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Zemet R, Van den Veyver IB. Impact of prenatal genomics on clinical genetics practice. Best Pract Res Clin Obstet Gynaecol 2024; 97:102545. [PMID: 39265228 DOI: 10.1016/j.bpobgyn.2024.102545] [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: 06/04/2024] [Revised: 06/18/2024] [Accepted: 09/02/2024] [Indexed: 09/14/2024]
Abstract
Genetic testing for prenatal diagnosis in the pre-genomic era primarily focused on detecting common fetal aneuploidies, using methods that combine maternal factors and imaging findings. The genomic era, ushered in by the emergence of new technologies like chromosomal microarray analysis and next-generation sequencing, has transformed prenatal diagnosis. These new tools enable screening and testing for a broad spectrum of genetic conditions, from chromosomal to monogenic disorders, and significantly enhance diagnostic precision and efficacy. This chapter reviews the transition from traditional karyotyping to comprehensive sequencing-based genomic analyses. We discuss both the clinical utility and the challenges of integrating prenatal exome and genome sequencing into prenatal care and underscore the need for ethical frameworks, improved prenatal phenotypic characterization, and global collaboration to further advance the field.
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Affiliation(s)
- Roni Zemet
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.
| | - Ignatia B Van den Veyver
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA; Department of Obstetrics and Gynecology, Division of Maternal-Fetal Medicine, Division of Prenatal and Reproductive Genetics, Baylor College of Medicine, Houston, TX, USA.
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2
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Bhatia S, Pal S, Kulshrestha S, Gupta D, Soni A, Saxena R, Bijarnia-Mahay S, Verma IC, Puri RD. Role of next generation sequencing in diagnosis and management of critically ill children with suspected monogenic disorder. Eur J Hum Genet 2024; 32:1106-1115. [PMID: 38605122 PMCID: PMC11369102 DOI: 10.1038/s41431-024-01569-z] [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: 07/31/2023] [Revised: 01/19/2024] [Accepted: 02/12/2024] [Indexed: 04/13/2024] Open
Abstract
Next generation sequencing based diagnosis has emerged as a promising tool for evaluating critically ill neonates and children. However, there is limited data on its utility in developing countries. We assessed its diagnostic rate and clinical impact on management of pediatric patients with a suspected genetic disorder requiring critical care. The study was conducted at a single tertiary hospital in Northern India. We analyzed 70 children with an illness requiring intensive care and obtained a precise molecular diagnosis in 32 of 70 probands (45.3%) using diverse sequencing techniques such as clinical exome, whole exome, and whole genome. A significant change in clinical outcome was observed in 13 of 32 (40.6%) diagnosed probands with a change in medication in 11 subjects and redirection to palliative care in two subjects. Additional benefits included specific dietary management (three cases), avoidance of a major procedure (one case) and better reproductive counseling. Dramatic therapeutic responses were observed in three cases with SCN1A, SCN2A and KCNQ2-related epileptic encephalopathy. A delayed turn-around for sequencing results was perceived as a major limiting factor in the study, as rapid and ultra-rapid sequencing was not available. Achieving a precise molecular diagnosis has great utility in managing critically ill patients with suspected genetic disorders in developing countries.
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Affiliation(s)
- Sameer Bhatia
- Institute of Medical Genetics and Genomics, Sir Ganga Ram Hospital, New Delhi, India
| | - Swasti Pal
- Institute of Medical Genetics and Genomics, Sir Ganga Ram Hospital, New Delhi, India
| | - Samarth Kulshrestha
- Institute of Medical Genetics and Genomics, Sir Ganga Ram Hospital, New Delhi, India
| | - Dhiren Gupta
- Department of Paediatrics, Institute of Child Health, Sir Ganga Ram Hospital, New Delhi, India
| | - Arun Soni
- Department of Neonatology, Institute of Child Health, Sir Ganga Ram Hospital, New Delhi, India
| | - Renu Saxena
- Institute of Medical Genetics and Genomics, Sir Ganga Ram Hospital, New Delhi, India
| | - Sunita Bijarnia-Mahay
- Institute of Medical Genetics and Genomics, Sir Ganga Ram Hospital, New Delhi, India
| | - Ishwar Chander Verma
- Institute of Medical Genetics and Genomics, Sir Ganga Ram Hospital, New Delhi, India
| | - Ratna Dua Puri
- Institute of Medical Genetics and Genomics, Sir Ganga Ram Hospital, New Delhi, India.
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3
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Tasker RC. Editor's Choice Articles for August. Pediatr Crit Care Med 2024; 25:685-688. [PMID: 39101799 DOI: 10.1097/pcc.0000000000003568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 08/06/2024]
Affiliation(s)
- Robert C Tasker
- orcid.org/0000-0003-3647-8113
- Department of Anesthesiology, Critical Care and Pain Medicine, Boston Children's Hospital, Boston, MA
- Selwyn College, Cambridge University, Cambridge, United Kingdom
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4
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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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Affiliation(s)
- Ricardo G Branco
- Both authors: Pediatric Intensive Care Unit, Division of Critical Care, Sidra Medicine, Doha, Qatar
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Migliavacca MP, Sobreira J, Bermeo D, Gomes M, Alencar D, Sussuchi L, Souza CA, Silva JS, Kroll JE, Burger M, Guarischi-Sousa R, Villela D, Yamamoto GL, Milanezi F, Horigoshi N, Cesar RG, de Carvalho WB, Honjo RS, Bertola DR, Kim CA, de Souza L, Procianoy RS, Silveria RC, Rosenberg C, Giugliani R, Campana GA, Scapulatempo-Neto C, Sobreira N. Whole genome sequencing as a first-tier diagnostic test for infants in neonatal intensive care units: A pilot study in Brazil. Am J Med Genet A 2024; 194:e63544. [PMID: 38258498 DOI: 10.1002/ajmg.a.63544] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 12/27/2023] [Accepted: 12/28/2023] [Indexed: 01/24/2024]
Abstract
In this pilot study, we aimed to evaluate the feasibility of whole genome sequencing (WGS) as a first-tier diagnostic test for infants hospitalized in neonatal intensive care units in the Brazilian healthcare system. The cohort presented here results from a joint collaboration between private and public hospitals in Brazil considering the initiative of a clinical laboratory to provide timely diagnosis for critically ill infants. We performed trio (proband and parents) WGS in 21 infants suspected of a genetic disease with an urgent need for diagnosis to guide medical care. Overall, the primary indication for genetic testing was dysmorphic syndromes (n = 14, 67%) followed by inborn errors of metabolism (n = 6, 29%) and skeletal dysplasias (n = 1, 5%). The diagnostic yield in our cohort was 57% (12/21) based on cases that received a definitive or likely definitive diagnostic result from WGS analysis. A total of 16 pathogenic/likely pathogenic variants and 10 variants of unknown significance were detected, and in most cases inherited from an unaffected parent. In addition, the reported variants were of different types, but mainly missense (58%) and associated with autosomal diseases (19/26); only three were associated with X-linked diseases, detected in hemizygosity in the proband an inherited from an unaffected mother. Notably, we identified 10 novel variants, absent from public genomic databases, in our cohort. Considering the entire diagnostic process, the average turnaround time from enrollment to medical report in our study was 53 days. Our findings demonstrate the remarkable utility of WGS as a diagnostic tool, elevating the potential of transformative impact since it outperforms conventional genetic tests. Here, we address the main challenges associated with implementing WGS in the medical care system in Brazil, as well as discuss the potential benefits and limitations of WGS as a diagnostic tool in the neonatal care setting.
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Affiliation(s)
| | - Joselito Sobreira
- Diagnósticos da América S.A., DASA, São Paulo, Brazil
- Hospital Infantil Sabará, São Paulo, Brazil
| | - Diana Bermeo
- Diagnósticos da América S.A., DASA, São Paulo, Brazil
| | | | - Dayse Alencar
- Diagnósticos da América S.A., DASA, São Paulo, Brazil
| | | | | | | | | | | | | | | | - Guilherme L Yamamoto
- Diagnósticos da América S.A., DASA, São Paulo, Brazil
- Instituto da Criança, Faculdade de Medicina (FMUSP), Universidade de São Paulo, São Paulo, Brazil
| | | | | | | | | | - Rachel Sayuri Honjo
- Instituto da Criança, Faculdade de Medicina (FMUSP), Universidade de São Paulo, São Paulo, Brazil
| | | | - Chong Ae Kim
- Instituto da Criança, Faculdade de Medicina (FMUSP), Universidade de São Paulo, São Paulo, Brazil
| | - Lucian de Souza
- Hospital das Clínicas de Porto Alegre (HCPA), Porto Alegre, Brazil
| | | | - Rita C Silveria
- Hospital das Clínicas de Porto Alegre (HCPA), Porto Alegre, Brazil
| | | | - Roberto Giugliani
- Diagnósticos da América S.A., DASA, São Paulo, Brazil
- Hospital das Clínicas de Porto Alegre (HCPA), Porto Alegre, Brazil
| | | | | | - Nara Sobreira
- Diagnósticos da América S.A., DASA, São Paulo, Brazil
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
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Zhang R, Cui X, Zhang Y, Ma H, Gao J, Zhang Y, Shu J, Cai C, Liu Y. Whole-exome sequencing as the first-tier test for patients in neonatal intensive care unit: a Chinese single-center study. BMC Pediatr 2024; 24:351. [PMID: 38778310 PMCID: PMC11110365 DOI: 10.1186/s12887-024-04820-0] [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: 11/12/2023] [Accepted: 05/08/2024] [Indexed: 05/25/2024] Open
Abstract
BACKGROUND Genetic disorders significantly affect patients in neonatal intensive care units, where establishing a diagnosis can be challenging through routine tests and supplementary examinations. Whole-exome sequencing offers a molecular-based approach for diagnosing genetic disorders. This study aimed to assess the importance of whole-exome sequencing for neonates in intensive care through a retrospective observational study within a Chinese cohort. METHODS We gathered data from neonatal patients at Tianjin Children's Hospital between January 2018 and April 2021. These patients presented with acute illnesses and were suspected of having genetic disorders, which were investigated using whole-exome sequencing. Our retrospective analysis covered clinical data, genetic findings, and the correlation between phenotypes and genetic variations. RESULTS The study included 121 neonates. Disorders affected multiple organs or systems, predominantly the metabolic, neurological, and endocrine systems. The detection rate for whole-exome sequencing was 52.9% (64 out of 121 patients), identifying 84 pathogenic or likely pathogenic genetic variants in 64 neonates. These included 13 copy number variations and 71 single-nucleotide variants. The most frequent inheritance pattern was autosomal recessive (57.8%, 37 out of 64), followed by autosomal dominant (29.7%, 19 out of 64). In total, 40 diseases were identified through whole-exome sequencing. CONCLUSION This study underscores the value and clinical utility of whole-exome sequencing as a primary diagnostic tool for neonates in intensive care units with suspected genetic disorders. Whole-exome sequencing not only aids in diagnosis but also offers significant benefits to patients and their families by providing clarity in uncertain diagnostic situations.
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Affiliation(s)
- Ruiping Zhang
- Department of Neonatology, Tianjin Children's Hospital/Tianjin University Children's Hospital, Beichen District, Tianjin, China
| | - Xiaoyu Cui
- Department of Neonatology, Tianjin Children's Hospital/Tianjin University Children's Hospital, Beichen District, Tianjin, China
| | - Yan Zhang
- Department of Neonatology, Tianjin Children's Hospital/Tianjin University Children's Hospital, Beichen District, Tianjin, China
- Graduate College, Tianjin Medical University, Heping District, Tianjin, China
| | - Huiqing Ma
- Graduate College, Tianjin Medical University, Heping District, Tianjin, China
| | - Jing Gao
- Graduate College, Tianjin Medical University, Heping District, Tianjin, China
| | - Ying Zhang
- Department of Neonatology, Tianjin Children's Hospital/Tianjin University Children's Hospital, Beichen District, Tianjin, China
| | - Jianbo Shu
- Tianjin Pediatric Research Institute, Tianjin Children's Hospital/Tianjin University Children's Hospital, Beichen District, Tianjin, China.
- Tianjin Key Laboratory of Birth Defects for Prevention and Treatment, Beichen District, Tianjin, China.
| | - Chunquan Cai
- Tianjin Pediatric Research Institute, Tianjin Children's Hospital/Tianjin University Children's Hospital, Beichen District, Tianjin, China.
- Tianjin Key Laboratory of Birth Defects for Prevention and Treatment, Beichen District, Tianjin, China.
| | - Yang Liu
- Department of Neonatology, Tianjin Children's Hospital/Tianjin University Children's Hospital, Beichen District, Tianjin, China.
- The Pediatric Clinical College in Tianjin Medical University, Heping District, Tianjin, China.
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Sloper E, Jezkova J, Thomas J, Dawson K, Halstead J, Gardner J, Burke K, Oruganti S, Calvert J, Evans J, Anderson S, Corrin S, Pottinger C, Murch O. Wales Infants' and childreN's Genome Service (WINGS): providing rapid genetic diagnoses for unwell children. Arch Dis Child 2024; 109:409-413. [PMID: 38320813 DOI: 10.1136/archdischild-2023-326579] [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: 11/06/2023] [Accepted: 01/24/2024] [Indexed: 04/20/2024]
Abstract
INTRODUCTION This study reviews the first 3 years of delivery of the first National Health Service (NHS)-commissioned trio rapid whole genome sequencing (rWGS) service for acutely unwell infants and children in Wales. METHODS Demographic and phenotypic data were prospectively collected as patients and their families were enrolled in the Wales Infants' and childreN's Genome Service (WINGS). These data were reviewed alongside trio rWGS results. RESULTS From April 2020 to March 2023, 82 families underwent WINGS, with a diagnostic yield of 34.1%. The highest diagnostic yields were noted in skeletal dysplasias, neurological or metabolic phenotypes. Mean time to reporting was 9 days. CONCLUSION This study demonstrates that trio rWGS is having a positive impact on the care of acutely unwell infants and children in an NHS setting. In particular, the study shows that rWGS can be applied in an NHS setting, achieving a diagnostic yield comparable with the previously published diagnostic yields achieved in research settings, while also helping to improve patient care and management.
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Affiliation(s)
- Emily Sloper
- All Wales Medical Genomics Service, University Hospital of Wales Healthcare NHS Trust, Cardiff, UK
| | - Jana Jezkova
- All Wales Medical Genomics Service, University Hospital of Wales Healthcare NHS Trust, Cardiff, UK
| | - Joanne Thomas
- Faculty of Life Science and Education, University of South Wales, Pontypridd, UK
| | | | - Joseph Halstead
- All Wales Medical Genomics Service, University Hospital of Wales Healthcare NHS Trust, Cardiff, UK
| | - Jennifer Gardner
- All Wales Medical Genomics Service, University Hospital of Wales Healthcare NHS Trust, Cardiff, UK
| | - Katherine Burke
- Neonatal Intensive Care Unit, Singleton Hospital, Swansea, UK
| | - Sivakumar Oruganti
- Paediatric Critical Care Unit, Noah's Ark Children's Hospital for Wales, Cardiff, UK
- College of Biomedical and Life Sciences, Cardiff University, Cardiff, UK
| | - Jennifer Calvert
- Neonatal Intensive Care Unit, University Hospital of Wales Healthcare NHS Trust, Cardiff, UK
| | - Jennifer Evans
- Child Health, Children's Hospital for Wales, Cardiff, UK
| | - Sarah Anderson
- All Wales Medical Genomics Service, University Hospital of Wales Healthcare NHS Trust, Cardiff, UK
| | - Sian Corrin
- All Wales Medical Genomics Service, University Hospital of Wales Healthcare NHS Trust, Cardiff, UK
| | - Caroline Pottinger
- All Wales Medical Genomics Service, University Hospital of Wales Healthcare NHS Trust, Cardiff, UK
| | - Oliver Murch
- All Wales Medical Genomics Service, University Hospital of Wales Healthcare NHS Trust, Cardiff, UK
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Schildt A, Stevenson DA, Yu L, Anguiano B, Suarez CJ. Time to diagnosis in rapid exome/genome sequencing in the clinical inpatient setting. Am J Med Genet A 2024; 194:e63483. [PMID: 38017634 DOI: 10.1002/ajmg.a.63483] [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: 11/03/2023] [Revised: 11/15/2023] [Accepted: 11/16/2023] [Indexed: 11/30/2023]
Abstract
Exome and genome sequencing are clinically available, with many laboratories offering expedited testing (e.g., "rapid" and "ultra-rapid"). With the increase in uptake of expedited testing, there is a need for the development of inpatient protocols for best practices based on real-life data. A retrospective 2-year review (October 2019-November 2021) of the utilization of rapid exome and genome sequencing for inpatient cases at a tertiary care center using a utilization management tracking database with subsequent chart review was performed. Thirty-three expedited "rapid/priority" exome/genome tests were performed clinically. The average total turnaround time (TAT) was 17.88 days (5-43 days) with an average TAT of 13.97 days (3-41 days) for the performing laboratory. There were 5 positive diagnostic results (15.2%), 3 likely positive diagnostic results (9%), 2 noncontributory results (6%), and 26 nondiagnostic results (69.7%). Real-life data suggest that there is an approximately 3.91-day lag in getting samples to the performing laboratory. Although laboratories may advertise their expected TAT, a number of factors can potentially impact the actual time from test order placement to communication of the results for clinical use. Understanding the points of delay will enable the development of internal protocols and policies to improve time to diagnosis.
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Affiliation(s)
- Alison Schildt
- Department of Pediatrics, Division of Medical Genetics, Stanford University, Palo Alto, California, USA
| | - David A Stevenson
- Department of Pediatrics, Division of Medical Genetics, Stanford University, Palo Alto, California, USA
| | - Linbo Yu
- Genetic Testing Optimization Service, Stanford Hospitals and Clinics, Palo Alto, California, USA
| | - Beatriz Anguiano
- Genetic Testing Optimization Service, Stanford Hospitals and Clinics, Palo Alto, California, USA
| | - Carlos J Suarez
- Department of Pathology, Stanford University, Palo Alto, California, USA
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Azuelos C, Marquis MA, Laberge AM. A systematic review of the assessment of the clinical utility of genomic sequencing: Implications of the lack of standard definitions and measures of clinical utility. Eur J Med Genet 2024; 68:104925. [PMID: 38432472 DOI: 10.1016/j.ejmg.2024.104925] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 12/31/2023] [Accepted: 02/11/2024] [Indexed: 03/05/2024]
Abstract
PURPOSE Exome sequencing (ES) and genome sequencing (GS) are diagnostic tests for rare genetic diseases. Studies report clinical utility of ES/GS. The goal of this systematic review is to establish how clinical utility is defined and measured in studies evaluating the impacts of ES/GS results for pediatric patients. METHODS Relevant articles were identified in PubMed, Medline, Embase, and Web of Science. Eligible studies assessed clinical utility of ES/GS for pediatric patients published before 2021. Other relevant articles were added based on articles' references. Articles were coded to assess definitions and measures of clinical utility. RESULTS Of 1346 articles, 83 articles met eligibility criteria. Clinical utility was not clearly defined in 19% of studies and 92% did not use an explicit measure of clinical utility. When present, definitions of clinical utility diverged from recommended definitions and varied greatly, from narrow (diagnostic yield of ES/GS) to broad (including decisions about withdrawal of care/palliative care and/or impacts on other family members). CONCLUSION Clinical utility is used to guide policy and practice decisions about test use. The lack of a standard definition of clinical utility of ES/GS may lead to under- or overestimations of clinical utility, complicating policymaking and raising ethical issues.
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Affiliation(s)
- Claudia Azuelos
- Medical Genetics, Dept of Pediatrics, CHU Sainte-Justine and Université de Montréal, Canada.
| | - Marc-Antoine Marquis
- Palliative Care, Dept of Pediatrics, CHU Sainte-Justine and Université de Montréal, Canada
| | - Anne-Marie Laberge
- Medical Genetics, Dept of Pediatrics, CHU Sainte-Justine and Université de Montréal, Canada.
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Calvo M, Stefani S, Migliorisi G. Bacterial Infections in Intensive Care Units: Epidemiological and Microbiological Aspects. Antibiotics (Basel) 2024; 13:238. [PMID: 38534673 DOI: 10.3390/antibiotics13030238] [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: 02/16/2024] [Revised: 03/01/2024] [Accepted: 03/04/2024] [Indexed: 03/28/2024] Open
Abstract
Intensive care units constitute a critical setting for the management of infections. The patients' fragilities and spread of multidrug-resistant microorganisms lead to relevant difficulties in the patients' care. Recent epidemiological surveys documented the Gram-negative bacteria supremacy among intensive care unit (ICU) infection aetiologies, accounting for numerous multidrug-resistant isolates. Regarding this specific setting, clinical microbiology support holds a crucial role in the definition of diagnostic algorithms. Eventually, the complete patient evaluation requires integrating local epidemiological knowledge into the best practice and the standardization of antimicrobial stewardship programs. Clinical laboratories usually receive respiratory tract and blood samples from ICU patients, which express a significant predisposition to severe infections. Therefore, conventional or rapid diagnostic workflows should be modified depending on patients' urgency and preliminary colonization data. Additionally, it is essential to complete each microbiological report with rapid phenotypic minimum inhibitory concentration (MIC) values and information about resistance markers. Microbiologists also help in the eventual integration of ultimate genome analysis techniques into complicated diagnostic workflows. Herein, we want to emphasize the role of the microbiologist in the decisional process of critical patient management.
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Affiliation(s)
- Maddalena Calvo
- U.O.C. Laboratory Analysis Unit, A.O.U. "Policlinico-San Marco", Via S. Sofia 78, 95123 Catania, Italy
| | - Stefania Stefani
- U.O.C. Laboratory Analysis Unit, A.O.U. "Policlinico-San Marco", Via S. Sofia 78, 95123 Catania, Italy
- Department of Biomedical and Biotechnological Sciences (BIOMETEC), University of Catania, 95123 Catania, Italy
| | - Giuseppe Migliorisi
- U.O.C. Laboratory Analysis Unit, A.O. "G.F. Ingrassia", Corso Calatafimi 1002, 90131 Palermo, Italy
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Liu Y, Qian S. Current situation and prospect for the diagnosis and treatment of pediatric critical rare diseases in China. Pediatr Investig 2024; 8:66-71. [PMID: 38516143 PMCID: PMC10951483 DOI: 10.1002/ped4.12419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Accepted: 01/16/2024] [Indexed: 03/23/2024] Open
Abstract
The onset of critical rare diseases (RDs) in children is rapid and dangerous, accompanied by a high mortality rate, which brings a heavy burden to both families and society. Multiple malformations, neuromuscular diseases, metabolic diseases, and heart diseases are the most common types of RDs in children of China, often manifesting with multiple organ dysfunction. At present, the diagnosis and treatment of critical RDs in children face challenges such as prolonged diagnosis time, a high misdiagnosis rate, limited treatment modalities, and a significant disease burden. However, with the progress in genetic testing technology, the establishment of multidisciplinary diagnosis and treatment platforms, and the implementation of relevant RD policies in China, children with critical RDs will received enhanced medical services, experience improved prognoses, and reintegrate into social life.
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Affiliation(s)
- Yingchao Liu
- Pediatric Intensive Care Unit, Beijing Children's Hospital, Capital Medical UniversityNational Center for Children's HealthBeijingChina
| | - Suyun Qian
- Pediatric Intensive Care Unit, Beijing Children's Hospital, Capital Medical UniversityNational Center for Children's HealthBeijingChina
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Kingsmore SF, Nofsinger R, Ellsworth K. Rapid genomic sequencing for genetic disease diagnosis and therapy in intensive care units: a review. NPJ Genom Med 2024; 9:17. [PMID: 38413639 PMCID: PMC10899612 DOI: 10.1038/s41525-024-00404-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 02/15/2024] [Indexed: 02/29/2024] Open
Abstract
Single locus (Mendelian) diseases are a leading cause of childhood hospitalization, intensive care unit (ICU) admission, mortality, and healthcare cost. Rapid genome sequencing (RGS), ultra-rapid genome sequencing (URGS), and rapid exome sequencing (RES) are diagnostic tests for genetic diseases for ICU patients. In 44 studies of children in ICUs with diseases of unknown etiology, 37% received a genetic diagnosis, 26% had consequent changes in management, and net healthcare costs were reduced by $14,265 per child tested by URGS, RGS, or RES. URGS outperformed RGS and RES with faster time to diagnosis, and higher rate of diagnosis and clinical utility. Diagnostic and clinical outcomes will improve as methods evolve, costs decrease, and testing is implemented within precision medicine delivery systems attuned to ICU needs. URGS, RGS, and RES are currently performed in <5% of the ~200,000 children likely to benefit annually due to lack of payor coverage, inadequate reimbursement, hospital policies, hospitalist unfamiliarity, under-recognition of possible genetic diseases, and current formatting as tests rather than as a rapid precision medicine delivery system. The gap between actual and optimal outcomes in children in ICUs is currently increasing since expanded use of URGS, RGS, and RES lags growth in those likely to benefit through new therapies. There is sufficient evidence to conclude that URGS, RGS, or RES should be considered in all children with diseases of uncertain etiology at ICU admission. Minimally, diagnostic URGS, RGS, or RES should be ordered early during admissions of critically ill infants and children with suspected genetic diseases.
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Affiliation(s)
- Stephen F Kingsmore
- Rady Children's Institute for Genomic Medicine, Rady Children's Hospital, San Diego, CA, USA.
| | - Russell Nofsinger
- Rady Children's Institute for Genomic Medicine, Rady Children's Hospital, San Diego, CA, USA
| | - Kasia Ellsworth
- Rady Children's Institute for Genomic Medicine, Rady Children's Hospital, San Diego, CA, USA
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Wigby KM, Brockman D, Costain G, Hale C, Taylor SL, Belmont J, Bick D, Dimmock D, Fernbach S, Greally J, Jobanputra V, Kulkarni S, Spiteri E, Taft RJ. Evidence review and considerations for use of first line genome sequencing to diagnose rare genetic disorders. NPJ Genom Med 2024; 9:15. [PMID: 38409289 PMCID: PMC10897481 DOI: 10.1038/s41525-024-00396-x] [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: 06/11/2023] [Accepted: 01/26/2024] [Indexed: 02/28/2024] Open
Abstract
Early use of genome sequencing (GS) in the diagnostic odyssey can reduce suffering and improve care, but questions remain about which patient populations are most amenable to GS as a first-line diagnostic test. To address this, the Medical Genome Initiative conducted a literature review to identify appropriate clinical indications for GS. Studies published from January 2011 to August 2022 that reported on the diagnostic yield (DY) or clinical utility of GS were included. An exploratory meta-analysis using a random effects model evaluated DY based on cohort size and diagnosed cases per cohort. Seventy-one studies met inclusion criteria, comprising over 13,000 patients who received GS in one of the following settings: hospitalized pediatric patients, pediatric outpatients, adult outpatients, or mixed. GS was the first-line test in 38% (27/71). The unweighted mean DY of first-line GS was 45% (12-73%), 33% (6-86%) in cohorts with prior genetic testing, and 33% (9-60%) in exome-negative cohorts. Clinical utility was reported in 81% of first-line GS studies in hospitalized pediatric patients. Changes in management varied by cohort and underlying molecular diagnosis (24-100%). To develop evidence-informed points to consider, the quality of all 71 studies was assessed using modified American College of Radiology (ACR) criteria, with five core points to consider developed, including recommendations for use of GS in the N/PICU, in lieu of sequential testing and when disorders with substantial allelic heterogeneity are suspected. Future large and controlled studies in the pediatric and adult populations may support further refinement of these recommendations.
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Affiliation(s)
- Kristen M Wigby
- University of California, Davis, CA, USA.
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA.
| | | | | | | | | | - John Belmont
- Genetics & Genomics Services Inc, Houston, TX, USA
| | | | - David Dimmock
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
| | | | - John Greally
- Albert Einstein College of Medicine, Bronx, NY, USA
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15
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Thompson L, Larson A, Salz L, Veith R, Tsai JP, Jayakar A, Chapman R, Gupta A, Kingsmore SF, Dimmock D, Bedrick A, Galindo MK, Casas K, Mohamed M, Straight L, Khan MA, Salyakina D. Multi-center implementation of rapid whole genome sequencing provides additional evidence of its utility in the pediatric inpatient setting. Front Pediatr 2024; 12:1349519. [PMID: 38440187 PMCID: PMC10909823 DOI: 10.3389/fped.2024.1349519] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Accepted: 02/01/2024] [Indexed: 03/06/2024] Open
Abstract
Objective Multi-center implementation of rapid whole genome sequencing with assessment of the clinical utility of rapid whole genome sequencing (rWGS), including positive, negative and uncertain results, in admitted infants with a suspected genetic disease. Study design rWGS tests were ordered at eight hospitals between November 2017 and April 2020. Investigators completed a survey of demographic data, Human Phenotype Ontology (HPO) terms, test results and impacts of results on clinical care. Results A total of 188 patients, on general hospital floors and intensive care unit (ICU) settings, underwent rWGS testing. Racial and ethnic characteristics of the tested infants were broadly representative of births in the country at large. 35% of infants received a diagnostic result in a median of 6 days. The most common HPO terms for tested infants indicated an abnormality of the nervous system, followed by the cardiovascular system, the digestive system, the respiratory system and the head and neck. Providers indicated a major change in clinical management because of rWGS for 32% of infants tested overall and 70% of those with a diagnostic result. Also, 7% of infants with a negative rWGS result and 23% with a variant of unknown significance (VUS) had a major change in management due to testing. Conclusions Our study demonstrates that the implementation of rWGS is feasible across diverse institutions, and provides additional evidence to support the clinical utility of rWGS in a demographically representative sample of admitted infants and includes assessment of the clinical impact of uncertain rWGS results in addition to both positive and negative results.
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Affiliation(s)
- Lauren Thompson
- Division of Genetics and Metabolism, Nicklaus Children’s Hospital, Miami, FL, United States
| | - Austin Larson
- Department of Pediatrics, Children’s Hospital Colorado, Aurora, CO, United States
- Department of Pediatrics, University of Colorado School of Medicine, Aurora, CO, United States
| | - Lisa Salz
- RCIGM, Rady Children’s Hospital San Diego, San Diego, CA, United States
| | - Regan Veith
- Genomic Medicine, Children’s Minnesota, Minneapolis, MN, United States
| | - John-Paul Tsai
- Department of Pediatrics, University of Colorado School of Medicine, Aurora, CO, United States
| | - Anuj Jayakar
- Division of Genetics and Metabolism, Nicklaus Children’s Hospital, Miami, FL, United States
| | - Rachel Chapman
- Fetal & Neonatal Institute, Children’s Hospital Los Angeles, Los Angeles, CA, United States
- Department of Pediatrics, USC Keck School of Medicine, Los Angeles, CA, United States
| | - Apeksha Gupta
- Division of Genetics and Metabolism, Nicklaus Children’s Hospital, Miami, FL, United States
| | | | - David Dimmock
- RCIGM, Rady Children’s Hospital San Diego, San Diego, CA, United States
| | - Alan Bedrick
- Department of Pediatrics, Banner Diamond Children’s Medical Center, Tucson, AZ, United States
- Department of Pediatrics, University of Arizona College of Medicine, Tucson, AZ, United States
| | - Maureen Kelly Galindo
- Department of Pediatrics, Banner Diamond Children’s Medical Center, Tucson, AZ, United States
| | - Kari Casas
- Department of Pediatrics, Sanford Children’s Fargo, Fargo, SD, United States
| | - Mohamed Mohamed
- Department of Pediatrics, Sanford Children’s Fargo, Fargo, SD, United States
| | - Lisa Straight
- Department of Pediatrics, Sanford Children’s Sioux Falls, Sioux Falls, SD, United States
| | - M. Akram Khan
- Department of Pediatrics, Sanford Children’s Sioux Falls, Sioux Falls, SD, United States
| | - Daria Salyakina
- Division of Genetics and Metabolism, Nicklaus Children’s Hospital, Miami, FL, United States
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Marouane A, Neveling K, Deden AC, van den Heuvel S, Zafeiropoulou D, Castelein S, van de Veerdonk F, Koolen DA, Simons A, Rodenburg R, Westra D, Mensenkamp AR, de Leeuw N, Ligtenberg M, Matthijsse R, Pfundt R, Kamsteeg EJ, Brunner HG, Gilissen C, Feenstra I, de Boode WP, Yntema HG, van Zelst-Stams WAG, Nelen M, Vissers LELM. Lessons learned from rapid exome sequencing for 575 critically ill patients across the broad spectrum of rare disease. Front Genet 2024; 14:1304520. [PMID: 38259611 PMCID: PMC10800954 DOI: 10.3389/fgene.2023.1304520] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Accepted: 12/18/2023] [Indexed: 01/24/2024] Open
Abstract
Introduction: Rapid exome sequencing (rES) has become the first-choice genetic test for critically ill patients, mostly neonates, young infants, or fetuses in prenatal care, in time-sensitive situations and when it is expected that the genetic test result may guide clinical decision making. The implementation of rES has revolutionized medicine by enabling timely identification of genetic causes for various rare diseases. The utilization of rES has increasingly been recognized as an essential diagnostic tool for the identification of complex and undiagnosed genetic disorders. Methods: We conducted a retrospective evaluation of our experiences with rES performed on 575 critically ill patients from various age groups (prenatal to adulthood), over a four-year period (2016-2019). These patients presented with a wide spectrum of rare diseases, including but not limited to neurological disorders, severe combined immune deficiency, and cancer. Results: During the study period, there was a significant increase in rES referrals, with a rise from a total of two referrals in Q1-2016 to 10 referrals per week in Q4-2019. The median turnaround time (TAT) decreased from 17 to 11 days in the period 2016-2019, with an overall median TAT of 11 days (IQR 8-15 days). The overall diagnostic yield for this cohort was 30.4%, and did not significantly differ between the different age groups (e.g. adults 22.2% vs children 31.0%; p-value 0.35). However, variability in yield was observed between clinical entities: craniofacial anomalies yielded 58.3%, while for three clinical entities (severe combined immune deficiency, aneurysm, and hypogonadotropic hypogonadism) no diagnoses were obtained. Discussion: Importantly, whereas clinical significance is often only attributed to a conclusive diagnosis, we also observed impact on clinical decision-making for individuals in whom no genetic diagnosis was established. Hence, our experience shows that rES has an important role for patients of all ages and across the broad spectrum of rare diseases to impact clinical outcomes.
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Affiliation(s)
- Abderrahim Marouane
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands
- Department of Neonatology, Radboud University Medical Center, Radboud Institute for Health Sciences, Amalia Children’s Hospital, Nijmegen, Netherlands
| | - Kornelia Neveling
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands
- Research Institute for Medical Innovation, Radboud University Medical Center, Nijmegen, Netherlands
| | - A. Chantal Deden
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands
| | - Simone van den Heuvel
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands
| | - Dimitra Zafeiropoulou
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands
| | - Steven Castelein
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands
| | - Frank van de Veerdonk
- Department of Internal Medicine, Radboud University Medical Center, Radboud Institute for Health Sciences, Nijmegen, Netherlands
| | - David A. Koolen
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands
| | - Annet Simons
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands
| | - Richard Rodenburg
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands
| | - Dineke Westra
- Research Institute for Medical Innovation, Radboud University Medical Center, Nijmegen, Netherlands
| | - Arjen R. Mensenkamp
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands
| | - Nicole de Leeuw
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands
| | - Marjolijn Ligtenberg
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands
| | - Rene Matthijsse
- Department of Neonatology, Radboud University Medical Center, Radboud Institute for Health Sciences, Amalia Children’s Hospital, Nijmegen, Netherlands
| | - Rolph Pfundt
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands
| | - Erik Jan Kamsteeg
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands
| | - Han G. Brunner
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands
| | - Christian Gilissen
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands
| | - Ilse Feenstra
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands
| | - Willem P. de Boode
- Department of Neonatology, Radboud University Medical Center, Radboud Institute for Health Sciences, Amalia Children’s Hospital, Nijmegen, Netherlands
| | - Helger G. Yntema
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands
| | | | - Marcel Nelen
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands
| | - Lisenka E. L. M. Vissers
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands
- Research Institute for Medical Innovation, Radboud University Medical Center, Nijmegen, Netherlands
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Kim S, Pistawka C, Langlois S, Osiovich H, Virani A, Kitchin V, Elliott AM. Genetic counselling considerations with genetic/genomic testing in Neonatal and Pediatric Intensive Care Units: A scoping review. Clin Genet 2024; 105:13-33. [PMID: 37927209 DOI: 10.1111/cge.14446] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 09/23/2023] [Accepted: 10/15/2023] [Indexed: 11/07/2023]
Abstract
Genetic and genomic technologies can effectively diagnose numerous genetic disorders. Patients benefit when genetic counselling accompanies genetic testing and international guidelines recommend pre- and post-test genetic counselling with genome-wide sequencing. However, there is a gap in knowledge regarding the unique genetic counselling considerations with different types of genetic testing in the Neonatal Intensive Care Unit (NICU) and the Pediatric Intensive Care Unit (PICU). This scoping review was conducted to identify the gaps in care with respect to genetic counselling for infants/pediatric patients undergoing genetic and genomic testing in NICUs and PICUs and understand areas in need of improvement in order to optimize clinical care for patients, caregivers, and healthcare providers. Five databases (MEDLINE [Ovid], Embase [Ovid], PsycINFO [Ebsco], CENTRAL [Ovid], and CINHAL [Ebsco]) and grey literature were searched. A total of 170 studies were included and used for data extraction and analysis. This scoping review includes descriptive analysis, followed by a narrative account of the extracted data. Results were divided into three groups: pre-test, post-test, and comprehensive (both pre- and post-test) genetic counselling considerations based on indication for testing. More studies were conducted in the NICU than the PICU. Comprehensive genetic counselling was discussed in only 31% of all the included studies demonstrating the need for both pre-test and post-test genetic counselling for different clinical indications in addition to the need to account for different cultural aspects based on ethnicity and geographic factors.
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Affiliation(s)
- Sunu Kim
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Carly Pistawka
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Sylvie Langlois
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
- BC Children's Hospital Research Institute, Vancouver, British Columbia, Canada
- Women's Health Research Institute, Vancouver, British Columbia, Canada
| | - Horacio Osiovich
- BC Children's Hospital Research Institute, Vancouver, British Columbia, Canada
- Women's Health Research Institute, Vancouver, British Columbia, Canada
- Department of Pediatrics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Alice Virani
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
- Ethics Service, Provincial Health Services Authority, Vancouver, British Columbia, Canada
| | - Vanessa Kitchin
- Woodward Library, University of British Columbia, Vancouver, British Columbia, Canada
| | - Alison M Elliott
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
- BC Children's Hospital Research Institute, Vancouver, British Columbia, Canada
- Women's Health Research Institute, Vancouver, British Columbia, Canada
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18
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Schuler BA, Mosera M, Hatch LD, Grochowsky A, Wheeler F. Collaborative efforts to improve genetic testing in the neonatal intensive care unit. J Perinatol 2023; 43:1500-1505. [PMID: 37914812 DOI: 10.1038/s41372-023-01817-y] [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: 05/01/2023] [Revised: 09/22/2023] [Accepted: 10/23/2023] [Indexed: 11/03/2023]
Abstract
OBJECTIVE To reduce unnecessary simultaneous karyotype analysis and chromosomal microarray (CMA) testing in the neonatal intensive care unit (NICU). STUDY DESIGN This quality improvement study investigated the effect of collaborative efforts between the NICU, cytogenetics, and clinical genetics on numbers of genetic tests, rates of abnormal tests, and number of genetics consults comparing baseline and 5-month intervention periods. RESULTS Simultaneous karyotype analyses and CMAs decreased due to a decrease in karyotype testing (11.3% [68/600] vs. 0.98% [6/614], p < 0.01). Karyotype analyses were more likely to be abnormal (13.8% [12/87] vs. 64.0% [16/25], p < 0.01). Frequency of genetics consultation did not change (7.0% [42/600] vs. 9.4% [58/614], p = 0.12). CONCLUSION Collaborative efforts between the NICU, cytogenetics, and clinical genetics decreased redundant genetic testing, which demonstrated potential cost savings to our institution. Ongoing collaborative efforts could facilitate genetic testing practices in the NICU that readily evolve in tandem with genetic testing recommendations.
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Affiliation(s)
- Bryce A Schuler
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN, USA.
| | - Mackenzie Mosera
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - L Dupree Hatch
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Angela Grochowsky
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Ferrin Wheeler
- Department of Pathology, Vanderbilt University Medical Center, Nashville, TN, USA
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19
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Kumar RD, Saba LF, Streff H, Shaw CA, Mizerik E, Snyder MT, Lopez-Terrada D, Scull J. Clinical genome sequencing: Three years' experience at a tertiary children's hospital. Genet Med 2023; 25:100916. [PMID: 37334785 DOI: 10.1016/j.gim.2023.100916] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 06/08/2023] [Accepted: 06/09/2023] [Indexed: 06/20/2023] Open
Abstract
PURPOSE Genome sequencing (GS) may shorten the diagnostic odyssey for patients, but clinical experience with this assay in nonresearch settings remains limited. Texas Children's Hospital began offering GS as a clinical test to admitted patients in 2020, providing an opportunity to study GS utilization, possibilities for test optimization, and testing outcomes. METHODS We retrospectively reviewed GS orders for admitted patients for a nearly 3-year period from March 2020 through December 2022. We gathered anonymized clinical data from the electronic health record to answer the study questions. RESULTS The diagnostic yield over 97 admitted patients was 35%. The majority of GS clinical indications were neurologic or metabolic (61%) and most patients were in intensive care (58%). Tests were often characterized as candidates for intervention/improvement (56%), frequently because of redundancy with prior testing. Patients receiving GS without prior exome sequencing (ES) had higher diagnostic rates (45%) than the cohort as a whole. In 2 cases, GS revealed a molecular diagnosis that is unlikely to be detected by ES. CONCLUSION The performance of GS in clinical settings likely justifies its use as a first-line diagnostic test, but the incremental benefit for patients with prior ES may be limited.
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Affiliation(s)
- Runjun D Kumar
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX; Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX.
| | - Lisa F Saba
- Department of Pathology, Texas Children's Hospital, Houston, TX
| | - Haley Streff
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX; Department of Pathology, Texas Children's Hospital, Houston, TX
| | - Chad A Shaw
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX; Department of Statistics, Rice University, Houston, TX
| | - Elizabeth Mizerik
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX
| | - Matthew T Snyder
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX
| | - Dolores Lopez-Terrada
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX; Department of Pathology, Texas Children's Hospital, Houston, TX; Department of Pediatrics, Baylor College of Medicine, Houston, TX
| | - Jennifer Scull
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX; Department of Pathology, Texas Children's Hospital, Houston, TX.
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Heath O, Pandithan D, Pitt J, Savva E, Raiti L, Bracken J, Vandeleur M, Delatycki MB, Yaplito‐Lee J, Hardikar W, Halligan R. Interstitial lung disease and pancreatic exocrine insufficiency in CADDS: Phenotypic expansion and literature review. JIMD Rep 2023; 64:337-345. [PMID: 37701323 PMCID: PMC10494507 DOI: 10.1002/jmd2.12390] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/02/2023] [Revised: 08/02/2023] [Accepted: 08/07/2023] [Indexed: 09/14/2023] Open
Abstract
Contiguous ABCD1/ DXS1357E deletion syndrome (CADDS) is a rare deletion syndrome involving two contiguous genes on Xq28, ABCD1 and BCAP31 (formerly known as DXS1357E). Only nine individuals with this diagnosis have been reported in the medical literature to date. Intragenic loss-of-function variants in BCAP31 cause the deafness, dystonia, and cerebral hypomyelination syndrome (DDCH). Isolated pathogenic intragenic variants in ABCD1 are associated with the most common peroxisomal disorder, X-linked adrenoleukodystrophy (X-ALD), a single transporter deficiency, which in its more severe cerebral form is characterised by childhood-onset neurodegeneration and high levels of very-long-chain fatty acids (VLCFA). While increased VLCFA levels also feature in CADDS, the few patients described to date all presented as neonates with a severe phenotype. Here we report a tenth individual with CADDS, a male infant with dysmorphic facial features who was diagnosed through ultra-rapid whole genome sequencing (WGS) in the setting of persistent cholestatic liver disease, sensorineural hearing loss, hypotonia and growth failure and developmental delay. Biochemical studies showed elevated VLCFA and mildly reduced plasmalogens. He died at 7 months having developed pancreatic exocrine deficiency and interstitial lung disease, two features we propose to be possible extensions to the CADDS phenotype. We also review the genetic, phenotypic, and biochemical features in previously reported individuals with CADDS.
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Affiliation(s)
- Oliver Heath
- Department of Metabolic MedicineThe Royal Children's HospitalMelbourneAustralia
- Victorian Clinical Genetics ServicesMurdoch Children's Research InstituteMelbourneAustralia
| | - Dinusha Pandithan
- Department of Metabolic MedicineThe Royal Children's HospitalMelbourneAustralia
| | - James Pitt
- Victorian Clinical Genetics ServicesMurdoch Children's Research InstituteMelbourneAustralia
| | - Elena Savva
- Victorian Clinical Genetics ServicesMurdoch Children's Research InstituteMelbourneAustralia
| | - Laura Raiti
- Victorian Clinical Genetics ServicesMurdoch Children's Research InstituteMelbourneAustralia
| | - Jenny Bracken
- Department of RadiologyThe Royal Children's HospitalMelbourneAustralia
| | - Moya Vandeleur
- Department of Respiratory MedicineThe Royal Children's HospitalMelbourneAustralia
| | - Martin B. Delatycki
- Victorian Clinical Genetics ServicesMurdoch Children's Research InstituteMelbourneAustralia
| | - Joy Yaplito‐Lee
- Department of Metabolic MedicineThe Royal Children's HospitalMelbourneAustralia
- Victorian Clinical Genetics ServicesMurdoch Children's Research InstituteMelbourneAustralia
| | - Winita Hardikar
- Department of GastroenterologyThe Royal Children's HospitalMelbourneAustralia
| | - Rebecca Halligan
- Department of Metabolic MedicineThe Royal Children's HospitalMelbourneAustralia
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21
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Bonser D, Malone Jenkins S, Palmquist R, Guthery S, Bonkowsky JL, Jaramillo C. Rapid Genome Sequencing Diagnosis in Pediatric Patients with Liver Dysfunction. J Pediatr 2023; 260:113534. [PMID: 37269902 DOI: 10.1016/j.jpeds.2023.113534] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 04/16/2023] [Accepted: 05/29/2023] [Indexed: 06/05/2023]
Abstract
OBJECTIVE To describe the usefulness of rapid whole genome sequencing (rWGS) in a cohort of children presenting with acute liver dysfunction. STUDY DESIGN This was a retrospective, population-based cohort study conducted at Primary Children's Hospital in Salt Lake City, Utah. Children meeting criteria for acute liver dysfunction who received rWGS between August 2019 and December 2021 were included. rWGS was performed on blood samples from the patient and parents (1 or both depending on availability). The clinical characteristics of patients with positive rWGS results were compared with those with negative results. RESULTS Eighteen patients with pediatric acute liver dysfunction who had rWGS were identified. The median turnaround time from the date rWGS testing was ordered to the date an initial report was received was 8 days with a shorter turnaround time in patients with a diagnostic rWGS (4 days vs 10 days; P = .03). A diagnostic result was identified in 7 of 18 patients (39%). Subsequently, 4 patients in this cohort, who had negative rWGS results, were found to have a toxic exposure accounting for their liver dysfunction. With removal of these patients, the diagnostic rate of rWGS was 7 of 14 (50%). The use of rWGS led to a change in management for 6 of 18 patients (33%). CONCLUSIONS We found that rWGS provided a diagnosis in up to 50% of pediatric acute liver dysfunction. rWGS allows for higher diagnostic rates in an expedited fashion that affects clinical management. These data support the routine use of rWGS for life-threatening disorders in children, specifically acute liver dysfunction.
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Affiliation(s)
| | - Sabrina Malone Jenkins
- Division of Neonatology, Department of Pediatrics, University of Utah School of Medicine, Primary Children's Hospital, Salt Lake City, UT; Center for Personalized Medicine, Primary Children's Hospital, Salt Lake City, UT
| | - Rachel Palmquist
- Center for Personalized Medicine, Primary Children's Hospital, Salt Lake City, UT; Division of Pediatric Neurology, Department of Pediatrics, University of Utah School of Medicine, Salt Lake City, UT
| | - Stephen Guthery
- Division of Pediatric Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, University of Utah School of Medicine, Primary Children's Hospital, Salt Lake City, UT
| | - Joshua L Bonkowsky
- Center for Personalized Medicine, Primary Children's Hospital, Salt Lake City, UT; Division of Pediatric Neurology, Department of Pediatrics, University of Utah School of Medicine, Salt Lake City, UT
| | - Catalina Jaramillo
- Division of Pediatric Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, University of Utah School of Medicine, Primary Children's Hospital, Salt Lake City, UT.
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Chung CCY, Hue SPY, Ng NYT, Doong PHL, Chu ATW, Chung BHY. Meta-analysis of the diagnostic and clinical utility of exome and genome sequencing in pediatric and adult patients with rare diseases across diverse populations. Genet Med 2023; 25:100896. [PMID: 37191093 DOI: 10.1016/j.gim.2023.100896] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 05/07/2023] [Accepted: 05/10/2023] [Indexed: 05/17/2023] Open
Abstract
PURPOSE This meta-analysis aims to compare the diagnostic and clinical utility of exome sequencing (ES) vs genome sequencing (GS) in pediatric and adult patients with rare diseases across diverse populations. METHODS A meta-analysis was conducted to identify studies from 2011 to 2021. RESULTS One hundred sixty-one studies across 31 countries/regions were eligible, featuring 50,417 probands of diverse populations. Diagnostic rates of ES (0.38, 95% CI 0.36-0.40) and GS (0.34, 95% CI 0.30-0.38) were similar (P = .1). Within-cohort comparison illustrated 1.2-times odds of diagnosis by GS over ES (95% CI 0.79-1.83, P = .38). GS studies discovered a higher range of novel genes than ES studies; yet, the rate of variant of unknown significance did not differ (P = .78). Among high-quality studies, clinical utility of GS (0.77, 95% CI 0.64-0.90) was higher than that of ES (0.44, 95% CI 0.30-0.58) (P < .01). CONCLUSION This meta-analysis provides an important update to demonstrate the similar diagnostic rates between ES and GS and the higher clinical utility of GS over ES. With the newly published recommendations for clinical interpretation of variants found in noncoding regions of the genome and the trend of decreasing variant of unknown significance and GS cost, it is expected that GS will be more widely used in clinical settings.
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Affiliation(s)
| | - Shirley P Y Hue
- Hong Kong Genome Institute, Hong Kong Special Administrative Region
| | - Nicole Y T Ng
- Department of Paediatrics and Adolescent Medicine, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region
| | - Phoenix H L Doong
- Department of Paediatrics and Adolescent Medicine, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region
| | - Annie T W Chu
- Hong Kong Genome Institute, Hong Kong Special Administrative Region.
| | - Brian H Y Chung
- Hong Kong Genome Institute, Hong Kong Special Administrative Region; Department of Paediatrics and Adolescent Medicine, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region.
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Richards JL, Knight SJ. Parents' Perspectives on Secondary Genetic Ancestry Findings in Pediatric Genomic Medicine. Clin Ther 2023; 45:719-728. [PMID: 37573223 PMCID: PMC11182349 DOI: 10.1016/j.clinthera.2023.06.001] [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: 02/22/2023] [Revised: 05/17/2023] [Accepted: 06/02/2023] [Indexed: 08/14/2023]
Abstract
PURPOSE With advances in genome sequencing technologies, large-scale genome-wide sequencing has advanced our understanding of disease risk and etiology and contributes to the rapidly expanding genomic health services in pediatric settings. Because it is possible to return ancestry estimates following clinical genomic sequencing, it is important to understand the interest in ancestry results among families who may have the option of receiving these results. METHODS We conducted 26 semi-structured qualitative telephone interviews of parents with children/newborns with likely genetic conditions from two studies of clinical genome sequencing. Using a purposive sampling approach, we selected parents from the SouthSeq cohort, Clinical Sequencing Evidence-Generating Research (CSER Phase 2) project active in Alabama, Mississippi, and Louisiana, or an earlier Clinical Sequencing Exploratory Research (CSER Phase 1) initiative based in the same region. Our interviews focused on parental knowledge about, attitudes on, interest in, and preferences for receiving genetic ancestry results following clinical genome sequencing in the neonatal intensive care unit or in pediatric clinics. FINDINGS Overall, parents prioritized clinical results or results that would help guide the diagnosis and treatment of their child, but they were also interested in any genetic result, including genetic ancestry, that potentially could enhance the meaning of information on disease risk, prevention and screening guidance, or family planning. While parents thought that ancestry results would help them learn about themselves and their heritage, the had concerns over the privacy, security, and accuracy of genetic ancestry information, although parents indicated that they had greater trust in ancestry findings provided as part of clinical care compared with those offered commercially. Parents also wanted ancestry results to be returned in a timely manner by knowledgeable staff, with kid-friendly materials and online tools available to aid, as needed, in the understanding of their results. IMPLICATIONS Taken together, our results highlight that despite being in high-stress situations, such as having a newborn in the neonatal intensive care unit, parents were interested in receiving genetic ancestry results along with their clinically relevant findings.
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Affiliation(s)
- Jaimie L Richards
- Department of Genetics, The University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Sara J Knight
- Department of Internal Medicine, Division of Epidemiology, University of Utah, School of Medicine, Salt Lake City, Utah, USA; Informatics, Decision-Enhancement, and Analytical Sciences Center of Innovation, Salt Lake City VA Healthcare System, Salt Lake City, Utah, USA.
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24
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Reiley J, Botas P, Miller CE, Zhao J, Malone Jenkins S, Best H, Grubb PH, Mao R, Isla J, Brunelli L. Open-Source Artificial Intelligence System Supports Diagnosis of Mendelian Diseases in Acutely Ill Infants. CHILDREN (BASEL, SWITZERLAND) 2023; 10:991. [PMID: 37371223 PMCID: PMC10296792 DOI: 10.3390/children10060991] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2023] [Revised: 05/18/2023] [Accepted: 05/30/2023] [Indexed: 06/29/2023]
Abstract
Mendelian disorders are prevalent in neonatal and pediatric intensive care units and are a leading cause of morbidity and mortality in these settings. Current diagnostic pipelines that integrate phenotypic and genotypic data are expert-dependent and time-intensive. Artificial intelligence (AI) tools may help address these challenges. Dx29 is an open-source AI tool designed for use by clinicians. It analyzes the patient's phenotype and genotype to generate a ranked differential diagnosis. We used Dx29 to retrospectively analyze 25 acutely ill infants who had been diagnosed with a Mendelian disorder, using a targeted panel of ~5000 genes. For each case, a trio (proband and both parents) file containing gene variant information was analyzed, alongside patient phenotype, which was provided to Dx29 by three approaches: (1) AI extraction from medical records, (2) AI extraction with manual review/editing, and (3) manual entry. We then identified the rank of the correct diagnosis in Dx29's differential diagnosis. With these three approaches, Dx29 ranked the correct diagnosis in the top 10 in 92-96% of cases. These results suggest that non-expert use of Dx29's automated phenotyping and subsequent data analysis may compare favorably to standard workflows utilized by bioinformatics experts to analyze genomic data and diagnose Mendelian diseases.
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Affiliation(s)
- Joseph Reiley
- Division of Neonatology, Department of Pediatrics, University of Utah School of Medicine, Salt Lake City, UT 84108, USA
| | - Pablo Botas
- Foundation Twenty-Nine, 28223 Madrid, Spain
- Nostos Genomics, 10625 Berlin, Germany
| | - Christine E. Miller
- ARUP Laboratories, University of Utah Health Sciences Center, Salt Lake City, UT 84108, USA
- Valley Children’s Healthcare, Madera, CA 93636, USA
| | - Jian Zhao
- ARUP Laboratories, University of Utah Health Sciences Center, Salt Lake City, UT 84108, USA
- Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT 84132, USA
| | - Sabrina Malone Jenkins
- Division of Neonatology, Department of Pediatrics, University of Utah School of Medicine, Salt Lake City, UT 84108, USA
| | - Hunter Best
- ARUP Laboratories, University of Utah Health Sciences Center, Salt Lake City, UT 84108, USA
- Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT 84132, USA
| | - Peter H. Grubb
- Division of Neonatology, Department of Pediatrics, University of Utah School of Medicine, Salt Lake City, UT 84108, USA
| | - Rong Mao
- ARUP Laboratories, University of Utah Health Sciences Center, Salt Lake City, UT 84108, USA
- Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT 84132, USA
| | | | - Luca Brunelli
- Division of Neonatology, Department of Pediatrics, University of Utah School of Medicine, Salt Lake City, UT 84108, USA
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25
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Nurchis MC, Altamura G, Riccardi MT, Radio FC, Chillemi G, Bertini ES, Garlasco J, Tartaglia M, Dallapiccola B, Damiani G. Whole genome sequencing diagnostic yield for paediatric patients with suspected genetic disorders: systematic review, meta-analysis, and GRADE assessment. Arch Public Health 2023; 81:93. [PMID: 37231492 DOI: 10.1186/s13690-023-01112-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Accepted: 05/18/2023] [Indexed: 05/27/2023] Open
Abstract
BACKGROUND About 80% of the roughly 7,000 known rare diseases are single gene disorders, about 85% of which are ultra-rare, affecting less than one in one million individuals. NGS technologies, in particular whole genome sequencing (WGS) in paediatric patients suffering from severe disorders of likely genetic origin improve the diagnostic yield allowing targeted, effective care and management. The aim of this study is to perform a systematic review and meta-analysis to assess the effectiveness of WGS, with respect to whole exome sequencing (WES) and/or usual care, for the diagnosis of suspected genetic disorders among the paediatric population. METHODS A systematic review of the literature was conducted querying relevant electronic databases, including MEDLINE, EMBASE, ISI Web of Science, and Scopus from January 2010 to June 2022. A random-effect meta-analysis was run to inspect the diagnostic yield of different techniques. A network meta-analysis was also performed to directly assess the comparison between WGS and WES. RESULTS Of the 4,927 initially retrieved articles, thirty-nine met the inclusion criteria. Overall results highlighted a significantly higher pooled diagnostic yield for WGS, 38.6% (95% CI: [32.6 - 45.0]), in respect to WES, 37.8% (95% CI: [32.9 - 42.9]) and usual care, 7.8% (95% CI: [4.4 - 13.2]). The meta-regression output suggested a higher diagnostic yield of the WGS compared to WES after controlling for the type of disease (monogenic vs non-monogenic), with a tendency to better diagnostic performances for Mendelian diseases. The network meta-analysis showed a higher diagnostic yield for WGS compared to WES (OR = 1.54, 95%CI: [1.11 - 2.12]). CONCLUSIONS Although whole genome sequencing for the paediatric population with suspected genetic disorders provided an accurate and early genetic diagnosis in a high proportion of cases, further research is needed for evaluating costs, effectiveness, and cost-effectiveness of WGS and achieving an informed decision-making process. TRIAL REGISTRATION This systematic review has not been registered.
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Grants
- RF-2018-12,366,391, 2018 Ministero della Salute
- RF-2018-12,366,391, 2018 Ministero della Salute
- RF-2018-12,366,391, 2018 Ministero della Salute
- RF-2018-12,366,391, 2018 Ministero della Salute
- RF-2018-12,366,391, 2018 Ministero della Salute
- RF-2018-12,366,391, 2018 Ministero della Salute
- RF-2018-12,366,391, 2018 Ministero della Salute
- RF-2018-12,366,391, 2018 Ministero della Salute
- RF-2018-12,366,391, 2018 Ministero della Salute
- RF-2018-12,366,391, 2018 Ministero della Salute
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Affiliation(s)
- Mario Cesare Nurchis
- Department of Woman and Child Health and Public Health, Fondazione Policlinico Universitario A. Gemelli IRCCS, 00168, Rome, Italy
- School of Economics, Università Cattolica del Sacro Cuore, 00168, Rome, Italy
| | - Gerardo Altamura
- Department of Health Sciences and Public Health, Section of Hygiene, Università Cattolica del Sacro Cuore, Largo Francesco Vito 1, 00168, Rome, Italy.
| | - Maria Teresa Riccardi
- Department of Health Sciences and Public Health, Section of Hygiene, Università Cattolica del Sacro Cuore, Largo Francesco Vito 1, 00168, Rome, Italy
| | - Francesca Clementina Radio
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù IRCCS, 00146, Rome, Italy
| | - Giovanni Chillemi
- Department for Innovation in Biological Agro-Food and Forest Systems (DIBAF), University of Tuscia, 01100, Viterbo, Italy
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, Centro Nazionale Delle Ricerche, 70126, Bari, Italy
| | - Enrico Silvio Bertini
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù IRCCS, 00146, Rome, Italy
| | - Jacopo Garlasco
- Department of Public Health Sciences and Paediatrics, University of Turin, 10126, Turin, Italy
| | - Marco Tartaglia
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù IRCCS, 00146, Rome, Italy
| | - Bruno Dallapiccola
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù IRCCS, 00146, Rome, Italy
| | - Gianfranco Damiani
- Department of Woman and Child Health and Public Health, Fondazione Policlinico Universitario A. Gemelli IRCCS, 00168, Rome, Italy
- Department of Health Sciences and Public Health, Section of Hygiene, Università Cattolica del Sacro Cuore, Largo Francesco Vito 1, 00168, Rome, Italy
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26
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von Hardenberg S, Wallaschek H, Du C, Schmidt G, Auber B. A holistic approach to maximise diagnostic output in trio exome sequencing. Front Pediatr 2023; 11:1183891. [PMID: 37274821 PMCID: PMC10238563 DOI: 10.3389/fped.2023.1183891] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 05/02/2023] [Indexed: 06/07/2023] Open
Abstract
Introduction Rare genetic diseases are a major cause for severe illness in children. Whole exome sequencing (WES) is a powerful tool for identifying genetic causes of rare diseases. For a better and faster assessment of the vast number of variants that are identified in the index patient in WES, parental sequencing can be applied ("trio WES"). Methods We assessed the diagnostic rate of routine trio WES including analysis of copy number variants in 224 pediatric patients during an evaluation period of three years. Results Trio WES provided a diagnosis in 67 (30%) of all 224 analysed children. The turnaround time of trio WES analysis has been reduced significantly from 41 days in 2019 to 23 days in 2021. Copy number variants could be identified to be causative in 10 cases (4.5%), underlying the importance of copy number variant analysis. Variants in three genes which were previously not associated with a clinical condition (GAD1, TMEM222 and ZNFX1) were identified using the matching tool GeneMatcher and were part of the first description of a new syndrome. Discussion Trio WES has proven to have a high diagnostic yield and to shorten the process of identifying the correct diagnosis in paediatric patients. Re-evaluation of all 224 trio WES 1-3 years after initial analysis did not establish new diagnoses. Initiating (trio) WES as a first-tier diagnostics including copy number variant detection should be considered as early as possible, especially for children treated in ICU, if a monogenetic disease is suspected.
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Affiliation(s)
| | | | | | | | - Bernd Auber
- Correspondence: Sandra von Hardenberg Bernd Auber
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27
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Sergi MM, Keinath MC, Fanaroff J, Miller KE. Ethical Considerations of Genome Sequencing for Pediatric Patients. Semin Pediatr Neurol 2023; 45:101039. [PMID: 37003628 DOI: 10.1016/j.spen.2023.101039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 02/20/2023] [Accepted: 02/23/2023] [Indexed: 04/03/2023]
Abstract
Advancements in genetic testing in the healthcare setting, most recently genomic sequencing, has enhanced our ability to diagnose genetic conditions. These advances include increased accessibility and affordability of genomic technologies. With expanded use comes the potential for significant ethical challenges for clinicians, particularly considering the implications of testing a child for one condition and incidentally finding a different condition or health risk. In this focused review, we address various ethical considerations from informed consent to the rights of a child undergoing genetic testing.
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Affiliation(s)
- Michelle M Sergi
- From theUniversity Hospitals Rainbow Babies & Children's Hospital, Cleveland, OH; Case Western Reserve University School of Medicine, Cleveland, OH; University Hospitals Cleveland Medical Center, Cleveland, OH; MacLean Center for Clinical Medical Ethics, University of Chicago, Chicago, IL.
| | - Melissa C Keinath
- Case Western Reserve University School of Medicine, Cleveland, OH; University Hospitals Cleveland Medical Center, Cleveland, OH
| | - Jonathan Fanaroff
- From theUniversity Hospitals Rainbow Babies & Children's Hospital, Cleveland, OH; Case Western Reserve University School of Medicine, Cleveland, OH
| | - Kathryn E Miller
- From theUniversity Hospitals Rainbow Babies & Children's Hospital, Cleveland, OH
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28
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Dahmer M, Jennings A, Parker M, Sanchez-Pinto LN, Thompson A, Traube C, Zimmerman JJ. Pediatric Critical Care in the Twenty-first Century and Beyond. Crit Care Clin 2023; 39:407-425. [PMID: 36898782 DOI: 10.1016/j.ccc.2022.09.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Pediatric critical care addresses prevention, diagnosis, and treatment of organ dysfunction in the setting of increasingly complex patients, therapies, and environments. Soon burgeoning data science will enable all aspects of intensive care: driving facilitated diagnostics, empowering a learning health-care environment, promoting continuous advancement of care, and informing the continuum of critical care outside the intensive care unit preceding and following critical illness/injury. Although novel technology will progressively objectify personalized critical care, humanism, practiced at the bedside, defines the essence of pediatric critical care now and in the future.
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Affiliation(s)
- Mary Dahmer
- Division of Critical Care, Department of Pediatrics, University of Michigan, 1500 East Medical Center Drive, F6790/5243, Ann Arbor, MI, USA
| | - Aimee Jennings
- Division of Critical Care Medicine, Advanced Practice, FA.2.112, Seattle Children's Hospital, 4800 Sandpoint Way Northeast, Seattle, WA 98105, USA
| | - Margaret Parker
- Department of Pediatrics, Stony Brook University, 7762 Bloomfield Road, Easton, MD 21601, USA
| | - Lazaro N Sanchez-Pinto
- Department of Pediatrics, Ann and Robert H Lurie Children's Hospital of Chicago, Northwestern University Feinberg School of Medicine, 225 East Chicago Avenue, Box 73, Chicago, IL 60611-2605, USA
| | - Ann Thompson
- Department of Critical Care Medicine, University of Pittsburgh, 3550 Terrace Street, Pittsburgh, PA 15261, USA
| | - Chani Traube
- Department of Pediatrics, Weill Cornell Medicine, 525 East 68th Street, Box 225, New York, NY 10065, USA
| | - Jerry J Zimmerman
- Department of Pediatrics, FA.2.300B Seattle Children's Hospital, 4800 Sandpoint Way Northeast, Seattle, WA 98105, USA; Pediatric Critical Care Medicine, Seattle Children's Hospital, Harborview Medical Center, University of Washington, School of Medicine, FA.2.300B, Seattle Children's Hospital, 4800 Sand Point Way Northeast, Seattle, WA 98105, USA.
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29
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Spillmann RC, Tan QKG, Reuter C, Schoch K, Kohler J, Bonner D, Zastrow D, Alkelai A, Baugh E, Cope H, Marwaha S, Wheeler MT, Bernstein JA, Shashi V. A concurrent dual analysis of genomic data augments diagnoses: Experiences of 2 clinical sites in the Undiagnosed Diseases Network. Genet Med 2023; 25:100353. [PMID: 36481303 PMCID: PMC10506157 DOI: 10.1016/j.gim.2022.12.001] [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: 08/02/2022] [Revised: 11/28/2022] [Accepted: 12/01/2022] [Indexed: 12/12/2022] Open
Abstract
PURPOSE Next-generation sequencing (NGS) has revolutionized the diagnostic process for rare/ultrarare conditions. However, diagnosis rates differ between analytical pipelines. In the National Institutes of Health-Undiagnosed Diseases Network (UDN) study, each individual's NGS data are concurrently analyzed by the UDN sequencing core laboratory and the clinical sites. We examined the outcomes of this practice. METHODS A retrospective review was performed at 2 UDN clinical sites to compare the variants and diagnoses/candidate genes identified with the dual analyses of the NGS data. RESULTS In total, 95 individuals had 100 diagnoses/candidate genes. There was 59% concordance between the UDN sequencing core laboratories and the clinical sites in identifying diagnoses/candidate genes. The core laboratory provided more diagnoses, whereas the clinical sites prioritized more research variants/candidate genes (P < .001). The clinical sites solely identified 15% of the diagnoses/candidate genes. The differences between the 2 pipelines were more often because of variant prioritization disparities than variant detection. CONCLUSION The unique dual analysis of NGS data in the UDN synergistically enhances outcomes. The core laboratory provided a clinical analysis with more diagnoses and the clinical sites prioritized more research variants/candidate genes. Implementing such concurrent dual analyses in other genomic research studies and clinical settings can improve both variant detection and prioritization.
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Affiliation(s)
- Rebecca C Spillmann
- Division of Medical Genetics, Department of Pediatrics, Duke University School of Medicine, Durham, NC
| | - Queenie K-G Tan
- Division of Medical Genetics, Department of Pediatrics, Duke University School of Medicine, Durham, NC
| | - Chloe Reuter
- Stanford Center for Inherited Cardiovascular Disease, Division of Cardiovascular Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, CA; Stanford Center for Undiagnosed Diseases, Stanford University, and Department of Pediatrics, Stanford University School of Medicine, Stanford, CA
| | - Kelly Schoch
- Division of Medical Genetics, Department of Pediatrics, Duke University School of Medicine, Durham, NC
| | - Jennefer Kohler
- Stanford Center for Undiagnosed Diseases, Stanford University, and Department of Pediatrics, Stanford University School of Medicine, Stanford, CA
| | - Devon Bonner
- Stanford Center for Undiagnosed Diseases, Stanford University, and Department of Pediatrics, Stanford University School of Medicine, Stanford, CA
| | - Diane Zastrow
- Stanford Center for Undiagnosed Diseases, Stanford University, and Department of Pediatrics, Stanford University School of Medicine, Stanford, CA
| | - Anna Alkelai
- Institute for Genome Medicine, Columbia University Medical Center, New York, NY
| | - Evan Baugh
- Institute for Genome Medicine, Columbia University Medical Center, New York, NY
| | - Heidi Cope
- Division of Medical Genetics, Department of Pediatrics, Duke University School of Medicine, Durham, NC
| | - Shruti Marwaha
- Stanford Center for Undiagnosed Diseases, Stanford University, and Department of Pediatrics, Stanford University School of Medicine, Stanford, CA
| | - Matthew T Wheeler
- Stanford Center for Inherited Cardiovascular Disease, Division of Cardiovascular Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, CA; Stanford Center for Undiagnosed Diseases, Stanford University, and Department of Pediatrics, Stanford University School of Medicine, Stanford, CA
| | - Jonathan A Bernstein
- Stanford Center for Undiagnosed Diseases, Stanford University, and Department of Pediatrics, Stanford University School of Medicine, Stanford, CA
| | - Vandana Shashi
- Division of Medical Genetics, Department of Pediatrics, Duke University School of Medicine, Durham, NC.
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30
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Peterson B, Hernandez EJ, Hobbs C, Malone Jenkins S, Moore B, Rosales E, Zoucha S, Sanford E, Bainbridge MN, Frise E, Oriol A, Brunelli L, Kingsmore SF, Yandell M. Automated prioritization of sick newborns for whole genome sequencing using clinical natural language processing and machine learning. Genome Med 2023; 15:18. [PMID: 36927505 PMCID: PMC10018992 DOI: 10.1186/s13073-023-01166-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Accepted: 02/27/2023] [Indexed: 03/18/2023] Open
Abstract
BACKGROUND Rapidly and efficiently identifying critically ill infants for whole genome sequencing (WGS) is a costly and challenging task currently performed by scarce, highly trained experts and is a major bottleneck for application of WGS in the NICU. There is a dire need for automated means to prioritize patients for WGS. METHODS Institutional databases of electronic health records (EHRs) are logical starting points for identifying patients with undiagnosed Mendelian diseases. We have developed automated means to prioritize patients for rapid and whole genome sequencing (rWGS and WGS) directly from clinical notes. Our approach combines a clinical natural language processing (CNLP) workflow with a machine learning-based prioritization tool named Mendelian Phenotype Search Engine (MPSE). RESULTS MPSE accurately and robustly identified NICU patients selected for WGS by clinical experts from Rady Children's Hospital in San Diego (AUC 0.86) and the University of Utah (AUC 0.85). In addition to effectively identifying patients for WGS, MPSE scores also strongly prioritize diagnostic cases over non-diagnostic cases, with projected diagnostic yields exceeding 50% throughout the first and second quartiles of score-ranked patients. CONCLUSIONS Our results indicate that an automated pipeline for selecting acutely ill infants in neonatal intensive care units (NICU) for WGS can meet or exceed diagnostic yields obtained through current selection procedures, which require time-consuming manual review of clinical notes and histories by specialized personnel.
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Affiliation(s)
- Bennet Peterson
- Department of Biomedical Informatics, University of Utah, Salt Lake City, UT, USA
| | - Edgar Javier Hernandez
- Department of Human Genetics, Utah Center for Genetic Discovery, University of Utah, Salt Lake City, UT, USA
| | - Charlotte Hobbs
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
| | - Sabrina Malone Jenkins
- Division of Neonatology, Department of Pediatrics, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Barry Moore
- Department of Human Genetics, Utah Center for Genetic Discovery, University of Utah, Salt Lake City, UT, USA
| | - Edwin Rosales
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
| | - Samuel Zoucha
- Division of Neonatology, Department of Pediatrics, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Erica Sanford
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA.,Department of Pediatrics, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | | | | | | | - Luca Brunelli
- Division of Neonatology, Department of Pediatrics, University of Utah School of Medicine, Salt Lake City, UT, USA
| | | | - Mark Yandell
- Department of Human Genetics, Utah Center for Genetic Discovery, University of Utah, Salt Lake City, UT, USA.
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31
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Vockley J, Aartsma-Rus A, Cohen JL, Cowsert LM, Howell RR, Yu TW, Wasserstein MP, Defay T. Whole-genome sequencing holds the key to the success of gene-targeted therapies. AMERICAN JOURNAL OF MEDICAL GENETICS. PART C, SEMINARS IN MEDICAL GENETICS 2023; 193:19-29. [PMID: 36453229 DOI: 10.1002/ajmg.c.32017] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 10/12/2022] [Accepted: 11/15/2022] [Indexed: 12/02/2022]
Abstract
Rare genetic disorders affect as many as 3%-5% of all babies born. Approximately 10,000 such disorders have been identified or hypothesized to exist. Treatment is supportive except in a limited number of instances where specific therapies exist. Development of new therapies has been hampered by at least two major factors: difficulty in diagnosing diseases early enough to enable treatment before irreversible damage occurs, and the high cost of developing new drugs and getting them approved by regulatory agencies. Whole-genome sequencing (WGS) techniques have become exponentially less expensive and more rapid since the beginning of the human genome project, such that return of clinical data can now be achieved in days rather than years and at a cost that is comparable to other less expansive genetic testing. Thus, it is likely that WGS will ultimately become a mainstream, first-tier NBS technique at least for those disorders without appropriate high-throughput functional tests. However, there are likely to be several steps in the evolution to this end. The clinical implications of these advances are profound but highlight the bottlenecks in drug development that still limit transition to treatments. This article summarizes discussions arising from a recent National Institute of Health conference on nucleic acid therapy, with a focus on the impact of WGS in the identification of diagnosis and treatment of rare genetic disorders.
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Affiliation(s)
- Jerry Vockley
- Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
- Department of Human Genetics, University of Pittsburgh School of Public Health, Pittsburgh, Pennsylvania, USA
| | | | - Jennifer L Cohen
- Department of Pediatrics, Duke University Medical Center, Durham, North Carolina, USA
| | - Lex M Cowsert
- National Phenylketonuria Alliance, Eau Claire, Wisconsin, USA
| | - R Rodney Howell
- Miller School of Medicine, University of Miami, Miami, Florida, USA
| | - Timothy W Yu
- Department of Pediatrics, Harvard Medical School, Boston, Massachusetts, USA
| | - Melissa P Wasserstein
- Department of Pediatrics, Albert Einstein College of Medicine and the Children's Hospital at Montefiore, Bronx, New York, USA
| | - Thomas Defay
- Alexion AstraZeneca Rare Diseases, Boston, Massachusetts, USA
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Owen MJ, Wright MS, Batalov S, Kwon Y, Ding Y, Chau KK, Chowdhury S, Sweeney NM, Kiernan E, Richardson A, Batton E, Baer RJ, Bandoli G, Gleeson JG, Bainbridge M, Chambers CD, Kingsmore SF. Reclassification of the Etiology of Infant Mortality With Whole-Genome Sequencing. JAMA Netw Open 2023; 6:e2254069. [PMID: 36757698 PMCID: PMC9912130 DOI: 10.1001/jamanetworkopen.2022.54069] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Accepted: 11/27/2022] [Indexed: 02/10/2023] Open
Abstract
Importance Understanding the causes of infant mortality shapes public health, surveillance, and research investments. However, the association of single-locus (mendelian) genetic diseases with infant mortality is poorly understood. Objective To determine the association of genetic diseases with infant mortality. Design, Setting, and Participants This cohort study was conducted at a large pediatric hospital system in San Diego County (California) and included 546 infants (112 infant deaths [20.5%] and 434 infants [79.5%] with acute illness who survived; age, 0 to 1 year) who underwent diagnostic whole-genome sequencing (WGS) between January 2015 and December 2020. Data analysis was conducted between 2015 and 2022. Exposure Infants underwent WGS either premortem or postmortem with semiautomated phenotyping and diagnostic interpretation. Main Outcomes and Measures Proportion of infant deaths associated with single-locus genetic diseases. Results Among 112 infant deaths (54 girls [48.2%]; 8 [7.1%] African American or Black, 1 [0.9%] American Indian or Alaska Native, 8 [7.1%] Asian, 48 [42.9%] Hispanic, 1 [0.9%] Native Hawaiian or Pacific Islander, and 34 [30.4%] White infants) in San Diego County between 2015 and 2020, single-locus genetic diseases were the most common identifiable cause of infant mortality, with 47 genetic diseases identified in 46 infants (41%). Thirty-nine (83%) of these diseases had been previously reported to be associated with childhood mortality. Twenty-eight death certificates (62%) for 45 of the 46 infants did not mention a genetic etiology. Treatments that can improve outcomes were available for 14 (30%) of the genetic diseases. In 5 of 7 infants in whom genetic diseases were identified postmortem, death might have been avoided had rapid, diagnostic WGS been performed at time of symptom onset or regional intensive care unit admission. Conclusions and Relevance In this cohort study of 112 infant deaths, the association of genetic diseases with infant mortality was higher than previously recognized. Strategies to increase neonatal diagnosis of genetic diseases and immediately implement treatment may decrease infant mortality. Additional study is required to explore the generalizability of these findings and measure reduction in infant mortality.
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Affiliation(s)
- Mallory J. Owen
- Rady Children’s Institute for Genomic Medicine, Rady Children’s Hospital, San Diego, California
- Department of Pediatrics, University of California, San Diego, La Jolla
| | - Meredith S. Wright
- Rady Children’s Institute for Genomic Medicine, Rady Children’s Hospital, San Diego, California
| | - Sergey Batalov
- Rady Children’s Institute for Genomic Medicine, Rady Children’s Hospital, San Diego, California
| | - Yonghyun Kwon
- Rady Children’s Institute for Genomic Medicine, Rady Children’s Hospital, San Diego, California
| | - Yan Ding
- Rady Children’s Institute for Genomic Medicine, Rady Children’s Hospital, San Diego, California
| | - Kevin K. Chau
- Rady Children’s Institute for Genomic Medicine, Rady Children’s Hospital, San Diego, California
| | - Shimul Chowdhury
- Rady Children’s Institute for Genomic Medicine, Rady Children’s Hospital, San Diego, California
| | - Nathaly M. Sweeney
- Rady Children’s Institute for Genomic Medicine, Rady Children’s Hospital, San Diego, California
- Department of Pediatrics, University of California, San Diego, La Jolla
| | - Elizabeth Kiernan
- Rady Children’s Institute for Genomic Medicine, Rady Children’s Hospital, San Diego, California
| | - Andrew Richardson
- Rady Children’s Institute for Genomic Medicine, Rady Children’s Hospital, San Diego, California
| | - Emily Batton
- Department of Pediatrics, University of California, San Diego, La Jolla
| | - Rebecca J. Baer
- Department of Pediatrics, University of California, San Diego, La Jolla
- California Preterm Birth Initiative, University of California, San Francisco
| | - Gretchen Bandoli
- Department of Pediatrics, University of California, San Diego, La Jolla
| | - Joseph G. Gleeson
- Rady Children’s Institute for Genomic Medicine, Rady Children’s Hospital, San Diego, California
- Department of Pediatrics, University of California, San Diego, La Jolla
| | - Matthew Bainbridge
- Rady Children’s Institute for Genomic Medicine, Rady Children’s Hospital, San Diego, California
| | | | - Stephen F. Kingsmore
- Rady Children’s Institute for Genomic Medicine, Rady Children’s Hospital, San Diego, California
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Vora NL, Norton ME. Prenatal exome and genome sequencing for fetal structural abnormalities. Am J Obstet Gynecol 2023; 228:140-149. [PMID: 36027950 PMCID: PMC9877148 DOI: 10.1016/j.ajog.2022.08.040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Revised: 08/07/2022] [Accepted: 08/17/2022] [Indexed: 01/28/2023]
Abstract
As prenatal exome sequencing becomes integrated into clinical care, it is critical that providers caring for women with fetal anomalies recognize not only the benefits, but also the challenges and considerations related to this technology. This overview of prenatal sequencing includes information about indications for sequencing, methods, diagnostic yield, clinical utility, variant interpretation, ethical considerations and dilemmas, practical considerations (ie, turnaround time and cost), pre- and posttest counseling points, and psychological impact of testing on families.
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Affiliation(s)
- Neeta L Vora
- Division of Maternal-Fetal Medicine, Department of Obstetrics and Gynecology, University of North Carolina at Chapel Hill, Chapel Hill, NC.
| | - Mary E Norton
- Division of Maternal-Fetal Medicine, Department of Obstetrics, Gynecology and Reproductive Sciences, University of California, San Francisco, San Francisco, CA
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Félix TM, Fischinger Moura de Souza C, Oliveira JB, Rico-Restrepo M, Zanoteli E, Zatz M, Giugliani R. Challenges and recommendations to increasing the use of exome sequencing and whole genome sequencing for diagnosing rare diseases in Brazil: an expert perspective. Int J Equity Health 2023; 22:11. [PMID: 36639662 PMCID: PMC9837951 DOI: 10.1186/s12939-022-01809-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Accepted: 12/14/2022] [Indexed: 01/15/2023] Open
Abstract
Early diagnosis of genetic rare diseases is an unmet need in Brazil, where an estimated 10-13 million people live with these conditions. Increased use of chromosome microarray assays, exome sequencing, and whole genome sequencing as first-tier testing techniques in suitable indications can shorten the diagnostic odyssey, eliminate unnecessary tests, procedures, and treatments, and lower healthcare expenditures. A selected panel of Brazilian experts in fields related to rare diseases was provided with a series of relevant questions to address before a multi-day conference. Within this conference, each narrative was discussed and edited through numerous rounds of discussion until agreement was achieved. The widespread adoption of exome sequencing and whole genome sequencing in Brazil is limited by various factors: cost and lack of funding, reimbursement, awareness and education, specialist shortages, and policy issues. To reduce the burden of rare diseases and increase early diagnosis, the Brazilian healthcare authorities/government must address the barriers to equitable access to early diagnostic methods for these conditions. Recommendations are provided, including broadening approved testing indications, increasing awareness and education efforts, increasing specialist training opportunities, and ensuring sufficient funding for genetic testing.
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Affiliation(s)
- Têmis Maria Félix
- grid.414449.80000 0001 0125 3761Medical Genetics Service, Hospital de Clinicas de Porto Alegre, Rua Ramiro Barcelos, 2350, Porto Alegre, 90,035–903 Brazil
| | - Carolina Fischinger Moura de Souza
- grid.414449.80000 0001 0125 3761Medical Genetics Service, Hospital de Clinicas de Porto Alegre, Rua Ramiro Barcelos, 2350, Porto Alegre, 90,035–903 Brazil
| | - João Bosco Oliveira
- grid.413562.70000 0001 0385 1941Hospital Israelita Albert Einstein, São Paulo, Brazil
| | | | - Edmar Zanoteli
- grid.11899.380000 0004 1937 0722Faculdade de Medicina, Universidade de São Paulo (FMUSP), São Paulo, Brazil
| | - Mayana Zatz
- grid.11899.380000 0004 1937 0722Human Genome and Stem-cell Research Center, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
| | - Roberto Giugliani
- grid.414449.80000 0001 0125 3761Medical Genetics Service, Hospital de Clinicas de Porto Alegre, Rua Ramiro Barcelos, 2350, Porto Alegre, 90,035–903 Brazil ,House of Rares, Porto Alegre, Rio Grande do Sul Brazil
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Owen MJ, Batalov S, Ellsworth KA, Wright M, Breeding S, Hugh K, Kingsmore SF, Ding Y. Rapid Whole Genome Sequencing for Diagnosis of Single Locus Genetic Diseases in Critically Ill Children. Methods Mol Biol 2023; 2621:217-239. [PMID: 37041447 DOI: 10.1007/978-1-0716-2950-5_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/13/2023]
Abstract
Upon admission to intensive care units (ICU), the differential diagnosis of almost all infants with diseases of unclear etiology includes single locus genetic diseases. Rapid whole genome sequencing (rWGS), including sample preparation, short-read sequencing-by-synthesis, informatics pipelining, and semiautomated interpretation, can now identify nucleotide and structural variants associated with most genetic diseases with robust analytic and diagnostic performance in as little as 13.5 h. Early diagnosis of genetic diseases transforms medical and surgical management of infants in ICUs, minimizing both the duration of empiric treatment and the delay to start of specific treatment. Both positive and negative rWGS tests have clinical utility and can improve outcomes. Since first described 10 years ago, rWGS has evolved considerably. Here we describe our current methods for routine diagnostic testing for genetic diseases by rWGS in as little as 18 h.
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Affiliation(s)
- Mallory J Owen
- Rady Children's Institute for Genomic Medicine, Rady Children's Hospital, San Diego, CA, USA
| | - Sergey Batalov
- Rady Children's Institute for Genomic Medicine, Rady Children's Hospital, San Diego, CA, USA
| | - Katarzyna A Ellsworth
- Rady Children's Institute for Genomic Medicine, Rady Children's Hospital, San Diego, CA, USA
| | - Meredith Wright
- Rady Children's Institute for Genomic Medicine, Rady Children's Hospital, San Diego, CA, USA
| | - Sylvia Breeding
- Rady Children's Institute for Genomic Medicine, Rady Children's Hospital, San Diego, CA, USA
| | - Kwon Hugh
- Rady Children's Institute for Genomic Medicine, Rady Children's Hospital, San Diego, CA, USA
| | - Stephen F Kingsmore
- Rady Children's Institute for Genomic Medicine, Rady Children's Hospital, San Diego, CA, USA.
| | - Yan Ding
- Rady Children's Institute for Genomic Medicine, Rady Children's Hospital, San Diego, CA, USA.
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36
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Senaratne TN, Saitta SC. Evaluating Genetic Disorders in the Neonate: The Role of Exome Sequencing in the NICU. Neoreviews 2022; 23:e829-e840. [PMID: 36450644 DOI: 10.1542/neo.23-12-e829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
With recent advances in the technologies used for genetic diagnosis as well as our understanding of the genetic basis of disease, a growing list of options is available for providers when caring for a newborn with features suggesting an underlying genetic etiology. The choice of the most appropriate genetic test for a specific situation includes clinical considerations such as the phenotypic features and type of genetic abnormality suspected, as well as practical considerations such as cost and turnaround time. In this review, we discuss clinical exome sequencing in the context of genetic evaluation of newborns, including technical considerations, variant interpretation, and incidental/secondary findings. Strengths and limitations of exome sequencing are discussed and compared with those of other commonly known tests such as karyotype analysis, fluorescence in situ hybridization, chromosomal microarray, and sequencing panels, along with integration of results from prenatal testing if available. We also review future directions including genome sequencing and other emerging technologies that are starting to be used in clinical settings.
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Affiliation(s)
- T Niroshi Senaratne
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA
| | - Sulagna C Saitta
- Division of Clinical Genetics, Department of Pediatrics, Division of Reproductive Genetics, Department of Obstetrics and Gynecology, David Geffen School of Medicine at UCLA, Los Angeles, CA
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Beaman M, Fisher K, McDonald M, Tan QKG, Jackson D, Cocanougher BT, Landstrom AP, Hobbs CA, Cotten M, Cohen JL. Rapid Whole Genome Sequencing in Critically Ill Neonates Enables Precision Medicine Pipeline. J Pers Med 2022; 12:1924. [PMID: 36422100 PMCID: PMC9694815 DOI: 10.3390/jpm12111924] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 10/24/2022] [Accepted: 11/05/2022] [Indexed: 09/07/2023] Open
Abstract
Rapid genome sequencing in critically ill infants is increasingly identified as a crucial test for providing targeted and informed patient care. We report the outcomes of a pilot study wherein eight critically ill neonates received rapid whole genome sequencing with parental samples in an effort to establish a prompt diagnosis. Our pilot study resulted in a 37.5% diagnostic rate by whole genome sequencing alone and an overall 50% diagnostic rate for the cohort. We describe how the diagnoses led to identification of additional affected relatives and a change in management, the limitations of rapid genome sequencing, and some of the challenges with sample collection. Alongside this pilot study, our site simultaneously established a research protocol pipeline that will allow us to conduct research-based genomic testing in the cases for which a diagnosis was not reached by rapid genome sequencing or other available clinical testing. Here we describe the benefits, limitations, challenges, and potential for rapid whole genome sequencing to be incorporated into routine clinical evaluation in the neonatal period.
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Affiliation(s)
- Makenzie Beaman
- Duke University Medical Scientist Training Program, Durham, NC 27710, USA
- Duke University Department of Pediatrics, Division of Medical Genetics, Durham, NC 27710, USA
| | - Kimberley Fisher
- Duke University Department of Pediatrics, Division of Neonatology, Durham, NC 27710, USA
| | - Marie McDonald
- Duke University Department of Pediatrics, Division of Medical Genetics, Durham, NC 27710, USA
| | - Queenie K. G. Tan
- Duke University Department of Pediatrics, Division of Medical Genetics, Durham, NC 27710, USA
| | - David Jackson
- Duke University Department of Pediatrics, Division of Medical Genetics, Durham, NC 27710, USA
| | - Benjamin T. Cocanougher
- Duke University Department of Pediatrics, Division of Medical Genetics, Durham, NC 27710, USA
| | - Andrew P. Landstrom
- Duke University Department of Pediatrics, Division of Cardiology, Durham, NC 27710, USA
| | - Charlotte A. Hobbs
- Rady Children’s Institute for Genomic Medicine, Rady Children’s Hospital, San Diego, CA 92123, USA
| | - Michael Cotten
- Duke University Department of Pediatrics, Division of Neonatology, Durham, NC 27710, USA
| | - Jennifer L. Cohen
- Duke University Department of Pediatrics, Division of Medical Genetics, Durham, NC 27710, USA
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Evaluating use of changing technologies for rapid next-generation sequencing in pediatrics. Pediatr Res 2022; 92:1364-1369. [PMID: 35115709 PMCID: PMC10024604 DOI: 10.1038/s41390-022-01965-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 01/17/2022] [Accepted: 01/20/2022] [Indexed: 02/03/2023]
Abstract
BACKGROUND Rapid next-generation sequencing (NGS) offers the potential to shorten the diagnostic process and improve the care of acutely ill children. The goal of this study was to report our findings, including benefits and limitations, of a targeted NGS panel and rapid genome sequencing (rGS) in neonatal and pediatric acute clinical care settings. METHODS Retrospective analysis of patient characteristics, diagnostic yields, turnaround time, and changes in management for infants and children receiving either RapSeq, a targeted NGS panel for 4500+ genes, or rGS, at the University of Utah Hospital and Primary Children's Hospital, from 2015 to 2020. RESULTS Over a 5-year period, 142 probands underwent rapid NGS: 66 received RapSeq and 76 rGS. Overall diagnostic yield was 39%. In the majority of diagnostic cases, there were one or more changes in clinical care management. Of note, 7% of diagnoses identified by rGS would not have been identified by RapSeq. CONCLUSIONS Our results indicate that rapid NGS impacts acute pediatric care in real-life clinical settings. Although affected by patient selection criteria, diagnostic yields were similar to those from clinical trial settings. Future studies are needed to determine relative advantages, including cost, turnaround time, and benefits for patients, of each approach in specific clinical circumstances. IMPACT The use of comprehensive Mendelian gene panels and genome sequencing in the clinical setting allows for early diagnosis of patients in neonatal, pediatric, and cardiac intensive care units and impactful change in management. Diagnoses led to significant changes in management for several patients in lower acuity inpatient units supporting further exploration of the utility of rapid sequencing in these settings. This study reviews the limitations of comparing sequencing platforms in the clinical setting and the variables that should be considered in evaluating diagnostic rates across studies.
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Sanford Kobayashi E, Batalov S, Wenger AM, Lambert C, Dhillon H, Hall RJ, Baybayan P, Ding Y, Rego S, Wigby K, Friedman J, Hobbs C, Bainbridge MN. Approaches to long-read sequencing in a clinical setting to improve diagnostic rate. Sci Rep 2022; 12:16945. [PMID: 36210382 PMCID: PMC9548499 DOI: 10.1038/s41598-022-20113-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2022] [Accepted: 09/08/2022] [Indexed: 12/29/2022] Open
Abstract
Over the past decade, advances in genetic testing, particularly the advent of next-generation sequencing, have led to a paradigm shift in the diagnosis of molecular diseases and disorders. Despite our present collective ability to interrogate more than 90% of the human genome, portions of the genome have eluded us, resulting in stagnation of diagnostic yield with existing methodologies. Here we show how application of a new technology, long-read sequencing, has the potential to improve molecular diagnostic rates. Whole genome sequencing by long reads was able to cover 98% of next-generation sequencing dead zones, which are areas of the genome that are not interpretable by conventional industry-standard short-read sequencing. Through the ability of long-read sequencing to unambiguously call variants in these regions, we discovered an immunodeficiency due to a variant in IKBKG in a subject who had previously received a negative genome sequencing result. Additionally, we demonstrate the ability of long-read sequencing to detect small variants on par with short-read sequencing, its superior performance in identifying structural variants, and thirdly, its capacity to determine genomic methylation defects in native DNA. Though the latter technical abilities have been demonstrated, we demonstrate the clinical application of this technology to successfully identify multiple types of variants using a single test.
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Affiliation(s)
- Erica Sanford Kobayashi
- Rady Institute for Genomic Medicine, San Diego, CA USA ,grid.50956.3f0000 0001 2152 9905Department of Pediatrics, Cedars-Sinai Medical Center, Los Angeles, CA USA
| | - Serge Batalov
- Rady Institute for Genomic Medicine, San Diego, CA USA
| | - Aaron M. Wenger
- grid.423340.20000 0004 0640 9878Pacific Biosciences, Menlo Park, CA USA
| | - Christine Lambert
- grid.423340.20000 0004 0640 9878Pacific Biosciences, Menlo Park, CA USA
| | - Harsharan Dhillon
- grid.423340.20000 0004 0640 9878Pacific Biosciences, Menlo Park, CA USA
| | - Richard J. Hall
- grid.423340.20000 0004 0640 9878Pacific Biosciences, Menlo Park, CA USA
| | - Primo Baybayan
- grid.423340.20000 0004 0640 9878Pacific Biosciences, Menlo Park, CA USA
| | - Yan Ding
- Rady Institute for Genomic Medicine, San Diego, CA USA
| | - Seema Rego
- Rady Institute for Genomic Medicine, San Diego, CA USA
| | - Kristen Wigby
- Rady Institute for Genomic Medicine, San Diego, CA USA ,grid.266100.30000 0001 2107 4242Department of Pediatrics, University of California San Diego and Rady Children’s Hospital, San Diego, CA USA
| | - Jennifer Friedman
- Rady Institute for Genomic Medicine, San Diego, CA USA ,grid.266100.30000 0001 2107 4242Department of Pediatrics, University of California San Diego and Rady Children’s Hospital, San Diego, CA USA ,grid.266100.30000 0001 2107 4242Department of Neuroscience, University of California San Diego and Rady Children’s Hospital, San Diego, CA USA
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Motelow JE, Lippa NC, Hostyk J, Feldman E, Nelligan M, Ren Z, Alkelai A, Milner JD, Gharavi AG, Tang Y, Goldstein DB, Kernie SG. Risk Variants in the Exomes of Children With Critical Illness. JAMA Netw Open 2022; 5:e2239122. [PMID: 36306130 PMCID: PMC9617179 DOI: 10.1001/jamanetworkopen.2022.39122] [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] [Indexed: 11/14/2022] Open
Abstract
IMPORTANCE Diagnostic genetic testing can lead to changes in management in the pediatric intensive care unit. Genetic risk in children with critical illness but nondiagnostic exome sequencing (ES) has not been explored. OBJECTIVE To assess the association between loss-of-function (LOF) variants and pediatric critical illness. DESIGN, SETTING, AND PARTICIPANTS This genetic association study examined ES first screened for causative variants among 267 children at the Morgan Stanley Children's Hospital of NewYork-Presbyterian, of whom 22 were otherwise healthy with viral respiratory failure; 18 deceased children with bronchiolitis from the Office of the Chief Medical Examiner of New York City, of whom 14 were previously healthy; and 9990 controls from the Institute for Genomic Medicine at Columbia University Irving Medical Center. The ES data were generated between January 1, 2015, and December 31, 2020, and analyzed between January 1, 2017, and September 2, 2022. EXPOSURE Critical illness. MAIN OUTCOMES AND MEASURES Odds ratios and P values for genes and gene-sets enriched for rare LOF variants and the loss-of-function observed/expected upper bound fraction (LOEUF) score at which cases have a significant enrichment. RESULTS This study included 285 children with critical illness (median [range] age, 4.1 [0-18.9] years; 148 [52%] male) and 9990 controls. A total of 228 children (80%) did not receive a genetic diagnosis. After quality control (QC), 231 children harbored excess rare LOF variants in genes with a LOEUF score of 0.680 or less (intolerant genes) (P = 1.0 × 10-5). After QC, 176 children without a diagnosis harbored excess ultrarare LOF variants in intolerant genes but only in those without a known disease association (odds ratio, 1.8; 95% CI, 1.3-2.5). After QC, 25 children with viral respiratory failure harbored excess ultrarare LOF variants in intolerant genes but only in those without a known disease association (odds ratio, 2.8; 95% CI, 1.1-6.6). A total of 114 undiagnosed children were enriched for de novo LOF variants in genes without a known disease association (observed, 14; expected, 6.8; enrichment, 2.05). CONCLUSIONS AND RELEVANCE In this genetic association study, excess LOF variants were observed among critically ill children despite nondiagnostic ES. Variants lay in genes without a known disease association, suggesting future investigation may connect phenotypes to causative genes.
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Affiliation(s)
- Joshua E. Motelow
- Institute for Genomic Medicine, Columbia University Medical Center, New York, New York
- Division of Critical Care and Hospital Medicine, Department of Pediatrics, Columbia University Irving Medical Center, NewYork-Presbyterian Morgan Stanley Children's Hospital, New York, New York
| | - Natalie C. Lippa
- Institute for Genomic Medicine, Columbia University Medical Center, New York, New York
| | - Joseph Hostyk
- Institute for Genomic Medicine, Columbia University Medical Center, New York, New York
| | - Evin Feldman
- Division of Critical Care and Hospital Medicine, Department of Pediatrics, Columbia University Irving Medical Center, NewYork-Presbyterian Morgan Stanley Children's Hospital, New York, New York
| | - Matthew Nelligan
- Division of Critical Care and Hospital Medicine, Department of Pediatrics, Columbia University Irving Medical Center, NewYork-Presbyterian Morgan Stanley Children's Hospital, New York, New York
| | - Zhong Ren
- Institute for Genomic Medicine, Columbia University Medical Center, New York, New York
| | - Anna Alkelai
- Institute for Genomic Medicine, Columbia University Medical Center, New York, New York
- Regeneron Genetics Center, Regeneron Pharmaceuticals, Tarrytown, New York
| | | | - Ali G. Gharavi
- Institute for Genomic Medicine, Columbia University Medical Center, New York, New York
- Division of Nephrology, Department of Medicine, Columbia University Irving Medical Center, NewYork-Presbyterian, New York, New York
| | - Yingying Tang
- Molecular Genetics Laboratory, New York City Office of Chief Medical Examiner, New York, New York
| | - David B. Goldstein
- Institute for Genomic Medicine, Columbia University Medical Center, New York, New York
| | - Steven G. Kernie
- Division of Critical Care and Hospital Medicine, Department of Pediatrics, Columbia University Irving Medical Center, NewYork-Presbyterian Morgan Stanley Children's Hospital, New York, New York
- NewYork-Presbyterian Hospital, New York, New York
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Chad L, Anderson J, Cagliero D, Hayeems RZ, Ly LG, Szuto A. Rapid Genetic Testing in Pediatric and Neonatal Critical Care: A Scoping Review of Emerging Ethical Issues. Hosp Pediatr 2022; 12:e347-e359. [PMID: 36161483 DOI: 10.1542/hpeds.2022-006654] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
BACKGROUND Rapid genome-wide sequencing (rGWS) is being increasingly used to aid in prognostication and decision-making for critically ill newborns and children. Although its feasibility in this fast-paced setting has been described, this new paradigm of inpatient genetic care raises new ethical challenges. OBJECTIVE A scoping review was performed to (1) identify salient ethical issues in this area of practice; and (2) bring attention to gaps and ethical tensions that warrant more deliberate exploration. METHODS Data sources, Ovid Medline and Cochrane Central Register of Controlled Trials, were searched up to November 2021. Articles included were those in English relating to rGWS deployed rapidly in a critical care setting. Publications were examined for ethical themes and were further characterized as including a superficial or in-depth discussion of that theme. New themes were inductively identified as they emerged. RESULTS Ninety-nine studies, published in 2012 or thereafter, met inclusion criteria. Themes identified elaborated upon established ethical principles related to beneficence and nonmaleficence (ie, clinical utility, medical uncertainty, impact on family, and data security) autonomy (ie, informed consent), and justice (ie, resource allocation and disability rights). Many themes were only narrowly discussed. CONCLUSIONS The application of rGWS in neonatal and pediatric acute care is inherently tied to ethically charged issues, some of which are reported here. Attention to the ethical costs and benefits of rGWS is not always discussed, with important gaps and unanswered questions that call for ongoing focus on these ethical considerations in this next application of acute care genomics.
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Affiliation(s)
- Lauren Chad
- Divisions of Clinical and Metabolic Genetics.,Departments of Bioethics.,Departments of Paediatrics
| | | | | | - Robin Z Hayeems
- Child Health Evaluative Sciences, Hospital for Sick Children Research Institute,Toronto, Ontario, Canada.,Institute of Health Policy, Management, and Evaluation, University of Toronto,Toronto, Ontario, Canada
| | - Linh G Ly
- Neonatology.,Departments of Paediatrics
| | - Anna Szuto
- Genetic Counselling, Hospital for Sick Children,Toronto, Ontario, Canada.,Molecular Genetics
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Al-Ali S, Jeffries L, Faustino EVS, Ji W, Mis E, Konstantino M, Zerillo C, Jiang YH, Spencer-Manzon M, Bale A, Zhang H, McGlynn J, McGrath JM, Tremblay T, Brodsky NN, Lucas CL, Pierce R, Deniz E, Khokha MK, Lakhani SA. A retrospective cohort analysis of the Yale pediatric genomics discovery program. Am J Med Genet A 2022; 188:2869-2878. [PMID: 35899841 PMCID: PMC9474639 DOI: 10.1002/ajmg.a.62918] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 05/29/2022] [Accepted: 07/10/2022] [Indexed: 01/31/2023]
Abstract
The Pediatric Genomics Discovery Program (PGDP) at Yale uses next-generation sequencing (NGS) and translational research to evaluate complex patients with a wide range of phenotypes suspected to have rare genetic diseases. We conducted a retrospective cohort analysis of 356 PGDP probands evaluated between June 2015 and July 2020, querying our database for participant demographics, clinical characteristics, NGS results, and diagnostic and research findings. The three most common phenotypes among the entire studied cohort (n = 356) were immune system abnormalities (n = 105, 29%), syndromic or multisystem disease (n = 103, 29%), and cardiovascular system abnormalities (n = 62, 17%). Of 216 patients with final classifications, 77 (36%) received new diagnoses and 139 (64%) were undiagnosed; the remaining 140 patients were still actively being investigated. Monogenetic diagnoses were found in 67 (89%); the largest group had variants in known disease genes but with new contributions such as novel variants (n = 31, 40%) or expanded phenotypes (n = 14, 18%). Finally, five PGDP diagnoses (8%) were suggestive of novel gene-to-phenotype relationships. A broad range of patients can benefit from single subject studies combining NGS and functional molecular analyses. All pediatric providers should consider further genetics evaluations for patients lacking precise molecular diagnoses.
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Affiliation(s)
- Samir Al-Ali
- Pediatric Genomics Discovery Program, Department of Pediatrics, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Lauren Jeffries
- Pediatric Genomics Discovery Program, Department of Pediatrics, Yale University School of Medicine, New Haven, Connecticut, USA
| | - E. Vincent S. Faustino
- Pediatric Genomics Discovery Program, Department of Pediatrics, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Weizhen Ji
- Pediatric Genomics Discovery Program, Department of Pediatrics, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Emily Mis
- Pediatric Genomics Discovery Program, Department of Pediatrics, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Monica Konstantino
- Pediatric Genomics Discovery Program, Department of Pediatrics, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Cynthia Zerillo
- Pediatric Genomics Discovery Program, Department of Pediatrics, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Yong-hui Jiang
- Pediatric Genomics Discovery Program, Department of Pediatrics, Yale University School of Medicine, New Haven, Connecticut, USA
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, US
| | - Michele Spencer-Manzon
- Pediatric Genomics Discovery Program, Department of Pediatrics, Yale University School of Medicine, New Haven, Connecticut, USA
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, US
| | - Allen Bale
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, US
| | - Hui Zhang
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, US
| | - Julie McGlynn
- Pediatric Genomics Discovery Program, Department of Pediatrics, Yale University School of Medicine, New Haven, Connecticut, USA
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, US
| | - James M. McGrath
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, US
| | | | - Nina N. Brodsky
- Pediatric Genomics Discovery Program, Department of Pediatrics, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Carrie L. Lucas
- Department of Immunobiology, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Richard Pierce
- Pediatric Genomics Discovery Program, Department of Pediatrics, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Engin Deniz
- Pediatric Genomics Discovery Program, Department of Pediatrics, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Mustafa K. Khokha
- Pediatric Genomics Discovery Program, Department of Pediatrics, Yale University School of Medicine, New Haven, Connecticut, USA
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, US
| | - Saquib A. Lakhani
- Pediatric Genomics Discovery Program, Department of Pediatrics, Yale University School of Medicine, New Haven, Connecticut, USA
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Kingsmore SF, Smith LD, Kunard CM, Bainbridge M, Batalov S, Benson W, Blincow E, Caylor S, Chambers C, Del Angel G, Dimmock DP, Ding Y, Ellsworth K, Feigenbaum A, Frise E, Green RC, Guidugli L, Hall KP, Hansen C, Hobbs CA, Kahn SD, Kiel M, Van Der Kraan L, Krilow C, Kwon YH, Madhavrao L, Le J, Lefebvre S, Mardach R, Mowrey WR, Oh D, Owen MJ, Powley G, Scharer G, Shelnutt S, Tokita M, Mehtalia SS, Oriol A, Papadopoulos S, Perry J, Rosales E, Sanford E, Schwartz S, Tran D, Reese MG, Wright M, Veeraraghavan N, Wigby K, Willis MJ, Wolen AR, Defay T. A genome sequencing system for universal newborn screening, diagnosis, and precision medicine for severe genetic diseases. Am J Hum Genet 2022; 109:1605-1619. [PMID: 36007526 PMCID: PMC9502059 DOI: 10.1016/j.ajhg.2022.08.003] [Citation(s) in RCA: 58] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 08/01/2022] [Indexed: 12/31/2022] Open
Abstract
Newborn screening (NBS) dramatically improves outcomes in severe childhood disorders by treatment before symptom onset. In many genetic diseases, however, outcomes remain poor because NBS has lagged behind drug development. Rapid whole-genome sequencing (rWGS) is attractive for comprehensive NBS because it concomitantly examines almost all genetic diseases and is gaining acceptance for genetic disease diagnosis in ill newborns. We describe prototypic methods for scalable, parentally consented, feedback-informed NBS and diagnosis of genetic diseases by rWGS and virtual, acute management guidance (NBS-rWGS). Using established criteria and the Delphi method, we reviewed 457 genetic diseases for NBS-rWGS, retaining 388 (85%) with effective treatments. Simulated NBS-rWGS in 454,707 UK Biobank subjects with 29,865 pathogenic or likely pathogenic variants associated with 388 disorders had a true negative rate (specificity) of 99.7% following root cause analysis. In 2,208 critically ill children with suspected genetic disorders and 2,168 of their parents, simulated NBS-rWGS for 388 disorders identified 104 (87%) of 119 diagnoses previously made by rWGS and 15 findings not previously reported (NBS-rWGS negative predictive value 99.6%, true positive rate [sensitivity] 88.8%). Retrospective NBS-rWGS diagnosed 15 children with disorders that had been undetected by conventional NBS. In 43 of the 104 children, had NBS-rWGS-based interventions been started on day of life 5, the Delphi consensus was that symptoms could have been avoided completely in seven critically ill children, mostly in 21, and partially in 13. We invite groups worldwide to refine these NBS-rWGS conditions and join us to prospectively examine clinical utility and cost effectiveness.
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Affiliation(s)
- Stephen F Kingsmore
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA; Rady Children's Hospital, San Diego, CA 92123, USA; Keck Graduate Institute, Claremont, CA 91711, USA.
| | - Laurie D Smith
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA
| | | | - Matthew Bainbridge
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA; Rady Children's Hospital, San Diego, CA 92123, USA
| | - Sergey Batalov
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA; Rady Children's Hospital, San Diego, CA 92123, USA
| | - Wendy Benson
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA; Rady Children's Hospital, San Diego, CA 92123, USA
| | - Eric Blincow
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA; Rady Children's Hospital, San Diego, CA 92123, USA
| | - Sara Caylor
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA; Rady Children's Hospital, San Diego, CA 92123, USA
| | - Christina Chambers
- Department of Pediatrics, University of California San Diego, San Diego, CA 92093, USA
| | | | - David P Dimmock
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA; Rady Children's Hospital, San Diego, CA 92123, USA
| | - Yan Ding
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA; Rady Children's Hospital, San Diego, CA 92123, USA
| | - Katarzyna Ellsworth
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA; Rady Children's Hospital, San Diego, CA 92123, USA
| | - Annette Feigenbaum
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA; Rady Children's Hospital, San Diego, CA 92123, USA; Department of Pediatrics, University of California San Diego, San Diego, CA 92093, USA
| | - Erwin Frise
- Fabric Genomics, Inc., Oakland, CA 94612, USA
| | - Robert C Green
- Mass General Brigham, Broad Institute, Ariadne Labs and Harvard Medical School, Boston, MA 02115, USA
| | - Lucia Guidugli
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA; Rady Children's Hospital, San Diego, CA 92123, USA
| | | | - Christian Hansen
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA; Rady Children's Hospital, San Diego, CA 92123, USA
| | - Charlotte A Hobbs
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA; Rady Children's Hospital, San Diego, CA 92123, USA
| | | | - Mark Kiel
- Genomenon Inc., Ann Arbor, MI 48108, USA
| | - Lucita Van Der Kraan
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA; Rady Children's Hospital, San Diego, CA 92123, USA
| | | | - Yong H Kwon
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA; Rady Children's Hospital, San Diego, CA 92123, USA
| | - Lakshminarasimha Madhavrao
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA; Rady Children's Hospital, San Diego, CA 92123, USA
| | - Jennie Le
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA; Rady Children's Hospital, San Diego, CA 92123, USA
| | | | - Rebecca Mardach
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA; Rady Children's Hospital, San Diego, CA 92123, USA; Department of Pediatrics, University of California San Diego, San Diego, CA 92093, USA
| | | | - Danny Oh
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA; Rady Children's Hospital, San Diego, CA 92123, USA
| | - Mallory J Owen
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA; Rady Children's Hospital, San Diego, CA 92123, USA
| | | | - Gunter Scharer
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA
| | | | - Mari Tokita
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA; Rady Children's Hospital, San Diego, CA 92123, USA
| | | | - Albert Oriol
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA; Rady Children's Hospital, San Diego, CA 92123, USA
| | | | - James Perry
- Rady Children's Hospital, San Diego, CA 92123, USA; Department of Pediatrics, University of California San Diego, San Diego, CA 92093, USA
| | - Edwin Rosales
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA; Rady Children's Hospital, San Diego, CA 92123, USA
| | - Erica Sanford
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA
| | | | - Duke Tran
- Illumina, Inc., San Diego, CA 92122, USA
| | | | - Meredith Wright
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA; Rady Children's Hospital, San Diego, CA 92123, USA
| | - Narayanan Veeraraghavan
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA; Rady Children's Hospital, San Diego, CA 92123, USA
| | - Kristen Wigby
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA; Rady Children's Hospital, San Diego, CA 92123, USA; Department of Pediatrics, University of California San Diego, San Diego, CA 92093, USA
| | - Mary J Willis
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA
| | | | - Thomas Defay
- Alexion, Astra Zeneca Rare Disease, Boston, MA 02210, USA
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Abstract
Genetic diseases disrupt the functionality of an infant's genome during fetal-neonatal adaptation and represent a leading cause of neonatal and infant mortality in the United States. Due to disease acuity, gene locus and allelic heterogeneity, and overlapping and diverse clinical phenotypes, diagnostic genome sequencing in neonatal intensive care units has required the development of methods to shorten turnaround times and improve genomic interpretation. From 2012 to 2021, 31 clinical studies documented the diagnostic and clinical utility of first-tier rapid or ultrarapid whole-genome sequencing through cost-effective identification of pathogenic genomic variants that change medical management, suggest new therapeutic strategies, and refine prognoses. Genomic diagnosis also permits prediction of reproductive recurrence risk for parents and surviving probands. Using implementation science and quality improvement, deployment of a genomic learning healthcare system will contribute to a reduction of neonatal and infant mortality through the integration of genome sequencing into best-practice neonatal intensive care.
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Affiliation(s)
- Stephen F. Kingsmore
- Rady Children’s Hospital Institute for Genomic Medicine, Rady Children’s Hospital-San Diego
| | - F. Sessions Cole
- Division of Newborn Medicine, Edward Mallinckrodt Department of Pediatrics, Washington University School of Medicine in St. Louis
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Callahan KP, Mueller R, Flibotte J, Largent EA, Feudtner C. Measures of Utility Among Studies of Genomic Medicine for Critically Ill Infants: A Systematic Review. JAMA Netw Open 2022; 5:e2225980. [PMID: 35947384 PMCID: PMC9366540 DOI: 10.1001/jamanetworkopen.2022.25980] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
IMPORTANCE Genomic medicine holds promise to revolutionize care for critically ill infants by tailoring treatments for patients and providing additional prognostic information to families. However, measuring the utility of genomic medicine is not straightforward and has important clinical and ethical implications. OBJECTIVE To review the ways that researchers measure or neglect to measure the utility of genomic medicine for critically ill infants. EVIDENCE REVIEW This systematic review included prospective full-text studies of genomic medicine of both whole exome and genome sequencing in critically ill infants younger than 1 year. PubMed, Embase, Scopus, and Cochrane Library databases, the Cochrane Database of Systematic Reviews, and the ClinicalTrials.gov register were searched with an English language restriction for articles published from the inception of each database through May 2022. Search terms included variations of the following: gene, sequencing, intensive care, critical care, and infant. From the included articles, information on how utility was defined and measured was extracted and synthesized. Information was also extracted from patient cases that authors highlighted by providing additional information. Spearman rank-order correlation was used to evaluate the association between study size and utility. FINDINGS Synthesized data from the 21 included studies reflected results from 1654 patients. A mean of 46% (range, 15%-72%) of patients had a positive genetic test result, and a mean of 37% (range, 13%-61%) met the criteria for experiencing utility. Despite heterogeneity in how studies measured and reported utility, a standardized framework was created with 5 categories of utility: treatment change, redirection of care, prognostic information, reproductive information, and screening or subspecialty referral. Most studies omitted important categories of utility, notably personal utility (patient-reported benefits) (20 studies [95%]), utility of negative or uncertain results (15 [71%]), and disutility (harms) (20 [95%]). Studies disproportionally highlighted patient cases that resulted in treatment change. Larger studies reported substantially lower utility (r = -0.65; P = .002). CONCLUSIONS AND RELEVANCE This systematic review found that genomic medicine offered various categories of utility for a substantial proportion of critically ill infants. Studies measured utility in heterogeneous ways and focused more on documenting change than assessing meaningful benefit. Authors' decisions about which cases to highlight suggest that some categories of utility may be more important than others. A more complete definition of utility that is used consistently may improve understanding of potential benefits and harms of genetic medicine.
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Affiliation(s)
- Katharine Press Callahan
- The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania
- Department of Medical Ethics and Health Policy, Perelman School of Medicine at the University of Pennsylvania, Philadelphia
| | - Rebecca Mueller
- Department of Medical Ethics and Health Policy, Perelman School of Medicine at the University of Pennsylvania, Philadelphia
| | - John Flibotte
- The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Emily A. Largent
- Department of Medical Ethics and Health Policy, Perelman School of Medicine at the University of Pennsylvania, Philadelphia
| | - Chris Feudtner
- The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania
- Department of Medical Ethics and Health Policy, Perelman School of Medicine at the University of Pennsylvania, Philadelphia
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Owen MJ, Lefebvre S, Hansen C, Kunard CM, Dimmock DP, Smith LD, Scharer G, Mardach R, Willis MJ, Feigenbaum A, Niemi AK, Ding Y, Van Der Kraan L, Ellsworth K, Guidugli L, Lajoie BR, McPhail TK, Mehtalia SS, Chau KK, Kwon YH, Zhu Z, Batalov S, Chowdhury S, Rego S, Perry J, Speziale M, Nespeca M, Wright MS, Reese MG, De La Vega FM, Azure J, Frise E, Rigby CS, White S, Hobbs CA, Gilmer S, Knight G, Oriol A, Lenberg J, Nahas SA, Perofsky K, Kim K, Carroll J, Coufal NG, Sanford E, Wigby K, Weir J, Thomson VS, Fraser L, Lazare SS, Shin YH, Grunenwald H, Lee R, Jones D, Tran D, Gross A, Daigle P, Case A, Lue M, Richardson JA, Reynders J, Defay T, Hall KP, Veeraraghavan N, Kingsmore SF. An automated 13.5 hour system for scalable diagnosis and acute management guidance for genetic diseases. Nat Commun 2022; 13:4057. [PMID: 35882841 PMCID: PMC9325884 DOI: 10.1038/s41467-022-31446-6] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Accepted: 06/08/2022] [Indexed: 12/31/2022] Open
Abstract
While many genetic diseases have effective treatments, they frequently progress rapidly to severe morbidity or mortality if those treatments are not implemented immediately. Since front-line physicians frequently lack familiarity with these diseases, timely molecular diagnosis may not improve outcomes. Herein we describe Genome-to-Treatment, an automated, virtual system for genetic disease diagnosis and acute management guidance. Diagnosis is achieved in 13.5 h by expedited whole genome sequencing, with superior analytic performance for structural and copy number variants. An expert panel adjudicated the indications, contraindications, efficacy, and evidence-of-efficacy of 9911 drug, device, dietary, and surgical interventions for 563 severe, childhood, genetic diseases. The 421 (75%) diseases and 1527 (15%) effective interventions retained are integrated with 13 genetic disease information resources and appended to diagnostic reports ( https://gtrx.radygenomiclab.com ). This system provided correct diagnoses in four retrospectively and two prospectively tested infants. The Genome-to-Treatment system facilitates optimal outcomes in children with rapidly progressive genetic diseases.
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Affiliation(s)
- Mallory J Owen
- Rady Children's Institute for Genomic Medicine, San Diego, CA, 92123, USA
- Rady Children's Hospital, San Diego, CA, 92123, USA
| | | | - Christian Hansen
- Rady Children's Institute for Genomic Medicine, San Diego, CA, 92123, USA
- Rady Children's Hospital, San Diego, CA, 92123, USA
| | | | - David P Dimmock
- Rady Children's Institute for Genomic Medicine, San Diego, CA, 92123, USA
- Rady Children's Hospital, San Diego, CA, 92123, USA
- Keck Graduate Institute, Claremont, CA, 91711, USA
| | - Laurie D Smith
- Rady Children's Institute for Genomic Medicine, San Diego, CA, 92123, USA
| | - Gunter Scharer
- Rady Children's Institute for Genomic Medicine, San Diego, CA, 92123, USA
| | - Rebecca Mardach
- Rady Children's Hospital, San Diego, CA, 92123, USA
- Department of Pediatrics, University of California San Diego, San Diego, CA, 92093, USA
| | - Mary J Willis
- Rady Children's Institute for Genomic Medicine, San Diego, CA, 92123, USA
| | - Annette Feigenbaum
- Rady Children's Hospital, San Diego, CA, 92123, USA
- Department of Pediatrics, University of California San Diego, San Diego, CA, 92093, USA
| | - Anna-Kaisa Niemi
- Rady Children's Hospital, San Diego, CA, 92123, USA
- Department of Pediatrics, University of California San Diego, San Diego, CA, 92093, USA
| | - Yan Ding
- Rady Children's Institute for Genomic Medicine, San Diego, CA, 92123, USA
- Rady Children's Hospital, San Diego, CA, 92123, USA
| | - Luca Van Der Kraan
- Rady Children's Institute for Genomic Medicine, San Diego, CA, 92123, USA
- Rady Children's Hospital, San Diego, CA, 92123, USA
| | - Katarzyna Ellsworth
- Rady Children's Institute for Genomic Medicine, San Diego, CA, 92123, USA
- Rady Children's Hospital, San Diego, CA, 92123, USA
| | - Lucia Guidugli
- Rady Children's Institute for Genomic Medicine, San Diego, CA, 92123, USA
- Rady Children's Hospital, San Diego, CA, 92123, USA
| | | | | | | | - Kevin K Chau
- Rady Children's Institute for Genomic Medicine, San Diego, CA, 92123, USA
- Rady Children's Hospital, San Diego, CA, 92123, USA
| | - Yong H Kwon
- Rady Children's Institute for Genomic Medicine, San Diego, CA, 92123, USA
- Rady Children's Hospital, San Diego, CA, 92123, USA
| | - Zhanyang Zhu
- Rady Children's Institute for Genomic Medicine, San Diego, CA, 92123, USA
- Rady Children's Hospital, San Diego, CA, 92123, USA
| | - Sergey Batalov
- Rady Children's Institute for Genomic Medicine, San Diego, CA, 92123, USA
- Rady Children's Hospital, San Diego, CA, 92123, USA
| | - Shimul Chowdhury
- Rady Children's Institute for Genomic Medicine, San Diego, CA, 92123, USA
- Rady Children's Hospital, San Diego, CA, 92123, USA
- Keck Graduate Institute, Claremont, CA, 91711, USA
| | - Seema Rego
- Rady Children's Institute for Genomic Medicine, San Diego, CA, 92123, USA
- Rady Children's Hospital, San Diego, CA, 92123, USA
| | - James Perry
- Rady Children's Hospital, San Diego, CA, 92123, USA
- Department of Pediatrics, University of California San Diego, San Diego, CA, 92093, USA
| | - Mark Speziale
- Rady Children's Hospital, San Diego, CA, 92123, USA
- Department of Pediatrics, University of California San Diego, San Diego, CA, 92093, USA
| | - Mark Nespeca
- Rady Children's Hospital, San Diego, CA, 92123, USA
- Department of Pediatrics, University of California San Diego, San Diego, CA, 92093, USA
- Department of Neuroscience, University of California San Diego, San Diego, CA, 92093, USA
| | - Meredith S Wright
- Rady Children's Institute for Genomic Medicine, San Diego, CA, 92123, USA
- Rady Children's Hospital, San Diego, CA, 92123, USA
- Keck Graduate Institute, Claremont, CA, 91711, USA
| | | | | | - Joe Azure
- Fabric Genomics, Inc., Oakland, CA, 94612, USA
| | - Erwin Frise
- Fabric Genomics, Inc., Oakland, CA, 94612, USA
| | | | - Sandy White
- Fabric Genomics, Inc., Oakland, CA, 94612, USA
| | - Charlotte A Hobbs
- Rady Children's Institute for Genomic Medicine, San Diego, CA, 92123, USA
- Rady Children's Hospital, San Diego, CA, 92123, USA
- Department of Pediatrics, University of California San Diego, San Diego, CA, 92093, USA
| | | | - Gail Knight
- Rady Children's Hospital, San Diego, CA, 92123, USA
- Department of Pediatrics, University of California San Diego, San Diego, CA, 92093, USA
| | - Albert Oriol
- Rady Children's Institute for Genomic Medicine, San Diego, CA, 92123, USA
- Rady Children's Hospital, San Diego, CA, 92123, USA
| | - Jerica Lenberg
- Rady Children's Institute for Genomic Medicine, San Diego, CA, 92123, USA
- Rady Children's Hospital, San Diego, CA, 92123, USA
- Keck Graduate Institute, Claremont, CA, 91711, USA
| | - Shareef A Nahas
- Rady Children's Institute for Genomic Medicine, San Diego, CA, 92123, USA
- Rady Children's Hospital, San Diego, CA, 92123, USA
| | - Kate Perofsky
- Rady Children's Institute for Genomic Medicine, San Diego, CA, 92123, USA
- Rady Children's Hospital, San Diego, CA, 92123, USA
- Department of Pediatrics, University of California San Diego, San Diego, CA, 92093, USA
| | - Kyu Kim
- Rady Children's Institute for Genomic Medicine, San Diego, CA, 92123, USA
- Rady Children's Hospital, San Diego, CA, 92123, USA
- Department of Pediatrics, University of California San Diego, San Diego, CA, 92093, USA
| | - Jeanne Carroll
- Rady Children's Institute for Genomic Medicine, San Diego, CA, 92123, USA
- Rady Children's Hospital, San Diego, CA, 92123, USA
- Department of Pediatrics, University of California San Diego, San Diego, CA, 92093, USA
| | - Nicole G Coufal
- Rady Children's Institute for Genomic Medicine, San Diego, CA, 92123, USA
- Rady Children's Hospital, San Diego, CA, 92123, USA
- Department of Pediatrics, University of California San Diego, San Diego, CA, 92093, USA
| | - Erica Sanford
- Rady Children's Institute for Genomic Medicine, San Diego, CA, 92123, USA
| | - Kristen Wigby
- Rady Children's Institute for Genomic Medicine, San Diego, CA, 92123, USA
- Rady Children's Hospital, San Diego, CA, 92123, USA
- Department of Pediatrics, University of California San Diego, San Diego, CA, 92093, USA
| | | | | | | | | | | | | | | | | | - Duke Tran
- Illumina, Inc., San Diego, CA, 92122, USA
| | | | | | - Anne Case
- Illumina, Inc., San Diego, CA, 92122, USA
| | - Marisa Lue
- Illumina, Inc., San Diego, CA, 92122, USA
| | | | - John Reynders
- Alexion Pharmaceuticals, Inc., Boston, MA, 02210, USA
| | - Thomas Defay
- Alexion Pharmaceuticals, Inc., Boston, MA, 02210, USA
| | | | - Narayanan Veeraraghavan
- Rady Children's Institute for Genomic Medicine, San Diego, CA, 92123, USA
- Rady Children's Hospital, San Diego, CA, 92123, USA
| | - Stephen F Kingsmore
- Rady Children's Institute for Genomic Medicine, San Diego, CA, 92123, USA.
- Rady Children's Hospital, San Diego, CA, 92123, USA.
- Keck Graduate Institute, Claremont, CA, 91711, USA.
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McDermott H, Sherlaw-Sturrock C, Baptista J, Hartles-Spencer L, Naik S. Rapid exome sequencing in critically ill children impacts acute and long-term management of patients and their families: A retrospective regional evaluation. Eur J Med Genet 2022; 65:104571. [PMID: 35842091 DOI: 10.1016/j.ejmg.2022.104571] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 05/12/2022] [Accepted: 07/10/2022] [Indexed: 11/03/2022]
Abstract
INTRODUCTION Genetic disorders are a significant cause of paediatric morbidity and mortality. Rapid exome sequencing was introduced by the National Health Service (NHS) in England on 1st October 2019 for acutely unwell children with a likely monogenic disorder, or to inform current pregnancy management where there was a previously affected child or fetus. We present results of a 12-month patient cohort from one large clinical genetics centre in England. METHODS Patients were identified through local genetics laboratory records. We included all cases which underwent rapid exome sequencing between 1st October 2020 and 30th September 2021. DNA was extracted, quality checked and exported to the Exeter Genomic laboratory where library preparation, exome sequencing of all known human genes, gene-agnostic bioinformatic analysis, variant interpretation, MDT discussions and reporting were performed. RESULTS Ninety-five probands were included. Trio analysis was performed in 90% (85), duo in 8% (8), singleton in 2% (2). The median turnaround time for preliminary reports was 11 days. The overall diagnostic yield was 40% (38 patients); 36% (34 patients) made solely on exome with a further 4% on concomitant exome and microarray analysis. Highest diagnostic rates were seen in patients with neuro-regression, skeletal dysplasia, neuromuscular and neurometabolic conditions. Where the diagnosis was made solely through exome sequencing, management was altered for the proband or family in 97% (33/34). For the proband, this was most commonly that the diagnosis was able to inform current management and prognosis (20 patients, 59%), as well as direct specialist referrals (10 patients, 29%). For families, the exome sequencing results provided accurate recurrence risk counselling in 88% (30/34) with cascade testing offered if indicated in some families. CONCLUSIONS In the majority of cases, the genetic diagnoses influenced acute and long-term management for critically ill children and their families. Paediatric and neonatal clinicians in the NHS now have direct access to exome sequencing for their patients. The rapid turnaround time was particularly helpful to alter the management in acute clinical settings and is a powerful tool for diagnosing monogenic conditions. This study is an example of a highly successful integration of a national rapid exome sequencing service with diagnostic rates comparable to previously reported literature.
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Affiliation(s)
- Helen McDermott
- West Midlands Regional Genetics Service, Birmingham Women's and Children's NHS Foundation Trust, Birmingham, UK
| | - Charlotte Sherlaw-Sturrock
- West Midlands Regional Genetics Service, Birmingham Women's and Children's NHS Foundation Trust, Birmingham, UK.
| | - Julia Baptista
- Exeter Genomics Laboratory, Royal Devon and Exeter NHS Foundation Trust, UK; Peninsula Medical School, Faculty of Health, University of Plymouth, UK
| | | | - Swati Naik
- West Midlands Regional Genetics Service, Birmingham Women's and Children's NHS Foundation Trust, Birmingham, UK
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Diaby V, Babcock A, Huang Y, Moussa RK, Espinal PS, Janvier M, Soler D, Gupta A, Jayakar P, Diaz-Barbosa M, Totapally B, Sasaki J, Jayakar A, Salyakina D. Real-world economic evaluation of prospective rapid whole-genome sequencing compared to a matched retrospective cohort of critically ill pediatric patients in the United States. THE PHARMACOGENOMICS JOURNAL 2022; 22:223-229. [PMID: 35436997 DOI: 10.1038/s41397-022-00277-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Revised: 03/03/2022] [Accepted: 03/17/2022] [Indexed: 02/04/2023]
Abstract
There is an increasing demand for supporting the adoption of rapid whole-genome sequencing (rWGS) by demonstrating its real-world value. We aimed to assess the cost-effectiveness of rWGS in critically ill pediatric patients with diseases of unknown cause. Data were collected prospectively of patients admitted to the Nicklaus Children's Hospital's intensive care units from March 2018 to September 2020, with rWGS (N = 65). Comparative data were collected in a matched retrospective cohort with standard diagnostic genetic testing. We determined total costs, diagnostic yield (DY), and incremental cost-effectiveness ratio (ICER) adjusted for selection bias and right censoring. Sensitivity analyses explored the robustness of ICER through bootstrapping. rWGS resulted in a diagnosis in 39.8% while standard testing in 13.5% (p = 0.026). rWGS resulted in a mean saving per person of $100,440 (SE = 26,497, p < 0.001) and a total of $6.53 M for 65 patients. rWGS in critically ill pediatric patients is cost-effective, cost-saving, shortens diagnostic odyssey, and triples the DY of traditional approaches.
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Affiliation(s)
- Vakaramoko Diaby
- Department of Pharmaceutical Outcomes and Policy (POP), College of Pharmacy, HPNP 3317, University of Florida 1225 Center Drive, Gainesville, FL, 32610, USA.
| | - Aram Babcock
- Department of Pharmaceutical Outcomes and Policy (POP), College of Pharmacy, HPNP 2309, University of Florida 1225 Center Drive Gainesville, Gainesville, FL, 32610, USA
| | - Yushi Huang
- Department of Pharmaceutical Outcomes and Policy (POP), College of Pharmacy, HPNP 2309, University of Florida 1225 Center Drive Gainesville, Gainesville, FL, 32610, USA
| | - Richard K Moussa
- Ecole Nationale Supérieure de Statistiques et d'Economie Appliquée (ENSEA), Côte d'Ivoire 08 BP 03, Abidjan, 08, Côte d'Ivoire
| | - Paula S Espinal
- Personalized Medicine and Health Outcomes Research, Nicklaus Children's Hospital, 3100 SW 62nd Ave, Miami, FL, 33155, USA
| | - Michelin Janvier
- Personalized Medicine and Health Outcomes Research, Nicklaus Children's Hospital, 3100 SW 62nd Ave, Miami, FL, 33155, USA
| | - Diana Soler
- Personalized Medicine and Health Outcomes Research, Nicklaus Children's Hospital, 3100 SW 62nd Ave, Miami, FL, 33155, USA
| | - Apeksha Gupta
- Personalized Medicine and Health Outcomes Research, Nicklaus Children's Hospital, 3100 SW 62nd Ave, Miami, FL, 33155, USA
| | - Parul Jayakar
- Division of Genetics and Metabolism, Nicklaus Children's Hospital, 3100 SW 62nd Ave, Miami, FL, 33155, USA
| | - Magaly Diaz-Barbosa
- Department of Pediatrics, Herbert Wertheim College of Medicine, Florida International University, 11200 SW 8th St, Miami, FL, 33199, USA.,Nicklaus Children's Hospital Miami, 3100 SW 62nd Ave, Miami, FL, 33155, USA
| | - Balagangadhar Totapally
- Division of Critical Care Medicine, Nicklaus Children's Hospital, 3100 SW, 62nd Avenue, Miami, FL, 33155, USA.,Herbert Wertheim College of Medicine, Florida International University, 11200 SW 8th St, Miami, FL, 33199, USA
| | - Jun Sasaki
- Nicklaus Children's Hospital Miami, 3100 SW 62nd Ave, Miami, FL, 33155, USA.,Department of Cardiology, Herbert Wertheim College of Medicine, Florida International University, 11200 SW 8th St, Miami, FL, 33199, USA
| | - Anuj Jayakar
- Neurocritical Care & Department of Neurology, Division of Epilepsy, Nicklaus Children's Hospital, 3100 SW, 62nd Avenue, Miami, FL, 33155, USA
| | - Daria Salyakina
- Personalized Medicine and Health Outcomes Research, Nicklaus Children's Hospital, 3100 SW 62nd Ave, Miami, FL, 33155, USA
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49
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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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50
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Lumaka A, Carstens N, Devriendt K, Krause A, Kulohoma B, Kumuthini J, Mubungu G, Mukisa J, Nel M, Olanrewaju TO, Lombard Z, Landouré G. Increasing African genomic data generation and sharing to resolve rare and undiagnosed diseases in Africa: a call-to-action by the H3Africa rare diseases working group. Orphanet J Rare Dis 2022; 17:230. [PMID: 35710439 PMCID: PMC9201791 DOI: 10.1186/s13023-022-02391-w] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Accepted: 06/06/2022] [Indexed: 11/10/2022] Open
Abstract
The rich and diverse genomics of African populations is significantly underrepresented in reference and in disease-associated databases. This renders interpreting the Next Generation Sequencing (NGS) data and reaching a diagnostic more difficult in Africa and for the African diaspora. It increases chances for false positives with variants being misclassified as pathogenic due to their novelty or rarity. We can increase African genomic data by (1) making consent for sharing aggregate frequency data an essential component of research toolkit; (2) encouraging investigators with African data to share available data through public resources such as gnomAD, AVGD, ClinVar, DECIPHER and to use MatchMaker Exchange; (3) educating African research participants on the meaning and value of sharing aggregate frequency data; and (4) increasing funding to scale-up the production of African genomic data that will be more representative of the geographical and ethno-linguistic variation on the continent. The RDWG of H3Africa is hereby calling to action because this underrepresentation accentuates the health disparities. Applying the NGS to shorten the diagnostic odyssey or to guide therapeutic options for rare diseases will fully work for Africans only when public repositories include sufficient data from African subjects.
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Affiliation(s)
- Aimé Lumaka
- Department of Pediatrics, Faculty of Medicine, Centre for Human Genetics, University of Kinshasa, Kinshasa, Congo. .,Laboratoire de Génétique Humaine, GIGA-Research Institute, University of Liège, Bât. B34 +2, Sart Tilman, Avenue de l'Hôpital 13, 4000, Liège, Belgium.
| | - Nadia Carstens
- Division of Human Genetics, National Health Laboratory Service, and School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Koenraad Devriendt
- Centre for Human Genetics, University Hospital, University of Leuven, Leuven, Belgium
| | - Amanda Krause
- Division of Human Genetics, National Health Laboratory Service, and School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Benard Kulohoma
- Centre for Biotechnology and Bioinformatics, University of Nairobi, Nairobi, Kenya.,ADVANCE, IAVI, Nairobi, Kenya
| | - Judit Kumuthini
- South African National Bioinformatics Institute (SANBI), University of Western Cape (UWC), Robert Sobukwe Road Bellville, Cape Town, 7535, Republic of South Africa
| | - Gerrye Mubungu
- Department of Pediatrics, Faculty of Medicine, Centre for Human Genetics, University of Kinshasa, Kinshasa, Congo.,Centre for Human Genetics, University Hospital, University of Leuven, Leuven, Belgium
| | - John Mukisa
- Department of Immunology and Molecular Biology, Makerere University College of Health Sciences, Third Floor, Pathology & Microbiology building Upper Mulago Hill, P.O.Box 7072, Kampala, Uganda
| | - Melissa Nel
- Neurology Research Group, Neuroscience Institute, University of Cape Town, Cape Town, 7925, South Africa
| | - Timothy O Olanrewaju
- Division of Nephrology, Department of Medicine, University of Ilorin and University of Ilorin Teaching Hospital, Tanke Road, PMB 1515, Ilorin, Kwara State, Nigeria.,Julius Global Health, Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Zané Lombard
- Division of Human Genetics, National Health Laboratory Service, and School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Guida Landouré
- Faculté de Médecine Et d'Odontostomatologie, USTTB, Bamako, Mali.,Service de Neurologie, Centre Hospitalier Universitaire du Point G, Bamako, Mali
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