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Dratch L, Bardakjian TM, Johnson K, Babaian N, Gonzalez-Alegre P, Elman L, Quinn C, Guo MH, Scherer SS, Amado DA. The Importance of Offering Exome or Genome Sequencing in Adult Neuromuscular Clinics. BIOLOGY 2024; 13:93. [PMID: 38392311 PMCID: PMC10886886 DOI: 10.3390/biology13020093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Revised: 01/29/2024] [Accepted: 01/30/2024] [Indexed: 02/24/2024]
Abstract
Advances in gene-specific therapeutics for patients with neuromuscular disorders (NMDs) have brought increased attention to the importance of genetic diagnosis. Genetic testing practices vary among adult neuromuscular clinics, with multi-gene panel testing currently being the most common approach; follow-up testing using broad-based methods, such as exome or genome sequencing, is less consistently offered. Here, we use five case examples to illustrate the unique ability of broad-based testing to improve diagnostic yield, resulting in identification of SORD-neuropathy, HADHB-related disease, ATXN2-ALS, MECP2 related progressive gait decline and spasticity, and DNMT1-related cerebellar ataxia, deafness, narcolepsy, and hereditary sensory neuropathy type 1E. We describe in each case the technological advantages that enabled identification of the causal gene, and the resultant clinical and personal implications for the patient, demonstrating the importance of offering exome or genome sequencing to adults with NMDs.
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Affiliation(s)
- Laynie Dratch
- Department of Neurology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Tanya M Bardakjian
- Department of Neurology, University of Pennsylvania, Philadelphia, PA 19104, USA
- Sarepta Therapeutics Inc., Cambridge, MA 02142, USA
| | - Kelsey Johnson
- Department of Neurology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Nareen Babaian
- Department of Neurology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Pedro Gonzalez-Alegre
- Department of Neurology, University of Pennsylvania, Philadelphia, PA 19104, USA
- Spark Therapeutics, Inc., Philadelphia, PA 19104, USA
| | - Lauren Elman
- Department of Neurology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Colin Quinn
- Department of Neurology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Michael H Guo
- Department of Neurology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Steven S Scherer
- Department of Neurology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Defne A Amado
- Department of Neurology, University of Pennsylvania, Philadelphia, PA 19104, USA
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2
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Gyngell C, Lynch F, Vears D, Bowman-Smart H, Savulescu J, Christodoulou J. Storing paediatric genomic data for sequential interrogation across the lifespan. JOURNAL OF MEDICAL ETHICS 2023:jme-2022-108471. [PMID: 37263770 DOI: 10.1136/jme-2022-108471] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Accepted: 03/02/2023] [Indexed: 06/03/2023]
Abstract
Genomic sequencing (GS) is increasingly used in paediatric medicine to aid in screening, research and treatment. Some health systems are trialling GS as a first-line test in newborn screening programmes. Questions about what to do with genomic data after it has been generated are becoming more pertinent. While other research has outlined the ethical reasons for storing deidentified genomic data to be used in research, the ethical case for storing data for future clinical use has not been explicated. In this paper, we examine the ethical case for storing genomic data with the intention of using it as a lifetime health resource. In this model, genomic data would be stored with the intention of reanalysis at certain points through one's life. We argue this could benefit individuals and create an important public resource. However, several ethical challenges must first be met to achieve these benefits. We explore issues related to privacy, consent, justice and equality. We conclude by arguing that health systems should be moving towards futures that allow for the sequential interrogation of genomic data throughout the lifespan.
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Affiliation(s)
- Christopher Gyngell
- Biomedical Ethics Research Group, Murdoch Children's Research Institute, Parkville, Victoria, Australia
- Department of Paediatrics, The University of Melbourne, Melbourne, Victoria, Australia
| | - Fiona Lynch
- Biomedical Ethics Research Group, Murdoch Children's Research Institute, Parkville, Victoria, Australia
- Melbourne Law School, The University of Melbourne, Parkville, VIC, Australia
| | - Danya Vears
- Biomedical Ethics Research Group, Murdoch Children's Research Institute, Parkville, Victoria, Australia
- Department of Paediatrics, The University of Melbourne, Melbourne, Victoria, Australia
| | - Hilary Bowman-Smart
- Biomedical Ethics Research Group, Murdoch Children's Research Institute, Parkville, Victoria, Australia
- University of South Australia, Adeliade, South Australia, Australia
| | - Julian Savulescu
- Biomedical Ethics Research Group, Murdoch Children's Research Institute, Parkville, Victoria, Australia
- Faculty of Philosophy, University of Oxford, Oxford, UK
- Centre for Biomedical Ethics - Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - John Christodoulou
- Department of Paediatrics, The University of Melbourne, Melbourne, Victoria, Australia
- Brain and Mitochondrial Research Group, Murdoch Children's Research Institute, Parkville, VIC, Australia
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Schuster ALR, Crossnohere NL, Bachini M, Blair CK, Carpten JD, Claus EB, Colditz GA, Ding L, Drake BF, Fields RC, Janeway KA, Kwan BM, Lenz HJ, Ma Q, Mishra SI, Paskett ED, Rebbeck TR, Ricker C, Stern MC, Sussman AL, Tiner JC, Trent JM, Verhaak RGW, Wagle N, Willman C, Bridges JFP. Priorities to Promote Participant Engagement in the Participant Engagement and Cancer Genome Sequencing (PE-CGS) Network. Cancer Epidemiol Biomarkers Prev 2023; 32:487-495. [PMID: 36791345 PMCID: PMC10068438 DOI: 10.1158/1055-9965.epi-22-0356] [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: 09/06/2022] [Revised: 11/21/2022] [Accepted: 02/07/2023] [Indexed: 02/17/2023] Open
Abstract
BACKGROUND Engaging diverse populations in cancer genomics research is of critical importance and is a fundamental goal of the NCI Participant Engagement and Cancer Genome Sequencing (PE-CGS) Network. Established as part of the Cancer Moonshot, PE-CGS is a consortium of stakeholders including clinicians, scientists, genetic counselors, and representatives of potential study participants and their communities. Participant engagement is an ongoing, bidirectional, and mutually beneficial interaction between study participants and researchers. PE-CGS sought to set priorities in participant engagement for conducting the network's research. METHODS PE-CGS deliberatively engaged its stakeholders in the following four-phase process to set the network's research priorities in participant engagement: (i) a brainstorming exercise to elicit potential priorities; (ii) a 2-day virtual meeting to discuss priorities; (iii) recommendations from the PE-CGS External Advisory Panel to refine priorities; and (iv) a virtual meeting to set priorities. RESULTS Nearly 150 PE-CGS stakeholders engaged in the process. Five priorities were set: (i) tailor education and communication materials for participants throughout the research process; (ii) identify measures of participant engagement; (iii) identify optimal participant engagement strategies; (iv) understand cancer disparities in the context of cancer genomics research; and (v) personalize the return of genomics findings to participants. CONCLUSIONS PE-CGS is pursuing these priorities to meaningfully engage diverse and underrepresented patients with cancer and posttreatment cancer survivors as participants in cancer genomics research and, subsequently, generate new discoveries. IMPACT Data from PE-CGS will be shared with the broader scientific community in a manner consistent with participant informed consent and community agreement.
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Affiliation(s)
- Anne LR. Schuster
- Department of Biomedical Informatics, The Ohio State University College of Medicine, Columbus, Ohio
| | - Norah L. Crossnohere
- Division of General Internal Medicine, Department of Internal Medicine, The Ohio State University, Columbus, Ohio
| | | | - Cindy K. Blair
- Department of Internal Medicine, University of New Mexico Comprehensive Cancer Center and Health Sciences Center, Albuquerque, New Mexico
| | - John D. Carpten
- Institute of Translational Genomics, Department of Translational Genomics, Keck School of Medicine USC, Norris Comprehensive Cancer Center, Los Angeles, California
| | - Elizabeth B. Claus
- Department of Biostatistics, Yale School of Public Health, New Haven, Connecticut
- Department of Neurosurgery, Brigham and Women's Hospital, Boston, Massachusetts
| | - Graham A. Colditz
- Department of Surgery, Washington University School of Medicine, Alvin J. Siteman Cancer Center, St. Louis, Missouri
| | - Li Ding
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri
| | - Bettina F. Drake
- Division of Public Health Sciences, Washington University School of Medicine, Alvin J. Siteman Cancer Center, St. Louis, Missouri
| | - Ryan C. Fields
- Division of General Surgery, Washington University School of Medicine, Alvin J. Siteman Cancer Center, St. Louis, Missouri
| | - Katherine A. Janeway
- Dana-Farber / Boston Children's Cancer and Blood Disorders Center, and Broad Institute of MIT and Harvard, Harvard Medical School, Boston, Massachusetts
| | - Bethany M. Kwan
- Department of Emergency Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado
| | - Heinz-Josef Lenz
- Keck School of Medicine of USC, Norris Comprehensive Cancer Center, Los Angeles, California
| | - Qin Ma
- Department of Biomedical Informatics, The Ohio State University College of Medicine, Columbus, Ohio
| | - Shiraz I. Mishra
- Departments of Pediatrics and Family and Community Medicine, University of New Mexico Comprehensive Cancer Center, University of New Mexico Health Sciences Center, Albuquerque, New Mexico
| | - Electra D. Paskett
- Division of Cancer Prevention and Control, Department of Internal Medicine, College of Medicine; Division of Epidemiology, College of Public Health, The Ohio State University, Columbus, Ohio
| | - Timothy R. Rebbeck
- Harvard TH Chan School of Public Health, Broad Institute of MIT and Harvard, and the Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Charité Ricker
- Division of Medical Oncology, Department of Medicine, Keck School of Medicine USC, Norris Comprehensive Cancer Center, Los Angeles, California
| | - Mariana C. Stern
- Department of Population and Public Health Sciences & Urology, Keck School of Medicine of USC, Norris Comprehensive Cancer Center, Los Angeles, California
| | - Andrew L. Sussman
- Department of Family and Community Medicine, University of New Mexico Comprehensive Cancer Center and Health Sciences Center, Albuquerque, New Mexico
| | - Jessica C. Tiner
- Epidemiology and Genomics Research Program, Division of Cancer Control and Population Sciences, National Cancer Institute, Bethesda, Maryland
| | - Jeffrey M. Trent
- Translational Genomics Research Institute part of City of Hope, Phoenix, Arizona
| | - Roel GW. Verhaak
- The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut
| | - Nikhil Wagle
- Dana-Farber Cancer Institute, Broad Institute of MIT and Harvard, Harvard Medical School, Dana-Farber/Harvard Cancer Center, and Count Me In, Boston, Massachusetts
| | - Cheryl Willman
- Department of Laboratory Medicine and Pathology, Mayo Clinic Comprehensive Cancer Center, Mayo Clinic, Rochester, Minnesota
- University of New Mexico School of Medicine and Comprehensive Cancer Center, Albuquerque, New Mexico
| | - John FP. Bridges
- Department of Biomedical Informatics, The Ohio State University College of Medicine, Columbus, Ohio
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Ståhlbom E, Molin J, Ynnerman A, Lundström C. The thorny complexities of visualization research for clinical settings: A case study from genomics. FRONTIERS IN BIOINFORMATICS 2023; 3:1112649. [PMID: 37063648 PMCID: PMC10090312 DOI: 10.3389/fbinf.2023.1112649] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 03/13/2023] [Indexed: 03/31/2023] Open
Abstract
In this perspective article we discuss a certain type of research on visualization for bioinformatics data, namely, methods targeting clinical use. We argue that in this subarea additional complex challenges come into play, particularly so in genomics. We here describe four such challenge areas, elicited from a domain characterization effort in clinical genomics. We also list opportunities for visualization research to address clinical challenges in genomics that were uncovered in the case study. The findings are shown to have parallels with experiences from the diagnostic imaging domain.
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Affiliation(s)
- Emilia Ståhlbom
- Department of Science and Technology, Linköping University, Linköping, Sweden
- Sectra AB, Linköping, Sweden
- *Correspondence: Emilia Ståhlbom,
| | | | - Anders Ynnerman
- Department of Science and Technology, Linköping University, Linköping, Sweden
| | - Claes Lundström
- Department of Science and Technology, Linköping University, Linköping, Sweden
- Sectra AB, Linköping, Sweden
- Center for Medical Image Science and Visualization, Linköping University, Linköping, Sweden
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Receiving results of uncertain clinical relevance from population genetic screening: systematic review & meta-synthesis of qualitative research. Eur J Hum Genet 2022; 30:520-531. [PMID: 35256770 PMCID: PMC9090782 DOI: 10.1038/s41431-022-01054-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 01/11/2022] [Accepted: 01/18/2022] [Indexed: 01/01/2023] Open
Abstract
Genetic screening can be hugely beneficial, yet its expansion poses clinical and ethical challenges due to results of uncertain clinical relevance (such as ‘cystic fibrosis screen positive, inconclusive diagnosis’/CFSPID). This review systematically identifies, appraises, and synthesises the qualitative research on experiences of receiving results of uncertain clinical relevance from population genetic screening. Eight databases were systematically searched for original qualitative research using the SPIDER framework, and checked against inclusion criteria by the research team and an independent researcher. Nine papers were included (from USA, Canada, UK, New Zealand). PRISMA, ENTREQ, and EMERGE guidance were used to report. Quality was appraised using criteria for qualitative research. All papers focused on parental responses to uncertain results from newborn screening. Data were synthesised using meta-ethnography and first- and second-order constructs. Findings suggest that results of uncertain clinical relevance are often experienced in the same way as a ‘full-blown’ diagnosis. This has significant emotional and behavioural impact, for example adoption of lifestyle-altering disease-focused behaviours. Analysis suggests this may be due to the results not fitting a common medical model, leading recipients to interpret the significance of the result maladaptively. Findings suggest scope for professionals to negotiate and reframe uncertain screening results. Clearer initial communication is needed to reassure recipients there is no immediate severe health risk from these types of results. Public understanding of an appropriate medical model, that accounts for uncertain genetic screening results in a non-threatening way, may be key to maximising the benefits of genomic medicine and minimising potential psychological harm.
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6
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Rebbeck TR, Bridges JFP, Mack JW, Gray SW, Trent JM, George S, Crossnohere NL, Paskett ED, Painter CA, Wagle N, Kano M, Nez Henderson P, Henderson JA, Mishra SI, Willman CL, Sussman AL. A Framework for Promoting Diversity, Equity, and Inclusion in Genetics and Genomics Research. JAMA HEALTH FORUM 2022; 3:e220603. [PMID: 35755401 PMCID: PMC9223088 DOI: 10.1001/jamahealthforum.2022.0603] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/13/2023] Open
Abstract
IMPORTANCE Research into the genetic and genomic ("genomics") foundations of disease is central to our understanding of disease prevention, early detection, diagnostic accuracy, and therapeutic intervention. Inequitable participation in genomics research by historically excluded populations limits the ability to translate genomic knowledge to achieve health equity and ensure that findings are generalizable to diverse populations. OBSERVATIONS We propose a novel framework for promoting diversity, equity, and inclusion in genomics research. Building on principles of community-based participatory research and collective impact frameworks, the framework can guide our understanding of the social, cultural, health system, policy, community, and individual contexts in which engagement and genomics research are being done. Our framework highlights the involvement of a multistakeholder team, including the participants and communities to be engaged, to ensure robust methods for recruitment, retention, return of genomic results, quality of engagement, follow-up, and monitoring of participants. CONCLUSIONS AND RELEVANCE The proposed engagement framework will guide investigators in optimizing equitable representation in research and enhancing the rigor of genomics investigation.
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Affiliation(s)
- Timothy R Rebbeck
- Harvard T.H. Chan School of Public Health, Boston, Massachusetts (Rebbeck); Dana-Farber Cancer Institute, Boston, Massachusetts (Rebbeck, Mack, George, Wagle); The Ohio State University, Columbus, Ohio (Bridges, Crossnohere, Paskett); City of Hope, Duarte, California (Gray); The Translational Genomics Research Institute, Phoenix, Arizona (Trent); Broad Institute to Broad Institute of MIT and Harvard and Count Me In, Cambridge, Massachusetts (Painter, Wagle); University of New Mexico Comprehensive Cancer Center and Health Sciences Center, Albuquerque (Kano, Mishra, Willman, Sussman); Black Hills Center for American Indian Health, Rapid City, South Dakota (Nez Henderson, Henderson); Mayo Clinic Comprehensive Cancer Center, Mayo Clinic, Rochester, Minnesota (Willman)
| | - John F P Bridges
- Harvard T.H. Chan School of Public Health, Boston, Massachusetts (Rebbeck); Dana-Farber Cancer Institute, Boston, Massachusetts (Rebbeck, Mack, George, Wagle); The Ohio State University, Columbus, Ohio (Bridges, Crossnohere, Paskett); City of Hope, Duarte, California (Gray); The Translational Genomics Research Institute, Phoenix, Arizona (Trent); Broad Institute to Broad Institute of MIT and Harvard and Count Me In, Cambridge, Massachusetts (Painter, Wagle); University of New Mexico Comprehensive Cancer Center and Health Sciences Center, Albuquerque (Kano, Mishra, Willman, Sussman); Black Hills Center for American Indian Health, Rapid City, South Dakota (Nez Henderson, Henderson); Mayo Clinic Comprehensive Cancer Center, Mayo Clinic, Rochester, Minnesota (Willman)
| | - Jennifer W Mack
- Harvard T.H. Chan School of Public Health, Boston, Massachusetts (Rebbeck); Dana-Farber Cancer Institute, Boston, Massachusetts (Rebbeck, Mack, George, Wagle); The Ohio State University, Columbus, Ohio (Bridges, Crossnohere, Paskett); City of Hope, Duarte, California (Gray); The Translational Genomics Research Institute, Phoenix, Arizona (Trent); Broad Institute to Broad Institute of MIT and Harvard and Count Me In, Cambridge, Massachusetts (Painter, Wagle); University of New Mexico Comprehensive Cancer Center and Health Sciences Center, Albuquerque (Kano, Mishra, Willman, Sussman); Black Hills Center for American Indian Health, Rapid City, South Dakota (Nez Henderson, Henderson); Mayo Clinic Comprehensive Cancer Center, Mayo Clinic, Rochester, Minnesota (Willman)
| | - Stacy W Gray
- Harvard T.H. Chan School of Public Health, Boston, Massachusetts (Rebbeck); Dana-Farber Cancer Institute, Boston, Massachusetts (Rebbeck, Mack, George, Wagle); The Ohio State University, Columbus, Ohio (Bridges, Crossnohere, Paskett); City of Hope, Duarte, California (Gray); The Translational Genomics Research Institute, Phoenix, Arizona (Trent); Broad Institute to Broad Institute of MIT and Harvard and Count Me In, Cambridge, Massachusetts (Painter, Wagle); University of New Mexico Comprehensive Cancer Center and Health Sciences Center, Albuquerque (Kano, Mishra, Willman, Sussman); Black Hills Center for American Indian Health, Rapid City, South Dakota (Nez Henderson, Henderson); Mayo Clinic Comprehensive Cancer Center, Mayo Clinic, Rochester, Minnesota (Willman)
| | - Jeffrey M Trent
- Harvard T.H. Chan School of Public Health, Boston, Massachusetts (Rebbeck); Dana-Farber Cancer Institute, Boston, Massachusetts (Rebbeck, Mack, George, Wagle); The Ohio State University, Columbus, Ohio (Bridges, Crossnohere, Paskett); City of Hope, Duarte, California (Gray); The Translational Genomics Research Institute, Phoenix, Arizona (Trent); Broad Institute to Broad Institute of MIT and Harvard and Count Me In, Cambridge, Massachusetts (Painter, Wagle); University of New Mexico Comprehensive Cancer Center and Health Sciences Center, Albuquerque (Kano, Mishra, Willman, Sussman); Black Hills Center for American Indian Health, Rapid City, South Dakota (Nez Henderson, Henderson); Mayo Clinic Comprehensive Cancer Center, Mayo Clinic, Rochester, Minnesota (Willman)
| | - Suzanne George
- Harvard T.H. Chan School of Public Health, Boston, Massachusetts (Rebbeck); Dana-Farber Cancer Institute, Boston, Massachusetts (Rebbeck, Mack, George, Wagle); The Ohio State University, Columbus, Ohio (Bridges, Crossnohere, Paskett); City of Hope, Duarte, California (Gray); The Translational Genomics Research Institute, Phoenix, Arizona (Trent); Broad Institute to Broad Institute of MIT and Harvard and Count Me In, Cambridge, Massachusetts (Painter, Wagle); University of New Mexico Comprehensive Cancer Center and Health Sciences Center, Albuquerque (Kano, Mishra, Willman, Sussman); Black Hills Center for American Indian Health, Rapid City, South Dakota (Nez Henderson, Henderson); Mayo Clinic Comprehensive Cancer Center, Mayo Clinic, Rochester, Minnesota (Willman)
| | - Norah L Crossnohere
- Harvard T.H. Chan School of Public Health, Boston, Massachusetts (Rebbeck); Dana-Farber Cancer Institute, Boston, Massachusetts (Rebbeck, Mack, George, Wagle); The Ohio State University, Columbus, Ohio (Bridges, Crossnohere, Paskett); City of Hope, Duarte, California (Gray); The Translational Genomics Research Institute, Phoenix, Arizona (Trent); Broad Institute to Broad Institute of MIT and Harvard and Count Me In, Cambridge, Massachusetts (Painter, Wagle); University of New Mexico Comprehensive Cancer Center and Health Sciences Center, Albuquerque (Kano, Mishra, Willman, Sussman); Black Hills Center for American Indian Health, Rapid City, South Dakota (Nez Henderson, Henderson); Mayo Clinic Comprehensive Cancer Center, Mayo Clinic, Rochester, Minnesota (Willman)
| | - Electra D Paskett
- Harvard T.H. Chan School of Public Health, Boston, Massachusetts (Rebbeck); Dana-Farber Cancer Institute, Boston, Massachusetts (Rebbeck, Mack, George, Wagle); The Ohio State University, Columbus, Ohio (Bridges, Crossnohere, Paskett); City of Hope, Duarte, California (Gray); The Translational Genomics Research Institute, Phoenix, Arizona (Trent); Broad Institute to Broad Institute of MIT and Harvard and Count Me In, Cambridge, Massachusetts (Painter, Wagle); University of New Mexico Comprehensive Cancer Center and Health Sciences Center, Albuquerque (Kano, Mishra, Willman, Sussman); Black Hills Center for American Indian Health, Rapid City, South Dakota (Nez Henderson, Henderson); Mayo Clinic Comprehensive Cancer Center, Mayo Clinic, Rochester, Minnesota (Willman)
| | - Corrie A Painter
- Harvard T.H. Chan School of Public Health, Boston, Massachusetts (Rebbeck); Dana-Farber Cancer Institute, Boston, Massachusetts (Rebbeck, Mack, George, Wagle); The Ohio State University, Columbus, Ohio (Bridges, Crossnohere, Paskett); City of Hope, Duarte, California (Gray); The Translational Genomics Research Institute, Phoenix, Arizona (Trent); Broad Institute to Broad Institute of MIT and Harvard and Count Me In, Cambridge, Massachusetts (Painter, Wagle); University of New Mexico Comprehensive Cancer Center and Health Sciences Center, Albuquerque (Kano, Mishra, Willman, Sussman); Black Hills Center for American Indian Health, Rapid City, South Dakota (Nez Henderson, Henderson); Mayo Clinic Comprehensive Cancer Center, Mayo Clinic, Rochester, Minnesota (Willman)
| | - Nikhil Wagle
- Harvard T.H. Chan School of Public Health, Boston, Massachusetts (Rebbeck); Dana-Farber Cancer Institute, Boston, Massachusetts (Rebbeck, Mack, George, Wagle); The Ohio State University, Columbus, Ohio (Bridges, Crossnohere, Paskett); City of Hope, Duarte, California (Gray); The Translational Genomics Research Institute, Phoenix, Arizona (Trent); Broad Institute to Broad Institute of MIT and Harvard and Count Me In, Cambridge, Massachusetts (Painter, Wagle); University of New Mexico Comprehensive Cancer Center and Health Sciences Center, Albuquerque (Kano, Mishra, Willman, Sussman); Black Hills Center for American Indian Health, Rapid City, South Dakota (Nez Henderson, Henderson); Mayo Clinic Comprehensive Cancer Center, Mayo Clinic, Rochester, Minnesota (Willman)
| | - Miria Kano
- Harvard T.H. Chan School of Public Health, Boston, Massachusetts (Rebbeck); Dana-Farber Cancer Institute, Boston, Massachusetts (Rebbeck, Mack, George, Wagle); The Ohio State University, Columbus, Ohio (Bridges, Crossnohere, Paskett); City of Hope, Duarte, California (Gray); The Translational Genomics Research Institute, Phoenix, Arizona (Trent); Broad Institute to Broad Institute of MIT and Harvard and Count Me In, Cambridge, Massachusetts (Painter, Wagle); University of New Mexico Comprehensive Cancer Center and Health Sciences Center, Albuquerque (Kano, Mishra, Willman, Sussman); Black Hills Center for American Indian Health, Rapid City, South Dakota (Nez Henderson, Henderson); Mayo Clinic Comprehensive Cancer Center, Mayo Clinic, Rochester, Minnesota (Willman)
| | - Patricia Nez Henderson
- Harvard T.H. Chan School of Public Health, Boston, Massachusetts (Rebbeck); Dana-Farber Cancer Institute, Boston, Massachusetts (Rebbeck, Mack, George, Wagle); The Ohio State University, Columbus, Ohio (Bridges, Crossnohere, Paskett); City of Hope, Duarte, California (Gray); The Translational Genomics Research Institute, Phoenix, Arizona (Trent); Broad Institute to Broad Institute of MIT and Harvard and Count Me In, Cambridge, Massachusetts (Painter, Wagle); University of New Mexico Comprehensive Cancer Center and Health Sciences Center, Albuquerque (Kano, Mishra, Willman, Sussman); Black Hills Center for American Indian Health, Rapid City, South Dakota (Nez Henderson, Henderson); Mayo Clinic Comprehensive Cancer Center, Mayo Clinic, Rochester, Minnesota (Willman)
| | - Jeffrey A Henderson
- Harvard T.H. Chan School of Public Health, Boston, Massachusetts (Rebbeck); Dana-Farber Cancer Institute, Boston, Massachusetts (Rebbeck, Mack, George, Wagle); The Ohio State University, Columbus, Ohio (Bridges, Crossnohere, Paskett); City of Hope, Duarte, California (Gray); The Translational Genomics Research Institute, Phoenix, Arizona (Trent); Broad Institute to Broad Institute of MIT and Harvard and Count Me In, Cambridge, Massachusetts (Painter, Wagle); University of New Mexico Comprehensive Cancer Center and Health Sciences Center, Albuquerque (Kano, Mishra, Willman, Sussman); Black Hills Center for American Indian Health, Rapid City, South Dakota (Nez Henderson, Henderson); Mayo Clinic Comprehensive Cancer Center, Mayo Clinic, Rochester, Minnesota (Willman)
| | - Shiraz I Mishra
- Harvard T.H. Chan School of Public Health, Boston, Massachusetts (Rebbeck); Dana-Farber Cancer Institute, Boston, Massachusetts (Rebbeck, Mack, George, Wagle); The Ohio State University, Columbus, Ohio (Bridges, Crossnohere, Paskett); City of Hope, Duarte, California (Gray); The Translational Genomics Research Institute, Phoenix, Arizona (Trent); Broad Institute to Broad Institute of MIT and Harvard and Count Me In, Cambridge, Massachusetts (Painter, Wagle); University of New Mexico Comprehensive Cancer Center and Health Sciences Center, Albuquerque (Kano, Mishra, Willman, Sussman); Black Hills Center for American Indian Health, Rapid City, South Dakota (Nez Henderson, Henderson); Mayo Clinic Comprehensive Cancer Center, Mayo Clinic, Rochester, Minnesota (Willman)
| | - Cheryl L Willman
- Harvard T.H. Chan School of Public Health, Boston, Massachusetts (Rebbeck); Dana-Farber Cancer Institute, Boston, Massachusetts (Rebbeck, Mack, George, Wagle); The Ohio State University, Columbus, Ohio (Bridges, Crossnohere, Paskett); City of Hope, Duarte, California (Gray); The Translational Genomics Research Institute, Phoenix, Arizona (Trent); Broad Institute to Broad Institute of MIT and Harvard and Count Me In, Cambridge, Massachusetts (Painter, Wagle); University of New Mexico Comprehensive Cancer Center and Health Sciences Center, Albuquerque (Kano, Mishra, Willman, Sussman); Black Hills Center for American Indian Health, Rapid City, South Dakota (Nez Henderson, Henderson); Mayo Clinic Comprehensive Cancer Center, Mayo Clinic, Rochester, Minnesota (Willman)
| | - Andrew L Sussman
- Harvard T.H. Chan School of Public Health, Boston, Massachusetts (Rebbeck); Dana-Farber Cancer Institute, Boston, Massachusetts (Rebbeck, Mack, George, Wagle); The Ohio State University, Columbus, Ohio (Bridges, Crossnohere, Paskett); City of Hope, Duarte, California (Gray); The Translational Genomics Research Institute, Phoenix, Arizona (Trent); Broad Institute to Broad Institute of MIT and Harvard and Count Me In, Cambridge, Massachusetts (Painter, Wagle); University of New Mexico Comprehensive Cancer Center and Health Sciences Center, Albuquerque (Kano, Mishra, Willman, Sussman); Black Hills Center for American Indian Health, Rapid City, South Dakota (Nez Henderson, Henderson); Mayo Clinic Comprehensive Cancer Center, Mayo Clinic, Rochester, Minnesota (Willman)
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7
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Clinical Phenotypes of Cardiovascular and Heart Failure Diseases Can Be Reversed? The Holistic Principle of Systems Biology in Multifaceted Heart Diseases. CARDIOGENETICS 2022. [DOI: 10.3390/cardiogenetics12020015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/07/2022] Open
Abstract
Recent advances in cardiology and biological sciences have improved quality of life in patients with complex cardiovascular diseases (CVDs) or heart failure (HF). Regardless of medical progress, complex cardiac diseases continue to have a prolonged clinical course with high morbidity and mortality. Interventional coronary techniques together with drug therapy improve quality and future prospects of life, but do not reverse the course of the atherosclerotic process that remains relentlessly progressive. The probability of CVDs and HF phenotypes to reverse can be supported by the advances made on the medical holistic principle of systems biology (SB) and on artificial intelligence (AI). Studies on clinical phenotypes reversal should be based on the research performed in large populations of patients following gathering and analyzing large amounts of relative data that embrace the concept of complexity. To decipher the complexity conundrum, a multiomics approach is needed with network analysis of the biological data. Only by understanding the complexity of chronic heart diseases and explaining the interrelationship between different interconnected biological networks can the probability for clinical phenotypes reversal be increased.
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8
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Dikow N, Ditzen B, Kölker S, Hoffmann GF, Schaaf CP. From newborn screening to genomic medicine: challenges and suggestions on how to incorporate genomic newborn screening in public health programs. MED GENET-BERLIN 2022; 34:13-20. [PMID: 38836020 PMCID: PMC11006367 DOI: 10.1515/medgen-2022-2113] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 02/17/2022] [Indexed: 06/06/2024]
Abstract
Newborn screening (NBS) programs are considered among the most effective and efficient measures of secondary prevention in medicine. In individuals with medical conditions, genomic sequencing has become available in routine healthcare, and results from exome or genome sequencing may help to guide treatment decisions. Genomic sequencing in healthy or asymptomatic newborns (gNBS) is feasible and reveals clinically relevant disorders that are not detectable by biochemical analyses alone. However, the implementation of genomic sequencing in population-based screening programs comes with technological, clinical, ethical, and psychological issues, as well as economic and legal topics. Here, we address and discuss the most important questions to be considered when implementing gNBS, such as "which categories of results should be reported" or "which is the best time to return results". We also offer ideas on how to balance expected benefits against possible harms to children and their families.
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Affiliation(s)
- Nicola Dikow
- Institute of Human Genetics, Heidelberg University, Heidelberg, Germany
| | - Beate Ditzen
- Institute of Medical Psychology, Center for Psychosocial Medicine, University Hospital Heidelberg, Heidelberg, Germany
| | - Stefan Kölker
- University Hospital Heidelberg, Center for Pediatric and Adolescent Medicine, Clinic I, Heidelberg, Germany
| | - Georg F Hoffmann
- University Hospital Heidelberg, Center for Pediatric and Adolescent Medicine, Clinic I, Heidelberg, Germany
| | - Christian P Schaaf
- Institute of Human Genetics, Heidelberg University, Heidelberg, Germany
- Baylor College of Medicine, Houston, Texas, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, Texas, USA
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9
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Nurchis MC, Riccardi MT, Radio FC, Chillemi G, Bertini ES, Tartaglia M, Cicchetti A, Dallapiccola B, Damiani G. Incremental net benefit of Whole Genome Sequencing for newborns and children with suspected genetic disorders: systematic review and meta-analysis of cost-effectiveness evidence. Health Policy 2022; 126:337-345. [DOI: 10.1016/j.healthpol.2022.03.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 02/16/2022] [Accepted: 03/01/2022] [Indexed: 11/16/2022]
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10
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Bui TA, Shatto J, Cuppens T, Droit A, Bolduc FV. Phenotypic Trade-Offs: Deciphering the Impact of Neurodiversity on Drug Development in Fragile X Syndrome. Front Psychiatry 2021; 12:730987. [PMID: 34733188 PMCID: PMC8558248 DOI: 10.3389/fpsyt.2021.730987] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Accepted: 09/20/2021] [Indexed: 11/24/2022] Open
Abstract
Fragile X syndrome (FXS) is the most common single-gene cause of intellectual disability and autism spectrum disorder. Individuals with FXS present with a wide range of severity in multiple phenotypes including cognitive delay, behavioral challenges, sleep issues, epilepsy, and anxiety. These symptoms are also shared by many individuals with other neurodevelopmental disorders (NDDs). Since the discovery of the FXS gene, FMR1, FXS has been the focus of intense preclinical investigation and is placed at the forefront of clinical trials in the field of NDDs. So far, most studies have aimed to translate the rescue of specific phenotypes in animal models, for example, learning, or improving general cognitive or behavioral functioning in individuals with FXS. Trial design, selection of outcome measures, and interpretation of results of recent trials have shown limitations in this type of approach. We propose a new paradigm in which all phenotypes involved in individuals with FXS would be considered and, more importantly, the possible interactions between these phenotypes. This approach would be implemented both at the baseline, meaning when entering a trial or when studying a patient population, and also after the intervention when the study subjects have been exposed to the investigational product. This approach would allow us to further understand potential trade-offs underlying the varying effects of the treatment on different individuals in clinical trials, and to connect the results to individual genetic differences. To better understand the interplay between different phenotypes, we emphasize the need for preclinical studies to investigate various interrelated biological and behavioral outcomes when assessing a specific treatment. In this paper, we present how such a conceptual shift in preclinical design could shed new light on clinical trial results. Future clinical studies should take into account the rich neurodiversity of individuals with FXS specifically and NDDs in general, and incorporate the idea of trade-offs in their designs.
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Affiliation(s)
- Truong An Bui
- Department of Pediatrics, University of Alberta, Edmonton, AB, Canada
| | - Julie Shatto
- Department of Pediatrics, University of Alberta, Edmonton, AB, Canada
| | - Tania Cuppens
- Centre de Recherche du CHU de Québec-Université Laval et Département de Médecine Moléculaire de l'Université Laval, Laval, QC, Canada
| | - Arnaud Droit
- Centre de Recherche du CHU de Québec-Université Laval et Département de Médecine Moléculaire de l'Université Laval, Laval, QC, Canada
| | - François V. Bolduc
- Department of Pediatrics, University of Alberta, Edmonton, AB, Canada
- Department of Medical Genetics, University of Alberta, Edmonton, AB, Canada
- Neuroscience and Mental Health Institute, University of Alberta, Edmonton, AB, Canada
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11
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Cléophat JE, Dorval M, El Haffaf Z, Chiquette J, Collins S, Malo B, Fradet V, Joly Y, Nabi H. Whether, when, how, and how much? General public's and cancer patients' views about the disclosure of genomic secondary findings. BMC Med Genomics 2021; 14:167. [PMID: 34174888 PMCID: PMC8236159 DOI: 10.1186/s12920-021-01016-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Accepted: 06/16/2021] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Data on the modalities of disclosing genomic secondary findings (SFs) remain scarce. We explore cancer patients' and the general public's perspectives about disclosing genomic SFs and the modalities of such disclosure. METHODS Sixty-one cancer patients (n = 29) and members of the public (n = 32) participated in eight focus groups in Montreal and Quebec City, Canada. They were asked to provide their perspectives of five fictitious vignettes related to medically actionable and non-actionable SFs. Two researchers used a codification framework to conduct a thematic content analysis of the group discussion transcripts. RESULTS Cancer patients and members of the public were open to receive genomic SFs, considering their potential clinical and personal utility. They believed that the right to know or not and share or not such findings should remain the patient's decision. They thought that the disclosure of SFs should be made mainly in person by the prescribing clinician. Maintaining confidentiality when so requested and preventing genetic discrimination were considered essential. CONCLUSION Participants in this study welcomed the prospect of disclosing genomic SFs, as long as the right to choose to know or not to know is preserved. They called for the development of policies and practice guidelines that aim to protect genetic information confidentiality as well as the autonomy, physical and psychosocial wellbeing of patients and families.
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Affiliation(s)
- Jude Emmanuel Cléophat
- Faculty of Pharmacy, Laval University, Quebec City, QC, Canada.,Oncology Division, Research Center of the CHU de Québec-Laval University, Hôpital du Saint-Sacrement, 1050, chemin Sainte-Foy, Québec, QC, G1S 4L8, Canada
| | - Michel Dorval
- Faculty of Pharmacy, Laval University, Quebec City, QC, Canada.,Oncology Division, Research Center of the CHU de Québec-Laval University, Hôpital du Saint-Sacrement, 1050, chemin Sainte-Foy, Québec, QC, G1S 4L8, Canada.,Laval University Cancer Research Center, Quebec City, QC, Canada.,Research Center of the Chaudière-Appalaches Integrated Center for Health and Social Services, Lévis, QC, Canada
| | - Zaki El Haffaf
- Division of Genetics, Department of Medicine, Hospital Center of the University of Montreal, Montreal, QC, Canada.,Oncology Division, Research Center of the Hospital Center of the University of Montreal, Montreal, QC, Canada
| | - Jocelyne Chiquette
- Oncology Division, Research Center of the CHU de Québec-Laval University, Hôpital du Saint-Sacrement, 1050, chemin Sainte-Foy, Québec, QC, G1S 4L8, Canada.,Department of Family Medicine and Emergency Medicine, Faculty of Medicine, Laval University, Quebec City, QC, Canada
| | | | - Benjamin Malo
- Infectious and Immune Diseases Division, Research center of the Quebec City University Hospital, Quebec City, QC, Canada
| | - Vincent Fradet
- Oncology Division, Research Center of the CHU de Québec-Laval University, Hôpital du Saint-Sacrement, 1050, chemin Sainte-Foy, Québec, QC, G1S 4L8, Canada.,Laval University Cancer Research Center, Quebec City, QC, Canada.,Department of Surgery, Faculty of Medicine, Laval University, Quebec City, QC, Canada
| | - Yann Joly
- Center of Genomics and Policy, McGill University, Montreal, QC, Canada
| | - Hermann Nabi
- Oncology Division, Research Center of the CHU de Québec-Laval University, Hôpital du Saint-Sacrement, 1050, chemin Sainte-Foy, Québec, QC, G1S 4L8, Canada. .,Laval University Cancer Research Center, Quebec City, QC, Canada. .,Department of Social and Preventive Medicine, Faculty of Medicine, Laval University, Quebec City, QC, Canada.
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12
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Sun H, Shen XR, Fang ZB, Jiang ZZ, Wei XJ, Wang ZY, Yu XF. Next-Generation Sequencing Technologies and Neurogenetic Diseases. Life (Basel) 2021; 11:life11040361. [PMID: 33921670 PMCID: PMC8072598 DOI: 10.3390/life11040361] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 04/05/2021] [Accepted: 04/16/2021] [Indexed: 12/18/2022] Open
Abstract
Next-generation sequencing (NGS) technology has led to great advances in understanding the causes of Mendelian and complex neurological diseases. Owing to the complexity of genetic diseases, the genetic factors contributing to many rare and common neurological diseases remain poorly understood. Selecting the correct genetic test based on cost-effectiveness, coverage area, and sequencing range can improve diagnosis, treatments, and prevention. Whole-exome sequencing and whole-genome sequencing are suitable methods for finding new mutations, and gene panels are suitable for exploring the roles of specific genes in neurogenetic diseases. Here, we provide an overview of the classifications, applications, advantages, and limitations of NGS in research on neurological diseases. We further provide examples of NGS-based explorations and insights of the genetic causes of neurogenetic diseases, including Charcot-Marie-Tooth disease, spinocerebellar ataxias, epilepsy, and multiple sclerosis. In addition, we focus on issues related to NGS-based analyses, including interpretations of variants of uncertain significance, de novo mutations, congenital genetic diseases with complex phenotypes, and single-molecule real-time approaches.
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Affiliation(s)
| | | | | | | | | | | | - Xue-Fan Yu
- Correspondence: ; Tel.: +86-157-5430-1836
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13
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Cushman-Vokoun A, Lauring J, Pfeifer J, Olson DR, Berry A, Thorson J, Voelkerding K, Myles J, Barbeau J, Chandra P, Li M, Vance GH, Jensen BW, Hansen MY, Yohe S. Laboratory and Clinical Implications of Incidental and Secondary Germline Findings During Tumor Testing. Arch Pathol Lab Med 2021; 146:70-77. [PMID: 33769456 DOI: 10.5858/arpa.2020-0025-cp] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/13/2021] [Indexed: 11/06/2022]
Abstract
CONTEXT.— Next-generation sequencing is a powerful clinical tool for cancer management but can produce incidental/secondary findings that require special consideration. OBJECTIVE.— To discuss clinical and laboratory issues related to incidental or secondary germline findings in the clinical setting of tumor testing and inform future guidelines in this area. DESIGN.— A College of American Pathologists workgroup including representation from the American Society of Clinical Oncology, the Association for Molecular Pathology, and the American College of Medical Genetics and Genomics created a review of items that should be considered when developing guidelines for incidental or secondary findings when performing clinical tumor testing. RESULTS.— Testing recommendations should be cognizant of the differences among anticipated incidental, unanticipated incidental, and secondary findings, and whether normal tissue is also tested. In addition to defining which variants will be reported, robust recommendations must also take into account test design and validation, reimbursement, cost, infrastructure, impact on reflex testing, and maintenance of proficiency. Care providers need to consider the potential of a test to uncover incidental or secondary findings, the recommendation of upfront counseling, the need for consent, the timing of testing and counseling, and that the exact significance of a finding may not be clear. CONCLUSIONS.— As clinical oncology testing panels have become a mainstay of clinical cancer care, guidelines addressing the unique aspects of incidental and secondary findings in oncology testing are needed. This paper highlights clinical and laboratory considerations with regard to incidental/secondary findings and is a clarion call to create recommendations.
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Affiliation(s)
- Allison Cushman-Vokoun
- From the Department of Pathology and Microbiology, University of Nebraska Medical Center Nebraska Medicine, Omaha (Cushman-Vokoun)
| | - Josh Lauring
- the Breast and Ovarian Cancer Program, The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, Maryland (Lauring)
| | - John Pfeifer
- the Department of Pathology, Washington University School of Medicine, Saint Louis, Missouri (Pfeifer)
| | - Damon R Olson
- the Department of Pathology, Children's Hospitals and Clinics of Minnesota, Minneapolis (Olson)
| | - Anna Berry
- Molecular Pathology Genomics, Swedish Cancer Institute Lab, Seattle, Washington (Berry)
| | - John Thorson
- the Department of Pathology, University of California, San Diego (Thorson)
| | - Karl Voelkerding
- the Department of Pathology, University of Utah, ARUP Laboratories Institute for Clinical and Experimental Pathology, Salt Lake City (Voelkerding)
| | - Jonathan Myles
- the Department of Anatomic Pathology, Cleveland Clinic, Cleveland, Ohio (Myles)
| | - James Barbeau
- the Department of Pathology and Laboratory Medicine, Brown University Alpert Medical School, Lifespan Academic Medical Center, Providence, Rhode Island (Barbeau)
| | - Pranil Chandra
- the Department of Molecular and Clinical Pathology, PathGroup Lab LLC, Nashville, Tennessee (Chandra)
| | - Marilyn Li
- the Department of Genomic Diagnostics, Children's Hospital of Philadelphia, Perelman School of Medicine, University of Pennsylvania, Philadelphia (Li)
| | - Gail H Vance
- the Department of Medical and Molecular Genetics, Indiana University, Indianapolis (Vance)
| | - Brad W Jensen
- the Department of Anatomic and Clinical Pathology, PeaceHealth Medical Center, Vancouver, Washington (Jensen)
| | - Molly Y Hansen
- Proficiency Testing, College of American Pathologists, Northfield, Illinois (Hansen)
| | - Sophia Yohe
- the Department of Laboratory Medicine and Pathology, University of Minnesota Medical Center, Minneapolis (Yohe)
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14
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Carruth ED, Beer D, Alsaid A, Schwartz MLB, McMinn M, Kelly MA, Buchanan AH, Nevius CD, Calkins H, James CA, Murray B, Tichnell C, Matsumura ME, Kirchner HL, Fornwalt BK, Sturm AC, Haggerty CM. Clinical Findings and Diagnostic Yield of Arrhythmogenic Cardiomyopathy Through Genomic Screening of Pathogenic or Likely Pathogenic Desmosome Gene Variants. CIRCULATION-GENOMIC AND PRECISION MEDICINE 2021; 14:e003302. [PMID: 33684294 DOI: 10.1161/circgen.120.003302] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
BACKGROUND Genomic screening holds great promise for presymptomatic identification of hidden disease, and prevention of dramatic events, including sudden cardiac death associated with arrhythmogenic cardiomyopathy (ACM). Herein, we present findings from clinical follow-up of carriers of ACM-associated pathogenic/likely pathogenic desmosome variants ascertained through genomic screening. METHODS Of 64 548 eligible participants in Geisinger MyCode Genomic Screening and Counseling program (2015-present), 92 individuals (0.14%) identified with pathogenic/likely pathogenic desmosome variants by clinical laboratory testing were referred for evaluation. We reviewed preresult medical history, patient-reported family history, and diagnostic testing results to assess both arrhythmogenic right ventricular cardiomyopathy and left-dominant ACM. RESULTS One carrier had a prior diagnosis of dilated cardiomyopathy with arrhythmia; no other related diagnoses or diagnostic family history criteria were reported. Fifty-nine carriers (64%) had diagnostic testing in follow-up. Excluding the variant, 21/59 carriers satisfied at least one arrhythmogenic right ventricular cardiomyopathy task force criterion, 11 (52%) of whom harbored DSP variants, but only 5 exhibited multiple criteria. Six (10%) carriers demonstrated evidence of left-dominant ACM, including high rates of atypical late gadolinium enhancement by magnetic resonance imaging and nonsustained ventricular tachycardia. Two individuals received new cardiomyopathy diagnoses and received defibrillators for primary prevention. CONCLUSIONS Genomic screening for pathogenic/likely pathogenic variants in desmosome genes can uncover both left- and right-dominant ACM. Findings of overt cardiomyopathy were limited but were most common in DSP-variant carriers and notably absent in PKP2-variant carriers. Consideration of the pathogenic/likely pathogenic variant as a major criterion for diagnosis is inappropriate in the setting of genomic screening.
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Affiliation(s)
- Eric D Carruth
- Department of Translational Data Science and Informatics (E.D.C., C.D.N., B.K.F., C.M.H.), Geisinger, Danville, PA
| | - Dominik Beer
- The Heart Institute (D.B., A.A., M.E.M., B.K.F., A.C.S., C.M.H.), Geisinger, Danville, PA
| | - Amro Alsaid
- The Heart Institute (D.B., A.A., M.E.M., B.K.F., A.C.S., C.M.H.), Geisinger, Danville, PA
| | - Marci L B Schwartz
- Genomic Medicine Institute (M.L.B.S., M.M., M.A.K., A.H.B., A.C.S.), Geisinger, Danville, PA
| | - Megan McMinn
- Genomic Medicine Institute (M.L.B.S., M.M., M.A.K., A.H.B., A.C.S.), Geisinger, Danville, PA
| | - Melissa A Kelly
- Genomic Medicine Institute (M.L.B.S., M.M., M.A.K., A.H.B., A.C.S.), Geisinger, Danville, PA
| | - Adam H Buchanan
- Genomic Medicine Institute (M.L.B.S., M.M., M.A.K., A.H.B., A.C.S.), Geisinger, Danville, PA
| | - Christopher D Nevius
- Department of Translational Data Science and Informatics (E.D.C., C.D.N., B.K.F., C.M.H.), Geisinger, Danville, PA
| | - Hugh Calkins
- Division of Cardiology, Department of Medicine, Johns Hopkins Medical Center, Baltimore, MD (H.C., C.A.J., B.M., C.T.)
| | - Cynthia A James
- Division of Cardiology, Department of Medicine, Johns Hopkins Medical Center, Baltimore, MD (H.C., C.A.J., B.M., C.T.)
| | - Brittney Murray
- Division of Cardiology, Department of Medicine, Johns Hopkins Medical Center, Baltimore, MD (H.C., C.A.J., B.M., C.T.)
| | - Crystal Tichnell
- Division of Cardiology, Department of Medicine, Johns Hopkins Medical Center, Baltimore, MD (H.C., C.A.J., B.M., C.T.)
| | - Martin E Matsumura
- The Heart Institute (D.B., A.A., M.E.M., B.K.F., A.C.S., C.M.H.), Geisinger, Danville, PA
| | - H Lester Kirchner
- Department of Population Health Sciences (H.L.K.), Geisinger, Danville, PA
| | - Brandon K Fornwalt
- Department of Translational Data Science and Informatics (E.D.C., C.D.N., B.K.F., C.M.H.), Geisinger, Danville, PA.,The Heart Institute (D.B., A.A., M.E.M., B.K.F., A.C.S., C.M.H.), Geisinger, Danville, PA.,Department of Radiology (B.K.F.), Geisinger, Danville, PA
| | - Amy C Sturm
- The Heart Institute (D.B., A.A., M.E.M., B.K.F., A.C.S., C.M.H.), Geisinger, Danville, PA.,Genomic Medicine Institute (M.L.B.S., M.M., M.A.K., A.H.B., A.C.S.), Geisinger, Danville, PA
| | - Christopher M Haggerty
- Department of Translational Data Science and Informatics (E.D.C., C.D.N., B.K.F., C.M.H.), Geisinger, Danville, PA.,The Heart Institute (D.B., A.A., M.E.M., B.K.F., A.C.S., C.M.H.), Geisinger, Danville, PA
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15
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Godino L, Varesco L, Bruno W, Bruzzone C, Battistuzzi L, Franiuk M, Miccoli S, Bertonazzi B, Graziano C, Seri M, Turchetti D. Preferences of Italian patients for return of secondary findings from clinical genome/exome sequencing. J Genet Couns 2020; 30:665-675. [PMID: 33142017 DOI: 10.1002/jgc4.1350] [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: 05/07/2020] [Revised: 09/28/2020] [Accepted: 09/28/2020] [Indexed: 02/03/2023]
Abstract
Exome/genome sequencing (ES/GS) is increasingly becoming routine in clinical genetic diagnosis, yet issues regarding how to disclose and manage secondary findings (SFs) remain to be addressed, and limited evidence is available on patients' preferences. We carried out semi-structured interviews with 307 individuals undergoing clinical genetic testing to explore their preferences for return of SFs in the hypothetical scenario that their test would be performed using ES/GS. Participants were 254 females (82.7%) and 53 males (17.3%), aged 18-86 years; 73.9% (81.1% of those with lower education levels) reported no prior knowledge of ES/GS. Prior knowledge of ES/GS was more common among patients tested for Mendelian conditions (34.5%), compared to those undergoing cancer genetic testing (22.3%) or carrier screening (7.4%). Despite this reported lack of knowledge, most participants (213, 69.6%) stated they would prefer to be informed of all possible results. Reasons in favor of disclosure included wanting to be aware of any risks (168; 83.6%) and to help relatives (23; 11.4%), but also hope that preventive measures might become available in the future (10, 5%). Conversely, potential negative impact on quality of life was the commonest motivation against disclosure. Among 179 participants seen for cancer genetic counseling who were interviewed again after test disclosure, 81.9% had not heard about ES/GS in the meantime; however, the proportion of participants opting for disclosure of any variants was lower (116; 64.8%), with 36 (20.1%) changing opinion compared to the first interview. Based on these findings, we conclude that genetic counseling for ES/GS should involve enhanced education and decision-making support to enable informed consent to SFs disclosure.
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Affiliation(s)
- Lea Godino
- Division of Medical Genetics, Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy.,Dipartimento di Scienze Mediche e Chirurgiche: Centro di Ricerca sui Tumori Ereditari, Università di Bologna, Bologna, Italy
| | - Liliana Varesco
- UOS Tumori Ereditari, IRCCS Ospedale Policlinico San Martino, Genova, Italy
| | - William Bruno
- SSD Genetica dei Tumori Rari, IRCCS Ospedale Policlinico San Martino, Genova - Dipartimento di Medicina Interna e Specialità Mediche, Università degli Studi di Genova, Genova, Italy
| | - Carla Bruzzone
- UOS Tumori Ereditari, IRCCS Ospedale Policlinico San Martino, Genova, Italy
| | - Linda Battistuzzi
- Dipartimento di Informatica, Bioingegneria, Robotica e Ingegneria dei Sistemi, Università degli Studi di Genova, Genova, Italy
| | - Marzena Franiuk
- UOS Tumori Ereditari, IRCCS Ospedale Policlinico San Martino, Genova, Italy
| | - Sara Miccoli
- Division of Medical Genetics, Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy.,Dipartimento di Scienze Mediche e Chirurgiche: Centro di Ricerca sui Tumori Ereditari, Università di Bologna, Bologna, Italy
| | - Benedetta Bertonazzi
- Division of Medical Genetics, Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
| | - Claudio Graziano
- Division of Medical Genetics, Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
| | - Marco Seri
- Division of Medical Genetics, Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
| | - Daniela Turchetti
- Division of Medical Genetics, Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy.,Dipartimento di Scienze Mediche e Chirurgiche: Centro di Ricerca sui Tumori Ereditari, Università di Bologna, Bologna, Italy
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16
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Health-care practitioners' preferences for the return of secondary findings from next-generation sequencing: a discrete choice experiment. Genet Med 2020; 22:2011-2019. [PMID: 32820245 DOI: 10.1038/s41436-020-0927-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Revised: 07/24/2020] [Accepted: 07/27/2020] [Indexed: 11/08/2022] Open
Abstract
PURPOSE Health-care practitioners' (HCPs) preferences for returning secondary findings (SFs) will influence guideline compliance, shared decision-making, and patient health outcomes. This study aimed to estimate HCPs' preferences and willingness to support the return (WTSR) of SFs in Canada. METHODS A discrete choice experiment estimated HCPs' preferences for the following attributes: disease risk, clinical utility, health consequences, prior experience, and patient preference. We analyzed responses with an error component mixed logit model and predicted WTSR using scenario analyses. RESULTS Two hundred fifty participants of 583 completed the questionnaire (completion rate: 42.9%). WTSR was significantly influenced by patient preference and SF outcome characteristics. HCPs' WTSR was 78% (95% confidence interval: 74-81%) when returning SFs with available medical treatment, high penetrance, severe health consequences, and patient's preference for return. Genetics professionals had a higher WTSR than HCPs of other types when returning SFs with clinical utility and patient preference to know. HCPs >55 years of age were more likely to return SFs compared with younger HCPs. CONCLUSION This study identified factors that influence WTSR of SFs and indicates that HCPs make tradeoffs between patient preference and other outcome characteristics. The results can inform clinical scenarios and models aiming to understand shared decision-making, patient and family opportunity to benefit, and cost-effectiveness.
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17
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Reid AE, Ferrer RA, Kadirvel S, Biesecker BB, Lewis KL, Biesecker LG, Klein WMP. Roles of attitudes and injunctive norms in decisional conflict and disclosure following receipt of genome sequencing results. Soc Sci Med 2020; 262:113147. [PMID: 32624263 DOI: 10.1016/j.socscimed.2020.113147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Revised: 05/05/2020] [Accepted: 06/13/2020] [Indexed: 10/24/2022]
Abstract
RATIONALE Individuals who choose to obtain genetic information may learn that their genetic profile confers health risks to themselves or offspring. Individuals may react more negatively to this information when personal attitudes, perceived norms, and/or the decision to receive results conflict with one another. OBJECTIVE We predicted that holding more negative attitudes (personal evaluations) or injunctive norms (perceptions of others' approval) toward obtaining genetic test results would prospectively predict greater conflict about the decision to undergo sequencing and less disclosure of sequencing results to family members. We also expected attitudes and norms to interact, such that attitudes would be negatively associated with decisional conflict and positively associated with disclosure when injunctive norms were positive, but weakly associated with outcomes when injunctive norms were negative. METHOD Participants (N=312) were enrolled in a genomic sequencing trial focused on identifying carrier genetic variants, reflecting a variant that might affect their biological children's or grandchildren's health. Participants reported attitudes and injunctive norms, underwent sequencing, and later received results indicating carrier status for at least one variant. Decisional conflict was assessed at immediate post-test, and 1- and 6-month follow-ups. Disclosure of results to children and siblings were assessed at 1 and 6 months. RESULTS In structural equation models with covariates, attitudes were negatively associated with post-test and 1-month decisional conflict. Injunctive norms were negatively associated with decisional conflict at 1 and 6 months and positively associated with disclosure to children and siblings at 1 month. The significant attitudes by injunctive norms interaction predicting post-test decisional conflict supported lower decisional conflict when attitudes, norms, and the decision to receive results were all aligned. Exploratory analyses supported indirect effects of attitudes and norms on 6-month sibling disclosure via 1- month decisional conflict. CONCLUSION Results support roles of psychosocial factors in decisional conflict and disclosure after receiving sequencing results.
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Affiliation(s)
- Allecia E Reid
- Department of Psychological and Brain Sciences, University of Massachusetts, Amherst, USA.
| | | | - Sanjana Kadirvel
- Department of Psychological and Brain Sciences, University of Massachusetts, Amherst, USA
| | | | - Katie L Lewis
- National Human Genome Research Institute, National Institutes of Health, USA
| | - Leslie G Biesecker
- National Human Genome Research Institute, National Institutes of Health, USA
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Wynn J, Wei W, Li X, So YS, Bakken S, Weng C, Chung WK. User engagement with web-based genomics education videos and implications for designing scalable patient education materials. AMIA ... ANNUAL SYMPOSIUM PROCEEDINGS. AMIA SYMPOSIUM 2020; 2019:923-932. [PMID: 32308889 PMCID: PMC7153116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Genomic medicine has created an urgent need for scalable genomic education. One promising approach is self-guided learning platforms. Understanding how these platforms are used is critical to guide their effective development and implementation. This study contributes a log-based method to study user engagement with online genomic educational videos among participants in a genomic screening study. We collected baseline demographics, logged participant usage and compared pre- and post-education genomic knowledge. Participants (N=390) who chose website access differed from those who declined access (N=81) and were more likely to be non-Latino, English speaking, younger, and have higher educational attainment. Only 45% who accessed the website viewed at least one video. The average video exposure time was 12 minutes. Longer exposure was not associated with an improvement in the user's genomic knowledge. Our study and future studies of user analytics should be used to guide the development of effective, scalable genomic education methods.
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Affiliation(s)
- Julia Wynn
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY
- Ms. Wynn and Dr. Wei contributed equally to this work b Dr. Chung and Dr. Weng contributed equally to this work
| | - Wei Wei
- Department of Biomedical Informatics, Columbia University Irving Medical Center, New York, NY, USA
- Ms. Wynn and Dr. Wei contributed equally to this work b Dr. Chung and Dr. Weng contributed equally to this work
| | - Xinhang Li
- Department of Biomedical Informatics, Columbia University Irving Medical Center, New York, NY, USA
| | - Yat S So
- Irving Institute of Clinical and Translational Research, Columbia University Irving Medical Center, New York, NY, USA
| | - Suzanne Bakken
- Department of Biomedical Informatics, Columbia University Irving Medical Center, New York, NY, USA
- School of Nursing, Columbia University Irving Medical Center, New York, NY, USA
| | - Chunhua Weng
- Department of Biomedical Informatics, Columbia University Irving Medical Center, New York, NY, USA
- Dr. Chung and Dr. Weng contributed equally to this work
| | - Wendy K Chung
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY
- Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA
- Dr. Chung and Dr. Weng contributed equally to this work
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Rowe CA, Wright CF. Expanded universal carrier screening and its implementation within a publicly funded healthcare service. J Community Genet 2019; 11:21-38. [PMID: 31828606 PMCID: PMC6962405 DOI: 10.1007/s12687-019-00443-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Accepted: 10/28/2019] [Indexed: 11/25/2022] Open
Abstract
Carrier screening, a well-established clinical initiative, has been slow to take advantage of the new possibilities offered by high-throughput next generation sequencing technologies. There is evidence of significant benefit in expanding carrier screening to include multiple autosomal recessive conditions and offering a ‘universal’ carrier screen that could be used for a pan-ethnic population. However, the challenges of implementing such a programme and the difficulties of demonstrating efficacy worthy of public health investment are significant barriers. In order for such a programme to be successful, it would need to be applicable and acceptable to the population, which may be ethnically and culturally diverse. There are significant practical and ethical implications associated with determining which variants, genes and conditions to include whilst maintaining adequate sensitivity and accuracy. Although preconception screening would maximise the potential benefits from universal carrier screening, the resource implications of different modes of delivery need to be carefully evaluated and balanced against maximising reproductive autonomy and ensuring equity of access. Currently, although a number of existing initiatives are increasing access to carrier screening, there is insufficient evidence to inform the development of a publicly funded, expanded, universal carrier screening programme that would justify investment over other healthcare interventions.
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Affiliation(s)
- Charlotte A Rowe
- University of Exeter, St Luke's Campus, 79 Heavitree Rd, Exeter, EX1 1TX, UK. .,Post Graduate Centre, Royal Cornwall Hospitals NHS Trust, Treliske, Truro, Cornwall, TR1 3LQ, UK.
| | - Caroline F Wright
- Institute of Biomedical and Clinical Science, College of Medicine and Health, University of Exeter, RILD Building, RD&E, Barrack Road, Exeter, EX2 5DW, UK.
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20
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Akras Z, Bungo B, Leach BH, Marquard J, Ahluwalia M, Carraway H, Grivas P, Sohal DP, Funchain P. Primer on Hereditary Cancer Predisposition Genes Included Within Somatic Next-Generation Sequencing Panels. JCO Precis Oncol 2019; 3:1-11. [DOI: 10.1200/po.18.00258] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
PURPOSE It has been estimated that 5% to 10% of cancers are due to hereditary causes. Recent data sets indicate that the incidence of hereditary cancer may be as high as 17.5% in patients with cancer, and a notable subset is missed if screening is solely by family history and current syndrome-based testing guidelines. Identification of germline variants has implications for both patients and their families. There is currently no comprehensive overview of cancer susceptibility genes or inclusion of these genes in commercially available somatic testing. We aimed to summarize genes linked to hereditary cancer and the somatic and germline panels that include such genes. METHODS Germline predisposition genes were chosen if commercially available for testing. Penetrance was defined as low, moderate, or high according to whether the gene conferred a 0% to 20%, 20% to 50%, or 50% to 100% lifetime risk of developing the cancer or, when percentages were not available, was estimated on the basis of existing literature descriptions. RESULTS We identified a total of 89 genes linked to hereditary cancer predisposition, and we summarized these genes alphabetically and by organ system. We considered four germline and six somatic commercially available panel tests and quantified the coverage of germline genes across them. Comparison between the number of genes that had germline importance and the number of genes included in somatic testing showed that many but not all germline genes are tested by frequently used somatic panels. CONCLUSION The inclusion of cancer-predisposing genes in somatic variant testing panels makes incidental germline findings likely. Although somatic testing can be used to screen for germline variants, this strategy is inadequate for comprehensive screening. Access to genetic counseling is essential for interpretation of germline implications of somatic testing and implementation of appropriate screening and follow-up.
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21
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Watkins NA, Charames GS. Implementing Next-Generation Sequencing in Clinical Practice. J Appl Lab Med 2019; 3:338-341. [PMID: 33636945 DOI: 10.1373/jalm.2017.025791] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Accepted: 06/29/2018] [Indexed: 01/09/2023]
Affiliation(s)
- Nicholas A Watkins
- Department of Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, Canada.,Departments of Molecular Genetics
| | - George S Charames
- Department of Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, Canada.,Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada.,Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Canada
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22
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Lo Surdo P, Calderone A, Iannuccelli M, Licata L, Peluso D, Castagnoli L, Cesareni G, Perfetto L. DISNOR: a disease network open resource. Nucleic Acids Res 2019; 46:D527-D534. [PMID: 29036667 PMCID: PMC5753342 DOI: 10.1093/nar/gkx876] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2017] [Accepted: 09/25/2017] [Indexed: 12/13/2022] Open
Abstract
DISNOR is a new resource that aims at exploiting the explosion of data on the identification of disease-associated genes to assemble inferred disease pathways. This may help dissecting the signaling events whose disruption causes the pathological phenotypes and may contribute to build a platform for precision medicine. To this end we combine the gene-disease association (GDA) data annotated in the DisGeNET resource with a new curation effort aimed at populating the SIGNOR database with causal interactions related to disease genes with the highest possible coverage. DISNOR can be freely accessed at http://DISNOR.uniroma2.it/ where >3700 disease-networks, linking ∼2600 disease genes, can be explored. For each disease curated in DisGeNET, DISNOR links disease genes by manually annotated causal relationships and offers an intuitive visualization of the inferred ‘patho-pathways’ at different complexity levels. User-defined gene lists are also accepted in the query pipeline. In addition, for each list of query genes—either annotated in DisGeNET or user-defined—DISNOR performs a gene set enrichment analysis on KEGG-defined pathways or on the lists of proteins associated with the inferred disease pathways. This function offers additional information on disease-associated cellular pathways and disease similarity.
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Affiliation(s)
- Prisca Lo Surdo
- Bioinformatics and Computational Biology Unit, Department of Biology, University of Rome 'Tor Vergata', 00133 Rome, Italy
| | - Alberto Calderone
- Bioinformatics and Computational Biology Unit, Department of Biology, University of Rome 'Tor Vergata', 00133 Rome, Italy
| | - Marta Iannuccelli
- Bioinformatics and Computational Biology Unit, Department of Biology, University of Rome 'Tor Vergata', 00133 Rome, Italy
| | - Luana Licata
- Bioinformatics and Computational Biology Unit, Department of Biology, University of Rome 'Tor Vergata', 00133 Rome, Italy
| | - Daniele Peluso
- Bioinformatics and Computational Biology Unit, Department of Biology, University of Rome 'Tor Vergata', 00133 Rome, Italy.,Laboratory of Bioinformatic, IRCCS Fondazione Santa Lucia, 00143 Rome, Italy
| | - Luisa Castagnoli
- Bioinformatics and Computational Biology Unit, Department of Biology, University of Rome 'Tor Vergata', 00133 Rome, Italy
| | - Gianni Cesareni
- Bioinformatics and Computational Biology Unit, Department of Biology, University of Rome 'Tor Vergata', 00133 Rome, Italy
| | - Livia Perfetto
- Bioinformatics and Computational Biology Unit, Department of Biology, University of Rome 'Tor Vergata', 00133 Rome, Italy
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23
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McVeigh E, Jones H, Black G, Hall G. The psychosocial and service delivery impact of genomic testing for inherited retinal dystrophies. J Community Genet 2019; 10:425-434. [PMID: 30680631 PMCID: PMC6591333 DOI: 10.1007/s12687-019-00406-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Accepted: 01/02/2019] [Indexed: 11/25/2022] Open
Abstract
Next-generation sequencing (NGS) provides diagnostic information for many rare conditions. The evolution of NGS for panel, exome, and genome testing is set to be the platform for transforming genomic diagnosis in the National Health Service (NHS). Inherited retinal dystrophies (IRDs) are a highly genetically heterogeneous disease group causing progressive visual impairment. IRDs are ideal for an NGS panel approach due to phenotypic overlap and were one of the first diagnostic panels to be developed in the NHS. While diagnostic yield for patients with IRD has improved significantly with NGS, a proportion of patients remain without a diagnosis. The clinical value of NGS testing is well understood; however, the patient experience of panel testing is not well documented. Semi-structured qualitative telephone interviews were conducted with 23 participants with IRD who had undergone NGS testing. Interviews were transcribed verbatim and analysed using interpretative phenomenological analysis. Participants' experiences were interpreted to explore the psychosocial and service delivery impact of this testing technology, inclusive of those who received a pathogenic, negative, carrier status or variant of uncertain significance result. Collectively, three core themes were identified: (1) the journey towards a genomic diagnosis, (2) the impact of NGS testing, (3) service delivery of NGS tests. Disclosure of results had no reported adverse implications. Participants appreciated an open discussion about the potential for an uncertain or unexpected result, prior to testing. They valued pre-test counselling discussions, expert opinions and on-going care from genomic services.
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Affiliation(s)
- Eleanor McVeigh
- Clinical Genetics Service, Birmingham Women's and Children's NHS Foundation Trust, Birmingham Women's Hospital, Birmingham, UK.
| | - Harriet Jones
- Clinical Genetics Service, Birmingham Women's and Children's NHS Foundation Trust, Birmingham Women's Hospital, Birmingham, UK.
- Genetics Health Service, Northern Hub, Auckland City Hospital, Aukland, New Zealand.
| | - Graeme Black
- Manchester Centre for Genomic Medicine, Central Manchester University Hospitals NHS Foundation Trust, St Mary's Hospital, Manchester, UK
| | - Georgina Hall
- Manchester Centre for Genomic Medicine, Central Manchester University Hospitals NHS Foundation Trust, St Mary's Hospital, Manchester, UK
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24
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Wright CF, Ware JS, Lucassen AM, Hall A, Middleton A, Rahman N, Ellard S, Firth HV. Genomic variant sharing: a position statement. Wellcome Open Res 2019; 4:22. [PMID: 31886409 PMCID: PMC6913213 DOI: 10.12688/wellcomeopenres.15090.2] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/01/2019] [Indexed: 12/12/2022] Open
Abstract
Sharing de-identified genetic variant data is essential for the practice of genomic medicine and is demonstrably beneficial to patients. Robust genetic diagnoses that inform medical management cannot be made accurately without reference to genetic test results from other patients, as well as population controls. Errors in this process can result in delayed, missed or erroneous diagnoses, leading to inappropriate or missed medical interventions for the patient and their family. The benefits of sharing individual genetic variants, and the harms of not sharing them, are numerous and well-established. Databases and mechanisms already exist to facilitate deposition and sharing of pseudonomised genetic variants, but clarity and transparency around best practice is needed to encourage widespread use, prevent inconsistencies between different communities, maximise individual privacy and ensure public trust. We therefore recommend that widespread sharing of a small number of individual genetic variants associated with limited clinical information should become standard practice in genomic medicine. Information robustly linking genetic variants with specific conditions is fundamental biological knowledge, not personal information, and therefore should not require consent to share. For additional case-level detail about individual patients or more extensive genomic information, which is often essential for clinical interpretation, it may be more appropriate to use a controlled-access model for data sharing, with the ultimate aim of making as much information as open and de-identified as possible with appropriate consent.
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Affiliation(s)
- Caroline F. Wright
- Institute of Biomedical and Clinical Science, University of Exeter, Exeter, UK
| | - James S. Ware
- National Heart and Lung Institute, Imperial Centre for Translational and Experimental Medicine, London, UK
| | - Anneke M. Lucassen
- Department of Clinical Ethics and Law, Faculty of Medicine, University of Southampton, Southampton, UK
| | | | - Anna Middleton
- Faculty of Education, University of Cambridge, Cambridge, UK
- Connecting Science, Wellcome Genome Campus, Cambridge, UK
| | - Nazneen Rahman
- Division of Genetics and Epidemiology, Institute of Cancer Research, UK, London, UK
| | - Sian Ellard
- Institute of Biomedical and Clinical Science, University of Exeter, Exeter, UK
| | - Helen V. Firth
- Department of Clinical Genetics, University of Cambridge Addenbrooke's Hospital Cambridge, Cambridge, UK
- Wellcome Trust Sanger Institute, Cambridge, UK
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25
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Wright CF, Ware JS, Lucassen AM, Hall A, Middleton A, Rahman N, Ellard S, Firth HV. Genomic variant sharing: a position statement. Wellcome Open Res 2019. [DOI: 10.12688/wellcomeopenres.15090.1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Sharing de-identified genetic variant data is essential for the practice of genomic medicine and is demonstrably beneficial to patients. Robust genetic diagnoses that inform medical management cannot be made accurately without reference to genetic test results from other patients, as well as population controls. Errors in this process can result in delayed, missed or erroneous diagnoses, leading to inappropriate or missed medical interventions for the patient and their family. The benefits of sharing individual genetic variants, and the harms of not sharing them, are numerous and well-established. Databases and mechanisms already exist to facilitate deposition and sharing of pseudonomised genetic variants, but clarity and transparency around best practice is needed to encourage widespread use, prevent inconsistencies between different communities, maximise individual privacy and ensure public trust. We therefore recommend that widespread sharing of a small number of individual genetic variants associated with limited clinical information should become standard practice in genomic medicine. Information robustly linking genetic variants with specific conditions is fundamental biological knowledge, not personal information, and therefore should not require consent to share. For additional case-level detail about individual patients or more extensive genomic information, which is often essential for clinical interpretation, it may be more appropriate to use a controlled-access model for data sharing, with the ultimate aim of making as much information as open and de-identified as possible with appropriate consent.
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26
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Lantos JD. Ethical and Psychosocial Issues in Whole Genome Sequencing (WGS) for Newborns. Pediatrics 2019; 143:S1-S5. [PMID: 30600264 DOI: 10.1542/peds.2018-1099b] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 07/03/2018] [Indexed: 11/24/2022] Open
Abstract
In this article, I review some of the ethical issues that have arisen in the past when genetic testing has been done in newborns. I then suggest how whole genome sequencing may raise a new set of issues. Finally, I introduce a series of other articles in which the authors address different controversies that arise when whole genome sequencing is used in the newborn period.
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Affiliation(s)
- John D Lantos
- Bioethics Center, Children's Mercy Hospital and University of Missouri - Kansas City, Kansas City, Missouri
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27
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Yang M, Fang X, Li J, Xu D, Xiao Q, Yu S, Hu H, Weng S, Ding K, Yuan Y. Afatinib treatment for her-2 amplified metastatic colorectal cancer based on patient-derived xenograft models and next generation sequencing. Cancer Biol Ther 2018; 20:391-396. [PMID: 30307354 DOI: 10.1080/15384047.2018.1529120] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND Substantial progress has been made in metastatic colorectal cancer (mCRC) treatment, but there is still a fraction of patients cannot find any effective therapeutic strategy after guideline-recommended standard chemotherapy and molecular targeted therapy. CASE PRESENTATION Here we present a KRAS/NRAS/BRAF wild-type mCRC patient who has been previously treated with FOLFIRI (fluorouracil, leucovorin, and irinotecan), XELOX (capecitabine and oxaliplatin), cetuximab and bevacizumab, and then received the next generation sequencing (NGS) and whose metastatic subcutaneous nodule was resected to generate patient-derived xenograft (PDX) models. The NGS revealed HER-2 amplification as well as an activating mutation S310F and PDX models tested several drugs finding that afatinib was the optimal agent with notable efficacy and well tolerance among 6 regimens. Therefore, this patient started to take afatinib orally and achieved 3 months progression-free survival (PFS) and relief of clinical symptoms without severe adverse effects. CONCLUSIONS NGS and PDX models have great significance for precision and individualized medicine in the mCRC treatment, especially for patients whose diseases have been progressed after multiline standard therapies.
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Affiliation(s)
- Mengyuan Yang
- a Department of Medical Oncology, the Second Affiliated Hospital , Zhejiang University School of Medicine , Hangzhou , Zhejiang , China
| | - Xuefeng Fang
- a Department of Medical Oncology, the Second Affiliated Hospital , Zhejiang University School of Medicine , Hangzhou , Zhejiang , China
| | - Jun Li
- b Department of Surgical Oncology, the Second Affiliated Hospital , Zhejiang University School of Medicine , Hangzhou , Zhejiang , China
| | - Dong Xu
- b Department of Surgical Oncology, the Second Affiliated Hospital , Zhejiang University School of Medicine , Hangzhou , Zhejiang , China
| | - Qian Xiao
- b Department of Surgical Oncology, the Second Affiliated Hospital , Zhejiang University School of Medicine , Hangzhou , Zhejiang , China
| | - Shaojun Yu
- b Department of Surgical Oncology, the Second Affiliated Hospital , Zhejiang University School of Medicine , Hangzhou , Zhejiang , China
| | - Hanguang Hu
- a Department of Medical Oncology, the Second Affiliated Hospital , Zhejiang University School of Medicine , Hangzhou , Zhejiang , China
| | - Shanshan Weng
- a Department of Medical Oncology, the Second Affiliated Hospital , Zhejiang University School of Medicine , Hangzhou , Zhejiang , China
| | - Kefeng Ding
- b Department of Surgical Oncology, the Second Affiliated Hospital , Zhejiang University School of Medicine , Hangzhou , Zhejiang , China
| | - Ying Yuan
- a Department of Medical Oncology, the Second Affiliated Hospital , Zhejiang University School of Medicine , Hangzhou , Zhejiang , China
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28
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Affiliation(s)
- David R Adams
- From the Office of the Clinical Director, National Human Genome Research Institute, and the Undiagnosed Diseases Program, National Institutes of Health, Bethesda, MD (D.R.A.); and the Department of Molecular and Human Genetics, Baylor College of Medicine, and Baylor Genetics - both in Houston (C.M.E.)
| | - Christine M Eng
- From the Office of the Clinical Director, National Human Genome Research Institute, and the Undiagnosed Diseases Program, National Institutes of Health, Bethesda, MD (D.R.A.); and the Department of Molecular and Human Genetics, Baylor College of Medicine, and Baylor Genetics - both in Houston (C.M.E.)
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29
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Johnston J, Lantos JD, Goldenberg A, Chen F, Parens E, Koenig BA. Sequencing Newborns: A Call for Nuanced Use of Genomic Technologies. Hastings Cent Rep 2018; 48 Suppl 2:S2-S6. [PMID: 30133723 PMCID: PMC6901349 DOI: 10.1002/hast.874] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Many scientists and doctors hope that affordable genome sequencing will lead to more personalized medical care and improve public health in ways that will benefit children, families, and society more broadly. One hope in particular is that all newborns could be sequenced at birth, thereby setting the stage for a lifetime of medical care and self-directed preventive actions tailored to each child's genome. Indeed, commentators often suggest that universal genome sequencing is inevitable. Such optimism can come with the presumption that discussing the potential limits, cost, and downsides of widespread application of genomic technologies is pointless, excessively pessimistic, or overly cautious. We disagree. Given the pragmatic challenges associated with determining what sequencing data mean for the health of individuals, the economic costs associated with interpreting and acting on such data, and the psychosocial costs of predicting one's own or one's child's future life plans based on uncertain testing results, we think this hope and optimism deserve to be tempered. In the analysis that follows, we distinguish between two reasons for using sequencing: to diagnose individual infants who have been identified as sick and to screen populations of infants who appear to be healthy. We also distinguish among three contexts in which sequencing for either diagnosis or screening could be deployed: in clinical medicine, in public health programs, and as a direct-to-consumer service. Each of these contexts comes with different professional norms, policy considerations, and public expectations. Finally, we distinguish between two main types of genome sequencing: targeted sequencing, where only specific genes are sequenced or analyzed, and whole-exome or whole-genome sequencing, where all the DNA or all the coding segments of all genes are sequenced and analyzed. In a symptomatic newborn, targeted or genome-wide sequencing can help guide other tests for diagnosis or for specific treatment that is urgently needed. Clinicians use the infant's symptoms (or phenotype) to interrogate the sequencing data. These same complexities and uncertainties, however, limit the usefulness of genome-wide sequencing as a population screening tool. While we recognize considerable benefit in using targeted sequencing to screen for or detect specific conditions that meet the criteria for inclusion in newborn screening panels, use of genome-wide sequencing as a sole screening tool for newborns is at best premature. We conclude that sequencing technology can be beneficially used in newborns when that use is nuanced and attentive to context.
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Genomic information and a person's right not to know: A closer look at variations in hypothetical informational preferences in a German sample. PLoS One 2018; 13:e0198249. [PMID: 29924808 PMCID: PMC6010220 DOI: 10.1371/journal.pone.0198249] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2016] [Accepted: 05/16/2018] [Indexed: 01/02/2023] Open
Abstract
In clinical practice and in research, there is an ongoing debate on how to return incidental and secondary findings of genetic tests to patients and research participants. Previous investigations have found that most of the people most of the time are in favor of full disclosure of results. Yet, the option to reject disclosure, based on the so-called right not to know, can be valuable especially for some vulnerable subgroups of recipients. In the present study we investigated variations in informational preferences in the context of genetic testing in a large and diverse German sample. This survey examined health care professionals, patients, participants of genetic counseling sessions and members of the general population (N = 518). Survey participants were assessed regarding their openness to learning about findings under various hypothetical scenarios, as well as their attitudes about the doctor-patient-relationship in a disclosure situation and about informational transfer to third parties. While the majority of participants wanted to learn about their findings, the extent of support of disclosure varied with features of the hypothetical diagnostic scenarios (e.g., controllability of disease; abstract vs. concrete scenario description) and demographic characteristics of the subjects. For example, subjects with higher levels of education were more selective with regards to the kind of information they want to receive than those with lower levels of education. We discuss implications of these findings for the debate about the right not to know and for the clinical practice of informed consent procedures.
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Reid AE, Taber JM, Ferrer RA, Biesecker BB, Lewis KL, Biesecker LG, Klein WMP. Associations of perceived norms with intentions to learn genomic sequencing results: Roles for attitudes and ambivalence. Health Psychol 2018; 37:553-561. [PMID: 29745680 PMCID: PMC5962407 DOI: 10.1037/hea0000579] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
OBJECTIVE Genomic sequencing is becoming increasingly accessible, highlighting the need to understand the social and psychological factors that drive interest in receiving testing results. These decisions may depend on perceived descriptive norms (how most others behave) and injunctive norms (what is approved of by others). We predicted that descriptive norms would be directly associated with intentions to learn genomic sequencing results, whereas injunctive norms would be associated indirectly, via attitudes. These differential associations with intentions versus attitudes were hypothesized to be strongest when individuals held ambivalent attitudes toward obtaining results. METHOD Participants enrolled in a genomic sequencing trial (n = 372) reported intentions to learn medically actionable, nonmedically actionable, and carrier sequencing results. Descriptive norms items referenced other study participants. Injunctive norms were analyzed separately for close friends and family members. Attitudes, attitudinal ambivalence, and sociodemographic covariates were also assessed. RESULTS In structural equation models, both descriptive norms and friend injunctive norms were associated with intentions to receive all sequencing results (ps < .004). Attitudes consistently mediated all friend injunctive norms-intentions associations, but not the descriptive norms-intentions associations. Attitudinal ambivalence moderated the association between friend injunctive norms (p ≤ .001), but not descriptive norms (p = .16), and attitudes. Injunctive norms were significantly associated with attitudes when ambivalence was high, but were unrelated when ambivalence was low. Results replicated for family injunctive norms. CONCLUSIONS Descriptive and injunctive norms play roles in genomic sequencing decisions. Considering mediators and moderators of these processes enhances ability to optimize use of normative information to support informed decision making. (PsycINFO Database Record
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Affiliation(s)
| | | | | | | | - Katie L. Lewis
- National Human, Research Institute, National Institutes of Health
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32
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Wynn J, Lewis K, Amendola LM, Bernhardt BA, Biswas S, Joshi M, McMullen C, Scollon S. Clinical providers' experiences with returning results from genomic sequencing: an interview study. BMC Med Genomics 2018; 11:45. [PMID: 29739461 PMCID: PMC5941324 DOI: 10.1186/s12920-018-0360-z] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Accepted: 04/19/2018] [Indexed: 12/12/2022] Open
Abstract
Background Current medical practice includes the application of genomic sequencing (GS) in clinical and research settings. Despite expanded use of this technology, the process of disclosure of genomic results to patients and research participants has not been thoroughly examined and there are no established best practices. Methods We conducted semi-structured interviews with 21 genetic and non-genetic clinicians returning results of GS as part of the NIH funded Clinical Sequencing Exploratory Research (CSER) Consortium projects. Interviews focused on the logistics of sessions, participant/patient reactions and factors influencing them, how the sessions changed with experience, and resources and training recommended to return genomic results. Results The length of preparation and disclosure sessions varied depending on the type and number of results and their implications. Internal and external databases, online resources and result review meetings were used to prepare. Respondents reported that participants’ reactions were variable and ranged from enthusiasm and relief to confusion and disappointment. Factors influencing reactions were types of results, expectations and health status. A recurrent challenge was managing inflated expectations about GS. Other challenges included returning multiple, unanticipated and/or uncertain results and navigating a rare diagnosis. Methods to address these challenges included traditional genetic counseling techniques and modifying practice over time in order to provide anticipatory guidance and modulate expectations. Respondents made recommendations to improve access to genomic resources and genetic referrals to prepare future providers as the uptake of GS increases in both genetic and non-genetic settings. Conclusions These findings indicate that returning genomic results is similar to return of results in traditional genetic testing but is magnified by the additional complexity and potential uncertainty of the results. Managing patient expectations, initially identified in studies of informed consent, remains an ongoing challenge and highlights the need to address this issue throughout the testing process. The results of this study will help to guide future providers in the disclosure of genomic results and highlight educational needs and resources necessary to prepare providers. Future research on the patient experience, understanding and follow-up of recommendations is needed to more fully understand the disclosure process. Electronic supplementary material The online version of this article (10.1186/s12920-018-0360-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Julia Wynn
- Department of Pediatrics, Columbia University Medical Center, New York, NY, USA
| | - Katie Lewis
- Medical Genomics and Metabolic Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Laura M Amendola
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Barbara A Bernhardt
- Division of Translational Medicine and Human Genetics, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Sawona Biswas
- Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Manasi Joshi
- The Center for Health Research, Rice University, Houston, TX, USA
| | - Carmit McMullen
- Center for Health Research - Kaiser Permanente Northwest, Portland, OR, USA
| | - Sarah Scollon
- Department of Pediatrics, Baylor College of Medicine, 1102 Bates St. FC 1200, Houston, TX, 77030, USA.
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Burke W, Beskow LM, Trinidad SB, Fullerton SM, Brelsford K. Informed Consent in Translational Genomics: Insufficient Without Trustworthy Governance. THE JOURNAL OF LAW, MEDICINE & ETHICS : A JOURNAL OF THE AMERICAN SOCIETY OF LAW, MEDICINE & ETHICS 2018; 46:79-86. [PMID: 29962827 PMCID: PMC6023399 DOI: 10.1177/1073110518766023] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Neither the range of potential results from genomic research that might be returned to participants nor future uses of stored data and biospecimens can be fully predicted at the outset of a study. Informed consent procedures require clear explanations about how and by whom decisions are made and what principles and criteria apply. To ensure trustworthy research governance, there is also a need for empirical studies incorporating public input to evaluate and strengthen these processes.
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Affiliation(s)
- Wylie Burke
- Department of Bioethics and Humanities, Box 357120, University of Washington, Seattle WA 98195; Work phone: 206-221-5482; Home phone 206-232-6760; Cell phone: 206-619-3191
| | - Laura M Beskow
- Center for Biomedical Ethics and Society, Vanderbilt University Medical Center, 2525 West End Aves, Suite 400, Nashville TN 37203; Work phone: 615-936-2686
| | - Susan Brown Trinidad
- Department of Bioethics and Humanities, Box 357120, University of Washington, Seattle WA 98195; Work phone:206-543-2508;Home phone: 206-842-9241;Cell phone: 360-850-3428
| | - Stephanie M Fullerton
- Department of Bioethics and Humanities, Box 357120, University of Washington, Seattle WA 98195; Work phone: 206-616-1864; Home phone: 206-297-1005; Cell phone: 206-529-7029
| | - Kathleen Brelsford
- Center for Biomedical Ethics and Society, Vanderbilt University Medical Center, 2525 West End Aves, Suite 400, Nashville TN 37203; Work phone: 615-936-2686
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Abstract
The majority of rare diseases affect children, most of whom have an underlying genetic cause for their condition. However, making a molecular diagnosis with current technologies and knowledge is often still a challenge. Paediatric genomics is an immature but rapidly evolving field that tackles this issue by incorporating next-generation sequencing technologies, especially whole-exome sequencing and whole-genome sequencing, into research and clinical workflows. This complex multidisciplinary approach, coupled with the increasing availability of population genetic variation data, has already resulted in an increased discovery rate of causative genes and in improved diagnosis of rare paediatric disease. Importantly, for affected families, a better understanding of the genetic basis of rare disease translates to more accurate prognosis, management, surveillance and genetic advice; stimulates research into new therapies; and enables provision of better support.
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Al Kawam A, Sen A, Datta A, Dickey N. Understanding the Bioinformatics Challenges of Integrating Genomics into Healthcare. IEEE J Biomed Health Inform 2017; 22:1672-1683. [PMID: 29990071 DOI: 10.1109/jbhi.2017.2778263] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Genomic data is paving the way towards personalized healthcare. By unveiling genetic disease-contributing factors, genomic data can aid in the detection, diagnosis, and treatment of a wide range of complex diseases. Integrating genomic data into healthcare is riddled with a wide range of challenges spanning social, ethical, legal, educational, economic, and technical aspects. Bioinformatics is a core integration aspect presenting an overwhelming number of unaddressed challenges. In this paper we tackle the fundamental bioinformatics integration concerns including: genomic data generation, storage, representation, and utilization in conjunction with clinical data. We divide the bioinformatics challenges into a series of seven intertwined integration aspects spanning the areas of informatics, knowledge management, and communication. For each aspect, we provide a detailed discussion of the current research directions, outstanding challenges, and possible resolutions. This paper seeks to help narrow the gap between the genomic applications, which are being predominantly utilized in research settings, and the clinical adoption of these applications.
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Pinto AM, Ariani F, Bianciardi L, Daga S, Renieri A. Exploiting the potential of next-generation sequencing in genomic medicine. Expert Rev Mol Diagn 2017; 16:1037-47. [PMID: 27574853 DOI: 10.1080/14737159.2016.1224181] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
INTRODUCTION The review highlights the impact of next-generation sequencing (NGS) on genomic medicine and the consequences of the progression from a single-gene panel technology to a whole exome sequencing approach. AREAS COVERED We brought together literature-based evidences, personal unpublished data and clinical experience to provide a critical overview of the impact of NGS on our daily clinical practice. Expert commentary: NGS has changed the role of clinical geneticist and has broadened the view accomplishing a transition from a monogenic Mendelian perspective to an oligogenic approach to disorders. Thus, it is a compelling new expertise which combines clinical evaluation with big omics data interpretation and moves forward to phenotype re-evaluation in light of data analysis. We introduced the term, 'exotyping', to highlight this holistic approach. Further, the review discusses the impact that the combination of genetic reprogramming and transcriptome analysis will have on the discovery of evidence-based therapies.
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Affiliation(s)
- Anna Maria Pinto
- a Medical Genetics , University of Siena , Siena , Italy.,b Genetica Medica , Azienda Ospedaliera Universitaria Senese , Siena , Italy
| | - Francesca Ariani
- a Medical Genetics , University of Siena , Siena , Italy.,b Genetica Medica , Azienda Ospedaliera Universitaria Senese , Siena , Italy
| | | | - Sergio Daga
- a Medical Genetics , University of Siena , Siena , Italy
| | - Alessandra Renieri
- a Medical Genetics , University of Siena , Siena , Italy.,b Genetica Medica , Azienda Ospedaliera Universitaria Senese , Siena , Italy
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37
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Chen SC, Wasserman DT. A Framework for Unrestricted Prenatal Whole-Genome Sequencing: Respecting and Enhancing the Autonomy of Prospective Parents. THE AMERICAN JOURNAL OF BIOETHICS : AJOB 2017; 17:3-18. [PMID: 27996923 DOI: 10.1080/15265161.2016.1251632] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Noninvasive, prenatal whole genome sequencing (NIPW) may be a technological reality in the near future, making available a vast array of genetic information early in pregnancy at no risk to the fetus or mother. Many worry that the timing, safety, and ease of the test will lead to informational overload and reproductive consumerism. The prevailing response among commentators has been to restrict conditions eligible for testing based on medical severity, which imposes disputed value judgments and devalues those living with eligible conditions. To avoid these difficulties, we propose an unrestricted testing policy, under which prospective parents could obtain information on any variant of known significance after a careful informed consent process that uses an interactive decision aid to deliver a mandatory presentation on the purposes, techniques, and limitations of genomic testing, as well as optional resources for reflection and consultation. This process would encourage thoughtful, informed deliberation by prospective parents before deciding whether or how to use NIPW.
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McGraw SA, Garber J, Jänne PA, Lindeman N, Oliver N, Sholl LM, Van Allen EM, Wagle N, Garraway LA, Joffe S, Gray SW. The fuzzy world of precision medicine: deliberations of a precision medicine tumor board. Per Med 2017; 14:37-50. [PMID: 28757884 PMCID: PMC5480788 DOI: 10.2217/pme-2016-0074] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Accepted: 10/21/2016] [Indexed: 01/18/2023]
Abstract
AIM To understand how a cancer precision medicine tumor board (CPM-TB) made choices about return of results. MATERIALS & METHODS Observed CPM-TB deliberations and completed in-depth interviews with committee members. RESULTS Responding to complex evidence of ambiguous significance, deliberations of the CPM-TB were predicated on analytic validity and clinical utility. Members had concerns both about potential harms due to returning results based on weak evidence and about withholding potentially meaningful results. Group dynamics and the clinical experiences of individual committee members shaped their work. CONCLUSION Both scientific evidence and the social context surrounding deliberations of a CPM-TB influenced decisions about return of results. Subjective elements, while present in any scientific endeavor, may carry more weight in the face of ambiguous findings.
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Affiliation(s)
| | - Judy Garber
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Department of Medicine, Brigham & Women's Hospital, Boston, MA, USA
| | - Pasi A Jänne
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Department of Medicine, Brigham & Women's Hospital, Boston, MA, USA
| | - Neal Lindeman
- Harvard Medical School, Boston, MA, USA
- Department of Pathology, Brigham & Woman's Hospital, Boston, MA, USA
| | - Nelly Oliver
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Lynette M Sholl
- Harvard Medical School, Boston, MA, USA
- Department of Pathology, Brigham & Woman's Hospital, Boston, MA, USA
| | - Eliezer M Van Allen
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Department of Medicine, Brigham & Women's Hospital, Boston, MA, USA
- Broad Institute, Cambridge, MA, USA
| | - Nikhil Wagle
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Department of Medicine, Brigham & Women's Hospital, Boston, MA, USA
- Broad Institute, Cambridge, MA, USA
| | - Levi A Garraway
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Department of Medicine, Brigham & Women's Hospital, Boston, MA, USA
- Broad Institute, Cambridge, MA, USA
| | - Steven Joffe
- Department of Medical Ethics & Health Policy, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
- Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Stacy W Gray
- Department of Population Sciences, City of Hope Comprehensive Cancer Center, Duarte, CA, USA
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Engagement and communication among participants in the ClinSeq Genomic Sequencing Study. Genet Med 2016; 19:98-103. [PMID: 27763633 DOI: 10.1038/gim.2016.71] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Accepted: 04/21/2016] [Indexed: 12/15/2022] Open
Abstract
PURPOSE As clinical genome sequencing expand its reach, understanding how individuals engage with this process are of critical importance. In this study, we aimed to describe internal engagement and its correlates among a ClinSeq cohort of adults consented to genome sequencing and receipt of results. METHODS This study was framed using the precaution adoption process model (PAPM), in which knowledge predicts engagement and engagement predicts subsequent behaviors. Prior to receipt of sequencing results, 630 participants in the study completed a baseline survey. Engagement was assessed as the frequency with which participants thought about their participation in ClinSeq since enrollment. RESULTS Results were consistent with the PAPM: those with higher genomics knowledge reported higher engagement (r = 0.13, P = 0.001) and those who were more engaged reported more frequent communication with their physicians (r = 0.28, P < 0.001) and family members (r = 0.35, P < 0.001) about ClinSeq. Characteristics of those with higher engagement included poorer overall health (r = -0.13, P = 0.002), greater seeking of health information (r = 0.16, P < 0.001), and more recent study enrollment (r = -0.21, P < 0.001). CONCLUSION These data support the importance of internal engagement in communication related to genomic sequencing.Genet Med 19 1, 98-103.
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40
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Pinard A, Salgado D, Desvignes JP, Rai G, Hanna N, Arnaud P, Guien C, Martinez M, Faivre L, Jondeau G, Boileau C, Zaffran S, Béroud C, Collod-Béroud G. WES/WGS Reporting of Mutations from Cardiovascular "Actionable" Genes in Clinical Practice: A Key Role for UMD Knowledgebases in the Era of Big Databases. Hum Mutat 2016; 37:1308-1317. [PMID: 27647783 DOI: 10.1002/humu.23119] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2016] [Revised: 08/22/2016] [Accepted: 09/12/2016] [Indexed: 12/27/2022]
Abstract
High-throughput next-generation sequencing such as whole-exome and whole-genome sequencing are being rapidly integrated into clinical practice. The use of these techniques leads to the identification of secondary variants for which decisions about the reporting or not to the patient need to be made. The American College of Medical Genetics and Genomics recently published recommendations for the reporting of these variants in clinical practice for 56 "actionable" genes. Among these, seven are involved in Marfan Syndrome And Related Disorders (MSARD) resulting from mutations of the FBN1, TGFBR1 and 2, ACTA2, SMAD3, MYH11 and MYLK genes. Here, we show that mutations collected in UMD databases for MSARD genes (UMD-MSARD) are rarely reported, including the most frequent ones, in global scale initiatives for variant annotation such as the NHLBI GO Exome Sequencing Project (ESP), the Exome Aggregation Consortium (ExAC), and ClinVar. The predicted pathogenic mutations reported in global scale initiatives but absent in locus-specific databases (LSDBs) mainly correspond to rare events. UMD-MSARD databases are therefore the only resources providing access to the full spectrum of known pathogenic mutations. They are the most comprehensive resources for clinicians and geneticists to interpret MSARD-related variations not only primary variants but also secondary variants.
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Affiliation(s)
| | | | | | - Ghadi Rai
- Aix Marseille Univ, INSERM, GMGF, Marseille, France
| | - Nadine Hanna
- Département de Génétique, Hôpital Bichat AP-HP, Paris, France.,Inserm U1148 LVTS, Equipe 2 Maladies Structurelles Cardiovasculaires, Hôpital Bichat, Université Paris Diderot, Sorbonne Paris Cité.,Centre National de Référence Maladies Rares, Syndrome de Marfan et pathologies apparentées, Hôpital Bichat, AP-HP, Paris, France
| | - Pauline Arnaud
- Département de Génétique, Hôpital Bichat AP-HP, Paris, France.,Inserm U1148 LVTS, Equipe 2 Maladies Structurelles Cardiovasculaires, Hôpital Bichat, Université Paris Diderot, Sorbonne Paris Cité.,Centre National de Référence Maladies Rares, Syndrome de Marfan et pathologies apparentées, Hôpital Bichat, AP-HP, Paris, France
| | - Céline Guien
- Aix Marseille Univ, INSERM, GMGF, Marseille, France
| | - Maria Martinez
- IRSD, INSERM, INRA, ENVT, UPS, Université de Toulouse, Toulouse, France
| | - Laurence Faivre
- Fédération Hospitalo-Universitaire Médecine Translationnelle et Anomalies du Développement (TRANSLAD), Centre Hospitalier Universitaire Dijon, Dijon, France.,Centre de Génétique et Centre de Référence, Anomalies du Développement et Syndromes Malformatifs de l'Inter-région Est, Centre Hospitalier Universitaire Dijon, Dijon, France.,EA 4271 GAD, Université de Bourgogne Franche-Comté, Dijon, France
| | - Guillaume Jondeau
- Centre National de Référence Maladies Rares, Syndrome de Marfan et pathologies apparentées, Hôpital Bichat, AP-HP, Paris, France.,Service de Cardiologie, AP-HP, Hôpital Bichat, Paris, France.,AP-HP, Centre de référence pour les syndromes de Marfan et apparentés, Service de Cardiologie, Hôpital Bichat, Paris, France
| | - Catherine Boileau
- Inserm U1148 LVTS, Equipe 2 Maladies Structurelles Cardiovasculaires, Hôpital Bichat, Université Paris Diderot, Sorbonne Paris Cité.,Centre National de Référence Maladies Rares, Syndrome de Marfan et pathologies apparentées, Hôpital Bichat, AP-HP, Paris, France.,AP-HP, Centre de référence pour les syndromes de Marfan et apparentés, Service de Cardiologie, Hôpital Bichat, Paris, France
| | | | - Christophe Béroud
- Aix Marseille Univ, INSERM, GMGF, Marseille, France.,AP-HM, Département de Génétique Médicale, Hôpital Timone Enfants, Marseille, France
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Van Allen EM, Robinson D, Morrissey C, Pritchard C, Imamovic A, Carter S, Rosenberg M, McKenna A, Wu YM, Cao X, Chinnaiyan A, Garraway L, Nelson PS. A comparative assessment of clinical whole exome and transcriptome profiling across sequencing centers: implications for precision cancer medicine. Oncotarget 2016; 7:52888-52899. [PMID: 27167109 PMCID: PMC5288156 DOI: 10.18632/oncotarget.9184] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2015] [Accepted: 03/29/2016] [Indexed: 11/25/2022] Open
Abstract
Advances in next generation sequencing technologies provide approaches to comprehensively determine genomic alterations within a tumor that occur as a cause or consequence of neoplastic growth. Though providers offering various cancer genomics assays have multiplied, the level of reproducibility in terms of the technical sensitivity and the conclusions resulting from the data analyses have not been assessed.We sought to determine the reproducibility of ascertaining tumor genome aberrations using whole exome sequencing (WES) and RNAseq. Samples of the same metastatic tumors were independently processed and subjected to WES of tumor and constitutional DNA, and RNAseq of RNA, at two sequencing centers. Overall, the sequencing results were highly comparable. Concordant mutation calls ranged from 88% to 93% of all variants including 100% agreement across 154 cancer-associated genes. Regions of copy losses and gains were uniformly identified and called by each sequencing center and chromosomal plots showed nearly identical patterns. Transcript abundance levels also exhibited a high degree of concordance (r2 ≥ 0.78;Pearson). Biologically-relevant gene fusion events were concordantly called. Exome sequencing of germline DNA samples provided a minimum of 30X coverage depth across 56 genes where incidental findings are recommended to be reported. One possible pathogenic variant in the APC gene was identified by both sequencing centers.The findings from this study demonstrate that results of somatic and germline sequencing are highly concordant across sequencing centers that have substantial experience in the technological requirements for preparing, sequencing and annotating DNA and RNA from human biospecimens.
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Affiliation(s)
- Eliezer M Van Allen
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, 02142, MA, USA
| | - Dan Robinson
- Michigan Center for Translational Pathology, University of Michigan Medical School, Ann Arbor, 48109, MI, USA
| | - Colm Morrissey
- Department of Urology, University of Washington, Seattle, 98195, WA, USA
| | - Colin Pritchard
- Department of Laboratory Medicine, University of Washington, Seattle, 98195, WA, USA
| | - Alma Imamovic
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, 02142, MA, USA
| | - Scott Carter
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, 02142, MA, USA
| | - Mara Rosenberg
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, 02142, MA, USA
| | - Aaron McKenna
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, 02142, MA, USA
| | - Yi-Mi Wu
- Michigan Center for Translational Pathology, University of Michigan Medical School, Ann Arbor, 48109, MI, USA
| | - Xuhong Cao
- Michigan Center for Translational Pathology, University of Michigan Medical School, Ann Arbor, 48109, MI, USA
| | - Arul Chinnaiyan
- Michigan Center for Translational Pathology, University of Michigan Medical School, Ann Arbor, 48109, MI, USA
| | - Levi Garraway
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, 02142, MA, USA
| | - Peter S Nelson
- Department of Urology, University of Washington, Seattle, 98195, WA, USA
- Department of Medicine, University of Washington, Seattle, 98195, WA, USA
- Divisions of Human Biology and Clinical Research, Fred Hutchinson Cancer Research Center, Seattle, 98109, WA, USA
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Sweet K, Sturm AC, Schmidlen T, Hovick S, Peng J, Manickam K, Salikhova A, McElroy J, Scheinfeldt L, Toland AE, Roberts JS, Christman M. EMR documentation of physician-patient communication following genomic counseling for actionable complex disease and pharmacogenomic results. Clin Genet 2016; 91:545-556. [PMID: 27322592 DOI: 10.1111/cge.12820] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2016] [Revised: 06/01/2016] [Accepted: 06/06/2016] [Indexed: 01/06/2023]
Abstract
Genomic risk information for potentially actionable complex diseases and pharmacogenomics communicated through genomic counseling (GC) may motivate physicians and patients to take preventive actions. The Ohio State University-Coriell Personalized Medicine Collaborative is a randomized trial to measure the effects of in-person GC on chronic disease patients provided with multiplex results. Nine personalized genomic risk reports were provided to patients through a web portal, and to physicians via electronic medical record (EMR). Active arm participants (98, 39% female) received GC within 1 month of report viewing; control arm subjects (101, 54% female) could access counseling 3-months post-report viewing. We examined whether GC affected documentation of physician-patient communication by reviewing the first clinical note following the patient's GC visit or report upload to the EMR. Multivariable logistic regression modeling estimated the independent effect of GC on physician-patient communication, as intention to treat (ITT) and per protocol (PP), adjusted for physician educational intervention. Counselees in the active arm had more physician-patient communications than control subjects [ITT, odds ratio (OR): 3.76 (95% confidence interval (CI): 1.38-10.22, p < 0.0094); PP, OR: 5.53 (95% CI: 2.20-13.90, p = 0.0017). In conclusion, GC appreciably affected physician-patient communication following receipt of potentially actionable genomic risk information.
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Affiliation(s)
- K Sweet
- Division of Human Genetics, Ohio State University Wexner Medical Center, Columbus, OH, USA
| | - A C Sturm
- Division of Human Genetics, Ohio State University Wexner Medical Center, Columbus, OH, USA
| | - T Schmidlen
- Coriell Personalized Medicine Collaborative, Coriell Institute for Medical Research, Camden, NJ, USA
| | - S Hovick
- School of Communication, Ohio State University, Columbus, OH, USA
| | - J Peng
- Department of Biomedical Informatics, Center for Biostatistics, Columbus, OH, USA
| | - K Manickam
- Division of Human Genetics, Ohio State University Wexner Medical Center, Columbus, OH, USA.,Geisinger Health System, Genomic Medicine Institute, Precision Health Center, Forty Fort, PA, USA
| | - A Salikhova
- Ohio State University Comprehensive Cancer Center, Columbus, OH, USA
| | - J McElroy
- Department of Biomedical Informatics, Center for Biostatistics, Columbus, OH, USA
| | - L Scheinfeldt
- Coriell Personalized Medicine Collaborative, Coriell Institute for Medical Research, Camden, NJ, USA.,Department of Biology, Temple University, Philadelphia, PA, USA
| | - A E Toland
- Division of Human Genetics, Ohio State University Wexner Medical Center, Columbus, OH, USA
| | - J S Roberts
- Department of Health Behaviour & Health Education, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - M Christman
- Coriell Personalized Medicine Collaborative, Coriell Institute for Medical Research, Camden, NJ, USA
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Fokstuen S, Makrythanasis P, Hammar E, Guipponi M, Ranza E, Varvagiannis K, Santoni FA, Albarca-Aguilera M, Poleggi ME, Couchepin F, Brockmann C, Mauron A, Hurst SA, Moret C, Gehrig C, Vannier A, Bevillard J, Araud T, Gimelli S, Stathaki E, Paoloni-Giacobino A, Bottani A, Sloan-Béna F, Sizonenko LD, Mostafavi M, Hamamy H, Nouspikel T, Blouin JL, Antonarakis SE. Experience of a multidisciplinary task force with exome sequencing for Mendelian disorders. Hum Genomics 2016; 10:24. [PMID: 27353043 PMCID: PMC4924303 DOI: 10.1186/s40246-016-0080-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Accepted: 06/17/2016] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND In order to optimally integrate the use of high-throughput sequencing (HTS) as a tool in clinical diagnostics of likely monogenic disorders, we have created a multidisciplinary "Genome Clinic Task Force" at the University Hospitals of Geneva, which is composed of clinical and molecular geneticists, bioinformaticians, technicians, bioethicists, and a coordinator. METHODS AND RESULTS We have implemented whole exome sequencing (WES) with subsequent targeted bioinformatics analysis of gene lists for specific disorders. Clinical cases of heterogeneous Mendelian disorders that could potentially benefit from HTS are presented and discussed during the sessions of the task force. Debate concerning the interpretation of identified variants and the content of the final report constitutes a major part of the task force's work. Furthermore, issues related to bioethics, genetic counseling, quality control, and reimbursement are also addressed. CONCLUSIONS This multidisciplinary task force has enabled us to create a platform for regular exchanges between all involved experts in order to deal with the multiple complex issues related to HTS in clinical practice and to continuously improve the diagnostic use of HTS. In addition, this task force was instrumental to formally approve the reimbursement of HTS for molecular diagnosis of Mendelian disorders in Switzerland.
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Affiliation(s)
- S Fokstuen
- Service of Genetic Medicine, University Hospitals of Geneva, Geneva, Switzerland
| | - P Makrythanasis
- Service of Genetic Medicine, University Hospitals of Geneva, Geneva, Switzerland.,Department of Genetic Medicine and Development, University of Geneva, 1 rue Michel-Servet, 1211, Geneva, Switzerland
| | - E Hammar
- Service of Genetic Medicine, University Hospitals of Geneva, Geneva, Switzerland
| | - M Guipponi
- Service of Genetic Medicine, University Hospitals of Geneva, Geneva, Switzerland.,Department of Genetic Medicine and Development, University of Geneva, 1 rue Michel-Servet, 1211, Geneva, Switzerland
| | - E Ranza
- Service of Genetic Medicine, University Hospitals of Geneva, Geneva, Switzerland
| | - K Varvagiannis
- Service of Genetic Medicine, University Hospitals of Geneva, Geneva, Switzerland.,Department of Genetic Medicine and Development, University of Geneva, 1 rue Michel-Servet, 1211, Geneva, Switzerland
| | - F A Santoni
- Service of Genetic Medicine, University Hospitals of Geneva, Geneva, Switzerland.,Department of Genetic Medicine and Development, University of Geneva, 1 rue Michel-Servet, 1211, Geneva, Switzerland
| | - M Albarca-Aguilera
- Service of Genetic Medicine, University Hospitals of Geneva, Geneva, Switzerland
| | - M E Poleggi
- Service of Genetic Medicine, University Hospitals of Geneva, Geneva, Switzerland
| | - F Couchepin
- Service of Genetic Medicine, University Hospitals of Geneva, Geneva, Switzerland
| | - C Brockmann
- Service of Genetic Medicine, University Hospitals of Geneva, Geneva, Switzerland
| | - A Mauron
- Institute for Ethics, History, and the Humanities, Geneva University Medical School, Geneva, Switzerland
| | - S A Hurst
- Institute for Ethics, History, and the Humanities, Geneva University Medical School, Geneva, Switzerland
| | - C Moret
- Institute for Ethics, History, and the Humanities, Geneva University Medical School, Geneva, Switzerland
| | - C Gehrig
- Service of Genetic Medicine, University Hospitals of Geneva, Geneva, Switzerland
| | - A Vannier
- Service of Genetic Medicine, University Hospitals of Geneva, Geneva, Switzerland
| | - J Bevillard
- Department of Genetic Medicine and Development, University of Geneva, 1 rue Michel-Servet, 1211, Geneva, Switzerland
| | - T Araud
- Service of Genetic Medicine, University Hospitals of Geneva, Geneva, Switzerland
| | - S Gimelli
- Service of Genetic Medicine, University Hospitals of Geneva, Geneva, Switzerland
| | - E Stathaki
- Service of Genetic Medicine, University Hospitals of Geneva, Geneva, Switzerland
| | - A Paoloni-Giacobino
- Service of Genetic Medicine, University Hospitals of Geneva, Geneva, Switzerland
| | - A Bottani
- Service of Genetic Medicine, University Hospitals of Geneva, Geneva, Switzerland
| | - F Sloan-Béna
- Service of Genetic Medicine, University Hospitals of Geneva, Geneva, Switzerland
| | - L D'Amato Sizonenko
- Service of Genetic Medicine, University Hospitals of Geneva, Geneva, Switzerland
| | - M Mostafavi
- Service of Genetic Medicine, University Hospitals of Geneva, Geneva, Switzerland
| | - H Hamamy
- Department of Genetic Medicine and Development, University of Geneva, 1 rue Michel-Servet, 1211, Geneva, Switzerland
| | - T Nouspikel
- Service of Genetic Medicine, University Hospitals of Geneva, Geneva, Switzerland
| | - J L Blouin
- Service of Genetic Medicine, University Hospitals of Geneva, Geneva, Switzerland
| | - S E Antonarakis
- Service of Genetic Medicine, University Hospitals of Geneva, Geneva, Switzerland. .,Department of Genetic Medicine and Development, University of Geneva, 1 rue Michel-Servet, 1211, Geneva, Switzerland. .,iGE3, Institute of Genetics and Genomics of Geneva, Geneva, Switzerland.
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Unsolicited findings of next-generation sequencing for tumor analysis within a Dutch consortium: clinical daily practice reconsidered. Eur J Hum Genet 2016; 24:1496-500. [PMID: 27071717 DOI: 10.1038/ejhg.2016.27] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2015] [Revised: 01/11/2016] [Accepted: 02/10/2016] [Indexed: 12/24/2022] Open
Abstract
Cancer patients participating in studies involving experimental or diagnostic next-generation sequencing (NGS) procedures are confronted with the possibility of unsolicited findings. The Center for Personalized Cancer Treatment (CPCT), a Dutch consortium of cancer centers, is offering centralized large-scale NGS for the discovery of somatic tumor mutations with their germline DNA as reference. The CPCT aims to give all cancer patients with advanced disease stages access to tumor DNA analysis in order to improve selection for experimental therapy. In this article, our experiences at the CPCT will serve as an example to discuss the ethical and practical aspects regarding the management of unsolicited findings in personalized cancer research and treatment. Generic issues, relevant for all researchers in this field are discussed and illustrated by description of three patients faced with an unsolicited DNA finding, while they intended to be candidate for future anticancer treatment by participating in a trial that included NGS of both somatic and germline DNA. As options for DNA analysis expand and costs decrease rapidly, more and more patients are offered large-scale NGS testing. After reviewing current recommendations in literature, we conclude that classical informed consent procedures need to be adapted to become more explicit in asking patients if they want to be informed about unsolicited findings and if so, what level of detail of genetic risk information exactly they want to be returned after the analysis.
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Mucaki EJ, Caminsky NG, Perri AM, Lu R, Laederach A, Halvorsen M, Knoll JHM, Rogan PK. A unified analytic framework for prioritization of non-coding variants of uncertain significance in heritable breast and ovarian cancer. BMC Med Genomics 2016; 9:19. [PMID: 27067391 PMCID: PMC4828881 DOI: 10.1186/s12920-016-0178-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2015] [Accepted: 03/15/2016] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Sequencing of both healthy and disease singletons yields many novel and low frequency variants of uncertain significance (VUS). Complete gene and genome sequencing by next generation sequencing (NGS) significantly increases the number of VUS detected. While prior studies have emphasized protein coding variants, non-coding sequence variants have also been proven to significantly contribute to high penetrance disorders, such as hereditary breast and ovarian cancer (HBOC). We present a strategy for analyzing different functional classes of non-coding variants based on information theory (IT) and prioritizing patients with large intragenic deletions. METHODS We captured and enriched for coding and non-coding variants in genes known to harbor mutations that increase HBOC risk. Custom oligonucleotide baits spanning the complete coding, non-coding, and intergenic regions 10 kb up- and downstream of ATM, BRCA1, BRCA2, CDH1, CHEK2, PALB2, and TP53 were synthesized for solution hybridization enrichment. Unique and divergent repetitive sequences were sequenced in 102 high-risk, anonymized patients without identified mutations in BRCA1/2. Aside from protein coding and copy number changes, IT-based sequence analysis was used to identify and prioritize pathogenic non-coding variants that occurred within sequence elements predicted to be recognized by proteins or protein complexes involved in mRNA splicing, transcription, and untranslated region (UTR) binding and structure. This approach was supplemented by in silico and laboratory analysis of UTR structure. RESULTS 15,311 unique variants were identified, of which 245 occurred in coding regions. With the unified IT-framework, 132 variants were identified and 87 functionally significant VUS were further prioritized. An intragenic 32.1 kb interval in BRCA2 that was likely hemizygous was detected in one patient. We also identified 4 stop-gain variants and 3 reading-frame altering exonic insertions/deletions (indels). CONCLUSIONS We have presented a strategy for complete gene sequence analysis followed by a unified framework for interpreting non-coding variants that may affect gene expression. This approach distills large numbers of variants detected by NGS to a limited set of variants prioritized as potential deleterious changes.
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Affiliation(s)
- Eliseos J Mucaki
- Department of Biochemistry, Schulich School of Medicine and Dentistry, Western University, London, ON, N6A 2C1, Canada
| | - Natasha G Caminsky
- Department of Biochemistry, Schulich School of Medicine and Dentistry, Western University, London, ON, N6A 2C1, Canada
| | - Ami M Perri
- Department of Biochemistry, Schulich School of Medicine and Dentistry, Western University, London, ON, N6A 2C1, Canada
| | - Ruipeng Lu
- Department of Computer Science, Faculty of Science, Western University, London, N6A 2C1, Canada
| | - Alain Laederach
- Department of Biology, University of North Carolina, Chapel Hill, NC, 27599-3290, USA
| | - Matthew Halvorsen
- Institute for Genomic Medicine, Columbia University Medical Center, New York, NY, 10032, USA
| | - Joan H M Knoll
- Department of Pathology and Laboratory Medicine, Schulich School of Medicine and Dentistry, Western University, London, N6A 2C1, Canada
- Cytognomix Inc., London, Canada
| | - Peter K Rogan
- Department of Biochemistry, Schulich School of Medicine and Dentistry, Western University, London, ON, N6A 2C1, Canada.
- Department of Computer Science, Faculty of Science, Western University, London, N6A 2C1, Canada.
- Cytognomix Inc., London, Canada.
- Department of Oncology, Schulich School of Medicine and Dentistry, Western University, London, N6A 2C1, Canada.
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Abstract
In this review, we lay out 3 areas currently being evaluated for incorporation of genetic information into clinical practice related to atherosclerosis. The first, familial hypercholesterolemia, is the clearest case for utility of genetic testing in diagnosis and potentially guiding treatment. Already in use for confirmatory testing of familial hypercholesterolemia and for cascade screening of relatives, genetic testing is likely to expand to help establish diagnoses and facilitate research related to most effective therapies, including new agents, such as PCSK9 inhibitors. The second area, adding genetic information to cardiovascular risk prediction for primary prevention, is not currently recommended. Although identification of additional variants may add substantially to prediction in the future, combining known variants has not yet demonstrated sufficient improvement in prediction for incorporation into commonly used risk scores. The third area, pharmacogenetics, has utility for some therapies today. Future utility for pharmacogenetics will wax or wane depending on the nature of available drugs and therapeutic strategies.
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Affiliation(s)
- Nina P. Paynter
- From the Division of Preventive Medicine, Department of Medicine, Brigham and Women’s Hospital, Boston, MA
| | - Paul M Ridker
- From the Division of Preventive Medicine, Department of Medicine, Brigham and Women’s Hospital, Boston, MA
| | - Daniel I. Chasman
- From the Division of Preventive Medicine, Department of Medicine, Brigham and Women’s Hospital, Boston, MA
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Boers SN, van Delden JJM, Knoers NV, Bredenoord AL. Postmortem disclosure of genetic information to family members: active or passive? Trends Mol Med 2016; 21:148-53. [PMID: 25743261 DOI: 10.1016/j.molmed.2015.01.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2014] [Revised: 12/22/2014] [Accepted: 01/07/2015] [Indexed: 01/19/2023]
Abstract
Advances in next-generation DNA sequencing (NGS) now make it possible, and affordable, to sequence the entire genome of an individual. Routine clinical application is on the horizon. There is a consensus that some subsets of genetic information should be disclosed to patients, but disclosure to their relatives is less consensual. This issue becomes especially salient after a patient's death, when permission can no longer be sought. There has however been little debate on postmortem disclosure. We identify and explain the arguments in favor of and against disclosure of genetic information to the relatives of a deceased patient. We conclude that there are valid reasons to communicate some subsets of genetic information to family members after death, and we propose a passive postmortem disclosure policy.
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Affiliation(s)
- Sarah N Boers
- Department of Medical Humanities, Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Str 6.131, PO Box 85500, 3508 GA Utrecht, The Netherlands.
| | - Johannes J M van Delden
- Department of Medical Humanities, Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Str 6.131, PO Box 85500, 3508 GA Utrecht, The Netherlands
| | - Nine V Knoers
- Department of Medical Genetics, University Medical Center Utrecht, KC04.084.2, PO Box 85090, 3508 GA Utrecht, The Netherlands
| | - Annelien L Bredenoord
- Department of Medical Humanities, Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Str 6.131, PO Box 85500, 3508 GA Utrecht, The Netherlands
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48
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Beckmann JS. Can we afford to sequence every newborn baby's genome? Hum Mutat 2015; 36:283-6. [PMID: 25546530 DOI: 10.1002/humu.22748] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2014] [Accepted: 12/17/2014] [Indexed: 01/19/2023]
Abstract
Whole-exome sequencing and whole-genome sequencing are gradually entering into the clinical arena. Drops in sequencing prices have led some to suggest that these analyses could be extended to the screening of whole populations or subsets thereof. Herein, we argue that this optimism is presently still unfounded. While cost estimates take into account the generation of sequence data, they fail to properly evaluate both the price of accurate and efficient interpretation and of the proper return of genomic information to the consulting individuals. Thus, short of inventing new, cost-effective ways of achieving these goals, the latter are likely to ruin our healthcare systems. We posit that due to lack of available resources, generalization of this practice remains, for the time being, unrealistic.
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Affiliation(s)
- Jacques S Beckmann
- Clinical Bioinformatics, SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
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49
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Cherukuri PF, Maduro V, Fuentes-Fajardo KV, Lam K, Adams DR, Tifft CJ, Mullikin JC, Gahl WA, Boerkoel CF. Replicate exome-sequencing in a multiple-generation family: improved interpretation of next-generation sequencing data. BMC Genomics 2015; 16:998. [PMID: 26602380 PMCID: PMC4659195 DOI: 10.1186/s12864-015-2107-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2014] [Accepted: 10/16/2015] [Indexed: 12/18/2022] Open
Abstract
Background Whole-exome sequencing (WES) is rapidly evolving into a tool of choice for rapid, and inexpensive identification of molecular genetic lesions within targeted regions of the human genome. While biases in WES coverage of nucleotides in targeted regions are recognized, it is not well understood how repetition of WES improves the interpretation of sequencing results in a clinical diagnostic setting. Method To address this, we compared independently generated exome-capture of six individuals from three-generations sequenced in triplicate. This generated between 48x-86x mean target depth of high-quality mapped bases (>Q20) for each technical replicate library. Cumulatively, we achieved 179 - 208x average target coverage for each individual in the pedigree. Using this experimental design, we evaluated stochastics in WES interpretation, genotyping sensitivity, and accuracy to detect de novo variants. Results In this study, we show that repetition of WES improved the interpretation of the capture target regions after aggregating the data (93.5 - 93.9 %). Compared to 81.2 - 89.6 % (50.2-55.4 Mb of 61.7 M) coverage of targeted bases at ≥20x in the individual technical replicates, the aggregated data covered 93.5 - 93.9 % of targeted bases (57.7 – 58.0 of 61.7 M) at ≥20x threshold, suggesting a 4.3 – 12.7 % improvement in coverage. Each individual’s aggregate dataset recovered 3.4 – 6.4 million bases within variable targeted regions. We uncovered technical variability (2-5 %) inherent to WES technique. We also show improved interpretation in assessing clinically important regions that lack interpretation under current conditions, affecting 12–16 of the 56 genes recommended for secondary analysis by American College of Medical Genetics (ACMG). We demonstrate that comparing technical replicate WES datasets and their derived aggregate data can effectively address overall WES genotyping discrepancies. Conclusion We describe a method to evaluate the reproducibility and stochastics in exome library preparation, and delineate the advantages of aggregating the data derived from technical replicates. The implications of this study are directly applicable to improved experimental design and provide an opportunity to rapidly, efficiently, and accurately arrive at reliable candidate nucleotide variants. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-2107-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Praveen F Cherukuri
- NIH Undiagnosed Diseases Program, Common Fund, Office of the Director, NIH, Bethesda, MD, USA. .,Inova Translational Medicine Institute, Inova Health System, Falls Church, VA, USA.
| | - Valerie Maduro
- NIH Undiagnosed Diseases Program, Common Fund, Office of the Director, NIH, Bethesda, MD, USA.
| | - Karin V Fuentes-Fajardo
- NIH Undiagnosed Diseases Program, Common Fund, Office of the Director, NIH, Bethesda, MD, USA.
| | - Kevin Lam
- NIH Undiagnosed Diseases Program, Common Fund, Office of the Director, NIH, Bethesda, MD, USA.
| | | | - David R Adams
- NIH Undiagnosed Diseases Program, Common Fund, Office of the Director, NIH, Bethesda, MD, USA. .,Office of the Clinical Director, National Human Genome Research Institute, NIH, Bethesda, MD, USA.
| | - Cynthia J Tifft
- NIH Undiagnosed Diseases Program, Common Fund, Office of the Director, NIH, Bethesda, MD, USA. .,Office of the Clinical Director, National Human Genome Research Institute, NIH, Bethesda, MD, USA.
| | - James C Mullikin
- NIH Intramural Sequencing Center, National Human Genome Research Institute, NIH, Bethesda, MD, USA.
| | - William A Gahl
- NIH Undiagnosed Diseases Program, Common Fund, Office of the Director, NIH, Bethesda, MD, USA. .,Office of the Clinical Director, National Human Genome Research Institute, NIH, Bethesda, MD, USA.
| | - Cornelius F Boerkoel
- NIH Undiagnosed Diseases Program, Common Fund, Office of the Director, NIH, Bethesda, MD, USA.
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Blazer KR, Nehoray B, Solomon I, Niell-Swiller M, Culver JO, Uman GC, Weitzel JN. Next-Generation Testing for Cancer Risk: Perceptions, Experiences, and Needs Among Early Adopters in Community Healthcare Settings. Genet Test Mol Biomarkers 2015; 19:657-65. [PMID: 26539620 DOI: 10.1089/gtmb.2015.0061] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Advances in next-generation sequencing (NGS) technologies are driving a shift from single-gene to multigene panel testing for clinical genetic cancer risk assessment (GCRA). This study explored perceptions, experiences, and challenges with NGS testing for GCRA among U.S. community-based clinicians. METHODS Surveys delivered at initial and 8-month time points, and 12-month tracking of cases presented in a multidisciplinary web-based case conference series, were conducted with GCRA providers who participated in a 235-member nationwide community of practice. RESULTS The proportion of respondents ordering panel tests rose from 29% at initial survey (27/94) to 44% (46/107) within 8 months. Respondents reported significantly less confidence about interpreting and counseling about NGS compared with single-gene test results (p < 0.0001 for all comparisons). The most cited reasons for not ordering NGS tests included concerns about clinical utility, interpreting and communicating results, and lack of knowledge/skills. Multigene panels were used in 204/668 cases presented during 2013, yielding 37 (18%) deleterious (7% in low/moderate-penetrance genes), 88 (43%) with ≥1 variant of uncertain significance, 77 (38%) uninformative negative, and 2 (1%) inconclusive results. CONCLUSIONS Despite concerns about utility and ability to interpret/counsel about NGS results, a rapidly increasing uptake of NGS testing among community clinicians was documented. Challenges identified in case discussions point to the need for ongoing education, practice-based support, and opportunities to partner in research that contributes to characterization of lesser known genes.
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Affiliation(s)
- Kathleen R Blazer
- 1 City of Hope, Division of Clinical Cancer Genetics , Duarte, California
| | - Bita Nehoray
- 1 City of Hope, Division of Clinical Cancer Genetics , Duarte, California
| | - Ilana Solomon
- 1 City of Hope, Division of Clinical Cancer Genetics , Duarte, California
| | | | - Julie O Culver
- 1 City of Hope, Division of Clinical Cancer Genetics , Duarte, California
| | | | - Jeffrey N Weitzel
- 1 City of Hope, Division of Clinical Cancer Genetics , Duarte, California
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