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Juarez EF, Peterson B, Kobayashi ES, Gilmer S, Tobin LE, Schultz B, Lenberg J, Carroll J, Bai-Tong S, Sweeney NM, Beebe C, Stewart L, Olsen L, Reinke J, Kiernan EA, Reimers R, Wigby K, Tackaberry C, Yandell M, Hobbs C, Bainbridge MN. A Machine Learning Decision Support Tool Optimizes Whole Genome Sequencing Utilization in a Neonatal Intensive Care Unit. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.07.05.24310008. [PMID: 39006422 PMCID: PMC11245077 DOI: 10.1101/2024.07.05.24310008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/16/2024]
Abstract
The Mendelian Phenotype Search Engine (MPSE), a clinical decision support tool using Natural Language Processing and Machine Learning, helped neonatologists expedite decisions to whole genome sequencing (WGS) to diagnose patients in the Neonatal Intensive Care Unit. After the MPSE was introduced, utilization of WGS increased, time to ordering WGS decreased, and WGS diagnostic yield increased.
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2
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Coleman TF, Pugh J, Kelley WV, East KM, Greve V, Finnila CR, Henson A, Korf BR, Barsh GS, Cooper GM, Cochran ME. Errors in genome sequencing result disclosures: A randomized controlled trial comparing neonatology non-genetics healthcare professionals and genetic counselors. Genet Med 2024; 26:101198. [PMID: 38943479 DOI: 10.1016/j.gim.2024.101198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Revised: 06/18/2024] [Accepted: 06/21/2024] [Indexed: 07/01/2024] Open
Abstract
PURPOSE We compared the rate of errors in genome sequencing (GS) result disclosures by genetic counselors (GC) and trained non-genetics healthcare professionals (NGHPs) in SouthSeq, a randomized trial utilizing GS in critically ill infants. METHODS Over 400 recorded GS result disclosures were analyzed for major and minor errors. We used Fisher's exact test to compare error rates between GCs and NGHPs and performed a qualitative content analysis to characterize error themes. RESULTS Major errors were identified in 7.5% of disclosures by NGHPs and in no disclosures by GCs. Minor errors were identified in 32.1% of disclosures by NGHPs and in 11.4% of disclosures by GCs. Although most disclosures lacked errors, NGHPs were significantly more likely to make any error than GCs for all result types (positive, negative, or uncertain). Common major error themes include omission of critical information, overstating a negative result, and overinterpreting an uncertain result. The most common minor error was failing to disclose negative secondary findings. CONCLUSION Trained NGHPs made clinically significant errors in GS result disclosures. Characterizing common errors in result disclosure can illuminate gaps in education to inform the development of future genomics training and alternative service delivery models.
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Affiliation(s)
| | - Jada Pugh
- HudsonAlpha Institute for Biotechnology, Huntsville, AL
| | | | - Kelly M East
- HudsonAlpha Institute for Biotechnology, Huntsville, AL
| | | | | | - Ava Henson
- HudsonAlpha Institute for Biotechnology, Huntsville, AL; Graduate School of Biomedical Sciences, University of Texas MD Anderson Cancer Center UTHealth Houston, Houston, TX
| | - Bruce R Korf
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL
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3
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D'Gama AM, Wojcik MH, Hills S, Douglas J, Yu TW, Agrawal PB, Parker MG. "It's hard to wait": Provider perspectives on current genomic care in safety-net NICUs. Genet Med 2024; 26:101177. [PMID: 38855852 DOI: 10.1016/j.gim.2024.101177] [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: 02/09/2024] [Revised: 06/01/2024] [Accepted: 06/03/2024] [Indexed: 06/11/2024] Open
Abstract
PURPOSE Critically ill infants from marginalized populations disproportionately receive care in neonatal intensive care units (NICUs) that lack access to state-of-the-art genomic care, leading to inequitable outcomes. We sought provider perspectives to inform our implementation study (VIGOR) providing rapid genomic sequencing within these settings. METHODS We conducted semistructured focus groups with neonatal and genetics providers at 6 NICUs at safety-net hospitals, informed by the Promoting Action on Research Implementation in Health Services framework, which incorporates evidence, context, and facilitation domains. We iteratively developed codes and themes until thematic saturation was reached. RESULTS Regarding evidence, providers felt that genetic testing benefits infants and families. Regarding context, the major barriers identified to genomic care were genetic testing cost, lack of genetics expertise for disclosure and follow-up, and navigating the complexity of selecting and ordering genetic tests. Providers had negative feelings about the current status quo and inequity in genomic care across NICUs. Regarding facilitation, providers felt that a virtual support model such as VIGOR would address major barriers and foster family-centered care and collaboration. CONCLUSION NICU providers at safety-net hospitals believe that access to state-of-the-art genomic care is critical for optimizing infant outcomes; yet, substantial barriers exist that the VIGOR study may address.
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Affiliation(s)
- Alissa M D'Gama
- Division of Newborn Medicine, Department of Pediatrics, Boston Children's Hospital, Boston, MA; Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital, Boston, MA; Department of Pediatrics, Harvard Medical School, Boston, MA
| | - Monica H Wojcik
- Division of Newborn Medicine, Department of Pediatrics, Boston Children's Hospital, Boston, MA; Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital, Boston, MA; Department of Pediatrics, Harvard Medical School, Boston, MA; The Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA.
| | - Sonia Hills
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital, Boston, MA
| | - Jessica Douglas
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital, Boston, MA
| | - Timothy W Yu
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital, Boston, MA; Department of Pediatrics, Harvard Medical School, Boston, MA
| | - Pankaj B Agrawal
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital, Boston, MA; Department of Pediatrics, Harvard Medical School, Boston, MA; The Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA; Division of Neonatology, Department of Pediatrics, University of Miami Miller School of Medicine and Holtz Children's Hospital, Jackson Health System, Miami, FL
| | - Margaret G Parker
- Department of Pediatrics, UMass Chan School of Medicine, Worcester, MA
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4
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Mancl N, Myers MF, Miller EM, Jackson F, Widmeyer K. Preparedness and training of genetic counselors practicing in inpatient settings. J Genet Couns 2024; 33:539-553. [PMID: 37528675 DOI: 10.1002/jgc4.1754] [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: 04/21/2023] [Revised: 07/05/2023] [Accepted: 07/15/2023] [Indexed: 08/03/2023]
Abstract
As rapid genomic testing technology increasingly allows for real-time answers that could alter management for acutely ill patients, opportunities for genetic counselors to work in inpatient settings will increase. However, genetic counselors' preparedness and the training provided by graduate programs to work in inpatient settings are unknown. We conducted semi-structured interviews with 13 genetic counselors who provided services in varied inpatient settings to assess genetic counselors' readiness for inpatient positions. We also surveyed members of the Association of Genetic Counseling Program Directors (AGCPD) about inpatient training practices of genetic counseling graduate programs. Genetic counselors were recruited through the National Society of Genetic Counselors (NSGC) Inpatient Special Interest Group listserv and graduate program faculty were recruited through the AGCPD listserv. Some challenges reported by genetic counselors in inpatient settings included working in a fast-paced hospital environment which necessitated focused interactions with patients; collaborating with diverse providers who may not understand the role of genetic counselors; and navigating grief experiences of families and of themselves as a provider. Although genetic counselors felt that many of their skills developed in graduate school were transferrable to the inpatient setting, those who had minimal or no inpatient exposure in graduate school often described feeling unprepared for working in the inpatient setting. The majority of AGCPD respondents (23/28) indicated their program provided some type of exposure to the inpatient setting for students, the most common (22/23) being an inpatient clinical rotation, which suggests many graduate programs are already recognizing the importance of providing inpatient training. Our findings indicate that while many skills are transferrable to inpatient positions, genetic counselors face unique challenges in inpatient settings. Our results suggest that graduate exposure to the inpatient setting and professional support of inpatient genetic counselors are beneficial to support genetic counselors' preparedness to take on inpatient positions.
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Affiliation(s)
- Nelliann Mancl
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
- College of Medicine, University of Cincinnati, Cincinnati, Ohio, USA
| | - Melanie F Myers
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
- College of Medicine, University of Cincinnati, Cincinnati, Ohio, USA
| | - Erin M Miller
- College of Medicine, University of Cincinnati, Cincinnati, Ohio, USA
- Division of Cardiology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - Farrah Jackson
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - Kimberly Widmeyer
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
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5
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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 2024:10.1038/s41431-024-01569-z. [PMID: 38605122 DOI: 10.1038/s41431-024-01569-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [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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6
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Vears DF, Lynch F, Nisselle A, Ayres S, Stark Z. Rapid genomic testing in critically ill patients with genetic conditions: position statement by the Human Genetics Society of Australasia. Eur J Hum Genet 2024; 32:150-154. [PMID: 37864047 PMCID: PMC10853566 DOI: 10.1038/s41431-023-01477-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 09/13/2023] [Accepted: 10/02/2023] [Indexed: 10/22/2023] Open
Affiliation(s)
- Danya F Vears
- Murdoch Children's Research Institute, Melbourne, VIC, Australia
- The University of Melbourne, Melbourne, VIC, Australia
| | - Fiona Lynch
- Murdoch Children's Research Institute, Melbourne, VIC, Australia
- The University of Melbourne, Melbourne, VIC, Australia
| | - Amy Nisselle
- Murdoch Children's Research Institute, Melbourne, VIC, Australia
- The University of Melbourne, Melbourne, VIC, Australia
| | - Samantha Ayres
- Murdoch Children's Research Institute, Melbourne, VIC, Australia
- The University of Melbourne, Melbourne, VIC, Australia
| | - Zornitza Stark
- Murdoch Children's Research Institute, Melbourne, VIC, Australia.
- The University of Melbourne, Melbourne, VIC, Australia.
- Australian Genomics, Melbourne, VIC, Australia.
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7
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Kim S, Pistawka C, Langlois S, Osiovich H, Virani A, Kitchin V, Elliott AM. Genetic counselling considerations with genetic/genomic testing in Neonatal and Pediatric Intensive Care Units: A scoping review. Clin Genet 2024; 105:13-33. [PMID: 37927209 DOI: 10.1111/cge.14446] [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: 07/28/2023] [Revised: 09/23/2023] [Accepted: 10/15/2023] [Indexed: 11/07/2023]
Abstract
Genetic and genomic technologies can effectively diagnose numerous genetic disorders. Patients benefit when genetic counselling accompanies genetic testing and international guidelines recommend pre- and post-test genetic counselling with genome-wide sequencing. However, there is a gap in knowledge regarding the unique genetic counselling considerations with different types of genetic testing in the Neonatal Intensive Care Unit (NICU) and the Pediatric Intensive Care Unit (PICU). This scoping review was conducted to identify the gaps in care with respect to genetic counselling for infants/pediatric patients undergoing genetic and genomic testing in NICUs and PICUs and understand areas in need of improvement in order to optimize clinical care for patients, caregivers, and healthcare providers. Five databases (MEDLINE [Ovid], Embase [Ovid], PsycINFO [Ebsco], CENTRAL [Ovid], and CINHAL [Ebsco]) and grey literature were searched. A total of 170 studies were included and used for data extraction and analysis. This scoping review includes descriptive analysis, followed by a narrative account of the extracted data. Results were divided into three groups: pre-test, post-test, and comprehensive (both pre- and post-test) genetic counselling considerations based on indication for testing. More studies were conducted in the NICU than the PICU. Comprehensive genetic counselling was discussed in only 31% of all the included studies demonstrating the need for both pre-test and post-test genetic counselling for different clinical indications in addition to the need to account for different cultural aspects based on ethnicity and geographic factors.
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Affiliation(s)
- Sunu Kim
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Carly Pistawka
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Sylvie Langlois
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
- BC Children's Hospital Research Institute, Vancouver, British Columbia, Canada
- Women's Health Research Institute, Vancouver, British Columbia, Canada
| | - Horacio Osiovich
- BC Children's Hospital Research Institute, Vancouver, British Columbia, Canada
- Women's Health Research Institute, Vancouver, British Columbia, Canada
- Department of Pediatrics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Alice Virani
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
- Ethics Service, Provincial Health Services Authority, Vancouver, British Columbia, Canada
| | - Vanessa Kitchin
- Woodward Library, University of British Columbia, Vancouver, British Columbia, Canada
| | - Alison M Elliott
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
- BC Children's Hospital Research Institute, Vancouver, British Columbia, Canada
- Women's Health Research Institute, Vancouver, British Columbia, Canada
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8
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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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9
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Wojcik MH, Callahan KP, Antoniou A, Del Rosario MC, Brunelli L, ElHassan NO, Gogcu S, Murthy K, Rumpel JA, Wambach JA, Suhrie K, Fishler K, Chaudhari BP. Provision and availability of genomic medicine services in Level IV neonatal intensive care units. Genet Med 2023; 25:100926. [PMID: 37422715 PMCID: PMC10592224 DOI: 10.1016/j.gim.2023.100926] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 06/30/2023] [Accepted: 07/02/2023] [Indexed: 07/10/2023] Open
Abstract
PURPOSE To describe variation in genomic medicine services across level IV neonatal intensive care units (NICUs) in the United States and Canada. METHODS We developed and distributed a novel survey to the 43 level IV NICUs belonging to the Children's Hospitals Neonatal Consortium, requesting a single response per site from a clinician with knowledge of the provision of genomic medicine services. RESULTS Overall response rate was 74% (32/43). Although chromosomal microarray and exome or genome sequencing (ES or GS) were universally available, access was restricted for 22% (7/32) and 81% (26/32) of centers, respectively. The most common restriction on ES or GS was requiring approval by a specialist (41%, 13/32). Rapid ES/GS was available in 69% of NICUs (22/32). Availability of same-day genetics consultative services was limited (41%, 13/32 sites), and pre- and post-test counseling practices varied widely. CONCLUSION We observed large inter-center variation in genomic medicine services across level IV NICUs: most notably, access to rapid, comprehensive genetic testing in time frames relevant to critical care decision making was limited at many level IV Children's Hospitals Neonatal Consortium NICUs despite a significant burden of genetic disease. Further efforts are needed to improve access to neonatal genomic medicine services.
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Affiliation(s)
- Monica H Wojcik
- Divisions of Newborn Medicine and Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital and Harvard Medical School, Boston, MA; Neonatal Genomics Program, Department of Pediatrics, Boston Children's Hospital and Harvard Medical School, Boston, MA.
| | - Katharine P Callahan
- Division of Neonatology, Children's Hospital of Philadelphia, Philadelphia, PA; Division of Medical Ethics and Health Policy, University of Pennsylvania, Philadelphia, PA
| | - Austin Antoniou
- Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH
| | - Maya C Del Rosario
- Neonatal Genomics Program, Department of Pediatrics, Boston Children's Hospital and Harvard Medical School, Boston, MA
| | - Luca Brunelli
- Division of Neonatology, University of Utah Health and Primary Children's Hospital, Salt Lake City, UT
| | - Nahed O ElHassan
- Division of Neonatology, Arkansas Children's Hospital, University of Arkansas for Medical Sciences, Little Rock, AR
| | - Semsa Gogcu
- Wake Forest School of Medicine, Department of Pediatrics, Winston-Salem, NC
| | - Karna Murthy
- Ann & Robert H Lurie Children's Hospital of Chicago and Northwestern University, Chicago, IL; Children's Hospitals Neonatal Consortium, Dover, DE
| | - Jennifer A Rumpel
- Division of Neonatology, Arkansas Children's Hospital, University of Arkansas for Medical Sciences, Little Rock, AR
| | - Jennifer A Wambach
- Washington University School of Medicine and St Louis Children's Hospital, St Louis, MO
| | - Kristen Suhrie
- Department of Pediatrics, Division of Neonatal-Perinatal Medicine, and Department of Medical and Molecular Genetics, Riley Hospital for Children and Indiana University School of Medicine, Indianapolis, IN
| | - Kristen Fishler
- Munroe-Meyer Institute for Genetics and Rehabilitation, University of Nebraska Medical Center, Omaha, NE
| | - Bimal P Chaudhari
- Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH; Divisions of Neonatology and Genetics and Genomic Medicine, Department of Pediatrics, Nationwide Children's Hospital and The Ohio State University College of Medicine, Columbus, OH
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10
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Fishler KP, Steber HS, Brunelli L, Shope RJ. Exploring collaboration models between geneticists and intensivists for implementing rapid genome sequencing in critical care settings. Am J Med Genet A 2023; 191:2290-2299. [PMID: 37318250 DOI: 10.1002/ajmg.a.63318] [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: 02/16/2023] [Revised: 04/13/2023] [Accepted: 05/13/2023] [Indexed: 06/16/2023]
Abstract
The availability of rapid genome sequencing (rGS) for children in a critical-care setting is increasing. This study explored the perspectives of geneticists and intensivists on optimal collaboration and division of roles when implementing rGS in neonatal and pediatric intensive care units (ICUs). We conducted an explanatory mixed methods study involving a survey embedded within an interview with 13 genetics and intensive care providers. Interviews were recorded, transcribed, and coded. Geneticists endorsed higher confidence in performing a physical exam and interpreting/communicating positive results. Intensivists endorsed highest confidence in determining whether genetic testing was appropriate, communicating negative results, and consenting. Major qualitative themes that emerged were: (1) concerns with both "genetics-led" and "intensivist-led" models with workflows and sustainability (2) shift the role of determining rGS eligibility to ICU medical professionals, (3) continued role of geneticists to assess phenotype, and (4) include genetic counselors (GCs) and neonatal nurse practitioners to enhance workflow and care. All geneticists supported shifting decisions regarding eligibility for rGS to the ICU team to minimize time cost for the genetics workforce. Exploring models of geneticist-led phenotyping, intensivist-led phenotyping for some indications, and/or inclusion of a dedicated inpatient GC may help offset the time burden of consenting and other tasks associated with rGS.
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Affiliation(s)
- Kristen P Fishler
- Munroe-Meyer Institute for Genetics & Rehabilitation, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Hannah S Steber
- Munroe-Meyer Institute for Genetics & Rehabilitation, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Luca Brunelli
- Division of Neonatology, University of Utah School of Medicine, Salt Lake City, Utah, USA
| | - Ronald J Shope
- College of Allied Health Professions, University of Nebraska Medical Center, Omaha, Nebraska, USA
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11
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Bonser D, Malone Jenkins S, Palmquist R, Guthery S, Bonkowsky JL, Jaramillo C. Rapid Genome Sequencing Diagnosis in Pediatric Patients with Liver Dysfunction. J Pediatr 2023; 260:113534. [PMID: 37269902 DOI: 10.1016/j.jpeds.2023.113534] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 04/16/2023] [Accepted: 05/29/2023] [Indexed: 06/05/2023]
Abstract
OBJECTIVE To describe the usefulness of rapid whole genome sequencing (rWGS) in a cohort of children presenting with acute liver dysfunction. STUDY DESIGN This was a retrospective, population-based cohort study conducted at Primary Children's Hospital in Salt Lake City, Utah. Children meeting criteria for acute liver dysfunction who received rWGS between August 2019 and December 2021 were included. rWGS was performed on blood samples from the patient and parents (1 or both depending on availability). The clinical characteristics of patients with positive rWGS results were compared with those with negative results. RESULTS Eighteen patients with pediatric acute liver dysfunction who had rWGS were identified. The median turnaround time from the date rWGS testing was ordered to the date an initial report was received was 8 days with a shorter turnaround time in patients with a diagnostic rWGS (4 days vs 10 days; P = .03). A diagnostic result was identified in 7 of 18 patients (39%). Subsequently, 4 patients in this cohort, who had negative rWGS results, were found to have a toxic exposure accounting for their liver dysfunction. With removal of these patients, the diagnostic rate of rWGS was 7 of 14 (50%). The use of rWGS led to a change in management for 6 of 18 patients (33%). CONCLUSIONS We found that rWGS provided a diagnosis in up to 50% of pediatric acute liver dysfunction. rWGS allows for higher diagnostic rates in an expedited fashion that affects clinical management. These data support the routine use of rWGS for life-threatening disorders in children, specifically acute liver dysfunction.
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Affiliation(s)
| | - Sabrina Malone Jenkins
- Division of Neonatology, Department of Pediatrics, University of Utah School of Medicine, Primary Children's Hospital, Salt Lake City, UT; Center for Personalized Medicine, Primary Children's Hospital, Salt Lake City, UT
| | - Rachel Palmquist
- Center for Personalized Medicine, Primary Children's Hospital, Salt Lake City, UT; Division of Pediatric Neurology, Department of Pediatrics, University of Utah School of Medicine, Salt Lake City, UT
| | - Stephen Guthery
- Division of Pediatric Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, University of Utah School of Medicine, Primary Children's Hospital, Salt Lake City, UT
| | - Joshua L Bonkowsky
- Center for Personalized Medicine, Primary Children's Hospital, Salt Lake City, UT; Division of Pediatric Neurology, Department of Pediatrics, University of Utah School of Medicine, Salt Lake City, UT
| | - Catalina Jaramillo
- Division of Pediatric Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, University of Utah School of Medicine, Primary Children's Hospital, Salt Lake City, UT.
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12
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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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13
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Reiley J, Botas P, Miller CE, Zhao J, Malone Jenkins S, Best H, Grubb PH, Mao R, Isla J, Brunelli L. Open-Source Artificial Intelligence System Supports Diagnosis of Mendelian Diseases in Acutely Ill Infants. CHILDREN (BASEL, SWITZERLAND) 2023; 10:991. [PMID: 37371223 PMCID: PMC10296792 DOI: 10.3390/children10060991] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2023] [Revised: 05/18/2023] [Accepted: 05/30/2023] [Indexed: 06/29/2023]
Abstract
Mendelian disorders are prevalent in neonatal and pediatric intensive care units and are a leading cause of morbidity and mortality in these settings. Current diagnostic pipelines that integrate phenotypic and genotypic data are expert-dependent and time-intensive. Artificial intelligence (AI) tools may help address these challenges. Dx29 is an open-source AI tool designed for use by clinicians. It analyzes the patient's phenotype and genotype to generate a ranked differential diagnosis. We used Dx29 to retrospectively analyze 25 acutely ill infants who had been diagnosed with a Mendelian disorder, using a targeted panel of ~5000 genes. For each case, a trio (proband and both parents) file containing gene variant information was analyzed, alongside patient phenotype, which was provided to Dx29 by three approaches: (1) AI extraction from medical records, (2) AI extraction with manual review/editing, and (3) manual entry. We then identified the rank of the correct diagnosis in Dx29's differential diagnosis. With these three approaches, Dx29 ranked the correct diagnosis in the top 10 in 92-96% of cases. These results suggest that non-expert use of Dx29's automated phenotyping and subsequent data analysis may compare favorably to standard workflows utilized by bioinformatics experts to analyze genomic data and diagnose Mendelian diseases.
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Affiliation(s)
- Joseph Reiley
- Division of Neonatology, Department of Pediatrics, University of Utah School of Medicine, Salt Lake City, UT 84108, USA
| | - Pablo Botas
- Foundation Twenty-Nine, 28223 Madrid, Spain
- Nostos Genomics, 10625 Berlin, Germany
| | - Christine E. Miller
- ARUP Laboratories, University of Utah Health Sciences Center, Salt Lake City, UT 84108, USA
- Valley Children’s Healthcare, Madera, CA 93636, USA
| | - Jian Zhao
- ARUP Laboratories, University of Utah Health Sciences Center, Salt Lake City, UT 84108, USA
- Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT 84132, USA
| | - Sabrina Malone Jenkins
- Division of Neonatology, Department of Pediatrics, University of Utah School of Medicine, Salt Lake City, UT 84108, USA
| | - Hunter Best
- ARUP Laboratories, University of Utah Health Sciences Center, Salt Lake City, UT 84108, USA
- Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT 84132, USA
| | - Peter H. Grubb
- Division of Neonatology, Department of Pediatrics, University of Utah School of Medicine, Salt Lake City, UT 84108, USA
| | - Rong Mao
- ARUP Laboratories, University of Utah Health Sciences Center, Salt Lake City, UT 84108, USA
- Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT 84132, USA
| | | | - Luca Brunelli
- Division of Neonatology, Department of Pediatrics, University of Utah School of Medicine, Salt Lake City, UT 84108, USA
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14
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Nurchis MC, Raspolini GM, Heidar Alizadeh A, Altamura G, Radio FC, Tartaglia M, Dallapiccola B, Damiani G. Organizational Aspects of the Implementation and Use of Whole Genome Sequencing and Whole Exome Sequencing in the Pediatric Population in Italy: Results of a Survey. J Pers Med 2023; 13:899. [PMID: 37373888 DOI: 10.3390/jpm13060899] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 05/16/2023] [Accepted: 05/24/2023] [Indexed: 06/29/2023] Open
Abstract
This study explores the organizational aspects of whole genome sequencing (WGS) implementation for pediatric patients with suspected genetic disorders in Italy, comparing it with whole exome sequencing (WES). Health professionals' opinions were collected through an internet-based survey and analyzed using a qualitative summative content analysis methodology. Among the 16 respondents, most were clinical geneticists performing only WES, while 5 also used WGS. The key differences identified include higher needs for analyzing genome rearrangements following WES, greater data storage and security requirements for WGS, and WGS only being performed in specific research studies. No difference was detected in centralization and decentralization issues. The main cost factors included genetic consultations, library preparation and sequencing, bioinformatic analysis, interpretation and confirmation, data storage, and complementary diagnostic investigations. Both WES and WGS decreased the need for additional diagnostic analyses when not used as last-resort tests. Organizational aspects were similar for WGS and WES, but economic evidence gaps may exist for WGS in clinical settings. As sequencing costs decline, WGS will likely replace WES and traditional genetic testing. Tailored genomic policies and cost-effectiveness analyses are needed for WGS implementation in health systems. WGS shows promise for enhancing genetics knowledge and expediting diagnoses for pediatric patients with genetic disorders.
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Affiliation(s)
- Mario Cesare Nurchis
- Department of Woman and Child Health and Public Health, Fondazione Policlinico Universitario A. Gemelli IRCCS, 00168 Rome, Italy
- School of Economics, Università Cattolica del Sacro Cuore, 00168 Rome, Italy
| | - Gian Marco Raspolini
- Department of Health Sciences and Public Health, Section of Hygiene, Università Cattolica del Sacro Cuore, 00168 Rome, Italy
| | - Aurora Heidar Alizadeh
- Department of Health Sciences and Public Health, Section of Hygiene, Università Cattolica del Sacro Cuore, 00168 Rome, Italy
| | - Gerardo Altamura
- Department of Health Sciences and Public Health, Section of Hygiene, Università Cattolica del Sacro Cuore, 00168 Rome, Italy
| | | | - Marco Tartaglia
- Molecular Genetics and Functional Genomics, Ospedale Pediatrico Bambino Gesù IRCCS, 00146 Rome, Italy
| | - Bruno Dallapiccola
- Molecular Genetics and Functional Genomics, Ospedale Pediatrico Bambino Gesù IRCCS, 00146 Rome, Italy
| | - Gianfranco Damiani
- Department of Woman and Child Health and Public Health, Fondazione Policlinico Universitario A. Gemelli IRCCS, 00168 Rome, Italy
- Department of Health Sciences and Public Health, Section of Hygiene, Università Cattolica del Sacro Cuore, 00168 Rome, Italy
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15
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Olaye IM, Seixas AA. The Gap Between AI and Bedside: Participatory Workshop on the Barriers to the Integration, Translation, and Adoption of Digital Health Care and AI Startup Technology Into Clinical Practice. J Med Internet Res 2023; 25:e32962. [PMID: 37129947 PMCID: PMC10189623 DOI: 10.2196/32962] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 02/02/2022] [Accepted: 10/25/2022] [Indexed: 05/03/2023] Open
Abstract
BACKGROUND Artificial intelligence (AI) and digital health technological innovations from startup companies used in clinical practice can yield better health outcomes, reduce health care costs, and improve patients' experience. However, the integration, translation, and adoption of these technologies into clinical practice are plagued with many challenges and are lagging. Furthermore, explanations of the impediments to clinical translation are largely unknown and have not been systematically studied from the perspective of AI and digital health care startup founders and executives. OBJECTIVE The aim of this paper is to describe the barriers to integrating early-stage technologies in clinical practice and health care systems from the perspectives of digital health and health care AI founders and executives. METHODS A stakeholder focus group workshop was conducted with a sample of 10 early-stage digital health and health care AI founders and executives. Digital health, health care AI, digital health-focused venture capitalists, and physician executives were represented. Using an inductive thematic analysis approach, transcripts were organized, queried, and analyzed for thematic convergence. RESULTS We identified the following four categories of barriers in the integration of early-stage digital health innovations into clinical practice and health care systems: (1) lack of knowledge of health system technology procurement protocols and best practices, (2) demanding regulatory and validation requirements, (3) challenges within the health system technology procurement process, and (4) disadvantages of early-stage digital health companies compared to large technology conglomerates. Recommendations from the study participants were also synthesized to create a road map to mitigate the barriers to integrating early-stage or novel digital health technologies in clinical practice. CONCLUSIONS Early-stage digital health and health care AI entrepreneurs identified numerous barriers to integrating digital health solutions into clinical practice. Mitigation initiatives should create opportunities for early-stage digital health technology companies and health care providers to interact, develop relationships, and use evidence-based research and best practices during health care technology procurement and evaluation processes.
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Affiliation(s)
- Iredia M Olaye
- Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY, United States
- Covered By Group, Covered By Health, Newark, NJ, United States
| | - Azizi A Seixas
- Media and Innovation Lab, Department of Informatics and Health Data Science, The University of Miami Miller School of Medicine, Miami, FL, United States
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16
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Lumaka A, Fasquelle C, Debray FG, Alkan S, Jacquinet A, Harvengt J, Boemer F, Mulder A, Vaessen S, Viellevoye R, Palmeira L, Charloteaux B, Brysse A, Bulk S, Rigo V, Bours V. Rapid Whole Genome Sequencing Diagnoses and Guides Treatment in Critically Ill Children in Belgium in Less than 40 Hours. Int J Mol Sci 2023; 24:4003. [PMID: 36835410 PMCID: PMC9967120 DOI: 10.3390/ijms24044003] [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] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 02/05/2023] [Accepted: 02/13/2023] [Indexed: 02/18/2023] Open
Abstract
Rapid Whole Genome Sequencing (rWGS) represents a valuable exploration in critically ill pediatric patients. Early diagnosis allows care to be adjusted. We evaluated the feasibility, turnaround time (TAT), yield, and utility of rWGS in Belgium. Twenty-one unrelated critically ill patients were recruited from the neonatal intensive care units, the pediatric intensive care unit, and the neuropediatric unit, and offered rWGS as a first tier test. Libraries were prepared in the laboratory of human genetics of the University of Liège using Illumina DNA PCR-free protocol. Sequencing was performed on a NovaSeq 6000 in trio for 19 and in duo for two probands. The TAT was calculated from the sample reception to the validation of results. Clinical utility data were provided by treating physicians. A definite diagnosis was reached in twelve (57.5%) patients in 39.80 h on average (range: 37.05-43.7). An unsuspected diagnosis was identified in seven patients. rWGS guided care adjustments in diagnosed patients, including a gene therapy, an off-label drug trial and two condition-specific treatments. We successfully implemented the fastest rWGS platform in Europe and obtained one of the highest rWGS yields. This study establishes the path for a nationwide semi-centered rWGS network in Belgium.
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Affiliation(s)
- Aimé Lumaka
- Human Genetic Laboratory, GIGA Institute, University of Liège, 4000 Liège, Belgium
- Center for Human Genetics, Centre Hospitalier Universitaire, 4032 Liège, Belgium
| | - Corinne Fasquelle
- Center for Human Genetics, Centre Hospitalier Universitaire, 4032 Liège, Belgium
| | | | - Serpil Alkan
- Center for Human Genetics, Centre Hospitalier Universitaire, 4032 Liège, Belgium
- Neuropediatric Division, CHU de Liège—CHR de la Citadelle, University of Liège, 4000 Liège, Belgium
| | - Adeline Jacquinet
- Center for Human Genetics, Centre Hospitalier Universitaire, 4032 Liège, Belgium
| | - Julie Harvengt
- Center for Human Genetics, Centre Hospitalier Universitaire, 4032 Liège, Belgium
| | - François Boemer
- Center for Human Genetics, Centre Hospitalier Universitaire, 4032 Liège, Belgium
| | - André Mulder
- Department of Pediatrics, Division of Pediatric Critical Care Medicine, CHC Mont-Légia, 4000 Liège, Belgium
| | - Sandrine Vaessen
- Neuropediatric Division, CHU de Liège—CHR de la Citadelle, University of Liège, 4000 Liège, Belgium
| | - Renaud Viellevoye
- Neonatology Division, CHU de Liège—CHR de la Citadelle, University of Liège, 4000 Liège, Belgium
| | - Leonor Palmeira
- Center for Human Genetics, Centre Hospitalier Universitaire, 4032 Liège, Belgium
| | - Benoit Charloteaux
- Center for Human Genetics, Centre Hospitalier Universitaire, 4032 Liège, Belgium
| | - Anne Brysse
- Center for Human Genetics, Centre Hospitalier Universitaire, 4032 Liège, Belgium
| | - Saskia Bulk
- Center for Human Genetics, Centre Hospitalier Universitaire, 4032 Liège, Belgium
| | - Vincent Rigo
- Neonatology Division, CHU de Liège—CHR de la Citadelle, University of Liège, 4000 Liège, Belgium
| | - Vincent Bours
- Human Genetic Laboratory, GIGA Institute, University of Liège, 4000 Liège, Belgium
- Center for Human Genetics, Centre Hospitalier Universitaire, 4032 Liège, Belgium
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17
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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] [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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18
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Bupp CP, Ames EG, Arenchild MK, Caylor S, Dimmock DP, Fakhoury JD, Karna P, Lehman A, Meghea CI, Misra V, Nolan DA, O’Shea J, Sharangpani A, Franck LS, Scheurer-Monaghan A. Breaking Barriers to Rapid Whole Genome Sequencing in Pediatrics: Michigan's Project Baby Deer. CHILDREN (BASEL, SWITZERLAND) 2023; 10:children10010106. [PMID: 36670656 PMCID: PMC9857227 DOI: 10.3390/children10010106] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/13/2022] [Revised: 12/02/2022] [Accepted: 12/19/2022] [Indexed: 01/06/2023]
Abstract
The integration of precision medicine in the care of hospitalized children is ever evolving. However, access to new genomic diagnostics such as rapid whole genome sequencing (rWGS) is hindered by barriers in implementation. Michigan's Project Baby Deer (PBD) is a multi-center collaborative effort that sought to break down barriers to access by offering rWGS to critically ill neonatal and pediatric inpatients in Michigan. The clinical champion team used a standardized approach with inclusion and exclusion criteria, shared learning, and quality improvement evaluation of the project's impact on the clinical outcomes and economics of inpatient rWGS. Hospitals, including those without on-site geneticists or genetic counselors, noted positive clinical impacts, accelerating time to definitive treatment for project patients. Between 95-214 hospital days were avoided, net savings of $4155 per patient, and family experience of care was improved. The project spurred policy advancement when Michigan became the first state in the United States to have a Medicaid policy with carve-out payment to hospitals for rWGS testing. This state project demonstrates how front-line clinician champions can directly improve access to new technology for pediatric patients and serves as a roadmap for expanding clinical implementation of evidence-based precision medicine technologies.
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Affiliation(s)
- Caleb P. Bupp
- Corewell Health Helen DeVos Children’s Hospital, Grand Rapids, MI 49503, USA
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI 49503, USA
- Correspondence: (C.P.B.); (A.S.-M.); Tel.: +1-616-391-2700 (C.P.B.)
| | - Elizabeth G. Ames
- Sparrow Hospital, University of Michigan Health System, Lansing, MI 48912, USA
| | | | - Sara Caylor
- Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123, USA
| | - David P. Dimmock
- Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123, USA
| | - Joseph D. Fakhoury
- Pediatric Hospital Medicine, Bronson Children’s Hospital, Kalamazoo, MI 49007, USA
- Department of Pediatric and Adolescent Medicine, Homer Stryker School of Medicine, Western Michigan University, Kalamazoo, MI 49007, USA
| | - Padmani Karna
- Department of Obstetrics, Gynecology and Reproductive Biology, College of Human Medicine, Michigan State University, Lansing, MI 48912, USA
| | - April Lehman
- Children’s Hospital of Michigan, Central Michigan University, Detroit, MI 48201, USA
| | - Cristian I. Meghea
- Department of Obstetrics, Gynecology and Reproductive Biology, College of Human Medicine, Michigan State University, Lansing, MI 48912, USA
| | - Vinod Misra
- Children’s Hospital of Michigan, Central Michigan University, Detroit, MI 48201, USA
| | | | - Jessica O’Shea
- Sparrow Hospital, University of Michigan Health System, Lansing, MI 48912, USA
| | - Aditi Sharangpani
- Department of Obstetrics, Gynecology and Reproductive Biology, College of Human Medicine, Michigan State University, Lansing, MI 48912, USA
| | - Linda S. Franck
- Department of Family Health Care Nursing, University of California, San Francisco, CA 94143, USA
| | - Andrea Scheurer-Monaghan
- Department of Pediatric and Adolescent Medicine, Homer Stryker School of Medicine, Western Michigan University, Kalamazoo, MI 49007, USA
- Neonatal Intensive Care, Bronson Children’s Hospital, Kalamazoo, MI 49007, USA
- Correspondence: (C.P.B.); (A.S.-M.); Tel.: +1-616-391-2700 (C.P.B.)
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19
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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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20
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Lynch F, Nisselle A, Stark Z, Gaff CL, McClaren B. Genetics follow up after rapid genomic sequencing in intensive care: current practices and recommendations for service delivery. Eur J Hum Genet 2022; 30:1276-1282. [PMID: 35953518 PMCID: PMC9626620 DOI: 10.1038/s41431-022-01168-w] [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: 05/04/2022] [Revised: 07/17/2022] [Accepted: 07/26/2022] [Indexed: 02/04/2023] Open
Abstract
The delivery of rapid genomic sequencing (rGS) to critically unwell children in intensive care occurs at a time of immense pressure and stress for parents. Contact with families after result disclosure, particularly after hospital discharge, presents an opportunity to meet their psychological, medical and information needs as they evolve. This study explores the preferences and perspectives of health professionals and parents of genetics follow up after rGS. Semi-structured interviews were conducted with 30 parents, seven genetic counsellors (GCs) and four intensive care physicians with experience in rGS. Transcripts were analysed using reflexive thematic analysis. Current practices surrounding genetics follow up after rGS were highly variable, resulting in some families not receiving the ongoing care they needed. Reasons identified by families for wanting follow-up care represented only a subset of those identified by health professionals. While GCs routinely provided their details to allow parents to initiate further contact, this was not always sufficient for follow-up care. Health professionals identified both organisational and psychosocial barriers to conducting follow up. As rGS transforms the diagnostic pathway in rare disease, there is a need for a co-designed, standardised but flexible model for follow-up care with genetics professionals so that families' evolving needs are met.
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Affiliation(s)
- Fiona Lynch
- Australian Genomics Health Alliance, Melbourne, VIC, Australia
- Department of Paediatrics, The University of Melbourne, Melbourne, VIC, Australia
- Genomics in Society, Murdoch Children's Research Institute, Melbourne, VIC, Australia
- Centre for Ethics of Paediatric Genomics, Murdoch Children's Research Institute, Melbourne, VIC, Australia
| | - Amy Nisselle
- Australian Genomics Health Alliance, Melbourne, VIC, Australia
- Department of Paediatrics, The University of Melbourne, Melbourne, VIC, Australia
- Genomics in Society, Murdoch Children's Research Institute, Melbourne, VIC, Australia
| | - Zornitza Stark
- Australian Genomics Health Alliance, Melbourne, VIC, Australia
- Department of Paediatrics, The University of Melbourne, Melbourne, VIC, Australia
- Victorian Clinical Genetics Service, Murdoch Children's Research Institute, Melbourne, VIC, Australia
| | - Clara L Gaff
- Australian Genomics Health Alliance, Melbourne, VIC, Australia
- Department of Paediatrics, The University of Melbourne, Melbourne, VIC, Australia
- Genomics in Society, Murdoch Children's Research Institute, Melbourne, VIC, Australia
- Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
| | - Belinda McClaren
- Australian Genomics Health Alliance, Melbourne, VIC, Australia.
- Department of Paediatrics, The University of Melbourne, Melbourne, VIC, Australia.
- Genomics in Society, Murdoch Children's Research Institute, Melbourne, VIC, Australia.
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21
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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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22
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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: 11] [Impact Index Per Article: 5.5] [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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Abstract
Genetic diseases disrupt the functionality of an infant's genome during fetal-neonatal adaptation and represent a leading cause of neonatal and infant mortality in the United States. Due to disease acuity, gene locus and allelic heterogeneity, and overlapping and diverse clinical phenotypes, diagnostic genome sequencing in neonatal intensive care units has required the development of methods to shorten turnaround times and improve genomic interpretation. From 2012 to 2021, 31 clinical studies documented the diagnostic and clinical utility of first-tier rapid or ultrarapid whole-genome sequencing through cost-effective identification of pathogenic genomic variants that change medical management, suggest new therapeutic strategies, and refine prognoses. Genomic diagnosis also permits prediction of reproductive recurrence risk for parents and surviving probands. Using implementation science and quality improvement, deployment of a genomic learning healthcare system will contribute to a reduction of neonatal and infant mortality through the integration of genome sequencing into best-practice neonatal intensive care.
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Affiliation(s)
- Stephen F. Kingsmore
- Rady Children’s Hospital Institute for Genomic Medicine, Rady Children’s Hospital-San Diego
| | - F. Sessions Cole
- Division of Newborn Medicine, Edward Mallinckrodt Department of Pediatrics, Washington University School of Medicine in St. Louis
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Sanford Kobayashi EF, Dimmock DP. Better and faster is cheaper. Hum Mutat 2022; 43:1495-1506. [PMID: 35723630 DOI: 10.1002/humu.24422] [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: 02/11/2022] [Revised: 05/23/2022] [Accepted: 06/08/2022] [Indexed: 11/09/2022]
Abstract
The rapid pace of advancement in genomic sequencing technology has recently reached a new milestone, with a record-setting time to molecular diagnosis of a mere 8 h. The catalyst behind this achievement is the accumulation of evidence indicating that quicker results more often make an impact on patient care and lead to healthcare cost savings. Herein, we review the diagnostic and clinical utility of rapid whole genome and rapid whole exome sequencing, the associated reduction in healthcare costs, and the relationship between these outcome measures and time-to-diagnosis.
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Affiliation(s)
- Erica F Sanford Kobayashi
- Department of Pediatrics, Cedars-Sinai Medical Center, Los Angeles, California, USA.,Rady Children's Institute for Genomic Medicine, Rady Children's Hospital, San Diego, California, USA
| | - David P Dimmock
- Rady Children's Institute for Genomic Medicine, Rady Children's Hospital, San Diego, California, USA
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P. Fishler K, Euteneuer JC, Brunelli L. Ethical Considerations for Equitable Access to Genomic Sequencing for Critically Ill Neonates in the United States. Int J Neonatal Screen 2022; 8:ijns8010022. [PMID: 35323201 PMCID: PMC8950005 DOI: 10.3390/ijns8010022] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Revised: 03/12/2022] [Accepted: 03/14/2022] [Indexed: 11/16/2022] Open
Abstract
Rare diseases impact all socio-economic, geographic, and racial groups indiscriminately. Newborn screening (NBS) is an exemplary international public health initiative that identifies infants with rare conditions early in life to reduce morbidity and mortality. NBS theoretically promotes equity through universal access, regardless of financial ability. There is however heterogeneity in access to newborn screening and conditions that are screened throughout the world. In the United States and some other developed countries, NBS is provided to all babies, subsidized by the local or federal government. Although NBS is an equitable test, infants admitted to neonatal intensive care units (NICUs) may not receive similar benefits to healthier infants. Newborns in the NICU may receive delayed and/or multiple newborn screens due to known limitations in interpreting the results with prematurity, total parenteral nutrition, blood transfusions, infection, and life support. Thus, genomic technologies might be needed in addition to NBS for equitable care of this vulnerable population. Whole exome (WES) and genome sequencing (WGS) have been recently studied in critically ill newborns across the world and have shown promising results in shortening diagnostic odysseys and providing clinical utility. However, in certain circumstances several barriers might limit access to these tests. Here, we discuss some of the existing barriers to genomic sequencing in NICUs in the United States, explore the ethical implications related to low access, consider ways to increase access to genomic testing, and offer some suggestions for future research in these areas.
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Affiliation(s)
- Kristen P. Fishler
- Munroe-Meyer Institute for Genetics and Rehabilitation, University of Nebraska Medical Center, Omaha, NE 68198, USA
- Correspondence:
| | | | - Luca Brunelli
- Division of Neonatology, University of Utah School of Medicine, Salt Lake City, UT 84132, USA;
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East KM, Cochran ME, Kelley WV, Greve V, Finnila CR, Coleman T, Jennings M, Alexander L, Rahn EJ, Danila MI, Barsh G, Korf B, Cooper G. Education and Training of Non-Genetics Providers on the Return of Genome Sequencing Results in a NICU Setting. J Pers Med 2022; 12:jpm12030405. [PMID: 35330405 PMCID: PMC8949881 DOI: 10.3390/jpm12030405] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Revised: 02/21/2022] [Accepted: 03/04/2022] [Indexed: 01/23/2023] Open
Abstract
To meet current and expected future demand for genome sequencing in the neonatal intensive care unit (NICU), adjustments to traditional service delivery models are necessary. Effective programs for the training of non-genetics providers (NGPs) may address the known barriers to providing genetic services including limited genetics knowledge and lack of confidence. The SouthSeq project aims to use genome sequencing to make genomic diagnoses in the neonatal period and evaluate a scalable approach to delivering genome sequencing results to populations with limited access to genetics professionals. Thirty-three SouthSeq NGPs participated in a live, interactive training intervention and completed surveys before and after participation. Here, we describe the protocol for the provider training intervention utilized in the SouthSeq study and the associated impact on NGP knowledge and confidence in reviewing, interpreting, and using genome sequencing results. Participation in the live training intervention led to an increased level of confidence in critical skills needed for real-world implementation of genome sequencing. Providers reported a significant increase in confidence level in their ability to review, understand, and use genome sequencing result reports to guide patient care. Reported barriers to implementation of genome sequencing in a NICU setting included test cost, lack of insurance coverage, and turn around time. As implementation of genome sequencing in this setting progresses, effective education of NGPs is critical to provide access to high-quality and timely genomic medicine care.
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Affiliation(s)
- Kelly M. East
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA; (M.E.C.); (W.V.K.); (V.G.); (C.R.F.); (T.C.); (M.J.); (L.A.); (G.B.); (G.C.)
- Correspondence: ; Tel.: +1-256-327-0461
| | - Meagan E. Cochran
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA; (M.E.C.); (W.V.K.); (V.G.); (C.R.F.); (T.C.); (M.J.); (L.A.); (G.B.); (G.C.)
| | - Whitley V. Kelley
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA; (M.E.C.); (W.V.K.); (V.G.); (C.R.F.); (T.C.); (M.J.); (L.A.); (G.B.); (G.C.)
| | - Veronica Greve
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA; (M.E.C.); (W.V.K.); (V.G.); (C.R.F.); (T.C.); (M.J.); (L.A.); (G.B.); (G.C.)
| | - Candice R. Finnila
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA; (M.E.C.); (W.V.K.); (V.G.); (C.R.F.); (T.C.); (M.J.); (L.A.); (G.B.); (G.C.)
| | - Tanner Coleman
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA; (M.E.C.); (W.V.K.); (V.G.); (C.R.F.); (T.C.); (M.J.); (L.A.); (G.B.); (G.C.)
| | - Mikayla Jennings
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA; (M.E.C.); (W.V.K.); (V.G.); (C.R.F.); (T.C.); (M.J.); (L.A.); (G.B.); (G.C.)
| | - Latonya Alexander
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA; (M.E.C.); (W.V.K.); (V.G.); (C.R.F.); (T.C.); (M.J.); (L.A.); (G.B.); (G.C.)
| | - Elizabeth J. Rahn
- Division of Clinical Immunology/Rheumatology, University of Alabama at Birmingham, Birmingham, AL 35294, USA; (E.J.R.); (M.I.D.)
| | - Maria I. Danila
- Division of Clinical Immunology/Rheumatology, University of Alabama at Birmingham, Birmingham, AL 35294, USA; (E.J.R.); (M.I.D.)
| | - Greg Barsh
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA; (M.E.C.); (W.V.K.); (V.G.); (C.R.F.); (T.C.); (M.J.); (L.A.); (G.B.); (G.C.)
| | - Bruce Korf
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, USA;
| | - Greg Cooper
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA; (M.E.C.); (W.V.K.); (V.G.); (C.R.F.); (T.C.); (M.J.); (L.A.); (G.B.); (G.C.)
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Healthcare Professionals’ Attitudes toward Rapid Whole Genome Sequencing in Pediatric Acute Care. CHILDREN 2022; 9:children9030357. [PMID: 35327729 PMCID: PMC8947383 DOI: 10.3390/children9030357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Revised: 02/24/2022] [Accepted: 02/24/2022] [Indexed: 11/16/2022]
Abstract
We aimed to characterize knowledge and attitudes about rapid whole genome sequencing (rWGS) implementation of a broad constituency of healthcare professionals at hospitals participating in a statewide initiative to implement rWGS for hospitalized neonates and children up to 18 years of age meeting clinical criteria for testing. We surveyed 307 healthcare professionals from eight hospitals about their knowledge and attitudes regarding rWGS. We examined survey internal reliability using exploratory factor analysis and associations between respondent characteristics and attitudes toward rWGS with linear regression. We thematically analyzed free-text responses. Views about rWGS implementation in respondents’ own setting and respondents’ personal capability to implement rWGS were generally neutral (M = 3.44 (SD = 0.74); M = 3.30 (SD = 0.85), respectively). Views about the potential for rWGS in clinical practice were overall positive (M = 4.12 (SD = 0.57)). The degree of positivity of attitudes about rWGS was strongly influenced by perceived knowledge, clinical or non-clinical role, concerns about future insurance coverage for rWGS as a first-tier test, and future adverse impact of genomics health information on patients or families. We identified several actionable factors influencing attitudes toward rWGS of pediatric healthcare professionals. Expanded education and ongoing implementation research are needed for the full potential of rWGS in pediatrics to be realized.
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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: 19] [Impact Index Per Article: 9.5] [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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Franck LS, Dimmock D, Hobbs C, Kingsmore SF. Rapid whole-genome sequencing in critically Ill children: shifting from unease to evidence, education, and equitable implementation. J Pediatr 2021; 238:343. [PMID: 34390697 PMCID: PMC10865930 DOI: 10.1016/j.jpeds.2021.08.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 08/06/2021] [Indexed: 12/31/2022]
Affiliation(s)
- Linda S. Franck
- Department of Family Health Care Nursing, University of
California San Francisco, San Francisco, CA
| | - David Dimmock
- Rady Children’s Institute for Genomic Medicine, San
Diego, CA
- Rady Children’s Hospital, San Diego, CA
| | - Charlotte Hobbs
- Rady Children’s Institute for Genomic Medicine, San
Diego, CA
- Rady Children’s Hospital, San Diego, CA
| | - Stephen F. Kingsmore
- Rady Children’s Institute for Genomic Medicine, San
Diego, CA
- Rady Children’s Hospital, San Diego, CA
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Reply. J Pediatr 2021; 238:343-344. [PMID: 34390696 DOI: 10.1016/j.jpeds.2021.08.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 08/06/2021] [Indexed: 11/22/2022]
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31
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Sources of Unease About the Use of Genome Sequencing for Diagnosing Rare Diseases in Children. J Pediatr 2021; 237:13-15. [PMID: 34166672 DOI: 10.1016/j.jpeds.2021.06.042] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Accepted: 06/18/2021] [Indexed: 02/06/2023]
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