1
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Li M, Chen F, Yang Q, Tang Q, Xiao Z, Tong X, Zhang Y, Lei L, Li S. Biomaterial-Based CRISPR/Cas9 Delivery Systems for Tumor Treatment. Biomater Res 2024; 28:0023. [PMID: 38694229 PMCID: PMC11062511 DOI: 10.34133/bmr.0023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2023] [Accepted: 03/25/2024] [Indexed: 05/04/2024] Open
Abstract
CRISPR/Cas9 gene editing technology is characterized by high specificity and efficiency, and has been applied to the treatment of human diseases, especially tumors involving multiple genetic modifications. However, the clinical application of CRISPR/Cas9 still faces some major challenges, the most urgent of which is the development of optimized delivery vectors. Biomaterials are currently the best choice for use in CRISPR/Cas9 delivery vectors owing to their tunability, biocompatibility, and efficiency. As research on biomaterial vectors continues to progress, hope for the application of the CRISPR/Cas9 system for clinical oncology therapy builds. In this review, we first detail the CRISPR/Cas9 system and its potential applications in tumor therapy. Then, we introduce the different delivery forms and compare the physical, viral, and non-viral vectors. In addition, we analyze the characteristics of different types of biomaterial vectors. We further review recent research progress in the use of biomaterials as vectors for CRISPR/Cas9 delivery to treat specific tumors. Finally, we summarize the shortcomings and prospects of biomaterial-based CRISPR/Cas9 delivery systems.
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Affiliation(s)
- Mengmeng Li
- Department of Otorhinolaryngology Head and Neck Surgery, the Second Xiangya Hospital,
Central South University, Changsha 410011, Hunan, China
| | - Fenglei Chen
- College of Veterinary Medicine, Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses,
Yangzhou University, Yangzhou 225009, China
| | - Qian Yang
- Department of Otorhinolaryngology Head and Neck Surgery, the Second Xiangya Hospital,
Central South University, Changsha 410011, Hunan, China
| | - Qinglai Tang
- Department of Otorhinolaryngology Head and Neck Surgery, the Second Xiangya Hospital,
Central South University, Changsha 410011, Hunan, China
| | - Zian Xiao
- Department of Otorhinolaryngology Head and Neck Surgery, the Second Xiangya Hospital,
Central South University, Changsha 410011, Hunan, China
| | - Xinying Tong
- Department of Hemodialysis, the Second Xiangya Hospital,
Central South University, Changsha 410011, Hunan, China
| | - Ying Zhang
- Department of Otorhinolaryngology Head and Neck Surgery, the Second Xiangya Hospital,
Central South University, Changsha 410011, Hunan, China
| | - Lanjie Lei
- Institute of Translational Medicine,
Zhejiang Shuren University, Hangzhou 310015, Zhejiang, China
| | - Shisheng Li
- Department of Otorhinolaryngology Head and Neck Surgery, the Second Xiangya Hospital,
Central South University, Changsha 410011, Hunan, China
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2
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Wang X, Sun Y, Zhao JY, Guan XW, Wang YY, Hong DY, Zhang ZL, Li YH, Yang PY, Jiang T, Xu ZF. Utility, benefits, and risks of newborn genetic screening carrier reports for families. J Glob Health 2024; 14:04044. [PMID: 38389402 PMCID: PMC10884785 DOI: 10.7189/jogh.14.04044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2024] Open
Abstract
Background Newborn genetic screening (NBGS) based on next-generation sequencing offers enhanced disease detection and better detection rates than traditional newborn screening. However, challenges remain, especially around reporting the NBGS carrier results. Therefore, we aimed to investigate the NBGS carrier parents' views on NBGS and NBGS reports in China. Methods We distributed a survey querying demographic information, knowledge and perceptions of NBGS, the impact of NBGS on a total of 2930 parents, and their decision-making to parents of newborns reported as carriers in NBGS in Nanjing, China in 2022. Results The average age of the survey respondents was 30.7 years (standard deviation = 3.6). Most (68.38%) felt informed about NBGS, especially women, the highly educated, and high earners. Nearly all (98.74%) saw NBGS as crucial for early disease detection, with 73.18% believing it positively impacts their future. However, 19.16% felt it might cause anxiety, especially among the less educated. Concerns included potential discrimination due to exposed genetic data and strained family ties. Many suggested NBGS coverage by medical insurance to ease financial burdens. Conclusions Through our study, we gained insights into parents' perspectives and concerns regarding the NBGS carrier result reporting, thus providing relevant information for further refinement and clinical promotion of the NBGS project.
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Affiliation(s)
- Xin Wang
- Genetic Medicine Center, Women’s Hospital of Nanjing Medical University, Nanjing Women and Children’s Healthcare Hospital, Nanjing, China
| | - Yun Sun
- Genetic Medicine Center, Women’s Hospital of Nanjing Medical University, Nanjing Women and Children’s Healthcare Hospital, Nanjing, China
| | | | - Xian-Wei Guan
- Genetic Medicine Center, Women’s Hospital of Nanjing Medical University, Nanjing Women and Children’s Healthcare Hospital, Nanjing, China
| | - Yan-Yun Wang
- Genetic Medicine Center, Women’s Hospital of Nanjing Medical University, Nanjing Women and Children’s Healthcare Hospital, Nanjing, China
| | - Dong-Yang Hong
- Genetic Medicine Center, Women’s Hospital of Nanjing Medical University, Nanjing Women and Children’s Healthcare Hospital, Nanjing, China
| | - Zhi-Lei Zhang
- Genetic Medicine Center, Women’s Hospital of Nanjing Medical University, Nanjing Women and Children’s Healthcare Hospital, Nanjing, China
| | - Ya-Hong Li
- Genetic Medicine Center, Women’s Hospital of Nanjing Medical University, Nanjing Women and Children’s Healthcare Hospital, Nanjing, China
| | - Pei-Ying Yang
- Genetic Medicine Center, Women’s Hospital of Nanjing Medical University, Nanjing Women and Children’s Healthcare Hospital, Nanjing, China
| | - Tao Jiang
- Genetic Medicine Center, Women’s Hospital of Nanjing Medical University, Nanjing Women and Children’s Healthcare Hospital, Nanjing, China
| | - Zheng-Feng Xu
- Genetic Medicine Center, Women’s Hospital of Nanjing Medical University, Nanjing Women and Children’s Healthcare Hospital, Nanjing, China
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3
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Di Carlo C, Mighton C, Clausen M, Joshi E, Casalino S, Kim THM, Kowal C, Birken C, Maguire J, Bombard Y. Parents' attitudes towards research involving genome sequencing of their healthy children: a qualitative study. Eur J Hum Genet 2024; 32:171-175. [PMID: 37864046 PMCID: PMC10853502 DOI: 10.1038/s41431-023-01476-9] [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: 06/18/2023] [Revised: 07/28/2023] [Accepted: 09/26/2023] [Indexed: 10/22/2023] Open
Abstract
With widespread genomic sequencing research efforts, there is increasing impetus to return results to participants. Parents of healthy children are increasingly asked to participate in genomic research, yet there are limited studies of parental expectations for the return of results amongst healthy children. We explored parental attitudes towards their healthy children's participation in genomic research and expectations for return of results. Data collection involved semi-structured telephone interviews with parents of healthy children participating in a primary care research network. Transcripts were analyzed thematically using constant comparison. A total of 26 parents were interviewed: 22 were female, 19 self-reported as White/European, and 20 were aged 30-39. Three themes emerged: (1) Reciprocity; Parents preferred to receive medically actionable, childhood-onset results and expected recontact overtime in exchange for their research participation. (2) Downstream impacts of testing; Parents expected future clinical benefits but were concerned about the risk of genetic discrimination. (3) Power and empowerment; Some parents felt empowered to take preventative action for their child and relatives, while others did not want to limit their child's autonomy. Considering these tensions may help to inform participant-centered approaches to optimize parental decision-making and participation, as well as maximize the utility of results.
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Affiliation(s)
- Christina Di Carlo
- Genomics Health Services Research Program, Li Ka Shing Knowledge Institute, St. Michael's Hospital, Unity Health Toronto, Toronto, ON, Canada
- University of Ottawa Faculty of Medicine, Ottawa, ON, Canada
| | - Chloe Mighton
- Genomics Health Services Research Program, Li Ka Shing Knowledge Institute, St. Michael's Hospital, Unity Health Toronto, Toronto, ON, Canada
- Institute of Health Policy, Management, and Evaluation, University of Toronto, Toronto, ON, Canada
| | - Marc Clausen
- Genomics Health Services Research Program, Li Ka Shing Knowledge Institute, St. Michael's Hospital, Unity Health Toronto, Toronto, ON, Canada
| | - Esha Joshi
- Genomics Health Services Research Program, Li Ka Shing Knowledge Institute, St. Michael's Hospital, Unity Health Toronto, Toronto, ON, Canada
| | - Selina Casalino
- Genomics Health Services Research Program, Li Ka Shing Knowledge Institute, St. Michael's Hospital, Unity Health Toronto, Toronto, ON, Canada
| | - Theresa H M Kim
- Genomics Health Services Research Program, Li Ka Shing Knowledge Institute, St. Michael's Hospital, Unity Health Toronto, Toronto, ON, Canada
- The Hospital for Sick Children, Toronto, ON, Canada
| | | | - Catherine Birken
- The Hospital for Sick Children, Toronto, ON, Canada
- University of Toronto, Toronto, ON, Canada
| | - Jonathon Maguire
- Genomics Health Services Research Program, Li Ka Shing Knowledge Institute, St. Michael's Hospital, Unity Health Toronto, Toronto, ON, Canada
- Institute of Health Policy, Management, and Evaluation, University of Toronto, Toronto, ON, Canada
- University of Toronto, Toronto, ON, Canada
| | - Yvonne Bombard
- Genomics Health Services Research Program, Li Ka Shing Knowledge Institute, 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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4
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Solomon BD. The future of commercial genetic testing. Curr Opin Pediatr 2023; 35:615-619. [PMID: 37218641 PMCID: PMC10667560 DOI: 10.1097/mop.0000000000001260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
PURPOSE OF REVIEW There are thousands of different clinical genetic tests currently available. Genetic testing and its applications continue to change rapidly for multiple reasons. These reasons include technological advances, accruing evidence about the impact and effects of testing, and many complex financial and regulatory factors. RECENT FINDINGS This article considers a number of key issues and axes related to the current and future state of clinical genetic testing, including targeted versus broad testing, simple/Mendelian versus polygenic and multifactorial testing models, genetic testing for individuals with high suspicion of genetic conditions versus ascertainment through population screening, the rise of artificial intelligence in multiple aspects of the genetic testing process, and how developments such as rapid genetic testing and the growing availability of new therapies for genetic conditions may affect the field. SUMMARY Genetic testing is expanding and evolving, including into new clinical applications. Developments in the field of genetics will likely result in genetic testing becoming increasingly in the purview of a very broad range of clinicians, including general paediatricians as well as paediatric subspecialists.
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Affiliation(s)
- Benjamin D. Solomon
- Medical Genetics Branch, National Human Genome Research Institute, United States of America
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5
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D'Gama AM, Agrawal PB. Genomic medicine in neonatal care: progress and challenges. Eur J Hum Genet 2023; 31:1357-1363. [PMID: 37789085 PMCID: PMC10689757 DOI: 10.1038/s41431-023-01464-z] [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: 05/24/2023] [Revised: 09/01/2023] [Accepted: 09/13/2023] [Indexed: 10/05/2023] Open
Abstract
During the neonatal period, many genetic disorders present and contribute to neonatal morbidity and mortality. Genomic medicine-the use of genomic information in clinical care- has the potential to significantly reduce morbidity and mortality in the neonatal period and improve outcomes for this population. Diagnostic genomic testing for symptomatic newborns, especially rapid testing, has been shown to be feasible and have diagnostic and clinical utility, particularly in the short-term. Ongoing studies are assessing the feasibility and utility, including personal utility, of implementation in diverse populations. Genomic screening for asymptomatic newborns has also been studied, and the acceptability and feasibility of such an approach remains an active area of investigation. Emerging precision therapies, with examples even at the "n-of-1" level, highlight the promise of precision diagnostics to lead to early intervention and improve outcomes. To sustainably implement genomic medicine in neonatal care in an ethical, effective, and equitable manner, we need to ensure access to genetics and genomics knowledge, access to genomic tests, which is currently limited by payors, feasible processes for ordering these tests, and access to follow up in the clinical and research realms. Future studies will provide further insight into enablers and barriers to optimize implementation strategies.
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Affiliation(s)
- Alissa M D'Gama
- Division of Newborn Medicine, Department of Pediatrics, Boston Children's Hospital, Boston, MA, USA
- Epilepsy Genetics Program, Department of Neurology, Boston Children's Hospital, Boston, MA, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA
| | - Pankaj B Agrawal
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA.
- The Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA, USA.
- Division of Neonatology, Department of Pediatrics, University of Miami Miller School of Medicine, Holtz Children's Hospital, Jackson Health System, Miami, FL, USA.
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6
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Brennenstuhl H, Schaaf CP. [Genomic newborn screening-research approaches, challenges, and opportunities]. Bundesgesundheitsblatt Gesundheitsforschung Gesundheitsschutz 2023; 66:1232-1242. [PMID: 37831095 PMCID: PMC10622372 DOI: 10.1007/s00103-023-03777-2] [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: 02/23/2023] [Accepted: 09/12/2023] [Indexed: 10/14/2023]
Abstract
The application of high-throughput sequencing methods for population-based genomic newborn screening offers numerous opportunities for improving population health. The use of genome-based sequencing technology holds potential to enable the diagnosis of virtually any genetic disorder at an early stage and offers great flexibility when it comes to selection and expansion of target diseases. National and international efforts are therefore being made to investigate the ethical, legal, social, psychological, and technical aspects of genomic newborn screening. In addition to the many opportunities, there are numerous challenges and questions that remain to be answered: When and how should legal guardians be informed about such screening? Which diseases should be screened for? How should incidental findings or identification of a genetic predisposition be dealt with? Should data be stored long term and if so, how can this be done securely? Provided there is an appropriate regulatory framework and a transparent consent process, genomic newborn screening has the potential to fundamentally change the way in which we screen for congenital diseases. However, there is still much to be done. To achieve understanding and acceptance of genomic newborn screening amongst all stakeholders and thus to maximize its benefits for the population, a public discourse on the possibilities and limitations of genomic newborn screening is of critical importance. This article aims to provide an overview of the innovative technical developments in the field of human genetics, describe national and international approaches, and discuss challenges and opportunities of genomic newborn screening development.
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Affiliation(s)
- Heiko Brennenstuhl
- Institut für Humangenetik, Universität Heidelberg, Heidelberg, Baden-Württemberg, Deutschland
| | - Christian P Schaaf
- Institut für Humangenetik, Universität Heidelberg, Heidelberg, Baden-Württemberg, Deutschland.
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7
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Chan K, Hu Z, Bush LW, Cope H, Holm IA, Kingsmore SF, Wilhelm K, Scharfe C, Brower A. NBSTRN Tools to Advance Newborn Screening Research and Support Newborn Screening Stakeholders. Int J Neonatal Screen 2023; 9:63. [PMID: 37987476 PMCID: PMC10660757 DOI: 10.3390/ijns9040063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Revised: 10/17/2023] [Accepted: 10/19/2023] [Indexed: 11/22/2023] Open
Abstract
Rapid advances in the screening, diagnosis, and treatment of genetic disorders have increased the number of conditions that can be detected through universal newborn screening (NBS). However, the addition of conditions to the Recommended Uniform Screening Panel (RUSP) and the implementation of nationwide screening has been a slow process taking several years to accomplish for individual conditions. Here, we describe web-based tools and resources developed and implemented by the newborn screening translational research network (NBSTRN) to advance newborn screening research and support NBS stakeholders worldwide. The NBSTRN's tools include the Longitudinal Pediatric Data Resource (LPDR), the NBS Condition Resource (NBS-CR), the NBS Virtual Repository (NBS-VR), and the Ethical, Legal, and Social Issues (ELSI) Advantage. Research programs, including the Inborn Errors of Metabolism Information System (IBEM-IS), BabySeq, EarlyCheck, and Family Narratives Use Cases, have utilized NBSTRN's tools and, in turn, contributed research data to further expand and refine these resources. Additionally, we discuss ongoing tool development to facilitate the expansion of genetic disease screening in increasingly diverse populations. In conclusion, NBSTRN's tools and resources provide a trusted platform to enable NBS stakeholders to advance NBS research and improve clinical care for patients and their families.
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Affiliation(s)
- Kee Chan
- American College of Medical Genetics and Genomics, Bethesda, MD 20814, USA
| | - Zhanzhi Hu
- Department of Systems Biology, Columbia University, New York, NY 10032, USA
| | - Lynn W Bush
- Division Genetics and Genomics, Boston Children's Hospital Center, Boston, MA 02115, USA
- Department of Pediatrics and Center for Bioethics, Harvard Medical School, Boston, MA 02115, USA
| | - Heidi Cope
- GenOmics and Translational Research Center, RTI International, Research Triangle Park, NC 27709, USA
| | - Ingrid A Holm
- Division Genetics and Genomics, Boston Children's Hospital Center, Boston, MA 02115, USA
- Department of Pediatrics and Center for Bioethics, Harvard Medical School, Boston, MA 02115, USA
| | | | - Kevin Wilhelm
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Curt Scharfe
- Department of Genetics, Yale School of Medicine, New Haven, CT 06510, USA
| | - Amy Brower
- American College of Medical Genetics and Genomics, Bethesda, MD 20814, USA
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8
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Veldman A, Kiewiet MBG, Westra D, Bosch AM, Brands MMG, de Coo RIFM, Derks TGJ, Fuchs SA, van den Hout JMP, Huidekoper HH, Kluijtmans LAJ, Koop K, Lubout CMA, Mulder MF, Panis B, Rubio-Gozalbo ME, de Sain-van der Velden MG, Schaefers J, Schreuder AB, Visser G, Wevers RA, Wijburg FA, Heiner-Fokkema MR, van Spronsen FJ. A Delphi Survey Study to Formulate Statements on the Treatability of Inherited Metabolic Disorders to Decide on Eligibility for Newborn Screening. Int J Neonatal Screen 2023; 9:56. [PMID: 37873847 PMCID: PMC10594494 DOI: 10.3390/ijns9040056] [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: 09/10/2023] [Revised: 10/04/2023] [Accepted: 10/05/2023] [Indexed: 10/25/2023] Open
Abstract
The Wilson and Jungner (W&J) and Andermann criteria are meant to help select diseases eligible for population-based screening. With the introduction of next-generation sequencing (NGS) methods for newborn screening (NBS), more inherited metabolic diseases (IMDs) can technically be included, and a revision of the criteria was attempted. This study aimed to formulate statements and investigate whether those statements could elaborate on the criterion of treatability for IMDs to decide on eligibility for NBS. An online Delphi study was started among a panel of Dutch IMD experts (EPs). EPs evaluated, amended, and approved statements on treatability that were subsequently applied to 10 IMDs. After two rounds of Delphi, consensus was reached on 10 statements. Application of these statements selected 5 out of 10 IMDs proposed for this study as eligible for NBS, including 3 IMDs in the current Dutch NBS. The statement: 'The expected benefit/burden ratio of early treatment is positive and results in a significant health outcome' contributed most to decision-making. Our Delphi study resulted in 10 statements that can help to decide on eligibility for inclusion in NBS based on treatability, also showing that other criteria could be handled in a comparable way. Validation of the statements is required before these can be applied as guidance to authorities.
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Affiliation(s)
- Abigail Veldman
- Division of Metabolic Diseases, Beatrix Children’s Hospital, University of Groningen, University Medical Center Groningen, 9718 GZ Groningen, The Netherlands
| | - M. B. Gea Kiewiet
- Department of Genetics, University of Groningen, University Medical Center Groningen, 9718 GZ Groningen, The Netherlands
| | - Dineke Westra
- Department of Human Genetics, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Annet M. Bosch
- Department of Pediatrics, Division of Metabolic Disorders, Emma Children’s Hospital, Amsterdam University Medical Centre, 1105 AZ Amsterdam, The Netherlands
| | - Marion M. G. Brands
- Department of Pediatrics, Division of Metabolic Disorders, Emma Children’s Hospital, Amsterdam University Medical Centre, 1105 AZ Amsterdam, The Netherlands
| | - René I. F. M. de Coo
- Department of Toxicogenomics, Unit Clinical Genomics, MHeNs School for Mental Health and Neuroscience, Maastricht University, 6229 ER Maastricht, The Netherlands
| | - Terry G. J. Derks
- Division of Metabolic Diseases, Beatrix Children’s Hospital, University of Groningen, University Medical Center Groningen, 9718 GZ Groningen, The Netherlands
| | - Sabine A. Fuchs
- Department of Metabolic Diseases, University Medical Center Utrecht, Wilhelmina Children’s Hospital, 3584 EA Utrecht, The Netherlands
| | - Johanna. M. P. van den Hout
- Department of Pediatrics, Center for Lysosomal and Metabolic Diseases, Erasmus University Medical Center, 3015 GD Rotterdam, The Netherlands
| | - Hidde H. Huidekoper
- Department of Pediatrics, Center for Lysosomal and Metabolic Diseases, Erasmus University Medical Center, 3015 GD Rotterdam, The Netherlands
| | - Leo A. J. Kluijtmans
- Department of Human Genetics, Translational Metabolic Laboratory, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands (R.A.W.)
| | - Klaas Koop
- Department of Metabolic Diseases, University Medical Center Utrecht, Wilhelmina Children’s Hospital, 3584 EA Utrecht, The Netherlands
| | - Charlotte M. A. Lubout
- Division of Metabolic Diseases, Beatrix Children’s Hospital, University of Groningen, University Medical Center Groningen, 9718 GZ Groningen, The Netherlands
| | - Margaretha F. Mulder
- Department of Pediatrics, Division of Metabolic Disorders, Emma Children’s Hospital, Amsterdam University Medical Centre, 1105 AZ Amsterdam, The Netherlands
| | - Bianca Panis
- Department of Pediatrics, Maastricht University Medical Center, 6229 HX Maastricht, The Netherlands
| | - M. Estela Rubio-Gozalbo
- Department of Pediatrics and Clinical Genetics, Maastricht University Medical Center, 6229 HX Maastricht, The Netherlands
| | | | - Jaqueline Schaefers
- Department of Pediatrics, Maastricht University Medical Center, 6229 HX Maastricht, The Netherlands
| | - Andrea B. Schreuder
- Division of Metabolic Diseases, Beatrix Children’s Hospital, University of Groningen, University Medical Center Groningen, 9718 GZ Groningen, The Netherlands
| | - Gepke Visser
- Department of Pediatrics, Division of Metabolic Disorders, Emma Children’s Hospital, Amsterdam University Medical Centre, 1105 AZ Amsterdam, The Netherlands
- Department of Metabolic Diseases, University Medical Center Utrecht, Wilhelmina Children’s Hospital, 3584 EA Utrecht, The Netherlands
| | - Ron A. Wevers
- Department of Human Genetics, Translational Metabolic Laboratory, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands (R.A.W.)
| | - Frits A. Wijburg
- Department of Pediatrics, Division of Metabolic Disorders, Emma Children’s Hospital, Amsterdam University Medical Centre, 1105 AZ Amsterdam, The Netherlands
| | - M. Rebecca Heiner-Fokkema
- Department of Laboratory Medicine, Laboratory of Metabolic Diseases, University of Groningen, University Medical Center Groningen, 9718 GZ Groningen, The Netherlands
| | - Francjan J. van Spronsen
- Division of Metabolic Diseases, Beatrix Children’s Hospital, University of Groningen, University Medical Center Groningen, 9718 GZ Groningen, The Netherlands
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9
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Liang NSY, Watts-Dickens A, Chitayat D, Babul-Hirji R, Chakraborty P, Hayeems RZ. Parental Preferences for Expanded Newborn Screening: What Are the Limits? CHILDREN (BASEL, SWITZERLAND) 2023; 10:1362. [PMID: 37628361 PMCID: PMC10453746 DOI: 10.3390/children10081362] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 08/02/2023] [Accepted: 08/08/2023] [Indexed: 08/27/2023]
Abstract
The use of next-generation sequencing technologies such as genomic sequencing in newborn screening (NBS) could enable the detection of a broader range of conditions. We explored parental preferences and attitudes towards screening for conditions for which varying types of treatment exist with a cross-sectional survey completed by 100 parents of newborns who received NBS in Ontario, Canada. The survey included four vignettes illustrative of hypothetical screening targets, followed by questions assessing parental attitudes. Chi-square tests were used to compare frequency distributions of preferences. Results show that most parents supported NBS for conditions for which only supportive interventions are available, but to a significantly lesser degree than those with disease-specific treatments (99% vs. 82-87%, p ≤ 0.01). For conditions without an effective treatment, the type of supportive care and age of onset of the condition did not significantly alter parent perceptions of risks and benefits. Parents are interested in expanded NBS for conditions with only supportive interventions in childhood, despite lower levels of perceived benefit for the child and greater anticipated anxiety from screen-positive results. These preferences suggest that the expansion of NBS may require ongoing deliberation of perceived benefits and risks and enhanced approaches to education, consent, and support.
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Affiliation(s)
- Nicole S. Y. Liang
- Department of Genetic Counselling, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada
- Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada
| | - Abby Watts-Dickens
- Department of Genetic Counselling, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada
- Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - David Chitayat
- Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Riyana Babul-Hirji
- Department of Genetic Counselling, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada
- Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | | | - Robin Z. Hayeems
- Child Health Evaluative Sciences, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada
- Health Policy, Management and Evaluation, University of Toronto, ON M5T 3M6, Canada
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10
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Green RC, Shah N, Genetti CA, Yu T, Zettler B, Uveges MK, Ceyhan-Birsoy O, Lebo MS, Pereira S, Agrawal PB, Parad RB, McGuire AL, Christensen KD, Schwartz TS, Rehm HL, Holm IA, Beggs AH. Actionability of unanticipated monogenic disease risks in newborn genomic screening: Findings from the BabySeq Project. Am J Hum Genet 2023; 110:1034-1045. [PMID: 37279760 PMCID: PMC10357495 DOI: 10.1016/j.ajhg.2023.05.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 05/09/2023] [Accepted: 05/10/2023] [Indexed: 06/08/2023] Open
Abstract
Newborn genomic sequencing (NBSeq) to screen for medically important genetic information is of considerable interest but data characterizing the actionability of such findings, and the downstream medical efforts in response to discovery of unanticipated genetic risk variants, are lacking. From a clinical trial of comprehensive exome sequencing in 127 apparently healthy infants and 32 infants in intensive care, we previously identified 17 infants (10.7%) with unanticipated monogenic disease risks (uMDRs). In this analysis, we assessed actionability for each of these uMDRs with a modified ClinGen actionability semiquantitative metric (CASQM) and created radar plots representing degrees of penetrance of the condition, severity of the condition, effectiveness of intervention, and tolerability of intervention. In addition, we followed each of these infants for 3-5 years after disclosure and tracked the medical actions prompted by these findings. All 17 uMDR findings were scored as moderately or highly actionable on the CASQM (mean 9, range: 7-11 on a 0-12 scale) and several distinctive visual patterns emerged on the radar plots. In three infants, uMDRs revealed unsuspected genetic etiologies for existing phenotypes, and in the remaining 14 infants, uMDRs provided risk stratification for future medical surveillance. In 13 infants, uMDRs prompted screening for at-risk family members, three of whom underwent cancer-risk-reducing surgeries. Although assessments of clinical utility and cost-effectiveness will require larger datasets, these findings suggest that large-scale comprehensive sequencing of newborns will reveal numerous actionable uMDRs and precipitate substantial, and in some cases lifesaving, downstream medical care in newborns and their family members.
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Affiliation(s)
- Robert C Green
- Department of Medicine, Mass General Brigham, Boston, MA 02115, USA; Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Ariadne Labs, Boston, MA 02215, USA; Harvard Medical School, Boston, MA 02215, USA.
| | - Nidhi Shah
- Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Division of Genetics and Genomics, Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA 02115, USA; Dartmouth Health Children's, Lebanon, NH 03756, USA
| | - Casie A Genetti
- Division of Genetics and Genomics, Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA 02115, USA
| | - Timothy Yu
- Harvard Medical School, Boston, MA 02215, USA; Division of Genetics and Genomics, Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA 02115, USA
| | - Bethany Zettler
- Department of Medicine, Mass General Brigham, Boston, MA 02115, USA; Ariadne Labs, Boston, MA 02215, USA
| | - Melissa K Uveges
- William F. Connell School of Nursing, Boston College, Chestnut Hill, MA 02467, USA
| | - Ozge Ceyhan-Birsoy
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Matthew S Lebo
- Department of Medicine, Mass General Brigham, Boston, MA 02115, USA; Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Harvard Medical School, Boston, MA 02215, USA; Department of Pathology, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Stacey Pereira
- Center for Medical Ethics and Health Policy, Baylor College of Medicine; Houston, TX, USA
| | - Pankaj B Agrawal
- Harvard Medical School, Boston, MA 02215, USA; Division of Genetics and Genomics, Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA 02115, USA; Division of Neonatology, Department of Pediatrics, University of Miami Miller School of Medicine and Holtz Children's Hospital, Jackson Health System, Miami, FL, USA
| | - Richard B Parad
- Harvard Medical School, Boston, MA 02215, USA; Department of Pediatric Newborn Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Amy L McGuire
- Center for Medical Ethics and Health Policy, Baylor College of Medicine; Houston, TX, USA
| | - Kurt D Christensen
- Harvard Medical School, Boston, MA 02215, USA; Department of Population Medicine, Harvard Pilgrim Health Care Institute, Boston, MA 02215, USA
| | - Talia S Schwartz
- Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Heidi L Rehm
- Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Harvard Medical School, Boston, MA 02215, USA; Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Ingrid A Holm
- Harvard Medical School, Boston, MA 02215, USA; Division of Genetics and Genomics, Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA 02115, USA
| | - Alan H Beggs
- Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Harvard Medical School, Boston, MA 02215, USA; Division of Genetics and Genomics, Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA 02115, USA
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11
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Balciuniene J, Liu R, Bean L, Guo F, Nallamilli BRR, Guruju N, Chen-Deutsch X, Yousaf R, Fura K, Chin E, Mathur A, Ma Z, Carmichael J, da Silva C, Collins C, Hegde M. At-Risk Genomic Findings for Pediatric-Onset Disorders From Genome Sequencing vs Medically Actionable Gene Panel in Proactive Screening of Newborns and Children. JAMA Netw Open 2023; 6:e2326445. [PMID: 37523181 PMCID: PMC10391308 DOI: 10.1001/jamanetworkopen.2023.26445] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 08/01/2023] Open
Abstract
Importance Although the clinical utility of genome sequencing for critically ill children is well recognized, its utility for proactive pediatric screening is not well explored. Objective To evaluate molecular findings from screening ostensibly healthy children with genome sequencing compared with a gene panel for medically actionable pediatric conditions. Design, Setting, and Participants This case series study was conducted among consecutive, apparently healthy children undergoing proactive genetic screening for pediatric disorders by genome sequencing (n = 562) or an exome-based panel of 268 genes (n = 606) from March 1, 2018, through July 31, 2022. Exposures Genetic screening for pediatric-onset disorders using genome sequencing or an exome-based panel of 268 genes. Main Outcomes and Measures Molecular findings indicative of genetic disease risk. Results Of 562 apparently healthy children (286 girls [50.9%]; median age, 29 days [IQR, 9-117 days]) undergoing screening by genome sequencing, 46 (8.2%; 95% CI, 5.9%-10.5%) were found to be at risk for pediatric-onset disease, including 22 children (3.9%) at risk for high-penetrance disorders. Sequence analysis uncovered molecular diagnoses among 32 individuals (5.7%), while copy number variant analysis uncovered molecular diagnoses among 14 individuals (2.5%), including 4 individuals (0.7%) with chromosome scale abnormalities. Overall, there were 47 molecular diagnoses, with 1 individual receiving 2 diagnoses; of the 47 potential diagnoses, 22 (46.8%) were associated with high-penetrance conditions. Pathogenic variants in medically actionable pediatric genes were found in 6 individuals (1.1%), constituting 12.8% (6 of 47) of all diagnoses. At least 1 pharmacogenomic variant was reported for 89.0% (500 of 562) of the cohort. In contrast, of 606 children (293 girls [48.3%]; median age, 26 days [IQR, 10-67 days]) undergoing gene panel screening, only 13 (2.1%; 95% CI, 1.0%-3.3%) resulted in potential childhood-onset diagnoses, a significantly lower rate than those screened by genome sequencing (P < .001). Conclusions and Relevance In this case series study, genome sequencing as a proactive screening approach for children, due to its unrestrictive gene content and technical advantages in comparison with an exome-based gene panel for medically actionable childhood conditions, uncovered a wide range of heterogeneous high-penetrance pediatric conditions that could guide early interventions and medical management.
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Affiliation(s)
| | - Ruby Liu
- PerkinElmer Genomics, PerkinElmer Inc, Pittsburgh, Pennsylvania
| | - Lora Bean
- PerkinElmer Genomics, PerkinElmer Inc, Pittsburgh, Pennsylvania
| | - Fen Guo
- PerkinElmer Genomics, PerkinElmer Inc, Pittsburgh, Pennsylvania
| | | | - Naga Guruju
- PerkinElmer Genomics, PerkinElmer Inc, Pittsburgh, Pennsylvania
| | | | - Rizwan Yousaf
- PerkinElmer Genomics, PerkinElmer Inc, Pittsburgh, Pennsylvania
| | - Kristina Fura
- PerkinElmer Genomics, PerkinElmer Inc, Pittsburgh, Pennsylvania
| | - Ephrem Chin
- PerkinElmer Genomics, PerkinElmer Inc, Pittsburgh, Pennsylvania
| | - Abhinav Mathur
- PerkinElmer Genomics, PerkinElmer Inc, Pittsburgh, Pennsylvania
| | - Zeqiang Ma
- PerkinElmer Genomics, PerkinElmer Inc, Pittsburgh, Pennsylvania
| | | | | | | | - Madhuri Hegde
- PerkinElmer Genomics, PerkinElmer Inc, Pittsburgh, Pennsylvania
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12
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Suhrie K, Tillman EM. Pharmacogenetic informed care in early childhood: options for improving access and health equity. Pharmacogenomics 2023; 24:579-582. [PMID: 37466126 DOI: 10.2217/pgs-2023-0119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/20/2023] Open
Affiliation(s)
- Kristen Suhrie
- Department of Pediatrics, Division of Neonatology, & Department of Medical & Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Emma M Tillman
- Division of Clinical Pharmacology, Department of Medicine, Indiana University School of Medicine, Indianapolis, IN 46202, USA
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13
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Lemke AA, Thompson ML, Gimpel EC, McNamara KC, Rich CA, Finnila CR, Cochran ME, Lawlor JMJ, East KM, Bowling KM, Latner DR, Hiatt SM, Amaral MD, Kelley WV, Greve V, Gray DE, Felker SA, Meddaugh H, Cannon A, Luedecke A, Jackson KE, Hendon LG, Janani HM, Johnston M, Merin LA, Deans SL, Tuura C, Hughes T, Williams H, Laborde K, Neu MB, Patrick-Esteve J, Hurst ACE, Kirmse BM, Savich R, Spedale SB, Knight SJ, Barsh GS, Korf BR, Cooper GM, Brothers KB. Parents' Perspectives on the Utility of Genomic Sequencing in the Neonatal Intensive Care Unit. J Pers Med 2023; 13:1026. [PMID: 37511639 PMCID: PMC10382030 DOI: 10.3390/jpm13071026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Revised: 06/08/2023] [Accepted: 06/16/2023] [Indexed: 07/30/2023] Open
Abstract
BACKGROUND It is critical to understand the wide-ranging clinical and non-clinical effects of genome sequencing (GS) for parents in the NICU context. We assessed parents' experiences with GS as a first-line diagnostic tool for infants with suspected genetic conditions in the NICU. METHODS Parents of newborns (N = 62) suspected of having a genetic condition were recruited across five hospitals in the southeast United States as part of the SouthSeq study. Semi-structured interviews (N = 78) were conducted after parents received their child's sequencing result (positive, negative, or variants of unknown significance). Thematic analysis was performed on all interviews. RESULTS Key themes included that (1) GS in infancy is important for reproductive decision making, preparing for the child's future care, ending the diagnostic odyssey, and sharing results with care providers; (2) the timing of disclosure was acceptable for most parents, although many reported the NICU environment was overwhelming; and (3) parents deny that receiving GS results during infancy exacerbated parent-infant bonding, and reported variable impact on their feelings of guilt. CONCLUSION Parents reported that GS during the neonatal period was useful because it provided a "backbone" for their child's care. Parents did not consistently endorse negative impacts like interference with parent-infant bonding.
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Affiliation(s)
- Amy A Lemke
- Department of Pediatrics, Norton Children's Research Institute, University of Louisville School of Medicine, Louisville, KY 40202, USA
| | | | - Emily C Gimpel
- Department of Pediatrics, Norton Children's Research Institute, University of Louisville School of Medicine, Louisville, KY 40202, USA
| | - Katelyn C McNamara
- Department of Pediatrics, Norton Children's Research Institute, University of Louisville School of Medicine, Louisville, KY 40202, USA
| | - Carla A Rich
- Department of Pediatrics, Norton Children's Research Institute, University of Louisville School of Medicine, Louisville, KY 40202, USA
| | | | - Meagan E Cochran
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - James M J Lawlor
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - Kelly M East
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - Kevin M Bowling
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Donald R Latner
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - Susan M Hiatt
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | | | - Whitley V Kelley
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - Veronica Greve
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - David E Gray
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - Stephanie A Felker
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
- Department of Biological Sciences, University of Alabama in Huntsville, Huntsville, AL 35899, USA
| | - Hannah Meddaugh
- Department of Genetics, Ochsner Health System, New Orleans, LA 70121, USA
| | - Ashley Cannon
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Amanda Luedecke
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Kelly E Jackson
- Division of Genetics, Norton Children's Genetics Center, University of Louisville School of Medicine, Louisville, KY 40202, USA
| | - Laura G Hendon
- Department of Pediatrics, University of Mississippi Medical Center, Jackson, MS 39216, USA
| | - Hillary M Janani
- Neonatal Intensive Care Unit, Woman's Hospital, Baton Rouge, LA 70817, USA
| | - Marla Johnston
- Department of Pediatrics, Children's Hospital New Orleans, New Orleans, LA 70118, USA
| | - Lee Ann Merin
- Department of Pediatrics, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Sarah L Deans
- Department of Pediatrics, Norton Children's Research Institute, University of Louisville School of Medicine, Louisville, KY 40202, USA
| | - Carly Tuura
- Department of Pediatrics, University of Mississippi Medical Center, Jackson, MS 39216, USA
| | - Trent Hughes
- Department of Pediatrics, University of Mississippi Medical Center, Jackson, MS 39216, USA
| | - Heather Williams
- Department of Pediatrics, University of Mississippi Medical Center, Jackson, MS 39216, USA
| | - Kelly Laborde
- Neonatal Intensive Care Unit, Woman's Hospital, Baton Rouge, LA 70817, USA
| | - Matthew B Neu
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | | | - Anna C E Hurst
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Brian M Kirmse
- Department of Pediatrics, University of Mississippi Medical Center, Jackson, MS 39216, USA
| | - Renate Savich
- Pediatrics Neonatology Division, University of New Mexico Health Sciences Center, Albuquerque, NM 87106, USA
| | - Steven B Spedale
- Neonatal Intensive Care Unit, Woman's Hospital, Baton Rouge, LA 70817, USA
| | - Sara J Knight
- Department of Internal Medicine, University of Utah, Salt Lake City, UT 84112, USA
| | - Gregory S Barsh
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - Bruce R Korf
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Gregory M Cooper
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - Kyle B Brothers
- Department of Pediatrics, Norton Children's Research Institute, University of Louisville School of Medicine, Louisville, KY 40202, USA
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14
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Bouffler SE, Lee L, Lynch F, Martyn M, Lynch E, Macciocca I, Curnow L, McCorkell G, Lunke S, Chong B, Marum JE, Delatycki M, Downie L, Goranitis I, Vears DF, Best S, Clausen M, Bombard Y, Stark Z, Gaff CL. Two-step offer and return of multiple types of additional genomic findings to families after ultrarapid trio genomic testing in the acute care setting: a study protocol. BMJ Open 2023; 13:e072999. [PMID: 37270192 DOI: 10.1136/bmjopen-2023-072999] [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] [Indexed: 06/05/2023] Open
Abstract
INTRODUCTION As routine genomic testing expands, so too does the opportunity to look for additional health information unrelated to the original reason for testing, termed additional findings (AF). Analysis for many different types of AF may be available, particularly to families undergoing trio genomic testing. The optimal model for service delivery remains to be determined, especially when the original test occurs in the acute care setting. METHODS AND ANALYSIS Families enrolled in a national study providing ultrarapid genomic testing to critically ill children will be offered analysis for three types of AF on their stored genomic data: paediatric-onset conditions in the child, adult-onset conditions in each parent and reproductive carrier screening for the parents as a couple. The offer will be made 3-6 months after diagnostic testing. Parents will have access to a modified version of the Genetics Adviser web-based decision support tool before attending a genetic counselling appointment to discuss consent for AF. Parental experiences will be evaluated using qualitative and quantitative methods on data collected through surveys, appointment recordings and interviews at multiple time points. Evaluation will focus on parental preferences, uptake, decision support use and understanding of AF. Genetic health professionals' perspectives on acceptability and feasibility of AF will also be captured through surveys and interviews. ETHICS AND DISSEMINATION This project received ethics approval from the Melbourne Health Human Research Ethics Committee as part of the Australian Genomics Health Alliance protocol: HREC/16/MH/251. Findings will be disseminated through peer-review journal articles and at conferences nationally and internationally.
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Affiliation(s)
| | - Ling Lee
- Melbourne Genomics Health Alliance, Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia
- Murdoch Children's Research Institute, Parkville, Victoria, Australia
| | - Fiona Lynch
- Murdoch Children's Research Institute, Parkville, Victoria, Australia
- Department of Paediatrics, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Melbourne, Victoria, Australia
| | - Melissa Martyn
- Melbourne Genomics Health Alliance, Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia
- Murdoch Children's Research Institute, Parkville, Victoria, Australia
| | - Elly Lynch
- Melbourne Genomics Health Alliance, Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Parkville, Victoria, Australia
| | - Ivan Macciocca
- Department of Paediatrics, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Melbourne, Victoria, Australia
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Parkville, Victoria, Australia
| | - Lisette Curnow
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Parkville, Victoria, Australia
| | - Giulia McCorkell
- Australian Genomics Health Alliance, Parkville, Victoria, Australia
- Department of Paediatrics, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Melbourne, Victoria, Australia
| | - Sebastian Lunke
- Department of Paediatrics, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Melbourne, Victoria, Australia
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Parkville, Victoria, Australia
| | - Belinda Chong
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Parkville, Victoria, Australia
| | - Justine E Marum
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Parkville, Victoria, Australia
| | - Martin Delatycki
- Department of Paediatrics, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Melbourne, Victoria, Australia
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Parkville, Victoria, Australia
| | - Lilian Downie
- Murdoch Children's Research Institute, Parkville, Victoria, Australia
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Parkville, Victoria, Australia
| | - Ilias Goranitis
- Australian Genomics Health Alliance, Parkville, Victoria, Australia
- Health Economics Unit, Centre for Health Policy, Melbourne Schoold of Population and Global Health, The University of Melbourne, Melbourne, Victoria, Australia
| | - Danya F Vears
- Murdoch Children's Research Institute, Parkville, Victoria, Australia
- Department of Paediatrics, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Melbourne, Victoria, Australia
| | - Stephanie Best
- Australian Genomics Health Alliance, Parkville, Victoria, Australia
- Department of Health Services Research, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Marc Clausen
- Genomics Health Services Research Program, St. Michael's Hospital, Unity Health Toronto, Toronto, Ontario, Canada
| | - Yvonne Bombard
- Genomics Health Services Research Program, St. Michael's Hospital, Unity Health Toronto, Toronto, Ontario, Canada
- Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, Ontario, Canada
| | - Zornitza Stark
- Australian Genomics Health Alliance, Parkville, Victoria, Australia
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Parkville, Victoria, Australia
| | - Clara L Gaff
- Melbourne Genomics Health Alliance, Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia
- Murdoch Children's Research Institute, Parkville, Victoria, Australia
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15
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Zhang S, Zhou L, Zhang L, Wang Y, Wang H. Molecular genetic screening of full-term small for gestational age. BMC Pediatr 2023; 23:217. [PMID: 37147621 PMCID: PMC10161501 DOI: 10.1186/s12887-023-04030-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Accepted: 04/24/2023] [Indexed: 05/07/2023] Open
Abstract
OBJECTIVE To examine the clinical application of genomic screening in newborns small for gestational age (SGA), hoping to provide an efficient technique for early discovery of neonatal diseases, which is necessary to elevate survival rates and the quality of life in infants. METHODS Totally 93 full-term SGA newborns were assessed. Dried blood spot (DBS) samples were obtained at 72 h after birth, and tandem mass spectrometry (TMS) and Angel Care genomic screening (GS, using Targeted next generation sequencing) were carried out. RESULTS All 93 subjects were examined by Angel Care GS and TMS. No children showing inborn errors of metabolism (IEM) were detected by TMS, while 2 pediatric cases (2.15%, 2/93) were confirmed as thyroid dyshormonogenesis 6 (TDH6) by Angel Care GS. Additionally, 45 pediatric cases (48.4%) had one or more variants conferring a carrier status for recessive childhood-onset disorders, with 31 genes and 42 variants associated with 26 diseases. The top three gene-related diseases with carrier status were autosomal recessive deafness (DFNB), abnormal thyroid hormone and Krabbe disease. CONCLUSIONS SGA is tightly associated with genetic variation. Molecular Genetic Screening allows early detection of congenital hypothyroidism and may be a potent genomic sequencing technique for screening newborns.
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Affiliation(s)
- Shuman Zhang
- Department of Neonatology, Changzhou Maternity and Child Health Care Hospital, Changzhou Medical Center, Nanjing Medical University, Changzhou, Jiangsu Province, China
| | - Lingna Zhou
- Department of Medical Genetics, Changzhou Maternity and Child Health Care Hospital, Changzhou Medical Center, Nanjing Medical University, Changzhou, Jiangsu Province, China
| | - Lin Zhang
- Department of Neonatology, Changzhou Maternity and Child Health Care Hospital, Changzhou Medical Center, Nanjing Medical University, Changzhou, Jiangsu Province, China
| | - Yu Wang
- Department of Neonatology, Changzhou Maternity and Child Health Care Hospital, Changzhou Medical Center, Nanjing Medical University, Changzhou, Jiangsu Province, China.
| | - Huaiyan Wang
- Department of Neonatology, Changzhou Maternity and Child Health Care Hospital, Changzhou Medical Center, Nanjing Medical University, Changzhou, Jiangsu Province, China.
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16
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Ulph F, Bennett R. Psychological and Ethical Challenges of Introducing Whole Genome Sequencing into Routine Newborn Screening: Lessons Learned from Existing Newborn Screening. New Bioeth 2023; 29:52-74. [PMID: 36181705 DOI: 10.1080/20502877.2022.2124582] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/06/2023]
Abstract
As a psychologist and an ethicist, we have explored empirically newborn screening consent and communication processes. In this paper we consider the impact on families if newborn screening uses whole genome sequencing. We frame this within the World Health Organization's definition of health and contend that proposals to use whole genome sequencing in newborn screening take into account the ethical, practical and psychological impact of such screening. We argue that the important psychological processes occurring in the neonatal phase necessitate a clear justification that providing risk information at this stage provides a health benefit. We illustrate how research on current newborn screening can inform whole genome sequencing debates, whilst highlighting important gaps. Obtaining explicit, voluntary, and sufficiently informed consent for newborn screening is challenging, however we stress that such consent is ethically and legally appropriate and psychologically and practically important. We conclude by outling how this might be done.
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Affiliation(s)
- Fiona Ulph
- Division of Psychology & Mental Health, School of Health Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, UK
| | - Rebecca Bennett
- Centre for Social Ethics and Policy, Department of Law, School of Social Sciences, Faculty of Humanities, University of Manchester, Manchester, UK
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17
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Pereira S, Gutierrez AM, Robinson JO, Christensen KD, Genetti CA, Blout Zawatsky CL, Hsu RL, Zettler B, Uveges MK, Parad RB, Beggs AH, Holm IA, Green RC, McGuire AL. Parents' decision-making regarding whether to receive adult-onset only genetic findings for their children: Findings from the BabySeq Project. Genet Med 2023; 25:100002. [PMID: 36549595 PMCID: PMC9992280 DOI: 10.1016/j.gim.2022.100002] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 12/13/2022] [Accepted: 12/15/2022] [Indexed: 12/24/2022] Open
Abstract
PURPOSE Most professional guidelines recommend against genetic screening for adult-onset only (AO) conditions until adulthood, yet others argue that there may be benefit to disclosing such results. We explored parents' decision-making on this issue in the BabySeq Project, a clinical trial of newborn genomic sequencing. METHODS We conducted interviews with parents (N = 24) who were given the option to receive actionable AO results for their children. Interviews explored parents' motivations to receive and reasons to decline AO genetic disease risk information, their decision-making process, and their suggestions for supporting parents in making this decision. RESULTS Parents noted several motivations to receive and reasons to decline AO results. Most commonly, parents cited early intervention/surveillance (n = 11), implications for family health (n = 7), and the ability to prepare (n = 6) as motivations to receive these results. The most common reasons to decline were protection of the child's future autonomy (n = 4), negative effect on parenting (n = 3), and anxiety about future disease (n = 3). Parents identified a number of ways to support parents in making this decision. CONCLUSION Results show considerations to better support parental decision-making that aligns with their values when offering AO genetic information because it is more commonly integrated into pediatric clinical care.
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Affiliation(s)
- Stacey Pereira
- Center for Medical Ethics and Health Policy, Baylor College of Medicine, Houston, TX.
| | - Amanda M Gutierrez
- Center for Medical Ethics and Health Policy, Baylor College of Medicine, Houston, TX
| | - Jill Oliver Robinson
- Center for Medical Ethics and Health Policy, Baylor College of Medicine, Houston, TX
| | - Kurt D Christensen
- PRecisiOn Medicine Translational Research (PROMoTeR) Center, Department of Population Medicine at Harvard Pilgrim Health Care Institute, Boston, MA; Department of Population Medicine, Harvard Medical School, Boston, MA
| | - Casie A Genetti
- Division of Genetics and Genomics, The Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA
| | - Carrie L Blout Zawatsky
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA; Medical and Population Genetics, The Broad Institute, Cambridge, MA; Brigham and Women's Hospital and the Harvard T.H. Chan School of Public Health, Ariadne Labs, Boston, MA; The MGH Institute of Health Professions, Boston, MA
| | - Rebecca L Hsu
- Center for Medical Ethics and Health Policy, Baylor College of Medicine, Houston, TX
| | - Bethany Zettler
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA
| | | | - Richard B Parad
- Department of Pediatrics, Harvard Medical School, Boston, MA; Department of Pediatric Newborn Medicine, Brigham and Women's Hospital, Boston, MA
| | - Alan H Beggs
- Division of Genetics and Genomics, The Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA; Harvard Medical School, Boston, MA; The Broad Institute of MIT and Harvard, Cambridge, MA
| | - Ingrid A Holm
- Division of Genetics and Genomics, The Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA; Department of Pediatrics, Harvard Medical School, Boston, MA; Harvard Medical School, Boston, MA; The Broad Institute of MIT and Harvard, Cambridge, MA
| | - Robert C Green
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA; Brigham and Women's Hospital and the Harvard T.H. Chan School of Public Health, Ariadne Labs, Boston, MA; Harvard Medical School, Boston, MA; The Broad Institute of MIT and Harvard, Cambridge, MA
| | - Amy L McGuire
- Center for Medical Ethics and Health Policy, Baylor College of Medicine, Houston, TX
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Vockley J, Aartsma-Rus A, Cohen JL, Cowsert LM, Howell RR, Yu TW, Wasserstein MP, Defay T. Whole-genome sequencing holds the key to the success of gene-targeted therapies. AMERICAN JOURNAL OF MEDICAL GENETICS. PART C, SEMINARS IN MEDICAL GENETICS 2023; 193:19-29. [PMID: 36453229 DOI: 10.1002/ajmg.c.32017] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 10/12/2022] [Accepted: 11/15/2022] [Indexed: 12/02/2022]
Abstract
Rare genetic disorders affect as many as 3%-5% of all babies born. Approximately 10,000 such disorders have been identified or hypothesized to exist. Treatment is supportive except in a limited number of instances where specific therapies exist. Development of new therapies has been hampered by at least two major factors: difficulty in diagnosing diseases early enough to enable treatment before irreversible damage occurs, and the high cost of developing new drugs and getting them approved by regulatory agencies. Whole-genome sequencing (WGS) techniques have become exponentially less expensive and more rapid since the beginning of the human genome project, such that return of clinical data can now be achieved in days rather than years and at a cost that is comparable to other less expansive genetic testing. Thus, it is likely that WGS will ultimately become a mainstream, first-tier NBS technique at least for those disorders without appropriate high-throughput functional tests. However, there are likely to be several steps in the evolution to this end. The clinical implications of these advances are profound but highlight the bottlenecks in drug development that still limit transition to treatments. This article summarizes discussions arising from a recent National Institute of Health conference on nucleic acid therapy, with a focus on the impact of WGS in the identification of diagnosis and treatment of rare genetic disorders.
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Affiliation(s)
- Jerry Vockley
- Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
- Department of Human Genetics, University of Pittsburgh School of Public Health, Pittsburgh, Pennsylvania, USA
| | | | - Jennifer L Cohen
- Department of Pediatrics, Duke University Medical Center, Durham, North Carolina, USA
| | - Lex M Cowsert
- National Phenylketonuria Alliance, Eau Claire, Wisconsin, USA
| | - R Rodney Howell
- Miller School of Medicine, University of Miami, Miami, Florida, USA
| | - Timothy W Yu
- Department of Pediatrics, Harvard Medical School, Boston, Massachusetts, USA
| | - Melissa P Wasserstein
- Department of Pediatrics, Albert Einstein College of Medicine and the Children's Hospital at Montefiore, Bronx, New York, USA
| | - Thomas Defay
- Alexion AstraZeneca Rare Diseases, Boston, Massachusetts, USA
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Yang RL, Qian GL, Wu DW, Miao JK, Yang X, Wu BQ, Yan YQ, Li HB, Mao XM, He J, Shen H, Zou H, Xue SY, Li XZ, Niu TT, Xiao R, Zhao ZY. A multicenter prospective study of next-generation sequencing-based newborn screening for monogenic genetic diseases in China. World J Pediatr 2023:10.1007/s12519-022-00670-x. [PMID: 36847978 DOI: 10.1007/s12519-022-00670-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 11/30/2022] [Indexed: 03/01/2023]
Abstract
BACKGROUND Newborn screening (NBS) is an important and successful public health program that helps improve the long-term clinical outcomes of newborns by providing early diagnosis and treatment of certain inborn diseases. The development of next-generation sequencing (NGS) technology provides new opportunities to expand current newborn screening methodologies. METHODS We designed a a newborn genetic screening (NBGS) panel targeting 135 genes associated with 75 inborn disorders by multiplex PCR combined with NGS. With this panel, a large-scale, multicenter, prospective multidisease analysis was conducted on dried blood spot (DBS) profiles from 21,442 neonates nationwide. RESULTS We presented the positive detection rate and carrier frequency of diseases and related variants in different regions; and 168 (0.78%) positive cases were detected. Glucose-6-Phosphate Dehydrogenase deficiency (G6PDD) and phenylketonuria (PKU) had higher prevalence rates, which were significantly different in different regions. The positive detection of G6PD variants was quite common in south China, whereas PAH variants were most commonly identified in north China. In addition, NBGS identified 3 cases with DUOX2 variants and one with SLC25A13 variants, which were normal in conventional NBS, but were confirmed later as abnormal in repeated biochemical testing after recall. Eighty percent of high-frequency gene carriers and 60% of high-frequency variant carriers had obvious regional differences. On the premise that there was no significant difference in birth weight and gestational age, the biochemical indicators of SLC22A5 c.1400C > G and ACADSB c.1165A > G carriers were significantly different from those of non-carriers. CONCLUSIONS We demonstrated that NBGS is an effective strategy to identify neonates affected with treatable diseases as a supplement to current NBS methods. Our data also showed that the prevalence of diseases has significant regional characteristics, which provides a theoretical basis for screening diseases in different regions.
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Affiliation(s)
- Ru-Lai Yang
- National Clinical Research Center for Child Health, Children's Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Gu-Ling Qian
- National Clinical Research Center for Child Health, Children's Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Ding-Wen Wu
- National Clinical Research Center for Child Health, Children's Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Jing-Kun Miao
- Chongqing Health Center for Women and Children, Neonatal Screening Center, Chongqing, China
| | - Xue Yang
- Guiyang Maternal and Child Health Hospital, Guiyang, China
| | - Ben-Qing Wu
- University of the Chinese Academy of Science, Shenzhen Hospital, Shenzhen, 518000, Guangdong, China
| | - Ya-Qiong Yan
- Shanxi Children's Hospital Shanxi Maternal and Child Health Hospital, Taiyuan, Shanxi, China
| | - Hai-Bo Li
- The Central Laboratory of Birth Defects Prevention and Control, Ningbo Women and Children's Hospital, Ningbo, 315012, Zhejiang, China
| | - Xin-Mei Mao
- Maternal and Child Health Hospital of Ningxia Hui Autonomous Region, Yinchuan, China
| | - Jun He
- Changsha Maternal and Child Health Hospital, Changsha, Hunan, China
| | - Huan Shen
- Yunnan Maternal and Child Health Hospital, Kunming, Yunan, China
| | - Hui Zou
- Jinan Maternity and Child Care Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, China
| | - Shu-Yuan Xue
- Urumqi Maternal and Child Health Care Hospital, Xinjiang Uygur Autonomous Region, Urumqi City, China
| | - Xiao-Ze Li
- Medical Genetic Center, Changzhi Maternal and Child Health Care Hospital, Changzhi, Shanxi, China
| | - Ting-Ting Niu
- Maternal and Child Health Care Hospital of Shandong Province, Jinan, Shandong, China
| | - Rui Xiao
- National Engineering Laboratory for Key Technology of Birth Defect Control and Prevention, Screening and Diagnostic R and D Center, Hangzhou, China
| | - Zheng-Yan Zhao
- National Clinical Research Center for Child Health, Children's Hospital, Zhejiang University School of Medicine, Hangzhou, China.
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20
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Reactive gene curation to support interpretation and reporting of a clinical genome test for rare disease: Experience from over 1,000 cases. CELL GENOMICS 2023; 3:100258. [PMID: 36819666 PMCID: PMC9932986 DOI: 10.1016/j.xgen.2023.100258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 09/13/2022] [Accepted: 01/06/2023] [Indexed: 02/04/2023]
Abstract
Current standards in clinical genetics recognize the need to establish the validity of gene-disease relationships as a first step in the interpretation of sequence variants. We describe our experience incorporating the ClinGen Gene-Disease Clinical Validity framework in our interpretation and reporting workflow for a clinical genome sequencing (cGS) test for individuals with rare and undiagnosed genetic diseases. This "reactive" gene curation is completed upon identification of candidate variants during active case analysis and within the test turn-around time by focusing on the most impactful evidence and taking advantage of the broad applicability of the framework to cover a wide range of disease areas. We demonstrate that reactive gene curation can be successfully implemented in support of cGS in a clinical laboratory environment, enabling robust clinical decision making and allowing all variants to be fully and appropriately considered and their clinical significance confidently interpreted.
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21
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Kochetkova TO, Maslennikov DN, Tolmacheva ER, Shubina J, Bolshakova AS, Suvorova DI, Degtyareva AV, Orlovskaya IV, Kuznetsova MV, Rachkova AA, Sukhikh GT, Rebrikov DV, Trofimov DY. De Novo Variant in the KCNJ9 Gene as a Possible Cause of Neonatal Seizures. Genes (Basel) 2023; 14:genes14020366. [PMID: 36833293 PMCID: PMC9956824 DOI: 10.3390/genes14020366] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Revised: 01/16/2023] [Accepted: 01/25/2023] [Indexed: 02/01/2023] Open
Abstract
BACKGROUND The reduction in next-generation sequencing (NGS) costs allows for using this method for newborn screening for monogenic diseases (MDs). In this report, we describe a clinical case of a newborn participating in the EXAMEN project (ClinicalTrials.gov Identifier: NCT05325749). METHODS The child presented with convulsive syndrome on the third day of life. Generalized convulsive seizures were accompanied by electroencephalographic patterns corresponding to epileptiform activity. Proband WES expanded to trio sequencing was performed. RESULTS A differential diagnosis was made between symptomatic (dysmetabolic, structural, infectious) neonatal seizures and benign neonatal seizures. There were no data in favor of the dysmetabolic, structural, or infectious nature of seizures. Molecular karyotyping and whole exome sequencing were not informative. Trio WES revealed a de novo variant in the KCNJ9 gene (1:160087612T > C, p.Phe326Ser, NM_004983), for which, according to the OMIM database, no association with the disease has been described to date. Three-dimensional modeling was used to predict the structure of the KCNJ9 protein using the known structure of its homologs. According to the predictions, Phe326Ser change possibly disrupts the hydrophobic contacts with the valine side chain. Destabilization of the neighboring structures may undermine the formation of GIRK2/GIRK3 tetramers necessary for their proper functioning. CONCLUSIONS We believe that the identified variant may be the cause of the disease in this patient but further studies, including the search for other patients with the KCNJ9 variants, are needed.
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22
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Notini L, Gaff C, Savulescu J, Vears DF. Offering and Returning Secondary Findings in the Context of Exome Sequencing for Hearing Loss: Clinicians' Views and Experiences. AJOB Empir Bioeth 2023; 14:74-83. [PMID: 36595590 DOI: 10.1080/23294515.2022.2160507] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
BACKGROUND There is ongoing debate regarding whether and under which circumstances secondary findings (SF) should be offered in the pediatric context. Although studies have examined patient perspectives on receiving SF, little research has been conducted examining the experiences of clinicians offering SF to parents of newborns receiving genomic sequencing for a recently diagnosed medical condition. METHODS To address this, we conducted qualitative interviews exploring the views and experiences of 12 clinicians who offered SF to parents of infants who had diagnostic exome sequencing (ES) to identify the cause of their hearing loss. Interviews explored clinicians' accounts of parents' choices and decision-making about receiving SF, their views on whether and when to offer SF, their experiences returning SF, and any ethical challenges they encountered. Interviews were audio-recorded, transcribed and analyzed using inductive content analysis. RESULTS Clinicians reported parents who declined all SF often felt finding out about future conditions unrelated to their child's hearing loss may be unhelpful, or even harmful, or were overwhelmed by their child's diagnosis. Clinicians also reported that some parents chose SF because they felt obliged to, even if they did not want to receive them. They explained that while some parents experienced decision-making regarding SF as positive, for others, this process was challenging or distressing. While clinicians generally agreed SF should be offered, mainly to promote parental choice, most felt SF should be offered after disclosing diagnostic results, primarily to avoid overwhelming parents. Clinicians encountered several ethical challenges, including balancing parental autonomy with non-maleficence, wanting to report or not report certain SF, and questioning whether parents can make an autonomous choice regarding SF. CONCLUSIONS Our findings, which are novel as they relate to parents of young infants with a recent diagnosis of hearing loss, add new insights into clinicians' and parents' decision-making regarding SF in pediatrics.
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Affiliation(s)
- Lauren Notini
- University of Melbourne, Carlton, Australia.,Biomedical Ethics Research Group, Murdoch Children's Research Institute, Parkville, Australia
| | - Clara Gaff
- Genomics in Society, Murdoch Children's Research Institute, Parkville, Australia.,Department of Paediatrics, University of Melbourne, Parkville, Australia.,Melbourne Genomics Health Alliance, Parkville, Australia
| | - Julian Savulescu
- University of Melbourne, Carlton, Australia.,Biomedical Ethics Research Group, Murdoch Children's Research Institute, Parkville, Australia.,Chen Su Lan Centennial Professor in Medical Ethics, Centre for Biomedical Ethics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Danya F Vears
- University of Melbourne, Carlton, Australia.,Biomedical Ethics Research Group, Murdoch Children's Research Institute, Parkville, Australia.,Department of Paediatrics, University of Melbourne, Parkville, Australia.,Centre for Biomedical Ethics and Law, KU Leuven, Leuven, Belgium
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23
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van der Wouden CH, Guchelaar HJ, Swen JJ. Precision Medicine Using Pharmacogenomic Panel-Testing: Current Status and Future Perspectives. Clin Lab Med 2022; 42:587-602. [PMID: 36368784 DOI: 10.1016/j.cll.2022.09.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Cathelijne H van der Wouden
- Department of Clinical Pharmacy & Toxicology, Leiden University Medical Center, Albinusdreef 2, Leiden 2333ZA, The Netherlands; Leiden Network for Personalised Therapeutics, Leiden, The Netherlands
| | - Henk-Jan Guchelaar
- Department of Clinical Pharmacy & Toxicology, Leiden University Medical Center, Albinusdreef 2, Leiden 2333ZA, The Netherlands; Leiden Network for Personalised Therapeutics, Leiden, The Netherlands
| | - Jesse J Swen
- Department of Clinical Pharmacy & Toxicology, Leiden University Medical Center, Albinusdreef 2, Leiden 2333ZA, The Netherlands; Leiden Network for Personalised Therapeutics, Leiden, The Netherlands.
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24
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The genetics of monogenic intestinal epithelial disorders. Hum Genet 2022; 142:613-654. [PMID: 36422736 PMCID: PMC10182130 DOI: 10.1007/s00439-022-02501-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2022] [Accepted: 10/23/2022] [Indexed: 11/27/2022]
Abstract
Monogenic intestinal epithelial disorders, also known as congenital diarrheas and enteropathies (CoDEs), are a group of rare diseases that result from mutations in genes that primarily affect intestinal epithelial cell function. Patients with CoDE disorders generally present with infantile-onset diarrhea and poor growth, and often require intensive fluid and nutritional management. CoDE disorders can be classified into several categories that relate to broad areas of epithelial function, structure, and development. The advent of accessible and low-cost genetic sequencing has accelerated discovery in the field with over 45 different genes now associated with CoDE disorders. Despite this increasing knowledge in the causal genetics of disease, the underlying cellular pathophysiology remains incompletely understood for many disorders. Consequently, clinical management options for CoDE disorders are currently limited and there is an urgent need for new and disorder-specific therapies. In this review, we provide a general overview of CoDE disorders, including a historical perspective of the field and relationship to other monogenic disorders of the intestine. We describe the genetics, clinical presentation, and known pathophysiology for specific disorders. Lastly, we describe the major challenges relating to CoDE disorders, briefly outline key areas that need further study, and provide a perspective on the future genetic and therapeutic landscape.
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25
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Outcomes of Returning Medically Actionable Genomic Results in Pediatric Research. J Pers Med 2022; 12:jpm12111910. [PMID: 36422086 PMCID: PMC9694255 DOI: 10.3390/jpm12111910] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 11/07/2022] [Accepted: 11/09/2022] [Indexed: 11/17/2022] Open
Abstract
Purpose: The electronic Medical Records and Genomics (eMERGE) Phase III study was undertaken to assess clinical utility of returning medically actionable genomic screening results. We assessed pediatric clinical outcomes following return of pathogenic/likely pathogenic (P/LP) variants in autosomal dominant conditions with available effective interventions. Methods: The two eMERGE III pediatric sites collected outcome data and assessed changes in medical management at 6 and 12 months. Results: We returned P/LP results to 29 participants with outcome data. For 23 of the 29 participants, the P/LP results were previously unknown. Five of the 23 participants were already followed for conditions related to the P/LP variant. Of those receiving novel results and not being followed for the condition related to the P/LP result (n = 18), 14 (77.8%) had a change in healthcare after return of results (RoR). Following RoR, cascade testing of family members occurred for 10 of 23 (43.5%). Conclusions: The most common outcomes post-RoR included imaging/laboratory testing and health behavior recommendations. A change in healthcare was documented in 77.8% of those receiving results by 6 months. Our findings demonstrate how return of genomic screening results impacts healthcare in pediatric populations.
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Evaluating use of changing technologies for rapid next-generation sequencing in pediatrics. Pediatr Res 2022; 92:1364-1369. [PMID: 35115709 PMCID: PMC10024604 DOI: 10.1038/s41390-022-01965-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 01/17/2022] [Accepted: 01/20/2022] [Indexed: 02/03/2023]
Abstract
BACKGROUND Rapid next-generation sequencing (NGS) offers the potential to shorten the diagnostic process and improve the care of acutely ill children. The goal of this study was to report our findings, including benefits and limitations, of a targeted NGS panel and rapid genome sequencing (rGS) in neonatal and pediatric acute clinical care settings. METHODS Retrospective analysis of patient characteristics, diagnostic yields, turnaround time, and changes in management for infants and children receiving either RapSeq, a targeted NGS panel for 4500+ genes, or rGS, at the University of Utah Hospital and Primary Children's Hospital, from 2015 to 2020. RESULTS Over a 5-year period, 142 probands underwent rapid NGS: 66 received RapSeq and 76 rGS. Overall diagnostic yield was 39%. In the majority of diagnostic cases, there were one or more changes in clinical care management. Of note, 7% of diagnoses identified by rGS would not have been identified by RapSeq. CONCLUSIONS Our results indicate that rapid NGS impacts acute pediatric care in real-life clinical settings. Although affected by patient selection criteria, diagnostic yields were similar to those from clinical trial settings. Future studies are needed to determine relative advantages, including cost, turnaround time, and benefits for patients, of each approach in specific clinical circumstances. IMPACT The use of comprehensive Mendelian gene panels and genome sequencing in the clinical setting allows for early diagnosis of patients in neonatal, pediatric, and cardiac intensive care units and impactful change in management. Diagnoses led to significant changes in management for several patients in lower acuity inpatient units supporting further exploration of the utility of rapid sequencing in these settings. This study reviews the limitations of comparing sequencing platforms in the clinical setting and the variables that should be considered in evaluating diagnostic rates across studies.
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Baribeau DA, Hoang N, Selvanayagam T, Stavropoulos DJ, Costain G, Scherer SW, Vorstman J. Developmental implications of genetic testing for physical indications. Eur J Hum Genet 2022; 30:1297-1300. [PMID: 36068265 PMCID: PMC9626575 DOI: 10.1038/s41431-022-01181-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 07/12/2022] [Accepted: 08/16/2022] [Indexed: 02/04/2023] Open
Abstract
In children undergoing genetic testing for physical health concerns, we examined how often the results also revealed information about their risk for neurodevelopmental disorders. The study sample consisted of 3056 genetic tests (1686 chromosomal microarrays--CMAs, and 1378 next-generation sequencing--NGS panels) ordered at a tertiary pediatric hospital because of a physical/congenital health problem. Tests ordered to investigate developmental concerns were excluded. Pathogenic, or likely pathogenic variants were manually reviewed for diagnostic likelihood, and for evidence of an association with a neurodevelopmental disorder (e.g., autism or intellectual disability). A total of 169 CMAs (10%) and 232 NGS panels (17%) had likely diagnostic results. More than half (52%) of all diagnostic results had established evidence of a neurodevelopmental disorder association. In summary, there is a high prevalence of neurodevelopmental implications from genetic tests ordered for physical/congenital indications. This broad clinical utility suggests a growing need for genetics-first developmental care pathways.
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Affiliation(s)
- Danielle A Baribeau
- Department of Psychiatry, The Hospital for Sick Children, Toronto, ON, Canada
- Department of Psychiatry, The University of Toronto, Toronto, ON, Canada
- Bloorview Research Institute, Holland Bloorview Kids Rehabilitation Hospital, Toronto, ON, Canada
| | - Ny Hoang
- Department of Genetic Counselling, The Hospital for Sick Children, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
- Genetics and Genome Biology, SickKids Research Institute, Toronto, ON, Canada
| | - Thanuja Selvanayagam
- Department of Genetic Counselling, The Hospital for Sick Children, Toronto, ON, Canada
- Genetics and Genome Biology, SickKids Research Institute, Toronto, ON, Canada
| | - D James Stavropoulos
- Department of Laboratory Medicine & Pathobiology, The Hospital for Sick Children, Toronto, ON, Canada
| | - Gregory Costain
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
- Genetics and Genome Biology, SickKids Research Institute, Toronto, ON, Canada
- Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, ON, Canada
| | - Stephen W Scherer
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
- Genetics and Genome Biology, SickKids Research Institute, Toronto, ON, Canada
- The Centre for Applied Genomics, SickKids Research Institute, Toronto, ON, Canada
| | - Jacob Vorstman
- Department of Psychiatry, The Hospital for Sick Children, Toronto, ON, Canada.
- Department of Psychiatry, The University of Toronto, Toronto, ON, Canada.
- Genetics and Genome Biology, SickKids Research Institute, Toronto, ON, Canada.
- Autism Research Unit, The Hospital for Sick Children, 555 University Avenue, Toronto, ON, M5G 1X8, Canada.
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28
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Mew M, Caldwell KA, Caldwell GA. From bugs to bedside: functional annotation of human genetic variation for neurological disorders using invertebrate models. Hum Mol Genet 2022; 31:R37-R46. [PMID: 35994032 PMCID: PMC9585664 DOI: 10.1093/hmg/ddac203] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 08/11/2022] [Accepted: 08/17/2022] [Indexed: 02/02/2023] Open
Abstract
The exponential accumulation of DNA sequencing data has opened new avenues for discovering the causative roles of single-nucleotide polymorphisms (SNPs) in neurological diseases. The opportunities emerging from this are staggering, yet only as good as our abilities to glean insights from this surplus of information. Whereas computational biology continues to improve with respect to predictions and molecular modeling, the differences between in silico and in vivo analysis remain substantial. Invertebrate in vivo model systems represent technically advanced, experimentally mature, high-throughput, efficient and cost-effective resources for investigating a disease. With a decades-long track record of enabling investigators to discern function from DNA, fly (Drosophila) and worm (Caenorhabditis elegans) models have never been better poised to serve as living engines of discovery. Both of these animals have already proven useful in the classification of genetic variants as either pathogenic or benign across a range of neurodevelopmental and neurodegenerative disorders-including autism spectrum disorders, ciliopathies, amyotrophic lateral sclerosis, Alzheimer's and Parkinson's disease. Pathogenic SNPs typically display distinctive phenotypes in functional assays when compared with null alleles and frequently lead to protein products with gain-of-function or partial loss-of-function properties that contribute to neurological disease pathogenesis. The utility of invertebrates is logically limited by overt differences in anatomical and physiological characteristics, and also the evolutionary distance in genome structure. Nevertheless, functional annotation of disease-SNPs using invertebrate models can expedite the process of assigning cellular and organismal consequences to mutations, ascertain insights into mechanisms of action, and accelerate therapeutic target discovery and drug development for neurological conditions.
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Affiliation(s)
- Melanie Mew
- Department of Biological Sciences, The University of Alabama, Tuscaloosa, AL 35487, USA
| | - Kim A Caldwell
- Department of Biological Sciences, The University of Alabama, Tuscaloosa, AL 35487, USA
- Alabama Research Institute on Aging, The University of Alabama, Tuscaloosa, AL 35487, USA
- Center for Convergent Bioscience and Medicine, The University of Alabama, Tuscaloosa, AL 35487, USA
- Departments of Neurobiology and Neurology, Center for Neurodegeneration and Experimental Therapeutics, Nathan Shock Center of Excellence for Research in the Basic Biology of Aging, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Guy A Caldwell
- Department of Biological Sciences, The University of Alabama, Tuscaloosa, AL 35487, USA
- Center for Convergent Bioscience and Medicine, The University of Alabama, Tuscaloosa, AL 35487, USA
- Departments of Neurobiology and Neurology, Center for Neurodegeneration and Experimental Therapeutics, Nathan Shock Center of Excellence for Research in the Basic Biology of Aging, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA
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29
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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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Li MJ, Chien TW, Liao KW, Lai FJ. Using the Sankey diagram to visualize article features on the topics of whole-exome sequencing (WES) and whole-genome sequencing (WGS) since 2012: Bibliometric analysis. Medicine (Baltimore) 2022; 101:e30682. [PMID: 36197161 PMCID: PMC9509026 DOI: 10.1097/md.0000000000030682] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
BACKGROUND Sequencing technologies, such as whole-exome sequencing (WES) and whole-genome sequencing (WGS), have been increasingly applied to medical research in recent years. Which countries, journals, and institutes (called entities) contributed most to the fields (WES/WGS) remains unknown. Temporal bar graphs (TBGs) are frequently used in trend analysis of publications. However, how to draw the TBG on the Sankey diagram is not well understood in bibliometrics. We thus aimed to investigate the evolution of article entities in the WES/WGS fields using publication-based TBGs and compare the individual research achievements (IRAs) among entities. METHODS A total of 3599 abstracts downloaded from icite analysis were matched to entities, including article identity numbers, citations, publication years, journals, affiliated countries/regions of origin, and medical subject headings (MeSH terms) in PubMed on March 12, 2022. The relative citation ratio (RCR) was extracted from icite analysis to compute the hT index (denoting the IRA, taking both publications and citations into account) for each entity in the years between 2012 and 2021. Three types of visualizations were applied to display the trends of publications (e.g., choropleth maps and the enhanced TBGs) and IRAs (e.g., the flowchart on the Sankey diagram) for article entities in WES/WGS. RESULTS We observed that the 3 countries (the US, China, and the UK) occupied most articles in the WES/WGS fields since 2012, the 3 entities (i.e., top 5 journals, research institutes, and MeSH terms) were demonstrated on the enhanced TBGs, the top 2 MeSH terms were genetics and methods in WES and WGS, and the IRAs of 6 article entities with their hT-indices were succinctly and simultaneously displayed on a single Sankey diagram that was never launched in bibliographical studies. CONCLUSION The number of WES/WGS-related articles has dramatically increased since 2017. TBGs, particularly with hTs on the Sankey, are recommended for research on a topic (or in a discipline) to compare trends of publications and IRAs for entities in future bibliographical studies.
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Affiliation(s)
- Meng-Ju Li
- Department of Pediatrics, National Taiwan University Hsin-Chu Hospital, Hsinchu, Taiwan
- Department of Biological Science and Technology, College of Biological Science and Technology, National Yang Ming Chiao Tung University, Hsinchu, Taiwan
| | - Tsair-Wei Chien
- Department of Medical Research, Chi-Mei Medical Center, Tainan, Taiwan
| | - Kuang-Wen Liao
- Department of Biological Science and Technology, College of Biological Science and Technology, National Yang Ming Chiao Tung University, Hsinchu, Taiwan
- Institute of Molecular Medicine and Bioengineering, National Yang Ming Chiao Tung University, Hsinchu, Taiwan
| | - Feng-Jie Lai
- Department of Dermatology, Chi Mei Medical Center, Tainan, Taiwan
- Center for General Education, Southern Taiwan University of Science and Technology, Tainan, Taiwan
- *Correspondence: Feng-Jie Lai, Chi-Mei Medical Center, 901 Chung Hwa Road, Yung Kung Dist., Tainan 710, Taiwan (e-mail: )
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Wang X, Guan XW, Wang YY, Zhang ZL, Li YH, Yang PY, Sun Y, Jiang T. Current attitudes and preconceptions on newborn genetic screening in the Chinese reproductive-aged population. Orphanet J Rare Dis 2022; 17:322. [PMID: 36028855 PMCID: PMC9412816 DOI: 10.1186/s13023-022-02474-8] [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: 12/16/2021] [Accepted: 08/13/2022] [Indexed: 11/10/2022] Open
Abstract
Purpose Newborn screening (NBS) applications are limited as they can only cover a few genetic diseases and may have false positive or false negative rates. A new detection program called newborn genetic screening (NBGS) has been designed to address the potential defects of NBS. This study aimed to investigate the perceptions, acceptance, and expectations of childbearing people related to NBGS to provide the basis for the targeted improvement in the NBGS program carried out in Hospitals. Methods A questionnaire with 20 items was designed on www.wjx.cn. Individuals who came to the Nanjing maternity and child health care Hospital for consultation from June 2021 to August 2021 participated in the survey. The data of the study was arranged properly and analyzed after the investigation. Results A total of 1141 valid questionnaires were collected in the survey, in which the average age of the participants was 31 (± 4) years, and a 1:4 ratio of males to females. Additionally, 65.12% of the participants possessed a bachelor's degree or above qualification. Overall, 50.57% of participants had an annual household income of 100,000–250,000 RMB, while about 86.68% of the participants supported the development of NBGS. The participation cost to pay for NBGS depended on the family incomes; about 59.42% of them were willing to pay a participation fee of 1000–2000 RMB. Conclusion Our research provisionally demonstrated that the residents generally supported the use of NBGS, especially those with higher educational degrees, but the understanding of the genetic diseases and NBGS among the low-educated population still needs to be strengthened. Supplementary Information The online version contains supplementary material available at 10.1186/s13023-022-02474-8.
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Affiliation(s)
- Xin Wang
- Genetic Medicine Center, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, 123 Tianfei Lane, Mochou Road, Qinhuai District, Nanjing, 210004, Jiangsu Province, China
| | - Xian-Wei Guan
- Genetic Medicine Center, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, 123 Tianfei Lane, Mochou Road, Qinhuai District, Nanjing, 210004, Jiangsu Province, China
| | - Yan-Yun Wang
- Genetic Medicine Center, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, 123 Tianfei Lane, Mochou Road, Qinhuai District, Nanjing, 210004, Jiangsu Province, China
| | - Zhi-Lei Zhang
- Genetic Medicine Center, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, 123 Tianfei Lane, Mochou Road, Qinhuai District, Nanjing, 210004, Jiangsu Province, China
| | - Ya-Hong Li
- Genetic Medicine Center, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, 123 Tianfei Lane, Mochou Road, Qinhuai District, Nanjing, 210004, Jiangsu Province, China
| | - Pei-Ying Yang
- Genetic Medicine Center, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, 123 Tianfei Lane, Mochou Road, Qinhuai District, Nanjing, 210004, Jiangsu Province, China
| | - Yun Sun
- Genetic Medicine Center, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, 123 Tianfei Lane, Mochou Road, Qinhuai District, Nanjing, 210004, Jiangsu Province, China.
| | - Tao Jiang
- Genetic Medicine Center, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, 123 Tianfei Lane, Mochou Road, Qinhuai District, Nanjing, 210004, Jiangsu Province, China.
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Next Generation Sequencing after Invasive Prenatal Testing in Fetuses with Congenital Malformations: Prenatal or Neonatal Investigation. Genes (Basel) 2022; 13:genes13091517. [PMID: 36140685 PMCID: PMC9498826 DOI: 10.3390/genes13091517] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 08/21/2022] [Accepted: 08/21/2022] [Indexed: 11/24/2022] Open
Abstract
Congenital malformations diagnosed by ultrasound screening complicate 3–5% of pregnancies and many of these have an underlying genetic cause. Approximately 40% of prenatally diagnosed fetal malformations are associated with aneuploidy or copy number variants, detected by conventional karyotyping, QF-PCR and microarray techniques, however monogenic disorders are not diagnosed by these tests. Next generation sequencing as a secondary prenatal genetic test offers additional diagnostic yield for congenital abnormalities deemed to be potentially associated with an underlying genetic aetiology, as demonstrated by two large cohorts: the ‘Prenatal assessment of genomes and exomes’ (PAGE) study and ‘Whole-exome sequencing in the evaluation of fetal structural anomalies: a prospective cohort study’ performed at Columbia University in the US. These were large and prospective studies but relatively ‘unselected’ congenital malformations, with little Clinical Genetics input to the pre-test selection process. This review focuses on the incremental yield of next generation sequencing in single system congenital malformations, using evidence from the PAGE, Columbia and subsequent cohorts, with particularly high yields in those fetuses with cardiac and neurological anomalies, large nuchal translucency and non-immune fetal hydrops (of unknown aetiology). The total additional yield gained by exome sequencing in congenital heart disease was 12.7%, for neurological malformations 13.8%, 13.1% in increased nuchal translucency and 29% in non-immune fetal hydrops. This demonstrates significant incremental yield with exome sequencing in single-system anomalies and supports next generation sequencing as a secondary genetic test in routine clinical care of fetuses with congenital abnormalities.
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The Progress and Future of US Newborn Screening. Int J Neonatal Screen 2022; 8:ijns8030041. [PMID: 35892471 PMCID: PMC9326622 DOI: 10.3390/ijns8030041] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 07/11/2022] [Accepted: 07/11/2022] [Indexed: 01/12/2023] Open
Abstract
Progress in newborn screening (NBS) has been driven for 60 years by developments in science and technology, growing consumer advocacy, the actions of providers involved in the care of rare disease patients, and by federal and State government funding and policies. With the current explosion of clinical trials of treatments for rare diseases, the pressure for expansion has grown, and concerns about the capacity for improvement and growth are being expressed. Genome and exome sequencing (GS/ES) have now opened more opportunities for early identification and disease prevention at all points in the lifespan. The greatest challenge facing NBS stems from the conditions most amenable to screening, and new treatment development is that we are screening for rare genetic diseases. In addition, understanding the spectrum of severity requires vast amounts of population and genomic data. We propose recommendations on improving the NBS system and addressing specific demands to grow its capacity by: better defining the criteria by which screening targets are established; financing the NBS system's responsiveness to opportunities for expansion, including engagement and funding from stakeholders; creating a national quality assurance, data, IT, and communications infrastructure; and improving intra-governmental communications. While our recommendations may be specific to the United States, the underlying issues should be considered when working to improve NBS programs globally.
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Bick D, Ahmed A, Deen D, Ferlini A, Garnier N, Kasperaviciute D, Leblond M, Pichini A, Rendon A, Satija A, Tuff-Lacey A, Scott RH. Newborn Screening by Genomic Sequencing: Opportunities and Challenges. Int J Neonatal Screen 2022; 8:ijns8030040. [PMID: 35892470 PMCID: PMC9326745 DOI: 10.3390/ijns8030040] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 07/09/2022] [Accepted: 07/11/2022] [Indexed: 12/11/2022] Open
Abstract
Newborn screening for treatable disorders is one of the great public health success stories of the twentieth century worldwide. This commentary examines the potential use of a new technology, next generation sequencing, in newborn screening through the lens of the Wilson and Jungner criteria. Each of the ten criteria are examined to show how they might be applied by programmes using genomic sequencing as a screening tool. While there are obvious advantages to a method that can examine all disease-causing genes in a single assay at an ever-diminishing cost, implementation of genomic sequencing at scale presents numerous challenges, some which are intrinsic to screening for rare disease and some specifically linked to genomics-led screening. In addition to questions specific to routine screening considerations, the ethical, communication, data management, legal, and social implications of genomic screening programmes require consideration.
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Affiliation(s)
- David Bick
- Genomics England Ltd., Dawson Hall, Charterhouse Square, Barbican, London EC1M 6BQ, UK; (A.A.); (D.D.); (D.K.); (M.L.); (A.P.); (A.R.); (A.S.); (A.T.-L.); (R.H.S.)
- Correspondence:
| | - Arzoo Ahmed
- Genomics England Ltd., Dawson Hall, Charterhouse Square, Barbican, London EC1M 6BQ, UK; (A.A.); (D.D.); (D.K.); (M.L.); (A.P.); (A.R.); (A.S.); (A.T.-L.); (R.H.S.)
| | - Dasha Deen
- Genomics England Ltd., Dawson Hall, Charterhouse Square, Barbican, London EC1M 6BQ, UK; (A.A.); (D.D.); (D.K.); (M.L.); (A.P.); (A.R.); (A.S.); (A.T.-L.); (R.H.S.)
| | - Alessandra Ferlini
- Medical Genetics Unit, Department of Medical Sciences, University of Ferrara, 44121 Ferrara, Italy;
| | | | - Dalia Kasperaviciute
- Genomics England Ltd., Dawson Hall, Charterhouse Square, Barbican, London EC1M 6BQ, UK; (A.A.); (D.D.); (D.K.); (M.L.); (A.P.); (A.R.); (A.S.); (A.T.-L.); (R.H.S.)
| | - Mathilde Leblond
- Genomics England Ltd., Dawson Hall, Charterhouse Square, Barbican, London EC1M 6BQ, UK; (A.A.); (D.D.); (D.K.); (M.L.); (A.P.); (A.R.); (A.S.); (A.T.-L.); (R.H.S.)
| | - Amanda Pichini
- Genomics England Ltd., Dawson Hall, Charterhouse Square, Barbican, London EC1M 6BQ, UK; (A.A.); (D.D.); (D.K.); (M.L.); (A.P.); (A.R.); (A.S.); (A.T.-L.); (R.H.S.)
| | - Augusto Rendon
- Genomics England Ltd., Dawson Hall, Charterhouse Square, Barbican, London EC1M 6BQ, UK; (A.A.); (D.D.); (D.K.); (M.L.); (A.P.); (A.R.); (A.S.); (A.T.-L.); (R.H.S.)
| | - Aditi Satija
- Genomics England Ltd., Dawson Hall, Charterhouse Square, Barbican, London EC1M 6BQ, UK; (A.A.); (D.D.); (D.K.); (M.L.); (A.P.); (A.R.); (A.S.); (A.T.-L.); (R.H.S.)
| | - Alice Tuff-Lacey
- Genomics England Ltd., Dawson Hall, Charterhouse Square, Barbican, London EC1M 6BQ, UK; (A.A.); (D.D.); (D.K.); (M.L.); (A.P.); (A.R.); (A.S.); (A.T.-L.); (R.H.S.)
| | - Richard H. Scott
- Genomics England Ltd., Dawson Hall, Charterhouse Square, Barbican, London EC1M 6BQ, UK; (A.A.); (D.D.); (D.K.); (M.L.); (A.P.); (A.R.); (A.S.); (A.T.-L.); (R.H.S.)
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Rahimzadeh V, Friedman JM, de Wert G, Knoppers BM. Exome/Genome-Wide Testing in Newborn Screening: A Proportionate Path Forward. Front Genet 2022; 13:865400. [PMID: 35860465 PMCID: PMC9289115 DOI: 10.3389/fgene.2022.865400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Accepted: 05/27/2022] [Indexed: 11/20/2022] Open
Abstract
Population-based newborn screening (NBS) is among the most effective public health programs ever launched, improving health outcomes for newborns who screen positive worldwide through early detection and clinical intervention for genetic disorders discovered in the earliest hours of life. Key to the success of newborn screening programs has been near universal accessibility and participation. Interest has been building to expand newborn screening programs to also include many rare genetic diseases that can now be identified by exome or genome sequencing (ES/GS). Significant declines in sequencing costs as well as improvements to sequencing technologies have enabled researchers to elucidate novel gene-disease associations that motivate possible expansion of newborn screening programs. In this paper we consider recommendations from professional genetic societies in Europe and North America in light of scientific advances in ES/GS and our current understanding of the limitations of ES/GS approaches in the NBS context. We invoke the principle of proportionality—that benefits clearly outweigh associated risks—and the human right to benefit from science to argue that rigorous evidence is still needed for ES/GS that demonstrates clinical utility, accurate genomic variant interpretation, cost effectiveness and universal accessibility of testing and necessary follow-up care and treatment. Confirmatory or second-tier testing using ES/GS may be appropriate as an adjunct to conventional newborn screening in some circumstances. Such cases could serve as important testbeds from which to gather data on relevant programmatic barriers and facilitators to wider ES/GS implementation.
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Affiliation(s)
- Vasiliki Rahimzadeh
- Stanford Center for Biomedical Ethics, Stanford University, Stanford, CA, United States
- *Correspondence: Vasiliki Rahimzadeh,
| | - Jan M. Friedman
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Guido de Wert
- Department of Health, Ethics and Society, Maastricht University, Maastricht, Netherlands
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Precision medicine via the integration of phenotype-genotype information in neonatal genome project. FUNDAMENTAL RESEARCH 2022. [DOI: 10.1016/j.fmre.2022.07.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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Pichini A, Ahmed A, Patch C, Bick D, Leblond M, Kasperaviciute D, Deen D, Wilde S, Garcia Noriega S, Matoko C, Tuff-Lacey A, Wigley C, Scott RH. Developing a National Newborn Genomes Program: An Approach Driven by Ethics, Engagement and Co-design. Front Genet 2022; 13:866168. [PMID: 35711926 PMCID: PMC9195613 DOI: 10.3389/fgene.2022.866168] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Accepted: 04/28/2022] [Indexed: 11/13/2022] Open
Abstract
The transformative potential of whole genome sequencing (WGS) as a diagnostic tool in healthcare has been demonstrated by initiatives including the 100,000 Genomes Project and is now offered to certain patients in the National Health Service (NHS) in England. Building on these foundations, the utility of WGS in the newborn period can now be explored. Genomics England is working in partnership with NHS England and NHS Improvement and other healthcare, patient and public interest groups to design a research program embedded in the NHS to explore the potential challenges and implications of offering WGS in all newborns. The program will aim to: 1) evaluate the feasibility, utility and impact on the NHS of screening for childhood-onset rare actionable genetic conditions; 2) understand how, with consent, genomic and healthcare data could be used to enable research to develop new diagnostics and treatments; and 3) explore the implications of storing an individual's genome for use over their lifetime. Recognizing the important practical, scientific and ethical questions that we must explore in dialogue with the public and experts, we are taking a collaborative, evidence-based and ethically deliberate approach to designing the program. An iterative co-design process including a nationwide public dialogue has identified emergent themes and ethical considerations which are the focus of the program's design. These themes will be further developed through continued engagement with healthcare professionals, researchers, ethics experts, patient groups and the public, with an ongoing commitment to embedding ongoing ethics research and co-design into the delivery of the program.
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Affiliation(s)
| | | | - Christine Patch
- Genomics England, London, United Kingdom.,Engagement and Society, Wellcome Connecting Science, Wellcome Genome Campus, Hinxton, United Kingdom
| | - David Bick
- Genomics England, London, United Kingdom
| | | | | | - Dasha Deen
- Genomics England, London, United Kingdom
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Madden JA, Brothers KK, Williams JL, Myers MF, Leppig KA, Clayton EW, Wiesner GL, Holm IA. Impact of returning unsolicited genomic results to nongenetic health care providers in the eMERGE III Network. Genet Med 2022; 24:1297-1305. [PMID: 35341654 PMCID: PMC9940614 DOI: 10.1016/j.gim.2022.02.018] [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: 10/20/2021] [Revised: 02/22/2022] [Accepted: 02/28/2022] [Indexed: 10/18/2022] Open
Abstract
PURPOSE As genomic sequencing becomes more common, medically actionable secondary findings will increasingly be returned to health care providers (HCPs), who will be faced with managing the resulting patient care. These findings are generally unsolicited, ie, unrelated to the sequencing indication and/or ordered by another clinician. METHODS To understand the impact of receiving unsolicited results, we interviewed HCPs who received genomic results for patients enrolled in the Electronic Medical Records and Genomics (eMERGE) Phase III Network, which returned results on >100 actionable genes to eMERGE participants and HCPs. RESULTS In total, 16 HCPs across 3 eMERGE sites were interviewed about their experience of receiving a positive (likely pathogenic or pathogenic), negative, or variant of uncertain significance result for a patient enrolled in eMERGE Phase III and about managing their patient on the basis of the result. Although unsolicited, HCPs felt responsible for managing the patient's resulting medical care. HCPs indicated that clinical utility depended on the actionability of results, and whereas comfort levels varied, confidence was improved by the availability of subspecialist consults. HCPs were concerned about patient anxiety, insurability, and missing an actionable result in the electronic health record. CONCLUSION Our findings help inform best practices for return of unsolicited genomic screening findings in the future.
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Affiliation(s)
- Jill A. Madden
- Division of Genetics & Genomics and the Manton Center for Orphan Disease Research, Boston Children’s Hospital, Boston, MA
| | - Kyle K. Brothers
- Department of Pediatrics, School of Medicine, University of Louisville, Louisville, KY
| | | | - Melanie F. Myers
- Department of Pediatrics, Cincinnati Children’s Hospital Medical Center, and College of Medicine, University of Cincinnati, Cincinnati, OH
| | | | - Ellen Wright Clayton
- Center for Biomedical Ethics and Society and Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN
| | - Georgia L. Wiesner
- Division of Genetic Medicine, Department of Medicine, and Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN
| | - Ingrid A. Holm
- Division of Genetics & Genomics and the Manton Center for Orphan Disease Research, Boston Children’s Hospital, Boston, MA,Department of Pediatrics, Harvard Medical School, Boston, MA,Correspondence and requests for materials should be addressed to Ingrid A. Holm, Division of Genetics and Genomics and the Manton Center for Orphan Disease Research, Boston Children’s Hospital, Boston, MA.
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Armstrong B, Christensen KD, Genetti CA, Parad RB, Robinson JO, Blout Zawatsky CL, Zettler B, Beggs AH, Holm IA, Green RC, McGuire AL, Smith HS, Pereira S. Parental Attitudes Toward Standard Newborn Screening and Newborn Genomic Sequencing: Findings From the BabySeq Study. Front Genet 2022; 13:867371. [PMID: 35571041 PMCID: PMC9091188 DOI: 10.3389/fgene.2022.867371] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Accepted: 03/31/2022] [Indexed: 01/15/2023] Open
Abstract
Introduction: With increasing utility and decreasing cost of genomic sequencing, augmentation of standard newborn screening (NBS) programs with newborn genomic sequencing (nGS) has been proposed. Before nGS can be integrated into newborn screening, parents' perspectives must be better understood. Objective: Using data from surveys administered to parents of healthy newborns who were enrolled in the BabySeq Project, a randomized clinical trial of nGS alongside NBS, this paper reports parents' attitudes regarding population-based NBS and nGS assessed 3 months after results disclosure. Methods: Parental attitudes regarding whether all newborns should receive, and whether informed consent should be required for, NBS and nGS, as well as whether nGS should be mandated were assessed using 5-point scales from strongly disagree (=1) to strongly agree (=5). Parents' interest in receiving types of results from nGS was assessed on a 5-point scale from not at all interested (=1) to very interested (=5). Survey responses were analyzed using Fisher's exact tests, paired t-tests, and repeated measures ANOVA. Results: At 3 months post-disclosure, 248 parents of 174 healthy newborns submitted a survey. Support for every newborn receiving standard NBS (mean 4.67) was higher than that for every newborn receiving nGS (mean 3.60; p < 0.001). Support for required informed consent for NBS (mean 3.44) was lower than that for nGS (mean 4.27, p < 0.001). Parents' attitudes toward NBS and nGS were not significantly associated with self-reported political orientation. If hypothetically receiving nGS outside of the BabySeq Project, most parents reported being very interested in receiving information on their baby's risk of developing a disease in childhood that can be prevented, treated, or cured (86.8%) and their risk of developing a disease during adulthood that can be prevented, treated, or cured (84.6%). Discussion: Parents' opinions are crucial to inform design and delivery of public health programs, as the success of the program hinges on parents' trust and participation. To accommodate parents' preferences without affecting the current high participation rates in NBS, an optional add-on consent to nGS in addition to NBS may be a feasible approach. Trial Registration ClinicalTrials.gov Identifier: NCT02422511.
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Affiliation(s)
- Brittan Armstrong
- Center for Medical Ethics and Heath Policy, Baylor College of Medicine, Houston, TX, United States
| | - Kurt D. Christensen
- PRecisiOn Medicine Translational Research (PROMoTeR) Center, Department of Population Medicine, Harvard Pilgrim Health Care Institute, Boston, MA, United States
- Harvard Medical School, Boston, MA, United States
| | - Casie A. Genetti
- Division of Genetics and Genomics, The Manton Center for Orphan Disease Research, Boston Children’s Hospital, Boston, MA, United States
| | - Richard B. Parad
- Harvard Medical School, Boston, MA, United States
- Department of Pediatric Newborn Medicine, Brigham and Women’s Hospital, Boston, MA, United States
| | - Jill Oliver Robinson
- Center for Medical Ethics and Heath Policy, Baylor College of Medicine, Houston, TX, United States
| | - Carrie L. Blout Zawatsky
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital, Boston, MA, United States
- Medical and Population Genetics, The Broad Institute, Cambridge, MA, United States
- Ariadne Labs, Boston, MA, United States
- The MGH Institute of Health Professions, Boston, MA, United States
| | - Bethany Zettler
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital, Boston, MA, United States
| | - Alan H. Beggs
- Harvard Medical School, Boston, MA, United States
- Division of Genetics and Genomics, The Manton Center for Orphan Disease Research, Boston Children’s Hospital, Boston, MA, United States
- The Broad Institute of MIT and Harvard, Cambridge, MA, United States
| | - Ingrid A. Holm
- Harvard Medical School, Boston, MA, United States
- Division of Genetics and Genomics, The Manton Center for Orphan Disease Research, Boston Children’s Hospital, Boston, MA, United States
- The Broad Institute of MIT and Harvard, Cambridge, MA, United States
| | - Robert C. Green
- Harvard Medical School, Boston, MA, United States
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital, Boston, MA, United States
- Ariadne Labs, Boston, MA, United States
- The Broad Institute of MIT and Harvard, Cambridge, MA, United States
| | - Amy L. McGuire
- Center for Medical Ethics and Heath Policy, Baylor College of Medicine, Houston, TX, United States
| | - Hadley Stevens Smith
- Center for Medical Ethics and Heath Policy, Baylor College of Medicine, Houston, TX, United States
| | - Stacey Pereira
- Center for Medical Ethics and Heath Policy, Baylor College of Medicine, Houston, TX, United States
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40
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Tong F, Wang J, Xiao R, Wu BB, Zou CC, Wu DW, Wang H, Zou H, Han LS, Yang L, Zou L, Hei MY, Yang RL, Yuan TM, Wen W, Huang XW, Gu XF, Yang YL, Huang YL, Zhang YJ, Yu YG, Xu ZF, Zhou WH, Zhao ZY. Application of next generation sequencing in the screening of monogenic diseases in China, 2021: a consensus among Chinese newborn screening experts. World J Pediatr 2022; 18:235-242. [PMID: 35292922 DOI: 10.1007/s12519-022-00522-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Accepted: 01/23/2022] [Indexed: 11/24/2022]
Affiliation(s)
- Fan Tong
- Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, 3333 Binsheng Road, Binjiang District, Hangzhou, 310052, China
| | - Jian Wang
- Shanghai Children's Medical Center, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Rui Xiao
- National Engineering Laboratory for Key Technology of Birth Defect Control and Prevention, Screening and Diagnostic R and D Center, Hangzhou, China
| | - Bing-Bing Wu
- Center for Molecular Medicine, Children's Hospital of Fudan University, 399 Wan Yuan Road, Min Xing District, Shanghai, 200000, China
| | - Chao-Chun Zou
- Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, 3333 Binsheng Road, Binjiang District, Hangzhou, 310052, China
| | - Ding-Wen Wu
- Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, 3333 Binsheng Road, Binjiang District, Hangzhou, 310052, China
| | - Hua Wang
- National Health Commission Key Laboratory for Birth Defect Research and Prevention, Maternal and Child Health Hospital of Hunan Province, Changsha, China
| | - Hui Zou
- Jinan Maternity and Child Care Hospital Affiliated To Shandong First Medical University, Jinan, China
| | - Lian-Shu Han
- Xinhua Hospital, Shanghai Institute for Pediatric Research, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Lin Yang
- Clinical Genetic Center, Children's Hospital of Fudan University, Shanghai, China
| | - Lin Zou
- Children's Hospital, Shanghai Jiaotong University, Shanghai, China
| | - Ming-Yan Hei
- Neonatal Center, Beijing Children's Hospital, Capital Medical University, Beijing, China
| | - Ru-Lai Yang
- Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, 3333 Binsheng Road, Binjiang District, Hangzhou, 310052, China
| | - Tian-Ming Yuan
- Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, 3333 Binsheng Road, Binjiang District, Hangzhou, 310052, China
| | - Wei Wen
- Affiliated Shenzhen Maternity and Child Healthcare Hospital, Southern Medical University, Shenzhen, China
| | - Xin-Wen Huang
- Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, 3333 Binsheng Road, Binjiang District, Hangzhou, 310052, China
| | - Xue-Fan Gu
- Xinhua Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, China
| | | | - Yong-Lan Huang
- Guangzhou Women and Children's Medical Center, Guangzhou, China
| | - Yong-Jun Zhang
- Xinhua Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, China
| | - Yong-Guo Yu
- Xinhua Hospital, Shanghai Institute for Pediatric Research, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Zheng-Feng Xu
- Center of Genetic Medicine, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, China
| | - Wen-Hao Zhou
- Center for Molecular Medicine, Children's Hospital of Fudan University, 399 Wan Yuan Road, Min Xing District, Shanghai, 200000, China.
| | - Zheng-Yan Zhao
- Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, 3333 Binsheng Road, Binjiang District, Hangzhou, 310052, China.
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Powell SN, Byfield G, Bennetone A, Frantz AM, Harrison LK, James-Crook ER, Osborne H, Owens TH, Shaw JL, O’Daniel J, Milko LV. Parental Guidance Suggested: Engaging Parents as Partners in Research Studies of Genomic Screening for a Pediatric Population. Front Genet 2022; 13:867030. [PMID: 35401676 PMCID: PMC8990237 DOI: 10.3389/fgene.2022.867030] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 03/07/2022] [Indexed: 01/21/2023] Open
Abstract
Recent advances in genomic sequencing and genomic medicine are reshaping the landscape of clinical care. As a screening modality, genetic sequencing has the potential to dramatically expand the clinical utility of newborn screening (NBS), though significant barriers remain regarding ethical, legal, and social implications (ELSI) and technical and evidentiary challenges. Stakeholder-informed implementation research is poised to grapple with many of these barriers, and parents are crucial stakeholders in this process. We describe the formation and activities of a Community Research Board (CRB) composed of parents with diverse backgrounds assembled to participate in an ongoing research partnership with genomic and public health researchers at the University of North Carolina. The mission of the CRB is to provide insight into parental perspectives regarding the prospect of adding genomic sequencing to NBS and collaboratively develop strategies to ensure its equitable uptake. We describe how these contributions can improve the accessibility of research and recruitment methods and promote trust and inclusivity within diverse communities to maximize the societal benefit of population genomic screening in healthy children.
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Affiliation(s)
- Sabrina N. Powell
- Program for Precision Medicine in Health Care, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States,Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Grace Byfield
- Program for Precision Medicine in Health Care, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States,Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | | | - Annabelle M. Frantz
- Program for Precision Medicine in Health Care, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States,Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Langston K. Harrison
- Program for Precision Medicine in Health Care, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States,Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | | | - Heather Osborne
- Community Research Board Member, Mooresville, NC, United States
| | | | | | - Julianne O’Daniel
- Program for Precision Medicine in Health Care, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States,Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Laura V. Milko
- Program for Precision Medicine in Health Care, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States,Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States,*Correspondence: Laura V. Milko,
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42
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Veldman A, Kiewiet MBG, Heiner-Fokkema MR, Nelen MR, Sinke RJ, Sikkema-Raddatz B, Voorhoeve E, Westra D, Dollé MET, Schielen PCJI, van Spronsen FJ. Towards Next-Generation Sequencing (NGS)-Based Newborn Screening: A Technical Study to Prepare for the Challenges Ahead. Int J Neonatal Screen 2022; 8:ijns8010017. [PMID: 35323196 PMCID: PMC8949100 DOI: 10.3390/ijns8010017] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Revised: 01/28/2022] [Accepted: 02/08/2022] [Indexed: 01/27/2023] Open
Abstract
Newborn screening (NBS) aims to identify neonates with severe conditions for whom immediate treatment is required. Currently, a biochemistry-first approach is used to identify these disorders, which are predominantly inherited meta1bolic disorders (IMD). Next-generation sequencing (NGS) is expected to have some advantages over the current approach, for example the ability to detect IMDs that meet all screening criteria but lack an identifiable biochemical footprint. We have now designed a technical study to explore the use of NGS techniques as a first-tier approach in NBS. Here, we describe the aim and set-up of the NGS-first for the NBS (NGSf4NBS) project, which will proceed in three steps. In Step 1, we will identify IMDs eligible for NGS-first testing, based on treatability. In Step 2, we will investigate the feasibility, limitations and comparability of different technical NGS approaches and analysis workflows for NBS, eventually aiming to develop a rapid NGS-based workflow. Finally, in Step 3, we will prepare for the incorporation of this workflow into the existing Dutch NBS program and propose a protocol for referral of a child after a positive NGS test result. The results of this study will be the basis for an additional analytical route within NBS that will be further studied for its applicability within the NBS program, e.g., regarding the ethical, legal, financial and social implications.
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Affiliation(s)
- Abigail Veldman
- Division of Metabolic Diseases, Beatrix Children’s Hospital, University Medical Center Groningen, University of Groningen, 9713 GZ Groningen, The Netherlands;
- Correspondence: (A.V.); (M.B.G.K.)
| | - Mensiena B. G. Kiewiet
- Division of Metabolic Diseases, Beatrix Children’s Hospital, University Medical Center Groningen, University of Groningen, 9713 GZ Groningen, The Netherlands;
- Department of Genetics, University Medical Center Groningen, University of Groningen, 9713 GZ Groningen, The Netherlands; (R.J.S.); (B.S.-R.)
- Correspondence: (A.V.); (M.B.G.K.)
| | - Margaretha Rebecca Heiner-Fokkema
- Department of Laboratory Medicine, University Medical Center Groningen, University of Groningen, 9713 GZ Groningen, The Netherlands;
| | - Marcel R. Nelen
- Department of Human Genetics, Radboud University Medical Center, 6500 HB Nijmegen, The Netherlands; (M.R.N.); (D.W.)
| | - Richard J. Sinke
- Department of Genetics, University Medical Center Groningen, University of Groningen, 9713 GZ Groningen, The Netherlands; (R.J.S.); (B.S.-R.)
| | - Birgit Sikkema-Raddatz
- Department of Genetics, University Medical Center Groningen, University of Groningen, 9713 GZ Groningen, The Netherlands; (R.J.S.); (B.S.-R.)
| | - Els Voorhoeve
- Centre for Health Protection, National Institute for Public Health and the Environment, 3720 BA Bilthoven, The Netherlands; (E.V.); (M.E.T.D.)
| | - Dineke Westra
- Department of Human Genetics, Radboud University Medical Center, 6500 HB Nijmegen, The Netherlands; (M.R.N.); (D.W.)
| | - Martijn E. T. Dollé
- Centre for Health Protection, National Institute for Public Health and the Environment, 3720 BA Bilthoven, The Netherlands; (E.V.); (M.E.T.D.)
| | - Peter C. J. I. Schielen
- Centre for Population Screening, National Institute for Public Health and the Environment, 3720 BA Bilthoven, The Netherlands;
| | - Francjan J. van Spronsen
- Division of Metabolic Diseases, Beatrix Children’s Hospital, University Medical Center Groningen, University of Groningen, 9713 GZ Groningen, The Netherlands;
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43
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Huang X, Wu D, Zhu L, Wang W, Yang R, Yang J, He Q, Zhu B, You Y, Xiao R, Zhao Z. Application of a next-generation sequencing (NGS) panel in newborn screening efficiently identifies inborn disorders of neonates. Orphanet J Rare Dis 2022; 17:66. [PMID: 35193651 PMCID: PMC8862216 DOI: 10.1186/s13023-022-02231-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Accepted: 02/06/2022] [Indexed: 11/10/2022] Open
Abstract
Background Newborn screening (NBS) has been implemented for neonatal inborn disorders using various technology platforms, but false-positive and false-negative results are still common. In addition, target diseases of NBS are limited by suitable biomarkers. Here we sought to assess the feasibility of further improving the screening using next-generation sequencing technology. Methods We designed a newborn genetic sequencing (NBGS) panel based on multiplex PCR and next generation sequencing to analyze 134 genes of 74 inborn disorders, that were validated in 287 samples with previously known mutations. A retrospective cohort of 4986 newborns was analyzed and compared with the biochemical results to evaluate the performance of this panel. Results The accuracy of the panel was 99.65% with all samples, and 154 mutations from 287 samples were 100% detected. In 4986 newborns, a total of 113 newborns were detected with biallelic or hemizygous mutations, of which 36 newborns were positive for the same disorder by both NBGS and conventional NBS (C-NBS) and 77 individuals were NBGS positive/C-NBS negative. Importantly, 4 of the 77 newborns were diagnosed currently including 1 newborn with methylmalonic acidemia, 1 newborn with primary systemic carnitine deficiency and 2 newborns with Wilson’s disease. A total of 1326 newborns were found to be carriers with an overall carrier rate of 26.6%. Conclusion Analysis based on next generation sequencing could effectively identify neonates affected with more congenital disorders. Combined with C-NBS, this approach may improve the early and accurate identification of neonates with inborn disorders. Our study lays the foundation for prospective studies and for implementing NGS-based analysis in NBS. Supplementary Information The online version contains supplementary material available at 10.1186/s13023-022-02231-x.
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Affiliation(s)
- Xinwen Huang
- Department of Genetics and Metabolism, Children's Hospital of Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, People's Republic of China
| | - Dingwen Wu
- Department of Genetics and Metabolism, Children's Hospital of Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, People's Republic of China.,Zhejiang Neonatal Screening Center, Department of Genetics and Metabolism, Children's Hospital of Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, China
| | - Lin Zhu
- Hangzhou Biosan Clinical Laboratory Co. Ltd, 859 Shixiang West Road, Hangzhou, Zhejiang Province, People's Republic of China
| | - Wenjun Wang
- Hangzhou Biosan Clinical Laboratory Co. Ltd, 859 Shixiang West Road, Hangzhou, Zhejiang Province, People's Republic of China
| | - Rulai Yang
- Department of Genetics and Metabolism, Children's Hospital of Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, People's Republic of China
| | - Jianbin Yang
- Department of Genetics and Metabolism, Children's Hospital of Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, People's Republic of China
| | - Qunyan He
- Zhejiang Biosan Biochemical Technologies Co. Ltd, 859 Shixiang West Rd, Hangzhou, 310007, Zhejiang Province, People's Republic of China
| | - Bingquan Zhu
- Department of Genetics and Metabolism, Children's Hospital of Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, People's Republic of China.,Department of Child Healthcare, Children's Hospital of Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, People's Republic of China
| | - Ying You
- Zhejiang Biosan Biochemical Technologies Co. Ltd, 859 Shixiang West Rd, Hangzhou, 310007, Zhejiang Province, People's Republic of China
| | - Rui Xiao
- Zhejiang Biosan Biochemical Technologies Co. Ltd, 859 Shixiang West Rd, Hangzhou, 310007, Zhejiang Province, People's Republic of China.
| | - Zhengyan Zhao
- Department of Genetics and Metabolism, Children's Hospital of Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, People's Republic of China. .,Department of PediatricsChildren's Hospital of Zhejiang University School of Medicine, National Clinical Research Center for Child Health, 3333 Binsheng Rd, Hangzhou, 310052, Zhejiang Province, People's Republic of China.
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44
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Schwartz TS, Christensen KD, Uveges MK, Waisbren SE, McGuire AL, Pereira S, Robinson JO, Beggs AH, Green RC, Bachmann GA, Rabson AB, Holm IA. Effects of participation in a U.S. trial of newborn genomic sequencing on parents at risk for depression. J Genet Couns 2022; 31:218-229. [PMID: 34309124 PMCID: PMC8789951 DOI: 10.1002/jgc4.1475] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Revised: 06/15/2021] [Accepted: 06/27/2021] [Indexed: 02/03/2023]
Abstract
Much emphasis has been placed on participant's psychological safety within genomic research studies; however, few studies have addressed parental psychological health effects associated with their child's participation in genomic studies, particularly when parents meet the threshold for clinical concern for depression. We aimed to determine if parents' depressive symptoms were associated with their child's participation in a randomized-controlled trial of newborn exome sequencing. Parents completed the Edinburgh Postnatal Depression Scale (EPDS) at baseline, immediately post-disclosure, and 3 months post-disclosure. Mothers and fathers scoring at or above thresholds for clinical concern on the EPDS, 12 and 10, respectively, indicating possible Major Depressive Disorder with Peripartum Onset, were contacted by study staff for mental health screening. Parental concerns identified in follow-up conversations were coded for themes. Forty-five parents had EPDS scores above the clinical threshold at baseline, which decreased by an average of 2.9 points immediately post-disclosure and another 1.1 points 3 months post-disclosure (both p ≤ .014). For 28 parents, EPDS scores were below the threshold for clinical concern at baseline, increased by an average of 4.7 points into the elevated range immediately post-disclosure, and decreased by 3.8 points at 3 months post-disclosure (both p < .001). Nine parents scored above thresholds only at 3 months post-disclosure after increasing an average of 5.7 points from immediately post-disclosure (p < .001). Of the 82 parents who scored above the threshold at any time point, 43 (52.4%) were reached and 30 (69.7%) of these 43 parents attributed their elevated scores to parenting stress, balancing work and family responsibilities, and/or child health concerns. Only three parents (7.0%) raised concerns about their participation in the trial, particularly their randomization to the control arm. Elevated scores on the EPDS were typically transient and parents attributed their symptomatology to life stressors in the postpartum period rather than participation in a trial of newborn exome sequencing.
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Affiliation(s)
- Talia S Schwartz
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, Massachusetts, USA.,The Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, Massachusetts, USA.,Rutgers Robert Wood Johnson Medical School, Piscataway, New Jersey, USA
| | - Kurt D Christensen
- PRecisiOn Medicine Translational Research (PROMoTeR) Center, Department of Population Medicine, Harvard Pilgrim Health Care Institute, Boston, Massachusetts, USA.,The Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.,Harvard Medical School, Boston, Massachusetts, USA
| | - Melissa K Uveges
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA.,Connell School of Nursing, Boston College, Chestnut Hill, Massachusetts, USA
| | - Susan E Waisbren
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, Massachusetts, USA.,Harvard Medical School, Boston, Massachusetts, USA
| | - Amy L McGuire
- Center for Medical Ethics and Health Policy, Baylor College of Medicine, Houston, Texas, USA
| | - Stacey Pereira
- Center for Medical Ethics and Health Policy, Baylor College of Medicine, Houston, Texas, USA
| | - Jill O Robinson
- Center for Medical Ethics and Health Policy, Baylor College of Medicine, Houston, Texas, USA
| | - Alan H Beggs
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, Massachusetts, USA.,The Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, Massachusetts, USA.,Harvard Medical School, Boston, Massachusetts, USA
| | - Robert C Green
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.,Harvard Medical School, Boston, Massachusetts, USA.,Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | | | - Gloria A Bachmann
- Rutgers Robert Wood Johnson Medical School, Piscataway, New Jersey, USA
| | - Arnold B Rabson
- Rutgers Robert Wood Johnson Medical School, Piscataway, New Jersey, USA
| | - Ingrid A Holm
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, Massachusetts, USA.,The Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, Massachusetts, USA.,Harvard Medical School, Boston, Massachusetts, USA
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45
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Ward A, Velinder M, Di Sera T, Ekawade A, Malone Jenkins S, Moore B, Mao R, Bayrak-Toydemir P, Marth G. Clin.iobio: A Collaborative Diagnostic Workflow to Enable Team-Based Precision Genomics. J Pers Med 2022; 12:73. [PMID: 35055388 PMCID: PMC8780189 DOI: 10.3390/jpm12010073] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 12/31/2021] [Accepted: 01/04/2022] [Indexed: 12/12/2022] Open
Abstract
The primary goal of precision genomics is the identification of causative genetic variants in targeted or whole-genome sequencing data. The ultimate clinical hope is that these findings lead to an efficacious change in treatment for the patient. In current clinical practice, these findings are typically returned by expert analysts as static, text-based reports. Ideally, these reports summarize the quality of the data obtained, integrate known gene-phenotype associations, follow allele segregation and affected status within the sequenced samples, and weigh computational evidence of pathogenicity. These findings are used to prioritize the variant(s) most likely to cause the given patient's phenotypes. In most diagnostic settings, a team of experts contribute to these reports, including bioinformaticians, clinicians, and genetic counselors, among others. However, these experts often do not have the necessary tools to review genomic findings, test genetic hypotheses, or query specific gene and variant information. Additionally, team members often rely on different tools and methods based on their given expertise, resulting in further difficulties in communicating and discussing genomic findings. Here, we present clin.iobio-a web-based solution to collaborative genomic analysis that enables diagnostic team members to focus on their area of expertise within the diagnostic process, while allowing them to easily review and contribute to all steps of the diagnostic process. Clin.iobio integrates tools from the popular iobio genomic visualization suite into a comprehensive diagnostic workflow, encompassing (1) genomic data quality review, (2) dynamic phenotype-driven gene prioritization, (3) variant prioritization using a comprehensive set of knowledge bases and annotations, (4) and an exportable findings summary. In conclusion, clin.iobio is a comprehensive solution to team-based precision genomics, the findings of which stand to inform genomic considerations in clinical practice.
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Affiliation(s)
- Alistair Ward
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT 84112, USA; (M.V.); (T.D.S.); (A.E.); (B.M.)
- Frameshift Labs, Inc., Cambridge, MA 02142, USA
| | - Matt Velinder
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT 84112, USA; (M.V.); (T.D.S.); (A.E.); (B.M.)
| | - Tonya Di Sera
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT 84112, USA; (M.V.); (T.D.S.); (A.E.); (B.M.)
| | - Aditya Ekawade
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT 84112, USA; (M.V.); (T.D.S.); (A.E.); (B.M.)
| | - Sabrina Malone Jenkins
- Department of Pediatrics, University of Utah Scbool of Medicine, Salt Lake City, UT 84112, USA;
| | - Barry Moore
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT 84112, USA; (M.V.); (T.D.S.); (A.E.); (B.M.)
| | - Rong Mao
- ARUP Laboratories, Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT 84112, USA; (R.M.); (P.B.-T.)
| | - Pinar Bayrak-Toydemir
- ARUP Laboratories, Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT 84112, USA; (R.M.); (P.B.-T.)
| | - Gabor Marth
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT 84112, USA; (M.V.); (T.D.S.); (A.E.); (B.M.)
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46
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Shen EC, Srinivasan S, Passero LE, Allen CG, Dixon M, Foss K, Halliburton B, Milko LV, Smit AK, Carlson R, Roberts MC. Barriers and Facilitators for Population Genetic Screening in Healthy Populations: A Systematic Review. Front Genet 2022; 13:865384. [PMID: 35860476 PMCID: PMC9289280 DOI: 10.3389/fgene.2022.865384] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Accepted: 06/02/2022] [Indexed: 11/25/2022] Open
Abstract
Studies suggest that 1-3% of the general population in the United States unknowingly carry a genetic risk factor for a common hereditary disease. Population genetic screening is the process of offering otherwise healthy patients in the general population testing for genomic variants that predispose them to diseases that are clinically actionable, meaning that they can be prevented or mitigated if they are detected early. Population genetic screening may significantly reduce morbidity and mortality from these diseases by informing risk-specific prevention or treatment strategies and facilitating appropriate participation in early detection. To better understand current barriers, facilitators, perceptions, and outcomes related to the implementation of population genetic screening, we conducted a systematic review and searched PubMed, Embase, and Scopus for articles published from date of database inception to May 2020. We included articles that 1) detailed the perspectives of participants in population genetic screening programs and 2) described the barriers, facilitators, perceptions, and outcomes related to population genetic screening programs among patients, healthcare providers, and the public. We excluded articles that 1) focused on direct-to-consumer or risk-based genetic testing and 2) were published before January 2000. Thirty articles met these criteria. Barriers and facilitators to population genetic screening were organized by the Social Ecological Model and further categorized by themes. We found that research in population genetic screening has focused on stakeholder attitudes with all included studies designed to elucidate individuals' perceptions. Additionally, inadequate knowledge and perceived limited clinical utility presented a barrier for healthcare provider uptake. There were very few studies that conducted long-term follow-up and evaluation of population genetic screening. Our findings suggest that these and other factors, such as prescreen counseling and education, may play a role in the adoption and implementation of population genetic screening. Future studies to investigate macro-level determinants, strategies to increase provider buy-in and knowledge, delivery models for prescreen counseling, and long-term outcomes of population genetic screening are needed for the effective design and implementation of such programs. Systematic Review Registration: https://www.crd.york.ac.uk/prospero/display_record.php?ID=CRD42020198198.
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Affiliation(s)
- Emily C Shen
- College of Arts and Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States.,UNC Lineberger Comprehensive Cancer Center, School of Medicine, University of North Carolina, Chapel Hill, NC, United States
| | - Swetha Srinivasan
- Division of Pharmaceutical Outcomes and Policy, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC, United States
| | - Lauren E Passero
- Division of Pharmaceutical Outcomes and Policy, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC, United States
| | - Caitlin G Allen
- Department of Public Health Science, College of Medicine, Medical University of South Carolina, Charleston, SC, United States
| | - Madison Dixon
- Department of Behavioral, Social, and Health Education Science, Rollins School of Public Health, Emory University, Atlanta, GA, United States
| | - Kimberly Foss
- Department of Genetics, School of Medicine, University of North Carolina, Chapel Hill, NC, United States
| | - Brianna Halliburton
- College of Arts and Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Laura V Milko
- Department of Genetics, School of Medicine, University of North Carolina, Chapel Hill, NC, United States
| | - Amelia K Smit
- The Daffodil Centre, University of Sydney, A Joint Venture with Cancer Council NSW, Sydney, NSW, Australia.,Melanoma Institute Australia, University of Sydney, Sydney, NSW, Australia
| | - Rebecca Carlson
- Health Sciences Library, University of North Carolina, Chapel Hill, NC, United States
| | - Megan C Roberts
- Division of Pharmaceutical Outcomes and Policy, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC, United States
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Kingdom R, Wright CF. Incomplete Penetrance and Variable Expressivity: From Clinical Studies to Population Cohorts. Front Genet 2022; 13:920390. [PMID: 35983412 PMCID: PMC9380816 DOI: 10.3389/fgene.2022.920390] [Citation(s) in RCA: 53] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 06/09/2022] [Indexed: 12/20/2022] Open
Abstract
The same genetic variant found in different individuals can cause a range of diverse phenotypes, from no discernible clinical phenotype to severe disease, even among related individuals. Such variants can be said to display incomplete penetrance, a binary phenomenon where the genotype either causes the expected clinical phenotype or it does not, or they can be said to display variable expressivity, in which the same genotype can cause a wide range of clinical symptoms across a spectrum. Both incomplete penetrance and variable expressivity are thought to be caused by a range of factors, including common variants, variants in regulatory regions, epigenetics, environmental factors, and lifestyle. Many thousands of genetic variants have been identified as the cause of monogenic disorders, mostly determined through small clinical studies, and thus, the penetrance and expressivity of these variants may be overestimated when compared to their effect on the general population. With the wealth of population cohort data currently available, the penetrance and expressivity of such genetic variants can be investigated across a much wider contingent, potentially helping to reclassify variants that were previously thought to be completely penetrant. Research into the penetrance and expressivity of such genetic variants is important for clinical classification, both for determining causative mechanisms of disease in the affected population and for providing accurate risk information through genetic counseling. A genotype-based definition of the causes of rare diseases incorporating information from population cohorts and clinical studies is critical for our understanding of incomplete penetrance and variable expressivity. This review examines our current knowledge of the penetrance and expressivity of genetic variants in rare disease and across populations, as well as looking into the potential causes of the variation seen, including genetic modifiers, mosaicism, and polygenic factors, among others. We also considered the challenges that come with investigating penetrance and expressivity.
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Affiliation(s)
- Rebecca Kingdom
- Institute of Biomedical and Clinical Science, Royal Devon & Exeter Hospital, University of Exeter Medical School, Exeter, United Kingdom
| | - Caroline F Wright
- Institute of Biomedical and Clinical Science, Royal Devon & Exeter Hospital, University of Exeter Medical School, Exeter, United Kingdom
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Biochemical testing for inborn errors of metabolism: experience from a large tertiary neonatal centre. Eur J Pediatr 2022; 181:3725-3732. [PMID: 35945291 PMCID: PMC9508208 DOI: 10.1007/s00431-022-04588-4] [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] [Received: 04/01/2022] [Revised: 07/14/2022] [Accepted: 08/05/2022] [Indexed: 11/25/2022]
Abstract
UNLABELLED Inborn errors of metabolism are an individually rare but collectively significant cause of mortality and morbidity in the neonatal period. They are identified by either newborn screening programmes or clinician-initiated targeted biochemical screening. This study examines the relative contribution of these two methods to the identification of inborn errors of metabolism and describes the incidence of these conditions in a large, tertiary, neonatal unit. We also examined which factors could impact the reliability of metabolic testing in this cohort. This is a retrospective, single-site study examining infants in whom a targeted metabolic investigation was performed from January 2018 to December 2020 inclusive. Data was also provided by the national newborn screening laboratory regarding newborn screening diagnoses. Two hundred and four newborns received a clinician-initiated metabolic screen during the time period examined with 5 newborns being diagnosed with an inborn error of metabolism (IEM) (2.4%). Of the 25,240 infants born in the hospital during the period examined, a further 11 newborns had an inborn error of metabolism diagnosed on newborn screening. This produced an incidence in our unit over the time described of 6.34 per 10,000 births. This number reflects a minimum estimate, given that the conditions diagnosed refer to early-onset disorders and distinctive categories of IEM only. Efficiency of the clinician-initiated metabolic screening process was also examined. The only statistically significant variable in requiring repeat metabolic screening was early day of life (z-score = - 2.58, p = 0.0098). A total of 28.4% was missing one of three key metabolic investigation parameters of blood glucose, ammonia or lactate concentration with ammonia the most common investigation missing. While hypoglycemia was the most common clinical rationale for a clinician-initiated metabolic test, it was a poor predictor of inborn error of metabolism with no newborns of 25 screened were diagnosed with a metabolic disorder. CONCLUSION Clinician-targeted metabolic screening had a high diagnostic yield given the relatively low prevalence of inborn errors of metabolism in the general population. Thoughts should be given to the rationale behind each targeted metabolic test and what specific metabolic disease or category of inborn error of metabolism they are concerned along with commencing targeted testing. WHAT IS KNOWN • Inborn errors of metabolism are a rare but potentially treatable cause of newborn mortality and morbidity. • A previous study conducted in a tertiary unit in an area with limited newborn screening demonstrated a diagnostic yield of 5.4%. WHAT IS NEW • Clinician-initiated targeted metabolic screening has a good diagnostic performance even with a more expanded newborn screening programme. • Further optimisation could be achieved by examining the best timing and also the rationale of metabolic testing in the newborn period.
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NeoSeq: a new method of genomic sequencing for newborn screening. Orphanet J Rare Dis 2021; 16:481. [PMID: 34794485 PMCID: PMC8600711 DOI: 10.1186/s13023-021-02116-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 11/06/2021] [Indexed: 12/16/2022] Open
Abstract
Objective To explore the clinical application of NeoSeq in newborn screening. Methods Based on the results obtained from traditional newborn screening (NBS) with tandem mass spectrometry (TMS), three cohorts were recruited into the present study: 36 true positive cases (TPC), 60 false-positive cases (FPC), and 100 negative cases. The dried blood spots of the infants were analyzed with NeoSeq, which is based on multiplex PCR amplicon sequencing. Results Overall, the sensitivity of NeoSeq was 55.6% (20/36) in the detection of TPC. NeoSeq detected disease-related genes in 20 of 36 TPC infants, while it could not identify these genes in eight children. Five cases (3.1%) with disease risk were additionally found in the FPC and NC cohorts. There was a significant difference in the diagnostic time between the two methods—10 days for NeoSeq vs. 43 days for traditional NBS. Conclusions NeoSeq is an economic genomic screening test for newborn screening. It can detect most inborn errors of metabolism, reduce the rate of false positive results, shorten the porting cycles, and reduce the screening cost. However, it is still necessary to further optimize the panel design and add more clinically relevant genomic variants to increase its sensitivity. Supplementary Information The online version contains supplementary material available at 10.1186/s13023-021-02116-5.
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Biesecker LG, Green ED, Manolio T, Solomon BD, Curtis D. Should all babies have their genome sequenced at birth? BMJ 2021; 375:n2679. [PMID: 34789511 DOI: 10.1136/bmj.n2679] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
| | - Eric D Green
- National Human Genome Research Institute, Bethesda, Maryland, USA
| | - Teri Manolio
- National Human Genome Research Institute, Bethesda, Maryland, USA
| | | | - David Curtis
- UCL Genetics Institute, University College London, UK
- Centre for Psychiatry, Queen Mary University of London, UK
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