1
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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2
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Rodriguez AM, Schain K, Jayakar P, Wright MS, Chowdhury S, Salyakina D. Report of two cases of Schaaf-Yang syndrome: Same genotype and different phenotype. Clin Case Rep 2023; 11:e7753. [PMID: 37529132 PMCID: PMC10387585 DOI: 10.1002/ccr3.7753] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 07/06/2023] [Accepted: 07/12/2023] [Indexed: 08/03/2023] Open
Abstract
We report two, genotypically identical but phenotypically distinct cases of Schaaf-Yang syndrome and propose the early use of Genome Sequencing in patients with nonspecific presentations to facilitate the early diagnosis of children with rare genetic diseases and improve overall health care outcomes.
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Affiliation(s)
- Ana Maria Rodriguez
- Division of Genetics and MetabolismNicklaus Children's Hospital Pediatric SpecialistsMiamiFloridaUSA
| | - Katherine Schain
- Division of Genetics and MetabolismNicklaus Children's Hospital Pediatric SpecialistsMiamiFloridaUSA
| | - Parul Jayakar
- Division of Genetics and MetabolismNicklaus Children's Hospital Pediatric SpecialistsMiamiFloridaUSA
| | - Meredith S. Wright
- Rady Children's Institute for Genomic MedicineSan DiegoCaliforniaUSA
- Keck Graduate InstituteClaremontCaliforniaUSA
| | - Shimul Chowdhury
- Rady Children's Institute for Genomic MedicineSan DiegoCaliforniaUSA
| | - Daria Salyakina
- Personalized Medicine & Health Outcomes Research, Nicklaus Children's Hospital Pediatric SpecialistsMiamiFloridaUSA
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3
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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4
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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) 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] [What about the content of this article? (0)] [Affiliation(s)] [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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5
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Beaman M, Fisher K, McDonald M, Tan QKG, Jackson D, Cocanougher BT, Landstrom AP, Hobbs CA, Cotten M, Cohen JL. Rapid Whole Genome Sequencing in Critically Ill Neonates Enables Precision Medicine Pipeline. J Pers Med 2022; 12:1924. [PMID: 36422100 PMCID: PMC9694815 DOI: 10.3390/jpm12111924] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 10/24/2022] [Accepted: 11/05/2022] [Indexed: 09/07/2023] Open
Abstract
Rapid genome sequencing in critically ill infants is increasingly identified as a crucial test for providing targeted and informed patient care. We report the outcomes of a pilot study wherein eight critically ill neonates received rapid whole genome sequencing with parental samples in an effort to establish a prompt diagnosis. Our pilot study resulted in a 37.5% diagnostic rate by whole genome sequencing alone and an overall 50% diagnostic rate for the cohort. We describe how the diagnoses led to identification of additional affected relatives and a change in management, the limitations of rapid genome sequencing, and some of the challenges with sample collection. Alongside this pilot study, our site simultaneously established a research protocol pipeline that will allow us to conduct research-based genomic testing in the cases for which a diagnosis was not reached by rapid genome sequencing or other available clinical testing. Here we describe the benefits, limitations, challenges, and potential for rapid whole genome sequencing to be incorporated into routine clinical evaluation in the neonatal period.
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Affiliation(s)
- Makenzie Beaman
- Duke University Medical Scientist Training Program, Durham, NC 27710, USA
- Duke University Department of Pediatrics, Division of Medical Genetics, Durham, NC 27710, USA
| | - Kimberley Fisher
- Duke University Department of Pediatrics, Division of Neonatology, Durham, NC 27710, USA
| | - Marie McDonald
- Duke University Department of Pediatrics, Division of Medical Genetics, Durham, NC 27710, USA
| | - Queenie K. G. Tan
- Duke University Department of Pediatrics, Division of Medical Genetics, Durham, NC 27710, USA
| | - David Jackson
- Duke University Department of Pediatrics, Division of Medical Genetics, Durham, NC 27710, USA
| | - Benjamin T. Cocanougher
- Duke University Department of Pediatrics, Division of Medical Genetics, Durham, NC 27710, USA
| | - Andrew P. Landstrom
- Duke University Department of Pediatrics, Division of Cardiology, Durham, NC 27710, USA
| | - Charlotte A. Hobbs
- Rady Children’s Institute for Genomic Medicine, Rady Children’s Hospital, San Diego, CA 92123, USA
| | - Michael Cotten
- Duke University Department of Pediatrics, Division of Neonatology, Durham, NC 27710, USA
| | - Jennifer L. Cohen
- Duke University Department of Pediatrics, Division of Medical Genetics, Durham, NC 27710, USA
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6
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Kingsmore SF. Dispatches from Biotech beginning BeginNGS: Rapid newborn genome sequencing to end the diagnostic and therapeutic odyssey. Am J Med Genet C Semin Med Genet 2022; 190:243-256. [PMID: 36218021 PMCID: PMC9588745 DOI: 10.1002/ajmg.c.32005] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 08/29/2022] [Accepted: 08/29/2022] [Indexed: 01/11/2023]
Abstract
In this Dispatch from Biotech, we briefly review the urgent need for extensive expansion of newborn screening (NBS) by genomic sequencing, and the reasons why early attempts had limited success. During the next decade transformative developments will continue in society and in the pharmaceutical, biotechnology, informatics, and medical sectors that enable prompt addition of genetic disorders to NBS by rapid whole genome sequencing (rWGS) upon introduction of new therapies that qualify them according to the Wilson and Jungner criteria (Wilson, J. M. G., & Jungner, G., World Health Organization. (1968). Principles and Practice of Screening for Disease. World Health Organization. Retrieved from https://apps.who.int/iris/handle/10665/37650). Herein we describe plans, progress, and clinical trial designs for BeginNGS (Newborn Genome Sequencing to end the diagnostic and therapeutic odyssey), a new international, pre-competitive, public-private consortium that proposes to implement a self-learning healthcare delivery system for screening all newborns for over 400 hundred genetic diseases, diagnostic confirmation, implementation of effective treatment, and acceleration of orphan drug development. We invite investigators and stakeholders worldwide to join the consortium in a prospective, multi-center, international trial of the clinical utility and cost effectiveness of BeginNGS.
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Affiliation(s)
- Stephen F. Kingsmore
- Rady Children's Institute for Genomic Medicine, Rady Children's HospitalSan DiegoCaliforniaUSA
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7
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Sen K, Harmon J, Gropman AL. Select Ethical Aspects of Next-Generation Sequencing Tests for Newborn Screening and Diagnostic Evaluation of Critically Ill Newborns. Int J Neonatal Screen 2021; 7:ijns7040076. [PMID: 34842609 PMCID: PMC8628939 DOI: 10.3390/ijns7040076] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Revised: 11/02/2021] [Accepted: 11/04/2021] [Indexed: 12/26/2022] Open
Abstract
In this review, we analyze medical and select ethical aspects of the increasing use of next-generation sequencing (NGS) based tests in newborn medicine. In the last five years, there have been several studies exploring the role of rapid exome sequencing (ES) and genome sequencing (GS) in critically ill newborns. While the advantages include a high diagnostic yield with potential changes in interventions, there have been ethical dilemmas surrounding consent, information about adult-onset diseases and resolution of variants of uncertain significance. Another active area of research includes a cohort of studies funded under Newborn Sequencing in Genomic Medicine and Public Health pertaining to the use of ES and GS in newborn screening (NBS). While these techniques may allow for screening for several genetic disorders that do not have a detectable biochemical marker, the high costs and long turnaround times of these tests are barriers in their utilization as public health screening tests. Discordant results between conventional NBS and ES-based NBS, as well as challenges with consent, are other potential pitfalls of this approach. Please see the Bush, Al-Hertani and Bodamer article in this Special Issue for the broader scope and further discussion.
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Affiliation(s)
- Kuntal Sen
- Division of Neurogenetics and Developmental Pediatrics, Center for Neuroscience and Behavioral Medicine, Children’s National Hospital, Washington, DC 20010, USA;
| | - Jennifer Harmon
- Rare Disease Institute, Children’s National Hospital, Washington, DC 20010, USA;
| | - Andrea L. Gropman
- Division of Neurogenetics and Developmental Pediatrics, Center for Neuroscience and Behavioral Medicine, Children’s National Hospital, Washington, DC 20010, USA;
- Correspondence: ; Tel.: +1-202-476-3511; Fax: +1-202-476-4336
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8
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Werner KM, Cox AJ, Qian E, Jain P, Ji W, Tikhonova I, Castaldi C, Bilguvar K, Knight J, Ferdinandusse S, Fawaz R, Jiang YH, Gallagher PG, Bizzarro M, Gruen JR, Bale A, Zhang H. D-bifunctional protein deficiency caused by splicing variants in a neonate with severe peroxisomal dysfunction and persistent hypoglycemia. Am J Med Genet A 2021; 188:357-363. [PMID: 34623748 DOI: 10.1002/ajmg.a.62520] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2021] [Revised: 08/31/2021] [Accepted: 09/03/2021] [Indexed: 01/27/2023]
Abstract
D-bifunctional protein (DBP) deficiency is a rare, autosomal recessive peroxisomal enzyme deficiency resulting in a high burden of morbidity and early mortality. Patients with DBP deficiency resemble those with a severe Zellweger phenotype, with neonatal hypotonia, seizures, craniofacial dysmorphisms, psychomotor delay, deafness, blindness, and death typically within the first 2 years of life, although patients with residual enzyme function can survive longer. The clinical severity of the disease depends on the degree of enzyme deficiency. Loss-of-function variants typically result in no residual enzyme activity; however, splice variants may result in protein with residual function. We describe a full-term newborn presenting with hypotonia, seizures, and unexplained hypoglycemia, who was later found to have rickets at follow up. Rapid whole genome sequencing identified two HSD17B4 variants in trans; one likely pathogenic variant and one variant of uncertain significance (VUS) located in the polypyrimidine tract of intron 13. To determine the functional consequence of the VUS, we analyzed RNA from the patient's father with RNA-seq which showed skipping of Exon 14, resulting in a frameshift mutation three amino acids from the new reading frame. This RNA-seq analysis was correlated with virtually absent enzyme activity, elevated very-long-chain fatty acids in fibroblasts, and a clinically severe phenotype. Both variants are reclassified as pathogenic. Due to the clinical spectrum of DBP deficiency, this provides important prognostic information, including early mortality. Furthermore, we add persistent hypoglycemia to the clinical spectrum of the disease, and advocate for the early management of fat-soluble vitamin deficiencies to reduce complications.
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Affiliation(s)
- Kelly M Werner
- Department of Pediatrics, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Allison J Cox
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, USA.,PreventionGenetics LLC, Marshfield, Wisconsin, USA
| | - Emily Qian
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Preti Jain
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, USA.,Sema4, Stanford, CT, USA
| | - Weizhen Ji
- Department of Pediatrics, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Irina Tikhonova
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Christopher Castaldi
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Kaya Bilguvar
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, USA
| | - James Knight
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Sacha Ferdinandusse
- Department of Clinical Chemistry, Amsterdam UMC Locatie AMC, Amsterdam, Netherlands
| | - Rima Fawaz
- Department of Pediatrics, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Yong-Hui Jiang
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Patrick G Gallagher
- Department of Pediatrics, Yale University School of Medicine, New Haven, Connecticut, USA.,Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, USA.,Department of Pathology, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Matthew Bizzarro
- Department of Pediatrics, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Jeffrey R Gruen
- Department of Pediatrics, Yale University School of Medicine, New Haven, Connecticut, USA.,Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Allen Bale
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Hui Zhang
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, USA
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9
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Sanford Kobayashi E, Waldman B, Engorn BM, Perofsky K, Allred E, Briggs B, Gatcliffe C, Ramchandar N, Gold JJ, Doshi A, Ingulli EG, Thornburg CD, Benson W, Farnaes L, Chowdhury S, Rego S, Hobbs C, Kingsmore SF, Dimmock DP, Coufal NG. Cost Efficacy of Rapid Whole Genome Sequencing in the Pediatric Intensive Care Unit. Front Pediatr 2021; 9:809536. [PMID: 35141181 PMCID: PMC8818891 DOI: 10.3389/fped.2021.809536] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Accepted: 12/29/2021] [Indexed: 11/26/2022] Open
Abstract
The diagnostic and clinical utility of rapid whole genome sequencing (rWGS) for critically ill children in the intensive care unit (ICU) has been substantiated by multiple studies, but comprehensive cost-effectiveness evaluation of rWGS in the ICU outside of the neonatal age group is lacking. In this study, we examined cost data retrospectively for a cohort of 38 children in a regional pediatric ICU (PICU) who received rWGS. We identified seven of 17 patients who received molecular diagnoses by rWGS and had resultant changes in clinical management with sufficient clarity to permit cost and quality adjusted life years (QALY) modeling. Cost of PICU care was estimated to be reduced by $184,846 and a total of 12.1 QALYs were gained among these seven patients. The total cost of rWGS for patients and families for the entire cohort (38 probands) was $239,400. Thus, the net cost of rWGS was $54,554, representing $4,509 per QALY gained. This quantitative, retrospective examination of healthcare utilization associated with rWGS-informed medicine interventions in the PICU revealed approximately one-third of a QALY gained per patient tested at a cost per QALY that was approximately one-tenth of that typically sought for cost-effective new medical interventions. This evidence suggests that performance of rWGS as a first-tier test in selected PICU children with diseases of unknown etiology is associated with acceptable cost-per-QALY gained.
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Affiliation(s)
- Erica Sanford Kobayashi
- Department of Pediatrics, Cedars-Sinai Medical Center, Los Angeles, CA, United States.,Rady Children's Institute for Genomic Medicine, San Diego, CA, United States
| | - Bryce Waldman
- Rady Children's Institute for Genomic Medicine, San Diego, CA, United States
| | - Branden M Engorn
- Rady Children's Hospital San Diego, San Diego, CA, United States
| | - Katherine Perofsky
- Rady Children's Institute for Genomic Medicine, San Diego, CA, United States.,Rady Children's Hospital San Diego, San Diego, CA, United States
| | - Erika Allred
- Rady Children's Institute for Genomic Medicine, San Diego, CA, United States.,Rady Children's Hospital San Diego, San Diego, CA, United States
| | - Benjamin Briggs
- Naval Medical Center San Diego, San Diego, CA, United States
| | - Chelsea Gatcliffe
- McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX, United States
| | - Nanda Ramchandar
- Rady Children's Institute for Genomic Medicine, San Diego, CA, United States.,Rady Children's Hospital San Diego, San Diego, CA, United States
| | - Jeffrey J Gold
- Rady Children's Hospital San Diego, San Diego, CA, United States.,Department of Neuroscience, University of California, San Diego, San Diego, CA, United States
| | - Ami Doshi
- Rady Children's Hospital San Diego, San Diego, CA, United States.,Department of Pediatrics, University of California, San Diego, San Diego, CA, United States
| | | | - Courtney D Thornburg
- Rady Children's Hospital San Diego, San Diego, CA, United States.,Department of Pediatrics, University of California, San Diego, San Diego, CA, United States
| | - Wendy Benson
- Rady Children's Institute for Genomic Medicine, San Diego, CA, United States
| | - Lauge Farnaes
- Department of Infectious Disease, University of California, San Diego, San Diego, CA, United States
| | - Shimul Chowdhury
- Rady Children's Institute for Genomic Medicine, San Diego, CA, United States
| | - Seema Rego
- Rady Children's Institute for Genomic Medicine, San Diego, CA, United States
| | - Charlotte Hobbs
- Rady Children's Institute for Genomic Medicine, San Diego, CA, United States
| | - Stephen F Kingsmore
- Rady Children's Institute for Genomic Medicine, San Diego, CA, United States
| | - David P Dimmock
- Rady Children's Institute for Genomic Medicine, San Diego, CA, United States
| | - Nicole G Coufal
- Rady Children's Institute for Genomic Medicine, San Diego, CA, United States.,Rady Children's Hospital San Diego, San Diego, CA, United States.,Department of Pediatrics, University of California, San Diego, San Diego, CA, United States
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Hussain SB, Quittner AL, Brown M, Li-Rosi AM. Understanding access to genomics in an ethnically diverse south Florida population: A comparison of demographics in odyssey and rapid whole genome sequencing programs. J Genet Couns 2020; 29:553-561. [PMID: 32277851 DOI: 10.1002/jgc4.1281] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Revised: 02/18/2020] [Accepted: 02/26/2020] [Indexed: 11/11/2022]
Abstract
Advances in genomic medicine have evolved to include rapid whole genome sequencing (rWGS) in pediatric intensive care settings. Traditionally, genetic testing was conducted in outpatient clinics, with stepwise genetic testing occurring over several years. This delayed the time to diagnosis, making it more difficult to include underrepresented groups, such as those who identify as Black and Latinx. National genetic sequencing programs have also struggled to engage these participants in their studies, leading to a significant disparity in access to new genetic technologies. The purpose of our study was to compare the demographic characteristics of families enrolled in both an Odyssey Program (N = 46), defined as outpatients in the Genetics Clinic who have had prior genetic testing, and a newly implemented rWGS (N = 52) sequencing program. Despite living in a large, ethnically diverse city, our results indicated that parents in the Odyssey program differed significantly from parents in the rWGS program in level of education, family income, and insurance status. For example, 71.5% of parents in the diagnostic Odyssey program had a college or advanced degree, whereas 42% of parents in the rWGS program had this level of education. Family income and insurance also differed, with 48.6% of families in the Odyssey program earning $100,000 or more versus 28.2% in rWGS; 56% of parents in the Odyssey program had private insurance with 26% on Medicaid whereas only 23% of parents in rWGS had private insurance, with the vast majority of children on Medicaid (69%). Thus, our Odyssey program illustrates some of the common pitfalls in implementing genomic testing in an ethnically diverse community, including lack of referrals, travel to outpatient visits, and a cultural mismatch with providers. The successful enrollment of underrepresented groups in the rWGS program demonstrates that given the opportunity to participate in genetic testing, families are interested and aware of the potential benefits of this testing for their child. As genomic sequencing transitions from outpatient to inpatient settings, an opportunity arises to close the health disparity gap. Recommendations for implementing rWGS in pediatric, intensive care settings that address the common barriers faced by underrepresented families are discussed.
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Affiliation(s)
- Saida B Hussain
- Research Institute, Nicklaus Children's Hospital, Miami, FL, USA
| | | | - Marilyn Brown
- Research Institute, Nicklaus Children's Hospital, Miami, FL, USA
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Kernan KF, Ghaloul-Gonzalez L, Vockley J, Carcillo JA. Rapid Whole Genome Sequencing and Fulfilling the Promise of Precision Pediatric Critical Care. Pediatr Crit Care Med 2019; 20:1085-6. [PMID: 31688677 DOI: 10.1097/PCC.0000000000002082] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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