Team (R.C.G.), Partners HealthCare Personalized Medicine, Cambridge, MA; and Howard Hughes Medical Institute, Chevy Chase, MD (C.E.S.)
| | - Matthew Lebo
- From the Cardiovascular Division (A.L.C., N.K.L., B.M., D.A., M.W., P.O., C.A.M., C.E.S., C.Y.H.), Department of Pathology (H.L.R.), and Division of Genetics (C.B., R.C.G., C.A.M.), Brigham and Women's Hospital, Boston, MA; Harvard Medical School, Boston, MA (N.K.L., B.M., D.A., M.W., P.O., H.L.R., R.C.G., C.A.M., C.E.S., C.Y.H.); Albany Medical College, NY (L.C.); Broad Institute of Harvard and MIT, Cambridge, MA (H.L.R., R.C.G., C.A.M.); Laboratory for Molecular Medicine (H.L.R., K.M., M.L.), Leadership Team (R.C.G.), Partners HealthCare Personalized Medicine, Cambridge, MA; and Howard Hughes Medical Institute, Chevy Chase, MD (C.E.S.)
| | - Carrie Blout
- From the Cardiovascular Division (A.L.C., N.K.L., B.M., D.A., M.W., P.O., C.A.M., C.E.S., C.Y.H.), Department of Pathology (H.L.R.), and Division of Genetics (C.B., R.C.G., C.A.M.), Brigham and Women's Hospital, Boston, MA; Harvard Medical School, Boston, MA (N.K.L., B.M., D.A., M.W., P.O., H.L.R., R.C.G., C.A.M., C.E.S., C.Y.H.); Albany Medical College, NY (L.C.); Broad Institute of Harvard and MIT, Cambridge, MA (H.L.R., R.C.G., C.A.M.); Laboratory for Molecular Medicine (H.L.R., K.M., M.L.), Leadership Team (R.C.G.), Partners HealthCare Personalized Medicine, Cambridge, MA; and Howard Hughes Medical Institute, Chevy Chase, MD (C.E.S.)
| | - Robert C Green
- From the Cardiovascular Division (A.L.C., N.K.L., B.M., D.A., M.W., P.O., C.A.M., C.E.S., C.Y.H.), Department of Pathology (H.L.R.), and Division of Genetics (C.B., R.C.G., C.A.M.), Brigham and Women's Hospital, Boston, MA; Harvard Medical School, Boston, MA (N.K.L., B.M., D.A., M.W., P.O., H.L.R., R.C.G., C.A.M., C.E.S., C.Y.H.); Albany Medical College, NY (L.C.); Broad Institute of Harvard and MIT, Cambridge, MA (H.L.R., R.C.G., C.A.M.); Laboratory for Molecular Medicine (H.L.R., K.M., M.L.), Leadership Team (R.C.G.), Partners HealthCare Personalized Medicine, Cambridge, MA; and Howard Hughes Medical Institute, Chevy Chase, MD (C.E.S.)
| | - Calum A MacRae
- From the Cardiovascular Division (A.L.C., N.K.L., B.M., D.A., M.W., P.O., C.A.M., C.E.S., C.Y.H.), Department of Pathology (H.L.R.), and Division of Genetics (C.B., R.C.G., C.A.M.), Brigham and Women's Hospital, Boston, MA; Harvard Medical School, Boston, MA (N.K.L., B.M., D.A., M.W., P.O., H.L.R., R.C.G., C.A.M., C.E.S., C.Y.H.); Albany Medical College, NY (L.C.); Broad Institute of Harvard and MIT, Cambridge, MA (H.L.R., R.C.G., C.A.M.); Laboratory for Molecular Medicine (H.L.R., K.M., M.L.), Leadership Team (R.C.G.), Partners HealthCare Personalized Medicine, Cambridge, MA; and Howard Hughes Medical Institute, Chevy Chase, MD (C.E.S.)
| | - Christine E Seidman
- From the Cardiovascular Division (A.L.C., N.K.L., B.M., D.A., M.W., P.O., C.A.M., C.E.S., C.Y.H.), Department of Pathology (H.L.R.), and Division of Genetics (C.B., R.C.G., C.A.M.), Brigham and Women's Hospital, Boston, MA; Harvard Medical School, Boston, MA (N.K.L., B.M., D.A., M.W., P.O., H.L.R., R.C.G., C.A.M., C.E.S., C.Y.H.); Albany Medical College, NY (L.C.); Broad Institute of Harvard and MIT, Cambridge, MA (H.L.R., R.C.G., C.A.M.); Laboratory for Molecular Medicine (H.L.R., K.M., M.L.), Leadership Team (R.C.G.), Partners HealthCare Personalized Medicine, Cambridge, MA; and Howard Hughes Medical Institute, Chevy Chase, MD (C.E.S.)
| | - Carolyn Y Ho
- From the Cardiovascular Division (A.L.C., N.K.L., B.M., D.A., M.W., P.O., C.A.M., C.E.S., C.Y.H.), Department of Pathology (H.L.R.), and Division of Genetics (C.B., R.C.G., C.A.M.), Brigham and Women's Hospital, Boston, MA; Harvard Medical School, Boston, MA (N.K.L., B.M., D.A., M.W., P.O., H.L.R., R.C.G., C.A.M., C.E.S., C.Y.H.); Albany Medical College, NY (L.C.); Broad Institute of Harvard and MIT, Cambridge, MA (H.L.R., R.C.G., C.A.M.); Laboratory for Molecular Medicine (H.L.R., K.M., M.L.), Leadership Team (R.C.G.), Partners HealthCare Personalized Medicine, Cambridge, MA; and Howard Hughes Medical Institute, Chevy Chase, MD (C.E.S.).
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25
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Arora NS, Davis JK, Kirby C, McGuire AL, Green RC, Blumenthal-Barby JS, Ubel PA. Communication challenges for nongeneticist physicians relaying clinical genomic results. Per Med 2017; 14:423-431. [PMID: 29181085 DOI: 10.2217/pme-2017-0008] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Accepted: 05/16/2017] [Indexed: 02/07/2023]
Abstract
Aim Identify the behavioral challenges to the use of genome sequencing (GS) in a clinical setting. Materials & methods We observed how general internists and nongenetic specialists delivered GS results to patients enrolled in the MedSeq Project. Using transcripts of such disclosure interactions, we made qualitative observations of communication behaviors that could limit the usefulness of GS results until reaching the point of thematic saturation. Results Findings included confusion regarding genomic terminology, difficulty with the volume or complexity of information and difficulties communicating complex risk information to patients. We observed a broad dismissal of clinical value of GS by some physicians and sometimes ineffective communication regarding health behavior change. Conclusion Overcoming these behavioral challenges is necessary to make full use of clinical GS results.
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Affiliation(s)
- Nonie S Arora
- University of Michigan Medical School, Ann Arbor, MI 48109, USA.,University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - J Kelly Davis
- Duke-Margolis Health Policy Center, Durham, NC 27708, USA.,Fuqua School of Business, Duke University, Durham, NC 27708, USA.,Duke-Margolis Health Policy Center, Durham, NC 27708, USA.,Fuqua School of Business, Duke University, Durham, NC 27708, USA
| | - Christine Kirby
- Duke-Margolis Health Policy Center, Durham, NC 27708, USA.,Fuqua School of Business, Duke University, Durham, NC 27708, USA.,Duke-Margolis Health Policy Center, Durham, NC 27708, USA.,Fuqua School of Business, Duke University, Durham, NC 27708, USA
| | - Amy L McGuire
- Center for Medical Ethics and Health Policy, Baylor College of Medicine, Houston, TX 77030, USA.,Center for Medical Ethics and Health Policy, Baylor College of Medicine, Houston, TX 77030, USA
| | - Robert C Green
- Division of Genetics, Department of Medicine, Brigham & Women's Hospital, Boston, MA 02115, USA.,Harvard Medical School, Boston, MA 02115, USA.,Partners Healthcare Personalized Medicine, Boston, MA 02139, USA.,Division of Genetics, Department of Medicine, Brigham & Women's Hospital, Boston, MA 02115, USA.,Harvard Medical School, Boston, MA 02115, USA.,Partners Healthcare Personalized Medicine, Boston, MA 02139, USA
| | - J S Blumenthal-Barby
- Center for Medical Ethics and Health Policy, Baylor College of Medicine, Houston, TX 77030, USA.,Center for Medical Ethics and Health Policy, Baylor College of Medicine, Houston, TX 77030, USA
| | - Peter A Ubel
- Duke-Margolis Health Policy Center, Durham, NC 27708, USA.,Fuqua School of Business, Duke University, Durham, NC 27708, USA.,Sanford School of Public Policy, Duke University, Durham, NC 27708, USA.,Duke University School of Medicine, Durham, NC 27710, USA.,Duke-Margolis Health Policy Center, Durham, NC 27708, USA.,Fuqua School of Business, Duke University, Durham, NC 27708, USA.,Sanford School of Public Policy, Duke University, Durham, NC 27708, USA.,Duke University School of Medicine, Durham, NC 27710, USA
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26
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Walser SA, Werner-Lin A, Mueller R, Miller VA, Biswas S, Bernhardt BA. How do providers discuss the results of pediatric exome sequencing with families? Per Med 2017; 14:409-422. [PMID: 28966657 DOI: 10.2217/pme-2017-0015] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
AIM This study provides preliminary data on the process and content of returning results from exome sequencing offered to children through one of the Clinical Sequencing Exploratory Research (CSER) projects. MATERIALS & METHODS We recorded 25 sessions where providers returned diagnostic and secondary sequencing results to families. Data interpretation utilized inductive thematic analysis. RESULTS Typically, providers followed a results report and discussed diagnostic findings using technical genomic and sequencing concepts. We identified four provider processes for returning results: teaching genetic concepts; assessing family response; personalizing findings; and strengthening patient-provider relationships. CONCLUSION Sessions should reflect family interest in medical management and next steps, and minimize detailed genomic concepts. As the scope and complexity of sequencing increase, the traditional information-laden counseling model requires revision.
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Affiliation(s)
- Sarah A Walser
- Translational Medicine & Human Genetics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Allison Werner-Lin
- School of Social Policy & Practice, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Rebecca Mueller
- Department of History & Sociology of Science, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Victoria A Miller
- Division of Adolescent Medicine, Department of Pediatrics, The Children's Hospital of Philadelphia & Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 9104, USA
| | - Sawona Biswas
- Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Barbara A Bernhardt
- Translational Medicine & Human Genetics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
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27
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Vassy JL, Christensen KD, Schonman EF, Blout CL, Robinson JO, Krier JB, Diamond PM, Lebo M, Machini K, Azzariti DR, Dukhovny D, Bates DW, MacRae CA, Murray MF, Rehm HL, McGuire AL, Green RC. The Impact of Whole-Genome Sequencing on the Primary Care and Outcomes of Healthy Adult Patients: A Pilot Randomized Trial. Ann Intern Med 2017; 167:159-169. [PMID: 28654958 PMCID: PMC5856654 DOI: 10.7326/m17-0188] [Citation(s) in RCA: 130] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Background Whole-genome sequencing (WGS) in asymptomatic adults might prevent disease but increase health care use without clinical value. Objective To describe the effect on clinical care and outcomes of adding WGS to standardized family history assessment in primary care. Design Pilot randomized trial. (ClinicalTrials.gov: NCT01736566). Setting Academic primary care practices. Participants 9 primary care physicians (PCPs) and 100 generally healthy patients recruited at ages 40 to 65 years. Intervention Patients were randomly assigned to receive a family history report alone (FH group) or in combination with an interpreted WGS report (FH + WGS group), which included monogenic disease risk (MDR) results (associated with Mendelian disorders), carrier variants, pharmacogenomic associations, and polygenic risk estimates for cardiometabolic traits. Each patient met with his or her PCP to discuss the report. Measurements Clinical outcomes and health care use through 6 months were obtained from medical records and audio-recorded discussions between PCPs and patients. Patients' health behavior changes were surveyed 6 months after receiving results. A panel of clinician-geneticists rated the appropriateness of how PCPs managed MDR results. Results Mean age was 55 years; 58% of patients were female. Eleven FH + WGS patients (22% [95% CI, 12% to 36%]) had new MDR results. Only 2 (4% [CI, 0.01% to 15%]) had evidence of the phenotypes predicted by an MDR result (fundus albipunctatus due to RDH5 and variegate porphyria due to PPOX). Primary care physicians recommended new clinical actions for 16% (CI, 8% to 30%) of FH patients and 34% (CI, 22% to 49%) of FH + WGS patients. Thirty percent (CI, 17% to 45%) and 41% (CI, 27% to 56%) of FH and FH + WGS patients, respectively, reported making a health behavior change after 6 months. Geneticists rated PCP management of 8 MDR results (73% [CI, 39% to 99%]) as appropriate and 2 results (18% [CI, 3% to 52%]) as inappropriate. Limitation Limited sample size and ancestral and socioeconomic diversity. Conclusion Adding WGS to primary care reveals new molecular findings of uncertain clinical utility. Nongeneticist providers may be able to manage WGS results appropriately, but WGS may prompt additional clinical actions of unclear value. Primary Funding Source National Institutes of Health.
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Affiliation(s)
- Jason L. Vassy
- VA Boston Healthcare System, Boston, MA
- Brigham and Women’s Hospital, Boston, MA
- Harvard Medical School, Boston, MA
| | | | | | | | | | - Joel B. Krier
- Brigham and Women’s Hospital, Boston, MA
- Harvard Medical School, Boston, MA
| | - Pamela M. Diamond
- Baylor College of Medicine, Houston, TX
- UTHealth School of Public Health, Houston, TX
| | - Matthew Lebo
- Brigham and Women’s Hospital, Boston, MA
- Harvard Medical School, Boston, MA
- Partners Healthcare Personalized Medicine, Boston, MA
| | - Kalotina Machini
- Brigham and Women’s Hospital, Boston, MA
- Harvard Medical School, Boston, MA
- Partners Healthcare Personalized Medicine, Boston, MA
| | | | | | - David W. Bates
- Brigham and Women’s Hospital, Boston, MA
- Harvard Medical School, Boston, MA
| | - Calum A. MacRae
- Brigham and Women’s Hospital, Boston, MA
- Harvard Medical School, Boston, MA
- Broad Institute of MIT and Harvard, Cambridge, MA
| | | | - Heidi L. Rehm
- Brigham and Women’s Hospital, Boston, MA
- Harvard Medical School, Boston, MA
- Partners Healthcare Personalized Medicine, Boston, MA
| | | | - Robert C. Green
- Brigham and Women’s Hospital, Boston, MA
- Harvard Medical School, Boston, MA
- Partners Healthcare Personalized Medicine, Boston, MA
- Broad Institute of MIT and Harvard, Cambridge, MA
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28
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Messner DA, Koay P, Al Naber J, Cook-Deegan R, Majumder M, Javitt G, Dvoskin R, Bollinger J, Curnutte M, McGuire AL. Barriers to clinical adoption of next-generation sequencing: a policy Delphi panel's solutions. Per Med 2017; 14:339-354. [PMID: 29230253 DOI: 10.2217/pme-2016-0104] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Aim Identify solutions to the most important policy barriers to the clinical adoption of next-generation sequencing. Materials & methods Four-round modified policy Delphi with a multistakeholder panel of 48 experts. The panel deliberated policy solutions to (previously reported) challenges deemed most important to address. Results The group advocated using consensus panels to promote consistency in payer policies and to standardize test reporting, and favored making genomic data-sharing a condition of regulatory clearance, certification, or accreditation processes. They were split on the role of US FDA. Conclusion Panelists found common ground on solutions for health plan coverage policy consistency, data-sharing, and standardizing reporting, but were sharply divided on the role of the FDA in mitigating risks to patients.
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Affiliation(s)
- Donna A Messner
- Center for Medical Technology Policy, Baltimore, MD 21202, USA
| | - Pei Koay
- Center for Medical Technology Policy, Baltimore, MD 21202, USA
| | | | - Robert Cook-Deegan
- School for the Future of Innovation in Society, and Consortium for Science, Policy & Outcomes, Arizona State University, Tempe, AZ 85281, USA
| | - Mary Majumder
- Center for Medical Ethics & Health Policy, Baylor College of Medicine, Houston, TX 77030, USA
| | - Gail Javitt
- Johns Hopkins Berman Institute of Bioethics, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Rachel Dvoskin
- Johns Hopkins Berman Institute of Bioethics, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Juli Bollinger
- Johns Hopkins Berman Institute of Bioethics, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Margaret Curnutte
- Center for Medical Ethics & Health Policy, Baylor College of Medicine, Houston, TX 77030, USA
| | - Amy L McGuire
- Center for Medical Ethics & Health Policy, Baylor College of Medicine, Houston, TX 77030, USA
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29
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Affiliation(s)
- Susanne B Haga
- Center for Applied Genomics & Precision Medicine, Duke University School of Medicine, 304 Research Drive, Box 90141, Durham, NC 27708, USA
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30
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Sweet K, Hovick S, Sturm AC, Schmidlen T, Gordon E, Bernhardt B, Wawak L, Wernke K, McElroy J, Scheinfeldt L, Toland AE, Roberts JS, Christman M. Counselees' Perspectives of Genomic Counseling Following Online Receipt of Multiple Actionable Complex Disease and Pharmacogenomic Results: a Qualitative Research Study. J Genet Couns 2016; 26:738-751. [PMID: 27921197 DOI: 10.1007/s10897-016-0044-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Accepted: 10/26/2016] [Indexed: 10/20/2022]
Abstract
Genomic applications raise multiple challenges including the optimization of genomic counseling (GC) services as part of the results delivery process. More information on patients' motivations, preferences, and informational needs are essential to guide the development of new, more efficient practice delivery models that capitalize on the existing strengths of a limited genetic counseling workforce. Semi-structured telephone interviews were conducted with a subset of counselees from the Coriell Personalized Medicine Collaborative following online receipt of multiple personalized genomic test reports. Participants previously had either in-person GC (chronic disease cohort, n = 20; mean age 60 years) or telephone GC (community cohort, n = 31; mean age 46.8 years). Transcripts were analyzed using a Grounded Theory framework. Major themes that emerged from the interviews include 1) primary reasons for seeking GC were to clarify results, put results into perspective relative to other health-related concerns, and to receive personalized recommendations; 2) there is need for a more participant driven approach in terms of mode of GC communication (in-person, phone, video), and refining the counseling agenda pre-session; and 3) there was strong interest in the option of follow up GC. By clarifying counselees' expectations, views and desired outcomes, we have uncovered a need for a more participant-driven GC model when potentially actionable genomic results are received online.
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Affiliation(s)
- Kevin Sweet
- Division of Human Genetics, Ohio State University Wexner Medical Center, 2012 Kenny Road, Columbus, OH, 43221, USA.
| | - Shelly Hovick
- School of Communication, Ohio State University, Columbus, OH, 43214, USA
| | - Amy C Sturm
- Division of Human Genetics, Ohio State University Wexner Medical Center, 2012 Kenny Road, Columbus, OH, 43221, USA.,Dorothy M. Davis Heart and Lung Research Institute, Ohio State University Wexner Medical Center, Columbus, OH, 43420, USA
| | - Tara Schmidlen
- Coriell Institute for Medical Research, 403 Haddon Avenue, Camden, NJ, 08103, USA
| | | | - Barbara Bernhardt
- Division of Translational Medicine and Human Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Lisa Wawak
- Coriell Institute for Medical Research, 403 Haddon Avenue, Camden, NJ, 08103, USA
| | - Karen Wernke
- Division of Human Genetics, Ohio State University Wexner Medical Center, 2012 Kenny Road, Columbus, OH, 43221, USA
| | - Joseph McElroy
- Department of Biomedical Informatics, Center for Biostatistics, Columbus, OH, 43221, USA
| | - Laura Scheinfeldt
- Coriell Institute for Medical Research, 403 Haddon Avenue, Camden, NJ, 08103, USA.,Temple University, SERC Building 1925 N. 12th St, Philadelphia, PA, 19122-1801, USA
| | - Amanda E Toland
- Division of Human Genetics, Ohio State University Wexner Medical Center, 2012 Kenny Road, Columbus, OH, 43221, USA
| | - J S Roberts
- Department of Health Behavior & Health Education, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Michael Christman
- Coriell Institute for Medical Research, 403 Haddon Avenue, Camden, NJ, 08103, USA
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31
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Cutting E, Banchero M, Beitelshees AL, Cimino JJ, Fiol GD, Gurses AP, Hoffman MA, Jeng LJB, Kawamoto K, Kelemen M, Pincus HA, Shuldiner AR, Williams MS, Pollin TI, Overby CL. User-centered design of multi-gene sequencing panel reports for clinicians. J Biomed Inform 2016; 63:1-10. [PMID: 27423699 DOI: 10.1016/j.jbi.2016.07.014] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2015] [Revised: 07/11/2016] [Accepted: 07/13/2016] [Indexed: 11/15/2022]
Abstract
The objective of this study was to develop a high-fidelity prototype for delivering multi-gene sequencing panel (GS) reports to clinicians that simulates the user experience of a final application. The delivery and use of GS reports can occur within complex and high-paced healthcare environments. We employ a user-centered software design approach in a focus group setting in order to facilitate gathering rich contextual information from a diverse group of stakeholders potentially impacted by the delivery of GS reports relevant to two precision medicine programs at the University of Maryland Medical Center. Responses from focus group sessions were transcribed, coded and analyzed by two team members. Notification mechanisms and information resources preferred by participants from our first phase of focus groups were incorporated into scenarios and the design of a software prototype for delivering GS reports. The goal of our second phase of focus group, to gain input on the prototype software design, was accomplished through conducting task walkthroughs with GS reporting scenarios. Preferences for notification, content and consultation from genetics specialists appeared to depend upon familiarity with scenarios for ordering and delivering GS reports. Despite familiarity with some aspects of the scenarios we proposed, many of our participants agreed that they would likely seek consultation from a genetics specialist after viewing the test reports. In addition, participants offered design and content recommendations. Findings illustrated a need to support customized notification approaches, user-specific information, and access to genetics specialists with GS reports. These design principles can be incorporated into software applications that deliver GS reports. Our user-centered approach to conduct this assessment and the specific input we received from clinicians may also be relevant to others working on similar projects.
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Affiliation(s)
- Elizabeth Cutting
- Program for Personalized and Genomic Medicine, University of Maryland School of Medicine, Baltimore, MD, United States
| | - Meghan Banchero
- Program for Personalized and Genomic Medicine, University of Maryland School of Medicine, Baltimore, MD, United States
| | - Amber L Beitelshees
- Program for Personalized and Genomic Medicine, University of Maryland School of Medicine, Baltimore, MD, United States
| | - James J Cimino
- Informatics Institute, School of Medicine, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Guilherme Del Fiol
- Department of Biomedical Informatics, University of Utah, Salt Lake City, UT, United States
| | - Ayse P Gurses
- Division of Health Sciences Informatics, Johns Hopkins University School of Medicine, United States; Armstrong Institute for Patient Safety and Quality, Johns Hopkins University School of Medicine, United States; Anesthesiology and Critical Care Medicine, Johns Hopkins University School of Medicine, United States
| | - Mark A Hoffman
- University of Missouri - Kansas City, Kansas City, MO, United States; Children's Mercy Hospital, Kansas City, MO, United States
| | - Linda Jo Bone Jeng
- Program for Personalized and Genomic Medicine, University of Maryland School of Medicine, Baltimore, MD, United States; Departments of Medicine, Pathology and Pediatrics, University of Maryland School of Medicine, Baltimore, MD, United States
| | - Kensaku Kawamoto
- Department of Biomedical Informatics, University of Utah, Salt Lake City, UT, United States
| | - Mark Kelemen
- University of Maryland Medical Center, Baltimore, MD, United States
| | - Harold Alan Pincus
- Columbia University and New York-Presbyterian Hospital, New York, NY, United States
| | - Alan R Shuldiner
- Program for Personalized and Genomic Medicine, University of Maryland School of Medicine, Baltimore, MD, United States
| | - Marc S Williams
- Genomic Medicine Institute, Geisinger Health System, Danville, PA, United States
| | - Toni I Pollin
- Program for Personalized and Genomic Medicine, University of Maryland School of Medicine, Baltimore, MD, United States
| | - Casey Lynnette Overby
- Program for Personalized and Genomic Medicine, University of Maryland School of Medicine, Baltimore, MD, United States; Division of Health Sciences Informatics, Johns Hopkins University School of Medicine, United States; Division of General Internal Medicine, Johns Hopkins University School of Medicine, United States.
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32
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Green RC, Goddard KAB, Jarvik GP, Amendola LM, Appelbaum PS, Berg JS, Bernhardt BA, Biesecker LG, Biswas S, Blout CL, Bowling KM, Brothers KB, Burke W, Caga-Anan CF, Chinnaiyan AM, Chung WK, Clayton EW, Cooper GM, East K, Evans JP, Fullerton SM, Garraway LA, Garrett JR, Gray SW, Henderson GE, Hindorff LA, Holm IA, Lewis MH, Hutter CM, Janne PA, Joffe S, Kaufman D, Knoppers BM, Koenig BA, Krantz ID, Manolio TA, McCullough L, McEwen J, McGuire A, Muzny D, Myers RM, Nickerson DA, Ou J, Parsons DW, Petersen GM, Plon SE, Rehm HL, Roberts JS, Robinson D, Salama JS, Scollon S, Sharp RR, Shirts B, Spinner NB, Tabor HK, Tarczy-Hornoch P, Veenstra DL, Wagle N, Weck K, Wilfond BS, Wilhelmsen K, Wolf SM, Wynn J, Yu JH. Clinical Sequencing Exploratory Research Consortium: Accelerating Evidence-Based Practice of Genomic Medicine. Am J Hum Genet 2016; 98:1051-1066. [PMID: 27181682 DOI: 10.1016/j.ajhg.2016.04.011] [Citation(s) in RCA: 109] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2015] [Accepted: 04/14/2016] [Indexed: 12/11/2022] Open
Abstract
Despite rapid technical progress and demonstrable effectiveness for some types of diagnosis and therapy, much remains to be learned about clinical genome and exome sequencing (CGES) and its role within the practice of medicine. The Clinical Sequencing Exploratory Research (CSER) consortium includes 18 extramural research projects, one National Human Genome Research Institute (NHGRI) intramural project, and a coordinating center funded by the NHGRI and National Cancer Institute. The consortium is exploring analytic and clinical validity and utility, as well as the ethical, legal, and social implications of sequencing via multidisciplinary approaches; it has thus far recruited 5,577 participants across a spectrum of symptomatic and healthy children and adults by utilizing both germline and cancer sequencing. The CSER consortium is analyzing data and creating publically available procedures and tools related to participant preferences and consent, variant classification, disclosure and management of primary and secondary findings, health outcomes, and integration with electronic health records. Future research directions will refine measures of clinical utility of CGES in both germline and somatic testing, evaluate the use of CGES for screening in healthy individuals, explore the penetrance of pathogenic variants through extensive phenotyping, reduce discordances in public databases of genes and variants, examine social and ethnic disparities in the provision of genomics services, explore regulatory issues, and estimate the value and downstream costs of sequencing. The CSER consortium has established a shared community of research sites by using diverse approaches to pursue the evidence-based development of best practices in genomic medicine.
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Affiliation(s)
- Robert C Green
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Harvard Medical School, Boston, MA 02115, USA; Partners Personalized Medicine, Boston, MA 02139, USA.
| | - Katrina A B Goddard
- Center for Health Research, Kaiser Permanente Northwest, Portland, OR 97227, USA
| | - Gail P Jarvik
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA; Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA 98195, USA; Clinical Sequencing Exploratory Research Coordinating Center, University of Washington, Seattle, WA 98195, USA
| | - Laura M Amendola
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA 98195, USA; Clinical Sequencing Exploratory Research Coordinating Center, University of Washington, Seattle, WA 98195, USA
| | - Paul S Appelbaum
- Department of Psychiatry, Columbia University Medical Center and New York State Psychiatric Institute, New York, NY 10032, USA
| | - Jonathan S Berg
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Barbara A Bernhardt
- Division of Translational Medicine and Human Genetics, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Leslie G Biesecker
- Medical Genomics and Metabolic Genetics Branch, National Human Genome Research Institute, NIH, Bethesda, MD 20892, USA
| | - Sawona Biswas
- Division of Translational Medicine and Human Genetics, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Carrie L Blout
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Kevin M Bowling
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - Kyle B Brothers
- Department of Pediatrics, University of Louisville, Louisville, KY 40202, USA
| | - Wylie Burke
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA 98195, USA; Clinical Sequencing Exploratory Research Coordinating Center, University of Washington, Seattle, WA 98195, USA; Department of Bioethics and Humanities, Department of Medicine, University of Washington, Seattle, WA 98195, USA
| | | | - Arul M Chinnaiyan
- Michigan Center for Translational Pathology, Ann Arbor, MI 48109, USA; Comprehensive Cancer Center, University of Michigan, Ann Arbor, MI 48109, USA; Departments of Pathology and Urology, University of Michigan, Ann Arbor, MI 48109, USA; Howard Hughes Medical Institute, Ann Arbor, MI 48109, USA
| | - Wendy K Chung
- Department of Pediatrics, Columbia University, New York, NY 10029, USA; Department of Medicine, Columbia University Medical Center, New York, NY 10032, USA
| | - Ellen W Clayton
- Center for Biomedical Ethics and Society, Vanderbilt University, Nashville, TN 37203, USA
| | - Gregory M Cooper
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - Kelly East
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - James P Evans
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Stephanie M Fullerton
- Department of Bioethics and Humanities, Department of Medicine, University of Washington, Seattle, WA 98195, USA
| | - Levi A Garraway
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Medical Oncology and Center for Cancer Precision Medicine, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Jeremy R Garrett
- Children's Mercy Bioethics Center, Children's Mercy Hospital, Kansas City, MO 64108, USA; Departments of Pediatrics and Philosophy, University of Missouri - Kansas City, Kansas City, MO 64110, USA
| | - Stacy W Gray
- Harvard Medical School, Boston, MA 02115, USA; Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Gail E Henderson
- Department of Social Medicine, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Lucia A Hindorff
- Division of Genomic Medicine, National Human Genome Research Institute, NIH, Bethesda, MD 20892, USA
| | - Ingrid A Holm
- Harvard Medical School, Boston, MA 02115, USA; Division of Genetics and Genomics and the Manton Center for Orphan Diseases Research, Boston Children's Hospital, Boston, MA 02115, USA
| | | | - Carolyn M Hutter
- Division of Genomic Medicine, National Human Genome Research Institute, NIH, Bethesda, MD 20892, USA
| | - Pasi A Janne
- Harvard Medical School, Boston, MA 02115, USA; Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Steven Joffe
- Department of Medical Ethics & Health Policy, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA
| | - David Kaufman
- Division of Genomics and Society, National Human Genome Research Institute, NIH, Bethesda, MD 20892, USA
| | - Bartha M Knoppers
- Centre of Genomics and Policy, Faculty of Medicine, Department of Human Genetics, McGill University, Montreal, QC H3A 1B1, Canada
| | - Barbara A Koenig
- Institute for Health and Aging, University of California, San Francisco, San Francisco, CA 94118, USA
| | - Ian D Krantz
- Division of Translational Medicine and Human Genetics, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Teri A Manolio
- Division of Genomic Medicine, National Human Genome Research Institute, NIH, Bethesda, MD 20892, USA
| | - Laurence McCullough
- Center for Medical Ethics and Health Policy, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jean McEwen
- Division of Genomics and Society, National Human Genome Research Institute, NIH, Bethesda, MD 20892, USA
| | - Amy McGuire
- Center for Medical Ethics and Health Policy, Baylor College of Medicine, Houston, TX 77030, USA
| | - Donna Muzny
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Richard M Myers
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - Deborah A Nickerson
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA; Clinical Sequencing Exploratory Research Coordinating Center, University of Washington, Seattle, WA 98195, USA
| | - Jeffrey Ou
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA 98195, USA; Clinical Sequencing Exploratory Research Coordinating Center, University of Washington, Seattle, WA 98195, USA
| | - Donald W Parsons
- Baylor College of Medicine and Texas Children's Cancer Center, Houston, TX 77030, USA
| | - Gloria M Petersen
- Department of Health Sciences Research, Mayo Clinic College of Medicine, Rochester, MN 55905, USA
| | - Sharon E Plon
- Baylor College of Medicine and Texas Children's Cancer Center, Houston, TX 77030, USA
| | - Heidi L Rehm
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Harvard Medical School, Boston, MA 02115, USA; Partners Personalized Medicine, Boston, MA 02139, USA; Laboratory for Molecular Medicine, Partners HealthCare, Cambridge, MA 02139, USA
| | - J Scott Roberts
- Department of Health Behavior & Health Education, University of Michigan School of Public Health, Ann Arbor, MI 48109, USA
| | - Dan Robinson
- Michigan Center for Translational Pathology, Ann Arbor, MI 48109, USA
| | - Joseph S Salama
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA 98195, USA; Clinical Sequencing Exploratory Research Coordinating Center, University of Washington, Seattle, WA 98195, USA
| | - Sarah Scollon
- Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Richard R Sharp
- Biomedical Ethics Research Program, Mayo Clinic College of Medicine, Rochester, MN 55905, USA
| | - Brian Shirts
- Department of Laboratory Medicine, University of Washington, Seattle, WA 98195, USA
| | - Nancy B Spinner
- Division of Translational Medicine and Human Genetics, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Holly K Tabor
- Department of Pediatrics and Seattle Children's Research Institute, University of Washington, Seattle, WA, USA
| | - Peter Tarczy-Hornoch
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA 98195, USA; University of Washington, Seattle, WA 98105, USA
| | - David L Veenstra
- Department of Pharmacy, University of Washington, Seattle, WA 98195, USA
| | - Nikhil Wagle
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Medical Oncology and Center for Cancer Precision Medicine, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Karen Weck
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, NC 27599, USA
| | - Benjamin S Wilfond
- Department of Pediatrics and Seattle Children's Research Institute, University of Washington, Seattle, WA, USA
| | - Kirk Wilhelmsen
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Susan M Wolf
- Law School, Medical School, and Consortium on Law and Values in Health, Environment, & the Life Sciences, Minneapolis, University of Minnesota, MN 55455, USA
| | - Julia Wynn
- Department of Pediatrics, Columbia University, New York, NY 10029, USA
| | - Joon-Ho Yu
- Department of Pediatrics, University of Washington, Seattle, WA 98195, USA
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Linderman MD, Nielsen DE, Green RC. Personal Genome Sequencing in Ostensibly Healthy Individuals and the PeopleSeq Consortium. J Pers Med 2016; 6:E14. [PMID: 27023617 PMCID: PMC4932461 DOI: 10.3390/jpm6020014] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Revised: 03/09/2016] [Accepted: 03/15/2016] [Indexed: 12/16/2022] Open
Abstract
Thousands of ostensibly healthy individuals have had their exome or genome sequenced, but a much smaller number of these individuals have received any personal genomic results from that sequencing. We term those projects in which ostensibly healthy participants can receive sequencing-derived genetic findings and may also have access to their genomic data as participatory predispositional personal genome sequencing (PPGS). Here we are focused on genome sequencing applied in a pre-symptomatic context and so define PPGS to exclude diagnostic genome sequencing intended to identify the molecular cause of suspected or diagnosed genetic disease. In this report we describe the design of completed and underway PPGS projects, briefly summarize the results reported to date and introduce the PeopleSeq Consortium, a newly formed collaboration of PPGS projects designed to collect much-needed longitudinal outcome data.
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Affiliation(s)
- Michael D Linderman
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
| | - Daiva E Nielsen
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA.
- Harvard Medical School, Boston, MA 02115, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
| | - Robert C Green
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA.
- Harvard Medical School, Boston, MA 02115, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
- Partners Personalized Medicine, Cambridge, MA 02139, USA.
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34
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Williams JL, Rahm AK, Stuckey H, Green J, Feldman L, Zallen DT, Bonhag M, Segal MM, Fan AL, Williams MS. Enhancing genomic laboratory reports: A qualitative analysis of provider review. Am J Med Genet A 2016; 170A:1134-41. [PMID: 26842872 PMCID: PMC5067598 DOI: 10.1002/ajmg.a.37573] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2015] [Accepted: 01/16/2016] [Indexed: 11/21/2022]
Abstract
This study reports on the responses of physicians who reviewed provider and patient versions of a genomic laboratory report designed to communicate results of whole genome sequencing. Semi‐structured interviews addressed concept communication, elements, and format of example genome reports. Analysis of the coded transcripts resulted in recognition of three constructs around communication of genome sequencing results: (1) Providers agreed that whole genomic sequencing results are complex and they welcomed a report that provided supportive interpretation information to accompany sequencing results; (2) Providers strongly endorsed a report that included active clinical guidance, such as reference to practice guidelines, if available; and (3) Providers valued the genomic report as a resource that would serve as the basis to facilitate communication of genome sequencing results with their patients and families. Providers valued both versions of the report, though they affirmed the need for a provider‐oriented report. Critical elements of the report included clear language to explain the result, as well as consolidated yet comprehensive prognostic information with clear guidance over time for the clinical care of the patient. Most importantly, it appears a report with this design has the potential not only to return results but also serves as a communication tool to help providers and patients discuss and coordinate care over time. © 2016 The Authors. American Journal of Medical Genetics Part A published by Wiley Periodicals, Inc.
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Affiliation(s)
| | | | - Heather Stuckey
- Penn State Hershey College of Medicine, Hershey, Pennsylvania
| | - Jamie Green
- Center for Health Research, Danville, Pennsylvania
| | - Lynn Feldman
- SimulConsult, Inc., Chestnut Hill, Massachusetts
| | | | | | | | - Audrey L Fan
- Geisinger Genomic Medicine, Danville, Pennsylvania
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35
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Smoller JW, Karlson EW, Green RC, Kathiresan S, MacArthur DG, Talkowski ME, Murphy SN, Weiss ST. An eMERGE Clinical Center at Partners Personalized Medicine. J Pers Med 2016; 6:E5. [PMID: 26805891 PMCID: PMC4810384 DOI: 10.3390/jpm6010005] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Revised: 01/12/2016] [Accepted: 01/13/2016] [Indexed: 02/06/2023] Open
Abstract
The integration of electronic medical records (EMRs) and genomic research has become a major component of efforts to advance personalized and precision medicine. The Electronic Medical Records and Genomics (eMERGE) network, initiated in 2007, is an NIH-funded consortium devoted to genomic discovery and implementation research by leveraging biorepositories linked to EMRs. In its most recent phase, eMERGE III, the network is focused on facilitating implementation of genomic medicine by detecting and disclosing rare pathogenic variants in clinically relevant genes. Partners Personalized Medicine (PPM) is a center dedicated to translating personalized medicine into clinical practice within Partners HealthCare. One component of the PPM is the Partners Healthcare Biobank, a biorepository comprising broadly consented DNA samples linked to the Partners longitudinal EMR. In 2015, PPM joined the eMERGE Phase III network. Here we describe the elements of the eMERGE clinical center at PPM, including plans for genomic discovery using EMR phenotypes, evaluation of rare variant penetrance and pleiotropy, and a novel randomized trial of the impact of returning genetic results to patients and clinicians.
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Affiliation(s)
- Jordan W Smoller
- Massachusetts General Hospital, Boston, MA 02114, USA.
- Partners Personalized Medicine, 65 Landsdowne Street, Cambridge, MA 02139, USA.
- Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02142, USA.
| | - Elizabeth W Karlson
- Partners Personalized Medicine, 65 Landsdowne Street, Cambridge, MA 02139, USA.
- Brigham and Women's Hospital, 75 Francis Street, Boston, MA 02115, USA.
| | - Robert C Green
- Partners Personalized Medicine, 65 Landsdowne Street, Cambridge, MA 02139, USA.
- Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02142, USA.
- Brigham and Women's Hospital, 75 Francis Street, Boston, MA 02115, USA.
| | - Sekar Kathiresan
- Massachusetts General Hospital, Boston, MA 02114, USA.
- Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02142, USA.
| | - Daniel G MacArthur
- Massachusetts General Hospital, Boston, MA 02114, USA.
- Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02142, USA.
| | - Michael E Talkowski
- Massachusetts General Hospital, Boston, MA 02114, USA.
- Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02142, USA.
| | - Shawn N Murphy
- Partners Personalized Medicine, 65 Landsdowne Street, Cambridge, MA 02139, USA.
- Brigham and Women's Hospital, 75 Francis Street, Boston, MA 02115, USA.
| | - Scott T Weiss
- Partners Personalized Medicine, 65 Landsdowne Street, Cambridge, MA 02139, USA.
- Brigham and Women's Hospital, 75 Francis Street, Boston, MA 02115, USA.
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