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Thorpe E, Williams T, Shaw C, Chekalin E, Ortega J, Robinson K, Button J, Jones MC, Campo MD, Basel D, McCarrier J, Keppen LD, Royer E, Foster-Bonds R, Duenas-Roque MM, Urraca N, Bosfield K, Brown CW, Lydigsen H, Mroczkowski HJ, Ward J, Sirchia F, Giorgio E, Vaux K, Salguero HP, Lumaka A, Mubungu G, Makay P, Ngole M, Lukusa PT, Vanderver A, Muirhead K, Sherbini O, Lah MD, Anderson K, Bazalar-Montoya J, Rodriguez RS, Cornejo-Olivas M, Milla-Neyra K, Shinawi M, Magoulas P, Henry D, Gibson K, Wiafe S, Jayakar P, Salyakina D, Masser-Frye D, Serize A, Perez JE, Taylor A, Shenbagam S, Abou Tayoun A, Malhotra A, Bennett M, Rajan V, Avecilla J, Warren A, Arseneault M, Kalista T, Crawford A, Ajay SS, Perry DL, Belmont J, Taft RJ. The impact of clinical genome sequencing in a global population with suspected rare genetic disease. Am J Hum Genet 2024; 111:1271-1281. [PMID: 38843839 DOI: 10.1016/j.ajhg.2024.05.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Revised: 05/03/2024] [Accepted: 05/06/2024] [Indexed: 07/03/2024] Open
Abstract
There is mounting evidence of the value of clinical genome sequencing (cGS) in individuals with suspected rare genetic disease (RGD), but cGS performance and impact on clinical care in a diverse population drawn from both high-income countries (HICs) and low- and middle-income countries (LMICs) has not been investigated. The iHope program, a philanthropic cGS initiative, established a network of 24 clinical sites in eight countries through which it provided cGS to individuals with signs or symptoms of an RGD and constrained access to molecular testing. A total of 1,004 individuals (median age, 6.5 years; 53.5% male) with diverse ancestral backgrounds (51.8% non-majority European) were assessed from June 2016 to September 2021. The diagnostic yield of cGS was 41.4% (416/1,004), with individuals from LMIC sites 1.7 times more likely to receive a positive test result compared to HIC sites (LMIC 56.5% [195/345] vs. HIC 33.5% [221/659], OR 2.6, 95% CI 1.9-3.4, p < 0.0001). A change in diagnostic evaluation occurred in 76.9% (514/668) of individuals. Change of management, inclusive of specialty referrals, imaging and testing, therapeutic interventions, and palliative care, was reported in 41.4% (285/694) of individuals, which increased to 69.2% (480/694) when genetic counseling and avoidance of additional testing were also included. Individuals from LMIC sites were as likely as their HIC counterparts to experience a change in diagnostic evaluation (OR 6.1, 95% CI 1.1-∞, p = 0.05) and change of management (OR 0.9, 95% CI 0.5-1.3, p = 0.49). Increased access to genomic testing may support diagnostic equity and the reduction of global health care disparities.
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Affiliation(s)
| | | | - Chad Shaw
- Genetic and Genomic Services PBC, Houston, TX, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA; Department of Statistics, Rice University, Houston, TX, USA
| | | | - Julia Ortega
- Illumina Inc, San Diego, CA, USA; C2N Diagnostics, St. Louis, MO, USA
| | | | | | - Marilyn C Jones
- Rady Children's Hospital, San Diego, CA, USA; University of California, San Diego, San Diego, CA, USA
| | - Miguel Del Campo
- Rady Children's Hospital, San Diego, CA, USA; University of California, San Diego, San Diego, CA, USA
| | - Donald Basel
- Department of Pediatrics, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Julie McCarrier
- Department of Pediatrics, Medical College of Wisconsin, Milwaukee, WI, USA
| | | | - Erin Royer
- Sanford Children's Specialty Clinics at Sanford Health, USD Sanford School of Medicine, Sioux Falls, SD, USA
| | | | | | - Nora Urraca
- University of Tennessee Health Science Center, Le Bonheur Children's Hospital, Memphis, TN, USA
| | - Kerri Bosfield
- University of Tennessee Health Science Center, Le Bonheur Children's Hospital, Memphis, TN, USA
| | - Chester W Brown
- University of Tennessee Health Science Center, Le Bonheur Children's Hospital, Memphis, TN, USA
| | - Holly Lydigsen
- University of Tennessee Health Science Center, Le Bonheur Children's Hospital, Memphis, TN, USA
| | - Henry J Mroczkowski
- University of Tennessee Health Science Center, Le Bonheur Children's Hospital, Memphis, TN, USA
| | - Jewell Ward
- University of Tennessee Health Science Center, Le Bonheur Children's Hospital, Memphis, TN, USA
| | - Fabio Sirchia
- Department of Molecular Medicine, University of Pavia, Pavia, Italy; Medical Genetics Unit, IRCCS San Matteo Foundation, Pavia, Italy
| | - Elisa Giorgio
- Department of Molecular Medicine, University of Pavia, Pavia, Italy; Medical Genetics Unit, IRCCS Mondino Foundation, Pavia, Italy
| | - Keith Vaux
- Point Loma Pediatrics, San Diego, CA, USA
| | | | - Aimé Lumaka
- Centre de Genetique Humaine, Universite de Kinshasa, Kinshasa, Democratic Republic of the Congo; Center for Human Genetics, Centre Hospitalier Universitaire, Liège, Belgium
| | - Gerrye Mubungu
- Centre de Genetique Humaine, Universite de Kinshasa, Kinshasa, Democratic Republic of the Congo
| | - Prince Makay
- Centre de Genetique Humaine, Universite de Kinshasa, Kinshasa, Democratic Republic of the Congo
| | - Mamy Ngole
- Centre de Genetique Humaine, Universite de Kinshasa, Kinshasa, Democratic Republic of the Congo
| | - Prosper Tshilobo Lukusa
- Centre de Genetique Humaine, Universite de Kinshasa, Kinshasa, Democratic Republic of the Congo
| | - Adeline Vanderver
- Division of Neurology, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, PA, USA; Department of Neurology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | | | - Omar Sherbini
- Division of Neurology, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Melissa D Lah
- Indiana University School of Medicine, Indianapolis, IN, USA
| | | | | | | | - Mario Cornejo-Olivas
- Neurogenetics Research Center, Instituto Nacional de Ciencias Neurologicas, Lima, Peru; Neurogenetics Working Group, Universidad Científica del Sur, Lima, Peru
| | - Karina Milla-Neyra
- Neurogenetics Research Center, Instituto Nacional de Ciencias Neurologicas, Lima, Peru
| | - Marwan Shinawi
- Washington University, St. Louis, MO, USA; St. Louis Children's Hospital, St. Louis, MO, USA
| | | | - Duncan Henry
- UCSF Benioff Children's Hospitals, San Francisco, CA, USA
| | - Kate Gibson
- Canterbury District Health Board, Canterbury, New Zealand
| | | | | | | | - Diane Masser-Frye
- Rady Children's Hospital, San Diego, CA, USA; San Diego-Imperial Counties Developmental Services, Inc., San Diego, CA, USA
| | | | | | - Alan Taylor
- Al Jalila Genomics Center of Excellence, Al Jalila Children's Specialty Hospital, Dubai, United Arab Emirates
| | - Shruti Shenbagam
- Al Jalila Genomics Center of Excellence, Al Jalila Children's Specialty Hospital, Dubai, United Arab Emirates
| | - Ahmad Abou Tayoun
- Al Jalila Genomics Center of Excellence, Al Jalila Children's Specialty Hospital, Dubai, United Arab Emirates; Center for Genomic Discovery, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates
| | | | | | - Vani Rajan
- Illumina Inc, San Diego, CA, USA; Veracyte, San Diego, CA, USA
| | | | | | | | | | | | | | | | - John Belmont
- Genetic and Genomic Services PBC, Houston, TX, USA
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Barjesteh van Waalwijk van Doorn-Khosrovani S, Kholmanskikh Van Criekingen O, Koole S, Thomas DM, Gelderblom H. Testing dilemmas in the clinic: Lessons learned from biomarker-based drug development. Cancer Cell 2024; 42:923-929. [PMID: 38861927 DOI: 10.1016/j.ccell.2024.05.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Revised: 05/08/2024] [Accepted: 05/14/2024] [Indexed: 06/13/2024]
Abstract
Various tests based on different biomarkers have been developed to identify the best candidates for poly(ADP-ribose) polymerase (PARP)-inhibitor therapy. However, due to the absence of harmonization regarding these complex biomarkers, along with various cutoff points and unknown spatial and temporal variations, it is difficult to define the clinical utility of each test and ensure uniformity in treatment decision-making. Here, we propose measures to align biomarker definitions and minimum analytical performance characteristics for diagnostics to ensure equitable and sustainable access to precision medicine.
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Affiliation(s)
| | | | - Simone Koole
- Medical Advisory Department, Zilveren Kruis, Zeist, the Netherlands
| | - David M Thomas
- Centre for Molecular Oncology, University of New South Wales, Sydney, NSW, Australia
| | - Hans Gelderblom
- Department of Medical Oncology, Leiden University Medical Centre, Leiden, the Netherlands
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Smith HS, Leo M, Goddard K, Muessig K, Angelo F, Knight S, Outram S, Kelly NR, Rini C. Measuring health-related quality of life in children with suspected genetic conditions: validation of the PedsQL proxy-report versions. Qual Life Res 2024; 33:1541-1553. [PMID: 38472717 PMCID: PMC11116065 DOI: 10.1007/s11136-024-03623-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/26/2024] [Indexed: 03/14/2024]
Abstract
PURPOSE Measuring health-related quality of life (HRQoL) of children with suspected genetic conditions is important for understanding the effect of interventions such as genomic sequencing (GS). The Pediatric Quality of Life Inventory (PedsQL) is a widely used generic measure of HRQoL in pediatric patients, but its psychometric properties have not yet been evaluated in children undergoing diagnostic GS. METHODS In this cross-sectional study, we surveyed caregivers at the time of their child's enrollment into GS research studies as part of the Clinical Sequencing Evidence Generating Research (CSER) consortium. To evaluate structural validity of the PedsQL 4.0 Generic Core Scales and PedsQL Infant Scales parent proxy-report versions, we performed a confirmatory factor analysis of the hypothesized factor structure. To evaluate convergent validity, we examined correlations between caregivers' reports of their child's health, assessed using the EQ VAS, and PedsQL scores by child age. We conducted linear regression analyses to examine whether age moderated the association between caregiver-reported child health and PedsQL scores. We assessed reliability using Cronbach's alpha. RESULTS We analyzed data for 766 patients across all PedsQL age group versions (1-12 months through 13-18 years). Model fit failed to meet criteria for good fit, even after modification. Neither age group (categorical) nor age (continuous) significantly moderated associations between PedsQL scores and caregiver-reported child health. Cronbach's alphas indicated satisfactory internal consistency for most PedsQL scales. CONCLUSION The PedsQL Generic Core Scales and Infant Scales may be appropriate to measure HRQoL in pediatric patients with suspected genetic conditions across a wide age range. While we found evidence of acceptable internal consistency and preliminary convergent validity in this sample, there were some potential problems with structural validity and reliability that require further attention.
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Affiliation(s)
- Hadley Stevens Smith
- Department of Population Medicine, Harvard Medical School, 401 Park Drive, Suite 401, Boston, MA, 02215, USA.
| | - Michael Leo
- Kaiser Permanente Center for Health Research, Portland, OR, USA
| | - Katrina Goddard
- Department of Translational and Applied Genomics (TAG), Kaiser Permanente Center for Health Research, Portland, OR, USA
| | - Kristin Muessig
- Department of Translational and Applied Genomics (TAG), Kaiser Permanente Center for Health Research, Portland, OR, USA
| | - Frank Angelo
- Institute for Sexual and Gender Minority Health and Wellbeing, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Sara Knight
- Department of Internal Medicine, Division of Epidemiology, University of Utah, Salt Lake City, UT, USA
| | - Simon Outram
- Program in Bioethics, University of California San Francisco, San Francisco, CA, USA
| | - Nicole R Kelly
- Department of Pediatrics, Division of Pediatric Genetic Medicine, Children's Hospital at Montefiore/Montefiore Medical Center/Albert Einstein College of Medicine, Bronx, NY, USA
| | - Christine Rini
- Department of Medical Social Sciences, Northwestern University Feinberg School of Medicine, The Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Chicago, IL, USA
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Fehlberg Z, Goranitis I, Mallett AJ, Stark Z, Best S. Determining priority indicators of utility for genomic testing in rare disease: A Delphi study. Genet Med 2024; 26:101116. [PMID: 38459833 DOI: 10.1016/j.gim.2024.101116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 03/01/2024] [Accepted: 03/04/2024] [Indexed: 03/10/2024] Open
Abstract
PURPOSE Determining the value of genomic tests in rare disease necessitates a broader conceptualization of genomic utility beyond diagnostic yield. Despite widespread discussion, consensus toward which aspects of value to consider is lacking. This study aimed to use expert opinion to identify and refine priority indicators of utility in rare disease genomic testing. METHODS We used 2 survey rounds following Delphi methodology to obtain consensus on indicators of utility among experts involved in policy, clinical, research, and consumer advocacy leadership in Australia. We analyzed quantitative and qualitative data to identify, define, and determine priority indicators. RESULTS Twenty-five experts completed round 1 and 18 completed both rounds. Twenty indicators reached consensus as a priority in value assessment, including those relating to prognostic information, timeliness of results, practical and health care outcomes, clinical accreditation, and diagnostic yield. Whereas indicators pertaining to discovery research, disutility, and factors secondary to primary reason for testing were considered less of a priority and were removed. CONCLUSION This study obtained expert consensus on different utility indicators that are considered a priority in determining the value of genomic testing in rare disease in Australia. Indicators may inform a standardized approach to evidence generation and assessment to guide future research, decision making, and implementation efforts.
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Affiliation(s)
- Zoe Fehlberg
- Australian Genomics, Melbourne, VIC, Australia; University of Melbourne, Melbourne, VIC, Australia
| | - Ilias Goranitis
- Australian Genomics, Melbourne, VIC, Australia; University of Melbourne, Melbourne, VIC, Australia
| | - Andrew J Mallett
- Australian Genomics, Melbourne, VIC, Australia; College of Medicine and Dentistry, James Cook University, Douglas, QLD, Australia; Institute for Molecular Bioscience, The University of Queensland, St Lucia, QLD, Australia; Department of Renal Medicine, Townsville University Hospital, Douglas, QLD, Australia
| | - Zornitza Stark
- Australian Genomics, Melbourne, VIC, Australia; University of Melbourne, Melbourne, VIC, Australia; Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, VIC, Australia
| | - Stephanie Best
- Australian Genomics, Melbourne, VIC, Australia; University of Melbourne, Melbourne, VIC, Australia; Department of Health Services Research, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia; Victorian Comprehensive Cancer Centre Alliance, Melbourne, VIC, Australia.
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Azuelos C, Marquis MA, Laberge AM. A systematic review of the assessment of the clinical utility of genomic sequencing: Implications of the lack of standard definitions and measures of clinical utility. Eur J Med Genet 2024; 68:104925. [PMID: 38432472 DOI: 10.1016/j.ejmg.2024.104925] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 12/31/2023] [Accepted: 02/11/2024] [Indexed: 03/05/2024]
Abstract
PURPOSE Exome sequencing (ES) and genome sequencing (GS) are diagnostic tests for rare genetic diseases. Studies report clinical utility of ES/GS. The goal of this systematic review is to establish how clinical utility is defined and measured in studies evaluating the impacts of ES/GS results for pediatric patients. METHODS Relevant articles were identified in PubMed, Medline, Embase, and Web of Science. Eligible studies assessed clinical utility of ES/GS for pediatric patients published before 2021. Other relevant articles were added based on articles' references. Articles were coded to assess definitions and measures of clinical utility. RESULTS Of 1346 articles, 83 articles met eligibility criteria. Clinical utility was not clearly defined in 19% of studies and 92% did not use an explicit measure of clinical utility. When present, definitions of clinical utility diverged from recommended definitions and varied greatly, from narrow (diagnostic yield of ES/GS) to broad (including decisions about withdrawal of care/palliative care and/or impacts on other family members). CONCLUSION Clinical utility is used to guide policy and practice decisions about test use. The lack of a standard definition of clinical utility of ES/GS may lead to under- or overestimations of clinical utility, complicating policymaking and raising ethical issues.
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Affiliation(s)
- Claudia Azuelos
- Medical Genetics, Dept of Pediatrics, CHU Sainte-Justine and Université de Montréal, Canada.
| | - Marc-Antoine Marquis
- Palliative Care, Dept of Pediatrics, CHU Sainte-Justine and Université de Montréal, Canada
| | - Anne-Marie Laberge
- Medical Genetics, Dept of Pediatrics, CHU Sainte-Justine and Université de Montréal, Canada.
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Brlek P, Bulić L, Bračić M, Projić P, Škaro V, Shah N, Shah P, Primorac D. Implementing Whole Genome Sequencing (WGS) in Clinical Practice: Advantages, Challenges, and Future Perspectives. Cells 2024; 13:504. [PMID: 38534348 DOI: 10.3390/cells13060504] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Revised: 03/04/2024] [Accepted: 03/11/2024] [Indexed: 03/28/2024] Open
Abstract
The integration of whole genome sequencing (WGS) into all aspects of modern medicine represents the next step in the evolution of healthcare. Using this technology, scientists and physicians can observe the entire human genome comprehensively, generating a plethora of new sequencing data. Modern computational analysis entails advanced algorithms for variant detection, as well as complex models for classification. Data science and machine learning play a crucial role in the processing and interpretation of results, using enormous databases and statistics to discover new and support current genotype-phenotype correlations. In clinical practice, this technology has greatly enabled the development of personalized medicine, approaching each patient individually and in accordance with their genetic and biochemical profile. The most propulsive areas include rare disease genomics, oncogenomics, pharmacogenomics, neonatal screening, and infectious disease genomics. Another crucial application of WGS lies in the field of multi-omics, working towards the complete integration of human biomolecular data. Further technological development of sequencing technologies has led to the birth of third and fourth-generation sequencing, which include long-read sequencing, single-cell genomics, and nanopore sequencing. These technologies, alongside their continued implementation into medical research and practice, show great promise for the future of the field of medicine.
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Affiliation(s)
- Petar Brlek
- St. Catherine Specialty Hospital, 10000 Zagreb, Croatia
- International Center for Applied Biological Research, 10000 Zagreb, Croatia
- School of Medicine, Josip Juraj Strossmayer University of Osijek, 31000 Osijek, Croatia
| | - Luka Bulić
- St. Catherine Specialty Hospital, 10000 Zagreb, Croatia
| | - Matea Bračić
- St. Catherine Specialty Hospital, 10000 Zagreb, Croatia
| | - Petar Projić
- International Center for Applied Biological Research, 10000 Zagreb, Croatia
| | | | - Nidhi Shah
- Dartmouth Hitchcock Medical Center, Lebannon, NH 03766, USA
| | - Parth Shah
- Dartmouth Hitchcock Medical Center, Lebannon, NH 03766, USA
| | - Dragan Primorac
- St. Catherine Specialty Hospital, 10000 Zagreb, Croatia
- International Center for Applied Biological Research, 10000 Zagreb, Croatia
- School of Medicine, Josip Juraj Strossmayer University of Osijek, 31000 Osijek, Croatia
- Medical School, University of Split, 21000 Split, Croatia
- Eberly College of Science, The Pennsylvania State University, State College, PA 16802, USA
- The Henry C. Lee College of Criminal Justice and Forensic Sciences, University of New Haven, West Haven, CT 06516, USA
- REGIOMED Kliniken, 96450 Coburg, Germany
- Medical School, University of Rijeka, 51000 Rijeka, Croatia
- Faculty of Dental Medicine and Health, Josip Juraj Strossmayer University of Osijek, 31000 Osijek, Croatia
- Medical School, University of Mostar, 88000 Mostar, Bosnia and Herzegovina
- National Forensic Sciences University, Gujarat 382007, India
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Hu J, Korchina V, Zouk H, Harden MV, Murdock D, Macbeth A, Harrison SM, Lennon N, Kovar C, Balasubramanian A, Zhang L, Chandanavelli G, Pasham D, Rowley R, Wiley K, Smith ME, Gordon A, Jarvik GP, Sleiman P, Kelly MA, Bland HT, Murugan M, Venner E, Boerwinkle E, Prows C, Mahanta L, Rehm HL, Gibbs RA, Muzny DM. Genetic sex validation for sample tracking in next-generation sequencing clinical testing. BMC Res Notes 2024; 17:62. [PMID: 38433186 PMCID: PMC10910835 DOI: 10.1186/s13104-024-06723-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Accepted: 02/16/2024] [Indexed: 03/05/2024] Open
Abstract
OBJECTIVE Data from DNA genotyping via a 96-SNP panel in a study of 25,015 clinical samples were utilized for quality control and tracking of sample identity in a clinical sequencing network. The study aimed to demonstrate the value of both the precise SNP tracking and the utility of the panel for predicting the sex-by-genotype of the participants, to identify possible sample mix-ups. RESULTS Precise SNP tracking showed no sample swap errors within the clinical testing laboratories. In contrast, when comparing predicted sex-by-genotype to the provided sex on the test requisition, we identified 110 inconsistencies from 25,015 clinical samples (0.44%), that had occurred during sample collection or accessioning. The genetic sex predictions were confirmed using additional SNP sites in the sequencing data or high-density genotyping arrays. It was determined that discrepancies resulted from clerical errors (49.09%), samples from transgender participants (3.64%) and stem cell or bone marrow transplant patients (7.27%) along with undetermined sample mix-ups (40%) for which sample swaps occurred prior to arrival at genome centers, however the exact cause of the events at the sampling sites resulting in the mix-ups were not able to be determined.
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Affiliation(s)
- Jianhong Hu
- Baylor College of Medicine, Human Genome Sequencing Center (HGSC), Houston, TX, USA
| | - Viktoriya Korchina
- Baylor College of Medicine, Human Genome Sequencing Center (HGSC), Houston, TX, USA
| | - Hana Zouk
- Laboratory for Molecular Medicine (LMM), Mass General Brigham, Cambridge, MA, USA
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | | | - David Murdock
- Baylor College of Medicine, Human Genome Sequencing Center (HGSC), Houston, TX, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | | | - Steven M Harrison
- Laboratory for Molecular Medicine (LMM), Mass General Brigham, Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Niall Lennon
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Christie Kovar
- Baylor College of Medicine, Human Genome Sequencing Center (HGSC), Houston, TX, USA
| | | | - Lan Zhang
- Baylor College of Medicine, Human Genome Sequencing Center (HGSC), Houston, TX, USA
| | | | - Divya Pasham
- Baylor College of Medicine, Human Genome Sequencing Center (HGSC), Houston, TX, USA
| | - Robb Rowley
- Division of Genomic Medicine, National Human Genome Research Institute, Bethesda, MD, USA
| | - Ken Wiley
- Division of Genomic Medicine, National Human Genome Research Institute, Bethesda, MD, USA
| | - Maureen E Smith
- Center for Genetic Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Adam Gordon
- Center for Genetic Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Gail P Jarvik
- Division of Medical Genetics, Department of Medicine, University of Washington Medical Center, Seattle, WA, USA
| | - Patrick Sleiman
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | | | - Harris T Bland
- Vanderbilt University Medical Center, Nashville, TN, USA
| | - Mullai Murugan
- Baylor College of Medicine, Human Genome Sequencing Center (HGSC), Houston, TX, USA
| | - Eric Venner
- Baylor College of Medicine, Human Genome Sequencing Center (HGSC), Houston, TX, USA
| | - Eric Boerwinkle
- Baylor College of Medicine, Human Genome Sequencing Center (HGSC), Houston, TX, USA
- Human Genetics Center, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Cynthia Prows
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Lisa Mahanta
- Laboratory for Molecular Medicine (LMM), Mass General Brigham, Cambridge, MA, USA
| | - Heidi L Rehm
- Laboratory for Molecular Medicine (LMM), Mass General Brigham, Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Richard A Gibbs
- Baylor College of Medicine, Human Genome Sequencing Center (HGSC), Houston, TX, USA
| | - Donna M Muzny
- Baylor College of Medicine, Human Genome Sequencing Center (HGSC), Houston, TX, USA.
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Callahan KP, Clayton EW, Lemke AA, Chaudhari BP, Wenger TL, Lyle ANJ, Brothers KB. Ethical and Legal Issues Surrounding Genetic Testing in the NICU. Neoreviews 2024; 25:e127-e138. [PMID: 38425196 PMCID: PMC10998684 DOI: 10.1542/neo.25-3-e127] [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] [Indexed: 03/02/2024]
Abstract
Clinicians practicing in a modern NICU are noticing an increase in the proportion of patients who undergo genetic testing as well as changes in the types of genetic testing patients receive. These trends are not surprising given the increasing recognition of the genetic causes of neonatal illness and recent advances in genetic technology. Yet, the expansion of genetic testing in the NICU also raises a number of ethical questions. In this article, we will review the ethical issues raised by genetic testing, with a focus on the practical implications for neonatologists. First, we outline the complexities of measuring benefit, or utility, for neonatal genetic testing. Next, we discuss potential harms such as inequity, unexpected findings, disability biases, and legal risks. Finally, we conclude with a discussion of ethical issues related to consent for genetic testing. Throughout this article, we highlight solutions to challenges toward the ultimate goal of minimizing harms and maximizing the substantial potential benefits of genetic medicine in the NICU.
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Affiliation(s)
- Katharine P. Callahan
- Division of Neonatology, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania
- Department of Medical Ethics and Health Policy, The Perelman School of Medicine at the University of Pennsylvania; Philadelphia, Pennsylvania
| | - Ellen W. Clayton
- Center for Biomedical Ethics and Society, Department of Pediatrics, Vanderbilt University Medical Center, and School of Law, Vanderbilt University, Nashville, Tennessee
| | - Amy A. Lemke
- Norton Children’s Research Institute Affiliated with the University of Louisville School of Medicine, Louisville, Kentucky
| | - Bimal P. Chaudhari
- Divisions of Neonatology, Genetics and Genomic Medicine, Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children’s Hospital, Columbus, Ohio
| | - Tara L. Wenger
- Division of Medical Genetics, University of Washington, Seattle, Washington
| | - Allison N. J. Lyle
- Division of Neonatology, Department of Pediatrics, University of Louisville School of Medicine, Louisville, KY
| | - Kyle B. Brothers
- Norton Children’s Research Institute Affiliated with the University of Louisville School of Medicine, Louisville, Kentucky
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Nolan J, Buchanan J, Taylor J, Almeida J, Bedenham T, Blair E, Broadgate S, Butler S, Cazeaux A, Craft J, Cranston T, Crawford G, Forrest J, Gabriel J, George E, Gillen D, Haeger A, Hastings Ward J, Hawkes L, Hodgkiss C, Hoffman J, Jones A, Karpe F, Kasperaviciute D, Kovacs E, Leigh S, Limb E, Lloyd-Jani A, Lopez J, Lucassen A, McFarlane C, O'Rourke AW, Pond E, Sherman C, Stewart H, Thomas E, Thomas S, Thomas T, Thomson K, Wakelin H, Walker S, Watson M, Williams E, Ormondroyd E. Secondary (additional) findings from the 100,000 Genomes Project: Disease manifestation, health care outcomes, and costs of disclosure. Genet Med 2024; 26:101051. [PMID: 38131308 DOI: 10.1016/j.gim.2023.101051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 12/15/2023] [Accepted: 12/15/2023] [Indexed: 12/23/2023] Open
Abstract
PURPOSE The UK 100,000 Genomes Project offered participants screening for additional findings (AFs) in genes associated with familial hypercholesterolemia (FH) or hereditary cancer syndromes including breast/ovarian cancer (HBOC), Lynch, familial adenomatous polyposis, MYH-associated polyposis, multiple endocrine neoplasia (MEN), and von Hippel-Lindau. Here, we report disclosure processes, manifestation of AF-related disease, outcomes, and costs. METHODS An observational study in an area representing one-fifth of England. RESULTS Data were collected from 89 adult AF recipients. At disclosure, among 57 recipients of a cancer-predisposition-associated AF and 32 recipients of an FH-associated AF, 35% and 88%, respectively, had personal and/or family history evidence of AF-related disease. During post-disclosure investigations, 4 cancer-AF recipients had evidence of disease, including 1 medullary thyroid cancer. Six women with an HBOC AF, 3 women with a Lynch syndrome AF, and 2 individuals with a MEN AF elected for risk-reducing surgery. New hyperlipidemia diagnoses were made in 6 FH-AF recipients and treatment (re-)initiated for 7 with prior hyperlipidemia. Generating and disclosing AFs in this region cost £1.4m; £8680 per clinically significant AF. CONCLUSION Generation and disclosure of AFs identifies individuals with and without personal or familial evidence of disease and prompts appropriate clinical interventions. Results can inform policy toward secondary findings.
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Affiliation(s)
- Joshua Nolan
- Radcliffe Department of Medicine, University of Oxford, United Kingdom
| | - James Buchanan
- Health Economics Research Centre, University of Oxford, United Kingdom
| | - John Taylor
- Oxford Genetic Laboratories, Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom
| | - Joao Almeida
- Genomics England, United Kingdom Department of Health and Social Care, United Kingdom
| | - Tina Bedenham
- Oxford Genetic Laboratories, Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom
| | - Edward Blair
- Oxford Centre for Genomic Medicine, Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom
| | - Suzanne Broadgate
- Oxford Genetic Laboratories, Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom
| | - Samantha Butler
- Birmingham Women's and Children's Hospitals NHS Foundation Trust, Birmingham, United Kingdom
| | - Angela Cazeaux
- University Hospitals Southampton NHS Foundation Trust, Southampton, United Kingdom
| | - Judith Craft
- Oxford Genetic Laboratories, Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom
| | - Treena Cranston
- Oxford Genetic Laboratories, Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom
| | - Gillian Crawford
- University Hospitals Southampton NHS Foundation Trust, Southampton, United Kingdom
| | - Jamie Forrest
- Oxford Centre for Genomic Medicine, Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom; University of Manchester, Manchester, United Kingdom
| | - Jessica Gabriel
- Oxford Genetic Laboratories, Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom
| | - Elaine George
- University Hospitals Birmingham NHS Foundation Trust, Birmingham, United Kingdom
| | - Donna Gillen
- University Hospitals Birmingham NHS Foundation Trust, Birmingham, United Kingdom
| | - Ash Haeger
- Oxford Genetic Laboratories, Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom
| | | | - Lara Hawkes
- Oxford Centre for Genomic Medicine, Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom
| | - Claire Hodgkiss
- Oxford Genetic Laboratories, Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom
| | - Jonathan Hoffman
- Birmingham Women's and Children's Hospitals NHS Foundation Trust, Birmingham, United Kingdom
| | - Alan Jones
- University Hospitals Birmingham NHS Foundation Trust, Birmingham, United Kingdom
| | - Fredrik Karpe
- Radcliffe Department of Medicine, University of Oxford, United Kingdom; NIHR Oxford Biomedical Research Centre, Oxford, United Kingdom
| | - Dalia Kasperaviciute
- Genomics England, United Kingdom Department of Health and Social Care, United Kingdom
| | - Erika Kovacs
- University Hospitals Southampton NHS Foundation Trust, Southampton, United Kingdom
| | - Sarah Leigh
- Genomics England, United Kingdom Department of Health and Social Care, United Kingdom
| | - Elizabeth Limb
- Population Health Research Institute, St George's University of London, London, United Kingdom
| | - Anjali Lloyd-Jani
- Oxford Genetic Laboratories, Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom
| | - Javier Lopez
- Genomics England, United Kingdom Department of Health and Social Care, United Kingdom
| | - Anneke Lucassen
- Oxford Centre for Genomic Medicine, Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom; Centre for Personalised Medicine, Nuffield Department of Medicine, University of Oxford, United Kingdom
| | - Carlos McFarlane
- Birmingham Women's and Children's Hospitals NHS Foundation Trust, Birmingham, United Kingdom
| | - Anthony W O'Rourke
- Oxford Genetic Laboratories, Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom
| | - Emily Pond
- University Hospitals Southampton NHS Foundation Trust, Southampton, United Kingdom
| | - Catherine Sherman
- University Hospitals Southampton NHS Foundation Trust, Southampton, United Kingdom
| | - Helen Stewart
- Oxford Centre for Genomic Medicine, Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom
| | - Ellen Thomas
- Genomics England, United Kingdom Department of Health and Social Care, United Kingdom
| | - Simon Thomas
- University Hospitals Southampton NHS Foundation Trust, Southampton, United Kingdom
| | - Tessy Thomas
- University Hospitals Southampton NHS Foundation Trust, Southampton, United Kingdom
| | - Kate Thomson
- Oxford Genetic Laboratories, Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom
| | - Hannah Wakelin
- Oxford Centre for Genomic Medicine, Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom
| | - Susan Walker
- Genomics England, United Kingdom Department of Health and Social Care, United Kingdom
| | - Melanie Watson
- University Hospitals Southampton NHS Foundation Trust, Southampton, United Kingdom
| | - Eleanor Williams
- Genomics England, United Kingdom Department of Health and Social Care, United Kingdom
| | - Elizabeth Ormondroyd
- Radcliffe Department of Medicine, University of Oxford, United Kingdom; NIHR Oxford Biomedical Research Centre, Oxford, United Kingdom.
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10
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Wigby KM, Brockman D, Costain G, Hale C, Taylor SL, Belmont J, Bick D, Dimmock D, Fernbach S, Greally J, Jobanputra V, Kulkarni S, Spiteri E, Taft RJ. Evidence review and considerations for use of first line genome sequencing to diagnose rare genetic disorders. NPJ Genom Med 2024; 9:15. [PMID: 38409289 PMCID: PMC10897481 DOI: 10.1038/s41525-024-00396-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2023] [Accepted: 01/26/2024] [Indexed: 02/28/2024] Open
Abstract
Early use of genome sequencing (GS) in the diagnostic odyssey can reduce suffering and improve care, but questions remain about which patient populations are most amenable to GS as a first-line diagnostic test. To address this, the Medical Genome Initiative conducted a literature review to identify appropriate clinical indications for GS. Studies published from January 2011 to August 2022 that reported on the diagnostic yield (DY) or clinical utility of GS were included. An exploratory meta-analysis using a random effects model evaluated DY based on cohort size and diagnosed cases per cohort. Seventy-one studies met inclusion criteria, comprising over 13,000 patients who received GS in one of the following settings: hospitalized pediatric patients, pediatric outpatients, adult outpatients, or mixed. GS was the first-line test in 38% (27/71). The unweighted mean DY of first-line GS was 45% (12-73%), 33% (6-86%) in cohorts with prior genetic testing, and 33% (9-60%) in exome-negative cohorts. Clinical utility was reported in 81% of first-line GS studies in hospitalized pediatric patients. Changes in management varied by cohort and underlying molecular diagnosis (24-100%). To develop evidence-informed points to consider, the quality of all 71 studies was assessed using modified American College of Radiology (ACR) criteria, with five core points to consider developed, including recommendations for use of GS in the N/PICU, in lieu of sequential testing and when disorders with substantial allelic heterogeneity are suspected. Future large and controlled studies in the pediatric and adult populations may support further refinement of these recommendations.
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Affiliation(s)
- Kristen M Wigby
- University of California, Davis, CA, USA.
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA.
| | | | | | | | | | - John Belmont
- Genetics & Genomics Services Inc, Houston, TX, USA
| | | | - David Dimmock
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
| | | | - John Greally
- Albert Einstein College of Medicine, Bronx, NY, USA
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11
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Waung MW, Ma F, Wheeler AG, Zai CC, So J. The Diagnostic Landscape of Adult Neurogenetic Disorders. BIOLOGY 2023; 12:1459. [PMID: 38132285 PMCID: PMC10740572 DOI: 10.3390/biology12121459] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2023] [Revised: 11/11/2023] [Accepted: 11/16/2023] [Indexed: 12/23/2023]
Abstract
Neurogenetic diseases affect individuals across the lifespan, but accurate diagnosis remains elusive for many patients. Adults with neurogenetic disorders often undergo a long diagnostic odyssey, with multiple specialist evaluations and countless investigations without a satisfactory diagnostic outcome. Reasons for these diagnostic challenges include: (1) clinical features of neurogenetic syndromes are diverse and under-recognized, particularly those of adult-onset, (2) neurogenetic syndromes may manifest with symptoms that span multiple neurological and medical subspecialties, and (3) a positive family history may not be present or readily apparent. Furthermore, there is a large gap in the understanding of how to apply genetic diagnostic tools in adult patients, as most of the published literature focuses on the pediatric population. Despite these challenges, accurate genetic diagnosis is imperative to provide affected individuals and their families guidance on prognosis, recurrence risk, and, for an increasing number of disorders, offer targeted treatment. Here, we provide a framework for recognizing adult neurogenetic syndromes, describe the current diagnostic approach, and highlight studies using next-generation sequencing in different neurological disease cohorts. We also discuss diagnostic pitfalls, barriers to achieving a definitive diagnosis, and emerging technology that may increase the diagnostic yield of testing.
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Affiliation(s)
- Maggie W. Waung
- Division of General Neurology, Department of Neurology, Weill Institute for Neurosciences, University of California, San Francisco, CA 94158, USA
| | - Fion Ma
- Institute for Human Genetics, University of California San Francisco School of Medicine, San Francisco, CA 94143, USA
| | - Allison G. Wheeler
- Institute for Human Genetics, University of California San Francisco School of Medicine, San Francisco, CA 94143, USA
- Department of Neurology, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Clement C. Zai
- Tanenbaum Centre for Pharmacogenetics, Molecular Brain Science, Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, ON M5T 1R8, Canada
- Department of Psychiatry, Institute of Medical Science, Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Joyce So
- Division of Medical Genetics, Department of Pediatrics, University of California, San Francisco, CA 94158, USA
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12
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Abstract
Rare diseases are a leading cause of infant mortality and lifelong disability. To improve outcomes, timely diagnosis and effective treatments are needed. Genomic sequencing has transformed the traditional diagnostic process, providing rapid, accurate and cost-effective genetic diagnoses to many. Incorporating genomic sequencing into newborn screening programmes at the population scale holds the promise of substantially expanding the early detection of treatable rare diseases, with stored genomic data potentially benefitting health over a lifetime and supporting further research. As several large-scale newborn genomic screening projects launch internationally, we review the challenges and opportunities presented, particularly the need to generate evidence of benefit and to address the ethical, legal and psychosocial issues that genomic newborn screening raises.
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Affiliation(s)
- Zornitza Stark
- Australian Genomics, Melbourne, Victoria, Australia.
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Victoria, Australia.
- Department of Paediatrics, University of Melbourne, Melbourne, Victoria, Australia.
| | - Richard H Scott
- Great Ormond Street Hospital for Children, London, UK
- UCL Great Ormond Street Institute of Child Health, London, UK
- Genomics England, London, UK
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13
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Tein I. Recent advances in neurometabolic diseases: The genetic role in the modern era. Epilepsy Behav 2023; 145:109338. [PMID: 37453291 DOI: 10.1016/j.yebeh.2023.109338] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 06/21/2023] [Accepted: 06/22/2023] [Indexed: 07/18/2023]
Abstract
The global birth prevalence of all inborn errors of metabolism (IEMs) in children (49 studies, 1980-2017) is approximately 50.9/100,000 live births. Regional pooled birth prevalence showed higher rates in Eastern Mediterranean regions (75.7/100,000 live births) and highest in Saudi Arabia (169/100,000) with higher parental consanguinity rates of ∼60%. Case fatality rates globally are estimated to be 33% or higher. IEMs are a group of >600 heterogeneous disorders often presenting in newborns and infants with drug-resistant seizures and/or encephalopathy. Early diagnosis and treatments are key in the prevention of morbidity, early mortality, and high lifetime health care costs, such as the early recognition of the newborn with pyridoxine- or pyridoxal-L-phosphate-dependent seizures which do not respond to standard antiepileptic drugs. The earlier the recognition and intervention in the specific cofactor- or vitamin-responsive epilepsies, the better the outcome and prevention of intractable seizures and encephalopathy leading to irreversible neurologic injury. In recent years, the genetics of IEMs has been transformed by the emergence of new molecular genetic technologies. Depending upon the clinical phenotype, current genetic testing may include chromosomal microarray (deletion/duplication analysis), single target gene sequencing, gene panels (sequencing and deletion/duplication analysis), DNA methylation analysis, mitochondrial nuclear gene panel, and mtDNA sequencing and/or trio WES or WGS (which have reduced in costs). A meta-analysis, showed WES and epilepsy gene panels to be the most cost-effective genetic tests for unknown epilepsies versus chromosomal microarray. Most recently, rapid genomic sequencing (RGS) has been associated with a shorter time to diagnosis (3 days) and increased diagnostic yield when compared with standard-of-care testing, including gene panels and microarrays. A randomized controlled trial (RCT) of rapid(r) WGS or rWES in acutely ill infants with diseases of unknown etiology in pediatric ICUs in San Diego, California found RGS to be highly clinically useful for 77% of 201 infants. RGS changed clinical management in 28% of infants and outcomes in 15%. An Australian study of ultra-rapid (ur) exome sequencing (mean time to genomic test report of 3.3 days) in 108 critically ill infants and children with suspected monogenic conditions, had a molecular diagnostic yield of 51% with 20% requiring further genetic analysis. In 42/55 (76%), ur exome sequencing was felt to have influenced clinical management for targeted treatments, surveillance, or palliative care, however, the study was not designed or powered to measure differences in major clinical outcomes compared to standard care of critically ill patients. Further research is needed to understand this tool's clinical value and generalizability balanced against its high costs. A paradigm shift is evolving from pattern- and evidence-based medicine toward algorithm-based, precision medicine targeted to individual mutations. Meticulous clinical phenotyping and pedigree analysis, combined with advances in high-throughput metabolomics, proteomics, transcriptomics (RNAseq in clinically relevant tissues), and genomics, have expedited the identification of novel pathomechanisms and new therapeutic targets. Evaluation of these therapies in IEMs, many of which manifest with encephalopathy and epilepsy, will depend on international registries of well-characterized phenotypes in RCTs and measurement of clinically relevant endpoints. The earlier the recognition and diagnosis and intervention with targeted therapies, the better the overall outcome in terms of the impact on intellectual disability and the effective management of the associated epilepsy.
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Affiliation(s)
- Ingrid Tein
- Division of Neurology, Dept. of Pediatrics and Dept. of Laboratory Medicine and Pathobiology, The Genetics and Genome Biology Program, The Research Institute, The Hospital for Sick Children, The University of Toronto, Toronto, Ontario, Canada M5G 1X8.
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14
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Zhang L, Parvin R, Chen M, Hu D, Fan Q, Ye F. High-throughput microfluidic droplets in biomolecular analytical system: A review. Biosens Bioelectron 2023; 228:115213. [PMID: 36906989 DOI: 10.1016/j.bios.2023.115213] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 02/13/2023] [Accepted: 03/06/2023] [Indexed: 03/11/2023]
Abstract
Droplet microfluidic technology has revolutionized biomolecular analytical research, as it has the capability to reserve the genotype-to-phenotype linkage and assist for revealing the heterogeneity. Massive and uniform picolitre droplets feature dividing solution to the level that single cell and single molecule in each droplet can be visualized, barcoded, and analyzed. Then, the droplet assays can unfold intensive genomic data, offer high sensitivity, and screen and sort from a large number of combinations or phenotypes. Based on these unique advantages, this review focuses on up-to-date research concerning diverse screening applications utilizing droplet microfluidic technology. The emerging progress of droplet microfluidic technology is first introduced, including efficient and scaling-up in droplets encapsulation, and prevalent batch operations. Then the new implementations of droplet-based digital detection assays and single-cell muti-omics sequencing are briefly examined, along with related applications such as drug susceptibility testing, multiplexing for cancer subtype identification, interactions of virus-to-host, and multimodal and spatiotemporal analysis. Meanwhile, we specialize in droplet-based large-scale combinational screening regarding desired phenotypes, with an emphasis on sorting for immune cells, antibodies, enzymatic properties, and proteins produced by directed evolution methods. Finally, some challenges, deployment and future perspective of droplet microfluidics technology in practice are also discussed.
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Affiliation(s)
- Lexiang Zhang
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), Wenzhou, Zhejiang, 325000, China; Zhejiang Engineering Research Center for Tissue Repair Materials, Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, Zhejiang, 325000, China
| | - Rokshana Parvin
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), Wenzhou, Zhejiang, 325000, China; Zhejiang Engineering Research Center for Tissue Repair Materials, Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, Zhejiang, 325000, China
| | - Mingshuo Chen
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), Wenzhou, Zhejiang, 325000, China; Zhejiang Engineering Research Center for Tissue Repair Materials, Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, Zhejiang, 325000, China
| | - Dingmeng Hu
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), Wenzhou, Zhejiang, 325000, China; Zhejiang Engineering Research Center for Tissue Repair Materials, Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, Zhejiang, 325000, China
| | - Qihui Fan
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), Wenzhou, Zhejiang, 325000, China; Zhejiang Engineering Research Center for Tissue Repair Materials, Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, Zhejiang, 325000, China; Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, 100190, China.
| | - Fangfu Ye
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), Wenzhou, Zhejiang, 325000, China; Zhejiang Engineering Research Center for Tissue Repair Materials, Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, Zhejiang, 325000, China; Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, 100190, China.
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15
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Parker G, Hunter S, Ghazi S, Hayeems RZ, Rousseau F, Miller FA. Decision impact studies, evidence of clinical utility for genomic assays in cancer: A scoping review. PLoS One 2023; 18:e0280582. [PMID: 36897859 PMCID: PMC10004522 DOI: 10.1371/journal.pone.0280582] [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: 08/14/2022] [Accepted: 01/03/2023] [Indexed: 03/11/2023] Open
Abstract
BACKGROUND Decision impact studies have become increasingly prevalent in cancer prognostic research in recent years. These studies aim to evaluate the impact of a genomic test on decision-making and appear to be a new form of evidence of clinical utility. The objectives of this review were to identify and characterize decision impact studies in genomic medicine in cancer care and categorize the types of clinical utility outcomes reported. METHODS We conducted a search of four databases, Medline, Embase, Scopus and Web of Science, from inception to June 2022. Empirical studies that reported a "decision impact" assessment of a genomic assay on treatment decisions or recommendations for cancer patients were included. We followed scoping review methodology and adapted the Fryback and Thornbury Model to collect and analyze data on clinical utility. The database searches identified 1803 unique articles for title/abstract screening; 269 articles moved to full-text review. RESULTS 87 studies met inclusion criteria. All studies were published in the last 12 years with the majority for breast cancer (72%); followed by other cancers (28%) (lung, prostate, colon). Studies reported on the impact of 19 different proprietary (18) and generic (1) assays. Across all four levels of clinical utility, outcomes were reported for 22 discrete measures, including the impact on provider/team decision-making (100%), provider confidence (31%); change in treatment received (46%); patient psychological impacts (17%); and costing or savings impacts (21%). Based on the data synthesis, we created a comprehensive table of outcomes reported for clinical utility. CONCLUSIONS This scoping review is a first step in understanding the evolution and uses of decision impact studies and their influence on the integration of emerging genomic technologies in cancer care. The results imply that DIS are positioned to provide evidence of clinical utility and impact clinical practice and reimbursement decision-making in cancer care. Systematic review registration: Open Science Framework osf.io/hm3jr.
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Affiliation(s)
- Gillian Parker
- Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, Ontario, Canada
| | - Sarah Hunter
- Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, Ontario, Canada
| | - Samer Ghazi
- Lawrence S. Bloomberg Faculty of Nursing, University of Toronto, Toronto, Ontario, Canada
| | - Robin Z. Hayeems
- Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, Ontario, Canada
- Child Health Evaluative Sciences Program, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Francois Rousseau
- Department of Molecular Biology, Medical Biochemistry, and Pathology, Faculty of Medicine, Université Laval, Québec City, Québec, Canada
| | - Fiona A. Miller
- Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, Ontario, Canada
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16
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Pan A, Scodellaro S, Khan T, Ushcatz I, Wu W, Curtis M, Cohen E, Cohn RD, Hayeems RZ, Meyn MS, Orkin J, Otal J, Reuter MS, Walker S, Scherer SW, Marshall CR, Cohn I, Costain G. Pharmacogenetic profiling via genome sequencing in children with medical complexity. Pediatr Res 2023; 93:905-910. [PMID: 36167815 PMCID: PMC10033400 DOI: 10.1038/s41390-022-02313-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 07/25/2022] [Accepted: 09/03/2022] [Indexed: 11/09/2022]
Abstract
BACKGROUND Children with medical complexity (CMC) are a priority pediatric population, with high resource use and associated costs. Genome-wide sequencing is increasingly organized for CMC early in life as a diagnostic test. Polypharmacy becomes common as CMC age. Clinically relevant pharmacogenetic (PGx) information can be extracted from existing genome sequencing (GS) data via GS-PGx profiling. The role of GS-PGx profiling in the CMC population is unclear. METHODS Prescribed medications were extracted from care plans of 802 eligible CMC enrolled in a structured Complex Care Program over a 10-year period. Drug-gene associations were annotated using curated Clinical Pharmacogenetics Implementation Consortium data. GS-PGx profiling was then performed for a subset of 50 CMC. RESULTS Overall, 546 CMC (68%) were prescribed at least one medication with an established PGx association. In the GS-PGx subgroup, 24 (48%) carried variants in pharmacogenes with drug-gene guidelines for one or more of their current medications. All had findings of potential relevance to some medications, including 32 (64%) with variants in CYP2C19 that could affect their metabolism of proton-pump inhibitors. CONCLUSION GS-PGx profiling at the time of diagnostics-focused genetic testing could be an efficient way to incorporate precision prescribing practices into the lifelong care of CMC. IMPACT Polypharmacy and genetic test utilization are both common in children with medical complexity. The role of repurposing genome sequencing data for pharmacogenetic profiling in children with medical complexity was previously unclear. We identified a high rate of medication use with clinically relevant drug-gene associations in this priority pediatric population and demonstrated that relevant pharmacogenetic information can be extracted from their existing genome sequencing data. Pharmacogenetic profiling at the time of diagnostics-focused genetic testing could be an efficient way to incorporate precision prescribing practices into the lifelong care of children with medical complexity.
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Affiliation(s)
- Amy Pan
- Genetics and Genome Biology, Research Institute, The Hospital for Sick Children, Toronto, ON, Canada
| | - Sierra Scodellaro
- Program in Translational Medicine, The Hospital for Sick Children, Toronto, ON, Canada
- Division of Clinical Pharmacology and Toxicology, Department of Paediatrics, The Hospital for Sick Children, University of Toronto, Toronto, ON, Canada
| | - Tayyaba Khan
- Genetics and Genome Biology, Research Institute, The Hospital for Sick Children, Toronto, ON, Canada
| | - Inna Ushcatz
- Genetics and Genome Biology, Research Institute, The Hospital for Sick Children, Toronto, ON, Canada
| | - Wendy Wu
- Genetics and Genome Biology, Research Institute, The Hospital for Sick Children, Toronto, ON, Canada
| | - Meredith Curtis
- Genetics and Genome Biology, Research Institute, The Hospital for Sick Children, Toronto, ON, Canada
| | - Eyal Cohen
- Department of Paediatrics, University of Toronto, Toronto, ON, Canada
- Division of Paediatric Medicine, The Hospital for Sick Children, Toronto, ON, Canada
- Child Health Evaluative Sciences, Research Institute, The Hospital for Sick Children, Toronto, ON, Canada
- Institute of Health Policy Management and Evaluation, University of Toronto, Toronto, ON, Canada
- Edwin S.H. Leong Centre for Healthy Children, University of Toronto, Toronto, ON, Canada
| | - Ronald D Cohn
- Genetics and Genome Biology, Research Institute, The Hospital for Sick Children, Toronto, ON, Canada
- Department of Paediatrics, University of Toronto, Toronto, ON, Canada
- Division of Paediatric Medicine, The Hospital for Sick Children, Toronto, ON, Canada
- Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Robin Z Hayeems
- Child Health Evaluative Sciences, Research Institute, The Hospital for Sick Children, Toronto, ON, Canada
- Institute of Health Policy Management and Evaluation, University of Toronto, Toronto, ON, Canada
- Centre for Genetic Medicine, The Hospital for Sick Children, Toronto, ON, Canada
| | - M Stephen Meyn
- Department of Paediatrics, University of Toronto, Toronto, ON, Canada
- Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
- Centre for Genetic Medicine, The Hospital for Sick Children, Toronto, ON, Canada
- Center for Human Genomics and Precision Medicine, University of Wisconsin, Madison, WI, USA
| | - Julia Orkin
- Department of Paediatrics, University of Toronto, Toronto, ON, Canada
- Division of Paediatric Medicine, The Hospital for Sick Children, Toronto, ON, Canada
- Child Health Evaluative Sciences, Research Institute, The Hospital for Sick Children, Toronto, ON, Canada
| | - Jaskiran Otal
- Division of Paediatric Medicine, The Hospital for Sick Children, Toronto, ON, Canada
| | - Miriam S Reuter
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON, Canada
| | - Susan Walker
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON, Canada
| | - Stephen W Scherer
- Genetics and Genome Biology, Research Institute, The Hospital for Sick Children, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
- Centre for Genetic Medicine, The Hospital for Sick Children, Toronto, ON, Canada
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON, Canada
| | - Christian R Marshall
- Centre for Genetic Medicine, The Hospital for Sick Children, Toronto, ON, Canada
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON, Canada
- Genome Diagnostics, Department of Paediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, ON, Canada
- Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| | - Iris Cohn
- Program in Translational Medicine, The Hospital for Sick Children, Toronto, ON, Canada
- Division of Clinical Pharmacology and Toxicology, Department of Paediatrics, The Hospital for Sick Children, University of Toronto, Toronto, ON, Canada
| | - Gregory Costain
- Genetics and Genome Biology, Research Institute, The Hospital for Sick Children, Toronto, ON, Canada.
- Department of Paediatrics, University of Toronto, Toronto, ON, Canada.
- Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, ON, Canada.
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.
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17
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Turbitt E, Kohler JN, Angelo F, Miller IM, Lewis KL, Goddard KAB, Wilfond BS, Biesecker BB, Leo MC. The PrU: Development and validation of a measure to assess personal utility of genomic results. Genet Med 2023; 25:100356. [PMID: 36516964 DOI: 10.1016/j.gim.2022.12.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 12/06/2022] [Accepted: 12/07/2022] [Indexed: 12/14/2022] Open
Abstract
PURPOSE People report experiencing value from learning genomic results even in the absence of clinically actionable information. Such personal utility has emerged as a key concept in genomic medicine. The lack of a validated patient-reported outcome measure of personal utility has impeded the ability to assess this concept among those receiving genomic results and evaluate the patient-perceived value of genomics. We aimed to construct and psychometrically evaluate a scale to measure personal utility of genomic results-the Personal Utility (PrU) scale. METHODS We used an evidence-based, operational definition of personal utility, with data from a systematic literature review and Delphi survey to build a novel scale. After piloting with 24 adults, the PrU was administered to healthy adults in a Clinical Sequencing Evidence-Generating Research Consortium study after receiving results. We investigated the responses using exploratory factor analysis. RESULTS The exploratory factor analysis (N = 841 participants) resulted in a 3-factor solution, accounting for 74% of the variance in items: (1) self-knowledge (α = 0.92), (2) reproductive planning (α = 0.89), and (3) practical benefits (α = 0.91). CONCLUSION Our findings support the use of the 3-factor PrU to assess personal utility of genomic results. Validation of the PrU in other samples will be important for more wide-spread application.
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Affiliation(s)
- Erin Turbitt
- Graduate School of Health, University of Technology Sydney, Ultimo, New South Wales, Australia.
| | - Jennefer N Kohler
- Stanford Center for Undiagnosed Diseases, Standard University, Stanford, CA
| | - Frank Angelo
- Department of Medical Social Sciences, Feinberg School of Medicine, Northwestern University, Chicago, IL
| | - Ilana M Miller
- Rare Disease Institute, Children's National Hospital, Washington, DC
| | - Katie L Lewis
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD
| | | | - Benjamin S Wilfond
- Treuman Katz Center for Pediatric Bioethics, Seattle Children's Hospital, Seattle, WA
| | - Barbara B Biesecker
- Genomics, Ethics, and Translational Research Program, RTI International, Washington, DC
| | - Michael C Leo
- Center for Health Research, Kaiser Permanente Northwest, Portland, OR
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18
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Handra J, Elbert A, Gazzaz N, Moller-Hansen A, Hyunh S, Lee HK, Boerkoel P, Alderman E, Anderson E, Clarke L, Hamilton S, Hamman R, Hughes S, Ip S, Langlois S, Lee M, Li L, Mackenzie F, Patel MS, Prentice LM, Sangha K, Sato L, Seath K, Seppelt M, Swenerton A, Warnock L, Zambonin JL, Boerkoel CF, Chin HL, Armstrong L. The practice of genomic medicine: A delineation of the process and its governing principles. Front Med (Lausanne) 2023; 9:1071348. [PMID: 36714130 PMCID: PMC9877428 DOI: 10.3389/fmed.2022.1071348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2022] [Accepted: 12/23/2022] [Indexed: 01/13/2023] Open
Abstract
Genomic medicine, an emerging medical discipline, applies the principles of evolution, developmental biology, functional genomics, and structural genomics within clinical care. Enabling widespread adoption and integration of genomic medicine into clinical practice is key to achieving precision medicine. We delineate a biological framework defining diagnostic utility of genomic testing and map the process of genomic medicine to inform integration into clinical practice. This process leverages collaboration and collective cognition of patients, principal care providers, clinical genomic specialists, laboratory geneticists, and payers. We detail considerations for referral, triage, patient intake, phenotyping, testing eligibility, variant analysis and interpretation, counseling, and management within the utilitarian limitations of health care systems. To reduce barriers for clinician engagement in genomic medicine, we provide several decision-making frameworks and tools and describe the implementation of the proposed workflow in a prototyped electronic platform that facilitates genomic care. Finally, we discuss a vision for the future of genomic medicine and comment on areas for continued efforts.
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Affiliation(s)
- Julia Handra
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada,Provincial Medical Genetics Program, British Columbia Women’s Hospital and Health Centre, Vancouver, BC, Canada
| | - Adrienne Elbert
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada,Provincial Medical Genetics Program, British Columbia Women’s Hospital and Health Centre, Vancouver, BC, Canada
| | - Nour Gazzaz
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada,Provincial Medical Genetics Program, British Columbia Women’s Hospital and Health Centre, Vancouver, BC, Canada,Department of Pediatrics, University of British Columbia, Vancouver, BC, Canada,Department of Pediatrics, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Ashley Moller-Hansen
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada,Provincial Medical Genetics Program, British Columbia Women’s Hospital and Health Centre, Vancouver, BC, Canada
| | - Stephanie Hyunh
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada,Provincial Medical Genetics Program, British Columbia Women’s Hospital and Health Centre, Vancouver, BC, Canada
| | - Hyun Kyung Lee
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada,Provincial Medical Genetics Program, British Columbia Women’s Hospital and Health Centre, Vancouver, BC, Canada
| | - Pierre Boerkoel
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Emily Alderman
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada,Provincial Medical Genetics Program, British Columbia Women’s Hospital and Health Centre, Vancouver, BC, Canada
| | - Erin Anderson
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada,Provincial Medical Genetics Program, British Columbia Women’s Hospital and Health Centre, Vancouver, BC, Canada
| | - Lorne Clarke
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada,Provincial Medical Genetics Program, British Columbia Women’s Hospital and Health Centre, Vancouver, BC, Canada
| | - Sara Hamilton
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada,Provincial Medical Genetics Program, British Columbia Women’s Hospital and Health Centre, Vancouver, BC, Canada
| | - Ronnalea Hamman
- Provincial Medical Genetics Program, British Columbia Women’s Hospital and Health Centre, Vancouver, BC, Canada
| | - Shevaun Hughes
- Clinical Research Informatics, Provincial Health Services Authority, Vancouver, BC, Canada
| | - Simon Ip
- Process & Systems Improvement, Provincial Health Services Authority, Vancouver, BC, Canada
| | - Sylvie Langlois
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada,Provincial Medical Genetics Program, British Columbia Women’s Hospital and Health Centre, Vancouver, BC, Canada
| | - Mary Lee
- Provincial Medical Genetics Program, British Columbia Women’s Hospital and Health Centre, Vancouver, BC, Canada
| | - Laura Li
- Breakthrough Genomics, Irvine, CA, United States
| | - Frannie Mackenzie
- Women’s Health Research Institute, British Columbia Women’s Hospital and Health Centre, Vancouver, BC, Canada
| | - Millan S. Patel
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada,Provincial Medical Genetics Program, British Columbia Women’s Hospital and Health Centre, Vancouver, BC, Canada
| | - Leah M. Prentice
- Provincial Medical Genetics Program, British Columbia Women’s Hospital and Health Centre, Vancouver, BC, Canada
| | - Karan Sangha
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada,Provincial Medical Genetics Program, British Columbia Women’s Hospital and Health Centre, Vancouver, BC, Canada
| | - Laura Sato
- Process & Systems Improvement, Provincial Health Services Authority, Vancouver, BC, Canada
| | - Kimberly Seath
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada,Provincial Medical Genetics Program, British Columbia Women’s Hospital and Health Centre, Vancouver, BC, Canada
| | - Margaret Seppelt
- Process & Systems Improvement, Provincial Health Services Authority, Vancouver, BC, Canada
| | - Anne Swenerton
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada,Provincial Medical Genetics Program, British Columbia Women’s Hospital and Health Centre, Vancouver, BC, Canada
| | - Lynn Warnock
- Provincial Medical Genetics Program, British Columbia Women’s Hospital and Health Centre, Vancouver, BC, Canada
| | - Jessica L. Zambonin
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada,Provincial Medical Genetics Program, British Columbia Women’s Hospital and Health Centre, Vancouver, BC, Canada
| | - Cornelius F. Boerkoel
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada,Provincial Medical Genetics Program, British Columbia Women’s Hospital and Health Centre, Vancouver, BC, Canada
| | - Hui-Lin Chin
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada,Provincial Medical Genetics Program, British Columbia Women’s Hospital and Health Centre, Vancouver, BC, Canada,Khoo Teck Puat-National University Children’s Medical Institute, National University Hospital, Singapore, Singapore,*Correspondence: Hui-Lin Chin,
| | - Linlea Armstrong
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada,Provincial Medical Genetics Program, British Columbia Women’s Hospital and Health Centre, Vancouver, BC, Canada
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19
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Hayeems RZ, Bernier F, Boycott KM, Hartley T, Michaels-Igbokwe C, Marshall DA. Positioning whole exome sequencing in the diagnostic pathway for rare disease to optimise utility: a protocol for an observational cohort study and an economic evaluation. BMJ Open 2022; 12:e061468. [PMID: 36216418 PMCID: PMC9557316 DOI: 10.1136/bmjopen-2022-061468] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
INTRODUCTION Despite the superior diagnostic performance of exome and genome sequencing compared with conventional genetic tests, evidence gaps related to clinical utility and cost effectiveness have limited their availability in routine clinical practice in many jurisdictions. To inform adoption and reimbursement policy, this protocol provides a chain of evidence approach to determining the diagnostic utility, clinical utility and cost-effectiveness of whole exome sequencing (WES) from seven medical genetic centres in two Canadian provinces. METHODS AND ANALYSIS Using a multicentre observational cohort design, we will extract data specific to the pre-WES diagnostic pathway and 1-year post-WES medical management from electronic medical records for 650 patients with rare disease of suspected genetic aetiology who receive WES. The date from the clinical record will be linked to provincial administrative health database to capture healthcare resource use and estimate costs. Our analysis will: (1) define and describe diagnostic testing pathways that occur prior to WES among patients with rare disease, (2) determine the diagnostic utility of WES, characterised as the proportion of patients for whom causative DNA variants are identified, (3) determine the clinical utility of WES, characterised as a change in medical management triggered by WES results, (4) determine the pattern and cost of health service utilisation prior and 1 year following WES among patients who receive a diagnosis, do not receive a diagnosis, or receive an uncertain diagnosis and (5) estimate the cost-effectiveness of WES compared with conventional diagnostic testing pathways, measured by the incremental cost per additional patient diagnosed by WES using simulation modelling. ETHICS AND DISSEMINATION This protocol was approved by Clinical Trials Ontario (CTO-1577) and research ethics boards at the University of Calgary (REB18-0744 and REB20-1449) and University of Alberta (Pro0009156). Findings will be disseminated through academic publications and policy reports.
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Affiliation(s)
- Robin Z Hayeems
- Child Health Evaluative Sciences, Hospital for Sick Children Research Institute, Toronto, Ontario, Canada
- Institute of Health Policy Management and Evaluation, University of Toronto, Toronto, Ontario, Canada
| | - Francois Bernier
- Department of Medical Genetics, Alberta Children's Hospital, Calgary, Alberta, Canada
- Cummings School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Kym M Boycott
- Department of Genetics, Children's Hospital of Eastern Ontario Research Institute, Ottawa, Ontario, Canada
- Department of Paediatrics, Facuty of Medicine, University of Ottawa, Ottawa, Ontario, Canada
| | - Taila Hartley
- Department of Genetics, Children's Hospital of Eastern Ontario Research Institute, Ottawa, Ontario, Canada
| | - Christine Michaels-Igbokwe
- Cummings School of Medicine, University of Calgary, Calgary, Alberta, Canada
- O'Brien Institute for Public Health, University of Calgary, Calgary, Alberta, Canada
| | - Deborah A Marshall
- Cummings School of Medicine, University of Calgary, Calgary, Alberta, Canada
- O'Brien Institute for Public Health, University of Calgary, Calgary, Alberta, Canada
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20
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Ferket BS, Baldwin Z, Murali P, Pai A, Mittendorf KF, Russell HV, Chen F, Lynch FL, Lich KH, Hindorff LA, Savich R, Slavotinek A, Smith HS, Gelb BD, Veenstra DL. Cost-effectiveness frameworks for comparing genome and exome sequencing versus conventional diagnostic pathways: A scoping review and recommended methods. Genet Med 2022; 24:2014-2027. [PMID: 35833928 PMCID: PMC9997042 DOI: 10.1016/j.gim.2022.06.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 06/13/2022] [Accepted: 06/15/2022] [Indexed: 01/21/2023] Open
Abstract
PURPOSE Methodological challenges have limited economic evaluations of genome sequencing (GS) and exome sequencing (ES). Our objective was to develop conceptual frameworks for model-based cost-effectiveness analyses (CEAs) of diagnostic GS/ES. METHODS We conducted a scoping review of economic analyses to develop and iterate with experts a set of conceptual CEA frameworks for GS/ES for prenatal testing, early diagnosis in pediatrics, diagnosis of delayed-onset disorders in pediatrics, genetic testing in cancer, screening of newborns, and general population screening. RESULTS Reflecting on 57 studies meeting inclusion criteria, we recommend the following considerations for each clinical scenario. For prenatal testing, performing comparative analyses of costs of ES strategies and postpartum care, as well as genetic diagnoses and pregnancy outcomes. For early diagnosis in pediatrics, modeling quality-adjusted life years (QALYs) and costs over ≥20 years for rapid turnaround GS/ES. For hereditary cancer syndrome testing, modeling cumulative costs and QALYs for the individual tested and first/second/third-degree relatives. For tumor profiling, not restricting to treatment uptake or response and including QALYs and costs of downstream outcomes. For screening, modeling lifetime costs and QALYs and considering consequences of low penetrance and GS/ES reanalysis. CONCLUSION Our frameworks can guide the design of model-based CEAs and ultimately foster robust evidence for the economic value of GS/ES.
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Affiliation(s)
- Bart S Ferket
- Institute for Healthcare Delivery Science, Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY.
| | - Zach Baldwin
- The Comparative Health Outcomes, Policy and Economics (CHOICE) Institute, School of Pharmacy, University of Washington, Seattle, WA
| | - Priyanka Murali
- Division of Medical Genetics, Department of Medicine, University of Washington Medical Center, University of Washington, Seattle, WA
| | - Akila Pai
- Institute for Healthcare Delivery Science, Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Kathleen F Mittendorf
- Department of Translational and Applied Genomics (TAG), Kaiser Permanente Center for Health Research, Kaiser Permanente Northwest, Portland, Oregon; Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN
| | - Heidi V Russell
- Texas Children's Cancer Center, Baylor College of Medicine, Houston, TX; Center for Medical Ethics and Health Policy, Baylor College of Medicine, Houston, TX
| | - Flavia Chen
- Program in Bioethics, University of California San Francisco, San Francisco, CA; Institute for Human Genetics, University of California San Francisco, San Francisco, CA
| | | | - Kristen Hassmiller Lich
- Department of Health Policy and Management, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Lucia A Hindorff
- Division of Genomic Medicine, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD
| | - Renate Savich
- Department of Pediatrics, University of Mississippi Medical Center, Jackson, MS; Division of Neonatology, School of Medicine, University of New Mexico Health Sciences Center, Albuquerque, NM
| | - Anne Slavotinek
- Department of Pediatrics, University of California San Francisco, San Francisco, CA
| | - Hadley Stevens Smith
- Center for Medical Ethics and Health Policy, Baylor College of Medicine, Houston, TX
| | - Bruce D Gelb
- Departments of Pediatrics and Genetics & Genomic Sciences, Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY
| | - David L Veenstra
- The Comparative Health Outcomes, Policy and Economics (CHOICE) Institute, School of Pharmacy, University of Washington, Seattle, WA
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21
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Alam A, Parfyonov M, Huang CY, Gill I, Connolly MB, Illes J. Targeted Whole Exome Sequencing in Children With Early-Onset Epilepsy: Parent Experiences. J Child Neurol 2022; 37:840-850. [PMID: 35921196 PMCID: PMC9554160 DOI: 10.1177/08830738221113901] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
This study investigated the experiences of 25 caregivers of children with early-onset, treatment-resistant epilepsy who pursued whole exome sequencing to determine the impact of the test results on their child's treatment. Caregivers who consented to be recontacted were recruited from a previous study investigating the diagnostic yield of whole exome sequencing. A semistructured interview addressed questions based on one of 2 study phases. The first phase discussed the decision-making process for genetic testing (15 interviews), which revealed 4 major themes: (1) prognosis, (2) engagement, (3) concerns, and (4) autonomy. The second phase discussed the impact of genetic testing on treatment (10 interviews), which revealed 3 major themes: (1) testing features, (2) emotional impact, and (3) treatment outcomes. Overall, parents pursued genetic testing to obtain a clear prognosis, inform treatment decisions, engage with other families, and exercise autonomy. Caregivers felt that early testing is warranted to inform their child's diagnostic odyssey.
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Affiliation(s)
- Armaghan Alam
- Neuroethics Canada, Division of Neurology, Department of Medicine, University of British Columbia, Vancouver, British Columbia, Canada,Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Maksim Parfyonov
- Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada,Department of Pediatrics, Division of Neurology, BC Children’s Hospital, Vancouver, British Columbia, Canada
| | - Camille Y. Huang
- Neuroethics Canada, Division of Neurology, Department of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Inderpal Gill
- Department of Pediatrics, Division of Neurology, BC Children’s Hospital, Vancouver, British Columbia, Canada
| | - Mary B. Connolly
- Department of Pediatrics, Division of Neurology, BC Children’s Hospital, Vancouver, British Columbia, Canada
| | - Judy Illes
- Neuroethics Canada, Division of Neurology, Department of Medicine, University of British Columbia, Vancouver, British Columbia, Canada,Judy Illes, CM, PhD, Professor of Neurology, Department of Medicine, University of British Columbia, 2211 Wesbrook Mall, Koerner S124, Vancouver, BC V6T 2B5 Canada.
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22
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Shickh S, Mighton C, Clausen M, Adi-Wauran E, Hirjikaka D, Kodida R, Krishnapillai S, Reble E, Sam J, Shaw A, Lerner-Ellis J, Baxter NN, Laupacis A, Bombard Y. "Doctors shouldn't have to cheat the system": Clinicians' real-world experiences of the utility of genomic sequencing. Genet Med 2022; 24:1888-1898. [PMID: 35612591 DOI: 10.1016/j.gim.2022.04.024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Revised: 04/27/2022] [Accepted: 04/28/2022] [Indexed: 11/24/2022] Open
Abstract
PURPOSE Emerging genetic tests such as genomic sequencing (GS) can generate a broad range of benefits, but funding criteria only prioritize diagnosis and clinical management. There is limited evidence on all types of benefits obtained from GS in practice. We aimed to explore real-world experiences of Canadian clinicians across specialties on the full range of benefits obtained from the results from GS. METHODS We conducted a qualitative study using semistructured interviews with Canadian clinicians. Transcripts were thematically analyzed using constant comparison. RESULTS In total, 25 clinicians participated, including 12 geneticists, 7 genetic counselors, 4 oncologists, 1 neurologist, and 1 family physician. Although diagnoses and management were the most valued benefits of GS, clinicians also prioritized nontraditional utility, such as access to community supports. However, clinicians felt "restricted" by funding bodies, which only approved funding when GS would inform diagnoses and management. Consequently, clinicians sought ways to "cheat the system" to access GS (eg, research testing) but acknowledged workarounds were burdensome, drove inequity, and undermined patient care. CONCLUSION Current governance structures undervalue real-world benefits of GS leading clinicians to adopt workarounds, which jeopardize patient care. These results support calls for the expansion of the definition of clinical utility and research to quantify the additional benefits.
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Affiliation(s)
- Salma Shickh
- Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, Ontario, Canada; Genomics Health Services and Policy Research Program, Li Ka Shing Knowledge Institute, St. Michael's Hospital, Unity Health Toronto, Toronto, Ontario, Canada
| | - Chloe Mighton
- Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, Ontario, Canada; Genomics Health Services and Policy Research Program, Li Ka Shing Knowledge Institute, St. Michael's Hospital, Unity Health Toronto, Toronto, Ontario, Canada
| | - Marc Clausen
- Genomics Health Services and Policy Research Program, Li Ka Shing Knowledge Institute, St. Michael's Hospital, Unity Health Toronto, Toronto, Ontario, Canada
| | - Ella Adi-Wauran
- Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, Ontario, Canada; Genomics Health Services and Policy Research Program, Li Ka Shing Knowledge Institute, St. Michael's Hospital, Unity Health Toronto, Toronto, Ontario, Canada
| | - Daena Hirjikaka
- Genomics Health Services and Policy Research Program, Li Ka Shing Knowledge Institute, St. Michael's Hospital, Unity Health Toronto, Toronto, Ontario, Canada
| | - Rita Kodida
- Genomics Health Services and Policy Research Program, Li Ka Shing Knowledge Institute, St. Michael's Hospital, Unity Health Toronto, Toronto, Ontario, Canada
| | - Suvetha Krishnapillai
- Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, Ontario, Canada; Genomics Health Services and Policy Research Program, Li Ka Shing Knowledge Institute, St. Michael's Hospital, Unity Health Toronto, Toronto, Ontario, Canada
| | - Emma Reble
- Genomics Health Services and Policy Research Program, Li Ka Shing Knowledge Institute, St. Michael's Hospital, Unity Health Toronto, Toronto, Ontario, Canada
| | - Jordan Sam
- Genomics Health Services and Policy Research Program, Li Ka Shing Knowledge Institute, St. Michael's Hospital, Unity Health Toronto, Toronto, Ontario, Canada
| | - Angela Shaw
- Genomics Health Services and Policy Research Program, Li Ka Shing Knowledge Institute, St. Michael's Hospital, Unity Health Toronto, Toronto, Ontario, Canada
| | - Jordan Lerner-Ellis
- Lunenfeld Tanenbaum Research Institute, Sinai Health, Toronto, Ontario, Canada; Pathology and Laboratory Medicine, Mount Sinai Hospital, Sinai Health, Toronto, Ontario, Canada; Department of Laboratory Medicine and Pathobiology, Temerty Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Nancy N Baxter
- Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, Ontario, Canada; Li Ka Shing Knowledge Institute, St. Michael's Hospital, Unity Health Toronto, Toronto, Ontario, Canada; Department of Surgery, Temerty Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada; Melbourne School of Population and Global Health, University of Melbourne, Melbourne, Victoria, Australia
| | - Andreas Laupacis
- Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, Ontario, Canada; Li Ka Shing Knowledge Institute, St. Michael's Hospital, Unity Health Toronto, Toronto, Ontario, Canada
| | - Yvonne Bombard
- Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, Ontario, Canada; Genomics Health Services and Policy Research Program, Li Ka Shing Knowledge Institute, St. Michael's Hospital, Unity Health Toronto, Toronto, Ontario, Canada; Ontario Institute for Cancer Research, Toronto, Ontario, Canada.
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23
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Hertz DL, McShane LM, Hayes DF. Defining Clinical Utility of Germline Indicators of Toxicity Risk: A Perspective. J Clin Oncol 2022; 40:1721-1731. [PMID: 35324346 PMCID: PMC9148690 DOI: 10.1200/jco.21.02209] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Affiliation(s)
- Daniel L Hertz
- Department of Clinical Pharmacy, University of Michigan College of Pharmacy, Ann Arbor, MI
| | - Lisa M McShane
- Biometric Research Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, Bethesda, MD
| | - Daniel F Hayes
- Stuart B. Padnos Professor of Breast Cancer Research, University of Michigan Rogel Cancer Center, Ann Arbor, MI
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24
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Liu Z, Roberts R, Mercer TR, Xu J, Sedlazeck FJ, Tong W. Towards accurate and reliable resolution of structural variants for clinical diagnosis. Genome Biol 2022; 23:68. [PMID: 35241127 PMCID: PMC8892125 DOI: 10.1186/s13059-022-02636-8] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Accepted: 02/15/2022] [Indexed: 12/17/2022] Open
Abstract
Structural variants (SVs) are a major source of human genetic diversity and have been associated with different diseases and phenotypes. The detection of SVs is difficult, and a diverse range of detection methods and data analysis protocols has been developed. This difficulty and diversity make the detection of SVs for clinical applications challenging and requires a framework to ensure accuracy and reproducibility. Here, we discuss current developments in the diagnosis of SVs and propose a roadmap for the accurate and reproducible detection of SVs that includes case studies provided from the FDA-led SEquencing Quality Control Phase II (SEQC-II) and other consortium efforts.
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Affiliation(s)
- Zhichao Liu
- National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR, 72079, USA
| | - Ruth Roberts
- ApconiX, BioHub at Alderley Park, Alderley Edge, SK10 4TG, UK.,University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Timothy R Mercer
- Australian Institute for Bioengineering and Nanotechnology, University of Queensland, Brisbane, QLD, Australia.,Garvan Institute of Medical Research, Sydney, NSW, Australia.,St Vincent's Clinical School, University of New South Wales, Sydney, NSW, Australia
| | - Joshua Xu
- National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR, 72079, USA
| | - Fritz J Sedlazeck
- Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA.
| | - Weida Tong
- National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR, 72079, USA.
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25
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Stark Z, Ellard S. Rapid genomic testing for critically ill children: time to become standard of care? Eur J Hum Genet 2022; 30:142-149. [PMID: 34744166 PMCID: PMC8821543 DOI: 10.1038/s41431-021-00990-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2021] [Accepted: 10/17/2021] [Indexed: 02/03/2023] Open
Abstract
Rapid genomic testing in critically ill neonatal and paediatric patients has transformed the paradigm of rare disease diagnosis, delivering results in real time to inform patient management. More than 20 studies totalling over 1500 patients from diverse healthcare settings worldwide have now been published, forming a compelling evidence base for healthcare system implementation. We review the reported diagnostic and clinical outcomes, as well as broader evaluations of family and professional experiences, cost effectiveness, implementation challenges and bioethical issues arising from rapid testing. As rapid genomic testing transitions from the research to the healthcare setting to become a 'standard of care' test, there is a need to develop effective service delivery models to support scalability at both the laboratory and clinical level and promote equity of access, prompt test initiation, integrated multidisciplinary input and holistic family support. Harnessing the high level of professional engagement with rapid genomic testing programmes will continue to drive innovation and adoption, while close integration with emerging precision medicine approaches will be necessary to deliver on the promise of reduced infant and child mortality.
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Affiliation(s)
- Zornitza Stark
- Australian Genomics, Melbourne, VIC Australia ,grid.1058.c0000 0000 9442 535XVictorian Clinical Genetics Services, Murdoch Children’s Research Institute, Melbourne, VIC Australia ,grid.1008.90000 0001 2179 088XDepartment of Paediatrics, University of Melbourne, Melbourne, VIC Australia
| | - Sian Ellard
- grid.419309.60000 0004 0495 6261Exeter Genomics Laboratory, South West Genomic Laboratory Hub, Royal Devon & Exeter NHS Foundation Trust, Exeter, UK ,grid.8391.30000 0004 1936 8024Institute of Biomedical and Clinical Science, University of Exeter Medical School, Exeter, UK
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26
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Leeb T, Roosje P, Welle M. Genetics of inherited skin disorders in dogs. Vet J 2021; 279:105782. [PMID: 34861369 DOI: 10.1016/j.tvjl.2021.105782] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 11/16/2021] [Accepted: 11/29/2021] [Indexed: 01/22/2023]
Abstract
Canine genodermatoses represent a broad spectrum of diseases with diverse phenotypes. Modern genetic technology including whole genome sequencing has expedited the identification of novel genes and greatly simplified the establishment of genetic diagnoses in such heterogeneous disorders. The precise genetic diagnosis of a heritable skin disorder is essential for the appropriate counselling of owners regarding the course of the disease, prognosis and implications for breeding. Understanding the underlying pathophysiology is a prerequisite to developing specific, targeted or individualized therapeutic approaches. This review aims to create a comprehensive overview of canine genodermatoses and their respective genetic aetiology known to date. Raising awareness of genodermatoses in dogs is important and this review may help clinicians to apply modern genetics in daily clinical practice, so that a precise diagnoses can be established in suspected genodermatoses.
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Affiliation(s)
- Tosso Leeb
- Institute of Genetics, Vetsuisse Faculty, University of Bern, 3001 Bern, Switzerland; Dermfocus, University of Bern, 3001 Bern, Switzerland.
| | - Petra Roosje
- Dermfocus, University of Bern, 3001 Bern, Switzerland; Division of Clinical Dermatology, Department of Clinical Veterinary Medicine, Vetsuisse Faculty, University of Bern, 3001 Bern, Switzerland
| | - Monika Welle
- Dermfocus, University of Bern, 3001 Bern, Switzerland; Institute of Animal Pathology, Vetsuisse Faculty, University of Bern, 3001 Bern, Switzerland
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27
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The Clinician-reported Genetic testing Utility InDEx (C-GUIDE): Preliminary evidence of validity and reliability. Genet Med 2021; 24:430-438. [PMID: 34906486 DOI: 10.1016/j.gim.2021.10.005] [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: 04/05/2021] [Revised: 08/25/2021] [Accepted: 10/06/2021] [Indexed: 12/15/2022] Open
Abstract
PURPOSE Demonstrating the clinical utility of genetic testing is fundamental to clinical adoption and reimbursement, but standardized definitions and measurement strategies for this construct do not exist. The Clinician-reported Genetic testing Utility InDEx (C-GUIDE) offers a novel measure to fill this gap. This study assessed its validity and inter-rater reliability. METHODS Genetics professionals completed C-GUIDE after disclosure of test results to patients. Construct validity was assessed using regression analysis to measure associations between C-GUIDE and global item scores as well as potentially explanatory variables. Inter-rater reliability was assessed by administering a vignette-based survey to genetics professionals and calculating Krippendorff's α. RESULTS On average, a 1-point increase in the global item score was associated with an increase of 3.0 in the C-GUIDE score (P < .001). Compared with diagnostic results, partially/potentially diagnostic and nondiagnostic results were associated with a reduction in C-GUIDE score of 9.5 (P < .001) and 10.2 (P < .001), respectively. Across 19 vignettes, Krippendorff's α was 0.68 (95% CI: 0.63-0.72). CONCLUSION C-GUIDE showed acceptable validity and inter-rater reliability. Although further evaluation is required, C-GUIDE version 1.2 can be useful as a standardized approach to assess the clinical utility of genetic testing.
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Abstract
Prior to integration into clinical care, a novel medical innovation is typically assessed in terms of its balance of benefits and risks, often referred to as utility. Members of multidisciplinary research teams may conceptualize and assess utility in different ways, which has implications within the translational genomics community and for the evidence base upon which clinical guidelines groups and healthcare payers make decisions. Ambiguity in the conceptualization of utility in translational genomics research can lead to communication challenges within research teams and to study designs that do not meet stakeholder needs. We seek to address the ambiguity challenge by describing the conceptual understanding of utility and use of the term by scholars in the fields of philosophy, medicine, and the social sciences of decision psychology and health economics. We illustrate applications of each field's orientation to translational genomics research by using examples from the Clinical Sequencing Evidence-Generating Research (CSER) consortium, and we provide recommendations for increasing clarity and cohesion in future research. Given that different understandings of utility will align to a greater or lesser degree with important stakeholders' views, more precise use of the term can help researchers to better integrate multidisciplinary investigations and communicate with stakeholders.
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29
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Shickh S, Mighton C, Uleryk E, Pechlivanoglou P, Bombard Y. The clinical utility of exome and genome sequencing across clinical indications: a systematic review. Hum Genet 2021; 140:1403-1416. [PMID: 34368901 DOI: 10.1007/s00439-021-02331-x] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Accepted: 07/31/2021] [Indexed: 12/15/2022]
Abstract
Exome sequencing and genome sequencing have the potential to improve clinical utility for patients undergoing genetic investigations. However, evidence of clinical utility is limited to pediatric populations; we aimed to fill this gap by conducting a systematic review of the literature on the clinical utility of exome/genome sequencing across disease indications in pediatric and adult populations. MEDLINE, EMBASE and Cochrane Library were searched between 2016 and 2020. Quantitative studies evaluating diagnostic yield were included; other measures of clinical utility such as changes to clinical management were documented if reported. Two reviewers screened, extracted data, and appraised risk of bias. Fifty studies met our inclusion criteria. All studies reported diagnostic yield, which ranged from 3 to 70%, with higher range of yields reported for neurological indications and acute illness ranging from 22 to 68% and 37-70%, respectively. Diagnoses triggered a range of clinical management changes including surveillance, reproductive-risk counseling, and identifying at-risk relatives in 4-100% of patients, with higher frequencies reported for acute illness ranging from 67 to 95%. The frequency of variants of uncertain significance ranged from 5 to 85% across studies with a potential trend of decreasing frequency over time and higher rates identified in patients of non-European ancestry. This review provides evidence for a higher range of diagnostic yield of exome/genome sequencing compared to standard genetic tests, particularly in neurological and acute indications. However, we identified significant heterogeneity in study procedures and outcomes, precluding a meaningful meta-analysis and certainty in the evidence available for decision-making. Future research that incorporates a comprehensive and consistent approach in capturing clinical utility of exome/genome sequencing across broader ancestral groups is necessary to improve diagnostic accuracy and yield and allow for analysis of trends over time.Prospero registration CRD42019094101.
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Affiliation(s)
- Salma Shickh
- Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, ON, Canada.,Genomics Health Services Research Program, Li Ka Shing Knowledge Institute, Unity Health Toronto, Toronto, ON, Canada
| | - Chloe Mighton
- Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, ON, Canada.,Genomics Health Services Research Program, Li Ka Shing Knowledge Institute, Unity Health Toronto, Toronto, ON, Canada
| | | | - Petros Pechlivanoglou
- Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, ON, Canada.,The Hospital for Sick Children, Toronto, ON, Canada
| | - Yvonne Bombard
- Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, ON, Canada. .,Genomics Health Services Research Program, Li Ka Shing Knowledge Institute, Unity Health Toronto, Toronto, ON, Canada. .,Li Ka Shing Knowledge Institute of St. Michael's Hospital, University of Toronto, 30 Bond Street, Toronto, ON, M5B 1W8, Canada.
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30
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Cochran M, East K, Greve V, Kelly M, Kelley W, Moore T, Myers RM, Odom K, Schroeder MC, Bick D. A study of elective genome sequencing and pharmacogenetic testing in an unselected population. Mol Genet Genomic Med 2021; 9:e1766. [PMID: 34313030 PMCID: PMC8457704 DOI: 10.1002/mgg3.1766] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 04/08/2021] [Accepted: 07/09/2021] [Indexed: 11/06/2022] Open
Abstract
BACKGROUND Genome sequencing (GS) of individuals without a medical indication, known as elective GS, is now available at a number of centers around the United States. Here we report the results of elective GS and pharmacogenetic panel testing in 52 individuals at a private genomics clinic in Alabama. METHODS Individuals seeking elective genomic testing and pharmacogenetic testing were recruited through a private genomics clinic in Huntsville, AL. Individuals underwent clinical genome sequencing with a separate pharmacogenetic testing panel. RESULTS Six participants (11.5%) had pathogenic or likely pathogenic variants that may explain one or more aspects of their medical history. Ten participants (19%) had variants that altered the risk of disease in the future, including two individuals with clonal hematopoiesis of indeterminate potential. Forty-four participants (85%) were carriers of a recessive or X-linked disorder. All individuals with pharmacogenetic testing had variants that affected current and/or future medications. CONCLUSION Our study highlights the importance of collecting detailed phenotype information to interpret results in elective GS.
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Affiliation(s)
- Meagan Cochran
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, USA
| | - Kelly East
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, USA
| | - Veronica Greve
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, USA
| | - Melissa Kelly
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, USA
| | - Whitley Kelley
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, USA
| | - Troy Moore
- Kailos Genetics, Huntsville, Alabama, USA
| | - Richard M Myers
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, USA
| | - Katherine Odom
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, USA
| | - Molly C Schroeder
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - David Bick
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, USA
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31
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Li H, Dawood M, Khayat MM, Farek JR, Jhangiani SN, Khan ZM, Mitani T, Coban-Akdemir Z, Lupski JR, Venner E, Posey JE, Sabo A, Gibbs RA. Exome variant discrepancies due to reference-genome differences. Am J Hum Genet 2021; 108:1239-1250. [PMID: 34129815 PMCID: PMC8322936 DOI: 10.1016/j.ajhg.2021.05.011] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Accepted: 05/19/2021] [Indexed: 12/15/2022] Open
Abstract
Despite release of the GRCh38 human reference genome more than seven years ago, GRCh37 remains more widely used by most research and clinical laboratories. To date, no study has quantified the impact of utilizing different reference assemblies for the identification of variants associated with rare and common diseases from large-scale exome-sequencing data. By calling variants on both the GRCh37 and GRCh38 references, we identified single-nucleotide variants (SNVs) and insertion-deletions (indels) in 1,572 exomes from participants with Mendelian diseases and their family members. We found that a total of 1.5% of SNVs and 2.0% of indels were discordant when different references were used. Notably, 76.6% of the discordant variants were clustered within discrete discordant reference patches (DISCREPs) comprising only 0.9% of loci targeted by exome sequencing. These DISCREPs were enriched for genomic elements including segmental duplications, fix patch sequences, and loci known to contain alternate haplotypes. We identified 206 genes significantly enriched for discordant variants, most of which were in DISCREPs and caused by multi-mapped reads on the reference assembly that lacked the variant call. Among these 206 genes, eight are implicated in known Mendelian diseases and 53 are associated with common phenotypes from genome-wide association studies. In addition, variant interpretations could also be influenced by the reference after lifting-over variant loci to another assembly. Overall, we identified genes and genomic loci affected by reference assembly choice, including genes associated with Mendelian disorders and complex human diseases that require careful evaluation in both research and clinical applications.
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Affiliation(s)
- He Li
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Moez Dawood
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Medical Scientist Training Program, Baylor College of Medicine, Houston, TX 77030, USA
| | - Michael M Khayat
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jesse R Farek
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Shalini N Jhangiani
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Ziad M Khan
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Tadahiro Mitani
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Zeynep Coban-Akdemir
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - James R Lupski
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Department of Pediatrics, Texas Children's Hospital, Houston, TX 77030, USA
| | - Eric Venner
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jennifer E Posey
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Aniko Sabo
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Richard A Gibbs
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA.
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32
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Remec ZI, Trebusak Podkrajsek K, Repic Lampret B, Kovac J, Groselj U, Tesovnik T, Battelino T, Debeljak M. Next-Generation Sequencing in Newborn Screening: A Review of Current State. Front Genet 2021; 12:662254. [PMID: 34122514 PMCID: PMC8188483 DOI: 10.3389/fgene.2021.662254] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Accepted: 04/13/2021] [Indexed: 12/27/2022] Open
Abstract
Newborn screening was first introduced at the beginning of the 1960s with the successful implementation of the first phenylketonuria screening programs. Early expansion of the included disorders was slow because each additional disorder screened required a separate test. Subsequently, the technological advancements of biochemical methodology enabled the scaling-up of newborn screening, most notably with the implementation of tandem mass spectrometry. In recent years, we have witnessed a remarkable progression of high-throughput sequencing technologies, which has resulted in a continuous decrease of both cost and time required for genetic analysis. This has enabled more widespread use of the massive multiparallel sequencing. Genomic sequencing is now frequently used in clinical applications, and its implementation in newborn screening has been intensively advocated. The expansion of newborn screening has raised many clinical, ethical, legal, psychological, sociological, and technological concerns over time. This review provides an overview of the current state of next-generation sequencing regarding newborn screening including current recommendations and potential challenges for the use of such technologies in newborn screening.
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Affiliation(s)
- Ziga I. Remec
- Clinical Institute for Special Laboratory Diagnostics, University Children’s Hospital, University Medical Centre Ljubljana, Ljubljana, Slovenia
| | - Katarina Trebusak Podkrajsek
- Clinical Institute for Special Laboratory Diagnostics, University Children’s Hospital, University Medical Centre Ljubljana, Ljubljana, Slovenia
- Faculty of Medicine, Institute of Biochemistry and Molecular Genetics, University of Ljubljana, Ljubljana, Slovenia
| | - Barbka Repic Lampret
- Clinical Institute for Special Laboratory Diagnostics, University Children’s Hospital, University Medical Centre Ljubljana, Ljubljana, Slovenia
| | - Jernej Kovac
- Clinical Institute for Special Laboratory Diagnostics, University Children’s Hospital, University Medical Centre Ljubljana, Ljubljana, Slovenia
| | - Urh Groselj
- Department of Endocrinology, Diabetes and Metabolic Diseases, University Children’s Hospital, University Medical Centre Ljubljana, Ljubljana, Slovenia
- Chair of Pediatrics, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Tine Tesovnik
- Clinical Institute for Special Laboratory Diagnostics, University Children’s Hospital, University Medical Centre Ljubljana, Ljubljana, Slovenia
| | - Tadej Battelino
- Department of Endocrinology, Diabetes and Metabolic Diseases, University Children’s Hospital, University Medical Centre Ljubljana, Ljubljana, Slovenia
- Chair of Pediatrics, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Marusa Debeljak
- Clinical Institute for Special Laboratory Diagnostics, University Children’s Hospital, University Medical Centre Ljubljana, Ljubljana, Slovenia
- Faculty of Medicine, Institute of Biochemistry and Molecular Genetics, University of Ljubljana, Ljubljana, Slovenia
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33
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Hayeems RZ, Luca S, Assamad D, Bhatt A, Ungar WJ. Utility of Genetic Testing from the Perspective of Parents/Caregivers: A Scoping Review. CHILDREN (BASEL, SWITZERLAND) 2021; 8:259. [PMID: 33801725 PMCID: PMC8067127 DOI: 10.3390/children8040259] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 03/23/2021] [Accepted: 03/25/2021] [Indexed: 11/16/2022]
Abstract
In genomics, perceived and personal utility have been proposed as constructs of value that include the subjective meanings and uses of genetic testing. Precisely what constitutes these constructs of utility and how they vary by stakeholder perspective remains unresolved. To advance methods for measuring the value of genetic testing in child health, we conducted a scoping review of the literature to characterize utility from the perspective of parents/caregivers. Peer reviewed literature that included empiric findings from parents/caregivers who received genetic test results for an index child and was written in English from 2016-2020 was included. Identified concepts of utility were coded according to Kohler's construct of personal utility. Of 2142 abstracts screened, 33 met inclusion criteria. Studies reflected a range of genetic test types; the majority of testing was pursued for children with developmental or neurodevelopmental concerns. Coding resulted in 15 elements of utility that mapped to Kohler's four domains of personal utility (affective, cognitive, behavioural and social) and one additional medical management domain. An adapted construct of utility for parents/caregivers may enable specific and standardized strategies for researchers to use to generate evidence of the post-test value of genetic testing. In turn, this will contribute to emerging methods for health technology assessment and policy decision making for genomics in child health.
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Affiliation(s)
- Robin Z. Hayeems
- Child Health Evaluative Sciences, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada; (S.L.); (D.A.); (A.B.); (W.J.U.)
- Institute of Health Policy Management and Evaluation, The University of Toronto, Toronto, ON M5T 3M6, Canada
| | - Stephanie Luca
- Child Health Evaluative Sciences, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada; (S.L.); (D.A.); (A.B.); (W.J.U.)
| | - Daniel Assamad
- Child Health Evaluative Sciences, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada; (S.L.); (D.A.); (A.B.); (W.J.U.)
| | - Ayushi Bhatt
- Child Health Evaluative Sciences, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada; (S.L.); (D.A.); (A.B.); (W.J.U.)
- Schulich School of Medicine and Dentistry, Western University, London, ON N6A 5C1, Canada
| | - Wendy J. Ungar
- Child Health Evaluative Sciences, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada; (S.L.); (D.A.); (A.B.); (W.J.U.)
- Institute of Health Policy Management and Evaluation, The University of Toronto, Toronto, ON M5T 3M6, Canada
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34
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Hyde C. Will better evidence on clinical utility bring about greater use of (genetic) tests? NPJ Genom Med 2021; 6:22. [PMID: 33664270 PMCID: PMC7933423 DOI: 10.1038/s41525-021-00187-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2020] [Accepted: 01/25/2021] [Indexed: 12/17/2022] Open
Abstract
Greater clarity on the nature of clinical utility is desirable. Of itself it may not bring about greater use of tests, including WGS (whole-genome sequencing), not least because clinical utility studies when performed may not confirm predicted changes in patient outcome. The notion that single “pivotal” clinical utility studies will achieve uptake needs to be questioned and that the evidence base for tests is likely to rely on patchworks of imperfect evidence embraced.
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Affiliation(s)
- Chris Hyde
- Exeter Test Group, Institute of Health Research, College of Medicine and Health, University of Exeter, Exeter, EX1 2LU, UK.
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