1
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Owens CEL, Tan O, Kuroiwa-Trzmielina J, Shrestha RN, O'Brien T, Tyrrell V, Schofield DJ. The economic costs of precision medicine for clinical translational research among children with high-risk cancer. NPJ Precis Oncol 2024; 8:224. [PMID: 39367129 PMCID: PMC11452525 DOI: 10.1038/s41698-024-00711-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Accepted: 09/17/2024] [Indexed: 10/06/2024] Open
Abstract
Embedding precision medicine in paediatric oncology shows promise to have a positive impact on how children with cancer will be treated in the future. While there are a number of studies of precision medicine in childhood cancer, there is limited evidence available on the cost of implementing the related testing. This is the first Australian study that systematically measures the cost of using precision medicine in the care of high-risk childhood cancers, through the Zero Childhood Cancer Precision Medicine Programme. In 2021 Australian dollars, the estimated costs inclusive of genomic and preclinical testing were: (A) $12,743 per patient for access; (B) $14,262 per identification of molecular cause; and (C) $21,769 per MTB recommendation. The information gained supports the understanding of the cost of reporting clinically significant outcomes relevant to the biology of the tumour, diagnosis, prognosis and potentially improving clinical management for a child.
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Affiliation(s)
- Christopher E L Owens
- Centre for Economic Impacts of Genomic Medicine, Macquarie Business School, Macquarie University, Sydney, NSW, Australia
| | - Owen Tan
- Centre for Economic Impacts of Genomic Medicine, Macquarie Business School, Macquarie University, Sydney, NSW, Australia
| | | | - Rupendra N Shrestha
- Centre for Economic Impacts of Genomic Medicine, Macquarie Business School, Macquarie University, Sydney, NSW, Australia.
| | - Tracey O'Brien
- School of Clinical Medicine, UNSW Medicine & Health, UNSW Sydney, Kensington, NSW, Australia
- Kids Cancer Centre, Sydney Children's Hospital, Randwick, NSW, Australia
| | - Vanessa Tyrrell
- Children's Cancer Institute, Sydney, NSW, Australia
- School of Clinical Medicine, UNSW Medicine & Health, UNSW Sydney, Kensington, NSW, Australia
| | - Deborah J Schofield
- Centre for Economic Impacts of Genomic Medicine, Macquarie Business School, Macquarie University, Sydney, NSW, Australia.
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2
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McCorkell G, Nisselle A, Halton D, Bouffler SE, Patel C, Christodoulou J, Maher F, McClaren B, Brett GR, Sandaradura S, Boggs K, de Silva MG, Lynch F, Macciocca I, Lynch E, Martyn M, Best S, Stark Z, Gaff CL. A national education program for rapid genomics in pediatric acute care: Building workforce confidence, competence, and capability. Genet Med 2024; 26:101224. [PMID: 39092589 DOI: 10.1016/j.gim.2024.101224] [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: 01/01/2024] [Revised: 07/23/2024] [Accepted: 07/24/2024] [Indexed: 08/04/2024] Open
Abstract
PURPOSE To develop and evaluate a scalable national program to build confidence, competence and capability in the use of rapid genomic testing (rGT) in the acute pediatric setting. METHODS We used theory-informed approaches to design a modular, adaptive program of blended learning aimed at diverse professional groups involved in acute pediatric care. The program comprised 4 online learning modules and an online workshop and was centered on case-based learning. We evaluated the program using the Kirkpatrick 4-level model of training evaluation and report our findings using the Reporting Item Standards for Education and its Evaluation (RISE2) guidelines for genomics education and evaluation. RESULTS Two hundred and two participants engaged with at least 1 component of the program. Participants self-reported increased confidence in using rGT, (P < .001), and quiz responses objectively demonstrated increased competence (eg, correct responses to a question on pretest counseling increased from 30% to 64%; P < .001). Additionally, their capability in applying genomic principles to simulated clinical cases increased (P < .001), as did their desire to take on more responsibility for performing rGT. The clinical interpretation of more complex test results (such as negative results or variants of uncertain significance) appeared to be more challenging, indicating a need for targeted education in this area. CONCLUSION The program format was effective in delivering multidisciplinary and wide-scale genomics education in the acute care context. The modular approach we have developed now lends itself to application in other medical specialties or areas of health care.
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Affiliation(s)
- Giulia McCorkell
- Australian Genomics, Melbourne, Australia; The University of Melbourne, Melbourne, Australia; Royal Melbourne Institute of Technology, Melbourne, Australia; Murdoch Children's Research Institute, Melbourne, Australia
| | - Amy Nisselle
- The University of Melbourne, Melbourne, Australia; Murdoch Children's Research Institute, Melbourne, Australia; Melbourne Genomics Health Alliance, Melbourne, Australia
| | - Donna Halton
- Australian Genomics, Melbourne, Australia; The University of Melbourne, Melbourne, Australia; Melbourne Genomics Health Alliance, Melbourne, Australia
| | - Sophie E Bouffler
- Australian Genomics, Melbourne, Australia; Murdoch Children's Research Institute, Melbourne, Australia
| | - Chirag Patel
- Genetic Health Queensland, Royal Brisbane and Women's Hospital, Brisbane, Australia
| | - John Christodoulou
- The University of Melbourne, Melbourne, Australia; Murdoch Children's Research Institute, Melbourne, Australia
| | - Fran Maher
- The University of Melbourne, Melbourne, Australia; Murdoch Children's Research Institute, Melbourne, Australia; Melbourne Genomics Health Alliance, Melbourne, Australia; WEHI, Melbourne, Australia
| | - Belinda McClaren
- The University of Melbourne, Melbourne, Australia; Murdoch Children's Research Institute, Melbourne, Australia; Melbourne Genomics Health Alliance, Melbourne, Australia
| | - Gemma R Brett
- The University of Melbourne, Melbourne, Australia; Victorian Clinical Genetics Services, Melbourne, Australia
| | - Sarah Sandaradura
- Sydney Children's Hospitals Network-Westmead, Sydney, Australia; University of Sydney, Sydney, Australia
| | - Kirsten Boggs
- Australian Genomics, Melbourne, Australia; Sydney Children's Hospitals Network-Westmead, Sydney, Australia; Sydney Children's Hospitals Network-Randwick, Sydney, Australia
| | - Michelle G de Silva
- The University of Melbourne, Melbourne, Australia; Murdoch Children's Research Institute, Melbourne, Australia; Victorian Clinical Genetics Services, Melbourne, Australia
| | - Fiona Lynch
- The University of Melbourne, Melbourne, Australia; Murdoch Children's Research Institute, Melbourne, Australia
| | - Ivan Macciocca
- The University of Melbourne, Melbourne, Australia; Victorian Clinical Genetics Services, Melbourne, Australia
| | - Elly Lynch
- Melbourne Genomics Health Alliance, Melbourne, Australia; Victorian Clinical Genetics Services, Melbourne, Australia
| | - Melissa Martyn
- The University of Melbourne, Melbourne, Australia; Murdoch Children's Research Institute, Melbourne, Australia; Melbourne Genomics Health Alliance, Melbourne, Australia
| | - Stephanie Best
- Australian Genomics, Melbourne, Australia; Department of Health Services Research, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Zornitza Stark
- Australian Genomics, Melbourne, Australia; The University of Melbourne, Melbourne, Australia; Victorian Clinical Genetics Services, Melbourne, Australia.
| | - Clara L Gaff
- The University of Melbourne, Melbourne, Australia; Murdoch Children's Research Institute, Melbourne, Australia; Melbourne Genomics Health Alliance, Melbourne, Australia
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3
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Bhatia S, Pal S, Kulshrestha S, Gupta D, Soni A, Saxena R, Bijarnia-Mahay S, Verma IC, Puri RD. Role of next generation sequencing in diagnosis and management of critically ill children with suspected monogenic disorder. Eur J Hum Genet 2024; 32:1106-1115. [PMID: 38605122 PMCID: PMC11369102 DOI: 10.1038/s41431-024-01569-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 01/19/2024] [Accepted: 02/12/2024] [Indexed: 04/13/2024] Open
Abstract
Next generation sequencing based diagnosis has emerged as a promising tool for evaluating critically ill neonates and children. However, there is limited data on its utility in developing countries. We assessed its diagnostic rate and clinical impact on management of pediatric patients with a suspected genetic disorder requiring critical care. The study was conducted at a single tertiary hospital in Northern India. We analyzed 70 children with an illness requiring intensive care and obtained a precise molecular diagnosis in 32 of 70 probands (45.3%) using diverse sequencing techniques such as clinical exome, whole exome, and whole genome. A significant change in clinical outcome was observed in 13 of 32 (40.6%) diagnosed probands with a change in medication in 11 subjects and redirection to palliative care in two subjects. Additional benefits included specific dietary management (three cases), avoidance of a major procedure (one case) and better reproductive counseling. Dramatic therapeutic responses were observed in three cases with SCN1A, SCN2A and KCNQ2-related epileptic encephalopathy. A delayed turn-around for sequencing results was perceived as a major limiting factor in the study, as rapid and ultra-rapid sequencing was not available. Achieving a precise molecular diagnosis has great utility in managing critically ill patients with suspected genetic disorders in developing countries.
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Affiliation(s)
- Sameer Bhatia
- Institute of Medical Genetics and Genomics, Sir Ganga Ram Hospital, New Delhi, India
| | - Swasti Pal
- Institute of Medical Genetics and Genomics, Sir Ganga Ram Hospital, New Delhi, India
| | - Samarth Kulshrestha
- Institute of Medical Genetics and Genomics, Sir Ganga Ram Hospital, New Delhi, India
| | - Dhiren Gupta
- Department of Paediatrics, Institute of Child Health, Sir Ganga Ram Hospital, New Delhi, India
| | - Arun Soni
- Department of Neonatology, Institute of Child Health, Sir Ganga Ram Hospital, New Delhi, India
| | - Renu Saxena
- Institute of Medical Genetics and Genomics, Sir Ganga Ram Hospital, New Delhi, India
| | - Sunita Bijarnia-Mahay
- Institute of Medical Genetics and Genomics, Sir Ganga Ram Hospital, New Delhi, India
| | - Ishwar Chander Verma
- Institute of Medical Genetics and Genomics, Sir Ganga Ram Hospital, New Delhi, India
| | - Ratna Dua Puri
- Institute of Medical Genetics and Genomics, Sir Ganga Ram Hospital, New Delhi, India.
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4
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Do TT, Martyn M, McClaren B, McEwen A, Gaff C. Becoming agents for genomic change: genetic counsellors' views of patient care and implementation influences when genomics is mainstreamed. Eur J Hum Genet 2024:10.1038/s41431-024-01686-9. [PMID: 39210048 DOI: 10.1038/s41431-024-01686-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Revised: 04/16/2024] [Accepted: 08/12/2024] [Indexed: 09/04/2024] Open
Abstract
Genetic counsellors (GCs) across the world are increasingly transitioning beyond clinical genetics services to meet the growing demands for genomic healthcare. This presents a unique opportunity for GCs to be 'genomic change agents' as they work in alternative models of care. Through various innovative models of mainstream care funded through a change program, we explored the views of GCs regarding their position as 'genomic change agents' and what may hinder or drive the success of their evolving roles. Guided by the Diffusion of Innovation Theory, we conducted qualitative interviews with all twelve GCs employed by the change program in different models of providing genomics across five specialties in Australia. Audio-recordings of all interviews were transcribed verbatim and analysed using inductive content analysis. Findings show that early in these new roles, participants held varied descriptions of 'genomics mainstreaming': some envisioned it as an end state exclusive to medical specialists practicing genomics while others saw the involvement of GCs as crucial. Participants believed they were uniquely positioned to expedite patient access to genomic testing and counselling and enhance medical specialists' capability to use genomics. Challenges included hesitancy of some medical specialists regarding the value of genomics in healthcare and potential tension arising from distinct perspectives and practice between genetic and non-genetic professionals. Participants anticipated a decline in the standard of care when non-genetic colleagues managed consent discussion and result disclosure. Our study underscores leadership support and peer connection with those in similar roles as essential elements for GCs' success in mainstream settings.
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Affiliation(s)
- Trang Thu Do
- Murdoch Children's Research Institute, Melbourne, VIC, Australia
- Melbourne Genomics Health Alliance, Melbourne, VIC, Australia
- University of Melbourne, Melbourne, VIC, Australia
| | - Melissa Martyn
- Murdoch Children's Research Institute, Melbourne, VIC, Australia
- Melbourne Genomics Health Alliance, Melbourne, VIC, Australia
- University of Melbourne, Melbourne, VIC, Australia
| | - Belinda McClaren
- Murdoch Children's Research Institute, Melbourne, VIC, Australia
- Melbourne Genomics Health Alliance, Melbourne, VIC, Australia
- University of Melbourne, Melbourne, VIC, Australia
| | - Alison McEwen
- Graduate School of Health, University of Technology Sydney, Sydney, NSW, Australia
| | - Clara Gaff
- Murdoch Children's Research Institute, Melbourne, VIC, Australia.
- Melbourne Genomics Health Alliance, Melbourne, VIC, Australia.
- University of Melbourne, Melbourne, VIC, Australia.
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5
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Friedrich B, Vindrola-Padros C, Lucassen AM, Patch C, Clarke A, Lakhanpaul M, Lewis C. "A very big challenge": a qualitative study to explore the early barriers and enablers to implementing a national genomic medicine service in England. Front Genet 2024; 14:1282034. [PMID: 38239852 PMCID: PMC10794539 DOI: 10.3389/fgene.2023.1282034] [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: 08/23/2023] [Accepted: 11/27/2023] [Indexed: 01/22/2024] Open
Abstract
Background: The Genomic Medicine Service (GMS) was launched in 2018 in England to create a step-change in the use of genomics in the NHS, including offering whole genome sequencing (WGS) as part of routine care. In this qualitative study on pediatric rare disease diagnosis, we used an implementation science framework to identify enablers and barriers which have influenced rollout. Methods: Semi-structured interviews were conducted with seven participants tasked with designing the GMS and 14 tasked with leading the implementation across the seven Genomic Medicine Service Alliances (GMSAs) and/or Genomic Laboratory Hubs (GLHs) between October 2021 and February 2022. Results: Overall, those involved in delivering the service strongly support its aims and ambitions. Challenges include: 1) concerns around the lack of trained and available workforce (clinicians and scientists) to seek consent from patients, interpret findings and communicate results; 2) the lack of a digital, coordinated infrastructure in place to support and standardize delivery with knock-on effects including onerous administrative aspects required to consent patients and order WGS tests; 3) that the "mainstreaming agenda", whilst considered important, encountered reluctance to become engaged from those who did not see it as a priority or viewed it as being politically rather than clinically driven; 4) the timelines and targets set for the GMS were perceived by some as too ambitious. Interviewees discussed local adaptations and strategies employed to address the various challenges they had encountered, including 1) capacity-building, 2) employing genomic associates and other support staff to support the consent and test ordering process, 3) having "genomic champions" embedded in mainstream services to impart knowledge and best practice, 4) enhancing collaboration between genetic and mainstream specialties, 5) building evaluation into the service and 6) co-creating services with patients and the public. Conclusion: Our findings highlight the challenges of implementing system-wide change within a complex healthcare system. Local as well as national solutions can undoubtedly address many of these barriers over time.
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Affiliation(s)
- Bettina Friedrich
- Population, Policy and Practice, UCL Great Ormond Street Institute of Child Health, London, United Kingdom
| | - Cecilia Vindrola-Padros
- Department of Targeted Intervention and Rapid Research Evaluation and Appraisal Lab (RREAL), University College London, London, United Kingdom
| | - Anneke M. Lucassen
- Clinical Ethics and Law, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
- Centre for Personalised Medicine, The Wellcome Centre for Human Genetics, Oxford, United Kingdom
| | - Chris Patch
- Engagement and Society, Wellcome Connecting Science Wellcome Genome Campus, Hinxton, United Kingdom
| | - Angus Clarke
- Division of Cancer and Genetics, Cardiff University School of Medicine, Cardiff, United Kingdom
| | - Monica Lakhanpaul
- Population, Policy and Practice, UCL Great Ormond Street Institute of Child Health, London, United Kingdom
| | - Celine Lewis
- Population, Policy and Practice, UCL Great Ormond Street Institute of Child Health, London, United Kingdom
- London North Genomic Laboratory Hub, London, United Kingdom
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6
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D'Gama AM, Agrawal PB. Genomic medicine in neonatal care: progress and challenges. Eur J Hum Genet 2023; 31:1357-1363. [PMID: 37789085 PMCID: PMC10689757 DOI: 10.1038/s41431-023-01464-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 09/01/2023] [Accepted: 09/13/2023] [Indexed: 10/05/2023] Open
Abstract
During the neonatal period, many genetic disorders present and contribute to neonatal morbidity and mortality. Genomic medicine-the use of genomic information in clinical care- has the potential to significantly reduce morbidity and mortality in the neonatal period and improve outcomes for this population. Diagnostic genomic testing for symptomatic newborns, especially rapid testing, has been shown to be feasible and have diagnostic and clinical utility, particularly in the short-term. Ongoing studies are assessing the feasibility and utility, including personal utility, of implementation in diverse populations. Genomic screening for asymptomatic newborns has also been studied, and the acceptability and feasibility of such an approach remains an active area of investigation. Emerging precision therapies, with examples even at the "n-of-1" level, highlight the promise of precision diagnostics to lead to early intervention and improve outcomes. To sustainably implement genomic medicine in neonatal care in an ethical, effective, and equitable manner, we need to ensure access to genetics and genomics knowledge, access to genomic tests, which is currently limited by payors, feasible processes for ordering these tests, and access to follow up in the clinical and research realms. Future studies will provide further insight into enablers and barriers to optimize implementation strategies.
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Affiliation(s)
- Alissa M D'Gama
- Division of Newborn Medicine, Department of Pediatrics, Boston Children's Hospital, Boston, MA, USA
- Epilepsy Genetics Program, Department of Neurology, Boston Children's Hospital, Boston, MA, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA
| | - Pankaj B Agrawal
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA.
- The Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA, USA.
- Division of Neonatology, Department of Pediatrics, University of Miami Miller School of Medicine, Holtz Children's Hospital, Jackson Health System, Miami, FL, USA.
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7
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D'Gama AM, Agrawal PB. Role of genomic medicine and implementing equitable access for critically ill infants in neonatal intensive care units. J Perinatol 2023; 43:963-967. [PMID: 36774516 PMCID: PMC9918837 DOI: 10.1038/s41372-023-01630-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 01/27/2023] [Accepted: 01/31/2023] [Indexed: 02/13/2023]
Abstract
Genetic disorders are a leading cause of morbidity and mortality in infants admitted to neonatal intensive care units. This population has immense potential to benefit from genomic medicine, as early precision diagnosis is critical to early personalized management. However, the implementation of genomic medicine in neonatology thus far has arguably worsened health inequities, and strategies are urgently needed to achieve equitable access to genomics in neonatal care. In this perspective, we demonstrate the utility of genomic sequencing in critically ill infants and highlight three key recommendations to advance equitable access: recruitment of underrepresented populations, education of non-genetics providers to empower practice of genomic medicine, and development of innovative infrastructure to implement genomic medicine across diverse settings.
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Affiliation(s)
- Alissa M D'Gama
- Epilepsy Genetics Program, Division of Epilepsy and Neurophysiology, Department of Neurology, Boston Children's Hospital, Boston, MA, USA
- Neonatal Genomics Program, Division of Newborn Medicine, Boston Children's Hospital, Boston, MA, USA
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Pankaj B Agrawal
- Neonatal Genomics Program, Division of Newborn Medicine, Boston Children's Hospital, Boston, MA, USA.
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA.
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA.
- The Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
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8
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Lunke S, Bouffler SE, Patel CV, Sandaradura SA, Wilson M, Pinner J, Hunter MF, Barnett CP, Wallis M, Kamien B, Tan TY, Freckmann ML, Chong B, Phelan D, Francis D, Kassahn KS, Ha T, Gao S, Arts P, Jackson MR, Scott HS, Eggers S, Rowley S, Boggs K, Rakonjac A, Brett GR, de Silva MG, Springer A, Ward M, Stallard K, Simons C, Conway T, Halman A, Van Bergen NJ, Sikora T, Semcesen LN, Stroud DA, Compton AG, Thorburn DR, Bell KM, Sadedin S, North KN, Christodoulou J, Stark Z. Integrated multi-omics for rapid rare disease diagnosis on a national scale. Nat Med 2023:10.1038/s41591-023-02401-9. [PMID: 37291213 PMCID: PMC10353936 DOI: 10.1038/s41591-023-02401-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Accepted: 05/12/2023] [Indexed: 06/10/2023]
Abstract
Critically ill infants and children with rare diseases need equitable access to rapid and accurate diagnosis to direct clinical management. Over 2 years, the Acute Care Genomics program provided whole-genome sequencing to 290 families whose critically ill infants and children were admitted to hospitals throughout Australia with suspected genetic conditions. The average time to result was 2.9 d and diagnostic yield was 47%. We performed additional bioinformatic analyses and transcriptome sequencing in all patients who remained undiagnosed. Long-read sequencing and functional assays, ranging from clinically accredited enzyme analysis to bespoke quantitative proteomics, were deployed in selected cases. This resulted in an additional 19 diagnoses and an overall diagnostic yield of 54%. Diagnostic variants ranged from structural chromosomal abnormalities through to an intronic retrotransposon, disrupting splicing. Critical care management changed in 120 diagnosed patients (77%). This included major impacts, such as informing precision treatments, surgical and transplant decisions and palliation, in 94 patients (60%). Our results provide preliminary evidence of the clinical utility of integrating multi-omic approaches into mainstream diagnostic practice to fully realize the potential of rare disease genomic testing in a timely manner.
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Affiliation(s)
- Sebastian Lunke
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
- Medicine, Dentistry and Health Sciences, University of Melbourne, Melbourne, Victoria, Australia
- Australian Genomics, Melbourne, Victoria, Australia
| | | | - Chirag V Patel
- Genetic Health Queensland, Royal Brisbane and Women's Hospital, Brisbane, Queensland, Australia
| | - Sarah A Sandaradura
- Sydney Children's Hospitals Network - Westmead, Sydney, New South Wales, Australia
- Children's Hospital Westmead Clinical School, University of Sydney, Sydney, New South Wales, Australia
| | - Meredith Wilson
- Sydney Children's Hospitals Network - Westmead, Sydney, New South Wales, Australia
- Children's Hospital Westmead Clinical School, University of Sydney, Sydney, New South Wales, Australia
| | - Jason Pinner
- Sydney Children's Hospitals Network - Randwick, Sydney, New South Wales, Australia
- Medicine and Health, University of New South Wales, Sydney, New South Wales, Australia
| | - Matthew F Hunter
- Monash Genetics, Monash Health, Melbourne, Victoria, Australia
- Department of Paediatrics, Monash University, Melbourne, Victoria, Australia
| | - Christopher P Barnett
- Paediatric and Reproductive Genetics Unit, Women's and Children's Hospital, North Adelaide, South Australia, Australia
- Department of Genetics and Molecular Pathology, SA Pathology, Adelaide, South Australia, Australia
- Adelaide Medical School, The University of Adelaide, Adelaide, South Australia, Australia
| | - Mathew Wallis
- Tasmanian Clinical Genetics Service, Tasmanian Health Service, Hobart, Tasmania, Australia
- School of Medicine and Menzies Institute for Medical Research, University of Tasmania, Hobart, Tasmania, Australia
| | - Benjamin Kamien
- Genetic Services of Western Australia, Perth, Western Australia, Australia
| | - Tiong Y Tan
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
- Medicine, Dentistry and Health Sciences, University of Melbourne, Melbourne, Victoria, Australia
| | - Mary-Louise Freckmann
- Department of Clinical Genetics, The Canberra Hospital, Canberra, Australian Capital Territory, Australia
| | - Belinda Chong
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Dean Phelan
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - David Francis
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Karin S Kassahn
- Department of Genetics and Molecular Pathology, SA Pathology, Adelaide, South Australia, Australia
- Adelaide Medical School, The University of Adelaide, Adelaide, South Australia, Australia
| | - Thuong Ha
- Department of Genetics and Molecular Pathology, SA Pathology, Adelaide, South Australia, Australia
- Centre for Cancer Biology, An alliance between SA Pathology and the University of South Australia, Adelaide, South Australia
- UniSA Clinical and Health Sciences, University of South Australia, Adelaide, South Australia, Australia
| | - Song Gao
- Department of Genetics and Molecular Pathology, SA Pathology, Adelaide, South Australia, Australia
| | - Peer Arts
- Department of Genetics and Molecular Pathology, SA Pathology, Adelaide, South Australia, Australia
- Adelaide Medical School, The University of Adelaide, Adelaide, South Australia, Australia
- Centre for Cancer Biology, An alliance between SA Pathology and the University of South Australia, Adelaide, South Australia
- UniSA Clinical and Health Sciences, University of South Australia, Adelaide, South Australia, Australia
| | - Matilda R Jackson
- Australian Genomics, Melbourne, Victoria, Australia
- Department of Genetics and Molecular Pathology, SA Pathology, Adelaide, South Australia, Australia
| | - Hamish S Scott
- Australian Genomics, Melbourne, Victoria, Australia
- Department of Genetics and Molecular Pathology, SA Pathology, Adelaide, South Australia, Australia
- Adelaide Medical School, The University of Adelaide, Adelaide, South Australia, Australia
- Centre for Cancer Biology, An alliance between SA Pathology and the University of South Australia, Adelaide, South Australia
- UniSA Clinical and Health Sciences, University of South Australia, Adelaide, South Australia, Australia
| | - Stefanie Eggers
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Simone Rowley
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Kirsten Boggs
- Australian Genomics, Melbourne, Victoria, Australia
- Sydney Children's Hospitals Network - Westmead, Sydney, New South Wales, Australia
- Sydney Children's Hospitals Network - Randwick, Sydney, New South Wales, Australia
| | - Ana Rakonjac
- Australian Genomics, Melbourne, Victoria, Australia
- Sydney Children's Hospitals Network - Westmead, Sydney, New South Wales, Australia
- Sydney Children's Hospitals Network - Randwick, Sydney, New South Wales, Australia
| | - Gemma R Brett
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
- Medicine, Dentistry and Health Sciences, University of Melbourne, Melbourne, Victoria, Australia
| | - Michelle G de Silva
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
- Medicine, Dentistry and Health Sciences, University of Melbourne, Melbourne, Victoria, Australia
- Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Amanda Springer
- Monash Genetics, Monash Health, Melbourne, Victoria, Australia
- Department of Paediatrics, Monash University, Melbourne, Victoria, Australia
| | - Michelle Ward
- Genetic Services of Western Australia, Perth, Western Australia, Australia
| | - Kirsty Stallard
- Paediatric and Reproductive Genetics Unit, Women's and Children's Hospital, North Adelaide, South Australia, Australia
| | - Cas Simons
- Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Thomas Conway
- Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Andreas Halman
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Nicole J Van Bergen
- Medicine, Dentistry and Health Sciences, University of Melbourne, Melbourne, Victoria, Australia
- Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Tim Sikora
- Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Liana N Semcesen
- Medicine, Dentistry and Health Sciences, University of Melbourne, Melbourne, Victoria, Australia
| | - David A Stroud
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
- Medicine, Dentistry and Health Sciences, University of Melbourne, Melbourne, Victoria, Australia
- Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Alison G Compton
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
- Medicine, Dentistry and Health Sciences, University of Melbourne, Melbourne, Victoria, Australia
- Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - David R Thorburn
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
- Medicine, Dentistry and Health Sciences, University of Melbourne, Melbourne, Victoria, Australia
- Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Katrina M Bell
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
- Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Simon Sadedin
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
- Medicine, Dentistry and Health Sciences, University of Melbourne, Melbourne, Victoria, Australia
- Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Kathryn N North
- Medicine, Dentistry and Health Sciences, University of Melbourne, Melbourne, Victoria, Australia
- Australian Genomics, Melbourne, Victoria, Australia
- Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - John Christodoulou
- Medicine, Dentistry and Health Sciences, University of Melbourne, Melbourne, Victoria, Australia
- Australian Genomics, Melbourne, Victoria, Australia
- Children's Hospital Westmead Clinical School, University of Sydney, Sydney, New South Wales, Australia
- Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Zornitza Stark
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Victoria, Australia.
- Medicine, Dentistry and Health Sciences, University of Melbourne, Melbourne, Victoria, Australia.
- Australian Genomics, Melbourne, Victoria, Australia.
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9
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Owen MJ, Wright MS, Batalov S, Kwon Y, Ding Y, Chau KK, Chowdhury S, Sweeney NM, Kiernan E, Richardson A, Batton E, Baer RJ, Bandoli G, Gleeson JG, Bainbridge M, Chambers CD, Kingsmore SF. Reclassification of the Etiology of Infant Mortality With Whole-Genome Sequencing. JAMA Netw Open 2023; 6:e2254069. [PMID: 36757698 PMCID: PMC9912130 DOI: 10.1001/jamanetworkopen.2022.54069] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Accepted: 11/27/2022] [Indexed: 02/10/2023] Open
Abstract
Importance Understanding the causes of infant mortality shapes public health, surveillance, and research investments. However, the association of single-locus (mendelian) genetic diseases with infant mortality is poorly understood. Objective To determine the association of genetic diseases with infant mortality. Design, Setting, and Participants This cohort study was conducted at a large pediatric hospital system in San Diego County (California) and included 546 infants (112 infant deaths [20.5%] and 434 infants [79.5%] with acute illness who survived; age, 0 to 1 year) who underwent diagnostic whole-genome sequencing (WGS) between January 2015 and December 2020. Data analysis was conducted between 2015 and 2022. Exposure Infants underwent WGS either premortem or postmortem with semiautomated phenotyping and diagnostic interpretation. Main Outcomes and Measures Proportion of infant deaths associated with single-locus genetic diseases. Results Among 112 infant deaths (54 girls [48.2%]; 8 [7.1%] African American or Black, 1 [0.9%] American Indian or Alaska Native, 8 [7.1%] Asian, 48 [42.9%] Hispanic, 1 [0.9%] Native Hawaiian or Pacific Islander, and 34 [30.4%] White infants) in San Diego County between 2015 and 2020, single-locus genetic diseases were the most common identifiable cause of infant mortality, with 47 genetic diseases identified in 46 infants (41%). Thirty-nine (83%) of these diseases had been previously reported to be associated with childhood mortality. Twenty-eight death certificates (62%) for 45 of the 46 infants did not mention a genetic etiology. Treatments that can improve outcomes were available for 14 (30%) of the genetic diseases. In 5 of 7 infants in whom genetic diseases were identified postmortem, death might have been avoided had rapid, diagnostic WGS been performed at time of symptom onset or regional intensive care unit admission. Conclusions and Relevance In this cohort study of 112 infant deaths, the association of genetic diseases with infant mortality was higher than previously recognized. Strategies to increase neonatal diagnosis of genetic diseases and immediately implement treatment may decrease infant mortality. Additional study is required to explore the generalizability of these findings and measure reduction in infant mortality.
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Affiliation(s)
- Mallory J. Owen
- Rady Children’s Institute for Genomic Medicine, Rady Children’s Hospital, San Diego, California
- Department of Pediatrics, University of California, San Diego, La Jolla
| | - Meredith S. Wright
- Rady Children’s Institute for Genomic Medicine, Rady Children’s Hospital, San Diego, California
| | - Sergey Batalov
- Rady Children’s Institute for Genomic Medicine, Rady Children’s Hospital, San Diego, California
| | - Yonghyun Kwon
- Rady Children’s Institute for Genomic Medicine, Rady Children’s Hospital, San Diego, California
| | - Yan Ding
- Rady Children’s Institute for Genomic Medicine, Rady Children’s Hospital, San Diego, California
| | - Kevin K. Chau
- Rady Children’s Institute for Genomic Medicine, Rady Children’s Hospital, San Diego, California
| | - Shimul Chowdhury
- Rady Children’s Institute for Genomic Medicine, Rady Children’s Hospital, San Diego, California
| | - Nathaly M. Sweeney
- Rady Children’s Institute for Genomic Medicine, Rady Children’s Hospital, San Diego, California
- Department of Pediatrics, University of California, San Diego, La Jolla
| | - Elizabeth Kiernan
- Rady Children’s Institute for Genomic Medicine, Rady Children’s Hospital, San Diego, California
| | - Andrew Richardson
- Rady Children’s Institute for Genomic Medicine, Rady Children’s Hospital, San Diego, California
| | - Emily Batton
- Department of Pediatrics, University of California, San Diego, La Jolla
| | - Rebecca J. Baer
- Department of Pediatrics, University of California, San Diego, La Jolla
- California Preterm Birth Initiative, University of California, San Francisco
| | - Gretchen Bandoli
- Department of Pediatrics, University of California, San Diego, La Jolla
| | - Joseph G. Gleeson
- Rady Children’s Institute for Genomic Medicine, Rady Children’s Hospital, San Diego, California
- Department of Pediatrics, University of California, San Diego, La Jolla
| | - Matthew Bainbridge
- Rady Children’s Institute for Genomic Medicine, Rady Children’s Hospital, San Diego, California
| | | | - Stephen F. Kingsmore
- Rady Children’s Institute for Genomic Medicine, Rady Children’s Hospital, San Diego, California
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10
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Wojcik MH, D'Gama AM, Agrawal PB. A model to implement genomic medicine in the neonatal intensive care unit. J Perinatol 2023; 43:248-252. [PMID: 35750755 PMCID: PMC9789202 DOI: 10.1038/s41372-022-01428-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 06/07/2022] [Accepted: 06/08/2022] [Indexed: 02/06/2023]
Abstract
Rapid genomic sequencing has been shown to have a high diagnostic yield for critically ill infants, with multiple research studies demonstrating both diagnostic and clinical utility. However, clinical implementation of rapid sequencing in the neonatal intensive care unit (NICU), as well as other aspects of genomic medicine such as precision therapy, may be challenging. We describe the Neonatal Genomics Program, developed at our institution as a multidisciplinary approach to improve clinical genetic diagnosis and outcomes for infants in our NICU through genomic medicine. The creation of a dedicated program implementing genomic medicine to improve care in the NICU allows not only for improved access to genomic sequencing for rapid diagnosis, but also advancement of rare disease research and precision therapeutics. Ongoing efforts will help to define an optimal approach to genomic medicine in the NICU context.
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Affiliation(s)
- Monica H Wojcik
- Division of Newborn Medicine, Department of Pediatrics, Boston Children's Hospital and Harvard Medical School, Boston, MA, USA.
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital and Harvard Medical School, Boston, MA, USA.
- The Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA, USA.
- The Broad Institute, Cambridge, MA, USA.
| | - Alissa M D'Gama
- Division of Newborn Medicine, Department of Pediatrics, Boston Children's Hospital and Harvard Medical School, Boston, MA, USA
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital and Harvard Medical School, Boston, MA, USA
- Epilepsy Genetics Program, Division of Epilepsy and Neurophysiology, Department of Neurology, Boston Children's Hospital and Harvard Medical School, Boston, MA, USA
| | - Pankaj B Agrawal
- Division of Newborn Medicine, Department of Pediatrics, Boston Children's Hospital and Harvard Medical School, Boston, MA, USA.
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital and Harvard Medical School, Boston, MA, USA.
- The Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA, USA.
- The Broad Institute, Cambridge, MA, USA.
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11
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How I treat thrombotic microangiopathy in the era of rapid genomics. Blood 2023; 141:147-155. [PMID: 36347020 DOI: 10.1182/blood.2022015583] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 09/08/2022] [Accepted: 11/01/2022] [Indexed: 11/10/2022] Open
Abstract
Thrombotic microangiopathy (TMA) encompasses various genetically-driven diseases. The emergence of ultrafast genomic sequencing has recently opened up new avenues of research for genetic investigations in the setting of intensive care units. TMA is likely to be a suitable focus for fast-track genomic sequencing. By establishing an expeditious molecular diagnosis of patients with the complement-dependent hemolytic uremic syndrome, fast-track genomic sequencing allows for the timely implementation or withdrawal of anti-C5 treatment while averting unnecessary, costly, and potentially harmful therapy in patients testing negative for the syndrome. Furthermore, genomics has the potential to reshape the taxonomic classification of TMA owing to comprehensive genomic analysis. The most significant results from such analysis can be categorized as (1) new descriptions of genetic diseases previously not recognized as associated with TMA and (2) an enrichment of the phenotypic spectrum of diseases traditionally related to TMA. The latter draws on the concept of retrophenotyping, wherein genomic investigation precedes full clinical description. By taking precedence over a phenotypic approach, an unbiased genomic-focused analysis maximizes the chances of discovering new descriptions of a given variant. Presented here are 4 cases of TMA which highlight these issues and substantiate the promise of fast-track genomic sequencing.
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12
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Owen MJ, Batalov S, Ellsworth KA, Wright M, Breeding S, Hugh K, Kingsmore SF, Ding Y. Rapid Whole Genome Sequencing for Diagnosis of Single Locus Genetic Diseases in Critically Ill Children. Methods Mol Biol 2023; 2621:217-239. [PMID: 37041447 DOI: 10.1007/978-1-0716-2950-5_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/13/2023]
Abstract
Upon admission to intensive care units (ICU), the differential diagnosis of almost all infants with diseases of unclear etiology includes single locus genetic diseases. Rapid whole genome sequencing (rWGS), including sample preparation, short-read sequencing-by-synthesis, informatics pipelining, and semiautomated interpretation, can now identify nucleotide and structural variants associated with most genetic diseases with robust analytic and diagnostic performance in as little as 13.5 h. Early diagnosis of genetic diseases transforms medical and surgical management of infants in ICUs, minimizing both the duration of empiric treatment and the delay to start of specific treatment. Both positive and negative rWGS tests have clinical utility and can improve outcomes. Since first described 10 years ago, rWGS has evolved considerably. Here we describe our current methods for routine diagnostic testing for genetic diseases by rWGS in as little as 18 h.
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Affiliation(s)
- Mallory J Owen
- Rady Children's Institute for Genomic Medicine, Rady Children's Hospital, San Diego, CA, USA
| | - Sergey Batalov
- Rady Children's Institute for Genomic Medicine, Rady Children's Hospital, San Diego, CA, USA
| | - Katarzyna A Ellsworth
- Rady Children's Institute for Genomic Medicine, Rady Children's Hospital, San Diego, CA, USA
| | - Meredith Wright
- Rady Children's Institute for Genomic Medicine, Rady Children's Hospital, San Diego, CA, USA
| | - Sylvia Breeding
- Rady Children's Institute for Genomic Medicine, Rady Children's Hospital, San Diego, CA, USA
| | - Kwon Hugh
- Rady Children's Institute for Genomic Medicine, Rady Children's Hospital, San Diego, CA, USA
| | - Stephen F Kingsmore
- Rady Children's Institute for Genomic Medicine, Rady Children's Hospital, San Diego, CA, USA.
| | - Yan Ding
- Rady Children's Institute for Genomic Medicine, Rady Children's Hospital, San Diego, CA, USA.
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13
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O'Shea R, Ma AS, Jamieson RV, Rankin NM. Precision medicine in Australia: now is the time to get it right. Med J Aust 2022; 217:559-563. [PMID: 36436133 PMCID: PMC10100177 DOI: 10.5694/mja2.51777] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 08/01/2022] [Accepted: 08/08/2022] [Indexed: 11/29/2022]
Affiliation(s)
| | - Alan S Ma
- University of Sydney, Sydney, NSW.,Western Sydney Genetics Program, Children's Hospital at Westmead, Sydney Children's Hospitals Network, Sydney, NSW
| | - Robyn V Jamieson
- University of Sydney, Sydney, NSW.,Western Sydney Genetics Program, Children's Hospital at Westmead, Sydney Children's Hospitals Network, Sydney, NSW
| | - Nicole M Rankin
- University of Sydney, Sydney, NSW.,Centre for Health Policy, University of Melbourne, Melbourne, VIC
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14
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Jezkova J, Shaw S, Taverner NV, Williams HJ. Rapid genome sequencing for pediatrics. Hum Mutat 2022; 43:1507-1518. [PMID: 36086948 PMCID: PMC9826377 DOI: 10.1002/humu.24466] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 08/30/2022] [Accepted: 09/06/2022] [Indexed: 01/11/2023]
Abstract
The advancements made in next-generation sequencing (NGS) technology over the past two decades have transformed our understanding of genetic variation in humans and had a profound impact on our ability to diagnose patients with rare genetic diseases. In this review, we discuss the recently developed application of rapid NGS techniques, used to diagnose pediatric patients with suspected rare diseases who are critically ill. We highlight the challenges associated with performing such clinical diagnostics tests in terms of the laboratory infrastructure, bioinformatic analysis pipelines, and the ethical considerations that need to be addressed. We end by looking at what future developments in this field may look like and how they can be used to augment the genetic data to further improve the diagnostic rates for these high-priority patients.
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Affiliation(s)
- Jana Jezkova
- All Wales Medical Genomics Service, Cardiff and Vale NHS TrustHeath HospitalCardiffUK
| | - Sophie Shaw
- All Wales Medical Genomics Service, Cardiff and Vale NHS TrustHeath HospitalCardiffUK
| | - Nicola V. Taverner
- All Wales Medical Genomics Service, Cardiff and Vale NHS TrustHeath HospitalCardiffUK,Centre for Medical Education, School of MedicineCardiff UniversityHeath ParkCardiffUK
| | - Hywel J. Williams
- Division of Cancer and Genetics, Genetic and Genomic Medicine, School of MedicineCardiff UniversityHeath ParkCardiffUK
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15
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Theory Designed Strategies to Support Implementation of Genomics in Nephrology. Genes (Basel) 2022; 13:genes13101919. [PMID: 36292804 PMCID: PMC9601730 DOI: 10.3390/genes13101919] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 10/14/2022] [Accepted: 10/18/2022] [Indexed: 11/17/2022] Open
Abstract
(1) Background: Genomic testing is increasingly utilized as a clinical tool; however, its integration into nephrology remains limited. The purpose of this study was to identify barriers and prioritize interventions for the widespread implementation of genomics in nephrology. (2) Methods: Qualitative, semi-structured interviews were conducted with 25 Australian adult nephrologists to determine their perspectives on interventions and models of care to support implementation of genomics in nephrology. Interviews were guided by a validated theoretical framework for the implementation of genomic medicine-the Consolidated Framework of Implementation Research (CFIR). (3) Results: Nephrologists were from 18 hospitals, with 7 having a dedicated multidisciplinary kidney genetics service. Most practiced in the public healthcare system (n = 24), a large number were early-career (n = 13), and few had genomics experience (n = 4). The top three preferred interventions were increased funding, access to genomics champions, and education and training. Where interventions to barriers were not reported, we used the CFIR/Expert Recommendations for Implementing Change matching tool to generate theory-informed approaches. The preferred model of service delivery was a multidisciplinary kidney genetics clinic. (4) Conclusions: This study identified surmountable barriers and practical interventions for the implementation of genomics in nephrology, with multidisciplinary kidney genetics clinics identified as the preferred model of care. The integration of genomics education into nephrology training, secure funding for testing, and counselling along with the identification of genomics champions should be pursued by health services more broadly.
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16
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Chad L, Anderson J, Cagliero D, Hayeems RZ, Ly LG, Szuto A. Rapid Genetic Testing in Pediatric and Neonatal Critical Care: A Scoping Review of Emerging Ethical Issues. Hosp Pediatr 2022; 12:e347-e359. [PMID: 36161483 DOI: 10.1542/hpeds.2022-006654] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
BACKGROUND Rapid genome-wide sequencing (rGWS) is being increasingly used to aid in prognostication and decision-making for critically ill newborns and children. Although its feasibility in this fast-paced setting has been described, this new paradigm of inpatient genetic care raises new ethical challenges. OBJECTIVE A scoping review was performed to (1) identify salient ethical issues in this area of practice; and (2) bring attention to gaps and ethical tensions that warrant more deliberate exploration. METHODS Data sources, Ovid Medline and Cochrane Central Register of Controlled Trials, were searched up to November 2021. Articles included were those in English relating to rGWS deployed rapidly in a critical care setting. Publications were examined for ethical themes and were further characterized as including a superficial or in-depth discussion of that theme. New themes were inductively identified as they emerged. RESULTS Ninety-nine studies, published in 2012 or thereafter, met inclusion criteria. Themes identified elaborated upon established ethical principles related to beneficence and nonmaleficence (ie, clinical utility, medical uncertainty, impact on family, and data security) autonomy (ie, informed consent), and justice (ie, resource allocation and disability rights). Many themes were only narrowly discussed. CONCLUSIONS The application of rGWS in neonatal and pediatric acute care is inherently tied to ethically charged issues, some of which are reported here. Attention to the ethical costs and benefits of rGWS is not always discussed, with important gaps and unanswered questions that call for ongoing focus on these ethical considerations in this next application of acute care genomics.
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Affiliation(s)
- Lauren Chad
- Divisions of Clinical and Metabolic Genetics.,Departments of Bioethics.,Departments of Paediatrics
| | | | | | - Robin Z Hayeems
- Child Health Evaluative Sciences, Hospital for Sick Children Research Institute,Toronto, Ontario, Canada.,Institute of Health Policy, Management, and Evaluation, University of Toronto,Toronto, Ontario, Canada
| | - Linh G Ly
- Neonatology.,Departments of Paediatrics
| | - Anna Szuto
- Genetic Counselling, Hospital for Sick Children,Toronto, Ontario, Canada.,Molecular Genetics
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17
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Smith J, Braithwaite J, O'Brien TA, Smith S, Tyrrell VJ, Mould EVA, Long JC, Rapport F. The Voices of Stakeholders Involved in Precision Medicine: The Co-Design and Evaluation of Qualitative Indicators of Intervention Acceptability, Fidelity and Context in PRecISion Medicine for Children With Cancer in Australia. QUALITATIVE HEALTH RESEARCH 2022; 32:1865-1880. [PMID: 36066496 DOI: 10.1177/10497323221120501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
We report a novel approach of amalgamating implementation outcomes of acceptability and fidelity alongside context as a new way of qualitatively evaluating implementation outcomes and context of a precision medicine intervention. A rapid qualitative online proforma was co-designed with stakeholders and sent to a purposive sample of healthcare professionals involved in an early-phase clinical trial intervention. Data were analysed using Framework Analysis. A total of 24 out of 68 proformas were returned. Although some participants raised concerns about drug medication access issues, the main intervention was well accepted and understood across professional groups. Comprehension was enhanced through exposure to specialist multidisciplinary meeting arrangements. In conclusion, a rapid data collection tool and framework are now available to assess readily measurable, qualitative indicators of acceptability, fidelity of receipt and contextual fit within the dynamic precision medicine context.
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Affiliation(s)
- James Smith
- Centre for Healthcare Resilience and Implementation Science, 208044Australian Institute of Health Innovation, Macquarie University, Sydney, NSW, Australia
| | - Jeffrey Braithwaite
- Centre for Healthcare Resilience and Implementation Science, 208044Australian Institute of Health Innovation, Macquarie University, Sydney, NSW, Australia
| | - Tracey A O'Brien
- Faculty of Medicine, School of Women's and Children's Health, 7800University of New South Wales, Sydney, NSW, Australia
- Kids Cancer Centre, Sydney Children's Hospital, Randwick, NSW, Australia
| | - Stephanie Smith
- School of Population Health, 1649Curtin University, Perth, WA, Australia
- School of Nursing and Midwifery, Edith Cowan University, Perth, WA, Australia
- Perth Children's Hospital, Nedlands, WA, Australia
| | - Vanessa J Tyrrell
- Children's Cancer Institute, 188680Lowy Cancer Research Centre, University of New South Wales, Randwick, NSW, Australia
| | - Emily V A Mould
- Children's Cancer Institute, 188680Lowy Cancer Research Centre, University of New South Wales, Randwick, NSW, Australia
| | - Janet C Long
- Centre for Healthcare Resilience and Implementation Science, 208044Australian Institute of Health Innovation, Macquarie University, Sydney, NSW, Australia
| | - Frances Rapport
- Centre for Healthcare Resilience and Implementation Science, 208044Australian Institute of Health Innovation, Macquarie University, Sydney, NSW, Australia
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18
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Integrating rapid exome sequencing into NICU clinical care after a pilot research study. NPJ Genom Med 2022; 7:51. [PMID: 36064943 PMCID: PMC9441819 DOI: 10.1038/s41525-022-00326-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 08/22/2022] [Indexed: 11/29/2022] Open
Abstract
Genomic sequencing is a powerful diagnostic tool in critically ill infants, but performing exome or genome sequencing (ES/GS) in the context of a research study is different from implementing these tests clinically. We investigated the integration of rapid ES into routine clinical care after a pilot research study in a Level IV Neonatal Intensive Care Unit (NICU). We performed a retrospective cohort analysis of infants admitted with suspected genetic disorders to the NICU from December 1, 2018 to March 31, 2021 and compared results to those obtained from a previous research study cohort (March 1, 2017 to November 30, 2018). Clinical rapid ES was performed in 80/230 infants (35%) with a suspected genetic disorder and identified a genetic diagnosis in 22/80 infants (28%). The majority of diagnoses acutely impacted clinical management (14/22 (64%)). Compared to the previous research study, clinically integrated rapid ES had a significantly lower diagnostic yield and increased time from NICU admission and genetics consult to ES report, but identified four genetic diagnoses that may have been missed by the research study selection criteria. Compared to other genetic tests, rapid ES had similar or higher diagnostic yield and similar or decreased time to result. Overall, rapid ES was utilized in the NICU after the pilot research study, often as the first-tier sequencing test, and could identify the majority of disease-causing variants, shorten the diagnostic odyssey, and impact clinical care. Based on our experience, we have identified strategies to optimize the clinical implementation of rapid ES in the NICU.
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19
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Stark Z, Ellard S. Rapid genomic testing for critically ill children: time to become standard of care? Eur J Hum Genet 2022; 30:142-149. [PMID: 34744166 PMCID: PMC8821543 DOI: 10.1038/s41431-021-00990-y] [Citation(s) in RCA: 36] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2021] [Accepted: 10/17/2021] [Indexed: 02/03/2023] Open
Abstract
Rapid genomic testing in critically ill neonatal and paediatric patients has transformed the paradigm of rare disease diagnosis, delivering results in real time to inform patient management. More than 20 studies totalling over 1500 patients from diverse healthcare settings worldwide have now been published, forming a compelling evidence base for healthcare system implementation. We review the reported diagnostic and clinical outcomes, as well as broader evaluations of family and professional experiences, cost effectiveness, implementation challenges and bioethical issues arising from rapid testing. As rapid genomic testing transitions from the research to the healthcare setting to become a 'standard of care' test, there is a need to develop effective service delivery models to support scalability at both the laboratory and clinical level and promote equity of access, prompt test initiation, integrated multidisciplinary input and holistic family support. Harnessing the high level of professional engagement with rapid genomic testing programmes will continue to drive innovation and adoption, while close integration with emerging precision medicine approaches will be necessary to deliver on the promise of reduced infant and child mortality.
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Affiliation(s)
- Zornitza Stark
- Australian Genomics, Melbourne, VIC Australia ,grid.1058.c0000 0000 9442 535XVictorian Clinical Genetics Services, Murdoch Children’s Research Institute, Melbourne, VIC Australia ,grid.1008.90000 0001 2179 088XDepartment of Paediatrics, University of Melbourne, Melbourne, VIC Australia
| | - Sian Ellard
- grid.419309.60000 0004 0495 6261Exeter Genomics Laboratory, South West Genomic Laboratory Hub, Royal Devon & Exeter NHS Foundation Trust, Exeter, UK ,grid.8391.30000 0004 1936 8024Institute of Biomedical and Clinical Science, University of Exeter Medical School, Exeter, UK
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20
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Lewis C, Buchanan J, Clarke A, Clement E, Friedrich B, Hastings-Ward J, Hill M, Horn R, Lucassen AM, Patch C, Pickard A, Roberts L, Sanderson SC, Wynn SL, Vindrola-Padros C, Lakhanpaul M. Mixed-methods evaluation of the NHS Genomic Medicine Service for paediatric rare diseases: study protocol. NIHR OPEN RESEARCH 2021; 1:23. [PMID: 35098132 PMCID: PMC7612282 DOI: 10.3310/nihropenres.13236.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Accepted: 11/09/2021] [Indexed: 11/22/2022]
Abstract
Background A new nationally commissioned NHS England Genomic Medicine Service (GMS) was recently established to deliver genomic testing with equity of access for patients affected by rare diseases and cancer. The overarching aim of this research is to evaluate the implementation of the GMS during its early years, identify barriers and enablers to successful implementation, and provide recommendations for practice. The focus will be on the use of genomic testing for paediatric rare diseases. Methods This will be a four-year mixed-methods research programme using clinic observations, interviews and surveys. Study 1 consists of qualitative interviews with designers/implementers of the GMS in Year 1 of the research programme, along with documentary analysis to understand the intended outcomes for the Service. These will be revisited in Year 4 to compare intended outcomes with what happened in practice, and to identify barriers and facilitators that were encountered along the way. Study 2 consists of clinic observations (pre-test counselling and results disclosure) to examine the interaction between health professionals and parents, along with follow-up interviews with both after each observation. Study 3 consists of a longitudinal survey with parents at two timepoints (time of testing and 12 months post-results) along with follow-up interviews, to examine parent-reported experiences and outcomes. Study 4 consists of qualitative interviews and a cross-sectional survey with medical specialists to identify preparedness, facilitators and challenges to mainstreaming genomic testing. The use of theory-based and pre-specified constructs will help generalise the findings and enable integration across the various sub-studies. Dissemination We will disseminate our results to policymakers as findings emerge, so any suggested changes to service provision can be considered in a timely manner. A workshop with key stakeholders will be held in Year 4 to develop and agree a set of recommendations for practice.
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Affiliation(s)
- Celine Lewis
- Population, Policy and Practice, UCL GOS Institute of Child Health, London, UK
- London North Genomic Laboratory Hub, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - James Buchanan
- Health Economics Research Centre, Nuffield Department of Population Health, University of Oxford,, Oxford, UK
- NIHR Oxford Biomedical Research Centre, Oxford, UK
| | - Angus Clarke
- Division of Cancer and Genetics, Cardiff University School of Medicine, Cardiff, UK
| | - Emma Clement
- Clinical Genetics and Genomic Medicine, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Bettina Friedrich
- Population, Policy and Practice, UCL GOS Institute of Child Health, London, UK
| | | | - Melissa Hill
- London North Genomic Laboratory Hub, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
- Genetics and Genomic Medicine, UCL GOS Institute of Child Health, London, UK
| | - Ruth Horn
- The Ethox Centre and the Wellcome Centre for Ethics and Humanities, Department of Population Health, University of Oxford, Oxford, UK
| | - Anneke M. Lucassen
- Clinical Ethics and Law, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Chris Patch
- Genomics England, Queen Mary University of London, London, UK
- Counselling, Society and Ethics Research, Wellcome Genome Campus, Cambridge, UK
| | | | | | | | - Sarah L. Wynn
- Unique – the Rare Chromosome Disorder Support Group, Oxted, UK
| | - Cecilia Vindrola-Padros
- Department of Targeted Intervention and Rapid Research Evaluation and Appraisal Lab (RREAL),, University College London, London, UK
| | - Monica Lakhanpaul
- Population, Policy and Practice, UCL GOS Institute of Child Health, London, UK
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Best S, Long JC, Gaff C, Braithwaite J, Taylor N. Organizational perspectives on implementing complex health interventions: clinical genomics in Australia. J Health Organ Manag 2021; ahead-of-print. [PMID: 34283896 DOI: 10.1108/jhom-12-2020-0495] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
PURPOSE Clinical genomics is a complex, innovative medical speciality requiring clinical and organizational engagement to fulfil the clinical reward promised to date. Focus thus far has been on gene discovery and clinicians' perspectives. The purpose of this study was to use implementation science theory to identify organizational barriers and enablers to implementation of clinical genomics along an organizations' implementation journey from Preadoption through to Adoption and Implementation. DESIGN/METHODOLOGY/APPROACH We used a deductive qualitative approach study design drawing on implementation science theory - (1) Translation Science to Population Impact Framework, to inform semi structured interviews with organizational decision-makers collaborating with Australian and Melbourne Genomics, alongside and (2) Theoretical Domains Framework (TDF), to guide data analysis. FINDINGS We identified evolving organizational barriers across the implementation journey from Preadoption to Implementation. Initially the organizational focus is on understanding the value of clinical genomics (TDF code: belief about consequences) and setting the scene (TDF code: goals) before organizational (TDF codes: knowledge and belief about consequences) and clinician (TDF codes: belief about capability and intentions) willingness to adopt is apparent. Once at the stage of Implementation, leadership and clarity in organizational priorities (TDF codes: intentions, professional identity and emotion) that include clinical genomics are essential prerequisites to implementing clinical genomics in practice. Intuitive enablers were identified (e.g. 'providing multiple opportunities for people to come on board) and mapped hypothetically to barriers. ORIGINALITY/VALUE Attention to date has centred on the barriers facing clinicians when introducing clinical genomics into practice. This paper uses a combination of implementation science theories to begin to unravel the organizational perspectives of implementing this complex health intervention.
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Affiliation(s)
- Stephanie Best
- Australian Institute of Health Innovation, Macquarie University, North Ryde, Australia.,Australian Genomics, Murdoch Childrens Research Institute, Parkville, Australia
| | - Janet C Long
- Australian Institute of Health Innovation, Macquarie University, North Ryde, Australia
| | - Clara Gaff
- Melbourne Genomics Health Alliance, Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia.,The University of Melbourne, Melbourne, Australia
| | - Jeffrey Braithwaite
- Australian Institute of Health Innovation, Macquarie University, North Ryde, Australia
| | - Natalie Taylor
- Cancer Council New South Wales, Woolloomooloo, Australia.,The University of Sydney, Sydney, Australia
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