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Migliavacca MP, Sobreira J, Bermeo D, Gomes M, Alencar D, Sussuchi L, Souza CA, Silva JS, Kroll JE, Burger M, Guarischi-Sousa R, Villela D, Yamamoto GL, Milanezi F, Horigoshi N, Cesar RG, de Carvalho WB, Honjo RS, Bertola DR, Kim CA, de Souza L, Procianoy RS, Silveria RC, Rosenberg C, Giugliani R, Campana GA, Scapulatempo-Neto C, Sobreira N. Whole genome sequencing as a first-tier diagnostic test for infants in neonatal intensive care units: A pilot study in Brazil. Am J Med Genet A 2024; 194:e63544. [PMID: 38258498 DOI: 10.1002/ajmg.a.63544] [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] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 12/27/2023] [Accepted: 12/28/2023] [Indexed: 01/24/2024]
Abstract
In this pilot study, we aimed to evaluate the feasibility of whole genome sequencing (WGS) as a first-tier diagnostic test for infants hospitalized in neonatal intensive care units in the Brazilian healthcare system. The cohort presented here results from a joint collaboration between private and public hospitals in Brazil considering the initiative of a clinical laboratory to provide timely diagnosis for critically ill infants. We performed trio (proband and parents) WGS in 21 infants suspected of a genetic disease with an urgent need for diagnosis to guide medical care. Overall, the primary indication for genetic testing was dysmorphic syndromes (n = 14, 67%) followed by inborn errors of metabolism (n = 6, 29%) and skeletal dysplasias (n = 1, 5%). The diagnostic yield in our cohort was 57% (12/21) based on cases that received a definitive or likely definitive diagnostic result from WGS analysis. A total of 16 pathogenic/likely pathogenic variants and 10 variants of unknown significance were detected, and in most cases inherited from an unaffected parent. In addition, the reported variants were of different types, but mainly missense (58%) and associated with autosomal diseases (19/26); only three were associated with X-linked diseases, detected in hemizygosity in the proband an inherited from an unaffected mother. Notably, we identified 10 novel variants, absent from public genomic databases, in our cohort. Considering the entire diagnostic process, the average turnaround time from enrollment to medical report in our study was 53 days. Our findings demonstrate the remarkable utility of WGS as a diagnostic tool, elevating the potential of transformative impact since it outperforms conventional genetic tests. Here, we address the main challenges associated with implementing WGS in the medical care system in Brazil, as well as discuss the potential benefits and limitations of WGS as a diagnostic tool in the neonatal care setting.
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Affiliation(s)
| | - Joselito Sobreira
- Diagnósticos da América S.A., DASA, São Paulo, Brazil
- Hospital Infantil Sabará, São Paulo, Brazil
| | - Diana Bermeo
- Diagnósticos da América S.A., DASA, São Paulo, Brazil
| | | | - Dayse Alencar
- Diagnósticos da América S.A., DASA, São Paulo, Brazil
| | | | | | | | | | | | | | | | - Guilherme L Yamamoto
- Diagnósticos da América S.A., DASA, São Paulo, Brazil
- Instituto da Criança, Faculdade de Medicina (FMUSP), Universidade de São Paulo, São Paulo, Brazil
| | | | | | | | | | - Rachel Sayuri Honjo
- Instituto da Criança, Faculdade de Medicina (FMUSP), Universidade de São Paulo, São Paulo, Brazil
| | | | - Chong Ae Kim
- Instituto da Criança, Faculdade de Medicina (FMUSP), Universidade de São Paulo, São Paulo, Brazil
| | - Lucian de Souza
- Hospital das Clínicas de Porto Alegre (HCPA), Porto Alegre, Brazil
| | | | - Rita C Silveria
- Hospital das Clínicas de Porto Alegre (HCPA), Porto Alegre, Brazil
| | | | - Roberto Giugliani
- Diagnósticos da América S.A., DASA, São Paulo, Brazil
- Hospital das Clínicas de Porto Alegre (HCPA), Porto Alegre, Brazil
| | | | | | - Nara Sobreira
- Diagnósticos da América S.A., DASA, São Paulo, Brazil
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
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2
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Konkwo C, Chowdhury S, Vilarinho S. Genetics of liver disease in adults. Hepatol Commun 2024; 8:e0408. [PMID: 38551385 PMCID: PMC10984672 DOI: 10.1097/hc9.0000000000000408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/12/2023] [Accepted: 01/30/2024] [Indexed: 04/02/2024] Open
Abstract
Chronic liver disease stands as a significant global health problem with an estimated 2 million annual deaths across the globe. Combining the use of next-generation sequencing technologies with evolving knowledge in the interpretation of genetic variation across the human genome is propelling our understanding, diagnosis, and management of both rare and common liver diseases. Here, we review the contribution of risk and protective alleles to common forms of liver disease, the rising number of monogenic diseases affecting the liver, and the role of somatic genetic variants in the onset and progression of oncological and non-oncological liver diseases. The incorporation of genomic information in the diagnosis and management of patients with liver disease is driving the beginning of a new era of genomics-informed clinical hepatology practice, facilitating personalized medicine, and improving patient care.
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Affiliation(s)
- Chigoziri Konkwo
- Department of Internal Medicine, Section of Digestive Diseases, Yale School of Medicine, New Haven, Connecticut, USA
| | - Shanin Chowdhury
- Department of Internal Medicine, Section of Digestive Diseases, Yale School of Medicine, New Haven, Connecticut, USA
- Department of Pathology, Yale School of Medicine, New Haven, Connecticut, USA
| | - Silvia Vilarinho
- Department of Internal Medicine, Section of Digestive Diseases, Yale School of Medicine, New Haven, Connecticut, USA
- Department of Pathology, Yale School of Medicine, New Haven, Connecticut, USA
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3
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Berkalieva A, Kelly NR, Fisher A, Hohmann SF, Sebastin M, Di Biase M, Bonini KE, Marathe P, Odgis JA, Suckiel SA, Ramos MA, Rhodes R, Abul-Husn NS, Greally JM, Horowitz CR, Wasserstein MP, Kenny EE, Gelb BD, Ferket BS. Physician services and costs after disclosure of diagnostic sequencing results in the NYCKidSeq program. Genet Med 2024; 26:101011. [PMID: 37897232 PMCID: PMC10842442 DOI: 10.1016/j.gim.2023.101011] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 10/19/2023] [Accepted: 10/22/2023] [Indexed: 10/29/2023] Open
Abstract
PURPOSE To better understand the effects of returning diagnostic sequencing results on clinical actions and economic outcomes for pediatric patients with suspected genetic disorders. METHODS Longitudinal physician claims data after diagnostic sequencing were obtained for patients aged 0 to 21 years with neurologic, cardiac, and immunologic disorders with suspected genetic etiology. We assessed specialist consultation rates prompted by primary diagnostic results, as well as marginal effects on overall 18-month physician services and costs. RESULTS We included data on 857 patients (median age: 9.6 years) with a median follow-up of 17.3 months after disclosure of diagnostic sequencing results. The likelihood of having ≥1 recommendation for specialist consultation in 155 patients with positive findings was high (72%) vs 23% in 443 patients with uncertain findings and 21% in 259 patients with negative findings (P < .001). Follow-through consultation occurred in 30%. Increases in 18-month physician services and costs following a positive finding diminished after multivariable adjustment. Also, no significant differences between those with uncertain and negative findings were demonstrated. CONCLUSION Our study did not provide evidence for significant increases in downstream physician services and costs after returning positive or uncertain diagnostic sequencing findings. More large-scale longitudinal studies are needed to confirm these findings.
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Affiliation(s)
- Asem Berkalieva
- Institute for Healthcare Delivery Science, Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Nicole R Kelly
- Division of Pediatric Genetic Medicine, Department of Pediatrics, Children's Hospital at Montefiore/Montefiore Medical Center/Albert Einstein College of Medicine, Bronx, NY
| | | | | | - Monisha Sebastin
- Division of Pediatric Genetic Medicine, Department of Pediatrics, Children's Hospital at Montefiore/Montefiore Medical Center/Albert Einstein College of Medicine, Bronx, NY
| | - Miranda Di Biase
- Division of Pediatric Genetic Medicine, Department of Pediatrics, Children's Hospital at Montefiore/Montefiore Medical Center/Albert Einstein College of Medicine, Bronx, NY
| | - Katherine E Bonini
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Priya Marathe
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Jacqueline A Odgis
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Sabrina A Suckiel
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Michelle A Ramos
- Institute for Health Equity Research, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Rosamond Rhodes
- Department of Education, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Noura S Abul-Husn
- Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY; 23andMe Inc, Sunnyvale, CA
| | - John M Greally
- Division of Genomics, Department of Genetics, Children's Hospital at Montefiore/Montefiore Medical Center/Albert Einstein College of Medicine, Bronx, NY
| | - Carol R Horowitz
- Institute for Health Equity Research, Icahn School of Medicine at Mount Sinai, New York, NY; Division of General Internal Medicine, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Melissa P Wasserstein
- Division of Pediatric Genetic Medicine, Department of Pediatrics, Children's Hospital at Montefiore/Montefiore Medical Center/Albert Einstein College of Medicine, Bronx, NY
| | - Eimear E Kenny
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY; Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY; Division for Genomic Medicine, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Bruce D Gelb
- Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Bart S Ferket
- Institute for Healthcare Delivery Science, Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY.
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4
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Abstract
Exome sequencing (ES) and genome sequencing (GS) have radically transformed the diagnostic approach to undiagnosed rare/ultrarare Mendelian diseases. Next-generation sequencing (NGS), the technology integral for ES, GS, and most large (100+) gene panels, has enabled previously unimaginable diagnoses, changes in medical management, new treatments, and accurate reproductive risk assessments for patients, as well as new disease gene discoveries. Yet, challenges remain, as most individuals remain undiagnosed with current NGS. Improved NGS technology has resulted in long-read sequencing, which may resolve diagnoses in some patients who do not obtain a diagnosis with current short-read ES and GS, but its effectiveness is unclear, and it is expensive. Other challenges that persist include the resolution of variants of uncertain significance, the urgent need for patients with ultrarare disorders to have access to therapeutics, the need for equity in patient access to NGS-based testing, and the study of ethical concerns. However, the outlook for undiagnosed disease resolution is bright, due to continual advancements in the field.
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Affiliation(s)
- Jennifer A Sullivan
- Division of Medical Genetics, Department of Pediatrics, Duke University School of Medicine, Durham, North Carolina, USA;
| | - Kelly Schoch
- Division of Medical Genetics, Department of Pediatrics, Duke University School of Medicine, Durham, North Carolina, USA;
| | - Rebecca C Spillmann
- Division of Medical Genetics, Department of Pediatrics, Duke University School of Medicine, Durham, North Carolina, USA;
| | - Vandana Shashi
- Division of Medical Genetics, Department of Pediatrics, Duke University School of Medicine, Durham, North Carolina, USA;
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Hayeems RZ, Bernier F, Boycott KM, Hartley T, Michaels-Igbokwe C, Marshall DA. Positioning whole exome sequencing in the diagnostic pathway for rare disease to optimise utility: a protocol for an observational cohort study and an economic evaluation. BMJ Open 2022; 12:e061468. [PMID: 36216418 PMCID: PMC9557316 DOI: 10.1136/bmjopen-2022-061468] [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] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
INTRODUCTION Despite the superior diagnostic performance of exome and genome sequencing compared with conventional genetic tests, evidence gaps related to clinical utility and cost effectiveness have limited their availability in routine clinical practice in many jurisdictions. To inform adoption and reimbursement policy, this protocol provides a chain of evidence approach to determining the diagnostic utility, clinical utility and cost-effectiveness of whole exome sequencing (WES) from seven medical genetic centres in two Canadian provinces. METHODS AND ANALYSIS Using a multicentre observational cohort design, we will extract data specific to the pre-WES diagnostic pathway and 1-year post-WES medical management from electronic medical records for 650 patients with rare disease of suspected genetic aetiology who receive WES. The date from the clinical record will be linked to provincial administrative health database to capture healthcare resource use and estimate costs. Our analysis will: (1) define and describe diagnostic testing pathways that occur prior to WES among patients with rare disease, (2) determine the diagnostic utility of WES, characterised as the proportion of patients for whom causative DNA variants are identified, (3) determine the clinical utility of WES, characterised as a change in medical management triggered by WES results, (4) determine the pattern and cost of health service utilisation prior and 1 year following WES among patients who receive a diagnosis, do not receive a diagnosis, or receive an uncertain diagnosis and (5) estimate the cost-effectiveness of WES compared with conventional diagnostic testing pathways, measured by the incremental cost per additional patient diagnosed by WES using simulation modelling. ETHICS AND DISSEMINATION This protocol was approved by Clinical Trials Ontario (CTO-1577) and research ethics boards at the University of Calgary (REB18-0744 and REB20-1449) and University of Alberta (Pro0009156). Findings will be disseminated through academic publications and policy reports.
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Affiliation(s)
- 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
| | - Francois Bernier
- Department of Medical Genetics, Alberta Children's Hospital, Calgary, Alberta, Canada
- Cummings School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Kym M Boycott
- Department of Genetics, Children's Hospital of Eastern Ontario Research Institute, Ottawa, Ontario, Canada
- Department of Paediatrics, Facuty of Medicine, University of Ottawa, Ottawa, Ontario, Canada
| | - Taila Hartley
- Department of Genetics, Children's Hospital of Eastern Ontario Research Institute, Ottawa, Ontario, Canada
| | - Christine Michaels-Igbokwe
- Cummings School of Medicine, University of Calgary, Calgary, Alberta, Canada
- O'Brien Institute for Public Health, University of Calgary, Calgary, Alberta, Canada
| | - Deborah A Marshall
- Cummings School of Medicine, University of Calgary, Calgary, Alberta, Canada
- O'Brien Institute for Public Health, University of Calgary, Calgary, Alberta, Canada
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6
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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7
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Rodriguez Llorian E, Dragojlovic N, Campbell TM, Friedman JM, Osiovich H, Elliott AM, Lynd LD. The effect of rapid exome sequencing on downstream health care utilization for infants with suspected genetic disorders in an intensive care unit. Genet Med 2022; 24:1675-1683. [PMID: 35622065 DOI: 10.1016/j.gim.2022.04.014] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Revised: 04/05/2022] [Accepted: 04/06/2022] [Indexed: 01/12/2023] Open
Abstract
PURPOSE This study aimed to compare downstream utilization of medical services among critically ill infants admitted to intensive care units who received rapid exome sequencing (ES) and those who followed alternative diagnostic testing pathways. METHODS Using propensity score-weighted regression models including sex, age at admission, and severity indicators, we compared a group of 47 infants who underwent rapid ES with a group of 211 infants who did not receive rapid ES. Utilization and cost indicators were compared between cohorts using negative binomial models for utilization and two-part models for costs. RESULTS After controlling for patients' sociodemographic and clinical characteristics, we found no statistically significant difference in outpatient visits, hospitalizations, intensive care unit or total length of stay, or length of stay-associated costs between the cohorts at 12- or 26-month follow-up. Similarly, there was no evidence of higher utilization or costs by the ES group when infants who died were removed from the analysis. CONCLUSION When examining utilization during and beyond the diagnostic trajectory, there is no evidence that ES changes frequency of outpatient visits or use of in-hospital resources in critically ill infants with suspected genetic disorders.
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Affiliation(s)
- Elisabet Rodriguez Llorian
- Collaboration for Outcomes Research and Evaluation, Faculty of Pharmaceutical Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Nick Dragojlovic
- Collaboration for Outcomes Research and Evaluation, Faculty of Pharmaceutical Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Teresa M Campbell
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Jan M Friedman
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Horacio Osiovich
- Division of Neonatology, Department of Paediatrics, University of British Columbia, Vancouver, British Columbia, Canada
| | | | - Alison M Elliott
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Larry D Lynd
- Collaboration for Outcomes Research and Evaluation, Faculty of Pharmaceutical Sciences, University of British Columbia, Vancouver, British Columbia, Canada; Centre for Health Evaluation and Outcome Sciences, St. Paul's Hospital, Vancouver, British Columbia, Canada.
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8
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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] [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: 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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9
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Nurchis MC, Riccardi MT, Radio FC, Chillemi G, Bertini ES, Tartaglia M, Cicchetti A, Dallapiccola B, Damiani G. Incremental net benefit of Whole Genome Sequencing for newborns and children with suspected genetic disorders: systematic review and meta-analysis of cost-effectiveness evidence. Health Policy 2022; 126:337-345. [DOI: 10.1016/j.healthpol.2022.03.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 02/16/2022] [Accepted: 03/01/2022] [Indexed: 11/16/2022]
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10
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Johnson K, Saylor KW, Guynn I, Hicklin K, Berg JS, Lich KH. A systematic review of the methodological quality of economic evaluations in genetic screening and testing for monogenic disorders. Genet Med 2022; 24:262-288. [PMID: 34906467 PMCID: PMC8900524 DOI: 10.1016/j.gim.2021.10.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 10/13/2021] [Indexed: 10/19/2022] Open
Abstract
PURPOSE Understanding the value of genetic screening and testing for monogenic disorders requires high-quality, methodologically robust economic evaluations. This systematic review sought to assess the methodological quality among such studies and examined opportunities for improvement. METHODS We searched PubMed, Cochrane, Embase, and Web of Science for economic evaluations of genetic screening/testing (2013-2019). Methodological rigor and adherence to best practices were systematically assessed using the British Medical Journal checklist. RESULTS Across the 47 identified studies, there were substantial variations in modeling approaches, reporting detail, and sophistication. Models ranged from simple decision trees to individual-level microsimulations that compared between 2 and >20 alternative interventions. Many studies failed to report sufficient detail to enable replication or did not justify modeling assumptions, especially for costing methods and utility values. Meta-analyses, systematic reviews, or calibration were rarely used to derive parameter estimates. Nearly all studies conducted some sensitivity analysis, and more sophisticated studies implemented probabilistic sensitivity/uncertainty analysis, threshold analysis, and value of information analysis. CONCLUSION We describe a heterogeneous body of work and present recommendations and exemplar studies across the methodological domains of (1) perspective, scope, and parameter selection; (2) use of uncertainty/sensitivity analyses; and (3) reporting transparency for improvement in the economic evaluation of genetic screening/testing.
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Affiliation(s)
- Karl Johnson
- Department of Health Policy and Management, Gillings School of Global Public Health, The University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Katherine W Saylor
- Department of Public Policy, College of Arts and Sciences, The University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Isabella Guynn
- Department of Health Policy and Management, Gillings School of Global Public Health, The University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Karen Hicklin
- Department of Health Policy and Management, Gillings School of Global Public Health, The University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Jonathan S Berg
- Department of Genetics, School of Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Kristen Hassmiller Lich
- Department of Health Policy and Management, Gillings School of Global Public Health, The University of North Carolina at Chapel Hill, Chapel Hill, NC.
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11
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Olde Keizer RACM, Henneman L, Ploos van Amstel JK, Vissers LELM, Frederix GWJ. Economic evaluations of exome and genome sequencing in pediatric genetics: considerations towards a consensus strategy. J Med Econ 2021; 24:60-70. [PMID: 34915793 DOI: 10.1080/13696998.2021.2009725] [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] [Indexed: 10/19/2022]
Abstract
OBJECTIVE Next Generation Sequencing (NGS) is increasingly used for the diagnosis of rare genetic disorders. The aim of this study is to review the different approaches for economic evaluations of Next Generation Sequencing (NGS) in pediatric care used to date, to identify all costs, effects, and time horizons taken into account. METHODS A systematic literature review was conducted to identify published economic evaluations of NGS applications in pediatric diagnostics, i.e. exome sequencing (ES) and/or genome sequencing (GS). Information regarding methodological approach, costs, effects, and time horizon was abstracted from these publications. RESULTS Twenty-eight economic evaluations of ES/GS within pediatrics were identified. Costs included were mainly restricted to direct in-hospital healthcare costs and varied widely in inclusion of sort of costs and time-horizon. Nineteen studies included diagnostic yield and eight studies included cost-effectiveness as outcome measures. Studies varied greatly in terms of included sort of costs data, effects, and time horizon. CONCLUSION Large differences in inclusion of cost and effect parameters were identified between studies. Validity of outcomes can therefore be questioned, which hinders valid comparison and widespread generalization of conclusions. In addition to current health economic guidance, specific guidance for evaluations in pediatric care is therefore necessary to improve the validity of outcomes and furthermore facilitate comparable decision-making for implementing novel NGS-based diagnostic modalities in pediatric genetics and beyond.
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Affiliation(s)
- Richelle A C M Olde Keizer
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Nijmegen, The Netherlands
| | - Lidewij Henneman
- Department of Clinical Genetics, Amsterdam UMC, Vrije Universiteit, Amsterdam, The Netherlands
| | | | - Lisenka E L M Vissers
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Nijmegen, The Netherlands
| | - Gerardus W J Frederix
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
- Department of Genetics, Utrecht University Medical Center, Utrecht, The Netherlands
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12
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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. Project Baby Bear: Rapid precision care incorporating rWGS in 5 California children's hospitals demonstrates improved clinical outcomes and reduced costs of care. Am J Hum Genet 2021; 108:1231-1238. [PMID: 34089648 PMCID: PMC8322922 DOI: 10.1016/j.ajhg.2021.05.008] [Citation(s) in RCA: 118] [Impact Index Per Article: 39.3] [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: 02/09/2021] [Accepted: 05/14/2021] [Indexed: 12/31/2022] Open
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.
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Affiliation(s)
- David Dimmock
- Rady Children’s Institute for Genomic Medicine, San Diego, CA 92130, USA,Corresponding author
| | - Sara Caylor
- Rady Children’s Institute for Genomic Medicine, San Diego, CA 92130, USA
| | - Bryce Waldman
- Rady Children’s Institute for Genomic Medicine, San Diego, CA 92130, USA
| | - Wendy Benson
- Rady Children’s Institute for Genomic Medicine, San Diego, CA 92130, USA
| | | | | | - Jeanne Carroll
- Rady Children’s Institute for Genomic Medicine, San Diego, CA 92130, USA,University of California, San Diego, San Diego, CA 92093, USA
| | - Elaine Cham
- University of California, San Francisco, Benioff Children’s Hospital Oakland, Oakland, CA 94609, USA
| | - Shimul Chowdhury
- Rady Children’s Institute for Genomic Medicine, San Diego, CA 92130, USA
| | - John Cleary
- Children’s Hospital of Orange County, Orange, CA 92868, USA
| | - Arthur D’Harlingue
- University of California, San Francisco, Benioff Children’s Hospital Oakland, Oakland, CA 94609, USA
| | - A. Doshi
- Rady Children’s Institute for Genomic Medicine, San Diego, CA 92130, USA,University of California, San Diego, San Diego, CA 92093, USA
| | | | | | - Charlotte Hobbs
- Rady Children’s Institute for Genomic Medicine, San Diego, CA 92130, USA
| | - Kathleen Houtchens
- University of California, San Francisco, Benioff Children’s Hospital Oakland, Oakland, CA 94609, USA
| | - Juliette Hunt
- Children’s Hospital of Orange County, Orange, CA 92868, USA
| | - Priscilla Joe
- University of California, San Francisco, Benioff Children’s Hospital Oakland, Oakland, CA 94609, USA
| | | | | | | | - Jason Knight
- Children’s Hospital of Orange County, Orange, CA 92868, USA
| | | | - Richard G. Kronick
- Torrey Pines Health Group, Inc., San Diego, CA 92037, USA,Department of Family Medicine and Public Health, University of California, San Diego, San Diego, CA 92093, USA
| | - Jolie Limon
- Valley Children’s Hospital, Madera, CA 93636, USA
| | - Madelena Martin
- University of California, Davis and Davis Children’s Hospital, Sacramento, CA 95817, USA
| | - Katherine A. Rauen
- University of California, Davis and Davis Children’s Hospital, Sacramento, CA 95817, USA
| | - Adam Schwarz
- Children’s Hospital of Orange County, Orange, CA 92868, USA
| | - Suma P. Shankar
- University of California, Davis and Davis Children’s Hospital, Sacramento, CA 95817, USA
| | | | | | | | - Kristen Wigby
- Rady Children’s Institute for Genomic Medicine, San Diego, CA 92130, USA,University of California, San Diego, San Diego, CA 92093, USA
| | - Neda Zadeh
- Children’s Hospital of Orange County, Orange, CA 92868, USA
| | - Lauge Farnaes
- Rady Children’s Institute for Genomic Medicine, San Diego, CA 92130, USA
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13
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Woodring TS, Mirza MH, Benavides V, Ellsworth KA, Wright MS, Javed MJ, Ramiro S. Uncertain, Not Unimportant: Callosal Dysgenesis and Variants of Uncertain Significance in ROBO1. Pediatrics 2021; 148:e2020019000. [PMID: 34193621 DOI: 10.1542/peds.2020-019000] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 02/08/2021] [Indexed: 11/24/2022] Open
Abstract
Congenital anomalies affect 3% to 5% of births and remain the leading cause of infant death in the United States. As whole exome and genome sequencing are increasingly used to diagnose underlying genetic disease, the patient's clinical presentation remains the most important context for interpreting sequencing results, including frequently reported variants of uncertain significance (VUS). Classification of a variant as VUS acknowledges limits on evidence to establish whether a variant can be classified as pathogenic or benign according to the American College of Medical Genetics guidelines. Importantly, the VUS designation reflects limits on the breadth of evidence linking the genetic variant to a disease. However, available evidence, although limited, may be surprisingly relevant in an individual patient's case. Accordingly, a VUS result should be approached neither as nondiagnostic genetic result nor as automatically "uncertain" in its potential to guide clinical decision-making. In this article, we discuss a case of an infant born at 29 weeks 4 days without a corpus callosum, whose whole genome sequencing yielded compound heterozygous variants both classified as VUS in ROBO1, a gene encoding for a receptor involved in a canonical signaling mechanism that guides axons across midline. Approaching the VUS result as potentially pathogenic, we found the infant ultimately had pituitary dysfunction and renal anomalies consistent with other reported ROBO1 variants and basic science literature. Accordingly, we highlight resources for variant interpretation available to clinicians to evaluate VUS results, particularly as they inform the diagnosis of individually rare but collectively common rare diseases.
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Affiliation(s)
- Therese S Woodring
- University of Wisconsin Hospital and Clinics, Madison, Wisconsin
- College of Medicine Peoria, University of Illinois, Peoria, Illinois
| | - Mohammed H Mirza
- College of Medicine Peoria, University of Illinois, Peoria, Illinois
| | | | | | | | - M Jawad Javed
- College of Medicine Peoria, University of Illinois, Peoria, Illinois
- NICU, Children's Hospital of Illinois, Peoria, Illinois
| | - Susan Ramiro
- College of Medicine Peoria, University of Illinois, Peoria, Illinois
- NICU, Children's Hospital of Illinois, Peoria, Illinois
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14
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Mulder DJ, Khalouei S, Warner N, Gonzaga-Jauregui C, Church PC, Walters TD, Ramani AK, Griffiths AM, Cohn I, Muise AM. Utilization of Whole Exome Sequencing Data to Identify Clinically Relevant Pharmacogenomic Variants in Pediatric Inflammatory Bowel Disease. Clin Transl Gastroenterol 2020; 11:e00263. [PMID: 33512800 DOI: 10.14309/ctg.0000000000000263] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
INTRODUCTION We hypothesized that variants within clinically relevant pharmacogenes could be identified using a whole exome sequencing data set derived from a cohort of more than 1,000 patients with inflammatory bowel disease (IBD). METHODS Pediatric patients diagnosed with IBD underwent whole exome sequencing. We selected 18 genes with supporting literature where specific exonic variants would influence clinical care. RESULTS We identified actionable pharmacogenomic variants in 63% of patients. Importantly, 5% of patients with IBD were at risk for serious adverse effects from anesthesia and 3% were at increased risk for thrombosis. DISCUSSION We identified exonic variants in most of our patients with IBD that directly impact clinical care.
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15
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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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16
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Li C, Vandersluis S, Holubowich C, Ungar WJ, Goh ES, Boycott KM, Sikich N, Dhalla I, Ng V. Cost-effectiveness of genome-wide sequencing for unexplained developmental disabilities and multiple congenital anomalies. Genet Med 2020; 23:451-460. [PMID: 33110268 DOI: 10.1038/s41436-020-01012-w] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [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: 07/22/2020] [Revised: 10/06/2020] [Accepted: 10/07/2020] [Indexed: 12/22/2022] Open
Abstract
PURPOSE Genetic testing is routine practice for individuals with unexplained developmental disabilities and multiple congenital anomalies. However, current testing pathways can be costly and time consuming, and the diagnostic yield low. Genome-wide sequencing, including exome sequencing (ES) and genome sequencing (GS), can improve diagnosis, but at a higher cost. This study aimed to assess the cost-effectiveness of genome-wide sequencing in Ontario, Canada. METHODS A cost-effectiveness analysis was conducted using a discrete event simulation from a public payer perspective. Six strategies involving ES or GS were compared. Outcomes reported were direct medical costs, number of molecular diagnoses, number of positive findings, and number of active treatment changes. RESULTS If ES was used as a second-tier test (after the current first-tier, chromosomal microarray, fails to provide a diagnosis), it would be less costly and more effective than standard testing (CAN$6357 [95% CI: 6179-6520] vs. CAN$8783 per patient [95% CI: 2309-31,123]). If ES was used after standard testing, it would cost an additional CAN$15,228 to identify the genetic diagnosis for one additional patient compared with standard testing. The results remained robust when parameters and assumptions were varied. CONCLUSION ES would likely be cost-saving if used earlier in the diagnostic pathway.
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Affiliation(s)
- Chunmei Li
- Ontario Health (Quality), Toronto, ON, Canada.
| | | | | | - Wendy J Ungar
- Program of Child Health Evaluative Sciences, The Hospital for Sick Children Research Institute, Toronto, ON, Canada.,Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, ON, Canada
| | - Elaine S Goh
- Laboratory Medicine and Genetics, Trillium Health Partners, Mississauga, ON, Canada
| | - Kym M Boycott
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, ON, Canada
| | | | - Irfan Dhalla
- Ontario Health (Quality), Toronto, ON, Canada.,Unity Health Toronto, Toronto, ON, Canada
| | - Vivian Ng
- Ontario Health (Quality), Toronto, ON, Canada
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17
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Fung JLF, Yu MHC, Huang S, Chung CCY, Chan MCY, Pajusalu S, Mak CCY, Hui VCC, Tsang MHY, Yeung KS, Lek M, Chung BHY. A three-year follow-up study evaluating clinical utility of exome sequencing and diagnostic potential of reanalysis. NPJ Genom Med 2020; 5:37. [PMID: 32963807 DOI: 10.1038/s41525-020-00144-x] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Accepted: 08/14/2020] [Indexed: 01/05/2023] Open
Abstract
Exome sequencing (ES) has become one of the important diagnostic tools in clinical genetics with a reported diagnostic rate of 25–58%. Many studies have illustrated the diagnostic and immediate clinical impact of ES. However, up to 75% of individuals remain undiagnosed and there is scarce evidence supporting clinical utility beyond a follow-up period of >1 year. This is a 3-year follow-up analysis to our previous publication by Mak et al. (NPJ Genom. Med. 3:19, 2018), to evaluate the long-term clinical utility of ES and the diagnostic potential of exome reanalysis. The diagnostic yield of the initial study was 41% (43/104). Exome reanalysis in 46 undiagnosed individuals has achieved 12 new diagnoses. The additional yield compared with the initial analysis was at least 12% (increased from 41% to at least 53%). After a median follow-up period of 3.4 years, change in clinical management was observed in 72.2% of the individuals (26/36), leading to positive change in clinical outcome in four individuals (11%). There was a minimum healthcare cost saving of HKD$152,078 (USD$19,497; €17,282) annually for these four individuals. There were a total of six pregnancies from five families within the period. Prenatal diagnosis was performed in four pregnancies; one fetus was affected and resulted in termination. None of the parents underwent preimplantation genetic diagnosis. This 3-year follow-up study demonstrated the long-term clinical utility of ES at individual, familial and health system level, and the promising diagnostic potential of subsequent reanalysis. This highlights the benefits of implementing ES and regular reanalysis in the clinical setting.
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18
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Gordon LG, White NM, Elliott TM, Nones K, Beckhouse AG, Rodriguez-Acevedo AJ, Webb PM, Lee XJ, Graves N, Schofield DJ. Estimating the costs of genomic sequencing in cancer control. BMC Health Serv Res 2020; 20:492. [PMID: 32493298 DOI: 10.1186/s12913-020-05318-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Accepted: 05/11/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Despite the rapid uptake of genomic technologies within cancer care, few studies provide detailed information on the costs of sequencing across different applications. The objective of the study was to examine and categorise the complete costs involved in genomic sequencing for a range of applications within cancer settings. METHODS We performed a cost-analysis using gross and micro-costing approaches for genomic sequencing performed during 2017/2018 across different settings in Brisbane, Australia. Sequencing was undertaken for patients with lung, breast, oesophageal cancers, melanoma or mesothelioma. Aggregated resource data were captured for a total of 1433 patients and point estimates of per patient costs were generated. Deterministic sensitivity analyses addressed the uncertainty in the estimates. Estimated costs to the public health system for resources were categorised into seven distinct activities in the sequencing process: sampling, extraction, library preparation, sequencing, analysis, data storage and clinical reporting. Costs were also aggregated according to labour, consumables, testing, equipment and 'other' categories. RESULTS The per person costs were AU$347-429 (2018 US$240-297) for targeted panels, AU$871-$2788 (2018 US$604-1932) for exome sequencing, and AU$2895-4830 (2018 US$2006-3347) for whole genome sequencing. Cost proportions were highest for library preparation/sequencing materials (average 76.8% of total costs), sample extraction (8.1%), data analysis (9.2%) and data storage (2.6%). Capital costs for the sequencers were an additional AU$34-197 (2018 US$24-67) per person. CONCLUSIONS Total costs were most sensitive to consumables and sequencing activities driven by commercial prices. Per person sequencing costs for cancer are high when tumour/blood pairs require testing. Using the natural steps involved in sequencing and categorising resources accordingly, future evaluations of costs or cost-effectiveness of clinical genomics across cancer projects could be more standardised and facilitate easier comparison of cost drivers.
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19
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Ontario Health (Quality). Genome-Wide Sequencing for Unexplained Developmental Disabilities or Multiple Congenital Anomalies: A Health Technology Assessment. Ont Health Technol Assess Ser 2020; 20:1-178. [PMID: 32194879] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
BACKGROUND People with unexplained developmental disabilities or multiple congenital anomalies might have had many biochemical, metabolic, and genetic tests for a period of years without receiving a diagnosis. A genetic diagnosis can help these people and their families better understand their condition and may help them to connect with others who have the same condition. Ontario Health (Quality), in collaboration with the Canadian Agency for Drugs and Technologies in Health (CADTH) conducted a health technology assessment about the use of genome-wide sequencing for patients with unexplained developmental disabilities or multiple congenital anomalies. Ontario Health (Quality) evaluated the effectiveness, cost-effectiveness, and budget impact of publicly funding genome-wide sequencing. We also conducted interviews with patients and examined the quantitative evidence of preferences and values literature to better understand the patient preferences and values for these tests. METHODS Ontario Health (Quality) performed a systematic literature search of the clinical evidence. We assessed the risk of bias of each included study using the Risk of Bias Assessment tool for Non-randomized Studies (RoBANS) and the quality of the body of evidence according to the Grading of Recommendations Assessment, Development, and Evaluation (GRADE) Working Group criteria. We also performed a search of the quantitative evidence and undertook direct patient engagement to ascertain patient preferences for genetic testing for unexplained developmental disabilities or multiple congenital anomalies. CADTH performed a review of qualitative literature about patient perspectives and experiences, and a review of ethical issues.Ontario Health (Quality) performed an economic literature review of genome-wide sequencing in people with unexplained developmental disabilities or multiple congenital anomalies. Although we found eight published cost-effectiveness studies, none completely addressed our research question. Therefore, we conducted a primary economic evaluation using a discrete event simulation model. Owing to its high cost and early stage of clinical implementation, whole exome sequencing is primarily used for people who do not have a diagnosis from standard testing (referred to here as whole exome sequencing after standard testing; standard testing includes chromosomal microarray and targeted single-gene tests or gene panels). Therefore, in our first analysis, we evaluated the cost-effectiveness of whole exome sequencing after standard testing versus standard testing alone. In our second analysis, we explored the cost-effectiveness of whole exome and whole genome sequencing used at various times in the diagnostic pathway (e.g., first tier, second tier, after standard testing) versus standard testing. We also estimated the budget impact of publicly funding genome-wide sequencing in Ontario for the next 5 years. RESULTS Forty-four studies were included in the clinical evidence review. The overall diagnostic yield of genome-wide sequencing for people with unexplained development disability and multiple congenital anomalies was 37%, but we are very uncertain about this estimate (GRADE: Very Low). Compared with standard genetic testing of chromosomal microarray and targeted single-gene tests or gene panels, genome-wide sequencing could have a higher diagnostic yield (GRADE: Low). As well, for some who are tested, genome-wide sequencing prompts some changes to medications, treatments, and referrals to specialists (GRADE: Very Low).Whole exome sequencing after standard testing cost an additional $3,261 per patient but was more effective than standard testing alone. For every 1,000 persons tested, using whole exome sequencing after standard testing would lead to an additional 240 persons with a molecular diagnosis, 272 persons with any positive finding, and 46 persons with active treatment change (modifications to medications, procedures, or treatment). The resulting incremental cost-effectiveness ratios (ICERs) were $13,591 per additional molecular diagnosis. The use of genome-wide sequencing early in the diagnostic pathway (e.g., as a first- or second-tier test) can save on costs and improve diagnostic yields over those of standard testing. Results remained robust when parameters and assumptions were varied.Our budget impact analysis showed that, if whole exome sequencing after standard testing continues to be funded through Ontario's Out-of-Country Prior Approval Program, its budget impact would range from $4 to $5 million in years 1 to 5. If whole exome sequencing becomes publicly funded in Ontario (not through the Out-of-Country Prior Approval Program), the budget impact would be about $9 million yearly. We also found that using whole exome sequencing as a second-tier test would lead to cost savings ($3.4 million per 1,000 persons tested yearly).Participants demonstrated consistent motivations for and expectations of obtaining a diagnosis for unexplained developmental delay or congenital anomalies through genome-wide sequencing. Patients and families greatly value the support and information they receive through genetic counselling when considering genome-wide sequencing and learning of a diagnosis. CONCLUSIONS Genome-wide sequencing could have a higher diagnostic yield than standard testing for people with unexplained developmental disabilities or multiple congenital anomalies. Genome-wide sequencing can also prompt some changes to medications, treatments, and referrals to specialists for some people tested; however, we are very uncertain about this. Genome-wide sequencing could be a cost-effective strategy when used after standard testing to diagnose people with unexplained developmental disabilities or multiple congenital anomalies. It could also lead to cost savings when used earlier in the diagnostic pathway. Patients and families consistently noted a benefit from seeking a diagnosis through genetic testing.
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Weymann D, Dragojlovic N, Pollard S, Regier DA. Allocating healthcare resources to genomic testing in Canada: latest evidence and current challenges. J Community Genet 2019. [PMID: 31273679 DOI: 10.1007/s12687-019-00428-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Accepted: 06/14/2019] [Indexed: 12/30/2022] Open
Abstract
Precision medicine (PM) informed by next-generation sequencing (NGS) poses challenges for health technology assessment (HTA). To date, there has been limited reimbursement of genomic testing with NGS in Canada, particularly for whole-genome and whole-exome sequencing (WGS/WES). Through a structured literature review, we examine Canadian economic evidence and evidentiary challenges for the adoption of genomic testing. We searched Medline (PubMed) for published Canadian studies generating economic evidence for PM informed by NGS. Our search focused on studies examining the costs and/or value of NGS. We reviewed included studies and summarized results according to evaluation type, clinical context, NGS technology, and test strategy. We then grouped HTA challenges encountered by authors when evaluating NGS. Our review included twenty-five studies. To determine the economic impacts of NGS-informed PM in Canada, studies applied cost-effectiveness analysis (52%, n = 13), stated preference analysis (20%, n = 5), cost-consequence analysis (16%, n = 4), and healthcare resource utilization or costing analysis (12%, n = 3). NGS panels were the most common technology evaluated (n = 13), followed by WGS and/or WES (n = 8). The included studies highlighted multiple challenges when generating economic evidence, many of which remain unaddressed. Challenges were broadly related to (1) accounting for all NGS outcomes; (2) addressing uncertainty; and (3) improving consistency of economic approaches. Canadian studies are beginning to produce estimates of the economic impacts of NGS-informed PM, yet challenges for HTA remain. While solutions and real-world evidence are generated, lifecycle health technology management methods can be designed to better support resource allocation decisions for genomic testing in Canada.
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21
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Patrick AE, Wang W, Brokamp E, Graham TB, Aune TM, Duis JB. Juvenile idiopathic arthritis associated with a mutation in GATA3. Arthritis Res Ther 2019; 21:156. [PMID: 31238969 PMCID: PMC6593533 DOI: 10.1186/s13075-019-1946-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Accepted: 06/17/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND GATA3 is a transcription factor that is important during development and plays a role in differentiation and activity of immune cells, particularly T cells. Abnormal T cell function is found in autoimmune arthritis. We present the first known case of autoimmune arthritis associated with a novel GATA3 mutation. METHODS Whole exome sequencing of the proband was performed on a clinical basis. Peripheral blood mononuclear cells (PBMCs) were collected from the proband, healthy sibling, and parent. cDNA prepared from RNA was analyzed with polymerase chain reaction and Sanger sequencing. Intracellular proteins were assessed by immunoblot of PBMC homogenates. GATA3 in vitro activity was measured in HeLa cell cultures expressing a mammalian expression vector containing GATA3 or mutants generated by site-directed mutagenesis. GATA3 transcriptional activity was examined using a luciferase reporter assay system. T helper cell ex vivo function was evaluated by stimulating PBMCs to differentiate into effector T cells along Th0, Th1, Th2, and Th17 lineages, and re-stimulating effector cells to secrete cytokines. Cytokine production was measured by enzyme-linked immunosorbent assay. RESULTS The proband is the first known case of autoimmune arthritis associated with a mutation in GATA3. The proband M401VfsX106 protein is expressed and has a dominant negative function on GATA3 transcriptional activity. The proband PBMCs have markedly increased differentiation along the Th1 and Th17 pathways, with decreased differentiation along the Th2 pathway. Unexpectedly, Th0 cells from the proband express high levels of IFNγ. CONCLUSIONS Our research presents the first known case of autoimmune arthritis associated with a mutation in GATA3. This work expands the phenotypic spectrum of GATA3 mutations. It reveals the novel insight that decreased and altered GATA3 activity coincides with autoimmune arthritis. This work suggests that modulation of GATA3 may be a therapeutic approach for patients with autoimmune arthritis.
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Affiliation(s)
- Anna E Patrick
- Division of Rheumatology, Department of Pediatrics, Vanderbilt University Medical Center, 1211 Medical Center Drive, Nashville, TN, 37232, USA
| | - Wei Wang
- GeneDx, Inc, 207 Perry Parkway, Gaithersburg, MD, 20877, USA
| | - Elly Brokamp
- Division of Medical Genetics and Genomic Medicine, Department of Pediatrics, Vanderbilt University Medical Center, 1211 Medical Center Drive, Nashville, TN, 37232, USA
| | - Thomas Brent Graham
- Division of Rheumatology, Department of Pediatrics, Vanderbilt University Medical Center, 1211 Medical Center Drive, Nashville, TN, 37232, USA
| | - Thomas M Aune
- Division of Rheumatology and Immunology, Department of Medicine, Vanderbilt University Medical Center, 1211 Medical Center Drive, Nashville, TN, 37232, USA.
| | - Jessica B Duis
- Division of Medical Genetics and Genomic Medicine, Department of Pediatrics, Vanderbilt University Medical Center, 1211 Medical Center Drive, Nashville, TN, 37232, USA
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22
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Schofield D, Rynehart L, Shresthra R, White SM, Stark Z. Long-term economic impacts of exome sequencing for suspected monogenic disorders: diagnosis, management, and reproductive outcomes. Genet Med 2019; 21:2586-2593. [DOI: 10.1038/s41436-019-0534-x] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Accepted: 04/24/2019] [Indexed: 12/18/2022] Open
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23
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Mintzer V, Moran-Gilad J, Simon-Tuval T. Operational models and criteria for incorporating microbial whole genome sequencing in hospital microbiology - A systematic literature review. Clin Microbiol Infect 2019; 25:1086-1095. [PMID: 31039443 DOI: 10.1016/j.cmi.2019.04.019] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [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: 02/27/2019] [Revised: 04/17/2019] [Accepted: 04/18/2019] [Indexed: 12/12/2022]
Abstract
BACKGROUND Microbial whole genome sequencing (WGS) has many advantages over standard microbiological methods. However, it is not yet widely implemented in routine hospital diagnostics due to notable challenges. OBJECTIVES The aim was to extract managerial, financial and clinical criteria supporting the decision to implement WGS in routine diagnostic microbiology, across different operational models of implementation in the hospital setting. METHODS This was a systematic review of literature identified through PubMed and Web of Science. English literature studies discussing the applications of microbial WGS without limitation on publication date were eligible. A narrative approach for categorization and synthesis of the sources identified was adopted. RESULTS A total of 98 sources were included. Four main alternative operational models for incorporating WGS in clinical microbiology laboratories were identified: full in-house sequencing and analysis, full outsourcing of sequencing and analysis and two hybrid models combining in-house/outsourcing of the sequencing and analysis components. Six main criteria (and multiple related sub-criteria) for WGS implementation emerged from our review and included cost (e.g. the availability of resources for capital and operational investment); manpower (e.g. the ability to provide training programmes or recruit trained personnel), laboratory infrastructure (e.g. the availability of supplies and consumables or sequencing platforms), bioinformatics requirements (e.g. the availability of valid analysis tools); computational infrastructure (e.g. the availability of storage space or data safety arrangements); and quality control (e.g. the existence of standardized procedures). CONCLUSIONS The decision to incorporate WGS in routine diagnostics involves multiple, sometimes competing, criteria and sub-criteria. Mapping these criteria systematically is an essential stage in developing policies for adoption of this technology, e.g. using a multicriteria decision tool. Future research that will prioritize criteria and sub-criteria that were identified in our review in the context of operational models will inform decision-making at clinical and managerial levels with respect to effective implementation of WGS for routine use. Beyond WGS, similar decision-making challenges are expected with respect to future integration of clinical metagenomics.
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Affiliation(s)
- V Mintzer
- Department of Health Systems Management, Guilford Glazer Faculty of Business and Management and Faculty of Health Sciences, Ben-Gurion University of the Negev, Israel; Leumit Health Services, Israel
| | - J Moran-Gilad
- Department of Health Policy and Management, School of Public Health, Faculty of Health Sciences, Ben-Gurion University of the Negev, Israel; ESCMID Study Group for Genomic and Molecular Diagnostics (ESGMD), Basel, Switzerland
| | - T Simon-Tuval
- Department of Health Systems Management, Guilford Glazer Faculty of Business and Management and Faculty of Health Sciences, Ben-Gurion University of the Negev, Israel.
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24
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Matias M, Wusik K, Neilson D, Zhang X, Valencia CA, Collins K. Comparison of medical management and genetic counseling options pre- and post-whole exome sequencing for patients with positive and negative results. J Genet Couns 2019; 28:182-193. [PMID: 30648779 DOI: 10.1002/jgc4.1054] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [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: 05/16/2018] [Revised: 10/16/2018] [Accepted: 10/20/2018] [Indexed: 12/14/2022]
Abstract
Whole exome sequencing (WES) is expected to impact patient management, but data surrounding the types of downstream effects and how frequently these effects are observed depending on the type of WES results received is limited. This study investigated changes to medical management and genetic counseling (GC) options following WES for individuals with positive and negative results. Electronic medical records of patients who had positive (n = 37) or negative (n = 41) WES results from Cincinnati Children's Hospital were retrospectively reviewed. Pre- and post-WES management and GC options were analyzed as were differences between positive and negative results. Almost all participants (97%) were observed to have at least one difference in medical management and/or GC options following WES. Comparing pre- and post-WES detected significant differences (p ≤ 0.05) in genetic testing, imaging, and metabolic testing regardless of WES results. Participants with positive results also had significant differences in recurrence risk, reproductive options, testing for family members, and support groups. Pre- to post-WES differences were significantly different between participants with positive and negative results in specialist referrals, lifestyle recommendations, recurrence risk, and all GC options (p ≤ 0.05); specifically, participants with positive results were more likely to have differences in these categories. Overall, differences in medical management and/or GC options were observed for participants with both types of WES results (positive and negative). Results from this study may contribute to the understanding of how WES impacts patients and their care and thus improve its utilization.
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Affiliation(s)
- Margret Matias
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio.,Department of Pediatrics, College of Medicine, University of Cincinnati, Cincinnati, Ohio.,UnityPoint-Health Meriter Hospital, Center for Perinatal Care, Madison, Wisconsin
| | - Katie Wusik
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio.,Department of Pediatrics, College of Medicine, University of Cincinnati, Cincinnati, Ohio
| | - Derek Neilson
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - Xue Zhang
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - C Alexander Valencia
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - Kathleen Collins
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio.,Department of Pediatrics, College of Medicine, University of Cincinnati, Cincinnati, Ohio
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25
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Drozd HP, Karathanasis SF, Molosh AI, Lukkes JL, Clapp DW, Shekhar A. From bedside to bench and back: Translating ASD models. Prog Brain Res 2018; 241:113-158. [PMID: 30447753 DOI: 10.1016/bs.pbr.2018.10.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Autism spectrum disorders (ASD) represent a heterogeneous group of disorders defined by deficits in social interaction/communication and restricted interests, behaviors, or activities. Models of ASD, developed based on clinical data and observations, are used in basic science, the "bench," to better understand the pathophysiology of ASD and provide therapeutic options for patients in the clinic, the "bedside." Translational medicine creates a bridge between the bench and bedside that allows for clinical and basic science discoveries to challenge one another to improve the opportunities to bring novel therapies to patients. From the clinical side, biomarker work is expanding our understanding of possible mechanisms of ASD through measures of behavior, genetics, imaging modalities, and serum markers. These biomarkers could help to subclassify patients with ASD in order to better target treatments to a more homogeneous groups of patients most likely to respond to a candidate therapy. In turn, basic science has been responding to developments in clinical evaluation by improving bench models to mechanistically and phenotypically recapitulate the ASD phenotypes observed in clinic. While genetic models are identifying novel therapeutics targets at the bench, the clinical efforts are making progress by defining better outcome measures that are most representative of meaningful patient responses. In this review, we discuss some of these challenges in translational research in ASD and strategies for the bench and bedside to bridge the gap to achieve better benefits to patients.
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Affiliation(s)
- Hayley P Drozd
- Program in Medical Neurobiology, Stark Neurosciences Institute, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Sotirios F Karathanasis
- Program in Medical Neurobiology, Stark Neurosciences Institute, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Andrei I Molosh
- Department of Psychiatry, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Jodi L Lukkes
- Department of Psychiatry, Indiana University School of Medicine, Indianapolis, IN, United States
| | - D Wade Clapp
- Department of Pediatrics, Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN, United States; Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Anantha Shekhar
- Program in Medical Neurobiology, Stark Neurosciences Institute, Indiana University School of Medicine, Indianapolis, IN, United States; Department of Psychiatry, Indiana University School of Medicine, Indianapolis, IN, United States; Department of Pharmacology and Toxicology, Indiana University School of Medicine, Indianapolis, IN, United States; Indiana Clinical and Translation Sciences Institute, Indiana University School of Medicine, Indianapolis, IN, United States.
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26
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Friedman JM, Bombard Y, Cornel MC, Fernandez CV, Junker AK, Plon SE, Stark Z, Knoppers BM; Paediatric Task Team of the Global Alliance for Genomics and Health Regulatory and Ethics Work Stream. Genome-wide sequencing in acutely ill infants: genomic medicine's critical application? Genet Med 2019; 21:498-504. [PMID: 29895853 DOI: 10.1038/s41436-018-0055-z] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Accepted: 04/25/2018] [Indexed: 12/22/2022] Open
Abstract
Diagnostic genome-wide sequencing (exome or genome sequencing and data analysis for high-penetrance disease-causing variants) in acutely ill infants appears to be clinically useful, but the value of this diagnostic test should be rigorously demonstrated before it is accepted as a standard of care. This white paper was developed by the Paediatric Task Team of the Global Alliance for Genomics and Health's Regulatory and Ethics Work Stream to address the question of how we can determine the clinical value of genome-wide sequencing in infants in an intensive care setting. After reviewing available clinical and ethics literature on this question, we conclude that evaluating diagnostic genome-wide sequencing as a comprehensive scan for major genetic disease (rather than as a large panel of single-gene tests) provides a practical approach to assessing its clinical value in acutely ill infants. Comparing the clinical value of diagnostic genome-wide sequencing to chromosomal microarray analysis, the current evidence-based standard of care, per case of serious genetic disease diagnosed provides a practical means of assessing clinical value. Scientifically rigorous studies of this kind are needed to determine if clinical genome-wide sequencing should be established as a standard of care supported by healthcare systems and insurers for diagnosis of genetic disease in seriously ill newborn infants.
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27
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Stark Z, Schofield D, Martyn M, Rynehart L, Shrestha R, Alam K, Lunke S, Tan TY, Gaff CL, White SM. Does genomic sequencing early in the diagnostic trajectory make a difference? A follow-up study of clinical outcomes and cost-effectiveness. Genet Med 2018; 21:173-180. [DOI: 10.1038/s41436-018-0006-8] [Citation(s) in RCA: 90] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Accepted: 03/20/2018] [Indexed: 01/09/2023] Open
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28
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Farnaes L, Hildreth A, Sweeney NM, Clark MM, Chowdhury S, Nahas S, Cakici JA, Benson W, Kaplan RH, Kronick R, Bainbridge MN, Friedman J, Gold JJ, Ding Y, Veeraraghavan N, Dimmock D, Kingsmore SF. Rapid whole-genome sequencing decreases infant morbidity and cost of hospitalization. NPJ Genom Med 2018; 3:10. [PMID: 29644095 PMCID: PMC5884823 DOI: 10.1038/s41525-018-0049-4] [Citation(s) in RCA: 275] [Impact Index Per Article: 45.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Revised: 03/06/2018] [Accepted: 03/12/2018] [Indexed: 02/08/2023] Open
Abstract
Genetic disorders are a leading cause of morbidity and mortality in infants. Rapid whole-genome sequencing (rWGS) can diagnose genetic disorders in time to change acute medical or surgical management (clinical utility) and improve outcomes in acutely ill infants. We report a retrospective cohort study of acutely ill inpatient infants in a regional children's hospital from July 2016-March 2017. Forty-two families received rWGS for etiologic diagnosis of genetic disorders. Probands also received standard genetic testing as clinically indicated. Primary end-points were rate of diagnosis, clinical utility, and healthcare utilization. The latter was modelled in six infants by comparing actual utilization with matched historical controls and/or counterfactual utilization had rWGS been performed at different time points. The diagnostic sensitivity of rWGS was 43% (eighteen of 42 infants) and 10% (four of 42 infants) for standard genetic tests (P = .0005). The rate of clinical utility of rWGS (31%, thirteen of 42 infants) was significantly greater than for standard genetic tests (2%, one of 42; P = .0015). Eleven (26%) infants with diagnostic rWGS avoided morbidity, one had a 43% reduction in likelihood of mortality, and one started palliative care. In six of the eleven infants, the changes in management reduced inpatient cost by $800,000-$2,000,000. These findings replicate a prior study of the clinical utility of rWGS in acutely ill inpatient infants, and demonstrate improved outcomes and net healthcare savings. rWGS merits consideration as a first tier test in this setting.
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Affiliation(s)
- Lauge Farnaes
- Rady Children’s Institute for Genomic Medicine, San Diego, CA USA
- Department of Pediatrics, University of California San Diego, San Diego, CA USA
| | - Amber Hildreth
- Rady Children’s Institute for Genomic Medicine, San Diego, CA USA
- Department of Pediatrics, University of California San Diego, San Diego, CA USA
| | - Nathaly M. Sweeney
- Rady Children’s Institute for Genomic Medicine, San Diego, CA USA
- Department of Pediatrics, University of California San Diego, San Diego, CA USA
| | | | - Shimul Chowdhury
- Rady Children’s Institute for Genomic Medicine, San Diego, CA USA
| | - Shareef Nahas
- Rady Children’s Institute for Genomic Medicine, San Diego, CA USA
| | - Julie A. Cakici
- Rady Children’s Institute for Genomic Medicine, San Diego, CA USA
| | - Wendy Benson
- Rady Children’s Institute for Genomic Medicine, San Diego, CA USA
| | | | - Richard Kronick
- Department of Family Medicine and Public Health, University of California San Diego, San Diego, CA USA
| | | | - Jennifer Friedman
- Rady Children’s Institute for Genomic Medicine, San Diego, CA USA
- Department of Pediatrics, University of California San Diego, San Diego, CA USA
- Department of Neurosciences, University of California San Diego, San Diego, CA USA
| | - Jeffrey J. Gold
- Rady Children’s Institute for Genomic Medicine, San Diego, CA USA
- Department of Neurosciences, University of California San Diego, San Diego, CA USA
| | - Yan Ding
- Rady Children’s Institute for Genomic Medicine, San Diego, CA USA
| | | | - David Dimmock
- Rady Children’s Institute for Genomic Medicine, San Diego, CA USA
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