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Betzler IR, Hempel M, Mütze U, Kölker S, Winkler E, Dikow N, Garbade SF, Schaaf CP, Brennenstuhl H. Comparative analysis of gene and disease selection in genomic newborn screening studies. J Inherit Metab Dis 2024. [PMID: 38757337 DOI: 10.1002/jimd.12750] [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: 03/12/2024] [Revised: 04/19/2024] [Accepted: 04/30/2024] [Indexed: 05/18/2024]
Abstract
Genomic newborn screening (gNBS) is on the horizon given the decreasing costs of sequencing and the advanced understanding of the impact of genetic variants on health and diseases. Key to ongoing gNBS pilot studies is the selection of target diseases and associated genes to be included. In this study, we present a comprehensive analysis of seven published gene-disease lists from gNBS studies, evaluating gene-disease count, composition, group proportions, and ClinGen curations of individual disorders. Despite shared selection criteria, we observe substantial variation in total gene count (median 480, range 237-889) and disease group composition. An intersection was identified for 53 genes, primarily inherited metabolic diseases (83%, 44/53). Each study investigated a subset of exclusive gene-disease pairs, and the total number of exclusive gene-disease pairs was positively correlated with the total number of genes included per study. While most pairs receive "Definitive" or "Strong" ClinGen classifications, some are labeled as "Refuted" (n = 5) or "Disputed" (n = 28), particularly in genetic cardiac diseases. Importantly, 17%-48% of genes lack ClinGen curation. This study underscores the current absence of consensus recommendations for selection criteria for target diseases for gNBS resulting in diversity in proposed gene-disease pairs, their coupling with gene variations and the use of ClinGen curation. Our findings provide crucial insights into the selection of target diseases and accompanying gene variations for future gNBS program, emphasizing the necessity for ongoing collaboration and discussion about criteria harmonization for panel selection to ensure the screening's objectivity, integrity, and broad acceptance.
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Affiliation(s)
- Isabel R Betzler
- Institute of Human Genetics, Heidelberg University and University Hospital Heidelberg, Heidelberg, Germany
| | - Maja Hempel
- Institute of Human Genetics, Heidelberg University and University Hospital Heidelberg, Heidelberg, Germany
| | - Ulrike Mütze
- Centre for Child and Adolescent Medicine, Division of Child Neurology and Metabolic Medicine, Heidelberg University and University Hospital Heidelberg, Heidelberg, Germany
| | - Stefan Kölker
- Centre for Child and Adolescent Medicine, Division of Child Neurology and Metabolic Medicine, Heidelberg University and University Hospital Heidelberg, Heidelberg, Germany
| | - Eva Winkler
- Section of Translational Medical Ethics, National Center for Tumour Diseases, Heidelberg University and University Hospital Heidelberg, Heidelberg, Germany
| | - Nicola Dikow
- Institute of Human Genetics, Heidelberg University and University Hospital Heidelberg, Heidelberg, Germany
| | - Sven F Garbade
- Centre for Child and Adolescent Medicine, Division of Child Neurology and Metabolic Medicine, Heidelberg University and University Hospital Heidelberg, Heidelberg, Germany
| | - Christian P Schaaf
- Institute of Human Genetics, Heidelberg University and University Hospital Heidelberg, Heidelberg, Germany
| | - Heiko Brennenstuhl
- Institute of Human Genetics, Heidelberg University and University Hospital Heidelberg, Heidelberg, Germany
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Lynch F, Best S, Gaff C, Downie L, Archibald AD, Gyngell C, Goranitis I, Peters R, Savulescu J, Lunke S, Stark Z, Vears DF. Australian public perspectives on genomic newborn screening: which conditions should be included? Hum Genomics 2024; 18:45. [PMID: 38720401 PMCID: PMC11077791 DOI: 10.1186/s40246-024-00611-x] [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: 02/13/2024] [Accepted: 04/17/2024] [Indexed: 05/12/2024] Open
Abstract
BACKGROUND Implementing genomic sequencing into newborn screening programs allows for significant expansion in the number and scope of conditions detected. We sought to explore public preferences and perspectives on which conditions to include in genomic newborn screening (gNBS). METHODS We recruited English-speaking members of the Australian public over 18 years of age, using social media, and invited them to participate in online focus groups. RESULTS Seventy-five members of the public aged 23-72 participated in one of fifteen focus groups. Participants agreed that if prioritisation of conditions was necessary, childhood-onset conditions were more important to include than later-onset conditions. Despite the purpose of the focus groups being to elicit public preferences, participants wanted to defer to others, such as health professionals or those with a lived experience of each condition, to make decisions about which conditions to include. Many participants saw benefit in including conditions with no available treatment. Participants agreed that gNBS should be fully publicly funded. CONCLUSION How many and which conditions are included in a gNBS program will be a complex decision requiring detailed assessment of benefits and costs alongside public and professional engagement. Our study provides support for implementing gNBS for treatable childhood-onset conditions.
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Affiliation(s)
- Fiona Lynch
- Biomedical Ethics Research Group, Murdoch Children's Research Institute, Parkville, VIC, 3052, Australia
- Melbourne Law School, The University of Melbourne, Melbourne, VIC, 3052, Australia
| | - Stephanie Best
- Sir Peter MacCallum Cancer Centre Dept of Oncology, University of Melbourne, Melbourne, VIC, 3052, Australia
- Australian Genomics, Melbourne, VIC, 3052, Australia
- School of Health Sciences, University of Melbourne, Melbourne, VIC, 3052, Australia
| | - Clara Gaff
- Murdoch Children's Research Institute, Parkville, VIC, 3052, Australia
- Melbourne Genomics, Melbourne, VIC, 3052, Australia
- Department of Paediatrics, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Melbourne, VIC, 3052, Australia
| | - Lilian Downie
- Murdoch Children's Research Institute, Parkville, VIC, 3052, Australia
- Department of Paediatrics, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Melbourne, VIC, 3052, Australia
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Parkville, VIC, 3052, Australia
| | - Alison D Archibald
- Murdoch Children's Research Institute, Parkville, VIC, 3052, Australia
- Department of Paediatrics, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Melbourne, VIC, 3052, Australia
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Parkville, VIC, 3052, Australia
| | - Christopher Gyngell
- Biomedical Ethics Research Group, Murdoch Children's Research Institute, Parkville, VIC, 3052, Australia
- Department of Paediatrics, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Melbourne, VIC, 3052, Australia
| | - Ilias Goranitis
- Australian Genomics, Melbourne, VIC, 3052, Australia
- Economics of Genomics and Precision Medicine Unit, Centre for Health Policy, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, VIC, 3052, Australia
| | - Riccarda Peters
- Economics of Genomics and Precision Medicine Unit, Centre for Health Policy, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, VIC, 3052, Australia
| | - Julian Savulescu
- Biomedical Ethics Research Group, Murdoch Children's Research Institute, Parkville, VIC, 3052, Australia
- Melbourne Law School, The University of Melbourne, Melbourne, VIC, 3052, Australia
- Centre for Biomedical Ethics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117597, Singapore
- Uehiro Chair of Practical Ethics, The Oxford Uehiro Centre for Practical Ethics, Oxford University, Oxford, OX1 1PT, UK
| | - Sebastian Lunke
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Parkville, VIC, 3052, Australia
- Department of Pathology, The University of Melbourne, Melbourne, VIC, 3052, Australia
| | - Zornitza Stark
- Australian Genomics, Melbourne, VIC, 3052, Australia
- Department of Paediatrics, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Melbourne, VIC, 3052, Australia
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Parkville, VIC, 3052, Australia
| | - Danya F Vears
- Biomedical Ethics Research Group, Murdoch Children's Research Institute, Parkville, VIC, 3052, Australia.
- Melbourne Law School, The University of Melbourne, Melbourne, VIC, 3052, Australia.
- Department of Paediatrics, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Melbourne, VIC, 3052, Australia.
- Centre for Biomedical Ethics and Law, Department of Public Health and Primary Care, KU Leuven, Leuven, 3000, Belgium.
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Downie L, Bouffler SE, Amor DJ, Christodoulou J, Yeung A, Horton AE, Macciocca I, Archibald AD, Wall M, Caruana J, Lunke S, Stark Z. Gene selection for genomic newborn screening: Moving toward consensus? Genet Med 2024; 26:101077. [PMID: 38275146 DOI: 10.1016/j.gim.2024.101077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 01/15/2024] [Accepted: 01/18/2024] [Indexed: 01/27/2024] Open
Abstract
PURPOSE Gene selection for genomic newborn screening (gNBS) underpins the validity, acceptability, and ethical application of this technology. Existing gNBS gene lists are highly variable despite being based on shared principles of gene-disease validity, treatability, and age of onset. This study aimed to curate a gNBS gene list that builds upon existing efforts and provide a core consensus list of gene-disease pairs assessed by multiple expert groups worldwide. METHODS Our multidisciplinary expert team curated a gene list using an open platform and multiple existing curated resources. We included severe treatable disorders with age of disease onset <5 years with established gene-disease associations and reliable variant detection. We compared the final list with published lists from 5 other gNBS projects to determine consensus genes and to identify areas of discrepancy. RESULTS We reviewed 1279 genes and 604 met our inclusion criteria. Metabolic conditions comprised the largest group (25%), followed by immunodeficiencies (21%) and endocrine disorders (15%). We identified 55 consensus genes included by all 6 gNBS research projects. Common reasons for discrepancy included variable definitions of treatability and strength of gene-disease association. CONCLUSION We have identified a consensus gene list for gNBS that can be used as a basis for systematic harmonization efforts internationally.
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Affiliation(s)
- Lilian Downie
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, VIC, Australia; Murdoch Children's Research Institute, Melbourne, VIC, Australia; University of Melbourne, Melbourne, VIC, Australia
| | | | - David J Amor
- Murdoch Children's Research Institute, Melbourne, VIC, Australia; University of Melbourne, Melbourne, VIC, Australia
| | - John Christodoulou
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, VIC, Australia; Murdoch Children's Research Institute, Melbourne, VIC, Australia; University of Melbourne, Melbourne, VIC, Australia
| | - Alison Yeung
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, VIC, Australia; University of Melbourne, Melbourne, VIC, Australia
| | - Ari E Horton
- Victorian Heart Institute, Monash University, Melbourne, VIC, Australia; Public Health Genomics, School of Public Health and Preventive Medicine, Monash University, Melbourne, VIC, Australia
| | - Ivan Macciocca
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, VIC, Australia; University of Melbourne, Melbourne, VIC, Australia
| | - Alison D Archibald
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, VIC, Australia; Murdoch Children's Research Institute, Melbourne, VIC, Australia; University of Melbourne, Melbourne, VIC, Australia
| | - Meghan Wall
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, VIC, Australia; Murdoch Children's Research Institute, Melbourne, VIC, Australia; University of Melbourne, Melbourne, VIC, Australia
| | - Jade Caruana
- Murdoch Children's Research Institute, Melbourne, VIC, Australia
| | - Sebastian Lunke
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, VIC, Australia; University of Melbourne, Melbourne, VIC, Australia
| | - Zornitza Stark
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, VIC, Australia; University of Melbourne, Melbourne, VIC, Australia; Australian Genomics, Melbourne, VIC, Australia.
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Minten T, Gold NB, Bick S, Adelson S, Gehlenborg N, Amendola LM, Boemer F, Coffey AJ, Encina N, Russell BE, Servais L, Sund KL, Tsipouras P, Bick D, Taft RJ, Green RC. Determining the characteristics of genetic disorders that predict inclusion in newborn genomic sequencing programs. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.03.24.24304797. [PMID: 38585998 PMCID: PMC10996735 DOI: 10.1101/2024.03.24.24304797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
Over 30 international research studies and commercial laboratories are exploring the use of genomic sequencing to screen apparently healthy newborns for genetic disorders. These programs have individualized processes for determining which genes and genetic disorders are queried and reported in newborns. We compared lists of genes from 26 research and commercial newborn screening programs and found substantial heterogeneity among the genes included. A total of 1,750 genes were included in at least one newborn genome sequencing program, but only 74 genes were included on >80% of gene lists, 16 of which are not associated with conditions on the Recommended Uniform Screening Panel. We used a linear regression model to explore factors related to the inclusion of individual genes across programs, finding that a high evidence base as well as treatment efficacy were two of the most important factors for inclusion. We applied a machine learning model to predict how suitable a gene is for newborn sequencing. As knowledge about and treatments for genetic disorders expand, this model provides a dynamic tool to reassess genes for newborn screening implementation. This study highlights the complex landscape of gene list curation among genomic newborn screening programs and proposes an empirical path forward for determining the genes and disorders of highest priority for newborn screening programs.
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Cao Z, He X, Wang D, Gu M, Suo F, Qiang R, Zhang R, Song C, Wang X, Zhu B, Cao D, Yu H, Qu Y, Shen G, Wu J, Wang P, Wang J, Zhang H, Yan Z, Yu G, Zou L. Targeted exome sequencing strategy (NeoEXOME) for Chinese newborns using a pilot study with 3423 neonates. Mol Genet Genomic Med 2024; 12:e2357. [PMID: 38284445 PMCID: PMC10795095 DOI: 10.1002/mgg3.2357] [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: 02/01/2023] [Revised: 09/15/2023] [Accepted: 12/26/2023] [Indexed: 01/30/2024] Open
Abstract
BACKGROUND Newborn screening (NBS) aims to detect congenital anomalies, and next-generation sequencing (NGS) has shown promise in this aspect. However, the NBS strategy for monogenic inherited diseases in China remains insufficient. METHODS We developed a NeoEXOME panel comprising 601 genes that are relevant to the Chinese population found through extensive research on available databases. An interpretation system to grade the results into positive (high-risk, moderate-risk, and low-risk genotypes), negative, and carrier according to the American College of Medical Genetics (ACMG) guidelines was also developed. We validated the panel to evaluate its efficacy by using data from the "1000 Genomes Project" and conducted a pilot multicenter study involving 3423 neonates. RESULTS The NGS positive rate in the 1000 Genomes Project was 7.6% (23/301), whereas the rate was 12.0% in the multicenter study, including 3249 recruited neonates. Notably, in 200 neonates, positive per conventional NBS, 58.5% (69/118) showed results consistent with NGS. In the remaining 3049 neonates showing negative results in conventional NBS, 271 (8.9%) were positive per NGS, and nine of them were clinically diagnosed with diseases in the follow-up. CONCLUSION We successfully designed a NeoEXOME panel for targeted sequencing of monogenic inherited diseases in NBS. The panel demonstrated high performance in the Chinese population, particularly for the early detection of diseases with no biochemical markers.
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Affiliation(s)
- Ziyang Cao
- Clinical Research Unit, Shanghai Children's HospitalShanghai Jiao Tong University Medical SchoolShanghaiChina
- Institute of Pediatric Infection, Immunity, and Critical Care MedicineShanghai Jiao Tong University School of MedicineShanghaiChina
| | - Xiaoyan He
- Center for Clinical Molecular Laboratory Medicine of Children's Hospital of Chongqing Medical UniversityChongqingChina
| | - Dongjuan Wang
- Center for Clinical Molecular Laboratory Medicine of Children's Hospital of Chongqing Medical UniversityChongqingChina
| | - Maosheng Gu
- Center of Medical GeneticsXuzhou Maternal and Child Health Care HospitalXuzhouChina
| | - Feng Suo
- Center of Medical GeneticsXuzhou Maternal and Child Health Care HospitalXuzhouChina
| | - Rong Qiang
- Center of Medical GeneticsNorthwest Women and Children's HospitalXi'anChina
| | - Ruixue Zhang
- Center of Medical GeneticsNorthwest Women and Children's HospitalXi'anChina
| | - Chengrong Song
- Center of Medical GeneticsNorthwest Women and Children's HospitalXi'anChina
| | - Xiaohua Wang
- Center of Medical GeneticsInner Mongolia Maternal and Child Health Care HospitalHohhotChina
| | - Bo Zhu
- Center of Medical GeneticsInner Mongolia Maternal and Child Health Care HospitalHohhotChina
| | - Donghua Cao
- Medical Genetic LaboratoryDalian Municipal Women and Children's Medical Center (Group)DalianChina
- Genetic LaboratoryShenyang Jinghua Hospital Co., LtdShenyangChina
| | - Haihua Yu
- Medical Genetic LaboratoryDalian Municipal Women and Children's Medical Center (Group)DalianChina
| | - Yiping Qu
- Newborn Screening Center of Children's Hospital of Zhejiang University School of MedicineHangzhouChina
| | - Guosong Shen
- Medical Laboratory Center of Huzhou Maternal and Child Health Care HospitalHuzhouChina
| | - Jian Wu
- Research and Development DepartmentMyGenostics Inc.BeijingChina
| | - Pengpeng Wang
- Research and Development DepartmentMyGenostics Inc.BeijingChina
| | - Jinxia Wang
- Clinical Research Unit, Shanghai Children's HospitalShanghai Jiao Tong University Medical SchoolShanghaiChina
- Institute of Pediatric Infection, Immunity, and Critical Care MedicineShanghai Jiao Tong University School of MedicineShanghaiChina
| | - Hongyang Zhang
- Clinical Research Unit, Shanghai Children's HospitalShanghai Jiao Tong University Medical SchoolShanghaiChina
- Institute of Pediatric Infection, Immunity, and Critical Care MedicineShanghai Jiao Tong University School of MedicineShanghaiChina
| | - Zijun Yan
- Clinical Research Unit, Shanghai Children's HospitalShanghai Jiao Tong University Medical SchoolShanghaiChina
- Institute of Pediatric Infection, Immunity, and Critical Care MedicineShanghai Jiao Tong University School of MedicineShanghaiChina
| | - Guangjun Yu
- Clinical Research Unit, Shanghai Children's HospitalShanghai Jiao Tong University Medical SchoolShanghaiChina
- Institute of Pediatric Infection, Immunity, and Critical Care MedicineShanghai Jiao Tong University School of MedicineShanghaiChina
| | - Lin Zou
- Clinical Research Unit, Shanghai Children's HospitalShanghai Jiao Tong University Medical SchoolShanghaiChina
- Institute of Pediatric Infection, Immunity, and Critical Care MedicineShanghai Jiao Tong University School of MedicineShanghaiChina
- Center for Clinical Molecular Laboratory Medicine of Children's Hospital of Chongqing Medical UniversityChongqingChina
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Campbell L, Fredericks J, Mathivha K, Moshesh P, Coovadia A, Chirwa P, Dillon B, Ghoor A, Lawrence D, Nair L, Mabaso N, Mokwele D, Novellie M, Krause A, Carstens N. The implementation and utility of clinical exome sequencing in a South African infant cohort. Front Genet 2023; 14:1277948. [PMID: 38028619 PMCID: PMC10665497 DOI: 10.3389/fgene.2023.1277948] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Accepted: 10/23/2023] [Indexed: 12/01/2023] Open
Abstract
Genetic disorders are significant contributors to infant hospitalization and mortality globally. The early diagnosis of these conditions in infants remains a considerable challenge. Clinical exome sequencing (CES) has shown to be a successful tool for the early diagnosis of genetic conditions, however, its utility in African infant populations has not been investigated. The impact of the under-representation of African genomic data, the cost of testing, and genomic workforce shortages, need to be investigated and evidence-based implementation strategies accounting for locally available genetics expertise and diagnostic infrastructure need to be developed. We evaluated the diagnostic utility of singleton CES in a cohort of 32 ill, South African infants from two State hospitals in Johannesburg, South Africa. We analysed the data using a series of filtering approaches, including a curated virtual gene panel consisting of genes implicated in neonatal-and early childhood-onset conditions and genes with known founder and common variants in African populations. We reported a diagnostic yield of 22% and identified seven pathogenic variants in the NPHS1, COL2A1, OCRL, SHOC2, TPRV4, MTM1 and STAC3 genes. This study demonstrates the utility value of CES in the South African State healthcare setting, providing a diagnosis to patients who would otherwise not receive one and allowing for directed management. We anticipate an increase in the diagnostic yield of our workflow with further refinement of the study inclusion criteria. This study highlights important considerations for the implementation of genomic medicine in under-resourced settings and in under-represented African populations where variant interpretation remains a challenge.
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Affiliation(s)
- L. Campbell
- Division of Human Genetics, National Health Laboratory Service andSchool of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - J. Fredericks
- Department of Paediatrics and Child Health, School of Clinical Medicine, Rahima Moosa Mother and Child Hospital, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - K. Mathivha
- Department of Paediatrics and Child Health, School of Clinical Medicine, Nelson Mandela Children’s Hospital, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - P. Moshesh
- Department of Paediatrics and Child Health, School of Clinical Medicine, Nelson Mandela Children’s Hospital, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - A. Coovadia
- Department of Paediatrics and Child Health, School of Clinical Medicine, Rahima Moosa Mother and Child Hospital, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - P. Chirwa
- Nelson Mandela Children’s Hospital, Johannesburg, South Africa
| | - B. Dillon
- Division of Human Genetics, National Health Laboratory Service andSchool of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - A. Ghoor
- Department of Paediatrics and Child Health, School of Clinical Medicine, Rahima Moosa Mother and Child Hospital, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - D. Lawrence
- Department of Paediatrics and Child Health, School of Clinical Medicine, Rahima Moosa Mother and Child Hospital, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - L. Nair
- Department of Paediatrics and Child Health, School of Clinical Medicine, Rahima Moosa Mother and Child Hospital, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - N. Mabaso
- Division of Human Genetics, National Health Laboratory Service andSchool of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - D. Mokwele
- Division of Human Genetics, National Health Laboratory Service andSchool of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - M. Novellie
- Division of Human Genetics, National Health Laboratory Service andSchool of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - A. Krause
- Division of Human Genetics, National Health Laboratory Service andSchool of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - N. Carstens
- Division of Human Genetics, National Health Laboratory Service andSchool of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Genomics Platform, South African Medical Research Council, Cape Town, South Africa
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Abstract
Rare diseases are a leading cause of infant mortality and lifelong disability. To improve outcomes, timely diagnosis and effective treatments are needed. Genomic sequencing has transformed the traditional diagnostic process, providing rapid, accurate and cost-effective genetic diagnoses to many. Incorporating genomic sequencing into newborn screening programmes at the population scale holds the promise of substantially expanding the early detection of treatable rare diseases, with stored genomic data potentially benefitting health over a lifetime and supporting further research. As several large-scale newborn genomic screening projects launch internationally, we review the challenges and opportunities presented, particularly the need to generate evidence of benefit and to address the ethical, legal and psychosocial issues that genomic newborn screening raises.
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Affiliation(s)
- Zornitza Stark
- Australian Genomics, Melbourne, Victoria, Australia.
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Victoria, Australia.
- Department of Paediatrics, University of Melbourne, Melbourne, Victoria, Australia.
| | - Richard H Scott
- Great Ormond Street Hospital for Children, London, UK
- UCL Great Ormond Street Institute of Child Health, London, UK
- Genomics England, London, UK
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8
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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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9
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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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10
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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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11
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Milko LV, Berg JS. Age-Based Genomic Screening during Childhood: Ethical and Practical Considerations in Public Health Genomics Implementation. Int J Neonatal Screen 2023; 9:36. [PMID: 37489489 PMCID: PMC10366892 DOI: 10.3390/ijns9030036] [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: 04/15/2023] [Revised: 06/07/2023] [Accepted: 06/21/2023] [Indexed: 07/26/2023] Open
Abstract
Genomic sequencing offers an unprecedented opportunity to detect inherited variants that are implicated in rare Mendelian disorders, yet there are many challenges to overcome before this technology can routinely be applied in the healthy population. The age-based genomic screening (ABGS) approach is a novel alternative to genome-scale sequencing at birth that aims to provide highly actionable genetic information to parents over the course of their child's routine health care. ABGS utilizes an established metric to identify conditions with high clinical actionability and incorporates information about the age of onset and age of intervention to determine the optimal time to screen for any given condition. Ongoing partnerships with parents and providers are instrumental to the co-creation of educational resources and strategies to address potential implementation barriers. Implementation science frameworks and informative empirical data are used to evaluate strategies to establish this unique clinical application of targeted genomic sequencing. Ultimately, a pilot project conducted in primary care pediatrics clinics will assess patient and implementation outcomes, parent and provider perspectives, and the feasibility of ABGS. A validated, stakeholder-informed, and practical ABGS program will include hundreds of conditions that are actionable during infancy and childhood, setting the stage for a longitudinal implementation that can assess clinical and health economic outcomes.
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Affiliation(s)
- Laura V. Milko
- Department of Genetics, University of North Carolina at Chapel Hill, 120 Mason Farm Rd., Chapel Hill, NC 27599-7264, USA;
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12
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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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13
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Gold NB, Adelson SM, Shah N, Williams S, Bick SL, Zoltick ES, Gold JI, Strong A, Ganetzky R, Roberts AE, Walker M, Holtz AM, Sankaran VG, Delmonte O, Tan W, Holm IA, Thiagarajah JR, Kamihara J, Comander J, Place E, Wiggs J, Green RC. Perspectives of Rare Disease Experts on Newborn Genome Sequencing. JAMA Netw Open 2023; 6:e2312231. [PMID: 37155167 PMCID: PMC10167563 DOI: 10.1001/jamanetworkopen.2023.12231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 03/23/2023] [Indexed: 05/10/2023] Open
Abstract
Importance Newborn genome sequencing (NBSeq) can detect infants at risk for treatable disorders currently undetected by conventional newborn screening. Despite broad stakeholder support for NBSeq, the perspectives of rare disease experts regarding which diseases should be screened have not been ascertained. Objective To query rare disease experts about their perspectives on NBSeq and which gene-disease pairs they consider appropriate to evaluate in apparently healthy newborns. Design, Setting, and Participants This survey study, designed between November 2, 2021, and February 11, 2022, assessed experts' perspectives on 6 statements related to NBSeq. Experts were also asked to indicate whether they would recommend including each of 649 gene-disease pairs associated with potentially treatable conditions in NBSeq. The survey was administered between February 11 and September 23, 2022, to 386 experts, including all 144 directors of accredited medical and laboratory genetics training programs in the US. Exposures Expert perspectives on newborn screening using genome sequencing. Main Outcomes and Measures The proportion of experts indicating agreement or disagreement with each survey statement and those who selected inclusion of each gene-disease pair were tabulated. Exploratory analyses of responses by gender and age were conducted using t and χ2 tests. Results Of 386 experts invited, 238 (61.7%) responded (mean [SD] age, 52.6 [12.8] years [range 27-93 years]; 126 [52.9%] women and 112 [47.1%] men). Among the experts who responded, 161 (87.9%) agreed that NBSeq for monogenic treatable disorders should be made available to all newborns; 107 (58.5%) agreed that NBSeq should include genes associated with treatable disorders, even if those conditions were low penetrance; 68 (37.2%) agreed that actionable adult-onset conditions should be sequenced in newborns to facilitate cascade testing in parents, and 51 (27.9%) agreed that NBSeq should include screening for conditions with no established therapies or management guidelines. The following 25 genes were recommended by 85% or more of the experts: OTC, G6PC, SLC37A4, CYP11B1, ARSB, F8, F9, SLC2A1, CYP17A1, RB1, IDS, GUSB, DMD, GLUD1, CYP11A1, GALNS, CPS1, PLPBP, ALDH7A1, SLC26A3, SLC25A15, SMPD1, GATM, SLC7A7, and NAGS. Including these, 42 gene-disease pairs were endorsed by at least 80% of experts, and 432 genes were endorsed by at least 50% of experts. Conclusions and Relevance In this survey study, rare disease experts broadly supported NBSeq for treatable conditions and demonstrated substantial concordance regarding the inclusion of a specific subset of genes in NBSeq.
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Affiliation(s)
- Nina B. Gold
- Division of Medical Genetics and Metabolism, Massachusetts General Hospital for Children, Boston
- Department of Pediatrics, Harvard Medical School, Boston, Massachusetts
| | - Sophia M. Adelson
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital, Boston, Massachusetts
- Ariadne Labs, Boston, Massachusetts
| | - Nidhi Shah
- Dartmouth Hitchcock Medical Center, Lebanon, New Hampshire
- Geisel School of Medicine, Hanover, New Hampshire
- Division of Genetics and Genomics, Boston Children’s Hospital, Boston, Massachusetts
| | - Shardae Williams
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital, Boston, Massachusetts
- Ariadne Labs, Boston, Massachusetts
| | - Sarah L. Bick
- Department of Pediatrics, Harvard Medical School, Boston, Massachusetts
- Division of Genetics and Genomics, Boston Children’s Hospital, Boston, Massachusetts
| | - Emilie S. Zoltick
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital, Boston, Massachusetts
- Center for Healthcare Research in Pediatrics, Department of Population Medicine, Harvard Pilgrim Health Care Institute, Boston, Massachusetts
- Department of Population Medicine, Harvard Medical School, Boston, Massachusetts
| | - Jessica I. Gold
- Division of Human Genetics, Department of Pediatrics, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Alanna Strong
- Division of Human Genetics, Department of Pediatrics, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania
- Perelman School of Medicine, University of Pennsylvania, Philadelphia
| | - Rebecca Ganetzky
- Division of Human Genetics, Department of Pediatrics, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania
- Perelman School of Medicine, University of Pennsylvania, Philadelphia
| | - Amy E. Roberts
- Department of Pediatrics, Harvard Medical School, Boston, Massachusetts
- Department of Cardiology and Division of Genetics and Genomics, Department of Pediatrics, Boston Children’s Hospital, Boston, Massachusetts
| | - Melissa Walker
- Division of Pediatric Neurology, Massachusetts General Hospital for Children, Boston
- Department of Neurology, Harvard Medical School, Boston, Massachusetts
| | - Alexander M. Holtz
- Division of Genetics and Genomics, Boston Children’s Hospital, Boston, Massachusetts
| | - Vijay G. Sankaran
- Department of Pediatrics, Harvard Medical School, Boston, Massachusetts
- Division of Hematology/Oncology, Boston Children’s Hospital, Boston, Massachusetts
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Ottavia Delmonte
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland
| | - Weizhen Tan
- Department of Pediatrics, Harvard Medical School, Boston, Massachusetts
- Division of Pediatric Nephrology, Massachusetts General Hospital for Children, Boston
| | - Ingrid A. Holm
- Department of Pediatrics, Harvard Medical School, Boston, Massachusetts
- Division of Genetics and Genomics, Boston Children’s Hospital, Boston, Massachusetts
- Manton Center for Orphan Diseases Research, Boston Children’s Hospital, Boston, Massachusetts
| | - Jay R. Thiagarajah
- Department of Pediatrics, Harvard Medical School, Boston, Massachusetts
- Division of Gastroenterology, Hepatology and Nutrition, Boston Children’s Hospital, Boston, Massachusetts
| | - Junne Kamihara
- Department of Pediatrics, Harvard Medical School, Boston, Massachusetts
- Division of Hematology/Oncology, Boston Children’s Hospital, Boston, Massachusetts
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Jason Comander
- Department of Ophthalmology, Massachusetts Eye and Ear, Boston
- Department of Ophthalmology, Harvard Medical School, Boston, Massachusetts
| | - Emily Place
- Department of Ophthalmology, Massachusetts Eye and Ear, Boston
- Department of Ophthalmology, Harvard Medical School, Boston, Massachusetts
| | - Janey Wiggs
- Department of Ophthalmology, Massachusetts Eye and Ear, Boston
- Department of Ophthalmology, Harvard Medical School, Boston, Massachusetts
| | - Robert C. Green
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital, Boston, Massachusetts
- Ariadne Labs, Boston, Massachusetts
- Department of Medicine, Harvard Medical School, Boston, Massachusetts
- Broad Institute, Boston, Massachusetts
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14
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Christensen KD, McMahon PM, Galbraith LN, Yeh JM, Stout NK, Lu CY, Stein S, Zhao M, Hylind RJ, Wu AC. Benefits, harms, and costs of newborn genetic screening for hypertrophic cardiomyopathy: Estimates from the PreEMPT model. Genet Med 2023; 25:100797. [PMID: 36727595 PMCID: PMC10168130 DOI: 10.1016/j.gim.2023.100797] [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: 09/14/2022] [Revised: 01/20/2023] [Accepted: 01/23/2023] [Indexed: 02/02/2023] Open
Abstract
PURPOSE Population newborn genetic screening for hypertrophic cardiomyopathy (HCM) is feasible, however its benefits, harms, and cost-effectiveness are uncertain. METHODS We developed a microsimulation model to simulate a US birth cohort of 3.7 million newborns. Those identified with pathogenic/likely pathogenic variants associated with increased risk of HCM underwent surveillance and recommended treatment, whereas in usual care, individuals with family histories of HCM underwent surveillance. RESULTS In a cohort of 3.7 million newborns, newborn genetic screening would reduce HCM-related deaths through age 20 years by 44 (95% uncertainty interval [UI] = 10-103) however increase the numbers of children undergoing surveillance by 8127 (95% UI = 6308-9664). Compared with usual care, newborn genetic screening costs $267,000 per life year saved (95% UI, $106,000 to $919,000 per life year saved). CONCLUSION Newborn genetic screening for HCM could prevent deaths but at a high cost and would require many healthy children to undergo surveillance. This study shows how modeling can provide insights into the tradeoffs between benefits and costs that will need to be considered as newborn genetic screening is more widely adopted.
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Affiliation(s)
- Kurt D Christensen
- Department of Population Medicine, Harvard Medical School, Boston, MA; Department of Population Medicine, Harvard Pilgrim Health Care Institute, Boston, MA.
| | - Pamela M McMahon
- Department of Population Medicine, Harvard Pilgrim Health Care Institute, Boston, MA
| | - Lauren N Galbraith
- Department of Population Medicine, Harvard Pilgrim Health Care Institute, Boston, MA; Department of Epidemiology and Biostatistics, School of Public Health, Boston University, Boston, MA
| | - Jennifer M Yeh
- Division of General Pediatrics, Department of Pediatrics, Boston Children's Hospital, Boston, MA; Department of Pediatrics, Harvard Medical School, Boston, MA
| | - Natasha K Stout
- Department of Population Medicine, Harvard Medical School, Boston, MA; Department of Population Medicine, Harvard Pilgrim Health Care Institute, Boston, MA
| | - Christine Y Lu
- Department of Population Medicine, Harvard Medical School, Boston, MA; Department of Population Medicine, Harvard Pilgrim Health Care Institute, Boston, MA
| | - Sarah Stein
- Department of Population Medicine, Harvard Pilgrim Health Care Institute, Boston, MA
| | | | - Robyn J Hylind
- Inherited Cardiac Arrhythmia Program, Department of Cardiology, Boston Children's Hospital Boston, MA
| | - Ann Chen Wu
- Department of Population Medicine, Harvard Medical School, Boston, MA; Department of Population Medicine, Harvard Pilgrim Health Care Institute, Boston, MA; Division of General Pediatrics, Department of Pediatrics, Boston Children's Hospital, Boston, MA
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15
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Stoltze UK, Hagen CM, van Overeem Hansen T, Byrjalsen A, Gerdes AM, Yakimov V, Rasmussen S, Bækvad-Hansen M, Hougaard DM, Schmiegelow K, Hjalgrim H, Wadt K, Bybjerg-Grauholm J. Combinatorial batching of DNA for ultralow-cost detection of pathogenic variants. Genome Med 2023; 15:17. [PMID: 36918911 PMCID: PMC10013285 DOI: 10.1186/s13073-023-01167-6] [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: 11/12/2022] [Accepted: 02/28/2023] [Indexed: 03/16/2023] Open
Abstract
BACKGROUND Next-generation sequencing (NGS) based population screening holds great promise for disease prevention and earlier diagnosis, but the costs associated with screening millions of humans remain prohibitive. New methods for population genetic testing that lower the costs of NGS without compromising diagnostic power are needed. METHODS We developed double batched sequencing where DNA samples are batch-sequenced twice - directly pinpointing individuals with rare variants. We sequenced batches of at-birth blood spot DNA using a commercial 113-gene panel in an explorative (n = 100) and a validation (n = 100) cohort of children who went on to develop pediatric cancers. All results were benchmarked against individual whole genome sequencing data. RESULTS We demonstrated fully replicable detection of cancer-causing germline variants, with positive and negative predictive values of 100% (95% CI, 0.91-1.00 and 95% CI, 0.98-1.00, respectively). Pathogenic and clinically actionable variants were detected in RB1, TP53, BRCA2, APC, and 19 other genes. Analyses of larger batches indicated that our approach is highly scalable, yielding more than 95% cost reduction or less than 3 cents per gene screened for rare disease-causing mutations. We also show that double batched sequencing could cost-effectively prevent childhood cancer deaths through broad genomic testing. CONCLUSIONS Our ultracheap genetic diagnostic method, which uses existing sequencing hardware and standard newborn blood spots, should readily open up opportunities for population-wide risk stratification using genetic screening across many fields of clinical genetics and genomics.
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Affiliation(s)
- Ulrik Kristoffer Stoltze
- Department of Pediatrics and Adolescent Medicine, Rigshospitalet, Blegdamsvej 9, 2100, KBH Ø, Denmark. .,Department of Clinical Genetics, Rigshospitalet, Blegdamsvej 9, 2100, KBH Ø, Denmark.
| | - Christian Munch Hagen
- Department of Congenital Disorders, Statens Serum Institute, 2300, KBH S, Artillerivej 5, Denmark
| | - Thomas van Overeem Hansen
- Department of Clinical Genetics, Rigshospitalet, Blegdamsvej 9, 2100, KBH Ø, Denmark.,Department of Clinical Medicine, Copenhagen University, Blegdamsvej 3B, 2200, KBH N, Denmark
| | - Anna Byrjalsen
- Department of Clinical Genetics, Rigshospitalet, Blegdamsvej 9, 2100, KBH Ø, Denmark
| | - Anne-Marie Gerdes
- Department of Clinical Genetics, Rigshospitalet, Blegdamsvej 9, 2100, KBH Ø, Denmark
| | - Victor Yakimov
- Department of Congenital Disorders, Statens Serum Institute, 2300, KBH S, Artillerivej 5, Denmark
| | - Simon Rasmussen
- Novo Nordisk Foundation Center for Protein Research, Copenhagen University, Blegdamsvej 3B, 2200, KBH N, Denmark
| | - Marie Bækvad-Hansen
- Department of Congenital Disorders, Statens Serum Institute, 2300, KBH S, Artillerivej 5, Denmark
| | - David Michael Hougaard
- Department of Congenital Disorders, Statens Serum Institute, 2300, KBH S, Artillerivej 5, Denmark
| | - Kjeld Schmiegelow
- Department of Pediatrics and Adolescent Medicine, Rigshospitalet, Blegdamsvej 9, 2100, KBH Ø, Denmark.,Department of Clinical Medicine, Copenhagen University, Blegdamsvej 3B, 2200, KBH N, Denmark
| | - Henrik Hjalgrim
- Department of Clinical Medicine, Copenhagen University, Blegdamsvej 3B, 2200, KBH N, Denmark.,Danish Cancer Society Research Centre, Danish Cancer Society, Strandboulevarden 49, 2100, KBH Ø, Denmark.,Department of Epidemiology Research, Statens Serum Institut, 2300, KBH S, Artillerivej 5, Denmark.,Department of Haematology, Rigshospitalet, Blegdamsvej 9, 2100, Copenhagen Ø, Denmark
| | - Karin Wadt
- Department of Clinical Genetics, Rigshospitalet, Blegdamsvej 9, 2100, KBH Ø, Denmark
| | - Jonas Bybjerg-Grauholm
- Department of Congenital Disorders, Statens Serum Institute, 2300, KBH S, Artillerivej 5, Denmark.
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16
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Newborn Screening Is on a Collision Course with Public Health Ethics. Int J Neonatal Screen 2022; 8:ijns8040051. [PMID: 36278621 PMCID: PMC9590071 DOI: 10.3390/ijns8040051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 09/18/2022] [Accepted: 09/21/2022] [Indexed: 11/22/2022] Open
Abstract
Newborn screening was established over 50 years ago to identify cases of disorders that were serious, urgent, and treatable, mirroring the criteria of Wilson and Jungner. In the last decade, conditions have been added to newborn screening that do not strictly meet these criteria, and genomic newborn screening is beginning to be discussed. Some of these new and proposed additions to newborn screening entail serious public health ethical issues that need to be explored.
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17
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Kingsmore SF, Smith LD, Kunard CM, Bainbridge M, Batalov S, Benson W, Blincow E, Caylor S, Chambers C, Del Angel G, Dimmock DP, Ding Y, Ellsworth K, Feigenbaum A, Frise E, Green RC, Guidugli L, Hall KP, Hansen C, Hobbs CA, Kahn SD, Kiel M, Van Der Kraan L, Krilow C, Kwon YH, Madhavrao L, Le J, Lefebvre S, Mardach R, Mowrey WR, Oh D, Owen MJ, Powley G, Scharer G, Shelnutt S, Tokita M, Mehtalia SS, Oriol A, Papadopoulos S, Perry J, Rosales E, Sanford E, Schwartz S, Tran D, Reese MG, Wright M, Veeraraghavan N, Wigby K, Willis MJ, Wolen AR, Defay. T. A genome sequencing system for universal newborn screening, diagnosis, and precision medicine for severe genetic diseases. Am J Hum Genet 2022; 109:1605-1619. [PMID: 36007526 PMCID: PMC9502059 DOI: 10.1016/j.ajhg.2022.08.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 08/01/2022] [Indexed: 12/31/2022] Open
Abstract
Newborn screening (NBS) dramatically improves outcomes in severe childhood disorders by treatment before symptom onset. In many genetic diseases, however, outcomes remain poor because NBS has lagged behind drug development. Rapid whole-genome sequencing (rWGS) is attractive for comprehensive NBS because it concomitantly examines almost all genetic diseases and is gaining acceptance for genetic disease diagnosis in ill newborns. We describe prototypic methods for scalable, parentally consented, feedback-informed NBS and diagnosis of genetic diseases by rWGS and virtual, acute management guidance (NBS-rWGS). Using established criteria and the Delphi method, we reviewed 457 genetic diseases for NBS-rWGS, retaining 388 (85%) with effective treatments. Simulated NBS-rWGS in 454,707 UK Biobank subjects with 29,865 pathogenic or likely pathogenic variants associated with 388 disorders had a true negative rate (specificity) of 99.7% following root cause analysis. In 2,208 critically ill children with suspected genetic disorders and 2,168 of their parents, simulated NBS-rWGS for 388 disorders identified 104 (87%) of 119 diagnoses previously made by rWGS and 15 findings not previously reported (NBS-rWGS negative predictive value 99.6%, true positive rate [sensitivity] 88.8%). Retrospective NBS-rWGS diagnosed 15 children with disorders that had been undetected by conventional NBS. In 43 of the 104 children, had NBS-rWGS-based interventions been started on day of life 5, the Delphi consensus was that symptoms could have been avoided completely in seven critically ill children, mostly in 21, and partially in 13. We invite groups worldwide to refine these NBS-rWGS conditions and join us to prospectively examine clinical utility and cost effectiveness.
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Affiliation(s)
- Stephen F. Kingsmore
- Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123, USA,Rady Children’s Hospital, San Diego, CA 92123, USA,Keck Graduate Institute, Claremont, CA 91711, USA,Corresponding author
| | - Laurie D. Smith
- Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123, USA
| | | | - Matthew Bainbridge
- Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123, USA,Rady Children’s Hospital, San Diego, CA 92123, USA
| | - Sergey Batalov
- Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123, USA,Rady Children’s Hospital, San Diego, CA 92123, USA
| | - Wendy Benson
- Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123, USA,Rady Children’s Hospital, San Diego, CA 92123, USA
| | - Eric Blincow
- Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123, USA,Rady Children’s Hospital, San Diego, CA 92123, USA
| | - Sara Caylor
- Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123, USA,Rady Children’s Hospital, San Diego, CA 92123, USA
| | - Christina Chambers
- Department of Pediatrics, University of California San Diego, San Diego, CA 92093, USA
| | | | - David P. Dimmock
- Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123, USA,Rady Children’s Hospital, San Diego, CA 92123, USA
| | - Yan Ding
- Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123, USA,Rady Children’s Hospital, San Diego, CA 92123, USA
| | - Katarzyna Ellsworth
- Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123, USA,Rady Children’s Hospital, San Diego, CA 92123, USA
| | - Annette Feigenbaum
- Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123, USA,Rady Children’s Hospital, San Diego, CA 92123, USA,Department of Pediatrics, University of California San Diego, San Diego, CA 92093, USA
| | - Erwin Frise
- Fabric Genomics, Inc., Oakland, CA 94612, USA
| | - Robert C. Green
- Mass General Brigham, Broad Institute, Ariadne Labs and Harvard Medical School, Boston, MA 02115, USA
| | - Lucia Guidugli
- Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123, USA,Rady Children’s Hospital, San Diego, CA 92123, USA
| | | | - Christian Hansen
- Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123, USA,Rady Children’s Hospital, San Diego, CA 92123, USA
| | - Charlotte A. Hobbs
- Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123, USA,Rady Children’s Hospital, San Diego, CA 92123, USA
| | | | - Mark Kiel
- Genomenon Inc., Ann Arbor, MI 48108, USA
| | - Lucita Van Der Kraan
- Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123, USA,Rady Children’s Hospital, San Diego, CA 92123, USA
| | | | - Yong H. Kwon
- Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123, USA,Rady Children’s Hospital, San Diego, CA 92123, USA
| | - Lakshminarasimha Madhavrao
- Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123, USA,Rady Children’s Hospital, San Diego, CA 92123, USA
| | - Jennie Le
- Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123, USA,Rady Children’s Hospital, San Diego, CA 92123, USA
| | | | - Rebecca Mardach
- Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123, USA,Rady Children’s Hospital, San Diego, CA 92123, USA,Department of Pediatrics, University of California San Diego, San Diego, CA 92093, USA
| | | | - Danny Oh
- Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123, USA,Rady Children’s Hospital, San Diego, CA 92123, USA
| | - Mallory J. Owen
- Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123, USA,Rady Children’s Hospital, San Diego, CA 92123, USA
| | | | - Gunter Scharer
- Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123, USA
| | | | - Mari Tokita
- Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123, USA,Rady Children’s Hospital, San Diego, CA 92123, USA
| | | | - Albert Oriol
- Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123, USA,Rady Children’s Hospital, San Diego, CA 92123, USA
| | | | - James Perry
- Rady Children’s Hospital, San Diego, CA 92123, USA,Department of Pediatrics, University of California San Diego, San Diego, CA 92093, USA
| | - Edwin Rosales
- Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123, USA,Rady Children’s Hospital, San Diego, CA 92123, USA
| | - Erica Sanford
- Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123, USA
| | | | - Duke Tran
- Illumina, Inc., San Diego, CA 92122, USA
| | | | - Meredith Wright
- Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123, USA,Rady Children’s Hospital, San Diego, CA 92123, USA
| | - Narayanan Veeraraghavan
- Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123, USA,Rady Children’s Hospital, San Diego, CA 92123, USA
| | - Kristen Wigby
- Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123, USA,Rady Children’s Hospital, San Diego, CA 92123, USA,Department of Pediatrics, University of California San Diego, San Diego, CA 92093, USA
| | - Mary J. Willis
- Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123, USA
| | | | - Thomas Defay.
- Alexion, Astra Zeneca Rare Disease, Boston, MA 02210, USA
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18
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Chan K, Brower A, Williams MS. Population-based screening of newborns: Findings from the newborn screening expansion study (part two). Front Genet 2022; 13:867354. [PMID: 36118861 PMCID: PMC9476322 DOI: 10.3389/fgene.2022.867354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Accepted: 07/18/2022] [Indexed: 11/13/2022] Open
Abstract
Rapid advances in genomic technologies to screen, diagnose, and treat newborns will significantly increase the number of conditions in newborn screening (NBS). We previously identified four factors that delay and/or complicate NBS expansion: 1) variability in screening panels persists; 2) the short duration of pilots limits information about interventions and health outcomes; 3) recent recommended uniform screening panel (RUSP) additions are expanding the definition of NBS; and 4) the RUSP nomination and evidence review process has capacity constraints. In this paper, we developed a use case for each factor and suggested how model(s) could be used to evaluate changes and improvements. The literature on models was reviewed from a range of disciplines including system sciences, management, artificial intelligence, and machine learning. The results from our analysis highlighted that there is at least one model which could be applied to each of the four factors that has delayed and/or complicate NBS expansion. In conclusion, our paper supports the use of modeling to address the four challenges in the expansion of NBS.
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Affiliation(s)
- Kee Chan
- American College of Medical Genetics and Genomics, Bethesda, MD, United States
- *Correspondence: Kee Chan,
| | - Amy Brower
- American College of Medical Genetics and Genomics, Bethesda, MD, United States
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19
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Owen MJ, Lefebvre S, Hansen C, Kunard CM, Dimmock DP, Smith LD, Scharer G, Mardach R, Willis MJ, Feigenbaum A, Niemi AK, Ding Y, Van Der Kraan L, Ellsworth K, Guidugli L, Lajoie BR, McPhail TK, Mehtalia SS, Chau KK, Kwon YH, Zhu Z, Batalov S, Chowdhury S, Rego S, Perry J, Speziale M, Nespeca M, Wright MS, Reese MG, De La Vega FM, Azure J, Frise E, Rigby CS, White S, Hobbs CA, Gilmer S, Knight G, Oriol A, Lenberg J, Nahas SA, Perofsky K, Kim K, Carroll J, Coufal NG, Sanford E, Wigby K, Weir J, Thomson VS, Fraser L, Lazare SS, Shin YH, Grunenwald H, Lee R, Jones D, Tran D, Gross A, Daigle P, Case A, Lue M, Richardson JA, Reynders J, Defay T, Hall KP, Veeraraghavan N, Kingsmore SF. An automated 13.5 hour system for scalable diagnosis and acute management guidance for genetic diseases. Nat Commun 2022; 13:4057. [PMID: 35882841 PMCID: PMC9325884 DOI: 10.1038/s41467-022-31446-6] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Accepted: 06/08/2022] [Indexed: 12/31/2022] Open
Abstract
While many genetic diseases have effective treatments, they frequently progress rapidly to severe morbidity or mortality if those treatments are not implemented immediately. Since front-line physicians frequently lack familiarity with these diseases, timely molecular diagnosis may not improve outcomes. Herein we describe Genome-to-Treatment, an automated, virtual system for genetic disease diagnosis and acute management guidance. Diagnosis is achieved in 13.5 h by expedited whole genome sequencing, with superior analytic performance for structural and copy number variants. An expert panel adjudicated the indications, contraindications, efficacy, and evidence-of-efficacy of 9911 drug, device, dietary, and surgical interventions for 563 severe, childhood, genetic diseases. The 421 (75%) diseases and 1527 (15%) effective interventions retained are integrated with 13 genetic disease information resources and appended to diagnostic reports ( https://gtrx.radygenomiclab.com ). This system provided correct diagnoses in four retrospectively and two prospectively tested infants. The Genome-to-Treatment system facilitates optimal outcomes in children with rapidly progressive genetic diseases.
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Affiliation(s)
- Mallory J. Owen
- grid.286440.c0000 0004 0383 2910Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123 USA ,grid.286440.c0000 0004 0383 2910Rady Children’s Hospital, San Diego, CA 92123 USA
| | - Sebastien Lefebvre
- grid.422288.60000 0004 0408 0730Alexion Pharmaceuticals, Inc., Boston, MA 02210 USA
| | - Christian Hansen
- grid.286440.c0000 0004 0383 2910Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123 USA ,grid.286440.c0000 0004 0383 2910Rady Children’s Hospital, San Diego, CA 92123 USA
| | - Chris M. Kunard
- grid.185669.50000 0004 0507 3954Illumina, Inc., San Diego, CA 92122 USA
| | - David P. Dimmock
- grid.286440.c0000 0004 0383 2910Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123 USA ,grid.286440.c0000 0004 0383 2910Rady Children’s Hospital, San Diego, CA 92123 USA ,grid.419735.d0000 0004 0615 8415Keck Graduate Institute, Claremont, CA 91711 USA
| | - Laurie D. Smith
- grid.286440.c0000 0004 0383 2910Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123 USA
| | - Gunter Scharer
- grid.286440.c0000 0004 0383 2910Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123 USA
| | - Rebecca Mardach
- grid.286440.c0000 0004 0383 2910Rady Children’s Hospital, San Diego, CA 92123 USA ,grid.266100.30000 0001 2107 4242Department of Pediatrics, University of California San Diego, San Diego, CA 92093 USA
| | - Mary J. Willis
- grid.286440.c0000 0004 0383 2910Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123 USA
| | - Annette Feigenbaum
- grid.286440.c0000 0004 0383 2910Rady Children’s Hospital, San Diego, CA 92123 USA ,grid.266100.30000 0001 2107 4242Department of Pediatrics, University of California San Diego, San Diego, CA 92093 USA
| | - Anna-Kaisa Niemi
- grid.286440.c0000 0004 0383 2910Rady Children’s Hospital, San Diego, CA 92123 USA ,grid.266100.30000 0001 2107 4242Department of Pediatrics, University of California San Diego, San Diego, CA 92093 USA
| | - Yan Ding
- grid.286440.c0000 0004 0383 2910Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123 USA ,grid.286440.c0000 0004 0383 2910Rady Children’s Hospital, San Diego, CA 92123 USA
| | - Luca Van Der Kraan
- grid.286440.c0000 0004 0383 2910Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123 USA ,grid.286440.c0000 0004 0383 2910Rady Children’s Hospital, San Diego, CA 92123 USA
| | - Katarzyna Ellsworth
- grid.286440.c0000 0004 0383 2910Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123 USA ,grid.286440.c0000 0004 0383 2910Rady Children’s Hospital, San Diego, CA 92123 USA
| | - Lucia Guidugli
- grid.286440.c0000 0004 0383 2910Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123 USA ,grid.286440.c0000 0004 0383 2910Rady Children’s Hospital, San Diego, CA 92123 USA
| | - Bryan R. Lajoie
- grid.185669.50000 0004 0507 3954Illumina, Inc., San Diego, CA 92122 USA
| | | | | | - Kevin K. Chau
- grid.286440.c0000 0004 0383 2910Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123 USA ,grid.286440.c0000 0004 0383 2910Rady Children’s Hospital, San Diego, CA 92123 USA
| | - Yong H. Kwon
- grid.286440.c0000 0004 0383 2910Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123 USA ,grid.286440.c0000 0004 0383 2910Rady Children’s Hospital, San Diego, CA 92123 USA
| | - Zhanyang Zhu
- grid.286440.c0000 0004 0383 2910Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123 USA ,grid.286440.c0000 0004 0383 2910Rady Children’s Hospital, San Diego, CA 92123 USA
| | - Sergey Batalov
- grid.286440.c0000 0004 0383 2910Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123 USA ,grid.286440.c0000 0004 0383 2910Rady Children’s Hospital, San Diego, CA 92123 USA
| | - Shimul Chowdhury
- grid.286440.c0000 0004 0383 2910Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123 USA ,grid.286440.c0000 0004 0383 2910Rady Children’s Hospital, San Diego, CA 92123 USA ,grid.419735.d0000 0004 0615 8415Keck Graduate Institute, Claremont, CA 91711 USA
| | - Seema Rego
- grid.286440.c0000 0004 0383 2910Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123 USA ,grid.286440.c0000 0004 0383 2910Rady Children’s Hospital, San Diego, CA 92123 USA
| | - James Perry
- grid.286440.c0000 0004 0383 2910Rady Children’s Hospital, San Diego, CA 92123 USA ,grid.266100.30000 0001 2107 4242Department of Pediatrics, University of California San Diego, San Diego, CA 92093 USA
| | - Mark Speziale
- grid.286440.c0000 0004 0383 2910Rady Children’s Hospital, San Diego, CA 92123 USA ,grid.266100.30000 0001 2107 4242Department of Pediatrics, University of California San Diego, San Diego, CA 92093 USA
| | - Mark Nespeca
- grid.286440.c0000 0004 0383 2910Rady Children’s Hospital, San Diego, CA 92123 USA ,grid.266100.30000 0001 2107 4242Department of Pediatrics, University of California San Diego, San Diego, CA 92093 USA ,grid.266100.30000 0001 2107 4242Department of Neuroscience, University of California San Diego, San Diego, CA 92093 USA
| | - Meredith S. Wright
- grid.286440.c0000 0004 0383 2910Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123 USA ,grid.286440.c0000 0004 0383 2910Rady Children’s Hospital, San Diego, CA 92123 USA ,grid.419735.d0000 0004 0615 8415Keck Graduate Institute, Claremont, CA 91711 USA
| | | | | | - Joe Azure
- Fabric Genomics, Inc., Oakland, CA 94612 USA
| | - Erwin Frise
- Fabric Genomics, Inc., Oakland, CA 94612 USA
| | | | - Sandy White
- Fabric Genomics, Inc., Oakland, CA 94612 USA
| | - Charlotte A. Hobbs
- grid.286440.c0000 0004 0383 2910Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123 USA ,grid.286440.c0000 0004 0383 2910Rady Children’s Hospital, San Diego, CA 92123 USA ,grid.266100.30000 0001 2107 4242Department of Pediatrics, University of California San Diego, San Diego, CA 92093 USA
| | - Sheldon Gilmer
- grid.286440.c0000 0004 0383 2910Rady Children’s Hospital, San Diego, CA 92123 USA
| | - Gail Knight
- grid.286440.c0000 0004 0383 2910Rady Children’s Hospital, San Diego, CA 92123 USA ,grid.266100.30000 0001 2107 4242Department of Pediatrics, University of California San Diego, San Diego, CA 92093 USA
| | - Albert Oriol
- grid.286440.c0000 0004 0383 2910Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123 USA ,grid.286440.c0000 0004 0383 2910Rady Children’s Hospital, San Diego, CA 92123 USA
| | - Jerica Lenberg
- grid.286440.c0000 0004 0383 2910Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123 USA ,grid.286440.c0000 0004 0383 2910Rady Children’s Hospital, San Diego, CA 92123 USA ,grid.419735.d0000 0004 0615 8415Keck Graduate Institute, Claremont, CA 91711 USA
| | - Shareef A. Nahas
- grid.286440.c0000 0004 0383 2910Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123 USA ,grid.286440.c0000 0004 0383 2910Rady Children’s Hospital, San Diego, CA 92123 USA
| | - Kate Perofsky
- grid.286440.c0000 0004 0383 2910Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123 USA ,grid.286440.c0000 0004 0383 2910Rady Children’s Hospital, San Diego, CA 92123 USA ,grid.266100.30000 0001 2107 4242Department of Pediatrics, University of California San Diego, San Diego, CA 92093 USA
| | - Kyu Kim
- grid.286440.c0000 0004 0383 2910Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123 USA ,grid.286440.c0000 0004 0383 2910Rady Children’s Hospital, San Diego, CA 92123 USA ,grid.266100.30000 0001 2107 4242Department of Pediatrics, University of California San Diego, San Diego, CA 92093 USA
| | - Jeanne Carroll
- grid.286440.c0000 0004 0383 2910Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123 USA ,grid.286440.c0000 0004 0383 2910Rady Children’s Hospital, San Diego, CA 92123 USA ,grid.266100.30000 0001 2107 4242Department of Pediatrics, University of California San Diego, San Diego, CA 92093 USA
| | - Nicole G. Coufal
- grid.286440.c0000 0004 0383 2910Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123 USA ,grid.286440.c0000 0004 0383 2910Rady Children’s Hospital, San Diego, CA 92123 USA ,grid.266100.30000 0001 2107 4242Department of Pediatrics, University of California San Diego, San Diego, CA 92093 USA
| | - Erica Sanford
- grid.286440.c0000 0004 0383 2910Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123 USA
| | - Kristen Wigby
- grid.286440.c0000 0004 0383 2910Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123 USA ,grid.286440.c0000 0004 0383 2910Rady Children’s Hospital, San Diego, CA 92123 USA ,grid.266100.30000 0001 2107 4242Department of Pediatrics, University of California San Diego, San Diego, CA 92093 USA
| | - Jacqueline Weir
- grid.185669.50000 0004 0507 3954Illumina, Inc., San Diego, CA 92122 USA
| | - Vicki S. Thomson
- grid.185669.50000 0004 0507 3954Illumina, Inc., San Diego, CA 92122 USA
| | - Louise Fraser
- grid.185669.50000 0004 0507 3954Illumina, Inc., San Diego, CA 92122 USA
| | - Seka S. Lazare
- grid.185669.50000 0004 0507 3954Illumina, Inc., San Diego, CA 92122 USA
| | - Yoon H. Shin
- grid.185669.50000 0004 0507 3954Illumina, Inc., San Diego, CA 92122 USA
| | | | - Richard Lee
- grid.185669.50000 0004 0507 3954Illumina, Inc., San Diego, CA 92122 USA
| | - David Jones
- grid.185669.50000 0004 0507 3954Illumina, Inc., San Diego, CA 92122 USA
| | - Duke Tran
- grid.185669.50000 0004 0507 3954Illumina, Inc., San Diego, CA 92122 USA
| | - Andrew Gross
- grid.185669.50000 0004 0507 3954Illumina, Inc., San Diego, CA 92122 USA
| | - Patrick Daigle
- grid.185669.50000 0004 0507 3954Illumina, Inc., San Diego, CA 92122 USA
| | - Anne Case
- grid.185669.50000 0004 0507 3954Illumina, Inc., San Diego, CA 92122 USA
| | - Marisa Lue
- grid.185669.50000 0004 0507 3954Illumina, Inc., San Diego, CA 92122 USA
| | | | - John Reynders
- grid.422288.60000 0004 0408 0730Alexion Pharmaceuticals, Inc., Boston, MA 02210 USA
| | - Thomas Defay
- grid.422288.60000 0004 0408 0730Alexion Pharmaceuticals, Inc., Boston, MA 02210 USA
| | - Kevin P. Hall
- grid.185669.50000 0004 0507 3954Illumina, Inc., San Diego, CA 92122 USA
| | - Narayanan Veeraraghavan
- grid.286440.c0000 0004 0383 2910Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123 USA ,grid.286440.c0000 0004 0383 2910Rady Children’s Hospital, San Diego, CA 92123 USA
| | - Stephen F. Kingsmore
- grid.286440.c0000 0004 0383 2910Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123 USA ,grid.286440.c0000 0004 0383 2910Rady Children’s Hospital, San Diego, CA 92123 USA ,grid.419735.d0000 0004 0615 8415Keck Graduate Institute, Claremont, CA 91711 USA
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20
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Roberts MC, Foss KS, Henderson GE, Powell SN, Saylor KW, Weck KE, Milko LV. Public Interest in Population Genetic Screening for Cancer Risk. Front Genet 2022; 13:886640. [PMID: 35938028 PMCID: PMC9354961 DOI: 10.3389/fgene.2022.886640] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 06/06/2022] [Indexed: 01/04/2023] Open
Abstract
An emerging role for DNA sequencing is to identify people at risk for an inherited cancer syndrome in order to prevent or ameliorate the manifestation of symptoms. Two cancer syndromes, Hereditary Breast and Ovarian Cancer and Lynch Syndrome meet the “Tier 1” evidence threshold established by the Centers for Disease Control and Prevention (CDC) for routine testing of patients with a personal or family history of cancer. Advancements in genomic medicine have accelerated public health pilot programs for these highly medically actionable conditions. In this brief report, we provide descriptive statistics from a survey of 746 US respondents from a Qualtrics panel about the public’s awareness of genetic testing, interest in learning about their cancer risk, and likelihood of participating in a population genetic screening (PGS) test. Approximately of half the respondents were aware of genetic testing for inherited cancer risk (n = 377/745, 50.6%) and would choose to learn about their cancer risk (n-309/635, 48.7%). Characteristics of those interested in learning about their cancer risk differed by educational attainment, age, income, insurance status, having a primary care doctor, being aware of genetic testing, and likelihood of sharing information with family (p < 0.05). A sizeable majority of the respondents who were interested in about learning their cancer risk also said that they were likely to participate in a PGS test that involved a clinical appointment and blood draw, but no out-of-pocket cost (n = 255/309, 82.5%). Reasons for not wanting to participate included not finding test results interesting or important, concerns about costs, and feeling afraid to know the results. Overall, our results suggest that engaging and educating the general population about the benefits of learning about an inherited cancer predisposition may be an important strategy to address recruitment barriers to PGS.
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Affiliation(s)
- Megan C Roberts
- Division of Pharmaceutical Outcomes and Policy, UNC Eshelman School of Pharmacy, Chapel Hill, NC, United States
| | - Kimberly S Foss
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Gail E Henderson
- Department of Social Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Sabrina N Powell
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Katherine W Saylor
- Department of Medical Ethics and Health Policy, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Karen E Weck
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Laura V Milko
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
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21
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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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22
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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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23
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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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24
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Minear MA, Phillips MN, Kau A, Parisi MA. Newborn screening research sponsored by the NIH: From diagnostic paradigms to precision therapeutics. AMERICAN JOURNAL OF MEDICAL GENETICS. PART C, SEMINARS IN MEDICAL GENETICS 2022; 190:138-152. [PMID: 36102292 PMCID: PMC10328555 DOI: 10.1002/ajmg.c.31997] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 08/21/2022] [Accepted: 08/24/2022] [Indexed: 06/15/2023]
Abstract
Newborn screening (NBS) is a successful public health initiative that effectively identifies pre-symptomatic neonates so that treatment can be initiated before the onset of irreversible morbidity and mortality. Legislation passed in 2008 has supported a system of state screening programs, educational resources, and an evidence-based review process to add conditions to a recommended universal newborn screening panel (RUSP). The Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), NIH, has promoted NBS research to advance legislative goals by supporting research that will uncover fundamental mechanisms of disease, develop treatments for NBS disorders, and promote pilot studies to test implementation of new conditions. NICHD's partnerships with other federal agencies have contributed to activities that support nominations of new conditions to the RUSP. The NIH's Newborn Sequencing In Genomic Medicine and Public Health (NSIGHT) initiative funded research projects that considered how genomic sequencing could be integrated into NBS and its ethical ramifications. Recently, the workshop, "Gene Targeted Therapies: Early Diagnosis and Equitable Delivery," has explored the possibility of expanding NBS to include genetic diagnosis and precision, gene-based therapies. Although hurdles remain to realize such a vision, broad engagement of multiple stakeholders is essential to advance genomic medicine within NBS.
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Affiliation(s)
- Mollie A. Minear
- Intellectual and Developmental Disabilities Branch, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, USA
| | - Megan N. Phillips
- Intellectual and Developmental Disabilities Branch, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, USA
- Present address: Allen Institute for Brain Science, Seattle, WA, USA
| | - Alice Kau
- Intellectual and Developmental Disabilities Branch, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, USA
| | - Melissa A. Parisi
- Intellectual and Developmental Disabilities Branch, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, USA
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25
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Kingsmore SF. Dispatches from Biotech beginning BeginNGS: Rapid newborn genome sequencing to end the diagnostic and therapeutic odyssey. AMERICAN JOURNAL OF MEDICAL GENETICS. PART C, SEMINARS IN MEDICAL GENETICS 2022; 190:243-256. [PMID: 36218021 PMCID: PMC9588745 DOI: 10.1002/ajmg.c.32005] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 08/29/2022] [Accepted: 08/29/2022] [Indexed: 01/11/2023]
Abstract
In this Dispatch from Biotech, we briefly review the urgent need for extensive expansion of newborn screening (NBS) by genomic sequencing, and the reasons why early attempts had limited success. During the next decade transformative developments will continue in society and in the pharmaceutical, biotechnology, informatics, and medical sectors that enable prompt addition of genetic disorders to NBS by rapid whole genome sequencing (rWGS) upon introduction of new therapies that qualify them according to the Wilson and Jungner criteria (Wilson, J. M. G., & Jungner, G., World Health Organization. (1968). Principles and Practice of Screening for Disease. World Health Organization. Retrieved from https://apps.who.int/iris/handle/10665/37650). Herein we describe plans, progress, and clinical trial designs for BeginNGS (Newborn Genome Sequencing to end the diagnostic and therapeutic odyssey), a new international, pre-competitive, public-private consortium that proposes to implement a self-learning healthcare delivery system for screening all newborns for over 400 hundred genetic diseases, diagnostic confirmation, implementation of effective treatment, and acceleration of orphan drug development. We invite investigators and stakeholders worldwide to join the consortium in a prospective, multi-center, international trial of the clinical utility and cost effectiveness of BeginNGS.
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Affiliation(s)
- Stephen F. Kingsmore
- Rady Children's Institute for Genomic Medicine, Rady Children's HospitalSan DiegoCaliforniaUSA
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26
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Bush L, Davidson H, Gelles S, Lea D, Koehly LM. Experiences of Families Caring for Children with Newborn Screening-Related Conditions: Implications for the Expansion of Genomics in Population-Based Neonatal Public Health Programs. Int J Neonatal Screen 2022; 8:ijns8020035. [PMID: 35645289 PMCID: PMC9149923 DOI: 10.3390/ijns8020035] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 05/09/2022] [Accepted: 05/13/2022] [Indexed: 02/01/2023] Open
Abstract
With the expansion of newborn screening conditions globally and the increased use of genomic technologies for early detection, there is a need for ethically nuanced policies to guide the future integration of ever-more comprehensive genomics into population-based newborn screening programs. In the current paper, we consider the lived experiences of 169 family caregivers caring for 77 children with NBS-related conditions to identify lessons learned that can inform policy and practice related to population-based newborn screening using genomic technologies. Based on caregiver narratives obtained through in-depth interviews, we identify themes characterizing these families' diagnostic odyssey continuum, which fall within two domains: (1) medical management implications of a child diagnosed with an NBS-related condition and (2) psychological implications of a child diagnosed with an NBS-related condition. For Domain 1, family caregivers' experiences point to the need for educational resources for both health care professionals that serve children with NBS-related conditions and their families; empowerment programs for family caregivers; training for providers in patient-centered communication; and access to multi-disciplinary specialists. For Domain 2, caregivers' experiences suggest a need for access to continuous, long-term counseling resources; patient navigator resources; and peer support programs. These lessons learned can inform policy recommendations for the benefit of the child, the family, the healthcare system, and society.
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Affiliation(s)
- Lynn Bush
- Division of Genetics and Genomics, Boston Children’s Hospital and Center for Bioethics, Harvard Medical School, Boston, MA 02115, USA;
| | - Hannah Davidson
- National Human Genome Research Institute, Bethesda, MD 20892, USA; (H.D.); (S.G.); (D.L.)
| | - Shani Gelles
- National Human Genome Research Institute, Bethesda, MD 20892, USA; (H.D.); (S.G.); (D.L.)
| | - Dawn Lea
- National Human Genome Research Institute, Bethesda, MD 20892, USA; (H.D.); (S.G.); (D.L.)
| | - Laura M. Koehly
- National Human Genome Research Institute, Bethesda, MD 20892, USA; (H.D.); (S.G.); (D.L.)
- Correspondence: ; Tel.: +1-301-451-3999
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27
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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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28
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Goddard KAB, Lee K, Buchanan AH, Powell BC, Hunter JE. Establishing the Medical Actionability of Genomic Variants. Annu Rev Genomics Hum Genet 2022; 23:173-192. [PMID: 35363504 PMCID: PMC10184682 DOI: 10.1146/annurev-genom-111021-032401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Actionability is an important concept in medicine that does not have a well-accepted standard definition, nor is there a general consensus on how to establish it. Medical actionability is often conflated with clinical utility, a related but distinct concept. This lack of clarity contributes to practice variation and inconsistent coverage decisions in genomic medicine, leading to the potential for systematic bias in the use of evidence-based interventions. We clarify how medical actionability and clinical utility are distinct and then discuss the spectrum of actionability, including benefits for the person, the family, and society. We also describe applications across the life course, including prediction, diagnosis, and treatment. Current challenges in assessing the medical actionability of identified genomic variants include gaps in the evidence, limited contexts with practice guidelines, and subjective aspects of medical actionability. A standardized and authoritative assessment of medical actionability is critical to implementing genomic medicine in a fashion that improves population health outcomes and reduces health disparities. Expected final online publication date for the Annual Review of Genomics and Human Genetics, Volume 23 is October 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Katrina A B Goddard
- Department of Translational and Applied Genomics, Center for Health Research, Kaiser Permanente Northwest, Portland, Oregon, USA; .,Department of Genetics, University of North Carolina, Chapel Hill, North Carolina, USA; , .,Genomic Medicine Institute, Geisinger Health System, Danville, Pennsylvania, USA; .,Genomics, Ethics, and Translational Research Program, RTI International, Research Triangle Park, North Carolina, USA;
| | - Kristy Lee
- Department of Translational and Applied Genomics, Center for Health Research, Kaiser Permanente Northwest, Portland, Oregon, USA; .,Department of Genetics, University of North Carolina, Chapel Hill, North Carolina, USA; , .,Genomic Medicine Institute, Geisinger Health System, Danville, Pennsylvania, USA; .,Genomics, Ethics, and Translational Research Program, RTI International, Research Triangle Park, North Carolina, USA;
| | - Adam H Buchanan
- Department of Translational and Applied Genomics, Center for Health Research, Kaiser Permanente Northwest, Portland, Oregon, USA; .,Department of Genetics, University of North Carolina, Chapel Hill, North Carolina, USA; , .,Genomic Medicine Institute, Geisinger Health System, Danville, Pennsylvania, USA; .,Genomics, Ethics, and Translational Research Program, RTI International, Research Triangle Park, North Carolina, USA;
| | - Bradford C Powell
- Department of Translational and Applied Genomics, Center for Health Research, Kaiser Permanente Northwest, Portland, Oregon, USA; .,Department of Genetics, University of North Carolina, Chapel Hill, North Carolina, USA; , .,Genomic Medicine Institute, Geisinger Health System, Danville, Pennsylvania, USA; .,Genomics, Ethics, and Translational Research Program, RTI International, Research Triangle Park, North Carolina, USA;
| | - Jessica Ezzell Hunter
- Department of Translational and Applied Genomics, Center for Health Research, Kaiser Permanente Northwest, Portland, Oregon, USA; .,Department of Genetics, University of North Carolina, Chapel Hill, North Carolina, USA; , .,Genomic Medicine Institute, Geisinger Health System, Danville, Pennsylvania, USA; .,Genomics, Ethics, and Translational Research Program, RTI International, Research Triangle Park, North Carolina, USA;
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29
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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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30
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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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31
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Park JE, Lee T, Ha K, Cho EH, Ki CS. Carrier frequency and incidence estimation of familial hemophagocytic lymphohistiocytosis in East Asian populations by genome aggregation database (gnomAD) based analysis. Front Pediatr 2022; 10:975665. [PMID: 36440336 PMCID: PMC9692074 DOI: 10.3389/fped.2022.975665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Accepted: 10/24/2022] [Indexed: 11/13/2022] Open
Abstract
OBJECTIVES Hemophagocytic lymphohistiocytosis (HLH) is a clinical syndrome characterized by a life-threatening condition caused by severe hypercytokinemia. The hereditary forms of HLH, also called familial HLH (fHLH), have 4 different genes (PRF1, UNC13D, STX11, and STXBP2) and have been identified as being causative for fHLH. This study aimed to analyze the carrier frequency and expected incidence of fHLH in East Asians and Koreans using exome data from the Genome Aggregation Database (gnomAD). METHODS We analyzed 9,197 exomes for East Asian populations from gnomAD with 1,909 Korean for four fHLH genes. All identified variants were classified according to 2015 American College of Medical Genetics and Genomics and the Association for Molecular Pathology guideline. RESULTS 19 pathogenic variant/likely pathogenic variants (PV/LPVs) were identified in 30 East Asian individuals (0.33%). Among them, 7 PV/LPVs were identified in 17 Korean individuals (0.63%). The estimated incidence of fHLH was 1 in 1,105,652 for East Asians and l in 235,128 for Koreans. CONCLUSIONS This study is the first to identify carrier frequencies in East Asian and Korean populations for fHLH using gnomAD. It was confirmed that the carrier frequency of fHLH patients was high in Koreans among East Asians and the incidence was also predicted to be higher than that of other East Asians. The variant spectrum of fHLH genes in East Asian and Korean populations differed greatly from those of other ethnic groups.
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Affiliation(s)
- Jong Eun Park
- Department of Laboratory Medicine, Hanyang University Guri Hospital, Hanyang University College of Medicine, Guri, South Korea
| | | | | | - Eun Hye Cho
- Department of Laboratory Medicine, Kangbuk Samsung Hospital, Sungkyunkwan University School of Medicine, Seoul, South Korea
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Abstract
IMPORTANCE Genomic newborn screening (gNBS) may optimize the health and well-being of children and families. Screening programs are required to be evidence based, acceptable, and beneficial. OBJECTIVES To identify what has been discovered following the reporting of the first gNBS pilot projects and to provide a summary of key points for the design of gNBS. EVIDENCE REVIEW A systematic literature review was performed on April 14, 2021, identifying 36 articles that addressed the following questions: (1) what is the interest in and what would be the uptake of gNBS? (2) what diseases and genes should be included? (3) what is the validity and utility of gNBS? and (4) what are the ethical, legal, and social implications? Articles were only included if they generated new evidence; all opinion pieces were excluded. FINDINGS In the 36 articles included, there was high concordance, except for gene disease inclusion, which was highly variable. Key findings were the need for equitable access, appropriate educational materials, and informed and flexible consent. The process for selecting genes for testing should be transparent and reflect that parents value the certainty of prediction over actionability. Data should be analyzed in a way that minimizes uncertainty and incidental findings. The expansion of traditional newborn screening (tNBS) to identify more life-threatening and treatable diseases needs to be balanced against the complexity of consenting parents of newborns for genomic testing as well as the risk that overall uptake of tNBS may decline. The literature reflected that the right of a child to self-determination should be valued more than the possibility of the whole family benefiting from a newborn genomic test. CONCLUSIONS AND RELEVANCE The findings of this systematic review suggest that implementing gNBS will require a nuanced approach. There are gaps in our knowledge, such as the views of diverse populations, the capabilities of health systems, and health economic implications. It will be essential to rigorously evaluate outcomes and ensure programs can evolve to maximize benefit.
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Affiliation(s)
- Lilian Downie
- Murdoch Children’s Research Institute, Melbourne, Victoria, Australia
- Department of Paediatrics, University of Melbourne, Melbourne, Victoria, Australia
| | - Jane Halliday
- Murdoch Children’s Research Institute, Melbourne, Victoria, Australia
- Department of Paediatrics, University of Melbourne, Melbourne, Victoria, Australia
| | - Sharon Lewis
- Murdoch Children’s Research Institute, Melbourne, Victoria, Australia
- Department of Paediatrics, University of Melbourne, Melbourne, Victoria, Australia
| | - David J. Amor
- Murdoch Children’s Research Institute, Melbourne, Victoria, Australia
- Department of Paediatrics, University of Melbourne, Melbourne, Victoria, Australia
- Royal Children’s Hospital, Melbourne, Victoria, Australia
- Victorian Clinical Genetics Services, Melbourne, Victoria, Australia
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33
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Staley BS, Milko LV, Waltz M, Griesemer I, Mollison L, Grant TL, Farnan L, Roche M, Navas A, Lightfoot A, Foreman AKM, O'Daniel JM, O'Neill SC, Lin FC, Roman TS, Brandt A, Powell BC, Rini C, Berg JS, Bensen JT. Evaluating the clinical utility of early exome sequencing in diverse pediatric outpatient populations in the North Carolina Clinical Genomic Evaluation of Next-generation Exome Sequencing (NCGENES) 2 study: a randomized controlled trial. Trials 2021; 22:395. [PMID: 34127041 PMCID: PMC8201439 DOI: 10.1186/s13063-021-05341-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2021] [Accepted: 05/26/2021] [Indexed: 11/20/2022] Open
Abstract
BACKGROUND Exome sequencing (ES) has probable utility for shortening the diagnostic odyssey of children with suspected genetic disorders. This report describes the design and methods of a study evaluating the potential of ES as a routine clinical tool for pediatric patients who have suspected genetic conditions and who are in the early stages of the diagnostic odyssey. METHODS The North Carolina Clinical Genomic Evaluation by Next-generation Exome Sequencing (NCGENES) 2 study is an interdisciplinary, multi-site Phase III randomized controlled trial of two interventions: educational pre-visit preparation (PVP) and offer of first-line ES. In this full-factorial design, parent-child dyads are randomly assigned to one of four study arms (PVP + usual care, ES + usual care, PVP + ES + usual care, or usual care alone) in equal proportions. Participants are recruited from Pediatric Genetics or Neurology outpatient clinics in three North Carolina healthcare facilities. Eligible pediatric participants are < 16 years old and have a first visit to a participating clinic, a suspected genetic condition, and an eligible parent/guardian to attend the clinic visit and complete study measures. The study oversamples participants from underserved and under-represented populations. Participants assigned to the PVP arms receive an educational booklet and question prompt list before clinical interactions. Randomization to offer of first-line ES is revealed after a child's clinic visit. Parents complete measures at baseline, pre-clinic, post-clinic, and two follow-up timepoints. Study clinicians provide phenotypic data and complete measures after the clinic visit and after returning results. Reportable study-related research ES results are confirmed in a CLIA-certified clinical laboratory. Results are disclosed to the parent by the clinical team. A community consultation team contributed to the development of study materials and study implementation methods and remains engaged in the project. DISCUSSION NCGENES 2 will contribute valuable knowledge concerning technical, clinical, psychosocial, and health economic issues associated with using early diagnostic ES to shorten the diagnostic odyssey of pediatric patients with likely genetic conditions. Results will inform efforts to engage diverse populations in genomic medicine research and generate evidence that can inform policy, practice, and future research related to the utility of first-line diagnostic ES in health care. TRIAL REGISTRATION ClinicalTrials.gov NCT03548779 . Registered on June 07, 2018.
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Affiliation(s)
- Brooke S Staley
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Campus Box #7295, Chapel Hill, NC, 27599-7295, USA.
| | - Laura V Milko
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Margaret Waltz
- Department of Social Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Ida Griesemer
- Department of Heath Behavior, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
- Cecil G. Sheps Center for Health Services Research, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Lonna Mollison
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Tracey L Grant
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Laura Farnan
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Myra Roche
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
- Department of Pediatrics, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, 27599, USA
| | - Angelo Navas
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Alexandra Lightfoot
- Department of Heath Behavior, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
- Center for Health Promotion and Disease Prevention, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Ann Katherine M Foreman
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Julianne M O'Daniel
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Suzanne C O'Neill
- Department of Oncology, Georgetown University, Washington, DC, 20007, USA
| | - Feng-Chang Lin
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Tamara S Roman
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Alicia Brandt
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Bradford C Powell
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Christine Rini
- Department of Medical Social Sciences, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL, USA
| | - Jonathan S Berg
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Jeannette T Bensen
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Campus Box #7295, Chapel Hill, NC, 27599-7295, USA
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34
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Remec ZI, Trebusak Podkrajsek K, Repic Lampret B, Kovac J, Groselj U, Tesovnik T, Battelino T, Debeljak M. Next-Generation Sequencing in Newborn Screening: A Review of Current State. Front Genet 2021; 12:662254. [PMID: 34122514 PMCID: PMC8188483 DOI: 10.3389/fgene.2021.662254] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Accepted: 04/13/2021] [Indexed: 12/27/2022] Open
Abstract
Newborn screening was first introduced at the beginning of the 1960s with the successful implementation of the first phenylketonuria screening programs. Early expansion of the included disorders was slow because each additional disorder screened required a separate test. Subsequently, the technological advancements of biochemical methodology enabled the scaling-up of newborn screening, most notably with the implementation of tandem mass spectrometry. In recent years, we have witnessed a remarkable progression of high-throughput sequencing technologies, which has resulted in a continuous decrease of both cost and time required for genetic analysis. This has enabled more widespread use of the massive multiparallel sequencing. Genomic sequencing is now frequently used in clinical applications, and its implementation in newborn screening has been intensively advocated. The expansion of newborn screening has raised many clinical, ethical, legal, psychological, sociological, and technological concerns over time. This review provides an overview of the current state of next-generation sequencing regarding newborn screening including current recommendations and potential challenges for the use of such technologies in newborn screening.
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Affiliation(s)
- Ziga I. Remec
- Clinical Institute for Special Laboratory Diagnostics, University Children’s Hospital, University Medical Centre Ljubljana, Ljubljana, Slovenia
| | - Katarina Trebusak Podkrajsek
- Clinical Institute for Special Laboratory Diagnostics, University Children’s Hospital, University Medical Centre Ljubljana, Ljubljana, Slovenia
- Faculty of Medicine, Institute of Biochemistry and Molecular Genetics, University of Ljubljana, Ljubljana, Slovenia
| | - Barbka Repic Lampret
- Clinical Institute for Special Laboratory Diagnostics, University Children’s Hospital, University Medical Centre Ljubljana, Ljubljana, Slovenia
| | - Jernej Kovac
- Clinical Institute for Special Laboratory Diagnostics, University Children’s Hospital, University Medical Centre Ljubljana, Ljubljana, Slovenia
| | - Urh Groselj
- Department of Endocrinology, Diabetes and Metabolic Diseases, University Children’s Hospital, University Medical Centre Ljubljana, Ljubljana, Slovenia
- Chair of Pediatrics, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Tine Tesovnik
- Clinical Institute for Special Laboratory Diagnostics, University Children’s Hospital, University Medical Centre Ljubljana, Ljubljana, Slovenia
| | - Tadej Battelino
- Department of Endocrinology, Diabetes and Metabolic Diseases, University Children’s Hospital, University Medical Centre Ljubljana, Ljubljana, Slovenia
- Chair of Pediatrics, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Marusa Debeljak
- Clinical Institute for Special Laboratory Diagnostics, University Children’s Hospital, University Medical Centre Ljubljana, Ljubljana, Slovenia
- Faculty of Medicine, Institute of Biochemistry and Molecular Genetics, University of Ljubljana, Ljubljana, Slovenia
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35
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Rehder C, Bean LJH, Bick D, Chao E, Chung W, Das S, O'Daniel J, Rehm H, Shashi V, Vincent LM. Next-generation sequencing for constitutional variants in the clinical laboratory, 2021 revision: a technical standard of the American College of Medical Genetics and Genomics (ACMG). Genet Med 2021; 23:1399-1415. [PMID: 33927380 DOI: 10.1038/s41436-021-01139-4] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 02/25/2021] [Accepted: 02/26/2021] [Indexed: 12/17/2022] Open
Abstract
Next-generation sequencing (NGS) technologies are now established in clinical laboratories as a primary testing modality in genomic medicine. These technologies have reduced the cost of large-scale sequencing by several orders of magnitude. It is now cost-effective to analyze an individual with disease-targeted gene panels, exome sequencing, or genome sequencing to assist in the diagnosis of a wide array of clinical scenarios. While clinical validation and use of NGS in many settings is established, there are continuing challenges as technologies and the associated informatics evolve. To assist clinical laboratories with the validation of NGS methods and platforms, the ongoing monitoring of NGS testing to ensure quality results, and the interpretation and reporting of variants found using these technologies, the American College of Medical Genetics and Genomics (ACMG) has developed the following technical standards.
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Affiliation(s)
| | - Lora J H Bean
- Department of Human Genetics, Emory University, Atlanta, GA, USA
| | - David Bick
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Elizabeth Chao
- Division of Genetics and Genomics, Department of Pediatrics, University of California, Irvine, CA, USA
| | - Wendy Chung
- Departments of Pediatrics and Medicine, Columbia University, New York, NY, USA
| | - Soma Das
- Department of Human Genetics, University of Chicago, Chicago, IL, USA
| | - Julianne O'Daniel
- Department of Genetics, University of North Carolina, Chapel Hill, NC, USA
| | - Heidi Rehm
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Vandana Shashi
- Department of Pediatrics, Duke University, Durham, NC, USA
| | - Lisa M Vincent
- Division of Pathology & Laboratory Medicine, Children's National Health System, Washington, DC, USA.,Departments of Pathology and Pediatrics, George Washington University, Washington, DC, USA
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36
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DeCristo DM, Milko LV, O'Daniel JM, Foreman AKM, Mollison LF, Powell BC, Powell CM, Berg JS. Actionability of commercial laboratory sequencing panels for newborn screening and the importance of transparency for parental decision-making. Genome Med 2021; 13:50. [PMID: 33781310 PMCID: PMC8008582 DOI: 10.1186/s13073-021-00867-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Accepted: 03/12/2021] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Newborn screening aims to identify individual patients who could benefit from early management, treatment, and/or surveillance practices. As sequencing technologies have progressed and we move into the era of precision medicine, genomic sequencing has been introduced to this area with the hopes of detecting variants related to a vastly expanded number of conditions. Though implementation of genomic sequencing for newborn screening in public health and clinical settings is limited, commercial laboratories have begun to offer genomic screening panels for neonates. METHODS We examined genes listed on four commercial laboratory genomic screening panels for neonates and assessed their clinical actionability using an established age-based semi-quantitative metric to categorize them. We identified genes that were included on multiple panels or distinct between panels. RESULTS Three hundred and nine genes appeared on one or more commercial panels: 74 (23.9%) genes were included in all four commercial panels, 45 (14.6%) were on only three panels, 76 (24.6%) were on only two panels, and 114 (36.9%) genes were listed on only one of the four panels. Eighty-two genes (26.5%) listed on one or more panels were assessed by our method to be inappropriate for newborn screening and to require additional parental decision-making. Conversely, 249 genes that we previously identified as being highly actionable were not listed on any of the four commercial laboratory genomic screening panels. CONCLUSIONS Commercial neonatal genomic screening panels have heterogeneous content and may contain some conditions with lower actionability than would be expected for public health newborn screening; conversely, some conditions with higher actionability may be omitted from these panels. The lack of transparency about how conditions are selected suggests a need for greater detail about panel content in order for parents to make informed decisions. The nuanced activity of gene list selection for genomic screening should be iteratively refined with evidence-based approaches to provide maximal benefit and minimal harm to newborns.
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Affiliation(s)
- Daniela M DeCristo
- Department of Genetics, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, 27599, USA
| | - Laura V Milko
- Department of Genetics, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, 27599, USA
| | - Julianne M O'Daniel
- Department of Genetics, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, 27599, USA
| | - Ann Katherine M Foreman
- Department of Genetics, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, 27599, USA
| | - Lonna F Mollison
- Department of Genetics, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, 27599, USA
| | - Bradford C Powell
- Department of Genetics, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, 27599, USA
| | - Cynthia M Powell
- Department of Genetics, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, 27599, USA
- Department of Pediatrics, Division of Genetics and Metabolism, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, 27599, USA
| | - Jonathan S Berg
- Department of Genetics, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, 27599, USA.
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37
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Bick D, Bick SL, Dimmock DP, Fowler TA, Caulfield MJ, Scott RH. An online compendium of treatable genetic disorders. AMERICAN JOURNAL OF MEDICAL GENETICS PART C-SEMINARS IN MEDICAL GENETICS 2020; 187:48-54. [PMID: 33350578 PMCID: PMC7986124 DOI: 10.1002/ajmg.c.31874] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Revised: 11/20/2020] [Accepted: 11/24/2020] [Indexed: 11/21/2022]
Abstract
More than 4,000 genes have been associated with recognizable Mendelian/monogenic diseases. When faced with a new diagnosis of a rare genetic disorder, health care providers increasingly turn to internet resources for information to understand the disease and direct care. Unfortunately, it can be challenging to find information concerning treatment for rare diseases as key details are scattered across a number of authoritative websites and numerous journal articles. The website and associated mobile device application described in this article begin to address this challenge by providing a convenient, readily available starting point to find treatment information. The site, Rx-genes.com (https://www.rx-genes.com/), is focused on those conditions where the treatment is directed against the mechanism of the disease and thereby alters the natural history of the disease. The website currently contains 633 disease entries that include references to disease information and treatment guidance, a brief summary of treatments, the inheritance pattern, a disease frequency (if known), nonmolecular confirmatory testing (if available), and a link to experimental treatments. Existing entries are continuously updated, and new entries are added as novel treatments appear in the literature.
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Affiliation(s)
- David Bick
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, USA
| | - Sarah L Bick
- Nemours/Alfred I. duPont Hospital for Children, Wilmington, Delaware, USA
| | - David P Dimmock
- Rady Children's Institute for Genomic Medicine, San Diego, California, USA
| | - Tom A Fowler
- Genomics England Ltd., London, UK.,William Harvey Research Institute, Queen Mary University of London, London, UK
| | - Mark J Caulfield
- Genomics England Ltd., London, UK.,William Harvey Research Institute, Queen Mary University of London, London, UK
| | - Richard H Scott
- Genomics England Ltd., London, UK.,Department of Clinical Genetics, Great Ormond Street Hospital for Children National Health Service (NHS) Foundation Trust, London, UK
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38
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Snir M, Nazareth S, Simmons E, Hayward L, Ashcraft K, Bristow SL, Esplin ED, Aradhya S. Democratizing genomics: Leveraging software to make genetics an integral part of routine care. AMERICAN JOURNAL OF MEDICAL GENETICS. PART C, SEMINARS IN MEDICAL GENETICS 2020; 187:14-27. [PMID: 33296144 DOI: 10.1002/ajmg.c.31866] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 11/16/2020] [Accepted: 11/17/2020] [Indexed: 12/25/2022]
Abstract
Genetic testing can provide definitive molecular diagnoses and guide clinical management decisions from preconception through adulthood. Innovative solutions for scaling clinical genomics services are necessary if they are to transition from a niche specialty to a routine part of patient care. The expertise of specialists, like genetic counselors and medical geneticists, has traditionally been relied upon to facilitate testing and follow-up, and while ideal, this approach is limited in its ability to integrate genetics into primary care. As individuals, payors, and providers increasingly realize the value of genetics in mainstream medicine, several implementation challenges need to be overcome. These include electronic health record integration, patient and provider education, tools to stay abreast of guidelines, and simplification of the test ordering process. Currently, no single platform offers a holistic view of genetic testing that streamlines the entire process across specialties that begins with identifying at-risk patients in mainstream care settings, providing pretest education, facilitating consent and test ordering, and following up as a "genetic companion" for ongoing management. We describe our vision for using software that includes clinical-grade chatbots and decision support tools, with direct access to genetic counselors and pharmacists within a modular, integrated, end-to-end testing journey.
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39
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Roman TS, Crowley SB, Roche MI, Foreman AKM, O'Daniel JM, Seifert BA, Lee K, Brandt A, Gustafson C, DeCristo DM, Strande NT, Ramkissoon L, Milko LV, Owen P, Roy S, Xiong M, Paquin RS, Butterfield RM, Lewis MA, Souris KJ, Bailey DB, Rini C, Booker JK, Powell BC, Weck KE, Powell CM, Berg JS. Genomic Sequencing for Newborn Screening: Results of the NC NEXUS Project. Am J Hum Genet 2020; 107:596-611. [PMID: 32853555 PMCID: PMC7536575 DOI: 10.1016/j.ajhg.2020.08.001] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Accepted: 07/24/2020] [Indexed: 02/08/2023] Open
Abstract
Newborn screening (NBS) was established as a public health program in the 1960s and is crucial for facilitating detection of certain medical conditions in which early intervention can prevent serious, life-threatening health problems. Genomic sequencing can potentially expand the screening for rare hereditary disorders, but many questions surround its possible use for this purpose. We examined the use of exome sequencing (ES) for NBS in the North Carolina Newborn Exome Sequencing for Universal Screening (NC NEXUS) project, comparing the yield from ES used in a screening versus a diagnostic context. We enrolled healthy newborns and children with metabolic diseases or hearing loss (106 participants total). ES confirmed the participant's underlying diagnosis in 15 out of 17 (88%) children with metabolic disorders and in 5 out of 28 (∼18%) children with hearing loss. We discovered actionable findings in four participants that would not have been detected by standard NBS. A subset of parents was eligible to receive additional information for their child about childhood-onset conditions with low or no clinical actionability, clinically actionable adult-onset conditions, and carrier status for autosomal-recessive conditions. We found pathogenic variants associated with hereditary breast and/or ovarian cancer in two children, a likely pathogenic variant in the gene associated with Lowe syndrome in one child, and an average of 1.8 reportable variants per child for carrier results. These results highlight the benefits and limitations of using genomic sequencing for NBS and the challenges of using such technology in future precision medicine approaches.
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Affiliation(s)
- Tamara S Roman
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Stephanie B Crowley
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Myra I Roche
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Department of Pediatrics, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA
| | - Ann Katherine M Foreman
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Julianne M O'Daniel
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Bryce A Seifert
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Kristy Lee
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Alicia Brandt
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Chelsea Gustafson
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Daniela M DeCristo
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Natasha T Strande
- Department of Pathology and Laboratory Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Lori Ramkissoon
- Department of Pathology and Laboratory Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Laura V Milko
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Phillips Owen
- Renaissance Computing Institute, Chapel Hill, NC 27517, USA
| | - Sayanty Roy
- Department of Pathology and Laboratory Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Mai Xiong
- Department of Pathology and Laboratory Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Ryan S Paquin
- Center for Communication Science, RTI International, Research Triangle Park, NC 27709, USA
| | - Rita M Butterfield
- Department of Family Medicine and Community Health, Duke University School of Medicine, Durham, NC 27705, USA
| | - Megan A Lewis
- Center for Communication Science, RTI International, Research Triangle Park, NC 27709, USA
| | - Katherine J Souris
- Department of Health Behavior, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Donald B Bailey
- Genomics, Bioinformatics and Translational Research Center, RTI International, Research Triangle Park, NC 27709, USA
| | - Christine Rini
- Feinberg School of Medicine, Department of Medical Social Sciences, and the Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL 60611, USA
| | - Jessica K Booker
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Department of Pathology and Laboratory Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Bradford C Powell
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Karen E Weck
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Department of Pathology and Laboratory Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Cynthia M Powell
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Department of Pediatrics, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA
| | - Jonathan S Berg
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
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40
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Smith LD, Bainbridge MN, Parad RB, Bhattacharjee A. Second Tier Molecular Genetic Testing in Newborn Screening for Pompe Disease: Landscape and Challenges. Int J Neonatal Screen 2020; 6:32. [PMID: 32352041 PMCID: PMC7189780 DOI: 10.3390/ijns6020032] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Accepted: 04/03/2020] [Indexed: 02/06/2023] Open
Abstract
Pompe disease (PD) is screened by a two tier newborn screening (NBS) algorithm, the first tier of which is an enzymatic assay performed on newborn dried blood spots (DBS). As first tier enzymatic screening tests have false positive results, an immediate second tier test on the same sample is critical in resolving newborn health status. Two methodologies have been proposed for second tier testing: (a) measurement of enzymatic activities such as of Creatine/Creatinine over alpha-glucosidase ratio, and (b) DNA sequencing (a molecular genetics approach), such as targeted next generation sequencing. (tNGS). In this review, we discuss the tNGS approach, as well as the challenges in providing second tier screening and follow-up care. While tNGS can predict genotype-phenotype effects when known, these advantages may be diminished when the variants are novel, of unknown significance or not discoverable by current test methodologies. Due to the fact that criticisms of screening algorithms that utilize tNGS are based on perceived complexities, including variant detection and interpretation, we clarify the actual limitations and present the rationale that supports optimizing a molecular genetic testing approach with tNGS. Second tier tNGS can benefit clinical decision-making through the use of the initial NBS DBS punch and rapid turn-around time methodology for tNGS, that includes copy number variant analysis, variant effect prediction, and variant 'cut-off' tools for the reduction of false positive results. The availability of DNA sequence data will contribute to the improved understanding of genotype-phenotype associations and application of treatment. The ultimate goal of second tier testing should enable the earliest possible diagnosis for the earliest initiation of the most effective clinical interventions in infants with PD.
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Affiliation(s)
- Laurie D. Smith
- Department of Pediatrics, UNC Hospitals, Chapel Hill, NC 27599, USA;
- Laboratory Services Division, Baebies, Inc., Durham, NC 27709, USA
| | - Matthew N. Bainbridge
- Codified Genomics, Houston, TX 77004, USA;
- Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123, USA
| | - Richard B. Parad
- Department of Pediatric Newborn Medicine, Brigham & Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
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41
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Amor DJ, Chitty LS, Van den Veyver IB. Current controversies in prenatal diagnosis 2: The 59 genes ACMG recommends reporting as secondary findings when sequencing postnatally should be reported when detected on fetal (and parental) sequencing. Prenat Diagn 2020; 40:1508-1514. [PMID: 32091628 DOI: 10.1002/pd.5670] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Revised: 12/23/2019] [Accepted: 12/26/2019] [Indexed: 12/13/2022]
Abstract
Genome sequencing is increasingly being used to aid genetic diagnosis in fetuses with structural abnormalities detected on ultrasound examination. However, with clinical exome and genome sequencing, there is potential for the recognition and reporting of incidental or secondary findings unrelated to the indication for ordering the sequencing, but of potential medical value for patient care. In the postnatal setting, the American College of Medical Genetics and Genomics (ACMG) has clear guidelines that state that when offering sequencing, secondary findings should be reported in 59 genes for which ACMG consider there is a clinical evidence that pathogenic variants may result in disease that might be prevented or treated, with the option to opt out of receiving this information. However, these guidelines specifically exclude prenatal sequencing. Here, we report the debate on whether or not pathogenic findings in these 59 genes should or should not be reported in the prenatal setting. Although more were in favour of reporting before the debate, there was no significant consensus from the audience. After the debate there was a swing toward not reporting, but a slim majority (55%) remained in favour, indicating that this is an area requiring further research and the development of evidence-based guidelines applicable to prenatal proband and trio sequencing.
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Affiliation(s)
- David J Amor
- Department of Paediatrics, Royal Children's Hospital, University of Melbourne, Melbourne, Victoria, USA.,Department of Paediatrics, Murdoch Children's Research Institute, Melbourne, Victoria, USA
| | - Lyn S Chitty
- Great Ormond Street NHS Foundation Trust and UCL GOS Institute of Child Health, London, UK
| | - Ignatia B Van den Veyver
- Department of Obstetrics and Gynecology, Baylor College of Medicine, Houston, Texas, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
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42
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A pediatric perspective on genomics and prevention in the twenty-first century. Pediatr Res 2020; 87:338-344. [PMID: 31578042 DOI: 10.1038/s41390-019-0597-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Accepted: 09/18/2019] [Indexed: 12/19/2022]
Abstract
We present evidence from diverse disciplines and populations to identify the current and emerging role of genomics in prevention from both medical and public health perspectives as well as key challenges and potential untoward consequences of increasing the role of genomics in these endeavors. We begin by comparing screening in healthy populations (newborn screening), with testing in symptomatic populations, which may incidentally identify secondary findings and at-risk relatives. Emerging evidence suggests that variants in genes subject to the reporting of secondary findings are more common than expected in patients who otherwise would not meet the criteria for testing and population testing for variants in these genes may more precisely identify discrete populations to target for various prevention strategies starting in childhood. Conversely, despite its theoretical promise, recent studies attempting to demonstrate benefits of next-generation sequencing for newborn screening have instead demonstrated numerous barriers and pitfalls to this approach. We also examine the special cases of pharmacogenomics and polygenic risk scores as examples of ways genomics can contribute to prevention amongst a broader population than that affected by rare Mendelian disease. We conclude with unresolved questions which will benefit from future investigations of the role of genomics in disease prevention.
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43
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Milko LV, Chen F, Chan K, Brower AM, Agrawal PB, Beggs AH, Berg JS, Brenner SE, Holm IA, Koenig BA, Parad RB, Powell CM, Kingsmore SF. FDA oversight of NSIGHT genomic research: the need for an integrated systems approach to regulation. NPJ Genom Med 2019; 4:32. [PMID: 31839987 PMCID: PMC6904743 DOI: 10.1038/s41525-019-0105-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Accepted: 11/04/2019] [Indexed: 11/12/2022] Open
Abstract
The National Institutes of Health (NIH) funded the Newborn Sequencing In Genomic medicine and public HealTh (NSIGHT) Consortium to investigate the implications, challenges, and opportunities associated with the possible use of genomic sequence information in the newborn period. Following announcement of the NSIGHT awardees in 2013, the Food and Drug Administration (FDA) contacted investigators and requested that pre-submissions to investigational device exemptions (IDE) be submitted for the use of genomic sequencing under Title 21 of the Code of Federal Regulations (21 CFR) part 812. IDE regulation permits clinical investigation of medical devices that have not been approved by the FDA. To our knowledge, this marked the first time the FDA determined that NIH-funded clinical genomic research projects are subject to IDE regulation. Here, we review the history of and rationale behind FDA oversight of clinical research and the NSIGHT Consortium's experiences in navigating the IDE process. Overall, NSIGHT investigators found that FDA's application of existing IDE regulations and medical device definitions aligned imprecisely with the aims of publicly funded exploratory clinical research protocols. IDE risk assessments by the FDA were similar to, but distinct from, protocol risk assessments conducted by local Institutional Review Boards (IRBs), and had the potential to reflect novel oversight of emerging genomic technologies. However, the pre-IDE and IDE process delayed the start of NSIGHT research studies by an average of 10 months, and significantly limited the scope of investigation in two of the four NIH approved projects. Based on the experience of the NSIGHT Consortium, we conclude that policies and practices governing the development and use of novel genomic technologies in clinical research urgently need clarification in order to mitigate potentially conflicting or redundant oversight by IRBs, NIH, FDA, and state authorities.
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Affiliation(s)
- Laura V. Milko
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599 USA
| | - Flavia Chen
- Institute for Human Genetics, University of California, San Francisco, CA 94143 USA
- Program in Bioethics, University of California, San Francisco, CA 94118 USA
| | - Kee Chan
- Department of Health Policy and Administration, University of Illinois, Chicago, IL 60612 USA
| | - Amy M. Brower
- American College of Medical Genetics and Genomics, 7101 Wisconsin Avenue Suite 1101, Bethesda, MD 20814 USA
| | - Pankaj B. Agrawal
- Division of Genetics & Genomics, The Manton Center for Orphan Disease Research, Boston Children’s Hospital, Boston, MA 02115 USA
- Division of Newborn Medicine, Boston Children’s Hospital, Boston, MA 02115 USA
- Department of Pediatrics, Harvard Medical School, Boston, MA 02115 USA
| | - Alan H. Beggs
- Division of Genetics & Genomics, The Manton Center for Orphan Disease Research, Boston Children’s Hospital, Boston, MA 02115 USA
- Department of Pediatrics, Harvard Medical School, Boston, MA 02115 USA
| | - Jonathan S. Berg
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599 USA
| | - Steven E. Brenner
- Institute for Human Genetics, University of California, San Francisco, CA 94143 USA
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720 USA
| | - Ingrid A. Holm
- Division of Genetics & Genomics, The Manton Center for Orphan Disease Research, Boston Children’s Hospital, Boston, MA 02115 USA
- Department of Pediatrics, Harvard Medical School, Boston, MA 02115 USA
| | - Barbara A. Koenig
- Institute for Human Genetics, University of California, San Francisco, CA 94143 USA
- Program in Bioethics, University of California, San Francisco, CA 94118 USA
| | - Richard B. Parad
- Department of Pediatrics, Harvard Medical School, Boston, MA 02115 USA
- Department of Pediatric Newborn Medicine, Brigham and Women’s Hospital, Boston, MA 02115 USA
| | - Cynthia M. Powell
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599 USA
- Department of Pediatrics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599 USA
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44
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Hendricks-Sturrup RM, Linsky A, Lu CY, Vassy JL. Genomic testing is best integrated into clinical practice when it is actionable. Per Med 2019; 17:5-8. [PMID: 31795838 DOI: 10.2217/pme-2019-0106] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Rachele M Hendricks-Sturrup
- Department of Population Medicine, Harvard Pilgrim Health Care Institute, Boston, MA, USA.,Harvard Medical School, Boston, MA, USA
| | - Amy Linsky
- Boston University School of Medicine, Boston, MA, USA.,VA Boston Healthcare System, Boston, MA, USA
| | - Christine Y Lu
- Department of Population Medicine, Harvard Pilgrim Health Care Institute, Boston, MA, USA.,Harvard Medical School, Boston, MA, USA
| | - Jason L Vassy
- Harvard Medical School, Boston, MA, USA.,VA Boston Healthcare System, Boston, MA, USA
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45
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Hendricks-Sturrup RM, Lu CY. When should genomic and exome sequencing be implemented in newborns? A call for an update to newborn screening guidelines. Genet Med 2019; 22:809-810. [PMID: 31767983 DOI: 10.1038/s41436-019-0707-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Accepted: 11/12/2019] [Indexed: 12/19/2022] Open
Affiliation(s)
- Rachele M Hendricks-Sturrup
- Department of Population Medicine, Harvard Pilgrim Health Care Institute and Harvard Medical School, Boston, MA, USA.
| | - Christine Y Lu
- Department of Population Medicine, Harvard Pilgrim Health Care Institute and Harvard Medical School, Boston, MA, USA
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46
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Large Scale Next Generation Sequencing and Newborn Screening: Are We Ready? J Pediatr 2019; 209:9-10. [PMID: 30819502 DOI: 10.1016/j.jpeds.2019.01.037] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Accepted: 01/18/2019] [Indexed: 01/10/2023]
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