1
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Zhang R, Cui X, Zhang Y, Ma H, Gao J, Zhang Y, Shu J, Cai C, Liu Y. Whole-exome sequencing as the first-tier test for patients in neonatal intensive care unit: a Chinese single-center study. BMC Pediatr 2024; 24:351. [PMID: 38778310 PMCID: PMC11110365 DOI: 10.1186/s12887-024-04820-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/12/2023] [Accepted: 05/08/2024] [Indexed: 05/25/2024] Open
Abstract
BACKGROUND Genetic disorders significantly affect patients in neonatal intensive care units, where establishing a diagnosis can be challenging through routine tests and supplementary examinations. Whole-exome sequencing offers a molecular-based approach for diagnosing genetic disorders. This study aimed to assess the importance of whole-exome sequencing for neonates in intensive care through a retrospective observational study within a Chinese cohort. METHODS We gathered data from neonatal patients at Tianjin Children's Hospital between January 2018 and April 2021. These patients presented with acute illnesses and were suspected of having genetic disorders, which were investigated using whole-exome sequencing. Our retrospective analysis covered clinical data, genetic findings, and the correlation between phenotypes and genetic variations. RESULTS The study included 121 neonates. Disorders affected multiple organs or systems, predominantly the metabolic, neurological, and endocrine systems. The detection rate for whole-exome sequencing was 52.9% (64 out of 121 patients), identifying 84 pathogenic or likely pathogenic genetic variants in 64 neonates. These included 13 copy number variations and 71 single-nucleotide variants. The most frequent inheritance pattern was autosomal recessive (57.8%, 37 out of 64), followed by autosomal dominant (29.7%, 19 out of 64). In total, 40 diseases were identified through whole-exome sequencing. CONCLUSION This study underscores the value and clinical utility of whole-exome sequencing as a primary diagnostic tool for neonates in intensive care units with suspected genetic disorders. Whole-exome sequencing not only aids in diagnosis but also offers significant benefits to patients and their families by providing clarity in uncertain diagnostic situations.
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Affiliation(s)
- Ruiping Zhang
- Department of Neonatology, Tianjin Children's Hospital/Tianjin University Children's Hospital, Beichen District, Tianjin, China
| | - Xiaoyu Cui
- Department of Neonatology, Tianjin Children's Hospital/Tianjin University Children's Hospital, Beichen District, Tianjin, China
| | - Yan Zhang
- Department of Neonatology, Tianjin Children's Hospital/Tianjin University Children's Hospital, Beichen District, Tianjin, China
- Graduate College, Tianjin Medical University, Heping District, Tianjin, China
| | - Huiqing Ma
- Graduate College, Tianjin Medical University, Heping District, Tianjin, China
| | - Jing Gao
- Graduate College, Tianjin Medical University, Heping District, Tianjin, China
| | - Ying Zhang
- Department of Neonatology, Tianjin Children's Hospital/Tianjin University Children's Hospital, Beichen District, Tianjin, China
| | - Jianbo Shu
- Tianjin Pediatric Research Institute, Tianjin Children's Hospital/Tianjin University Children's Hospital, Beichen District, Tianjin, China.
- Tianjin Key Laboratory of Birth Defects for Prevention and Treatment, Beichen District, Tianjin, China.
| | - Chunquan Cai
- Tianjin Pediatric Research Institute, Tianjin Children's Hospital/Tianjin University Children's Hospital, Beichen District, Tianjin, China.
- Tianjin Key Laboratory of Birth Defects for Prevention and Treatment, Beichen District, Tianjin, China.
| | - Yang Liu
- Department of Neonatology, Tianjin Children's Hospital/Tianjin University Children's Hospital, Beichen District, Tianjin, China.
- The Pediatric Clinical College in Tianjin Medical University, Heping District, Tianjin, China.
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2
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Blout Zawatsky CL, Bick D, Bier L, Funke B, Lebo M, Lewis KL, Orlova E, Qian E, Ryan L, Schwartz MLB, Soper ER. Elective genomic testing: Practice resource of the National Society of Genetic Counselors. J Genet Couns 2023; 32:281-299. [PMID: 36597794 DOI: 10.1002/jgc4.1654] [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: 03/31/2022] [Revised: 10/24/2022] [Accepted: 10/28/2022] [Indexed: 01/05/2023]
Abstract
Genetic counseling for patients who are pursuing genetic testing in the absence of a medical indication, referred to as elective genomic testing (EGT), is becoming more common. This type of testing has the potential to detect genetic conditions before there is a significant health impact permitting earlier management and/or treatment. Pre- and post-test counseling for EGT is similar to indication-based genetic testing. Both require a complete family and medical history when ordering a test or interpreting a result. However, EGT counseling has some special considerations including greater uncertainties around penetrance and clinical utility and a lack of published guidelines. While certain considerations in the selection of a high-quality genetic testing laboratory are universal, there are some considerations that are unique to the selection of a laboratory performing EGT. This practice resource intends to provide guidance for genetic counselors and other healthcare providers caring for adults seeking pre- or post-test counseling for EGT. Genetic counselors and other genetics trained healthcare providers are the ideal medical professionals to supply accurate information to individuals seeking counseling about EGT enabling them to make informed decisions about testing and follow-up.
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Affiliation(s)
- Carrie L Blout Zawatsky
- Genomes2People, Brigham and Women's Hospital, Boston, Massachusetts, USA.,Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts, USA.,Ariadne Labs, Boston, Massachusetts, USA.,The MGH Institute of Health Professions, Boston, Massachusetts, USA
| | | | - Louise Bier
- Institute for Genomic Medicine, Columbia University Irving Medical Center, New York, New York, USA
| | | | - Matthew Lebo
- Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts, USA.,Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts, USA.,Department of Pathology, Harvard Medical School, Cambridge, Massachusetts, USA.,Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine, Boston, Massachusetts, USA
| | - Katie L Lewis
- Center for Precision Health Research, National Institutes of Health, Bethesda, Maryland, USA
| | - Ekaterina Orlova
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Emily Qian
- Department of Genetics, Yale University, New Haven, Connecticut, USA
| | | | - Marci L B Schwartz
- Cardiac Genome Clinic, Ted Rogers Centre for Heart Research, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Emily R Soper
- The Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
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3
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Miura MS, Suckiel SA, Naik H, Soper ER, Abul-Husn NS. Elective genetic testing: Genetics professionals' perspectives and practices. J Genet Couns 2022. [PMID: 36575824 DOI: 10.1002/jgc4.1666] [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: 07/20/2022] [Revised: 11/30/2022] [Accepted: 12/04/2022] [Indexed: 12/29/2022]
Abstract
Elective genetic testing (EGT) to identify disease risk in individuals who may or may not meet clinical criteria for testing is increasingly being offered in clinical practice. However, little is known about how EGT is currently implemented and how genetics professionals perceive this type of testing. We conducted a mixed-methods survey study to evaluate genetics professionals' perspectives and attitudes about EGT and describe the current landscape of EGT practices in the United States (U.S.) and Canada. Six clinical geneticists and 131 genetic counselors responded to the online survey, among whom 44% reported offering EGT in their practice. Over 84% of survey respondents agreed that EGT may improve health outcomes and understanding of genotype-phenotype correlations, and 85% agreed that potential risks include result misinterpretation and contribution to economic health disparities. Though most respondents felt comfortable providing pretest (77%) and post-test (86%) counseling for EGT, lack of provider resources (such as time and personnel) and prioritization of diagnostic testing were cited most frequently in free-text responses as reasons for not offering EGT. Of those offering EGT, 88% reported positive overall experiences. Qualitative analysis of open-ended questions identified benefits of EGT as expanding access to genetic testing, providing potential health benefits, and providing psychological benefits for patients. Disadvantages included prohibitive costs, limited clinical utility, and strain on resources. Overall, we found that genetics providers perceive both potential benefits and harms of EGT and that those offering this testing had generally positive experiences, although ethical reservations and practical limitations exist.
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Affiliation(s)
- Madison S Miura
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Sabrina A Suckiel
- Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,Division of Genomic Medicine, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Hetanshi Naik
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Emily R Soper
- Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,Division of Genomic Medicine, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Noura S Abul-Husn
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,Division of Genomic Medicine, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
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4
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Mighton C, Shickh S, Aguda V, Krishnapillai S, Adi-Wauran E, Bombard Y. From the patient to the population: Use of genomics for population screening. Front Genet 2022; 13:893832. [PMID: 36353115 PMCID: PMC9637971 DOI: 10.3389/fgene.2022.893832] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Accepted: 09/26/2022] [Indexed: 10/22/2023] Open
Abstract
Genomic medicine is expanding from a focus on diagnosis at the patient level to prevention at the population level given the ongoing under-ascertainment of high-risk and actionable genetic conditions using current strategies, particularly hereditary breast and ovarian cancer (HBOC), Lynch Syndrome (LS) and familial hypercholesterolemia (FH). The availability of large-scale next-generation sequencing strategies and preventive options for these conditions makes it increasingly feasible to screen pre-symptomatic individuals through public health-based approaches, rather than restricting testing to high-risk groups. This raises anew, and with urgency, questions about the limits of screening as well as the moral authority and capacity to screen for genetic conditions at a population level. We aimed to answer some of these critical questions by using the WHO Wilson and Jungner criteria to guide a synthesis of current evidence on population genomic screening for HBOC, LS, and FH.
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Affiliation(s)
- Chloe Mighton
- Genomics Health Services Research Program, St. Michael’s Hospital, Unity Health Toronto, Toronto, ON, Canada
- Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, ON, Canada
| | - Salma Shickh
- Genomics Health Services Research Program, St. Michael’s Hospital, Unity Health Toronto, Toronto, ON, Canada
- Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, ON, Canada
| | - Vernie Aguda
- Genomics Health Services Research Program, St. Michael’s Hospital, Unity Health Toronto, Toronto, ON, Canada
- Centre for Medical Education, School of Medicine, Cardiff University, Cardiff, United Kingdom
| | - Suvetha Krishnapillai
- Genomics Health Services Research Program, St. Michael’s Hospital, Unity Health Toronto, Toronto, ON, Canada
- Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, ON, Canada
| | - Ella Adi-Wauran
- Genomics Health Services Research Program, St. Michael’s Hospital, Unity Health Toronto, Toronto, ON, Canada
- Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, ON, Canada
| | - Yvonne Bombard
- Genomics Health Services Research Program, St. Michael’s Hospital, Unity Health Toronto, Toronto, ON, Canada
- Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, ON, Canada
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5
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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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6
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Rehder C, Bean LJH, Bick D, Chao E, Chung W, Das S, O'Daniel J, Rehm H, Shashi V, Vincent LM. Next-generation sequencing for constitutional variants in the clinical laboratory, 2021 revision: a technical standard of the American College of Medical Genetics and Genomics (ACMG). Genet Med 2021; 23:1399-1415. [PMID: 33927380 DOI: 10.1038/s41436-021-01139-4] [Citation(s) in RCA: 59] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 02/25/2021] [Accepted: 02/26/2021] [Indexed: 12/17/2022] Open
Abstract
Next-generation sequencing (NGS) technologies are now established in clinical laboratories as a primary testing modality in genomic medicine. These technologies have reduced the cost of large-scale sequencing by several orders of magnitude. It is now cost-effective to analyze an individual with disease-targeted gene panels, exome sequencing, or genome sequencing to assist in the diagnosis of a wide array of clinical scenarios. While clinical validation and use of NGS in many settings is established, there are continuing challenges as technologies and the associated informatics evolve. To assist clinical laboratories with the validation of NGS methods and platforms, the ongoing monitoring of NGS testing to ensure quality results, and the interpretation and reporting of variants found using these technologies, the American College of Medical Genetics and Genomics (ACMG) has developed the following technical standards.
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Affiliation(s)
| | - Lora J H Bean
- Department of Human Genetics, Emory University, Atlanta, GA, USA
| | - David Bick
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Elizabeth Chao
- Division of Genetics and Genomics, Department of Pediatrics, University of California, Irvine, CA, USA
| | - Wendy Chung
- Departments of Pediatrics and Medicine, Columbia University, New York, NY, USA
| | - Soma Das
- Department of Human Genetics, University of Chicago, Chicago, IL, USA
| | - Julianne O'Daniel
- Department of Genetics, University of North Carolina, Chapel Hill, NC, USA
| | - Heidi Rehm
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Vandana Shashi
- Department of Pediatrics, Duke University, Durham, NC, USA
| | - Lisa M Vincent
- Division of Pathology & Laboratory Medicine, Children's National Health System, Washington, DC, USA.,Departments of Pathology and Pediatrics, George Washington University, Washington, DC, USA
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7
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Schwartz MLB, Buchanan AH, Hallquist MLG, Haggerty CM, Sturm AC. Genetic counseling for patients with positive genomic screening results: Considerations for when the genetic test comes first. J Genet Couns 2021; 30:634-644. [PMID: 33786929 DOI: 10.1002/jgc4.1386] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Revised: 12/18/2020] [Accepted: 12/31/2020] [Indexed: 01/06/2023]
Abstract
Emerging genetic testing delivery models have enabled individuals to receive testing without a medical indication. This article will highlight key considerations for patient care in the setting of adult patients with positive results for monogenic disease identified through genomic screening. Suggestions for how to adapt genetic counseling to a genomic screening population will encompass topics such as phenotyping, risk assessments, and the use of existing guidelines and resources. Case examples will demonstrate principles of genotype-first patient care.
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Affiliation(s)
| | | | | | - Christopher M Haggerty
- The Heart Institute, Geisinger, Danville, PA, USA.,Department of Translational Data Science and Informatics, Geisinger, Danville, PA, USA
| | - Amy C Sturm
- Genomic Medicine Institute, Geisinger, Danville, PA, USA
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8
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Bean LJH, Scheuner MT, Murray MF, Biesecker LG, Green RC, Monaghan KG, Palomaki GE, Sharp RR, Trotter TL, Watson MS, Powell CM. DNA-based screening and personal health: a points to consider statement for individuals and health-care providers from the American College of Medical Genetics and Genomics (ACMG). Genet Med 2021; 23:979-988. [PMID: 33790423 DOI: 10.1038/s41436-020-01083-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 12/14/2020] [Accepted: 12/17/2020] [Indexed: 01/15/2023] Open
Affiliation(s)
- Lora J H Bean
- Department of Human Genetics, Emory University, Atlanta, GA, USA
| | - Maren T Scheuner
- Division of Medical Genetics, Department of Pediatrics, and Division of Hematology-Oncology, Department of Medicine, University of California San Francisco School of Medicine, San Francisco, CA, USA.,Clinical Genetics Program, San Francisco VA Health Care System, San Francisco, CA, USA
| | - Michael F Murray
- Department of Genetics, Yale School of Medicine, New Haven, CT, USA
| | - Leslie G Biesecker
- Medical Genomics and Metabolic Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Robert C Green
- Harvard Medical School, Boston, MA, USA.,Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA.,The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | - Glenn E Palomaki
- Department of Pathology and Laboratory Medicine, Alpert Medical School, Brown University, Providence, RI, USA.,Women and Infants Hospital, Providence, RI, USA
| | | | - Tracy L Trotter
- San Ramon Valley Primary Care Medical Group, San Ramon, CA, USA
| | | | - Cynthia M Powell
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.,Division of Genetics and Metabolism, Department of Pediatrics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
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9
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Edgar J, Bao A, Maga T, Schwartz M, Yates C, Spencer S. Adopted individuals' interest in elective genomic testing. J Med Genet 2021; 59:197-203. [PMID: 33443090 DOI: 10.1136/jmedgenet-2020-107503] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2020] [Revised: 11/28/2020] [Accepted: 11/30/2020] [Indexed: 11/04/2022]
Abstract
PURPOSE Adoptees are a population that could benefit from genetic testing to fill gaps in family health history (FHH). Elective genomic testing (EGT) provides adoptees with clinical genetic testing options to learn about genetic health risks in the absence of FHH. We assessed adoptees' interests in, motivations for and perceived utility of EGT. METHODS Adult adoptees and non-adoptees completed an anonymous, online survey regarding their interest and motivations for EGT, perceived utility of potential results and willingness to pay for EGT. A validated measure of social identity was included to measure the effects of social identity on testing interest. RESULTS There were 112 adoptees and 229 non-adoptees included in the study. Adoptees reported greater interest in EGT (OR 5.0, 95% CI 2.2 to 11.3) than non-adoptees. They were motivated by curiosity and a desire to learn information about risks to children and grandchildren more than non-adoptees. Adoptees with higher education and non-adoptees with higher incomes were significantly more likely to spend more on EGT. Adoptees with higher incomes and non-adoptees with higher education were not significantly more likely to spend more. Social identity was a significant mediator between adoption and testing motivation. CONCLUSION Understanding adoptees' unique motivations and interests in EGT will allow healthcare providers to better address the informational needs and desires of this population. Social identity provides a foundation for recognising adoptees' universal experiences that influence motivations for genetic testing.
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Affiliation(s)
- Jessica Edgar
- Center for Genetic Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Annie Bao
- Center for Genetic Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Tara Maga
- Center for Genetic Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA.,Hereditary Cancer Program, University of Illinois at Chicago, Chicago, Illinois, USA
| | - Marci Schwartz
- Genomic Medicine Institute, Geisinger, Danville, Pennsylvania, USA
| | | | - Sara Spencer
- Center for Genetic Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA.,Obstetrics and Gynecology, Northwestern Medicine, Chicago, Illinois, USA
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10
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Bick D, Bick SL, Dimmock DP, Fowler TA, Caulfield MJ, Scott RH. An online compendium of treatable genetic disorders. AMERICAN JOURNAL OF MEDICAL GENETICS PART C-SEMINARS IN MEDICAL GENETICS 2020; 187:48-54. [PMID: 33350578 PMCID: PMC7986124 DOI: 10.1002/ajmg.c.31874] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Revised: 11/20/2020] [Accepted: 11/24/2020] [Indexed: 11/21/2022]
Abstract
More than 4,000 genes have been associated with recognizable Mendelian/monogenic diseases. When faced with a new diagnosis of a rare genetic disorder, health care providers increasingly turn to internet resources for information to understand the disease and direct care. Unfortunately, it can be challenging to find information concerning treatment for rare diseases as key details are scattered across a number of authoritative websites and numerous journal articles. The website and associated mobile device application described in this article begin to address this challenge by providing a convenient, readily available starting point to find treatment information. The site, Rx-genes.com (https://www.rx-genes.com/), is focused on those conditions where the treatment is directed against the mechanism of the disease and thereby alters the natural history of the disease. The website currently contains 633 disease entries that include references to disease information and treatment guidance, a brief summary of treatments, the inheritance pattern, a disease frequency (if known), nonmolecular confirmatory testing (if available), and a link to experimental treatments. Existing entries are continuously updated, and new entries are added as novel treatments appear in the literature.
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Affiliation(s)
- David Bick
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, USA
| | - Sarah L Bick
- Nemours/Alfred I. duPont Hospital for Children, Wilmington, Delaware, USA
| | - David P Dimmock
- Rady Children's Institute for Genomic Medicine, San Diego, California, USA
| | - Tom A Fowler
- Genomics England Ltd., London, UK.,William Harvey Research Institute, Queen Mary University of London, London, UK
| | - Mark J Caulfield
- Genomics England Ltd., London, UK.,William Harvey Research Institute, Queen Mary University of London, London, UK
| | - Richard H Scott
- Genomics England Ltd., London, UK.,Department of Clinical Genetics, Great Ormond Street Hospital for Children National Health Service (NHS) Foundation Trust, London, UK
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11
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Hayeems RZ, Dimmock D, Bick D, Belmont JW, Green RC, Lanpher B, Jobanputra V, Mendoza R, Kulkarni S, Grove ME, Taylor SL, Ashley E. Clinical utility of genomic sequencing: a measurement toolkit. NPJ Genom Med 2020; 5:56. [PMID: 33319814 PMCID: PMC7738524 DOI: 10.1038/s41525-020-00164-7] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Accepted: 11/12/2020] [Indexed: 12/21/2022] Open
Abstract
Whole-genome sequencing (WGS) is positioned to become one of the most robust strategies for achieving timely diagnosis of rare genomic diseases. Despite its favorable diagnostic performance compared to conventional testing strategies, routine use and reimbursement of WGS are hampered by inconsistencies in the definition and measurement of clinical utility. For example, what constitutes clinical utility for WGS varies by stakeholder's perspective (physicians, patients, families, insurance companies, health-care organizations, and society), clinical context (prenatal, pediatric, critical care, adult medicine), and test purpose (diagnosis, screening, treatment selection). A rapidly evolving technology landscape and challenges associated with robust comparative study design in the context of rare disease further impede progress in this area of empiric research. To address this challenge, an expert working group of the Medical Genome Initiative was formed. Following a consensus-based process, we align with a broad definition of clinical utility and propose a conceptually-grounded and empirically-guided measurement toolkit focused on four domains of utility: diagnostic thinking efficacy, therapeutic efficacy, patient outcome efficacy, and societal efficacy. For each domain of utility, we offer specific indicators and measurement strategies. While we focus on diagnostic applications of WGS for rare germline diseases, this toolkit offers a flexible framework for best practices around measuring clinical utility for a range of WGS applications. While we expect this toolkit to evolve over time, it provides a resource for laboratories, clinicians, and researchers looking to characterize the value of WGS beyond the laboratory.
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Affiliation(s)
- Robin Z Hayeems
- Program in Child Health Evaluative Sciences, The Hospital for Sick Children and the Institute of Health Policy Management and Evaluation, University of Toronto, Toronto, ON, Canada.
| | - David Dimmock
- Rady Children's Hospital Institute for Genomic Medicine, San Diego, CA, USA
| | - David Bick
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | | | - Robert C Green
- Brigham and Women's Hospital Broad Institute and Harvard Medical School, Boston, MA, USA
| | | | - Vaidehi Jobanputra
- New York Genome Center, New York, NY, USA
- Department of Pathology and Cell Biology Columbia University Medical Center, New York, NY, USA
| | - Roberto Mendoza
- The Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, ON, Canada
| | - Shashi Kulkarni
- Baylor Genetics and Baylor College of Medicine, Houston, TX, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
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12
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Hoxhaj I, Govaerts L, Simoens S, Van Dyck W, Huys I, Gutiérrez-Ibarluzea I, Boccia S. A Systematic Review of the Value Assessment Frameworks Used within Health Technology Assessment of Omics Technologies and Their Actual Adoption from HTA Agencies. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2020; 17:E8001. [PMID: 33143182 PMCID: PMC7663163 DOI: 10.3390/ijerph17218001] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 10/20/2020] [Accepted: 10/22/2020] [Indexed: 11/16/2022]
Abstract
BACKGROUND Omics technologies, enabling the measurements of genes (genomics), mRNA (transcriptomics), proteins (proteomics) and metabolites (metabolomics), are valuable tools for personalized decision-making. We aimed to identify the existing value assessment frameworks used by health technology assessment (HTA) doers for the evaluation of omics technologies through a systematic review. METHODS PubMed, Scopus, Embase and Web of Science databases were searched to retrieve potential eligible articles published until 31 May 2020 in English. Additionally, through a desk research in HTA agencies' repositories, we retrieved the published reports on the practical use of these frameworks. RESULTS Twenty-three articles were included in the systematic review. Twenty-two frameworks, which addressed genetic and/or genomic technologies, were described. Most of them derived from the ACCE framework and evaluated the domains of analytical validity, clinical validity and clinical utility. We retrieved forty-five reports, which mainly addressed the commercial transcriptomic prognostics and next generation sequencing, and evaluated clinical effectiveness, economic aspects, and description and technical characteristics. CONCLUSIONS A value assessment framework for the HTA evaluation of omics technologies is not standardized and accepted, yet. Our work reports that the most evaluated domains are analytical validity, clinical validity and clinical utility and economic aspects.
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Affiliation(s)
- Ilda Hoxhaj
- Section of Hygiene, University Department of Life Sciences and Public Health, Università Cattolica del Sacro Cuore, 00168 Roma, Italy; (I.H.); (S.B.)
| | - Laurenz Govaerts
- Healthcare Management Centre, Vlerick Business School, 9000 Ghent, Belgium;
- Department of Pharmaceutical and Pharmacological Sciences, Catholic University of Leuven-KU Leuven, 3000 Leuven, Belgium; (S.S.); (I.H.)
| | - Steven Simoens
- Department of Pharmaceutical and Pharmacological Sciences, Catholic University of Leuven-KU Leuven, 3000 Leuven, Belgium; (S.S.); (I.H.)
| | - Walter Van Dyck
- Healthcare Management Centre, Vlerick Business School, 9000 Ghent, Belgium;
- Department of Pharmaceutical and Pharmacological Sciences, Catholic University of Leuven-KU Leuven, 3000 Leuven, Belgium; (S.S.); (I.H.)
| | - Isabelle Huys
- Department of Pharmaceutical and Pharmacological Sciences, Catholic University of Leuven-KU Leuven, 3000 Leuven, Belgium; (S.S.); (I.H.)
| | | | - Stefania Boccia
- Section of Hygiene, University Department of Life Sciences and Public Health, Università Cattolica del Sacro Cuore, 00168 Roma, Italy; (I.H.); (S.B.)
- Department of Woman and Child Health and Public Health-Public Health Area, Fondazione Policlinico Universitario A. Gemelli IRCCS, 00168 Roma, Italy
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Design and Reporting Considerations for Genetic Screening Tests. J Mol Diagn 2020; 22:599-609. [DOI: 10.1016/j.jmoldx.2020.01.014] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Revised: 01/16/2020] [Accepted: 01/30/2020] [Indexed: 11/20/2022] Open
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Diagnostic gene sequencing panels: from design to report-a technical standard of the American College of Medical Genetics and Genomics (ACMG). Genet Med 2019; 22:453-461. [PMID: 31732716 DOI: 10.1038/s41436-019-0666-z] [Citation(s) in RCA: 75] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Revised: 09/20/2019] [Accepted: 09/22/2019] [Indexed: 12/20/2022] Open
Abstract
Gene sequencing panels are a powerful diagnostic tool for many clinical presentations associated with genetic disorders. Advances in DNA sequencing technology have made gene panels more economical, flexible, and efficient. Because the genes included on gene panels vary widely between laboratories in gene content (e.g., number, reason for inclusion, evidence level for gene-disease association) and technical completeness (e.g., depth of coverage), standards that address technical and clinical aspects of gene panels are needed. This document serves as a technical standard for laboratories designing, offering, and reporting gene panel testing. Although these principles can apply to multiple indications for genetic testing, the primary focus is on diagnostic gene panels (as opposed to carrier screening or predictive testing) with emphasis on technical considerations for the specific genes being tested. This technical standard specifically addresses the impact of gene panel content on clinical sensitivity, specificity, and validity-in the context of gene evidence for contribution to and strength of evidence for gene-disease association-as well as technical considerations such as sequencing limitations, presence of pseudogenes/gene families, mosaicism, transcript choice, detection of copy-number variants, reporting, and disclosure of assay limitations.
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Senol-Cosar O, Schmidt RJ, Qian E, Hoskinson D, Mason-Suares H, Funke B, Lebo MS. Considerations for clinical curation, classification, and reporting of low-penetrance and low effect size variants associated with disease risk. Genet Med 2019; 21:2765-2773. [PMID: 31147632 DOI: 10.1038/s41436-019-0560-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Accepted: 05/21/2019] [Indexed: 01/08/2023] Open
Abstract
PURPOSE Clinically relevant variants exhibit a wide range of penetrance. Medical practice has traditionally focused on highly penetrant variants with large effect sizes and, consequently, classification and clinical reporting frameworks are tailored to that variant type. At the other end of the penetrance spectrum, where variants are often referred to as "risk alleles," traditional frameworks are no longer appropriate. This has led to inconsistency in how such variants are interpreted and classified. Here, we describe a conceptual framework to begin addressing this gap. METHODS We used a set of risk alleles to define data elements that can characterize the validity of reported disease associations. We assigned weight to these data elements and established classification categories expressing confidence levels. This framework was then expanded to develop criteria for inclusion of risk alleles on clinical reports. RESULTS Foundational data elements include cohort size, quality of phenotyping, statistical significance, and replication of results. Criteria for determining inclusion of risk alleles on clinical reports include presence of clinical management guidelines, effect size, severity of the associated phenotype, and effectiveness of intervention. CONCLUSION This framework represents an approach for classifying risk alleles and can serve as a foundation to catalyze community efforts for refinement.
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Affiliation(s)
- Ozlem Senol-Cosar
- Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine, Cambridge, MA, USA.,Department of Pathology, Harvard Medical School/Brigham and Women's Hospital, Boston, MA, USA
| | - Ryan J Schmidt
- Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Keck School of Medicine of USC, Los Angeles, CA, USA
| | | | - Derick Hoskinson
- Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine, Cambridge, MA, USA
| | - Heather Mason-Suares
- Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine, Cambridge, MA, USA.,Department of Pathology, Harvard Medical School/Brigham and Women's Hospital, Boston, MA, USA
| | - Birgit Funke
- Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine, Cambridge, MA, USA. .,Veritas Genetics, Cambridge, MA, USA. .,Department of Pathology, Harvard Medical School/Massachusetts General Hospital, Boston, MA, USA.
| | - Matthew S Lebo
- Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine, Cambridge, MA, USA. .,Department of Pathology, Harvard Medical School/Brigham and Women's Hospital, Boston, MA, USA.
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Translating Risk of Consumer-Initiated Genetic Testing. J Mol Diagn 2018; 21:1-2. [PMID: 30577885 DOI: 10.1016/j.jmoldx.2018.11.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Accepted: 11/09/2018] [Indexed: 11/21/2022] Open
Abstract
This editorial highlights the article by Bick and colleagues that proposes a framework for evaluating elective genomic testing.
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