Scientific Publications

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16 Results

2022

Healthcare Professionals’ Attitudes toward Rapid Whole Genome Sequencing in Pediatric Acute Care

Franck LS, Scheurer-Monaghan A, Bupp CP, Fakhoury JD, Hoffmann TJ, Deshpandey M, Arenchild M, Dimmock DP.

Children. 2022; 9(3):357. 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.
https://doi.org/10.3390/children9030357

March 4, 2022
RPM for NICU and PICUrWGS

Evaluating use of changing technologies for rapid next-generation sequencing in pediatrics

Palmquist R, Jenkins SM, Bentley D, Miller C, Mao R, Meibos B, Bayrak-Toydemir P, Tvrdik T, Nadauld LD, Bleyl SB, Chowdhury S, Ostrander B, Flores-Daboub J, Longo N, Tristani-Firouzi M, Hobbs C, Bonkowsky JL, Brunelli L.

Pediatr Res. 2022 Feb 3. doi: 10.1038/s41390-022-01965-5. Online ahead of print. ABSTRACT BACKGROUND: Rapid next-generation sequencing (NGS) offers the potential to shorten the diagnostic process and improve the care of acutely ill children. The goal of this study was to report our findings, including benefits and limitations, of a targeted NGS panel and rapid genome sequencing (rGS) in neonatal and pediatric acute clinical care settings. METHODS: Retrospective analysis of patient characteristics, diagnostic yields, turnaround time, and changes in management for infants and children receiving either RapSeq, a targeted NGS panel for 4500+ genes, or rGS, at the University of Utah Hospital and Primary Children’s Hospital, from 2015 to 2020. RESULTS: Over a 5-year period, 142 probands underwent rapid NGS: 66 received RapSeq and 76 rGS. Overall diagnostic yield was 39%. In the majority of diagnostic cases, there were one or more changes in clinical care management. Of note, 7% of diagnoses identified by rGS would not have been identified by RapSeq. CONCLUSIONS: Our results indicate that rapid NGS impacts acute pediatric care in real-life clinical settings. Although affected by patient selection criteria, diagnostic yields were similar to those from clinical trial settings. Future studies are needed to determine relative advantages, including cost, turnaround time, and benefits for patients, of each approach in specific clinical circumstances. IMPACT: The use of comprehensive Mendelian gene panels and genome sequencing in the clinical setting allows for early diagnosis of patients in neonatal, pediatric, and cardiac intensive care units and impactful change in management. Diagnoses led to significant changes in management for several patients in lower acuity inpatient units supporting further exploration of the utility of rapid sequencing in these settings. This study reviews the limitations of comparing sequencing platforms in the clinical setting and the variables that should be considered in evaluating diagnostic rates across studies. PMID:35115709 | DOI:10.1038/s41390-022-01965-5

February 3, 2022
RPM for NICU and PICUrWGS

Cost Efficacy of Rapid Whole Genome Sequencing in the Pediatric Intensive Care Unit 

Sanford Kobayashi Erica, Waldman Bryce, Engorn Branden M., Perofsky Katherine, Allred Erika, Briggs Benjamin, Gatcliffe Chelsea, Ramchandar Nanda, Gold Jeffrey J., Doshi Ami, Ingulli Elizabeth G., Thornburg Courtney D., Benson Wendy, Farnaes Lauge, Chowdhury Shimul, Rego Seema, Hobbs Charlotte, Kingsmore Stephen F., Dimmock David P., Coufal Nicole G.

Front. Pediatr., 24 January 2022. doi: 10.3389/fped.2021.809536. 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. PMID:35141181 | PMC:PMC8818891 | DOI:10.3389/fped.2021.809536

January 24, 2022
RPM for NICU and PICUrWGS

2021

Addressing ethical and laboratory challenges for initiation of a rapid whole genome sequencing program

Malone Jenkins S, Palmquist R, Kapron AL, Torr C, Best DH, Karren MA, Brunelli L, Yandell M, Tristani-Firouzi M, Dimmock D, Watts B, Botkin JR, Johnson A, Bonkowsky JL

J Clin Transl Sci. 2021 Aug 9;5(1):e177. doi: 10.1017/cts.2021.833. eCollection 2021. ABSTRACT Rapid whole genome sequencing (rapid WGS) is a powerful diagnostic tool that is becoming increasingly practical for widespread clinical use. However, protocols for its use are challenging to implement. A significant obstacle to clinical adoption is that laboratory certification requires an initial research development phase, which is constrained by regulations from returning results. Regulations preventing return of results have ethical implications in cases which might impact patient outcomes. Here, we describe our experience with the development of a rapid WGS research protocol, that balanced the requirements for laboratory-validated test development with the ethical needs of clinically relevant return of results. PMID:34849253 | PMC:PMC8596074 | DOI:10.1017/cts.2021.833

December 2, 2021
rWGS

Rapid whole genome sequencing in critically ill children: Shifting from unease to evidence, education and equitable implementation

Linda S. Franck, RN, PhD, David Dimmock, MD, FACMG DABP, Charlotte Hobbs, MD, PhD, Stephen F. Kingsmore, MD, DSc

J Pediatr. 2021 Aug 11:S0022-3476(21)00761-7. doi: 10.1016/j.jpeds.2021.08.006. Online ahead of print. NO ABSTRACT PMID:34390697 | DOI:10.1016/j.jpeds.2021.08.006

August 17, 2021
rWGS

Postmortem whole-genome sequencing on a dried blood spot identifies a novel homozygous SUOX variant causing isolated sulfite oxidase deficiency

Owen MJ, Lenberg J, Feigenbaum A, Gold J, Chau K, Bezares-Orin Z, Ding Y, Chowdhury S, Kingsmore SF. 

Cold Spring Harb Mol Case Stud. 2021 Jun 11;7(3):a006091. doi: 10.1101/mcs.a006091. Print 2021 Jun. ABSTRACT Rapid whole-genome sequencing (rWGS) has shown that genetic diseases are a common cause of infant mortality in neonatal intensive care units. Dried blood spots collected for newborn screening allow investigation of causes of infant mortality that were not diagnosed during life. Here, we present a neonate who developed seizures and encephalopathy on the third day of life that was refractory to antiepileptic medications. The patient died on day of life 16 after progressive respiratory failure and sepsis. The parents had lost two prior children after similar presentations, neither of whom had a definitive diagnosis. Postmortem rWGS of a dried blood spot identified a pathogenic homozygous frameshift variant in the SUOX gene associated with isolated sulfite oxidase deficiency (c.1390_1391del, p.Leu464GlyfsTer10). This case highlights that early, accurate molecular diagnosis has the potential to influence prenatal counseling and guide management in rare, genetic disorders and has added importance in cases of a strong family history and risk factors such as consanguinity. PMID:34117075 | DOI:10.1101/mcs.a006091

June 14, 2021
Infant MortalityrWGS

Project Baby Bear: Rapid precision care incorporating rWGS in 5 California children’s hospitals demonstrates improved clinical outcomes and reduced costs of care

Dimmock D, Caylor S, Waldman B, Benson W, Ashburner C, Carmichael JL, Carroll J, Cham E, Chowdhury S, Cleary J, D’Harlingue A, Doshi A, Ellsworth K, Galarreta CI, Hobbs C, Houtchens K, Hunt J, Joe P, Joseph M, Kaplan RH, Kingsmore SF, Knight J, Kochhar A, Kronick RG, Limon J, Martin M, Rauen KA, Schwarz A, Shankar SP, Spicer R, Rojas MA, Vargas-Shiraishi O, Wigby K, Zadeh N, Farnaes L. 

Am J Hum Genet. 2021 May 29:S0002-9297(21)00192-0. doi: 10.1016/j.ajhg.2021.05.008. Online ahead of print. ABSTRACT Genetic disorders are a leading contributor to mortality in neonatal and pediatric intensive care units (ICUs). Rapid whole-genome sequencing (rWGS)-based rapid precision medicine (RPM) is an intervention that has demonstrated improved clinical outcomes and reduced costs of care. However, the feasibility of broad clinical deployment has not been established. The objective of this study was to implement RPM based on rWGS and evaluate the clinical and economic impact of this implementation as a first line diagnostic test in the California Medicaid (Medi-Cal) program. Project Baby Bear was a payor funded, prospective, real-world quality improvement project in the regional ICUs of five tertiary care children’s hospitals. Participation was limited to acutely ill Medi-Cal beneficiaries who were admitted November 2018 to May 2020, were <1 year old and within one week of hospitalization, or had just developed an abnormal response to therapy. The whole cohort received RPM. There were two prespecified primary outcomes-changes in medical care reported by physicians and changes in the cost of care. The majority of infants were from underserved populations. Of 184 infants enrolled, 74 (40%) received a diagnosis by rWGS that explained their admission in a median time of 3 days. In 58 (32%) affected individuals, rWGS led to changes in medical care. Testing and precision medicine cost $1.7 million and led to $2.2-2.9 million cost savings. rWGS-based RPM had clinical utility and reduced net health care expenditures for infants in regional ICUs. rWGS should be considered early in ICU admission when the underlying etiology is unclear. PMID:34089648 | DOI:10.1016/j.ajhg.2021.05.008

June 7, 2021
RPM for NICU and PICUrWGS

Rapid Sequencing-Based Diagnosis of Thiamine Metabolism Dysfunction Syndrome

Owen MJ, Niemi AK, Dimmock DP, Speziale M, Nespeca M, Chau KK, Van Der Kraan L, Wright MS, Hansen C, Veeraraghavan N, Ding Y, Lenberg J, Chowdhury S, Hobbs CA, Batalov S, Zhu Z, Nahas SA, Gilmer S, Knight G, Lefebvre S, Reynders J, Defay T, Weir J, Thomson VS, Fraser L, Lajoie BR, McPhail TK, Mehtalia SS, Kunard CM, Hall KP, Kingsmore SF.

N Engl J Med. 2021 Jun 3;384(22):2159-2161. doi: 10.1056/NEJMc2100365. NO ABSTRACT PMID:34077649 | DOI:10.1056/NEJMc2100365

June 3, 2021
rWGS

Implementing Rapid Whole Genome Sequencing in Critical Care: A Qualitative Study of Facilitators and Barriers to New Technology Adoption

Franck LS, Kriz RM, Rego S, Garman K, Hobbs C, Dimmock D.

J Pediatr. 2021 May 20:S0022-3476(21)00496-0. doi: 10.1016/j.jpeds.2021.05.045. Online ahead of print. ABSTRACT OBJECTIVE: To characterize the views of members of the multi-disciplinary team regarding the implementation of Rapid Whole Genome Sequencing (rWGS) as a first-tier test for critically ill children in diverse children’s hospital settings. STUDY DESIGN: Qualitative interviews informed by implementation science theory were conducted with the multi-disciplinary patient care teams and hospital leaders at each of the five tertiary care children’s hospitals involved in a statewide rWGS implementation project. RESULTS: Our analysis revealed 5 key themes regarding the implementation process across the sites: the need for rWGS champions, educational needs and strategies, negotiating decision-making roles and processes, workflows and workarounds, and perceptions about rWGS. From the findings a composite clinical workflow diagram was developed to summarize all of the processes involved in the implementation of the test, and the key areas where implementation practices differed. CONCLUSIONS: These findings provide insights for design of interventions to support adoption, scale-up and sustainability of rWGS and other novel technologies in neonatal and pediatric critical care settings. PMID:34023348 | DOI:10.1016/j.jpeds.2021.05.045

May 24, 2021
rWGS

Expanding the genotypic spectrum of ACTG2-related visceral myopathy

James KN, Lau M, Shayan K, Lenberg J, Mardach R, Ignacio R Jr, Halbach J, Choi L, Kumar S, Ellsworth KA.

Cold Spring Harb Mol Case Stud. 2021 Apr 21:mcs.a006085. doi: 10.1101/mcs.a006085. Online ahead of print.

ABSTRACT

Visceral myopathies (VMs) encompass a spectrum of disorders characterized by chronic disruption of gastrointestinal function, with or without urinary system involvement. Pathogenic missense variation in smooth muscle gamma-actin gene (ACTG2) is associated with autosomal dominant VM. Whole genome sequencing of an infant presenting with chronic intestinal pseudo-obstruction revealed a homozygous 187 base pair (c.589_613+163del188) deletion spanning the exon 6-intron 6 boundary within ACTG2. The patient’s clinical course was marked by prolonged hospitalizations, multiple surgeries, and intermittent total parenteral nutrition dependence. This case supports the emerging understanding of allelic heterogeneity in ACTG2-related VM, in which both homozygous and heterozygous variants in ACTG2 are associated with gastrointestinal dysfunction of similar severity and overlapped clinical presentation. Moreover, it illustrates the clinical utility of rapid whole genome sequencing, which can comprehensively and precisely detect different types of genomic variants including small deletions, leading to guidance of clinical care decisions.

PMID:33883208 | DOI:10.1101/mcs.a006085

April 23, 2021
rWGS

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