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Wallis M, Bodek SD, Munro J, Rafehi H, Bennett MF, Ye Z, Schneider A, Gardiner F, Valente G, Murdoch E, Uebergang E, Hunter J, Stutterd C, Huq A, Salmon L, Scheffer I, Eratne D, Meyn S, Fong CY, John T, Mullen S, White SM, Brown NJ, McGillivray G, Chen J, Richmond C, Hughes A, Krzesinski E, Fennell A, Chambers B, Santoreneos R, Le Fevre A, Hildebrand MS, Bahlo M, Christodoulou J, Delatycki M, Berkovic SF. Experience of the first adult-focussed undiagnosed disease program in Australia (AHA-UDP): solving rare and puzzling genetic disorders is ageless. Orphanet J Rare Dis 2024; 19:288. [PMID: 39095811 PMCID: PMC11297648 DOI: 10.1186/s13023-024-03297-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Accepted: 07/26/2024] [Indexed: 08/04/2024] Open
Abstract
BACKGROUND Significant recent efforts have facilitated increased access to clinical genetics assessment and genomic sequencing for children with rare diseases in many centres, but there remains a service gap for adults. The Austin Health Adult Undiagnosed Disease Program (AHA-UDP) was designed to complement existing UDP programs that focus on paediatric rare diseases and address an area of unmet diagnostic need for adults with undiagnosed rare conditions in Victoria, Australia. It was conducted at a large Victorian hospital to demonstrate the benefits of bringing genomic techniques currently used predominantly in a research setting into hospital clinical practice, and identify the benefits of enrolling adults with undiagnosed rare diseases into a UDP program. The main objectives were to identify the causal mutation for a variety of diseases of individuals and families enrolled, and to discover novel disease genes. METHODS Unsolved patients in whom standard genomic diagnostic techniques such as targeted gene panel, exome-wide next generation sequencing, and/or chromosomal microarray, had already been performed were recruited. Genome sequencing and enhanced genomic analysis from the research setting were applied to aid novel gene discovery. RESULTS In total, 16/50 (32%) families/cases were solved. One or more candidate variants of uncertain significance were detected in 18/50 (36%) families. No candidate variants were identified in 16/50 (32%) families. Two novel disease genes (TOP3B, PRKACB) and two novel genotype-phenotype correlations (NARS, and KMT2C genes) were identified. Three out of eight patients with suspected mosaic tuberous sclerosis complex had their diagnosis confirmed which provided reproductive options for two patients. The utility of confirming diagnoses for patients with mosaic conditions (using high read depth sequencing and ddPCR) was not specifically envisaged at the onset of the project, but the flexibility to offer recruitment and analyses on an as-needed basis proved to be a strength of the AHA-UDP. CONCLUSION AHA-UDP demonstrates the utility of a UDP approach applying genome sequencing approaches in diagnosing adults with rare diseases who have had uninformative conventional genetic analysis, informing clinical management, recurrence risk, and recommendations for relatives.
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Affiliation(s)
- Mathew Wallis
- Austin Health Clinical Genetics Service, Austin Health, Melbourne, Australia
- Tasmanian Clinical Genetics Service, Tasmanian Health Service, Hobart, TAS, Australia
- School of Medicine and Menzies Institute for Medical Research, University of Tasmania, Hobart, Australia
| | - Simon D Bodek
- Austin Health Clinical Genetics Service, Austin Health, Melbourne, Australia.
- Medicine, Dentistry and Health Science, The University of Melbourne, Parkville, Australia.
| | - Jacob Munro
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Australia
| | - Haloom Rafehi
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Australia
| | - Mark F Bennett
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Australia
- Epilepsy Research Centre, University of Melbourne, Austin Health, Melbourne, Australia
| | - Zimeng Ye
- Epilepsy Research Centre, University of Melbourne, Austin Health, Melbourne, Australia
| | - Amy Schneider
- Epilepsy Research Centre, University of Melbourne, Austin Health, Melbourne, Australia
| | - Fiona Gardiner
- Epilepsy Research Centre, University of Melbourne, Austin Health, Melbourne, Australia
| | - Giulia Valente
- Austin Health Clinical Genetics Service, Austin Health, Melbourne, Australia
| | - Emma Murdoch
- Austin Health Clinical Genetics Service, Austin Health, Melbourne, Australia
| | - Eloise Uebergang
- Austin Health Clinical Genetics Service, Austin Health, Melbourne, Australia
- Murdoch Children's Research Institute, Melbourne, Parkville, Australia
| | - Jacquie Hunter
- Austin Health Clinical Genetics Service, Austin Health, Melbourne, Australia
| | - Chloe Stutterd
- Austin Health Clinical Genetics Service, Austin Health, Melbourne, Australia
- Victorian Clinical Genetics Service, Melbourne, Australia
- Murdoch Children's Research Institute, Melbourne, Parkville, Australia
- Department of Paediatrics, The University of Melbourne, Parkville, Australia
| | - Aamira Huq
- Austin Health Clinical Genetics Service, Austin Health, Melbourne, Australia
- Genetic Medicine Service, The Royal Melbourne Hospital, Melbourne, Australia
| | - Lucinda Salmon
- Austin Health Clinical Genetics Service, Austin Health, Melbourne, Australia
- Genetics Service, Royal Prince Alfred Hospital, Melbourne, Australia
| | - Ingrid Scheffer
- Austin Health Clinical Genetics Service, Austin Health, Melbourne, Australia
- Epilepsy Research Centre, University of Melbourne, Austin Health, Melbourne, Australia
- Department of Paediatrics, Austin Health, Melbourne, Australia
| | - Dhamidhu Eratne
- Austin Health Clinical Genetics Service, Austin Health, Melbourne, Australia
- Epilepsy Research Centre, University of Melbourne, Austin Health, Melbourne, Australia
- Neuropsychiatry, The Royal Melbourne Hospital, Melbourne, Australia
| | - Stephen Meyn
- Centre for Human Genomics and Precision Medicine, University of Wisconsin-Madison, Madison, WI, USA
| | - Chun Y Fong
- Austin Health Clinical Genetics Service, Austin Health, Melbourne, Australia
| | - Tom John
- Austin Health Clinical Genetics Service, Austin Health, Melbourne, Australia
- Medicine, Dentistry and Health Science, The University of Melbourne, Parkville, Australia
- Peter MacCallum Cancer Centre, Melbourne, Australia
| | - Saul Mullen
- Austin Health Clinical Genetics Service, Austin Health, Melbourne, Australia
- Epilepsy Research Centre, University of Melbourne, Austin Health, Melbourne, Australia
| | - Susan M White
- Victorian Clinical Genetics Service, Melbourne, Australia
- Murdoch Children's Research Institute, Melbourne, Parkville, Australia
- Department of Paediatrics, The University of Melbourne, Parkville, Australia
| | - Natasha J Brown
- Victorian Clinical Genetics Service, Melbourne, Australia
- Murdoch Children's Research Institute, Melbourne, Parkville, Australia
- Department of Paediatrics, The University of Melbourne, Parkville, Australia
| | - George McGillivray
- Victorian Clinical Genetics Service, Melbourne, Australia
- Genetics Service, Mercy Hospital for Women, Melbourne, Australia
| | - Jesse Chen
- Neurology Service, Austin Health, Melbourne, Australia
| | - Chris Richmond
- Royal Brisbane and Women's Hospital, Brisbane, QLD, Australia
| | - Andrew Hughes
- Austin Health Clinical Genetics Service, Austin Health, Melbourne, Australia
- Medicine, Dentistry and Health Science, The University of Melbourne, Parkville, Australia
| | | | - Andrew Fennell
- Austin Health Clinical Genetics Service, Austin Health, Melbourne, Australia
- Monash Health Genetics Clinic, Melbourne, Australia
| | - Brian Chambers
- Austin Health Clinical Genetics Service, Austin Health, Melbourne, Australia
- Medicine, Dentistry and Health Science, The University of Melbourne, Parkville, Australia
| | - Renee Santoreneos
- Austin Health Clinical Genetics Service, Austin Health, Melbourne, Australia
- Victorian Clinical Genetics Service, Melbourne, Australia
| | - Anna Le Fevre
- Austin Health Clinical Genetics Service, Austin Health, Melbourne, Australia
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
- Victorian Clinical Genetics Service, Melbourne, Australia
| | - Michael S Hildebrand
- Epilepsy Research Centre, University of Melbourne, Austin Health, Melbourne, Australia
| | - Melanie Bahlo
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Australia
| | - John Christodoulou
- Victorian Clinical Genetics Service, Melbourne, Australia
- Murdoch Children's Research Institute, Melbourne, Parkville, Australia
- Department of Paediatrics, The University of Melbourne, Parkville, Australia
| | - Martin Delatycki
- Austin Health Clinical Genetics Service, Austin Health, Melbourne, Australia
- Victorian Clinical Genetics Service, Melbourne, Australia
- Murdoch Children's Research Institute, Melbourne, Parkville, Australia
- Department of Paediatrics, The University of Melbourne, Parkville, Australia
| | - Samuel F Berkovic
- Austin Health Clinical Genetics Service, Austin Health, Melbourne, Australia
- Epilepsy Research Centre, University of Melbourne, Austin Health, Melbourne, Australia
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Rodriguez KM, Vaught J, Salz L, Foley J, Boulil Z, Van Dongen-Trimmer HM, Whalen D, Oluchukwu O, Liu KC, Burton J, Syngal P, Vargas-Shiraishi O, Kingsmore SF, Kobayashi ES, Coufal NG. Rapid Whole-Genome Sequencing and Clinical Management in the PICU: A Multicenter Cohort, 2016-2023. Pediatr Crit Care Med 2024; 25:699-709. [PMID: 38668387 PMCID: PMC11300160 DOI: 10.1097/pcc.0000000000003522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 08/06/2024]
Abstract
OBJECTIVES Analysis of the clinical utility of rapid whole-genome sequencing (rWGS) outside of the neonatal period is lacking. We describe the use of rWGS in PICU and cardiovascular ICU (CICU) patients across four institutions. DESIGN Ambidirectional multisite cohort study. SETTING Four tertiary children's hospitals. PATIENTS Children 0-18 years old in the PICU or CICU who underwent rWGS analysis, from May 2016 to June 2023. INTERVENTIONS None. MEASUREMENTS AND MAIN RESULTS A total of 133 patients underwent clinical, phenotype-driven rWGS analysis, 36 prospectively. A molecular diagnosis was identified in 79 patients (59%). Median (interquartile range [IQR]) age was 6 months (IQR 1.2 mo-4.6 yr). Median time for return of preliminary results was 3 days (IQR 2-4). In 79 patients with a molecular diagnosis, there was a change in ICU management in 19 patients (24%); and some change in clinical management in 63 patients (80%). Nondiagnosis changed management in 5 of 54 patients (9%). The clinical specialty ordering rWGS did not affect diagnostic rate. Factors associated with greater odds ratio (OR [95% CI]; OR [95% CI]) of diagnosis included dysmorphic features (OR 10.9 [95% CI, 1.8-105]) and congenital heart disease (OR 4.2 [95% CI, 1.3-16.8]). Variables associated with greater odds of changes in management included obtaining a genetic diagnosis (OR 16.6 [95% CI, 5.5-62]) and a shorter time to genetic result (OR 0.8 [95% CI, 0.76-0.9]). Surveys of pediatric intensivists indicated that rWGS-enhanced clinical prognostication ( p < 0.0001) and contributed to a decision to consult palliative care ( p < 0.02). CONCLUSIONS In this 2016-2023 multiple-PICU/CICU cohort, we have shown that timely genetic diagnosis is feasible across institutions. Application of rWGS had a 59% (95% CI, 51-67%) rate of diagnostic yield and was associated with changes in critical care management and long-term patient management.
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Affiliation(s)
- Katherine M. Rodriguez
- Rady Children’s Hospital, San Diego, CA
- Department of Pediatrics, University of California, San Diego
- Rady Children’s Institute for Genomic Medicine, San Diego, CA
| | - Jordan Vaught
- Rady Children’s Hospital, San Diego, CA
- Department of Pediatrics, University of California, San Diego
| | - Lisa Salz
- Rady Children’s Institute for Genomic Medicine, San Diego, CA
| | | | | | | | | | - Okonkwo Oluchukwu
- OSF Children’s Hospital of Illinois, Peoria, IL
- University of Illinois College of Medicine at Peoria, Peoria, IL
| | - Kuang Chuen Liu
- University of Illinois College of Medicine at Peoria, Peoria, IL
| | - Jennifer Burton
- OSF Children’s Hospital of Illinois, Peoria, IL
- University of Illinois College of Medicine at Peoria, Peoria, IL
| | - Prachi Syngal
- OSF Children’s Hospital of Illinois, Peoria, IL
- University of Illinois College of Medicine at Peoria, Peoria, IL
| | | | | | - Erica Sanford Kobayashi
- Rady Children’s Institute for Genomic Medicine, San Diego, CA
- Cedars-Sinai Medical Center, Department of Pediatrics, Los Angeles, CA
- Children’s Hospital of Orange County, Orange, CA
| | - Nicole G. Coufal
- Rady Children’s Hospital, San Diego, CA
- Department of Pediatrics, University of California, San Diego
- Rady Children’s Institute for Genomic Medicine, San Diego, CA
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3
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Cirillo L, Becherucci F. The evolving role of first-tier exome sequencing in medical diagnostics. Nephrol Dial Transplant 2024; 39:560-563. [PMID: 37858299 DOI: 10.1093/ndt/gfad222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Indexed: 10/21/2023] Open
Affiliation(s)
- Luigi Cirillo
- Nephrology and Dialysis Unit, Meyer Children's Hospital IRCCS, Florence, Italy
- Department of Biomedical, Experimental and Clinical Sciences "Mario Serio", University of Florence, Florence, Italy
| | - Francesca Becherucci
- Nephrology and Dialysis Unit, Meyer Children's Hospital IRCCS, Florence, Italy
- Department of Biomedical, Experimental and Clinical Sciences "Mario Serio", University of Florence, Florence, Italy
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4
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Nurchis MC, Radio FC, Salmasi L, Heidar Alizadeh A, Raspolini GM, Altamura G, Tartaglia M, Dallapiccola B, Pizzo E, Gianino MM, Damiani G. Cost-Effectiveness of Whole-Genome vs Whole-Exome Sequencing Among Children With Suspected Genetic Disorders. JAMA Netw Open 2024; 7:e2353514. [PMID: 38277144 PMCID: PMC10818217 DOI: 10.1001/jamanetworkopen.2023.53514] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 12/05/2023] [Indexed: 01/27/2024] Open
Abstract
Importance The diagnosis of rare diseases and other genetic conditions can be daunting due to vague or poorly defined clinical features that are not recognized even by experienced clinicians. Next-generation sequencing technologies, such as whole-genome sequencing (WGS) and whole-exome sequencing (WES), have greatly enhanced the diagnosis of genetic diseases by expanding the ability to sequence a large part of the genome, rendering a cost-effectiveness comparison between them necessary. Objective To assess the cost-effectiveness of WGS compared with WES and conventional testing in children with suspected genetic disorders. Design, Setting, and Participants In this economic evaluation, a bayesian Markov model was implemented from January 1 to June 30, 2023. The model was developed using data from a cohort of 870 pediatric patients with suspected genetic disorders who were enrolled and underwent testing in the Ospedale Pediatrico Bambino Gesù, Rome, Italy, from January 1, 2015, to December 31, 2022. The robustness of the model was assessed through probabilistic sensitivity analysis and value of information analysis. Main Outcomes and Measures Overall costs, number of definitive diagnoses, and incremental cost-effectiveness ratios per diagnosis were measured. The cost-effectiveness analyses involved 4 comparisons: first-tier WGS with standard of care; first-tier WGS with first-tier WES; first-tier WGS with second-tier WES; and first-tier WGS with second-tier WGS. Results The ages of the 870 participants ranged from 0 to 18 years (539 [62%] girls). The results of the analysis suggested that adopting WGS as a first-tier strategy would be cost-effective compared with all other explored options. For all threshold levels above €29 800 (US $32 408) per diagnosis that were tested up to €50 000 (US $54 375) per diagnosis, first-line WGS vs second-line WES strategy (ie, 54.6%) had the highest probability of being cost-effective, followed by first-line vs second-line WGS (ie, 54.3%), first-line WGS vs the standard of care alternative (ie, 53.2%), and first-line WGS vs first-line WES (ie, 51.1%). Based on sensitivity analyses, these estimates remained robust to assumptions and parameter uncertainty. Conclusions and Relevance The findings of this economic evaluation encourage the development of policy changes at various levels (ie, macro, meso, and micro) of international health systems to ensure an efficient adoption of WGS in clinical practice and its equitable access.
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Affiliation(s)
- Mario Cesare Nurchis
- School of Economics, Università Cattolica del Sacro Cuore, Rome, Italy
- Department of Woman and Child Health and Public Health, Fondazione Policlinico Universitario A. Gemelli Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Rome, Italy
| | | | - Luca Salmasi
- Department of Economics and Finance, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Aurora Heidar Alizadeh
- Department of Health Sciences and Public Health, Section of Hygiene, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Gian Marco Raspolini
- Department of Health Sciences and Public Health, Section of Hygiene, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Gerardo Altamura
- Department of Health Sciences and Public Health, Section of Hygiene, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Marco Tartaglia
- Molecular Genetics and Functional Genomics, Ospedale Pediatrico Bambino Gesù IRCCS, Rome, Italy
| | - Bruno Dallapiccola
- Molecular Genetics and Functional Genomics, Ospedale Pediatrico Bambino Gesù IRCCS, Rome, Italy
| | - Elena Pizzo
- Department of Applied Health Research, University College London, London, United Kingdom
| | - Maria Michela Gianino
- Department of Public Health Sciences and Paediatrics, Università di Torino, Turin, Italy
| | - Gianfranco Damiani
- Department of Woman and Child Health and Public Health, Fondazione Policlinico Universitario A. Gemelli Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Rome, Italy
- Department of Health Sciences and Public Health, Section of Hygiene, Università Cattolica del Sacro Cuore, Rome, Italy
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5
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Botos L, Szatmári E, Nagy GR. Prenatal and postnatal genetic testing toward personalized care: The non-invasive perinatal testing. Mol Cell Probes 2023; 72:101942. [PMID: 37951513 DOI: 10.1016/j.mcp.2023.101942] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 11/05/2023] [Accepted: 11/06/2023] [Indexed: 11/14/2023]
Abstract
This article investigates how non-invasive prenatal testing and the incorporation of genomic sequencing into newborn screening postnatally are transforming perinatal care. They improve the accuracy of prenatal and neonatal screening, allowing for early interventions and personalized therapies. Non-invasive prenatal testing before birth and saliva-sample-based newborn genomic sequencing after birth can be collectively referred to as non-invasive perinatal testing. Non-invasive prenatal testing is particularly useful for aneuploidy, whereas performance markers worsen as DNA abnormalities shrink in size. Screening for clinically actionable diseases in childhood would be crucial to personalized medical therapy, as the postnatal period remains appropriate for screening for the great majority of monogenic disorders. While genomic data can help diagnose uncommon diseases, challenges like ethics and equity necessitate joint approaches for appropriate integration in this revolutionary journey toward personalized care.
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Affiliation(s)
- Lilla Botos
- Department of Obstetrics and Gynecology, Baross Street Division, Semmelweis University, Budapest, Hungary
| | - Erzsébet Szatmári
- Department of Obstetrics and Gynecology, Baross Street Division, Semmelweis University, Budapest, Hungary
| | - Gyula Richárd Nagy
- Department of Obstetrics and Gynecology, Baross Street Division, Semmelweis University, Budapest, Hungary; Intelligenetic Healthcare Services Ltd., Budapest, Hungary.
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Abstract
Rare diseases are a leading cause of infant mortality and lifelong disability. To improve outcomes, timely diagnosis and effective treatments are needed. Genomic sequencing has transformed the traditional diagnostic process, providing rapid, accurate and cost-effective genetic diagnoses to many. Incorporating genomic sequencing into newborn screening programmes at the population scale holds the promise of substantially expanding the early detection of treatable rare diseases, with stored genomic data potentially benefitting health over a lifetime and supporting further research. As several large-scale newborn genomic screening projects launch internationally, we review the challenges and opportunities presented, particularly the need to generate evidence of benefit and to address the ethical, legal and psychosocial issues that genomic newborn screening raises.
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Affiliation(s)
- Zornitza Stark
- Australian Genomics, Melbourne, Victoria, Australia.
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Victoria, Australia.
- Department of Paediatrics, University of Melbourne, Melbourne, Victoria, Australia.
| | - Richard H Scott
- Great Ormond Street Hospital for Children, London, UK
- UCL Great Ormond Street Institute of Child Health, London, UK
- Genomics England, London, UK
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7
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Wu D, Wu Y, Lan Y, Lan S, Zhong Z, Li D, Zheng Z, Wang H, Ma L. Chromosomal Aberrations in Pediatric Patients With Moderate/Severe Developmental Delay/Intellectual Disability With Abundant Phenotypic Heterogeneities: A Single-Center Study. Pediatr Neurol 2023; 147:72-81. [PMID: 37566956 DOI: 10.1016/j.pediatrneurol.2023.06.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 05/26/2023] [Accepted: 06/06/2023] [Indexed: 08/13/2023]
Abstract
BACKGROUND This study aimed to examine the clinical usefulness of chromosome microarray (CMA) for selective implementation in patients with unexplained moderate or severe developmental delay/intellectual disability (DD/ID) and/or combined with different dysphonic features in the Han Chinese population. METHODS We retrospectively analyzed data on 122 pediatric patients with unexplained isolated moderate/severe DD/ID with or without autism spectrum disorders, epilepsy, dystonia, and congenital abnormalities from a single-center neurorehabilitation clinic in southern China. RESULTS A total of 46 probands (37.7%) had abnormal CMA results among the 122 study patients. With the exclusion of aneuploidies, uniparental disomies, and multiple homozygotes, 37 patients harbored 39 pathogenic copy number variations (pCNVs) (median [interquartile range] size: 3.57 [1.6 to 7.1] Mb; 33 deletions and 6 duplications), enriched in chromosomes 5, 7, 15, 17, and 22, with a markedly high prevalence of Angelman/Prader-Willi syndrome (24.3% [nine of 37]). Three rare deletions in the regions 5q33.2q34, 17p13.2, and 13q33.2 were reported, with specific delineation of clinical phenotypes. The frequencies of pCNVs were 18%, 33.3%, 38.89%, 41.67%, and 100% for patients with 1, 2, 3, 4, and 5 study phenotypes, respectively; patients with more concomitant abnormalities in the heart, brain, craniofacial region, and/or other organs had a higher CMA diagnostic yield and pCNV prevalence (P < 0.05). CONCLUSIONS Clinical application of CMA as a first-tier test among patients with moderate/severe DD/ID combined with congenital structural anomalies improved diagnostic yields and the quality of clinical management in this series of patients.
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Affiliation(s)
- Dan Wu
- Department of Pediatrics, Second Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong, China; Centre for Precision Health, School of Medical and Health Sciences, Edith Cowan University, Perth, WA, Australia
| | - Yi Wu
- Department of Pediatrics, Second Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong, China
| | - Yulong Lan
- Centre for Precision Health, School of Medical and Health Sciences, Edith Cowan University, Perth, WA, Australia; Department of Cardiology, Second Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong, China
| | - Shaocong Lan
- Guangdong Medical College, Zhanjiang, Guangdong, China
| | - Zhiwei Zhong
- Department of Neurosurgery, The First Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong, China
| | - Duo Li
- Department of Pediatrics, Second Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong, China
| | - Zexin Zheng
- Department of Pediatrics, Second Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong, China
| | - Hongwu Wang
- Department of Pediatrics, Second Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong, China.
| | - Lian Ma
- Department of Pediatrics, Second Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong, China; Department of Hematology and Oncology, Shenzhen Children's Hospital of China Medical University, Shenzhen, Guangdong, China; Shenzhen Public Service Platform of Molecular Medicine in Pediatric Hematology and Oncology, Shenzhen, Guangdong, China; Department of Pediatrics, The Third Affiliated Hospital of Guangzhou Medical University (The Women and Children's Hospital of Guangzhou Medical University), Guangzhou, Guangdong, China.
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8
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Mordaunt DA, Dalziel K, Goranitis I, Stark Z. Uptake of funded genomic testing for syndromic and non-syndromic intellectual disability in Australia. Eur J Hum Genet 2023; 31:977-979. [PMID: 37400487 PMCID: PMC10474079 DOI: 10.1038/s41431-023-01417-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2023] [Accepted: 06/16/2023] [Indexed: 07/05/2023] Open
Affiliation(s)
- Dylan A Mordaunt
- Health Economics Group, School of Population and Global Health, University of Melbourne, Parkville, VIC, Australia.
- Department of Paediatrics, University of Melbourne, Parkville, VIC, Australia.
- Murdoch Children's Research Institute, Melbourne, VIC, Australia.
| | - Kim Dalziel
- Health Economics Group, School of Population and Global Health, University of Melbourne, Parkville, VIC, Australia
- Department of Paediatrics, University of Melbourne, Parkville, VIC, Australia
| | - Ilias Goranitis
- Health Economics Group, School of Population and Global Health, University of Melbourne, Parkville, VIC, Australia
- Department of Paediatrics, University of Melbourne, Parkville, VIC, Australia
| | - Zornitza Stark
- Department of Paediatrics, University of Melbourne, Parkville, VIC, Australia
- Australian Genomics, Melbourne, VIC, Australia
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, VIC, Australia
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9
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Sharo AG, Zou Y, Adhikari AN, Brenner SE. ClinVar and HGMD genomic variant classification accuracy has improved over time, as measured by implied disease burden. Genome Med 2023; 15:51. [PMID: 37443081 PMCID: PMC10347827 DOI: 10.1186/s13073-023-01199-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2022] [Accepted: 05/31/2023] [Indexed: 07/15/2023] Open
Abstract
BACKGROUND Curated databases of genetic variants assist clinicians and researchers in interpreting genetic variation. Yet, these databases contain some misclassified variants. It is unclear whether variant misclassification is abating as these databases rapidly grow and implement new guidelines. METHODS Using archives of ClinVar and HGMD, we investigated how variant misclassification has changed over 6 years, across different ancestry groups. We considered inborn errors of metabolism (IEMs) screened in newborns as a model system because these disorders are often highly penetrant with neonatal phenotypes. We used samples from the 1000 Genomes Project (1KGP) to identify individuals with genotypes that were classified by the databases as pathogenic. Due to the rarity of IEMs, nearly all such classified pathogenic genotypes indicate likely variant misclassification in ClinVar or HGMD. RESULTS While the false-positive rates of both ClinVar and HGMD have improved over time, HGMD variants currently imply two orders of magnitude more affected individuals in 1KGP than ClinVar variants. We observed that African ancestry individuals have a significantly increased chance of being incorrectly indicated to be affected by a screened IEM when HGMD variants are used. However, this bias affecting genomes of African ancestry was no longer significant once common variants were removed in accordance with recent variant classification guidelines. We discovered that ClinVar variants classified as Pathogenic or Likely Pathogenic are reclassified sixfold more often than DM or DM? variants in HGMD, which has likely resulted in ClinVar's lower false-positive rate. CONCLUSIONS Considering misclassified variants that have since been reclassified reveals our increasing understanding of rare genetic variation. We found that variant classification guidelines and allele frequency databases comprising genetically diverse samples are important factors in reclassification. We also discovered that ClinVar variants common in European and South Asian individuals were more likely to be reclassified to a lower confidence category, perhaps due to an increased chance of these variants being classified by multiple submitters. We discuss features for variant classification databases that would support their continued improvement.
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Affiliation(s)
- Andrew G. Sharo
- Biophysics Graduate Group, University of California, Berkeley, CA 94720 USA
- Center for Computational Biology, University of California, Berkeley, CA 94720 USA
- Department of Ecology and Evolutionary Biology, University of California, 124 Biomed Building, 1156 High St., Santa Cruz, CA 95064 USA
| | - Yangyun Zou
- Center for Computational Biology, University of California, Berkeley, CA 94720 USA
- Department of Plant and Microbial Biology, University of California, 461 Koshland Hall, Berkeley, CA 94720 USA
- Currently at: Department of Clinical Research, Yikon Genomics Company, Ltd., Shanghai, China
| | - Aashish N. Adhikari
- Center for Computational Biology, University of California, Berkeley, CA 94720 USA
- Department of Plant and Microbial Biology, University of California, 461 Koshland Hall, Berkeley, CA 94720 USA
- Currently at: Illumina, Foster City, CA 94404 USA
| | - Steven E. Brenner
- Biophysics Graduate Group, University of California, Berkeley, CA 94720 USA
- Center for Computational Biology, University of California, Berkeley, CA 94720 USA
- Department of Plant and Microbial Biology, University of California, 461 Koshland Hall, Berkeley, CA 94720 USA
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10
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Stefka J, Streff H, Liu P, Towne M, Smith HS. Cascade testing after exome sequencing: Retrospective analysis of linked family data at 2 US laboratories. Genet Med 2023; 25:100818. [PMID: 36852743 DOI: 10.1016/j.gim.2023.100818] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 02/16/2023] [Accepted: 02/22/2023] [Indexed: 02/26/2023] Open
Abstract
PURPOSE Cascade testing, the process of testing a proband's at-risk relatives, is integral to realizing the full value of genomic sequencing. However, there is little empirical evidence on the uptake of cascade testing after a positive exome sequencing (ES) result in a population of probands with diverse clinical indications. METHODS We retrospectively reviewed administrative data from 2 US clinical laboratories that perform ES. For each proband with a positive ES result, we used linked family data to describe the frequency of relatives' cascade testing performed at the same laboratory, variant detection yield of cascade tests, and characteristics of probands and relatives categorized on the basis of cascade testing completion. RESULTS Among the 3723 positive ES results across both laboratories, 426 relatives of 282 probands completed cascade testing (uptake = 7.6%). An average of 1.5 relatives (SD = 0.9) were tested per proband. Of the 426 relatives tested, 200 had a variant of interest detected (variant detection yield = 47.0%). CONCLUSION In our real-world data analysis, a small proportion of probands with a positive ES result subsequently had relatives complete cascade testing at the same laboratory. However, approximately half of the tested relatives received a clinically significant result that could have implications for clinical management or reproductive planning. Additional research on ways to increase cascade testing uptake is warranted.
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Affiliation(s)
- Julie Stefka
- Genetic Counseling Program, School of Health Professions, Baylor College of Medicine, Houston, TX; Clinical Diagnostics, Ambry Genetics, Aliso Viejo, CA.
| | - Haley Streff
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX
| | - Pengfei Liu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX; Baylor Genetics, Houston, TX
| | - Meghan Towne
- Medical Sciences, Ambry Genetics, Aliso Viejo, CA
| | - Hadley Stevens Smith
- Center for Medical Ethics and Health Policy, Baylor College of Medicine, Houston, TX; Precision Medicine Translational Research Center (PROMoTeR), Department of Population Medicine, Harvard Medical School and Harvard Pilgrim Health Care Institute, Boston, MA
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11
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Rezapour A, Souresrafil A, Barzegar M, Sheikhy-Chaman M, Tatarpour P. Economic evaluation of next-generation sequencing techniques in diagnosis of genetic disorders: A systematic review. Clin Genet 2023; 103:513-528. [PMID: 36808726 DOI: 10.1111/cge.14313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 02/12/2023] [Accepted: 02/14/2023] [Indexed: 02/23/2023]
Abstract
In recent years, massively parallel sequencing or next generation sequencing (NGS) has considerably changed both the research and diagnostic fields, and rapid developments have led to the combination of NGS techniques in clinical practice, ease of analysis, and detection of genetic mutations. This article aimed at reviewing the economic evaluation studies of the NGS techniques in the diagnosis of genetic diseases. In this systematic review, scientific databases (PubMed, EMBASE, Web of Science, Cochrane, Scopus, and CEA registry) were searched from 2005 to 2022 to identify the related literature on the economic evaluation of NGS techniques in the diagnosis of genetic diseases. Full-text reviews and data extraction were all performed by two independent researchers. The quality of all the articles included in this study was evaluated using the Checklist of Quality of Health Economic Studies (QHES). Out of 20 521 screened abstracts, 36 studies met the inclusion criteria. The mean score of the QHES checklist for the studies was 0.78 (high quality). Seventeen studies were conducted based on modeling. Cost-effectiveness analysis, cost-utility analysis, and cost-minimization analysis were done in 26 studies, 13 studies, and 1 study, respectively. Based on the available evidence and findings, exome sequencing, which is one of the NGS techniques, could have the potential to be used as a cost-effective genomic test to diagnose children with suspected genetic diseases. The results of the present study support the cost-effectiveness of exome sequencing in diagnosing suspected genetic disorders. However, the use of exome sequencing as a first- or second-line diagnostic test is still controversial. Most studies have been conducted in high-income countries, and research on the cost-effectiveness of NGS methods is recommended in low- and middle-income countries.
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Affiliation(s)
- Aziz Rezapour
- Health Management and Economics Research Center, Health Management Research Institute, Iran University of Medical Sciences, Tehran, Iran
| | - Aghdas Souresrafil
- Department of Health Services and Health Promotion, School of Health, Occupational Environment Research Center, Rafsanjan University of Medical Sciences, Rafsanjan, Iran
| | - Mohammad Barzegar
- Department of English Language, School of Health Management and Information Sciences, Iran University of Medical Sciences, Tehran, Iran
| | - Mohammadreza Sheikhy-Chaman
- Department of Health Economics, School of Health Management and Information Sciences, Iran University of Medical Sciences, Tehran, Iran
| | - Parvin Tatarpour
- School of Health Management and Information Sciences, Iran University of Medical Sciences, Tehran, Iran
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12
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Gordon LG, Wood C, Tothill RW, Webb PM, Schofield P, Mileshkin L. Healthcare Costs Before and After Diagnosis of Cancer of Unknown Primary Versus Ovarian Cancer in Australia. PHARMACOECONOMICS - OPEN 2023; 7:111-120. [PMID: 36253664 PMCID: PMC9929003 DOI: 10.1007/s41669-022-00371-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Accepted: 08/25/2022] [Indexed: 06/16/2023]
Abstract
BACKGROUND Little is known about the healthcare resource usage and costs for patients with cancer of unknown primary (CUP). OBJECTIVE The aim of this study was to describe and quantify healthcare resource use and costs in Australia, 6 months prior to and after a diagnosis of CUP, and compare to those of women with ovarian cancer. METHODS Individual-level data combining baseline surveys, clinical records and Medicare Benefits Schedule (MBS) claim records were analysed for 149 patients with CUP and 480 patients with ovarian cancer from two prospective cohort studies. MBS data were aggregated for the period 6 months prior to diagnosis date and 6 months after diagnosis. Data included doctor consultations, pathology, diagnostics, therapeutic procedures, imaging, allied health and medicines. Generalised linear models were used to evaluate the cost differences between CUP and ovarian cancer using gamma family and log link functions. Models were adjusted for age, employment, marital status, surgery, chemotherapy and number of comorbidities. RESULTS The mean healthcare costs in the 6 months prior to diagnosis of CUP were Australian (AU) $3903 versus AU$1327 for ovarian cancer (adjusted cost ratio 2.94, 95% confidence interval [CI] 2.08-4.15). Mean healthcare costs 6 months post-diagnosis were higher for patients with CUP versus ovarian cancer (AU$20,339 vs AU$13,819, adjusted cost ratio 1.47, 95% CI 1.13-1.92). Higher costs for patients with CUP were driven by imaging (AU$1937 vs AU$1387), procedures (AU$5403 vs AU$2702) and prescribed medicines for all conditions (AU$10,111 vs AU$6717). CONCLUSIONS Pre-diagnosis costs for patients with CUP are nearly triple those for ovarian cancer. Six months after diagnosis, healthcare costs for CUP remained higher than for ovarian cancer due to imaging, procedures and medicines.
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Affiliation(s)
- Louisa G Gordon
- QIMR Berghofer Medical Research Institute, Population Health Department, Locked Bag 2000, Royal Brisbane Hospital, Herston, Brisbane, Australia.
- Queensland University of Technology (QUT), School of Nursing, Kelvin Grove, Australia.
- The University of Queensland, School of Medicine, Herston, Brisbane, Australia.
| | - C Wood
- Department of Medical Oncology, Peter MacCallum Cancer Centre and the Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, Australia
| | - R W Tothill
- Department of Medical Oncology, Peter MacCallum Cancer Centre and the Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, Australia
| | - P M Webb
- QIMR Berghofer Medical Research Institute, Population Health Department, Locked Bag 2000, Royal Brisbane Hospital, Herston, Brisbane, Australia
| | | | - L Mileshkin
- Department of Medical Oncology, Peter MacCallum Cancer Centre and the Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, Australia
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13
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Hopkins CE, Brock T, Caulfield TR, Bainbridge M. Phenotypic screening models for rapid diagnosis of genetic variants and discovery of personalized therapeutics. Mol Aspects Med 2022; 91:101153. [PMID: 36411139 PMCID: PMC10073243 DOI: 10.1016/j.mam.2022.101153] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 10/22/2022] [Accepted: 10/23/2022] [Indexed: 11/19/2022]
Abstract
Precision medicine strives for highly individualized treatments for disease under the notion that each individual's unique genetic makeup and environmental exposures imprints upon them not only a disposition to illness, but also an optimal therapeutic approach. In the realm of rare disorders, genetic predisposition is often the predominant mechanism driving disease presentation. For such, mostly, monogenic disorders, a causal gene to phenotype association is likely. As a result, it becomes important to query the patient's genome for the presence of pathogenic variations that are likely to cause the disease. Determining whether a variant is pathogenic or not is critical to these analyses and can be challenging, as many disease-causing variants are novel and, ergo, have no available functional data to help categorize them. This problem is exacerbated by the need for rapid evaluation of pathogenicity, since many genetic diseases present in young children who will experience increased morbidity and mortality without rapid diagnosis and therapeutics. Here, we discuss the utility of animal models, with a focus mainly on C. elegans, as a contrast to tissue culture and in silico approaches, with emphasis on how these systems are used in determining pathogenicity of variants with uncertain significance and then used to screen for novel therapeutics.
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Affiliation(s)
| | | | - Thomas R Caulfield
- Mayo Clinic, Department of Neuroscience, Department of Computational Biology, Department of Clinical Genomics, Jacksonville, FL, 32224, Rochester, MN, 55905, USA
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14
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Abbott M, McKenzie L, Moran BVG, Heidenreich S, Hernández R, Hocking-Mennie L, Clark C, Gomes J, Lampe A, Baty D, McGowan R, Miedzybrodzka Z, Ryan M. Continuing the sequence? Towards an economic evaluation of whole genome sequencing for the diagnosis of rare diseases in Scotland. J Community Genet 2022; 13:487-501. [PMID: 34415556 PMCID: PMC9530076 DOI: 10.1007/s12687-021-00541-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 07/15/2021] [Indexed: 11/21/2022] Open
Abstract
Novel developments in genomic medicine may reduce the length of the diagnostic odyssey for patients with rare diseases. Health providers must thus decide whether to offer genome sequencing for the diagnosis of rare conditions in a routine clinical setting. We estimated the costs of singleton standard genetic testing and trio-based whole genome sequencing (WGS), in the context of the Scottish Genomes Partnership (SGP) study. We also explored what users value about genomic sequencing. Insights from the costing and value assessments will inform a subsequent economic evaluation of genomic medicine in Scotland. An average cost of £1,841 per singleton was estimated for the standard genetic testing pathway, with significant variability between phenotypes. WGS cost £6625 per family trio, but this estimate reflects the use of WGS during the SGP project and large cost savings may be realised if sequencing was scaled up. Patients and families valued (i) the chance of receiving a diagnosis (and the peace of mind and closure that brings); (ii) the information provided by WGS (including implications for family planning and secondary findings); and (iii) contributions to future research. Our costings will be updated to address limitations of the current study for incorporation in budget impact modelling and cost-effectiveness analysis (cost per diagnostic yield). Our insights into the benefits of WGS will guide the development of a discrete choice experiment valuation study. This will inform a user-perspective cost-benefit analysis of genome-wide sequencing, accounting for the broader non-health outcomes. Taken together, our research will inform the long-term strategic development of NHS Scotland clinical genetics testing services, and will be of benefit to others seeking to undertake similar evaluations in different contexts.
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Affiliation(s)
- Michael Abbott
- Health Economics Research Unit, University of Aberdeen, Aberdeen, UK.
| | - Lynda McKenzie
- Health Economics Research Unit, University of Aberdeen, Aberdeen, UK
| | | | - Sebastian Heidenreich
- Health Economics Research Unit, University of Aberdeen, Aberdeen, UK
- Evidera Inc., London, UK
| | - Rodolfo Hernández
- Health Economics Research Unit, University of Aberdeen, Aberdeen, UK
| | | | - Caroline Clark
- Department of Medical Genetics, University of Aberdeen, Aberdeen, UK
- NHS Grampian Regional Genetics Service, Aberdeen Royal Infirmary, Aberdeen, UK
| | - Joana Gomes
- NHS Grampian Regional Genetics Service, Aberdeen Royal Infirmary, Aberdeen, UK
| | - Anne Lampe
- South East Scotland Clinical Genetics Service, Western General Hospital, Edinburgh, UK
| | - David Baty
- NHS Tayside Regional Genetics Service, Ninewells Hospital, Dundee, UK
| | - Ruth McGowan
- South East Scotland Clinical Genetics Service, Queen Elizabeth University Hospital, Glasgow, UK
| | | | - Mandy Ryan
- Health Economics Research Unit, University of Aberdeen, Aberdeen, UK
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15
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Sanford Kobayashi EF, Dimmock DP. Better and faster is cheaper. Hum Mutat 2022; 43:1495-1506. [PMID: 35723630 DOI: 10.1002/humu.24422] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 05/23/2022] [Accepted: 06/08/2022] [Indexed: 11/09/2022]
Abstract
The rapid pace of advancement in genomic sequencing technology has recently reached a new milestone, with a record-setting time to molecular diagnosis of a mere 8 h. The catalyst behind this achievement is the accumulation of evidence indicating that quicker results more often make an impact on patient care and lead to healthcare cost savings. Herein, we review the diagnostic and clinical utility of rapid whole genome and rapid whole exome sequencing, the associated reduction in healthcare costs, and the relationship between these outcome measures and time-to-diagnosis.
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Affiliation(s)
- Erica F Sanford Kobayashi
- Department of Pediatrics, Cedars-Sinai Medical Center, Los Angeles, California, USA.,Rady Children's Institute for Genomic Medicine, Rady Children's Hospital, San Diego, California, USA
| | - David P Dimmock
- Rady Children's Institute for Genomic Medicine, Rady Children's Hospital, San Diego, California, USA
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16
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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] [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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17
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Xie D, Duan R, Li C, Xie Z, Wang A, Xiong L, Wei J, Xi H, Fang J, Yan H, Wang J, Zhang Y, Mao X, Wang J, Wang H. Study on the Economic Burden of Neurodevelopmental Diseases on Patients With Genetic Diagnosis. Front Public Health 2022; 10:887796. [PMID: 35615033 PMCID: PMC9126321 DOI: 10.3389/fpubh.2022.887796] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 04/04/2022] [Indexed: 11/17/2022] Open
Abstract
Objective To study the burden of neurodevelopmental diseases (NDDs) via cost-of-illness analysis of Chinese patients with genetic diagnosis. Methods We recruited NDD patients (0–18 years old) with genetic diagnosis (GD) from September 1, 2020 to January 30, 2021. We gathered basic information on the details of diagnosis, as well as the direct medical cost, direct non-healthcare cost and indirect cost before and after receiving GD. We corrected the cost for time biases by calculating the cost per day for each patient. Results For the 502 patients with NDDs, the mean age was 4.08 ± 3.47. The household income was 0.6 (0.4, 1.0) 10,000 CNY per-month on average. The direct medical cost, direct non-healthcare cost and indirect cost were 12.27 (7.36, 22.23) 10,000 CNY, 1.45 (0.73, 2.69)10,000 CNY and 14.14(4.80, 28.25) 10,000 CNY per patient, respectively. Every patient received 1.20 (0.34, 3.60) 10,000 CNY on average (15.91%) from insurance. The daily total cost after receiving GD were ~62.48% lower than those before GD (191.59 CNY vs. 71.45 CNY). The descend range of lab cost (95.77%, P < 0.05) was the largest, followed by drugs (91.39%, P < 0.05), hospitalization (90.85%, P < 0.05), and consultation (57.41%, P < 0.05). The cost of rehabilitation kept slightly increasing but there were no significant differences (P > 0.05). The daily direct medical cost of each patient fell by 75.26% (P < 0.05) from 311.79 CNY to 77.14 CNY when the diagnostic age was younger than 1, and declined by 49.30% (P < 0.05) and 8.97% (P > 0.05) when the diagnostic age was 1–3 and older than 3, respectively. Conclusions Early genetic diagnosis is crucial for to reducing the burden of disease because of the amount of money spent was lower when they are diagnosed at younger age. Patients with NDDs can incur a heavy economic burden, especially in rehabilitation cost and indirect cost, because the insurance coverage for patients is low, so it is urgent for governments to pay more attention to these issues.
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Affiliation(s)
- Donghua Xie
- Department of Information Management, Maternal and Child Health Hospital of Hunan Province, Changsha, China
| | - Ruoyu Duan
- Department of Pediatrics, Peking University First Hospital, Beijing, China
- Department of Neurology, National Center for Children's Health, Beijing Children's Hospital, Capital Medical University, Beijing, China
| | - Chen Li
- Children Health Hospital of Shenzhen City, Shenzhen, China
| | - Zhiqun Xie
- Department of Information Management, Maternal and Child Health Hospital of Hunan Province, Changsha, China
| | - Aihua Wang
- Department of Information Management, Maternal and Child Health Hospital of Hunan Province, Changsha, China
| | - Lili Xiong
- Department of Information Management, Maternal and Child Health Hospital of Hunan Province, Changsha, China
| | - Jianhui Wei
- Xiangya School of Public Health, Central South University, Changsha, China
| | - Hui Xi
- Department of Information Management, Maternal and Child Health Hospital of Hunan Province, Changsha, China
| | - Junqu Fang
- Department of Information Management, Maternal and Child Health Hospital of Hunan Province, Changsha, China
| | - Huifang Yan
- Department of Pediatrics, Peking University First Hospital, Beijing, China
| | - Junyu Wang
- Department of Pediatrics, Peking University First Hospital, Beijing, China
| | - Yu Zhang
- Department of Pediatrics, Peking University First Hospital, Beijing, China
| | - Xiao Mao
- NHC Key Laboratory of Birth Defect for Research and Prevention (Maternal and Child Health Hospital of Hunan Province), Changsha, China
- *Correspondence: Xiao Mao
| | - Jingmin Wang
- Department of Pediatrics, Peking University First Hospital, Beijing, China
- Beijing Key Laboratory of Molecular Diagnosis and Study on Pediatric Genetic Diseases, Beijing, China
- Key Laboratory for Neuroscience, Ministry of Education/National Health and Family Planning Commission, Peking University, Beijing, China
- Jingmin Wang
| | - Hua Wang
- NHC Key Laboratory of Birth Defect for Research and Prevention (Maternal and Child Health Hospital of Hunan Province), Changsha, China
- Hua Wang
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18
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Binquet C, Lejeune C, Faivre L, Bouctot M, Asensio ML, Simon A, Deleuze JF, Boland A, Guillemin F, Seror V, Delmas C, Espérou H, Duffourd Y, Lyonnet S, Odent S, Heron D, Sanlaville D, Frebourg T, Gerard B, Dollfus H. Genome Sequencing for Genetics Diagnosis of Patients With Intellectual Disability: The DEFIDIAG Study. Front Genet 2022; 12:766964. [PMID: 35178068 PMCID: PMC8845475 DOI: 10.3389/fgene.2021.766964] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Accepted: 12/28/2021] [Indexed: 12/26/2022] Open
Abstract
Introduction: Intellectual Disability (ID) is the most common cause of referral to pediatric genetic centers, as it affects around 1–3% of the general population and is characterized by a wide genetic heterogeneity. The Genome Sequencing (GS) approach is expected to achieve a higher diagnostic yield than exome sequencing given its wider and more homogenous coverage, and, since theoretically, it can more accurately detect variations in regions traditionally not well captured and identify structural variants, or intergenic/deep intronic putatively pathological events. The decreasing cost of sequencing, the progress in data-management and bioinformatics, prompted us to assess GS efficiency as the first line procedure to identify the molecular diagnosis in patients without obvious ID etiology. This work is being carried out in the framework of the national French initiative for genomic medicine (Plan France Médecine Génomique 2025). Methods and Analysis: This multidisciplinary, prospective diagnostic study will compare the diagnostic yield of GS trio analysis (index case, father, mother) with the French core minimal reference strategy (Fragile-X testing, chromosomal microarray analysis and Gene Panel Strategy of 44 selected ID genes). Both strategies are applied in a blinded fashion, in parallel, in the same population of 1275 ID index cases with no obvious diagnosis (50% not previously investigated). Among them, a subgroup of 196 patients are randomized to undergo GS proband analysis in addition to GS trio analysis plus the French core minimal reference strategy, in order to compare their efficiency. The study also aims to identify the most appropriate strategy according to the clinical presentation of the patients, to evaluate the impact of deployment of GS on the families’ diagnostic odyssey and the modification of their care, and to identify the advantages/difficulties for the patients and their families. Ethics Statement: The protocol was approved by the Ethics Committee Sud Méditerranée I and the French data privacy commission (CNIL, authorization 919361). Trial Registration:ClinicalTrials.gov identifier NCT04154891 (07/11/2019).
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Affiliation(s)
- Christine Binquet
- Inserm, CHU Dijon-Bourgogne, CIC1432-Epidémiologie Clinique, Dijon, France.,CHU Dijon-Bourgogne, Fédération Hospitalo-Universitaire Médecine Translationnelle et Anomalies Du Développement (TRANSLAD), Dijon, France
| | - Catherine Lejeune
- Inserm, CHU Dijon-Bourgogne, CIC1432-Epidémiologie Clinique, Dijon, France.,CHU Dijon-Bourgogne, Fédération Hospitalo-Universitaire Médecine Translationnelle et Anomalies Du Développement (TRANSLAD), Dijon, France.,Inserm, Université de Bourgogne-Franche-Comté, UMR 1231, EPICAD, Dijon, France
| | - Laurence Faivre
- CHU Dijon-Bourgogne, Fédération Hospitalo-Universitaire Médecine Translationnelle et Anomalies Du Développement (TRANSLAD), Dijon, France.,Inserm, Université Bourgogne-Franche-Comté, UMR1231, équipe GAD, Dijon, France.,Service de Génétique Clinique, Centre de Référence Anomalies Du Développement CLAD Est, CHU de Dijon, ERN ITHACA, Dijon, France
| | - Marion Bouctot
- Inserm, CHU Dijon-Bourgogne, CIC1432-Epidémiologie Clinique, Dijon, France
| | | | - Alban Simon
- Service de Génétique Médicale, Institut de Génétique Médicale D'Alsace, Hôpitaux Universitaires de Strasbourg, Strasbourg, France
| | - Jean-François Deleuze
- Université Paris-Saclay, CEA, Centre National de Recherche en Génomique Humaine (CNRGH), Evry, France
| | - Anne Boland
- Université Paris-Saclay, CEA, Centre National de Recherche en Génomique Humaine (CNRGH), Evry, France
| | - Francis Guillemin
- CIC1433-Epidémiologie Clinique, Inserm, Centre Hospitalier Régional et Universitaire de Nancy, Université de Lorraine, Nancy, France
| | - Valérie Seror
- Aix Marseille Université, IRD, APHM, SSA, VITROME, IHU-Méditerranée Infection, Marseille, France
| | | | | | - Yannis Duffourd
- CHU Dijon-Bourgogne, Fédération Hospitalo-Universitaire Médecine Translationnelle et Anomalies Du Développement (TRANSLAD), Dijon, France.,Inserm, Université Bourgogne-Franche-Comté, UMR1231, équipe GAD, Dijon, France
| | - Stanislas Lyonnet
- Université de Paris, INSERM, IHU Imagine-Institut des maladies génétiques, Paris, France.,Fédération de Génétique et Médecine Génomique, GHU APHP.centre-Université de Paris, Hôpital Necker-Enfants Malades, Paris, France
| | - Sylvie Odent
- Service de Génétique Clinique, Centre de Référence Anomalies Du Développement CLAD- Ouest, Université de Rennes, CNRS, IGDR (Institut de Génétique et Développement de Rennes), ERN ITHACA, Rennes, France
| | - Delphine Heron
- Unité Fonctionnelle de Génétique Médicale et Centre de Référence « Déficiences Intellectuelles de Causes Rares », APHP Sorbonne Université, Groupe Hospitalier Pitié-Salpêtrière et Hôpital Trousseau, Paris, France
| | - Damien Sanlaville
- Hospices Civils de Lyon, GHE, Service de Génétique, Université Claude Bernard Lyon 1, Lyon, France
| | - Thierry Frebourg
- CHU de Rouen, Service de Génétique, Rouen, France.,Inserm, Université de Normandie, UMR1245, Centre de Génomique et de Médecine Personnalisée, Rouen, France
| | - Bénédicte Gerard
- Laboratoires de Diagnostic Génétique, Institut de Génétique Médicale D'Alsace, Hôpitaux Universitaires de Strasbourg, Strasbourg, France
| | - Hélène Dollfus
- Service de Génétique Médicale, Institut de Génétique Médicale D'Alsace, Hôpitaux Universitaires de Strasbourg, Strasbourg, France.,Inserm UMRS_1112, Institut de Génétique Médicale D'Alsace, Université de Strasbourg, France et CHRU, Strasbourg, France
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19
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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] [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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20
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Stark Z, Ellard S. Rapid genomic testing for critically ill children: time to become standard of care? Eur J Hum Genet 2022; 30:142-149. [PMID: 34744166 PMCID: PMC8821543 DOI: 10.1038/s41431-021-00990-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2021] [Accepted: 10/17/2021] [Indexed: 02/03/2023] Open
Abstract
Rapid genomic testing in critically ill neonatal and paediatric patients has transformed the paradigm of rare disease diagnosis, delivering results in real time to inform patient management. More than 20 studies totalling over 1500 patients from diverse healthcare settings worldwide have now been published, forming a compelling evidence base for healthcare system implementation. We review the reported diagnostic and clinical outcomes, as well as broader evaluations of family and professional experiences, cost effectiveness, implementation challenges and bioethical issues arising from rapid testing. As rapid genomic testing transitions from the research to the healthcare setting to become a 'standard of care' test, there is a need to develop effective service delivery models to support scalability at both the laboratory and clinical level and promote equity of access, prompt test initiation, integrated multidisciplinary input and holistic family support. Harnessing the high level of professional engagement with rapid genomic testing programmes will continue to drive innovation and adoption, while close integration with emerging precision medicine approaches will be necessary to deliver on the promise of reduced infant and child mortality.
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Affiliation(s)
- Zornitza Stark
- Australian Genomics, Melbourne, VIC Australia ,grid.1058.c0000 0000 9442 535XVictorian Clinical Genetics Services, Murdoch Children’s Research Institute, Melbourne, VIC Australia ,grid.1008.90000 0001 2179 088XDepartment of Paediatrics, University of Melbourne, Melbourne, VIC Australia
| | - Sian Ellard
- grid.419309.60000 0004 0495 6261Exeter Genomics Laboratory, South West Genomic Laboratory Hub, Royal Devon & Exeter NHS Foundation Trust, Exeter, UK ,grid.8391.30000 0004 1936 8024Institute of Biomedical and Clinical Science, University of Exeter Medical School, Exeter, UK
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21
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Sainio MT, Aaltio J, Hyttinen V, Kortelainen M, Ojanen S, Paetau A, Tienari P, Ylikallio E, Auranen M, Tyynismaa H. Effectiveness of clinical exome sequencing in adult patients with difficult-to-diagnose neurological disorders. Acta Neurol Scand 2022; 145:63-72. [PMID: 34418069 DOI: 10.1111/ane.13522] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Revised: 08/02/2021] [Accepted: 08/12/2021] [Indexed: 12/25/2022]
Abstract
OBJECTIVES Clinical diagnostics in adults with hereditary neurological diseases is complicated by clinical and genetic heterogeneity, as well as lifestyle effects. Here, we evaluate the effectiveness of exome sequencing and clinical costs in our difficult-to-diagnose adult patient cohort. Additionally, we expand the phenotypic and genetic spectrum of hereditary neurological disorders in Finland. METHODS We performed clinical exome sequencing (CES) to 100 adult patients from Finland with neurological symptoms of suspected genetic cause. The patients were classified as myopathy (n = 57), peripheral neuropathy (n = 16), ataxia (n = 15), spastic paraplegia (n = 4), Parkinsonism (n = 3), and mixed (n = 5). In addition, we gathered the costs of prior diagnostic work-up to retrospectively assess the cost-effectiveness of CES as a first-line diagnostic tool. RESULTS The overall diagnostic yield of CES was 27%. Pathogenic variants were found for 14 patients (in genes ANO5, CHCHD10, CLCN1, DES, DOK7, FKBP14, POLG, PYROXD1, SCN4A, TUBB3, and TTN) and likely pathogenic previously undescribed variants for 13 patients (in genes ABCD1, AFG3L2, ATL1, CACNA1A, COL6A1, DYSF, IRF2BPL, KCNA1, MT-ATP6, SAMD9L, SGCB, and TPM2). Age of onset below 40 years increased the probability of finding a genetic cause. Our cost evaluation of prior diagnostic work-up suggested that early CES would be cost-effective in this patient group, in which diagnostic costs increase linearly with prolonged investigations. CONCLUSIONS Based on our results, CES is a cost-effective, powerful first-line diagnostic tool in establishing the molecular diagnosis in adult neurological patients with variable symptoms. Importantly, CES can markedly shorten the diagnostic odysseys of about one third of patients.
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Affiliation(s)
- Markus T. Sainio
- Stem Cells and Metabolism Research Program Faculty of Medicine University of Helsinki Helsinki Finland
| | - Juho Aaltio
- Stem Cells and Metabolism Research Program Faculty of Medicine University of Helsinki Helsinki Finland
| | - Virva Hyttinen
- VATT Institute for Economic Research Helsinki Finland
- Department of Health and Social Management University of Eastern Finland Kuopio Finland
| | - Mika Kortelainen
- VATT Institute for Economic Research Helsinki Finland
- Department of Economics Turku School of Economics Turku Finland
| | - Simo Ojanen
- Department of Veterinary Biosciences Faculty of Veterinary Medicine University of Helsinki Helsinki Finland
| | - Anders Paetau
- Department of Pathology HUSLAB and University of Helsinki Helsinki Finland
| | - Pentti Tienari
- Clinical Neurosciences Neurology University of Helsinki and Helsinki University Hospital Helsinki Finland
- Translational Immunology Research Program Faculty of Medicine University of Helsinki Helsinki Finland
| | - Emil Ylikallio
- Stem Cells and Metabolism Research Program Faculty of Medicine University of Helsinki Helsinki Finland
- Clinical Neurosciences Neurology University of Helsinki and Helsinki University Hospital Helsinki Finland
| | - Mari Auranen
- Clinical Neurosciences Neurology University of Helsinki and Helsinki University Hospital Helsinki Finland
| | - Henna Tyynismaa
- Stem Cells and Metabolism Research Program Faculty of Medicine University of Helsinki Helsinki Finland
- Department of Medical and Clinical Genetics University of Helsinki Helsinki Finland
- Neuroscience Center Helsinki Institute of Life Science University of Helsinki Helsinki Finland
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22
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Jayasinghe K, Wu Y, Stark Z, Kerr PG, Mallett AJ, Gaff C, Martyn M, Goranitis I, Quinlan C. Cost-Effectiveness of Targeted Exome Analysis as a Diagnostic Test in Glomerular Diseases. Kidney Int Rep 2021; 6:2850-2861. [PMID: 34805637 PMCID: PMC8589690 DOI: 10.1016/j.ekir.2021.08.028] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 08/12/2021] [Accepted: 08/30/2021] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Despite the emergence of diagnostic and clinical utility evidence in nephrology, publicly funded access to genomic testing is restricted in most health care systems. To establish genomic sequencing as a clinical test, an evaluation of cost-effectiveness is urgently required. METHODS An economic evaluation, informed by a primary clinical study and available clinical evidence and guidelines in nephrology, was performed to evaluate the cost-effectiveness and optimal timing of exome sequencing (ES) in adults and children with suspected monogenic glomerular diseases compared with nongenomic investigations (NGIs). Six diagnostic strategies reflecting current practice and recommended models of care in Australia were modeled: (i) NGIs, (ii) late gene panel followed by ES, (iii) late ES, (iv) early gene panel, (v) early gene panel followed by ES, and (vi) early ES. RESULTS ES with targeted analysis achieved a diagnosis in 23 of 63 (36.5%) adults and 10 of 24 (41.6%) children. NGIs were estimated to diagnose 4.0% of children, with an average estimated cost of AU$6120 per child. Integrating ES as a first-line test in children was cost saving, with an incremental cost saving of AU$3230 per additional diagnosis compared with NGIs. In adults, NGIs was estimated to diagnose 8% of patients, with an average estimated cost of AU$1830 per person. In adults, integrating ES early resulted in an incremental cost per additional diagnosis of AU$5460 relative to NGIs. CONCLUSIONS Early ES with targeted analysis was effective for diagnosing monogenic kidney disease, with substantial cost savings in children.
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Affiliation(s)
- Kushani Jayasinghe
- Department of Nephrology, Monash Medical Centre, Melbourne, Australia
- Monash University, Melbourne, Australia
- Murdoch Children’s Research Institute, Melbourne, Australia
- The KidGen Collaborative, Australian Genomics Health Alliance, Melbourne, Australia
| | - You Wu
- Centre for Health Policy, University of Melbourne, Melbourne, VIC, Australia
- Australian Genomics Health Alliance, Melbourne, VIC, Australia
| | - Zornitza Stark
- Murdoch Children’s Research Institute, Melbourne, Australia
- The KidGen Collaborative, Australian Genomics Health Alliance, Melbourne, Australia
- Department of Pediatrics, University of Melbourne, Australia
- Victorian Clinical Genetics Services, Melbourne, Australia
| | - Peter G. Kerr
- Department of Nephrology, Monash Medical Centre, Melbourne, Australia
- Monash University, Melbourne, Australia
| | - Andrew J. Mallett
- The KidGen Collaborative, Australian Genomics Health Alliance, Melbourne, Australia
- Department of Renal Medicine, Townsville University Hospital, Townsville, QLD, Australia
- College of Medicine and Dentistry, James Cook University, Townsville, QLD, Australia
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Clara Gaff
- Department of Pediatrics, University of Melbourne, Australia
- Melbourne Genomics Health Alliance, Melbourne, Australia
| | - Melissa Martyn
- Murdoch Children’s Research Institute, Melbourne, Australia
- Melbourne Genomics Health Alliance, Melbourne, Australia
| | - Ilias Goranitis
- Centre for Health Policy, University of Melbourne, Melbourne, VIC, Australia
- Australian Genomics Health Alliance, Melbourne, VIC, Australia
| | - Catherine Quinlan
- Murdoch Children’s Research Institute, Melbourne, Australia
- The KidGen Collaborative, Australian Genomics Health Alliance, Melbourne, Australia
- Department of Pediatrics, University of Melbourne, Australia
- Department of Pediatric Nephrology, Royal Children’s Hospital, Melbourne, Australia
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23
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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] [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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24
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Klau J, Abou Jamra R, Radtke M, Oppermann H, Lemke JR, Beblo S, Popp B. Exome first approach to reduce diagnostic costs and time - retrospective analysis of 111 individuals with rare neurodevelopmental disorders. Eur J Hum Genet 2021; 30:117-125. [PMID: 34690354 PMCID: PMC8738730 DOI: 10.1038/s41431-021-00981-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 09/22/2021] [Accepted: 10/04/2021] [Indexed: 11/09/2022] Open
Abstract
This single-center study aims to determine the time, diagnostic procedure, and cost saving potential of early exome sequencing in a cohort of 111 individuals with genetically confirmed neurodevelopmental disorders. We retrospectively collected data regarding diagnostic time points and procedures from the individuals' medical histories and developed criteria for classifying diagnostic procedures in terms of requirement, followed by a cost allocation. All genetic variants were re-evaluated according to ACMG recommendations and considering the individuals' phenotype. Individuals who developed first symptoms of their underlying genetic disorder when Next Generation Sequencing (NGS) diagnostics were already available received a diagnosis significantly faster than individuals with first symptoms before this cutoff. The largest amount of potentially dispensable diagnostics was found in genetic, metabolic, and cranial magnetic resonance imaging examinations. Out of 407 performed genetic examinations, 296 (72.7%) were classified as potentially dispensable. The same applied to 36 (27.9%) of 129 cranial magnetic resonance imaging and 111 (31.8%) of 349 metabolic examinations. Dispensable genetic examinations accounted 302,947.07€ (90.2%) of the total 335,837.49€ in potentially savable costs in this cohort. The remaining 32,890.42€ (9.8%) are related to non-required metabolic and cranial magnetic resonance imaging diagnostics. On average, the total potentially savable costs in our study amount to €3,025.56 per individual. Cost savings by first tier exome sequencing lie primarily in genetic, metabolic, and cMRI testing in this German cohort, underscoring the utility of performing exome sequencing at the beginning of the diagnostic pathway and the potential for saving diagnostic costs and time.
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Affiliation(s)
- Julia Klau
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany
| | - Rami Abou Jamra
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany
| | - Maximilian Radtke
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany
| | - Henry Oppermann
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany
| | - Johannes R Lemke
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany.,Center for Rare Diseases, University of Leipzig Medical Center, Leipzig, Germany
| | - Skadi Beblo
- Center for Rare Diseases, University of Leipzig Medical Center, Leipzig, Germany
| | - Bernt Popp
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany.
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25
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Yang L, Wei Z, Chen X, Hu L, Peng X, Wang J, Lu C, Kong Y, Dong X, Ni Q, Lu Y, Wu B, Wang H, Meirelles K, Tian X, Zhang J, Chang F, Liu L, Li C, You W, Cheng G, Wang L, Cao Y, Chen C, Fang P, Tang S, Zhou W. Use of medical exome sequencing for identification of underlying genetic defects in NICU: Experience in a cohort of 2303 neonates in China. Clin Genet 2021; 101:101-109. [PMID: 34671977 DOI: 10.1111/cge.14075] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 09/27/2021] [Accepted: 10/15/2021] [Indexed: 12/17/2022]
Abstract
Emerging evidence demonstrates the clinical utility of genomic applications in newborn intensive care unit (NICU) patients with strong indications of Mendelian etiology. However, such applications' diagnostic yield and utility remain unclear for NICU cohorts with minimal phenotype selection. In this study, focused medical exome sequencing was used as a first-tier, singleton-focused diagnostic tool for 2303 unrelated sick neonates. Integrated analysis of single nucleotide variants (SNVs), small insertions and deletions (Indels), and large copy number variants (CNVs) was performed. The diagnostic rate in this NICU cohort is 12.3% (284/2303), with 190 probands with molecular diagnoses made from SNV/Indel analyses (66.9%), 93 patients with diagnostic aneuploidy/CNVs findings (32.8%), and 1 patient with both SNV and CNV (0.4%). In addition, 54 (2.3%) of patients had a reportable incidental finding. Multiple organ involvements, craniofacial abnormalities, and dermatologic abnormalities were the strongest positive predictors for a molecular diagnosis. Among the 190 cases with SNV/Indel defects, direct impacts on medical management were observed in 46.8% of patients after the results were reported. In this study, we demonstrate that focused medical exome sequencing is a powerful first-line diagnostic tool for NICU patients. Significant number of diagnosed NICU patients can benefit from more focused medical management and long-term care.
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Affiliation(s)
- Lin Yang
- Clinical Genetic Center, Children's Hospital of Fudan University, Shanghai, China.,Key Laboratory of Birth Defects, Children's Hospital of Fudan University, Shanghai, China
| | - Zejun Wei
- Key Laboratory of Birth Defects, Children's Hospital of Fudan University, Shanghai, China
| | - Xiang Chen
- Division of Neonatology, Children's Hospital of Fudan University, Shanghai, China
| | - Liyuan Hu
- Division of Neonatology, Children's Hospital of Fudan University, Shanghai, China
| | - Xiaomin Peng
- Key Laboratory of Birth Defects, Children's Hospital of Fudan University, Shanghai, China
| | - Jin Wang
- Division of Neonatology, Children's Hospital of Fudan University, Shanghai, China
| | - Chunmei Lu
- Division of Neonatology, Children's Hospital of Fudan University, Shanghai, China
| | - Yanting Kong
- Division of Neonatology, Children's Hospital of Fudan University, Shanghai, China
| | - Xinran Dong
- Key Laboratory of Birth Defects, Children's Hospital of Fudan University, Shanghai, China
| | - Qi Ni
- Key Laboratory of Birth Defects, Children's Hospital of Fudan University, Shanghai, China
| | - Yulan Lu
- Key Laboratory of Birth Defects, Children's Hospital of Fudan University, Shanghai, China
| | - Bingbing Wu
- Key Laboratory of Birth Defects, Children's Hospital of Fudan University, Shanghai, China.,Key Laboratory of Neonatal Diseases, Ministry of Health, Children's Hospital of Fudan University, Shanghai, China
| | - Huijun Wang
- Key Laboratory of Birth Defects, Children's Hospital of Fudan University, Shanghai, China.,Key Laboratory of Neonatal Diseases, Ministry of Health, Children's Hospital of Fudan University, Shanghai, China
| | | | - Xia Tian
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA
| | | | | | - Liu Liu
- Sema4, Branford, Connecticut, USA
| | | | - Wesley You
- Google LLC, Mountain View, California, USA
| | - Guoqiang Cheng
- Division of Neonatology, Children's Hospital of Fudan University, Shanghai, China
| | - Laishuan Wang
- Division of Neonatology, Children's Hospital of Fudan University, Shanghai, China
| | - Yun Cao
- Division of Neonatology, Children's Hospital of Fudan University, Shanghai, China
| | - Chao Chen
- Division of Neonatology, Children's Hospital of Fudan University, Shanghai, China
| | - Ping Fang
- KingMed Diagnostics, Guangzhou, China
| | - Sha Tang
- KingMed Diagnostics, Guangzhou, China
| | - Wenhao Zhou
- Clinical Genetic Center, Children's Hospital of Fudan University, Shanghai, China.,Division of Neonatology, Children's Hospital of Fudan University, Shanghai, China.,CAS Center for Excellence in Brain Science and Intelligence Technology (CEBSIT), Shanghai, China
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26
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Liu J, Zheng Y, Huang J, Zhu D, Zang P, Luo Z, Yang Y, Peng Y, Xiao Z, Zhu Y, Lu X. Expanding the genotypes and phenotypes for 19 rare diseases by exome sequencing performed in pediatric intensive care unit. Hum Mutat 2021; 42:1443-1460. [PMID: 34298581 PMCID: PMC9292147 DOI: 10.1002/humu.24266] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Revised: 06/30/2021] [Accepted: 07/21/2021] [Indexed: 12/30/2022]
Abstract
Phenotypes of some rare genetic diseases are atypical and it is a challenge for pediatric intensive care units (PICUs) to diagnose and manage such patients in an emergency. In this study, we investigated 58 PICU patients (39 deceased and 19 surviving) in critical ill status or died shortly without a clear etiology. Whole exome sequencing was performed of 103 DNA samples from their families. Disease-causing single-nucleotide variants (SNVs) and copy number variants (CNVs) were identified to do genotype-phenotypes analysis. In total, 27 (46.6%) patients received a genetic diagnosis. We identified 34 pathogenic or likely pathogenic SNVs from 26 genes, which are related to at least 19 rare diseases. Each rare disease involved an isolated patient except two patients caused by the same gene ACAT1. The genotypic spectrum was expanded by 23 novel SNVs from gene MARS1, PRRT2, TBCK, TOR1A, ECE1, ARX, ZEB2, ACAT1, CPS1, VWF, NBAS, COG4, and INVS. We also identified two novel pathogenic CNVs. Phenotypes associated with respiratory, multiple congenital anomalies, neuromuscular, or metabolic disorders were the most common. Twenty patients (74.1%) accompanied severe infection, 19 patients (70.1%) died. In summary, our findings expanded the genotypes and phenotypes of 19 rare diseases from PICU with complex characteristics.
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Affiliation(s)
- Juan Liu
- Pediatric Intensive Care Unit, Hunan Childrens Hospital, University of South China, Changsha, Hunan, China
| | - Yu Zheng
- Pediatrics Research Institute of Hunan Province, Hunan Children's Hospital, Changsha, Hunan, China.,Center for Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Jiaotian Huang
- Pediatric Intensive Care Unit, Hunan Childrens Hospital, University of South China, Changsha, Hunan, China
| | - Desheng Zhu
- Pediatric Intensive Care Unit, Hunan Childrens Hospital, University of South China, Changsha, Hunan, China
| | - Ping Zang
- Pediatric Intensive Care Unit, Hunan Childrens Hospital, University of South China, Changsha, Hunan, China
| | - Zhenqing Luo
- Pediatrics Research Institute of Hunan Province, Hunan Children's Hospital, Changsha, Hunan, China
| | - Yongjia Yang
- Pediatrics Research Institute of Hunan Province, Hunan Children's Hospital, Changsha, Hunan, China
| | - Yu Peng
- Pediatrics Research Institute of Hunan Province, Hunan Children's Hospital, Changsha, Hunan, China
| | - Zhenghui Xiao
- Pediatric Intensive Care Unit, Hunan Childrens Hospital, University of South China, Changsha, Hunan, China
| | - Yimin Zhu
- Emergency Medicine Institute of Hunan Province, Changsha, Hunan, China
| | - Xiulan Lu
- Pediatric Intensive Care Unit, Hunan Childrens Hospital, University of South China, Changsha, Hunan, China
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27
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Karamzade A, Babaei M, Saberi M, Golchin N, Khalil Nejad Sani Banaei A, Eshaghkhani Y, Golchehre Z, Keramatipour M. Identification of a novel truncating variant in AHI1 gene and a brief review on mutations spectrum. Mol Biol Rep 2021; 48:5339-5345. [PMID: 34191236 DOI: 10.1007/s11033-021-06508-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2021] [Accepted: 06/21/2021] [Indexed: 10/21/2022]
Abstract
Joubert syndrome (JS) is a rare inherited neurodevelopmental condition characterized by hypotonia, ataxia, developmental delay, abnormal eye movements, neonatal respiratory disturbance and unique midbrain-hindbrain malformation, known as the molar tooth sign. JS is a genetically heterogeneous disorder with nearly 35 ciliary genes are implicated in its pathogenesis. AHI1 gene is one of the most frequently mutated gene in JS patients which is accounted for 8-11% of cases, particularly in Arab population. AHI1 encodes a cilium-localized protein with a significant role in mediating vesicle trafficking, ciliogenesis and cell polarity. Here, we report a novel pathogenic variant in AHI1 gene and review previously published mutations in AHI1 gene briefly. Whole exome sequencing was employed to determine the causative mutation in an Iranian Arab family with JS from southwestern Iran. Segregation analysis of the candidate variant in the family members was performed using PCR-Sanger sequencing. This approach found a novel homozygous nonsense variant c.832C > T (p.Gln278Ter) in AHI1. Segregation analysis was consistent with individual's phenotype and an autosomal recessive pattern in the family. The variant residing in a relatively highly conserved region and fulfilled the criteria required to be classified as a pathogenic variant based on American College of Medical Genetics and Genomics guidelines. This study confirms the diagnosis of JS in this family and highlights the efficiency of next-generation sequencing-based technique to identify the genetic causes of hereditary disorders with locus heterogeneity.
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Affiliation(s)
- Arezou Karamzade
- Department of Medical Genetics, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran.,Watson Genetic Laboratory, North Kargar street, Tehran, Iran
| | - Meisam Babaei
- Department of Pediatrics, North Khorasan University of Medical Sciences, Bojnurd, Iran
| | - Mohammad Saberi
- Department of Medical Genetics, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Neda Golchin
- Watson Genetic Laboratory, North Kargar street, Tehran, Iran
| | | | - Yeganeh Eshaghkhani
- Department of Medical Genetics, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Zahra Golchehre
- Department of Medical Genetics, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Mohammad Keramatipour
- Department of Medical Genetics, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran. .,Watson Genetic Laboratory, North Kargar street, Tehran, Iran.
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28
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Cost or price of sequencing? Implications for economic evaluations in genomic medicine. Genet Med 2021; 23:1833-1835. [PMID: 34113006 DOI: 10.1038/s41436-021-01223-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 05/10/2021] [Accepted: 05/10/2021] [Indexed: 11/08/2022] Open
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29
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Pearson NM, Stolte C, Shi K, Beren F, Abul-Husn NS, Bertier G, Brown K, Diaz GA, Odgis JA, Suckiel SA, Horowitz CR, Wasserstein M, Gelb BD, Kenny EE, Gagnon C, Jobanputra V, Bloom T, Greally JM. GenomeDiver: a platform for phenotype-guided medical genomic diagnosis. Genet Med 2021; 23:1998-2002. [PMID: 34113009 PMCID: PMC8488006 DOI: 10.1038/s41436-021-01219-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2020] [Revised: 05/06/2021] [Accepted: 05/07/2021] [Indexed: 12/11/2022] Open
Abstract
Purpose: Making a diagnosis from clinical genomic sequencing requires well-structured phenotypic data to guide genotype interpretation. A patient’s phenotypic features can be documented using the Human Phenotype Ontology (HPO), generating terms used to prioritize genes potentially causing the patient’s disease. We have developed GenomeDiver to provide a user interface for clinicians that allows more effective collaboration with the clinical diagnostic laboratory, with the goal of improving the success of the diagnostic process. Methods: GenomeDiver uses genomic data to prompt reverse phenotyping of patients undergoing genetic testing, enriching the amount and quality of structured phenotype data for the diagnostic laboratory, and helping clinicians to explore and flag diseases potentially causing their patient’s presentation. Results: We show how GenomeDiver communicates the clinician’s informed insights to the diagnostic lab in the form of HPO terms for interpretation of genomic sequencing data. We describe our user-driven design process, the engineering of the software for efficiency, security and portability, and examples of the performance of GenomeDiver using genomic testing data. Conclusions: GenomeDiver is a first step in a new approach to genomic diagnostics that enhances laboratory-clinician interactions, with the goal of directly engaging clinicians to improve the outcome of genomic diagnostic testing.
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Affiliation(s)
| | - Christian Stolte
- New York Genome Center, New York, NY, USA.,Stolte Design, Islesboro, ME, USA
| | - Kevin Shi
- New York Genome Center, New York, NY, USA
| | - Faygel Beren
- Columbia University, Graduate School of Arts and Sciences, New York, NY, USA
| | - Noura S Abul-Husn
- Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | - Kaitlyn Brown
- Division of Genetics, Department of Pediatrics, Children's Hospital at Montefiore, Bronx, NY, USA
| | - George A Diaz
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jacqueline A Odgis
- Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Sabrina A Suckiel
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | - Melissa Wasserstein
- Division of Genetics, Department of Pediatrics, Children's Hospital at Montefiore, Bronx, NY, USA.,Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Bruce D Gelb
- Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Eimear E Kenny
- Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | | | - Toby Bloom
- New York Genome Center, New York, NY, USA.,eGenesis, Inc., Cambridge, MA, USA
| | - John M Greally
- Division of Genetics, Department of Pediatrics, Children's Hospital at Montefiore, Bronx, NY, USA. .,Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA. .,Center for Epigenomics, Albert Einstein College of Medicine, Bronx, NY, USA.
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30
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Kilby MD. The role of next-generation sequencing in the investigation of ultrasound-identified fetal structural anomalies. BJOG 2021; 128:420-429. [PMID: 32975887 PMCID: PMC8607475 DOI: 10.1111/1471-0528.16533] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/24/2020] [Indexed: 12/14/2022]
Abstract
Fetal structural anomalies have an impact on fetal mortality and morbidity. Next-generation sequencing (NGS) may be incorporated into clinical pathways for investigation of paediatric morbidity but can also be used to delineate the prognosis of fetal anomalies. This paper reviews the role of NGS in the investigation of fetal malformations, the literature defining the clinical utility, the technique most commonly used and potential promise and challenges for implementation into clinical practice. Prospective case selection with informative pre-test counselling by multidisciplinary teams is imperative. Regulated laboratory sequencing, bioinformatic pathways with potential variant identification and conservative matching with the phenotype is important. TWEETABLE ABSTRACT: Prenatal exome sequencing in fetal structural anomalies yields diagnostic information in up to 20% of cases.
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Affiliation(s)
- M D Kilby
- Fetal Medicine Centre, Birmingham Women's and Children's Foundation Trust, Birmingham, UK.,Institute of Metabolism and Systems Research, College of Medical & Dental Sciences, University of Birmingham, Birmingham, UK
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31
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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: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [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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32
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Kingsmore SF, Henderson A, Owen MJ, Clark MM, Hansen C, Dimmock D, Chambers CD, Jeliffe-Pawlowski LL, Hobbs C. Measurement of genetic diseases as a cause of mortality in infants receiving whole genome sequencing. NPJ Genom Med 2020; 5:49. [PMID: 33154820 PMCID: PMC7608690 DOI: 10.1038/s41525-020-00155-8] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Accepted: 10/02/2020] [Indexed: 12/19/2022] Open
Abstract
Understanding causes of infant mortality shapes public health policy and prioritizes diseases for investments in surveillance, intervention and medical research. Rapid genomic sequencing has created a novel opportunity to decrease infant mortality associated with treatable genetic diseases. Herein, we sought to measure the contribution of genetic diseases to mortality among infants by secondary analysis of babies enrolled in two clinical studies and a systematic literature review. Among 312 infants who had been admitted to an ICU at Rady Children's Hospital between November 2015 and September 2018 and received rapid genomic sequencing, 30 (10%) died in infancy. Ten (33%) of the infants who died were diagnosed with 11 genetic diseases. The San Diego Study of Outcomes in Mothers and Infants platform identified differences between in-hospital and out-of-hospital causes of infant death. Similarly, in six published studies, 195 (21%) of 918 infant deaths were associated with genetic diseases by genomic sequencing. In 195 infant deaths associated with genetic diseases, locus heterogeneity was 70%. Treatment guidelines existed for 70% of the genetic diseases diagnosed, suggesting that rapid genomic sequencing has substantial potential to decrease infant mortality among infants in ICUs. Further studies are needed in larger, comprehensive, unbiased patient sets to determine the generalizability of these findings.
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Affiliation(s)
| | - Audrey Henderson
- Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123 USA
| | - Mallory J. Owen
- Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123 USA
| | - Michelle M. Clark
- Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123 USA
| | - Christian Hansen
- Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123 USA
| | - David Dimmock
- Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123 USA
| | | | - Laura L. Jeliffe-Pawlowski
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA USA
| | - Charlotte Hobbs
- Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123 USA
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33
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Response to Ferket et al. Genet Med 2020; 22:1910. [PMID: 32606441 DOI: 10.1038/s41436-020-0889-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Accepted: 06/17/2020] [Indexed: 11/09/2022] Open
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34
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Stenton SL, Prokisch H. Genetics of mitochondrial diseases: Identifying mutations to help diagnosis. EBioMedicine 2020; 56:102784. [PMID: 32454403 PMCID: PMC7248429 DOI: 10.1016/j.ebiom.2020.102784] [Citation(s) in RCA: 117] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 04/21/2020] [Accepted: 04/22/2020] [Indexed: 12/15/2022] Open
Abstract
Mitochondrial diseases are amongst the most genetically and phenotypically diverse groups of inherited diseases. The vast phenotypic overlap with other disease entities together with the absence of reliable biomarkers act as driving forces for the integration of unbiased methodologies early in the diagnostic algorithm, such as whole exome sequencing (WES) and whole genome sequencing (WGS). Such approaches are used in variant discovery and in combination with high-throughput functional assays such as transcriptomics in simultaneous variant discovery and validation. By capturing all genes, they not only increase the diagnostic rate in heterogenous mitochondrial disease patients, but accelerate novel disease gene discovery, and are valuable in side-stepping the risk of overlooking unexpected or even treatable genetic disease diagnoses.
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Affiliation(s)
- Sarah L Stenton
- Institut für Humangenetik, Klinikum rechts der Isar, Technische Universität München, Trogerstraße 32, 81675 München, Germany; Institute of Neurogenomics, Helmholtz Zentrum München, Ingolstaedter Landstraße 1, D-85764 Neuherberg, Germany
| | - Holger Prokisch
- Institut für Humangenetik, Klinikum rechts der Isar, Technische Universität München, Trogerstraße 32, 81675 München, Germany; Institute of Neurogenomics, Helmholtz Zentrum München, Ingolstaedter Landstraße 1, D-85764 Neuherberg, Germany.
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35
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Fahr P, Buchanan J, Wordsworth S. A Review of Health Economic Studies Comparing Traditional and Massively Parallel Sequencing Diagnostic Pathways for Suspected Genetic Disorders. PHARMACOECONOMICS 2020; 38:143-158. [PMID: 31741314 DOI: 10.1007/s40273-019-00856-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Genetic disorders are clinically diverse and genetically heterogeneous, and are traditionally diagnosed based on an iterative phenotype-guided genetic assessment. However, such diagnostic approaches are long (diagnostic odysseys are common), misdiagnoses occur frequently, and diagnostic rates are low. Massively parallel sequencing (MPS) technologies may improve diagnostic rates and reduce the time to diagnosis for patients with suspected genetic disorders; however, MPS technologies are expensive and the health economic evidence base to support their use is limited. Several studies have compared the costs of traditional and MPS diagnostic pathways for patients with suspected genetic disorders, however costing methods and diagnostic scenarios are heterogeneous across studies. We conducted a literature review to identify and summarise information on these costing methods and diagnostic scenarios. Relevant studies were identified in MEDLINE, EMBASE, EconLit, University of York Centre for Reviews and Dissemination and the Cochrane Library, from 2010 to 2018. Twenty-four articles were included in the review. We observed considerable heterogeneity across studies with respect to the selection of items of resource use used to derive total diagnostic pathway cost estimates. We also observed structural differences in the diagnostic scenarios used to compare the traditional and MPS diagnostic pathways. There is a need for guidelines on the costing of diagnostic pathways to encourage the use of consistent methods. More micro-costing studies that evaluate diagnostic service delivery are also required. Greater homogeneity in costing approaches would facilitate more reliable comparisons between studies and improve the transferability of cost estimates across countries.
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Affiliation(s)
- Patrick Fahr
- Health Economics Research Centre, Nuffield Department of Population Health, University of Oxford, Old Road Campus, Oxford, OX3 7LF, UK.
| | - James Buchanan
- Health Economics Research Centre, Nuffield Department of Population Health, University of Oxford, Old Road Campus, Oxford, OX3 7LF, UK
- National Institute for Health Research Oxford Biomedical Research Centre, University of Oxford, Oxford, UK
| | - Sarah Wordsworth
- Health Economics Research Centre, Nuffield Department of Population Health, University of Oxford, Old Road Campus, Oxford, OX3 7LF, UK
- National Institute for Health Research Oxford Biomedical Research Centre, University of Oxford, Oxford, UK
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36
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The cost trajectory of the diagnostic care pathway for children with suspected genetic disorders. Genet Med 2019; 22:292-300. [DOI: 10.1038/s41436-019-0635-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Accepted: 07/30/2019] [Indexed: 12/22/2022] Open
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