Meeting the challenges of implementing rapid genomic testing in acute pediatric care.

Stark, Zornitza; Lunke, Sebastian; Brett, Gemma R.; Tan, Natalie B.; Stapleton, Rachel; Kumble, Smitha; Yeung, Alison; Phelan, Dean G.; Chong, Belinda; Fanjul-Fernandez, Miriam; Marum, Justine E.; Hunter, Matthew; Jarmolowicz, Anna; Prawer, Yael; Riseley, Jessica R.; Regan, Matthew; Elliott, Justine; Martyn, Melissa; Best, Stephanie; Tan, Tiong Y.; Gaff, Clara L.; White, Susan M.

doi:10.1038/gim.2018.37

Cited by 160Genomics and Rare DiseasesMetabolism and Genetic DisordersConnective tissue disorders research

Meeting the challenges of implementing rapid genomic testing in acute pediatric care.

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Stark, Zornitza, Lunke, Sebastian, Brett, Gemma R., Tan, Natalie B., Stapleton, Rachel, Kumble, Smitha, Yeung, Alison, Phelan, Dean G. +14 more·2018·Genetics in Medicine

DOI 10.1038/gim.2018.37

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Abstract

Purpose The purpose of the study was to implement and prospectively evaluate the outcomes of a rapid genomic diagnosis program at two pediatric tertiary centers.Methods Rapid singleton whole-exome sequencing (rWES) was performed in acutely unwell pediatric patients with suspected monogenic disorders. Laboratory and clinical barriers to implementation were addressed through continuous multidisciplinary review of process parameters. Diagnostic and clinical utility and cost-effectiveness of rWES were assessed.Results Of 40 enrolled patients, 21 (52.5%) received a diagnosis, with median time to report of 16 days (range 9-109 days). A result was provided during the first hospital admission in 28 of 36 inpatients (78%). Clinical management changed in 12 of the 21 diagnosed patients (57%), including the provision of lifesaving treatment, avoidance of invasive biopsies, and palliative care guidance. The cost per diagnosis was AU$13,388 (US$10,453). Additional cost savings from avoidance of planned tests and procedures and reduced length of stay are estimated to be around AU$543,178 (US$424,101). The clear relative advantage of rWES, joint clinical and laboratory leadership, and the creation of a multidisciplinary "rapid team" were key to successful implementation.Conclusion Rapid genomic testing in acute pediatrics is not only feasible but also cost-effective, and has high diagnostic and clinical utility. It requires a whole-of-system approach for successful implementation.

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Inadequate funding, insufficient pediatric workforce preparation, and the high resource demands of rapid testing are substantial barriers to wide adoption.
“The lack of health care funding, the underpreparedness of the pediatric workforce, and the resource-intensive nature of rapid testing represent significant barriers to widespread adoption.”
From Feasibility of Ultra-Rapid Exome Sequencing in Critically Ill Infants and Children With Suspected Monogenic Conditions in the Australian Public Health Care System (2020) · cites this paper as [8]
The study found a 3-fold reduction in the mean time from hospital admission to molecular diagnosis compared with the prior Australian rapid exome sequencing study conducted in 2016-2017 at 2 centers.
“with a 3-fold reduction in the mean time from hospital admission to molecular diagnosis compared with the prior Australian rapid exome sequencing study 8 conducted in 2016-2017 at 2 centers.”
From Feasibility of Ultra-Rapid Exome Sequencing in Critically Ill Infants and Children With Suspected Monogenic Conditions in the Australian Public Health Care System (2020) · cites this paper as [8]
Rapid genomic testing places demands on all stages of the clinical and laboratory process, calling for timely patient identification, skilled evaluation, appropriate counseling, and robust communication and coordination.
“rapid genomic testing challenges all the components of the clinical and laboratory pathway, necessitating timely patient identification, skilled assessment, appropriate counseling, and a high degree of communication and coordination in emotionally charged and rapidly evolving clinical situations.”
From Feasibility of Ultra-Rapid Exome Sequencing in Critically Ill Infants and Children With Suspected Monogenic Conditions in the Australian Public Health Care System (2020) · cites this paper as [8]
A greater proportion of reports were returned before hospital discharge or death, and the reports contributed to palliative care decisions in a greater proportion of patients who died.
“A greater proportion of reports were returned prior to hospital discharge or death and the reports formed part of the palliative care decisions in a greater proportion of the patients who died.”
From Feasibility of Ultra-Rapid Exome Sequencing in Critically Ill Infants and Children With Suspected Monogenic Conditions in the Australian Public Health Care System (2020) · cites this paper as [8]

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Identification of a deletion containing TBX4 in a neonate with acinar dysplasia by rapid exome sequencing
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Rapid exome sequencing in critically ill children impacts acute and long-term management of patients and their families: A retrospective regional evaluation
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The Impact of Next-Generation Sequencing on the Diagnosis, Treatment, and Prevention of Hereditary Neuromuscular Disorders
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A systematic review of knowledge, attitude and practice of pharmacogenomics in pediatric oncology patients
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Advances in our understanding of genetic kidney disease using kidney organoids
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Rapid Identification of Biallelic <b><i>SPTB</i></b> Mutation in a Neonate with Severe Congenital Hemolytic Anemia and Liver Failure
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Double homozygosity in CEP57 and DYNC2H1 genes detected by WES: Composite or expanded phenotype?
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Biallelic Variants in PYROXD2 Cause a Severe Infantile Metabolic Disorder Affecting Mitochondrial Function
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Attitudes towards genetic testing and information: does parenthood shape the views?
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Rapid exome sequencing and adjunct RNA studies confirm the pathogenicity of a novel homozygous ASNS splicing variant in a critically ill neonate
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Rapid Genetic Testing in Pediatric and Neonatal Critical Care: A Scoping Review of Emerging Ethical Issues
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A micro-costing study of mass-spectrometry based quantitative proteomics testing applied to the diagnostic pipeline of mitochondrial and other rare disorders
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Healthcare Professionals’ Attitudes toward Rapid Whole Genome Sequencing in Pediatric Acute Care
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Implementing genomics in the neonatal period: An assessment of parental decision making and anxiety
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Analysis of laboratory reporting practices using a quality assessment of a virtual patient
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Lessons learned from rapid exome sequencing for 575 critically ill patients across the broad spectrum of rare disease
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Using an experiment among clinical experts to determine the cost and clinical impact of rapid whole exome sequencing in acute pediatric settings
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Rapid whole-exome sequencing facilitates precision medicine in paediatric rare disease patients and reduces healthcare costs
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Rapid genomic testing in acute paediatric care: Is it worth the trouble?
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Implementation of First-Line Rapid Genome Sequencing in Non–Critical Care Pediatric Wards
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Rapid Whole-Genome Sequencing in Acutely Ill Children: A Single Pediatric Center Experience
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Authors: Stark, Z., Lunke, S., Brett, G. R., Tan, N. B., Stapleton, R., Kumble, S., Yeung, A., Phelan, D. G., Chong, B., Fanjul-Fernandez, M., Marum, J. E., Hunter, M., Jarmolowicz, A., Prawer, Y., Riseley, J. R., Regan, M., Elliott, J., Martyn, M., Best, S., Tan, T. Y., Gaff, C. L., & White, S. M.
Affiliations: The University of Melbourne (AU)
Victorian Clinical Genetics Services (AU)
Monash Children’s Hospital (AU)
Macquarie University (AU)
Corresponding author: Stark, Zornitza
ORCID: Stark, Zornitza
Lunke, Sebastian
Brett, Gemma R.
Tan, Natalie B.
Stapleton, Rachel
Kumble, Smitha
Yeung, Alison
Phelan, Dean G.
Chong, Belinda
Hunter, Matthew
Jarmolowicz, Anna
Prawer, Yael
Elliott, Justine
Martyn, Melissa
Best, Stephanie
Tan, Tiong Y.
Gaff, Clara L.
White, Susan M.
Venue: Genetics in Medicine
Publisher: Elsevier BV
Published: 2018-12
Volume: 20
Issue: 12
Pages: 1554-1563
ISSN: 1098-3600 (ISSN-L)
DOI: 10.1038/gim.2018.37
OpenAlex: W2793936903
Cited by: 159
References: 29
Citations by year: 2026: 6 · 2025: 16 · 2024: 15 · 2023: 13 · 2022: 27 · 2021: 19 · 2020: 32 · 2019: 24 · 2018: 6 · 2012: 1
FWCI: 12.42
Type: journal article
Language: en
Open access: bronze
doi.org
Licence: www.elsevier.com/tdm/userlicense/1.0/ (tdm)
www.elsevier.com/legal/tdmrep-license (tdm)
www.elsevier.com/open-access/userlicense/1.0/ (vor, 1145 d)
Locations: Genetics in Medicine (publishedVersion)
PubMed (publishedVersion)
Topics: Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genomics and Rare Diseases
Life Sciences › Biochemistry, Genetics and Molecular Biology › Clinical Biochemistry › Metabolism and Genetic Disorders
Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Connective tissue disorders research
Keywords: exome sequencing, monogenic disorders, diagnostic yield, time to diagnosis, cost-effectiveness, implementation barriers, clinical utility, length of hospital stay
MeSH terms: Exome Sequencing, Cost-Benefit Analysis, Female, Genetic Testing, Humans, Male, Pediatrics, Genome, Human, Genomics, Pathology, Molecular, Exome

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Meeting the challenges of implementing rapid genomic testing in acute pediatric care.

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