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Basu AP, Low K, Ratnaike T, Rowitch D. Genetic investigations in cerebral palsy. Dev Med Child Neurol 2024. [PMID: 39208295 DOI: 10.1111/dmcn.16080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/08/2024] [Revised: 07/23/2024] [Accepted: 07/29/2024] [Indexed: 09/04/2024]
Abstract
The original description of cerebral palsy (CP) contained case histories suggesting that perinatal environmental stressors resulted in brain injury and neurodevelopmental disability. While there are clear associations between environmental impact on brain development and CP, recent studies indicate an 11% to 40% incidence of monogenic conditions in patients given a diagnosis of CP. A genetic diagnosis supports the delivery of personalized medicine. In this review, we describe how the Wnt pathway exemplifies our understanding of pathophysiology related to a gene variant (CTNNB1) found in some children diagnosed with CP. We cover studies undertaken to establish the baseline prevalence of monogenic conditions in populations attending CP clinics. We list factors indicating increased likelihood of a genomic diagnosis; and we highlight the need for a comprehensive, accurate, genotype-phenotype reference data set to aid variant interpretation in CP cohorts. We also consider the wider societal implications of genomic management of CP including significance of the diagnostic label, benefits and pitfalls of a genetic diagnosis, logistics, and cost.
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Affiliation(s)
- Anna P Basu
- Population Health Sciences Institute, Newcastle University, Newcastle upon Tyne, UK
- Paediatric Neurology, Great North Children's Hospital, Newcastle upon Tyne, UK
| | - Karen Low
- Centre for Academic Child Health, University of Bristol, Bristol, UK
- Department of Clinical Genetics, University Hospitals Bristol and Weston NHS Trust, Bristol, UK
| | - Thiloka Ratnaike
- Department of Paediatrics, University of Cambridge, Cambridge, UK
- Paediatrics, Colchester Hospital, East Suffolk and North Essex NHS Foundation Trust, Colchester, UK
| | - David Rowitch
- Department of Paediatrics, University of Cambridge, Cambridge, UK
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2
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McCorkell G, Nisselle A, Halton D, Bouffler SE, Patel C, Christodoulou J, Maher F, McClaren B, Brett GR, Sandaradura S, Boggs K, de Silva MG, Lynch F, Macciocca I, Lynch E, Martyn M, Best S, Stark Z, Gaff CL. A national education program for rapid genomics in pediatric acute care: Building workforce confidence, competence, and capability. Genet Med 2024; 26:101224. [PMID: 39092589 DOI: 10.1016/j.gim.2024.101224] [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: 01/01/2024] [Revised: 07/23/2024] [Accepted: 07/24/2024] [Indexed: 08/04/2024] Open
Abstract
PURPOSE To develop and evaluate a scalable national program to build confidence, competence and capability in the use of rapid genomic testing (rGT) in the acute pediatric setting. METHODS We used theory-informed approaches to design a modular, adaptive program of blended learning aimed at diverse professional groups involved in acute pediatric care. The program comprised 4 online learning modules and an online workshop and was centered on case-based learning. We evaluated the program using the Kirkpatrick 4-level model of training evaluation and report our findings using the Reporting Item Standards for Education and its Evaluation (RISE2) guidelines for genomics education and evaluation. RESULTS Two hundred and two participants engaged with at least 1 component of the program. Participants self-reported increased confidence in using rGT, (P < .001), and quiz responses objectively demonstrated increased competence (eg, correct responses to a question on pretest counseling increased from 30% to 64%; P < .001). Additionally, their capability in applying genomic principles to simulated clinical cases increased (P < .001), as did their desire to take on more responsibility for performing rGT. The clinical interpretation of more complex test results (such as negative results or variants of uncertain significance) appeared to be more challenging, indicating a need for targeted education in this area. CONCLUSION The program format was effective in delivering multidisciplinary and wide-scale genomics education in the acute care context. The modular approach we have developed now lends itself to application in other medical specialties or areas of health care.
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Affiliation(s)
- Giulia McCorkell
- Australian Genomics, Melbourne, Australia; The University of Melbourne, Melbourne, Australia; Royal Melbourne Institute of Technology, Melbourne, Australia; Murdoch Children's Research Institute, Melbourne, Australia
| | - Amy Nisselle
- The University of Melbourne, Melbourne, Australia; Murdoch Children's Research Institute, Melbourne, Australia; Melbourne Genomics Health Alliance, Melbourne, Australia
| | - Donna Halton
- Australian Genomics, Melbourne, Australia; The University of Melbourne, Melbourne, Australia; Melbourne Genomics Health Alliance, Melbourne, Australia
| | - Sophie E Bouffler
- Australian Genomics, Melbourne, Australia; Murdoch Children's Research Institute, Melbourne, Australia
| | - Chirag Patel
- Genetic Health Queensland, Royal Brisbane and Women's Hospital, Brisbane, Australia
| | - John Christodoulou
- The University of Melbourne, Melbourne, Australia; Murdoch Children's Research Institute, Melbourne, Australia
| | - Fran Maher
- The University of Melbourne, Melbourne, Australia; Murdoch Children's Research Institute, Melbourne, Australia; Melbourne Genomics Health Alliance, Melbourne, Australia; WEHI, Melbourne, Australia
| | - Belinda McClaren
- The University of Melbourne, Melbourne, Australia; Murdoch Children's Research Institute, Melbourne, Australia; Melbourne Genomics Health Alliance, Melbourne, Australia
| | - Gemma R Brett
- The University of Melbourne, Melbourne, Australia; Victorian Clinical Genetics Services, Melbourne, Australia
| | - Sarah Sandaradura
- Sydney Children's Hospitals Network-Westmead, Sydney, Australia; University of Sydney, Sydney, Australia
| | - Kirsten Boggs
- Australian Genomics, Melbourne, Australia; Sydney Children's Hospitals Network-Westmead, Sydney, Australia; Sydney Children's Hospitals Network-Randwick, Sydney, Australia
| | - Michelle G de Silva
- The University of Melbourne, Melbourne, Australia; Murdoch Children's Research Institute, Melbourne, Australia; Victorian Clinical Genetics Services, Melbourne, Australia
| | - Fiona Lynch
- The University of Melbourne, Melbourne, Australia; Murdoch Children's Research Institute, Melbourne, Australia
| | - Ivan Macciocca
- The University of Melbourne, Melbourne, Australia; Victorian Clinical Genetics Services, Melbourne, Australia
| | - Elly Lynch
- Melbourne Genomics Health Alliance, Melbourne, Australia; Victorian Clinical Genetics Services, Melbourne, Australia
| | - Melissa Martyn
- The University of Melbourne, Melbourne, Australia; Murdoch Children's Research Institute, Melbourne, Australia; Melbourne Genomics Health Alliance, Melbourne, Australia
| | - Stephanie Best
- Australian Genomics, Melbourne, Australia; Department of Health Services Research, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Zornitza Stark
- Australian Genomics, Melbourne, Australia; The University of Melbourne, Melbourne, Australia; Victorian Clinical Genetics Services, Melbourne, Australia.
| | - Clara L Gaff
- The University of Melbourne, Melbourne, Australia; Murdoch Children's Research Institute, Melbourne, Australia; Melbourne Genomics Health Alliance, Melbourne, Australia
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3
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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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4
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Durbin MD, Helvaty LR, Posorske A, Zhang S, Huang M, Li M, Abreu D, Fairman K, Geddes GC, Helm BM, Landis BJ, McEntire A, Mitchell DK, Ware SM. Rapid Genome Sequencing Shows Diagnostic Utility In Infants With Congenital Heart Defects. RESEARCH SQUARE 2024:rs.3.rs-3976548. [PMID: 38562732 PMCID: PMC10984023 DOI: 10.21203/rs.3.rs-3976548/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Congenital heart disease (CHD) is the most common birth defect and a leading cause of infant mortality. CHD often has a genetic etiology and recent studies demonstrate utility in genetic testing. In clinical practice, decisions around genetic testing choices continue to evolve, and the incorporation of rapid genome sequencing (rGS) in CHD has not been well studied. Though smaller studies demonstrate the value of rGS, they also highlight the burden of results interpretation. We analyze genetic testing in CHD at two time-points, in 2018 and 2022-2023, across a change in clinical testing guidelines from chromosome microarray (CMA) to rGS. Analysis of 421 hospitalized infants with CHD demonstrated consistent genetic testing across time. Overall, after incorporation of rGS in 2022-2023, the diagnostic yield was 6.8% higher compared to 2018, and this pattern was consistent across all patient subtypes analyzed. In 2018, CMA was the most common test performed, with diagnostic results for CHD in 14.3%, while in 2022-2023, rGS was the most frequent test performed, with results diagnostic for CHD in 16.9%. Additionally, rGS identified 44% more unique genetic diagnoses than CMA. This is the largest study to highlight the value of rGS in CHD and has important implications for management.
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Affiliation(s)
- Matthew D Durbin
- Indiana University School of Medicine, Indianapolis, IN
- Herman B Wells Center for Pediatric Research, Indianapolis, IN
| | | | - Alyx Posorske
- Indiana University School of Medicine, Indianapolis, IN
| | - Samuel Zhang
- Indiana University School of Medicine, Indianapolis, IN
| | - Manyan Huang
- Indiana University Bloomington School of Public Health, Bloomington, IN
| | - Ming Li
- Indiana University Bloomington School of Public Health, Bloomington, IN
| | - Daniel Abreu
- Indiana University School of Medicine, Indianapolis, IN
| | | | | | | | - Benjamin J Landis
- Indiana University School of Medicine, Indianapolis, IN
- Herman B Wells Center for Pediatric Research, Indianapolis, IN
| | | | | | - Stephanie M Ware
- Indiana University School of Medicine, Indianapolis, IN
- Herman B Wells Center for Pediatric Research, Indianapolis, IN
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5
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Tran A, Wang A, Mickaill J, Strbenac D, Larance M, Vernon ST, Grieve SM, Figtree GA, Patrick E, Yang JYH. Construction and optimization of multi-platform precision pathways for precision medicine. Sci Rep 2024; 14:4248. [PMID: 38378802 PMCID: PMC10879206 DOI: 10.1038/s41598-024-54517-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Accepted: 02/13/2024] [Indexed: 02/22/2024] Open
Abstract
In the enduring challenge against disease, advancements in medical technology have empowered clinicians with novel diagnostic platforms. Whilst in some cases, a single test may provide a confident diagnosis, often additional tests are required. However, to strike a balance between diagnostic accuracy and cost-effectiveness, one must rigorously construct the clinical pathways. Here, we developed a framework to build multi-platform precision pathways in an automated, unbiased way, recommending the key steps a clinician would take to reach a diagnosis. We achieve this by developing a confidence score, used to simulate a clinical scenario, where at each stage, either a confident diagnosis is made, or another test is performed. Our framework provides a range of tools to interpret, visualize and compare the pathways, improving communication and enabling their evaluation on accuracy and cost, specific to different contexts. This framework will guide the development of novel diagnostic pathways for different diseases, accelerating the implementation of precision medicine into clinical practice.
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Affiliation(s)
- Andy Tran
- School of Mathematics and Statistics, The University of Sydney, Camperdown, NSW, Australia
- Charles Perkins Centre, The University of Sydney, Camperdown, NSW, Australia
- Sydney Precision Data Science Centre, The University of Sydney, Camperdown, NSW, Australia
| | - Andy Wang
- Westmead Medical Institute, Westmead, NSW, Australia
| | - Jamie Mickaill
- School of Mathematics and Statistics, The University of Sydney, Camperdown, NSW, Australia
- School of Computer Science, The University of Sydney, Camperdown, NSW, Australia
| | - Dario Strbenac
- School of Mathematics and Statistics, The University of Sydney, Camperdown, NSW, Australia
- Charles Perkins Centre, The University of Sydney, Camperdown, NSW, Australia
- Sydney Precision Data Science Centre, The University of Sydney, Camperdown, NSW, Australia
| | - Mark Larance
- Charles Perkins Centre, The University of Sydney, Camperdown, NSW, Australia
| | - Stephen T Vernon
- Charles Perkins Centre, The University of Sydney, Camperdown, NSW, Australia
- Kolling Institute of Medical Research, St Leonards, NSW, Australia
| | - Stuart M Grieve
- Charles Perkins Centre, The University of Sydney, Camperdown, NSW, Australia
- Department of Radiology, Royal Prince Alfred Hospital, Camperdown, Australia
| | - Gemma A Figtree
- Charles Perkins Centre, The University of Sydney, Camperdown, NSW, Australia
- Kolling Institute of Medical Research, St Leonards, NSW, Australia
| | - Ellis Patrick
- School of Mathematics and Statistics, The University of Sydney, Camperdown, NSW, Australia
- Charles Perkins Centre, The University of Sydney, Camperdown, NSW, Australia
- Sydney Precision Data Science Centre, The University of Sydney, Camperdown, NSW, Australia
- Laboratory of Data Discovery for Health Limited (D24H), Science Park, Hong Kong SAR, China
| | - Jean Yee Hwa Yang
- School of Mathematics and Statistics, The University of Sydney, Camperdown, NSW, Australia.
- Charles Perkins Centre, The University of Sydney, Camperdown, NSW, Australia.
- Sydney Precision Data Science Centre, The University of Sydney, Camperdown, NSW, Australia.
- Laboratory of Data Discovery for Health Limited (D24H), Science Park, Hong Kong SAR, China.
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6
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Marom D, Mory A, Reytan-Miron S, Amir Y, Kurolap A, Cohen JG, Morhi Y, Smolkin T, Cohen L, Zangen S, Shalata A, Riskin A, Peleg A, Lavie-Nevo K, Mandel D, Chervinsky E, Fisch CF, Fleisher Sheffer V, Falik-Zaccai TC, Rips J, Shlomai NO, Friedman SE, Shporen CH, Ben-Yehoshua SJ, Simmonds A, Yaacobi RG, Bauer-Rusek S, Omari H, Weiss K, Hochwald O, Koifman A, Globus O, Batzir NA, Yaron N, Segel R, Morag I, Reish O, Eliyahu A, Leibovitch L, Schwartz ME, Abramsky R, Hochberg A, Oron A, Banne E, Portnov I, Samra NN, Singer A, Baris Feldman H. National Rapid Genome Sequencing in Neonatal Intensive Care. JAMA Netw Open 2024; 7:e240146. [PMID: 38386321 PMCID: PMC10884880 DOI: 10.1001/jamanetworkopen.2024.0146] [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: 02/23/2024] Open
Abstract
Importance National implementation of rapid trio genome sequencing (rtGS) in a clinical acute setting is essential to ensure advanced and equitable care for ill neonates. Objective To evaluate the feasibility, diagnostic efficacy, and clinical utility of rtGS in neonatal intensive care units (NICUs) throughout Israel. Design, Setting, and Participants This prospective, public health care-based, multicenter cohort study was conducted from October 2021 to December 2022 with the Community Genetics Department of the Israeli Ministry of Health and all Israeli medical genetics institutes (n = 18) and NICUs (n = 25). Critically ill neonates suspected of having a genetic etiology were offered rtGS. All sequencing, analysis, and interpretation of data were performed in a central genomics center at Tel-Aviv Sourasky Medical Center. Rapid results were expected within 10 days. A secondary analysis report, issued within 60 days, focused mainly on cases with negative rapid results and actionable secondary findings. Pathogenic, likely pathogenic, and highly suspected variants of unknown significance (VUS) were reported. Main Outcomes and Measures Diagnostic rate, including highly suspected disease-causing VUS, and turnaround time for rapid results. Clinical utility was assessed via questionnaires circulated to treating neonatologists. Results A total of 130 neonates across Israel (70 [54%] male; 60 [46%] female) met inclusion criteria and were recruited. Mean (SD) age at enrollment was 12 (13) days. Mean (SD) turnaround time for rapid report was 7 (3) days. Diagnostic efficacy was 50% (65 of 130) for disease-causing variants, 11% (14 of 130) for VUS suspected to be causative, and 1 novel gene candidate (1%). Disease-causing variants included 12 chromosomal and 52 monogenic disorders as well as 1 neonate with uniparental disomy. Overall, the response rate for clinical utility questionnaires was 82% (107 of 130). Among respondents, genomic testing led to a change in medical management for 24 neonates (22%). Results led to immediate precision medicine for 6 of 65 diagnosed infants (9%), an additional 2 (3%) received palliative care, and 2 (3%) were transferred to nursing homes. Conclusions and Relevance In this national cohort study, rtGS in critically ill neonates was feasible and diagnostically beneficial in a public health care setting. This study is a prerequisite for implementation of rtGS for ill neonates into routine care and may aid in design of similar studies in other public health care systems.
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Affiliation(s)
- Daphna Marom
- The Genetics Institute and Genomics Center, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel
- Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Adi Mory
- The Genetics Institute and Genomics Center, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel
| | - Sivan Reytan-Miron
- The Genetics Institute and Genomics Center, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel
| | - Yam Amir
- The Genetics Institute and Genomics Center, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel
- Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Alina Kurolap
- The Genetics Institute and Genomics Center, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel
| | - Julia Grinshpun Cohen
- Community Genetics Department, Public Health Services, Ministry of Health, Ramat Gan, Israel
| | - Yocheved Morhi
- Ruth and Bruce Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
| | - Tatiana Smolkin
- Department of Neonatalogy, Baruch Padeh Medical Center, Tzafon Medical Center, Tiberias, Israel
- Azrieli Faculty of Medicine, Bar Ilan University, Ramat Gan, Israel
| | - Lior Cohen
- Genetics Unit, Barzilai University Medical Center, Ashkelon, Israel
- Faculty of Health Sciences, Ben-Gurion University of the Negev, Be'er-Sheva, Israel
| | - Shmuel Zangen
- Faculty of Health Sciences, Ben-Gurion University of the Negev, Be'er-Sheva, Israel
- Department of Neonatalogy, Barzilai University Medical Center, Ashkelon, Israel
| | - Adel Shalata
- Ruth and Bruce Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
- Genetics Institute, Bnai Zion Medical Center, Haifa, Israel
| | - Arieh Riskin
- Ruth and Bruce Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
- Department of Neonatalogy, Bnai Zion Medical Center, Haifa, Israel
| | - Amir Peleg
- Ruth and Bruce Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
- Genetics Institute, Carmel Medical Center, Haifa, Israel
| | - Karen Lavie-Nevo
- Ruth and Bruce Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
- Department of Neonatalogy, Carmel Medical Center, Haifa, Israel
| | - Dror Mandel
- Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- Department of Neonatalogy, Dana-Dwek Children's Hospital, Tel Aviv Medical Center, Tel Aviv, Israel
| | - Elana Chervinsky
- Ruth and Bruce Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
- The Genetics Institute and Center of Rare Diseases, Emek Medical Center, Afula, Israel
| | - Clari Felszer Fisch
- Ruth and Bruce Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
- Department of Neonatalogy, Emek Medical Center, Afula, Israel
| | - Vered Fleisher Sheffer
- Azrieli Faculty of Medicine, Bar Ilan University, Ramat Gan, Israel
- Department of Neonatalogy, Galilee Medical Center, Naharia, Israel
| | - Tzipora C Falik-Zaccai
- Azrieli Faculty of Medicine, Bar Ilan University, Ramat Gan, Israel
- Genetics Institute, Galilee Medical Center, Naharia, Israel
| | - Jonathan Rips
- Department of Genetics, Hadassah Medical Organization, Jerusalem, Israel
- Faculty of Medicine, The Hebrew University of Jerusalem, Ein Kerem, Jerusalem, Israel
| | - Noa Ofek Shlomai
- Faculty of Medicine, The Hebrew University of Jerusalem, Ein Kerem, Jerusalem, Israel
- Department of Neonatalogy, Hadassah Medical Organization, Jerusalem, Israel
| | - Smadar Eventov Friedman
- Faculty of Medicine, The Hebrew University of Jerusalem, Ein Kerem, Jerusalem, Israel
- Department of Neonatalogy, Hadassah Medical Organization, Jerusalem, Israel
| | - Calanit Hershkovich Shporen
- Faculty of Medicine, The Hebrew University of Jerusalem, Ein Kerem, Jerusalem, Israel
- Department of Neonatalogy, Kaplan Medical Center, Rehovot, Israel
| | - Sagie Josefsberg Ben-Yehoshua
- Faculty of Medicine, The Hebrew University of Jerusalem, Ein Kerem, Jerusalem, Israel
- Genetics Institute, Kaplan Medical Center, Rehovot, Israel
| | - Aryeh Simmonds
- Department of Neonatalogy, Laniado Hospital, Netanya, Israel
- Adelson School of Medicine, Ariel University, Ariel, Israel
| | - Racheli Goldfarb Yaacobi
- Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- Genetics Institute, Meir Medical Center, Kefar-Sava, Israel
| | - Sofia Bauer-Rusek
- Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- Department of Neonatalogy, Meir Medical Center, Kefar-Sava, Israel
| | - Hussam Omari
- Azrieli Faculty of Medicine, Bar Ilan University, Ramat Gan, Israel
- Department of Neonatalogy, Saint Vincent Hospital (French Hospital), Nazareth, Israel
| | - Karin Weiss
- Ruth and Bruce Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
- Genetics Institute, Rambam Medical Center, Haifa, Israel
| | - Ori Hochwald
- Ruth and Bruce Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
- Department of Neonatalogy, Rambam Medical Center, Haifa, Israel
| | - Arie Koifman
- Faculty of Health Sciences, Ben-Gurion University of the Negev, Be'er-Sheva, Israel
- Genetics Institute, Samson Assuta University Medical Center, Ashdod, Israel
| | - Omer Globus
- Faculty of Health Sciences, Ben-Gurion University of the Negev, Be'er-Sheva, Israel
- Department of Neonatalogy, Samson Assuta University Medical Center, Ashdod, Israel
| | - Nurit Assia Batzir
- Pediatric Genetics Unit, Schneider Children's Medical Center of Israel, Petach Tikva, Israel
| | - Naveh Yaron
- Faculty of Medicine, The Hebrew University of Jerusalem, Ein Kerem, Jerusalem, Israel
- Department of Neonatalogy, Shaare Zedek Medical Center, Jerusalem, Israel
| | - Reeval Segel
- Faculty of Medicine, The Hebrew University of Jerusalem, Ein Kerem, Jerusalem, Israel
- Medical Genetics Institute, Shaare Zedek Medical Center, Jerusalem, Israel
| | - Iris Morag
- Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- Department of Neonatalogy, Shamir Medical Center, Zerifin, Israel
| | - Orit Reish
- Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- Genetics Institute, Shamir Medical Center, Zerifin, Israel
| | - Aviva Eliyahu
- Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- The Danek Gertner Institute of Human Genetics, Sheba Medical Center, Tel-Hashomer, Israel
| | - Leah Leibovitch
- Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- Neonatology Department, Sheba Medical Center, Tel-Hashomer, Israel
| | - Marina Eskin Schwartz
- Faculty of Health Sciences, Ben-Gurion University of the Negev, Be'er-Sheva, Israel
- Genetics Institute, Soroka University Medical Center, Be'er Sheva, Israel
| | - Ramy Abramsky
- Faculty of Health Sciences, Ben-Gurion University of the Negev, Be'er-Sheva, Israel
- Department of Neonatalogy, Soroka University Medical Center, Be'er Sheva, Israel
| | - Amit Hochberg
- Ruth and Bruce Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
- Department of Neonatalogy, The Hillel Yaffe Medical Center, Hadera, Israel
| | - Anat Oron
- Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- Department of Neonatalogy, Wolfson Medical Center, Holon, Israel
| | - Ehud Banne
- Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- Genetics Institute, Wolfson Medical Center, Hadera, Israel
| | - Igor Portnov
- Azrieli Faculty of Medicine, Bar Ilan University, Ramat Gan, Israel
- Department of Neonatalogy, Ziv Medical Center Sefat, Tsfat, Israel
| | - Nadra Nasser Samra
- Azrieli Faculty of Medicine, Bar Ilan University, Ramat Gan, Israel
- Genetics Institute, Ziv Medical Center, Safed, Israel
| | - Amihood Singer
- Community Genetics Department, Public Health Services, Ministry of Health, Ramat Gan, Israel
| | - Hagit Baris Feldman
- The Genetics Institute and Genomics Center, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel
- Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
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7
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Aekka A, Weisman AG, Papadakis J, Yerkes E, Baker J, Keswani M, Weinstein J, Finlayson C. Clinical utility of early rapid genome sequencing in the evaluation of patients with differences of sex development. Am J Med Genet A 2024; 194:351-357. [PMID: 37789729 DOI: 10.1002/ajmg.a.63377] [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: 06/15/2023] [Revised: 08/08/2023] [Accepted: 08/09/2023] [Indexed: 10/05/2023]
Abstract
Establishing an early and accurate genetic diagnosis among patients with differences of sex development (DSD) is crucial in guiding the complex medical and psychosocial care they require. Genetic testing routinely utilized in clinical practice for this population is predicated upon physical exam findings and biochemical and endocrine profiling. This approach, however, is inefficient and unstandardized. Many patients with DSD, particularly those with 46,XY DSD, never receive a molecular genetic diagnosis. Rapid genome sequencing (rGS) is gaining momentum as a first-tier diagnostic instrument in the evaluation of patients with DSD given its ability to provide greater diagnostic yield and timely results. We present the case of a patient with nonbinary genitalia and systemic findings for whom rGS identified a novel variant of the WT1 gene and resulted in a molecular diagnosis within two weeks of life. This timeframe of diagnosis for syndromic DSD is largely unprecedented at our institution. Rapid GS expedited mobilization of a multidisciplinary medical team; enabled early understanding of clinical trajectory; informed planning of medical and surgical interventions; and guided individualized psychosocial support provided to the family. This case highlights the potential of early rGS in transforming the evaluation and care of patients with DSD.
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Affiliation(s)
- Apoorva Aekka
- Division of Endocrinology, Ann and Robert H. Lurie Children's Hospital of Chicago, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Allison Goetsch Weisman
- Division of Genetics, Genomics, and Metabolism, Ann and Robert H. Lurie Children's Hospital of Chicago, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Jaclyn Papadakis
- Department of Psychiatry and Behavioral Health, Ann and Robert H. Lurie Children's Hospital of Chicago, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Elizabeth Yerkes
- Division of Urology, Ann and Robert H. Lurie Children's Hospital of Chicago, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Joshua Baker
- Division of Genetics, Genomics, and Metabolism, Ann and Robert H. Lurie Children's Hospital of Chicago, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Mahima Keswani
- Division of Nephrology, Ann and Robert H. Lurie Children's Hospital of Chicago, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Joanna Weinstein
- Division of Hematology, Oncology, Neuro-Oncology and Stem Cell Transplantation, Ann and Robert H. Lurie Children's Hospital of Chicago, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Courtney Finlayson
- Division of Endocrinology, Ann and Robert H. Lurie Children's Hospital of Chicago, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
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8
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Vears DF, Lynch F, Nisselle A, Ayres S, Stark Z. Rapid genomic testing in critically ill patients with genetic conditions: position statement by the Human Genetics Society of Australasia. Eur J Hum Genet 2024; 32:150-154. [PMID: 37864047 PMCID: PMC10853566 DOI: 10.1038/s41431-023-01477-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 09/13/2023] [Accepted: 10/02/2023] [Indexed: 10/22/2023] Open
Affiliation(s)
- Danya F Vears
- Murdoch Children's Research Institute, Melbourne, VIC, Australia
- The University of Melbourne, Melbourne, VIC, Australia
| | - Fiona Lynch
- Murdoch Children's Research Institute, Melbourne, VIC, Australia
- The University of Melbourne, Melbourne, VIC, Australia
| | - Amy Nisselle
- Murdoch Children's Research Institute, Melbourne, VIC, Australia
- The University of Melbourne, Melbourne, VIC, Australia
| | - Samantha Ayres
- Murdoch Children's Research Institute, Melbourne, VIC, Australia
- The University of Melbourne, Melbourne, VIC, Australia
| | - Zornitza Stark
- Murdoch Children's Research Institute, Melbourne, VIC, Australia.
- The University of Melbourne, Melbourne, VIC, Australia.
- Australian Genomics, Melbourne, VIC, Australia.
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9
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Guo F, Liu R, Pan Y, Collins C, Bean L, Ma Z, Mathur A, Da Silva C, Nallamilli B, Guruju N, Chen-Deutsch X, Yousaf R, Chin E, Balciuniene J, Hegde M. Evidence from 2100 index cases supports genome sequencing as a first-tier genetic test. Genet Med 2024; 26:100995. [PMID: 37838930 DOI: 10.1016/j.gim.2023.100995] [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: 03/16/2023] [Revised: 10/04/2023] [Accepted: 10/06/2023] [Indexed: 10/16/2023] Open
Abstract
PURPOSE Genome sequencing (GS) is one of the most comprehensive assays that interrogate single-nucleotide variants, copy number variants, mitochondrial variants, repeat expansions, and structural variants in a single assay. Despite the clear technical superiority, the full clinical utility of GS has yet to be determined. METHODS We systematically evaluated 2100 clinical GS index cases performed in our laboratory to explore the diagnostic yield of GS as first-tier and as follow-up testing. RESULTS The overall diagnostic yield was 28% (585/2100). The diagnostic yield for GS as the first-tier test was 26% (294/1146). Among cases with prior non-diagnostic genetic tests, GS provided a diagnosis for 27% (247/910) of cases, including 56 cases with prior exome sequencing (ES). Although re-analysis of previous ES might have resolved the diagnosis in 29 cases, diagnoses for 27 cases would have been missed because of the technical inferiority of ES. Moreover, GS further disclosed additional genetic etiology in 3 out of 44 cases with existing partial diagnosis. CONCLUSION We present the largest-to-date GS data set of a clinically heterogeneous cohort from a single clinical laboratory. Our data demonstrate that GS should be considered as the first-tier genetic test that has the potential to shorten the diagnostic odyssey.
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Affiliation(s)
- Fen Guo
- Revvity Omics, Pittsburgh, PA.
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10
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Campbell L, Fredericks J, Mathivha K, Moshesh P, Coovadia A, Chirwa P, Dillon B, Ghoor A, Lawrence D, Nair L, Mabaso N, Mokwele D, Novellie M, Krause A, Carstens N. The implementation and utility of clinical exome sequencing in a South African infant cohort. Front Genet 2023; 14:1277948. [PMID: 38028619 PMCID: PMC10665497 DOI: 10.3389/fgene.2023.1277948] [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: 08/15/2023] [Accepted: 10/23/2023] [Indexed: 12/01/2023] Open
Abstract
Genetic disorders are significant contributors to infant hospitalization and mortality globally. The early diagnosis of these conditions in infants remains a considerable challenge. Clinical exome sequencing (CES) has shown to be a successful tool for the early diagnosis of genetic conditions, however, its utility in African infant populations has not been investigated. The impact of the under-representation of African genomic data, the cost of testing, and genomic workforce shortages, need to be investigated and evidence-based implementation strategies accounting for locally available genetics expertise and diagnostic infrastructure need to be developed. We evaluated the diagnostic utility of singleton CES in a cohort of 32 ill, South African infants from two State hospitals in Johannesburg, South Africa. We analysed the data using a series of filtering approaches, including a curated virtual gene panel consisting of genes implicated in neonatal-and early childhood-onset conditions and genes with known founder and common variants in African populations. We reported a diagnostic yield of 22% and identified seven pathogenic variants in the NPHS1, COL2A1, OCRL, SHOC2, TPRV4, MTM1 and STAC3 genes. This study demonstrates the utility value of CES in the South African State healthcare setting, providing a diagnosis to patients who would otherwise not receive one and allowing for directed management. We anticipate an increase in the diagnostic yield of our workflow with further refinement of the study inclusion criteria. This study highlights important considerations for the implementation of genomic medicine in under-resourced settings and in under-represented African populations where variant interpretation remains a challenge.
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Affiliation(s)
- L. Campbell
- Division of Human Genetics, National Health Laboratory Service andSchool of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - J. Fredericks
- Department of Paediatrics and Child Health, School of Clinical Medicine, Rahima Moosa Mother and Child Hospital, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - K. Mathivha
- Department of Paediatrics and Child Health, School of Clinical Medicine, Nelson Mandela Children’s Hospital, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - P. Moshesh
- Department of Paediatrics and Child Health, School of Clinical Medicine, Nelson Mandela Children’s Hospital, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - A. Coovadia
- Department of Paediatrics and Child Health, School of Clinical Medicine, Rahima Moosa Mother and Child Hospital, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - P. Chirwa
- Nelson Mandela Children’s Hospital, Johannesburg, South Africa
| | - B. Dillon
- Division of Human Genetics, National Health Laboratory Service andSchool of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - A. Ghoor
- Department of Paediatrics and Child Health, School of Clinical Medicine, Rahima Moosa Mother and Child Hospital, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - D. Lawrence
- Department of Paediatrics and Child Health, School of Clinical Medicine, Rahima Moosa Mother and Child Hospital, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - L. Nair
- Department of Paediatrics and Child Health, School of Clinical Medicine, Rahima Moosa Mother and Child Hospital, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - N. Mabaso
- Division of Human Genetics, National Health Laboratory Service andSchool of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - D. Mokwele
- Division of Human Genetics, National Health Laboratory Service andSchool of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - M. Novellie
- Division of Human Genetics, National Health Laboratory Service andSchool of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - A. Krause
- Division of Human Genetics, National Health Laboratory Service andSchool of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - N. Carstens
- Division of Human Genetics, National Health Laboratory Service andSchool of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Genomics Platform, South African Medical Research Council, Cape Town, South Africa
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11
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Guzman H, Yazdani S, Harmon JL, Chapman KA, Vitola B, Pyle L, McKnight H, Sigal W, Lord K, De Leon DD, Merchant N, Ganetzky R. Case report: Two unexpected cases of DGUOK-related mitochondrial DNA depletion syndrome presenting with hyperinsulinemic hypoglycemia. Front Endocrinol (Lausanne) 2023; 14:1268135. [PMID: 38027095 PMCID: PMC10646319 DOI: 10.3389/fendo.2023.1268135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 10/02/2023] [Indexed: 12/01/2023] Open
Abstract
Timely diagnosis of persistent neonatal hypoglycemia is critical to prevent neurological sequelae, but diagnosis is complicated by the heterogenicity of the causes. We discuss two cases at separate institutions in which clinical management was fundamentally altered by the results of molecular genetic testing. In both patients, critical samples demonstrated hypoketotic hypoglycemia and a partial glycemic response to glucagon stimulation, thereby suggesting hyperinsulinism (HI). However, due to rapid genetic testing, both patients were found to have deoxyguanosine kinase (DGUOK)-related mitochondrial DNA depletion syndrome, an unexpected diagnosis. Patients with this disease typically present with either hepatocerebral disease in the neonatal period or isolated hepatic failure in infancy. The characteristic features involved in the hepatocerebral form of the disease include lactic acidosis, hypoglycemia, cholestasis, progressive liver failure, and increasing neurologic dysfunction. Those with isolated liver involvement experience hepatomegaly, cholestasis, and liver failure. Although liver transplantation is considered, research has demonstrated that for patients with DGUOK-related mitochondrial DNA depletion syndrome and neurologic symptoms, early demise occurs. Our report advocates for the prompt initiation of genetic testing in patients presenting with persistent neonatal hypoglycemia and for the incorporation of mitochondrial DNA depletion syndromes in the differential diagnosis of HI.
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Affiliation(s)
- Herodes Guzman
- Division of Endocrinology and Diabetes, Children’s Hospital of Philadelphia, Philadelphia, PA, United States
- Division of Genetics, Children’s Hospital of Philadelphia, Philadelphia, PA, United States
| | - Sahr Yazdani
- Division of General Pediatrics, Children’s Hospital of Philadelphia, Philadelphia, PA, United States
| | - Jennifer L. Harmon
- Rare Disease Institute, Children’s National Hospital, Washington, DC, United States
| | - Kimberly A. Chapman
- Rare Disease Institute, Children’s National Hospital, Washington, DC, United States
| | - Bernadette Vitola
- Division of Gastroenterology, Hepatology and Nutrition, Children’s National Hospital, Washington, DC, United States
- Transplant Institute, MedStar Georgetown University Hospital, Washington, DC, United States
| | - Louise Pyle
- Rare Disease Institute, Children’s National Hospital, Washington, DC, United States
| | - Heather McKnight
- Division of Endocrinology and Diabetes, Children’s Hospital of Philadelphia, Philadelphia, PA, United States
| | - Winnie Sigal
- Division of Endocrinology and Diabetes, Children’s Hospital of Philadelphia, Philadelphia, PA, United States
- Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, United States
| | - Katherine Lord
- Division of Endocrinology and Diabetes, Children’s Hospital of Philadelphia, Philadelphia, PA, United States
- Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, United States
| | - Diva D. De Leon
- Division of Endocrinology and Diabetes, Children’s Hospital of Philadelphia, Philadelphia, PA, United States
- Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, United States
| | - Nadia Merchant
- Rare Disease Institute, Children’s National Hospital, Washington, DC, United States
- Division of Endocrinology and Diabetes, Children’s National Hospital, Washington, DC, United States
| | - Rebecca Ganetzky
- Division of Genetics, Children’s Hospital of Philadelphia, Philadelphia, PA, United States
- Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, United States
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12
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Abstract
Rare diseases are a leading cause of infant mortality and lifelong disability. To improve outcomes, timely diagnosis and effective treatments are needed. Genomic sequencing has transformed the traditional diagnostic process, providing rapid, accurate and cost-effective genetic diagnoses to many. Incorporating genomic sequencing into newborn screening programmes at the population scale holds the promise of substantially expanding the early detection of treatable rare diseases, with stored genomic data potentially benefitting health over a lifetime and supporting further research. As several large-scale newborn genomic screening projects launch internationally, we review the challenges and opportunities presented, particularly the need to generate evidence of benefit and to address the ethical, legal and psychosocial issues that genomic newborn screening raises.
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Affiliation(s)
- Zornitza Stark
- Australian Genomics, Melbourne, Victoria, Australia.
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Victoria, Australia.
- Department of Paediatrics, University of Melbourne, Melbourne, Victoria, Australia.
| | - Richard H Scott
- Great Ormond Street Hospital for Children, London, UK
- UCL Great Ormond Street Institute of Child Health, London, UK
- Genomics England, London, UK
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13
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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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14
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Multi-omics for better and faster rare disease diagnosis. Nat Med 2023:10.1038/s41591-023-02417-1. [PMID: 37400642 DOI: 10.1038/s41591-023-02417-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/05/2023]
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15
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Lunke S, Bouffler SE, Patel CV, Sandaradura SA, Wilson M, Pinner J, Hunter MF, Barnett CP, Wallis M, Kamien B, Tan TY, Freckmann ML, Chong B, Phelan D, Francis D, Kassahn KS, Ha T, Gao S, Arts P, Jackson MR, Scott HS, Eggers S, Rowley S, Boggs K, Rakonjac A, Brett GR, de Silva MG, Springer A, Ward M, Stallard K, Simons C, Conway T, Halman A, Van Bergen NJ, Sikora T, Semcesen LN, Stroud DA, Compton AG, Thorburn DR, Bell KM, Sadedin S, North KN, Christodoulou J, Stark Z. Integrated multi-omics for rapid rare disease diagnosis on a national scale. Nat Med 2023:10.1038/s41591-023-02401-9. [PMID: 37291213 PMCID: PMC10353936 DOI: 10.1038/s41591-023-02401-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Accepted: 05/12/2023] [Indexed: 06/10/2023]
Abstract
Critically ill infants and children with rare diseases need equitable access to rapid and accurate diagnosis to direct clinical management. Over 2 years, the Acute Care Genomics program provided whole-genome sequencing to 290 families whose critically ill infants and children were admitted to hospitals throughout Australia with suspected genetic conditions. The average time to result was 2.9 d and diagnostic yield was 47%. We performed additional bioinformatic analyses and transcriptome sequencing in all patients who remained undiagnosed. Long-read sequencing and functional assays, ranging from clinically accredited enzyme analysis to bespoke quantitative proteomics, were deployed in selected cases. This resulted in an additional 19 diagnoses and an overall diagnostic yield of 54%. Diagnostic variants ranged from structural chromosomal abnormalities through to an intronic retrotransposon, disrupting splicing. Critical care management changed in 120 diagnosed patients (77%). This included major impacts, such as informing precision treatments, surgical and transplant decisions and palliation, in 94 patients (60%). Our results provide preliminary evidence of the clinical utility of integrating multi-omic approaches into mainstream diagnostic practice to fully realize the potential of rare disease genomic testing in a timely manner.
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Affiliation(s)
- Sebastian Lunke
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
- Medicine, Dentistry and Health Sciences, University of Melbourne, Melbourne, Victoria, Australia
- Australian Genomics, Melbourne, Victoria, Australia
| | | | - Chirag V Patel
- Genetic Health Queensland, Royal Brisbane and Women's Hospital, Brisbane, Queensland, Australia
| | - Sarah A Sandaradura
- Sydney Children's Hospitals Network - Westmead, Sydney, New South Wales, Australia
- Children's Hospital Westmead Clinical School, University of Sydney, Sydney, New South Wales, Australia
| | - Meredith Wilson
- Sydney Children's Hospitals Network - Westmead, Sydney, New South Wales, Australia
- Children's Hospital Westmead Clinical School, University of Sydney, Sydney, New South Wales, Australia
| | - Jason Pinner
- Sydney Children's Hospitals Network - Randwick, Sydney, New South Wales, Australia
- Medicine and Health, University of New South Wales, Sydney, New South Wales, Australia
| | - Matthew F Hunter
- Monash Genetics, Monash Health, Melbourne, Victoria, Australia
- Department of Paediatrics, Monash University, Melbourne, Victoria, Australia
| | - Christopher P Barnett
- Paediatric and Reproductive Genetics Unit, Women's and Children's Hospital, North Adelaide, South Australia, Australia
- Department of Genetics and Molecular Pathology, SA Pathology, Adelaide, South Australia, Australia
- Adelaide Medical School, The University of Adelaide, Adelaide, South Australia, Australia
| | - Mathew Wallis
- Tasmanian Clinical Genetics Service, Tasmanian Health Service, Hobart, Tasmania, Australia
- School of Medicine and Menzies Institute for Medical Research, University of Tasmania, Hobart, Tasmania, Australia
| | - Benjamin Kamien
- Genetic Services of Western Australia, Perth, Western Australia, Australia
| | - Tiong Y Tan
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
- Medicine, Dentistry and Health Sciences, University of Melbourne, Melbourne, Victoria, Australia
| | - Mary-Louise Freckmann
- Department of Clinical Genetics, The Canberra Hospital, Canberra, Australian Capital Territory, Australia
| | - Belinda Chong
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Dean Phelan
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - David Francis
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Karin S Kassahn
- Department of Genetics and Molecular Pathology, SA Pathology, Adelaide, South Australia, Australia
- Adelaide Medical School, The University of Adelaide, Adelaide, South Australia, Australia
| | - Thuong Ha
- Department of Genetics and Molecular Pathology, SA Pathology, Adelaide, South Australia, Australia
- Centre for Cancer Biology, An alliance between SA Pathology and the University of South Australia, Adelaide, South Australia
- UniSA Clinical and Health Sciences, University of South Australia, Adelaide, South Australia, Australia
| | - Song Gao
- Department of Genetics and Molecular Pathology, SA Pathology, Adelaide, South Australia, Australia
| | - Peer Arts
- Department of Genetics and Molecular Pathology, SA Pathology, Adelaide, South Australia, Australia
- Adelaide Medical School, The University of Adelaide, Adelaide, South Australia, Australia
- Centre for Cancer Biology, An alliance between SA Pathology and the University of South Australia, Adelaide, South Australia
- UniSA Clinical and Health Sciences, University of South Australia, Adelaide, South Australia, Australia
| | - Matilda R Jackson
- Australian Genomics, Melbourne, Victoria, Australia
- Department of Genetics and Molecular Pathology, SA Pathology, Adelaide, South Australia, Australia
| | - Hamish S Scott
- Australian Genomics, Melbourne, Victoria, Australia
- Department of Genetics and Molecular Pathology, SA Pathology, Adelaide, South Australia, Australia
- Adelaide Medical School, The University of Adelaide, Adelaide, South Australia, Australia
- Centre for Cancer Biology, An alliance between SA Pathology and the University of South Australia, Adelaide, South Australia
- UniSA Clinical and Health Sciences, University of South Australia, Adelaide, South Australia, Australia
| | - Stefanie Eggers
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Simone Rowley
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Kirsten Boggs
- Australian Genomics, Melbourne, Victoria, Australia
- Sydney Children's Hospitals Network - Westmead, Sydney, New South Wales, Australia
- Sydney Children's Hospitals Network - Randwick, Sydney, New South Wales, Australia
| | - Ana Rakonjac
- Australian Genomics, Melbourne, Victoria, Australia
- Sydney Children's Hospitals Network - Westmead, Sydney, New South Wales, Australia
- Sydney Children's Hospitals Network - Randwick, Sydney, New South Wales, Australia
| | - Gemma R Brett
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
- Medicine, Dentistry and Health Sciences, University of Melbourne, Melbourne, Victoria, Australia
| | - Michelle G de Silva
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
- Medicine, Dentistry and Health Sciences, University of Melbourne, Melbourne, Victoria, Australia
- Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Amanda Springer
- Monash Genetics, Monash Health, Melbourne, Victoria, Australia
- Department of Paediatrics, Monash University, Melbourne, Victoria, Australia
| | - Michelle Ward
- Genetic Services of Western Australia, Perth, Western Australia, Australia
| | - Kirsty Stallard
- Paediatric and Reproductive Genetics Unit, Women's and Children's Hospital, North Adelaide, South Australia, Australia
| | - Cas Simons
- Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Thomas Conway
- Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Andreas Halman
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Nicole J Van Bergen
- Medicine, Dentistry and Health Sciences, University of Melbourne, Melbourne, Victoria, Australia
- Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Tim Sikora
- Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Liana N Semcesen
- Medicine, Dentistry and Health Sciences, University of Melbourne, Melbourne, Victoria, Australia
| | - David A Stroud
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
- Medicine, Dentistry and Health Sciences, University of Melbourne, Melbourne, Victoria, Australia
- Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Alison G Compton
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
- Medicine, Dentistry and Health Sciences, University of Melbourne, Melbourne, Victoria, Australia
- Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - David R Thorburn
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
- Medicine, Dentistry and Health Sciences, University of Melbourne, Melbourne, Victoria, Australia
- Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Katrina M Bell
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
- Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Simon Sadedin
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
- Medicine, Dentistry and Health Sciences, University of Melbourne, Melbourne, Victoria, Australia
- Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Kathryn N North
- Medicine, Dentistry and Health Sciences, University of Melbourne, Melbourne, Victoria, Australia
- Australian Genomics, Melbourne, Victoria, Australia
- Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - John Christodoulou
- Medicine, Dentistry and Health Sciences, University of Melbourne, Melbourne, Victoria, Australia
- Australian Genomics, Melbourne, Victoria, Australia
- Children's Hospital Westmead Clinical School, University of Sydney, Sydney, New South Wales, Australia
- Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Zornitza Stark
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Victoria, Australia.
- Medicine, Dentistry and Health Sciences, University of Melbourne, Melbourne, Victoria, Australia.
- Australian Genomics, Melbourne, Victoria, Australia.
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16
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Auber B, Schmidt G, Du C, von Hardenberg S. Diagnostic genomic sequencing in critically ill children. MED GENET-BERLIN 2023; 35:105-112. [PMID: 38840860 PMCID: PMC10842578 DOI: 10.1515/medgen-2023-2015] [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: 06/07/2024]
Abstract
Rare genetic diseases are a major cause of severe illnesses and deaths in new-borns and infants. Disease manifestation in critically ill children may be atypical or incomplete, making a monogenetic disease difficult to diagnose clinically. Rapid exome or genome ("genomic") sequencing in critically ill children demonstrated profound diagnostic and clinical value, and there is growing evidence that the faster a molecular diagnosis is established in such children, the more likely clinical management is influenced positively. An early molecular diagnosis enables treatment of critically ill children with precision medicine, has the potential to improve patient outcome and leads to healthcare cost savings. In this review, we outline the status quo of rapid genomic sequencing and possible future implications.
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Affiliation(s)
- Bernd Auber
- Hannover Medical SchoolDepartment of Human GeneticsHannoverGermany
| | - Gunnar Schmidt
- Hannover Medical SchoolDepartment of Human GeneticsHannoverGermany
| | - Chen Du
- Hannover Medical SchoolDepartment of Human GeneticsHannoverGermany
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17
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Poogoda S, Lynch F, Stark Z, Wilkinson D, Savulescu J, Vears D, Gyngell C. Intensive Care Clinicians' Perspectives on Ethical Challenges Raised by Rapid Genomic Testing in Critically Ill Infants. CHILDREN (BASEL, SWITZERLAND) 2023; 10:970. [PMID: 37371202 DOI: 10.3390/children10060970] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 05/21/2023] [Accepted: 05/26/2023] [Indexed: 06/29/2023]
Abstract
Rapid genomic testing (rGT) enables genomic information to be available in a matter of hours, allowing it to be used in time-critical settings, such as intensive care units. Although rGT has been shown to improve diagnostic rates in a cost-effective manner, it raises ethical questions around a range of different areas, including obtaining consent and clinical decision-making. While some research has examined the perspectives of parents and genetics health professionals, the attitudes of intensive care clinicians remain under-explored. To address this gap, we administered an online survey to English-speaking neonatal/paediatric intensivists in Europe, Australasia and North America. We posed two ethical scenarios: one relating to obtaining consent from the parents and the second assessing decision-making regarding the provision of life-sustaining treatments. Descriptive statistics were used to analyse the data. We received 40 responses from 12 countries. About 50-75% of intensivists felt that explicit parental consent was necessary for rGT. About 68-95% felt that a diagnosis from rGT should affect the provision of life-sustaining care. Results were mediated by intensivists' level of experience. Our findings show divergent attitudes toward ethical issues generated by rGT among intensivists and suggest the need for guidance regarding ethical decision-making for rGT.
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Affiliation(s)
- Sachini Poogoda
- Department of Paediatrics, University of Melbourne, Melbourne, VIC 3010, Australia
| | - Fiona Lynch
- Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, VIC 3052, Australia
| | - Zornitza Stark
- Department of Paediatrics, University of Melbourne, Melbourne, VIC 3010, Australia
- Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, VIC 3052, Australia
- Australian Genomics, Melbourne, VIC 3052, Australia
| | - Dominic Wilkinson
- Faculty of Philosophy, Oxford Uehiro Centre for Practical Ethics, University of Oxford, Oxford OX1 1PT, UK
| | - Julian Savulescu
- Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, VIC 3052, Australia
- Faculty of Philosophy, Oxford Uehiro Centre for Practical Ethics, University of Oxford, Oxford OX1 1PT, UK
- Centre for Biomedical Ethics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119077, Singapore
| | - Danya Vears
- Department of Paediatrics, University of Melbourne, Melbourne, VIC 3010, Australia
- Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, VIC 3052, Australia
- Centre for Biomedical Ethics and Law, KU Leuven, 3000 Leuven, Belgium
| | - Christopher Gyngell
- Department of Paediatrics, University of Melbourne, Melbourne, VIC 3010, Australia
- Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, VIC 3052, Australia
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18
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Arkell K, Gyngell C, Stark Z, Vears DF. Rapid Genomic Testing in Intensive Care: Health Professionals' Perspectives on Ethical Challenges. CHILDREN (BASEL, SWITZERLAND) 2023; 10:children10050824. [PMID: 37238372 DOI: 10.3390/children10050824] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 04/20/2023] [Accepted: 04/28/2023] [Indexed: 05/28/2023]
Abstract
Ultra-rapid genomic sequencing (urGS) is increasingly used in neonatal and pediatric intensive care settings (NICU/PICU), demonstrating high diagnostic and clinical utility. This study aimed to explore the perspectives of healthcare professionals (HPs) and the challenges raised by urGS, particularly when making treatment decisions. Four focus groups and two interviews were conducted with HPs who had experience using urGS in NICU/PICU. Inductive content analysis was used to analyze the data. Nineteen HPs participated overall (eight clinical geneticists, nine genetic counselors, and two intensivists). One challenging area of practice identified by HPs was setting realistic expectations for outcomes of urGS among HPs and families. HPs reported modifying pre-test counseling to include life-limiting diagnoses as a possible test outcome and felt concerned about the timing of the test and its impact on parent-child bonding. UrGS results of uncertain prognostic significance posed considerable challenges. Moral distress arose when families and HPs were misaligned regarding treatment goals following the urGS diagnosis. We identified areas of practice that remain ethically challenging for HPs using urGS in the NICU/PICU. HPs experiences of using urGS in the NICU/PICU could inform specialized training in withdrawal of treatment decision making for the genomics workforce.
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Affiliation(s)
- Katie Arkell
- Biomedical Ethics Research Group, Murdoch Children's Research Institute, Parkville, VIC 3052, Australia
- Department of Paediatrics, The University of Melbourne, Parkville, VIC 3052, Australia
| | - Christopher Gyngell
- Biomedical Ethics Research Group, Murdoch Children's Research Institute, Parkville, VIC 3052, Australia
- Department of Paediatrics, The University of Melbourne, Parkville, VIC 3052, Australia
- Melbourne Law School, The University of Melbourne, Carlton, VIC 3053, Australia
| | - Zornitza Stark
- Department of Paediatrics, The University of Melbourne, Parkville, VIC 3052, Australia
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Parkville, VIC 3052, Australia
- Australian Genomics, Parkville, VIC 3052, Australia
| | - Danya F Vears
- Biomedical Ethics Research Group, Murdoch Children's Research Institute, Parkville, VIC 3052, Australia
- Department of Paediatrics, The University of Melbourne, Parkville, VIC 3052, Australia
- Melbourne Law School, The University of Melbourne, Carlton, VIC 3053, Australia
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19
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Wyatt RC, Olek S, De Franco E, Samans B, Patel K, Houghton J, Walter S, Schulze J, Bacchetta R, Hattersley AT, Flanagan SE, Johnson MB. FOXP3 TSDR Measurement Could Assist Variant Classification and Diagnosis of IPEX Syndrome. J Clin Immunol 2023; 43:662-669. [PMID: 36600150 PMCID: PMC9957900 DOI: 10.1007/s10875-022-01428-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 12/21/2022] [Indexed: 01/06/2023]
Abstract
Pathogenic FOXP3 variants cause immune dysregulation polyendocrinopathy enteropathy X-linked (IPEX) syndrome, a progressive autoimmune disease resulting from disruption of the regulatory T cell (Treg) compartment. Assigning pathogenicity to novel variants in FOXP3 is challenging due to the heterogeneous phenotype and variable immunological abnormalities. The number of cells with demethylation at the Treg cell-specific demethylated region (TSDR) is an independent biomarker of IPEX. We aimed to investigate if diagnosing IPEX at presentation with isolated diabetes could allow for effective monitoring of disease progression and assess whether TSDR analysis can aid FOXP3 variant classification and predict disease course. We describe a large genetically diagnosed IPEX cohort (n = 65) and 13 individuals with other monogenic autoimmunity subtypes in whom we quantified the proportion of cells with FOXP3 TSDR demethylation, normalized to the number with CD4 demethylation (%TSDR/CD4) and compare them to 29 unaffected controls. IPEX patients presenting with isolated diabetes (50/65, 77%) often later developed enteropathy (20/50, 40%) with a median interval of 23.5 weeks. %TSDR/CD4 was a good discriminator of IPEX vs. unaffected controls (ROC-AUC 0.81, median 13.6% vs. 8.5%, p < 0.0001) with higher levels of demethylation associated with more severe disease. Patients with other monogenic autoimmunity had a similar %TSDR/CD4 to controls (median 8.7%, p = 1.0). Identifying increased %TSDR/CD4 in patients with novel FOXP3 mutations presenting with isolated diabetes facilitates diagnosis and could offer an opportunity to monitor patients and begin immune modulatory treatment before onset of severe enteropathy.
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Affiliation(s)
- Rebecca C Wyatt
- Clinical and Biomedical Science, Faculty of Health and Life Sciences, University of Exeter, Exeter, UK
| | - Sven Olek
- Ivana Türbachova Laboratory of Epigenetics, Precision for Medicine GmbH, Berlin, Germany
| | - Elisa De Franco
- Clinical and Biomedical Science, Faculty of Health and Life Sciences, University of Exeter, Exeter, UK
| | - Bjoern Samans
- Ivana Türbachova Laboratory of Epigenetics, Precision for Medicine GmbH, Berlin, Germany
| | - Kashyap Patel
- Clinical and Biomedical Science, Faculty of Health and Life Sciences, University of Exeter, Exeter, UK
| | - Jayne Houghton
- Exeter Genomics Laboratory, Royal Devon and Exeter NHS Foundation Trust, Exeter, UK
| | - Steffi Walter
- Research & Development, Epimune Diagnostics, Berlin, Germany
| | - Janika Schulze
- Research & Development, Epimune Diagnostics, Berlin, Germany
| | - Rosa Bacchetta
- Department of Pediatrics, Division of Hematology, Oncology, Stem Cell Transplantation and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, USA
- Center for Definitive and Curative Medicine (CDCM), Stanford University, Stanford, USA
| | - Andrew T Hattersley
- Clinical and Biomedical Science, Faculty of Health and Life Sciences, University of Exeter, Exeter, UK
| | - Sarah E Flanagan
- Clinical and Biomedical Science, Faculty of Health and Life Sciences, University of Exeter, Exeter, UK
| | - Matthew B Johnson
- Clinical and Biomedical Science, Faculty of Health and Life Sciences, University of Exeter, Exeter, UK.
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20
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Lumaka A, Fasquelle C, Debray FG, Alkan S, Jacquinet A, Harvengt J, Boemer F, Mulder A, Vaessen S, Viellevoye R, Palmeira L, Charloteaux B, Brysse A, Bulk S, Rigo V, Bours V. Rapid Whole Genome Sequencing Diagnoses and Guides Treatment in Critically Ill Children in Belgium in Less than 40 Hours. Int J Mol Sci 2023; 24:4003. [PMID: 36835410 PMCID: PMC9967120 DOI: 10.3390/ijms24044003] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 02/05/2023] [Accepted: 02/13/2023] [Indexed: 02/18/2023] Open
Abstract
Rapid Whole Genome Sequencing (rWGS) represents a valuable exploration in critically ill pediatric patients. Early diagnosis allows care to be adjusted. We evaluated the feasibility, turnaround time (TAT), yield, and utility of rWGS in Belgium. Twenty-one unrelated critically ill patients were recruited from the neonatal intensive care units, the pediatric intensive care unit, and the neuropediatric unit, and offered rWGS as a first tier test. Libraries were prepared in the laboratory of human genetics of the University of Liège using Illumina DNA PCR-free protocol. Sequencing was performed on a NovaSeq 6000 in trio for 19 and in duo for two probands. The TAT was calculated from the sample reception to the validation of results. Clinical utility data were provided by treating physicians. A definite diagnosis was reached in twelve (57.5%) patients in 39.80 h on average (range: 37.05-43.7). An unsuspected diagnosis was identified in seven patients. rWGS guided care adjustments in diagnosed patients, including a gene therapy, an off-label drug trial and two condition-specific treatments. We successfully implemented the fastest rWGS platform in Europe and obtained one of the highest rWGS yields. This study establishes the path for a nationwide semi-centered rWGS network in Belgium.
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Affiliation(s)
- Aimé Lumaka
- Human Genetic Laboratory, GIGA Institute, University of Liège, 4000 Liège, Belgium
- Center for Human Genetics, Centre Hospitalier Universitaire, 4032 Liège, Belgium
| | - Corinne Fasquelle
- Center for Human Genetics, Centre Hospitalier Universitaire, 4032 Liège, Belgium
| | | | - Serpil Alkan
- Center for Human Genetics, Centre Hospitalier Universitaire, 4032 Liège, Belgium
- Neuropediatric Division, CHU de Liège—CHR de la Citadelle, University of Liège, 4000 Liège, Belgium
| | - Adeline Jacquinet
- Center for Human Genetics, Centre Hospitalier Universitaire, 4032 Liège, Belgium
| | - Julie Harvengt
- Center for Human Genetics, Centre Hospitalier Universitaire, 4032 Liège, Belgium
| | - François Boemer
- Center for Human Genetics, Centre Hospitalier Universitaire, 4032 Liège, Belgium
| | - André Mulder
- Department of Pediatrics, Division of Pediatric Critical Care Medicine, CHC Mont-Légia, 4000 Liège, Belgium
| | - Sandrine Vaessen
- Neuropediatric Division, CHU de Liège—CHR de la Citadelle, University of Liège, 4000 Liège, Belgium
| | - Renaud Viellevoye
- Neonatology Division, CHU de Liège—CHR de la Citadelle, University of Liège, 4000 Liège, Belgium
| | - Leonor Palmeira
- Center for Human Genetics, Centre Hospitalier Universitaire, 4032 Liège, Belgium
| | - Benoit Charloteaux
- Center for Human Genetics, Centre Hospitalier Universitaire, 4032 Liège, Belgium
| | - Anne Brysse
- Center for Human Genetics, Centre Hospitalier Universitaire, 4032 Liège, Belgium
| | - Saskia Bulk
- Center for Human Genetics, Centre Hospitalier Universitaire, 4032 Liège, Belgium
| | - Vincent Rigo
- Neonatology Division, CHU de Liège—CHR de la Citadelle, University of Liège, 4000 Liège, Belgium
| | - Vincent Bours
- Human Genetic Laboratory, GIGA Institute, University of Liège, 4000 Liège, Belgium
- Center for Human Genetics, Centre Hospitalier Universitaire, 4032 Liège, Belgium
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21
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McNeill A. 2022: the year that was in the European Journal of Human Genetics. Eur J Hum Genet 2023; 31:131-133. [PMID: 36750730 PMCID: PMC9905485 DOI: 10.1038/s41431-023-01283-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2023] Open
Affiliation(s)
- Alisdair McNeill
- Department of Neuroscience, The University of Sheffield, Sheffield, UK.
- Sheffield Clinical Genetics Department, Sheffield Children's Hospital NHS Foundation Trust, Sheffield, UK.
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22
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Lynch F, Prentice T, Gillam L, Stark Z, Gyngell C. Rapid Genome Sequencing: Consent for New Technologies in the Neonatal Intensive Care Context. Pediatrics 2022; 150:190125. [PMID: 36443237 DOI: 10.1542/peds.2022-058222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 09/09/2022] [Indexed: 11/30/2022] Open
Abstract
The clinical utility of rapid genome sequencing (rGS) in critically unwell infants has been consistently demonstrated, and there are calls for rGS to be implemented as a first-line test in the NICU. A diagnosis from rGS can enable rapid initiation of precision treatment, making it potentially lifesaving. However, in many patients rGS leads to the diagnosis of severe and life-limiting conditions, prompting discussion with families about withdrawal of life-sustaining treatment. The complexity of information about rGS, together with the heightened emotions of parents in the NICU, poses significant challenges for informed decision making in this context. We present a case where both parents are unable to provide informed consent, and the treating team must decide whether to proceed with rGS. Our discussion highlights the important differences between genome sequencing and other types of genetic testing, and the crucial role played by pre-test counseling in facilitating informed consent and preparing parents for a range of possible outcomes. We then discuss the consent paradigms at play in NICUs; whereas admission generally comes with an understanding that the treating team will perform interventions thought to be in the best interest of the child, rGS is substantially different because of its long-term implications for patients and family members. Finally, we look at the ethical interplay between parental consent and the interests of the child. We conclude by showing how cases like this are resolved at our tertiary center and how they may be resolved differently in future.
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Affiliation(s)
- Fiona Lynch
- Murdoch Children's Research Institute, Melbourne, Australia.,Melbourne Law School, The University of Melbourne, Melbourne, Australia
| | - Trisha Prentice
- Murdoch Children's Research Institute, Melbourne, Australia.,The Royal Children's Hospital, Melbourne, Australia.,Department of Paediatrics, The University of Melbourne, Melbourne, Australia
| | - Lynn Gillam
- The Royal Children's Hospital, Melbourne, Australia.,Department of Paediatrics, The University of Melbourne, Melbourne, Australia
| | - Zornitza Stark
- Department of Paediatrics, The University of Melbourne, Melbourne, Australia.,Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Australia.,Australian Genomics Health Alliance, Melbourne, Australia
| | - Christopher Gyngell
- Murdoch Children's Research Institute, Melbourne, Australia.,Department of Paediatrics, The University of Melbourne, Melbourne, Australia.,Melbourne Law School, The University of Melbourne, Melbourne, Australia
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23
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Longstaff H, Flamenbaum J, Richer E, Egar J, McMaster CR, Zawati MH. Core elements of participant consent documents for Canadian human genomics research and the National Human Genome Library: guidance for policy. CMAJ 2022; 194:E1500-E1508. [PMID: 36379551 PMCID: PMC9828931 DOI: 10.1503/cmaj.212063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Affiliation(s)
- Holly Longstaff
- Provincial Health Services Authority of British Columbia (Longstaff); Faculty of Health Sciences (Longstaff), Simon Fraser University, Burnaby, BC; Ethics Office, Science and Policy Branch (Flamenbaum), Canadian Institutes of Health Research, Ottawa, Ont.; Institute of Genetics (Richer, Egar, McMaster) Canadian Institutes of Health Research, Halifax, NS; Centre of Genomics and Policy (Zawati), McGill University, Montréal, Que
| | - Jaime Flamenbaum
- Provincial Health Services Authority of British Columbia (Longstaff); Faculty of Health Sciences (Longstaff), Simon Fraser University, Burnaby, BC; Ethics Office, Science and Policy Branch (Flamenbaum), Canadian Institutes of Health Research, Ottawa, Ont.; Institute of Genetics (Richer, Egar, McMaster) Canadian Institutes of Health Research, Halifax, NS; Centre of Genomics and Policy (Zawati), McGill University, Montréal, Que
| | - Etienne Richer
- Provincial Health Services Authority of British Columbia (Longstaff); Faculty of Health Sciences (Longstaff), Simon Fraser University, Burnaby, BC; Ethics Office, Science and Policy Branch (Flamenbaum), Canadian Institutes of Health Research, Ottawa, Ont.; Institute of Genetics (Richer, Egar, McMaster) Canadian Institutes of Health Research, Halifax, NS; Centre of Genomics and Policy (Zawati), McGill University, Montréal, Que
| | - Jeanne Egar
- Provincial Health Services Authority of British Columbia (Longstaff); Faculty of Health Sciences (Longstaff), Simon Fraser University, Burnaby, BC; Ethics Office, Science and Policy Branch (Flamenbaum), Canadian Institutes of Health Research, Ottawa, Ont.; Institute of Genetics (Richer, Egar, McMaster) Canadian Institutes of Health Research, Halifax, NS; Centre of Genomics and Policy (Zawati), McGill University, Montréal, Que
| | - Christopher R McMaster
- Provincial Health Services Authority of British Columbia (Longstaff); Faculty of Health Sciences (Longstaff), Simon Fraser University, Burnaby, BC; Ethics Office, Science and Policy Branch (Flamenbaum), Canadian Institutes of Health Research, Ottawa, Ont.; Institute of Genetics (Richer, Egar, McMaster) Canadian Institutes of Health Research, Halifax, NS; Centre of Genomics and Policy (Zawati), McGill University, Montréal, Que.
| | - Ma'n H Zawati
- Provincial Health Services Authority of British Columbia (Longstaff); Faculty of Health Sciences (Longstaff), Simon Fraser University, Burnaby, BC; Ethics Office, Science and Policy Branch (Flamenbaum), Canadian Institutes of Health Research, Ottawa, Ont.; Institute of Genetics (Richer, Egar, McMaster) Canadian Institutes of Health Research, Halifax, NS; Centre of Genomics and Policy (Zawati), McGill University, Montréal, Que
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24
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Jezkova J, Shaw S, Taverner NV, Williams HJ. Rapid genome sequencing for pediatrics. Hum Mutat 2022; 43:1507-1518. [PMID: 36086948 PMCID: PMC9826377 DOI: 10.1002/humu.24466] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 08/30/2022] [Accepted: 09/06/2022] [Indexed: 01/11/2023]
Abstract
The advancements made in next-generation sequencing (NGS) technology over the past two decades have transformed our understanding of genetic variation in humans and had a profound impact on our ability to diagnose patients with rare genetic diseases. In this review, we discuss the recently developed application of rapid NGS techniques, used to diagnose pediatric patients with suspected rare diseases who are critically ill. We highlight the challenges associated with performing such clinical diagnostics tests in terms of the laboratory infrastructure, bioinformatic analysis pipelines, and the ethical considerations that need to be addressed. We end by looking at what future developments in this field may look like and how they can be used to augment the genetic data to further improve the diagnostic rates for these high-priority patients.
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Affiliation(s)
- Jana Jezkova
- All Wales Medical Genomics Service, Cardiff and Vale NHS TrustHeath HospitalCardiffUK
| | - Sophie Shaw
- All Wales Medical Genomics Service, Cardiff and Vale NHS TrustHeath HospitalCardiffUK
| | - Nicola V. Taverner
- All Wales Medical Genomics Service, Cardiff and Vale NHS TrustHeath HospitalCardiffUK,Centre for Medical Education, School of MedicineCardiff UniversityHeath ParkCardiffUK
| | - Hywel J. Williams
- Division of Cancer and Genetics, Genetic and Genomic Medicine, School of MedicineCardiff UniversityHeath ParkCardiffUK
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25
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Lynch F, Nisselle A, Stark Z, Gaff CL, McClaren B. Genetics follow up after rapid genomic sequencing in intensive care: current practices and recommendations for service delivery. Eur J Hum Genet 2022; 30:1276-1282. [PMID: 35953518 PMCID: PMC9626620 DOI: 10.1038/s41431-022-01168-w] [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: 05/04/2022] [Revised: 07/17/2022] [Accepted: 07/26/2022] [Indexed: 02/04/2023] Open
Abstract
The delivery of rapid genomic sequencing (rGS) to critically unwell children in intensive care occurs at a time of immense pressure and stress for parents. Contact with families after result disclosure, particularly after hospital discharge, presents an opportunity to meet their psychological, medical and information needs as they evolve. This study explores the preferences and perspectives of health professionals and parents of genetics follow up after rGS. Semi-structured interviews were conducted with 30 parents, seven genetic counsellors (GCs) and four intensive care physicians with experience in rGS. Transcripts were analysed using reflexive thematic analysis. Current practices surrounding genetics follow up after rGS were highly variable, resulting in some families not receiving the ongoing care they needed. Reasons identified by families for wanting follow-up care represented only a subset of those identified by health professionals. While GCs routinely provided their details to allow parents to initiate further contact, this was not always sufficient for follow-up care. Health professionals identified both organisational and psychosocial barriers to conducting follow up. As rGS transforms the diagnostic pathway in rare disease, there is a need for a co-designed, standardised but flexible model for follow-up care with genetics professionals so that families' evolving needs are met.
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Affiliation(s)
- Fiona Lynch
- Australian Genomics Health Alliance, Melbourne, VIC, Australia
- Department of Paediatrics, The University of Melbourne, Melbourne, VIC, Australia
- Genomics in Society, Murdoch Children's Research Institute, Melbourne, VIC, Australia
- Centre for Ethics of Paediatric Genomics, Murdoch Children's Research Institute, Melbourne, VIC, Australia
| | - Amy Nisselle
- Australian Genomics Health Alliance, Melbourne, VIC, Australia
- Department of Paediatrics, The University of Melbourne, Melbourne, VIC, Australia
- Genomics in Society, Murdoch Children's Research Institute, Melbourne, VIC, Australia
| | - Zornitza Stark
- Australian Genomics Health Alliance, Melbourne, VIC, Australia
- Department of Paediatrics, The University of Melbourne, Melbourne, VIC, Australia
- Victorian Clinical Genetics Service, Murdoch Children's Research Institute, Melbourne, VIC, Australia
| | - Clara L Gaff
- Australian Genomics Health Alliance, Melbourne, VIC, Australia
- Department of Paediatrics, The University of Melbourne, Melbourne, VIC, Australia
- Genomics in Society, Murdoch Children's Research Institute, Melbourne, VIC, Australia
- Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
| | - Belinda McClaren
- Australian Genomics Health Alliance, Melbourne, VIC, Australia.
- Department of Paediatrics, The University of Melbourne, Melbourne, VIC, Australia.
- Genomics in Society, Murdoch Children's Research Institute, Melbourne, VIC, Australia.
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26
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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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27
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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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28
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Wells CF, Boursier G, Yauy K, Ruiz-Pallares N, Mechin D, Ruault V, Tharreau M, Blanchet P, Pinson L, Coubes C, Fila M, Baleine J, Pidoux O, Badr M, Milesi C, Cambonie G, Mesnage R, Dereure M, Ardouin O, Guignard T, Geneviève D, Barat-Houari M, Willems M. Rapid exome sequencing in critically ill infants: implementation in routine care from French regional hospital's perspective. Eur J Hum Genet 2022; 30:1076-1082. [PMID: 35729264 PMCID: PMC9436918 DOI: 10.1038/s41431-022-01133-7] [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: 04/04/2022] [Revised: 05/18/2022] [Accepted: 06/09/2022] [Indexed: 01/15/2023] Open
Abstract
This monocentric study included fifteen children under a year old in intensive care with suspected monogenic conditions for rapid trio exome sequencing (rES) between April 2019 and April 2021. The primary outcome was the time from blood sampling to rapid exome sequencing report to parents. All results were available within 16 days and were reported to parents in or under 16 days in 13 of the 15 individuals (86%). Six individuals (40%) received a diagnosis with rES, two had a genetic condition not diagnosed by rES. Eight individuals had their care impacted by their rES results, four were discharged or died before the results. This small-scale study shows that rES can be implemented in a regional University hospital with rapid impactful diagnosis to improve care in critically ill infants.
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Affiliation(s)
- Constance F Wells
- Department of Medical Genetics, Rare diseases and Personalized medicine, CHU Montpellier, Univ Montpellier, Montpellier, France
| | - Guilaine Boursier
- Department of Medical Genetics, Rare diseases and Personalized medicine, CHU Montpellier, Univ Montpellier, Montpellier, France
| | - Kevin Yauy
- Department of Medical Genetics, Rare diseases and Personalized medicine, CHU Montpellier, Univ Montpellier, Montpellier, France
- Institute of Advanced Biosciences, Centre de recherche UGA, Inserm U 1209, CNRS UMR 5309, Grenoble, France
- SeqOne Genomics, Montpellier, France
| | - Nathalie Ruiz-Pallares
- Department of Medical Genetics, Rare diseases and Personalized medicine, CHU Montpellier, Univ Montpellier, Montpellier, France
| | - Déborah Mechin
- Department of Medical Genetics, Rare diseases and Personalized medicine, CHU Montpellier, Univ Montpellier, Montpellier, France
| | - Valentin Ruault
- Department of Medical Genetics, Rare diseases and Personalized medicine, CHU Montpellier, Univ Montpellier, Montpellier, France
| | - Mylène Tharreau
- Department of Medical Genetics, Rare diseases and Personalized medicine, CHU Montpellier, Univ Montpellier, Montpellier, France
| | - Patricia Blanchet
- Department of Medical Genetics, Rare diseases and Personalized medicine, CHU Montpellier, Univ Montpellier, Montpellier, France
| | - Lucile Pinson
- Department of Medical Genetics, Rare diseases and Personalized medicine, CHU Montpellier, Univ Montpellier, Montpellier, France
| | - Christine Coubes
- Department of Medical Genetics, Rare diseases and Personalized medicine, CHU Montpellier, Univ Montpellier, Montpellier, France
| | - Marc Fila
- Pediatric Nephrology department, Montpellier university hospital, Univ, Montpellier, France
| | - Julien Baleine
- Department of Neonatal Medicine and Pediatric Intensive Care, Montpellier university Hospital, Univ, Montpellier, France
| | - Odile Pidoux
- Department of Neonatal Medicine and Pediatric Intensive Care, Montpellier university Hospital, Univ, Montpellier, France
| | - Maliha Badr
- Department of Neonatal Medicine and Pediatric Intensive Care, Montpellier university Hospital, Univ, Montpellier, France
| | - Christophe Milesi
- Department of Neonatal Medicine and Pediatric Intensive Care, Montpellier university Hospital, Univ, Montpellier, France
| | - Gilles Cambonie
- Department of Neonatal Medicine and Pediatric Intensive Care, Montpellier university Hospital, Univ, Montpellier, France
| | - Renaud Mesnage
- Department of Neonatal Medicine and Pediatric Intensive Care, Montpellier university Hospital, Univ, Montpellier, France
| | - Maëlle Dereure
- Clinical research and epidemiology department, Montpellier university hospital, Univ, Montpellier, France
| | - Olivier Ardouin
- Molecular medicine and genomics platform, Montpellier university hospital, Montpellier, France
| | - Thomas Guignard
- Unit of Chromosomal Genetics and Research Plateform Chromostem, Montpellier university hospital, Univ, Montpellier, France
| | - David Geneviève
- Department of Medical Genetics, Rare diseases and Personalized medicine, CHU Montpellier, Univ Montpellier, Montpellier, France
| | - Mouna Barat-Houari
- Department of Medical Genetics, Rare diseases and Personalized medicine, CHU Montpellier, Univ Montpellier, Montpellier, France
| | - Marjolaine Willems
- Department of Medical Genetics, Rare diseases and Personalized medicine, CHU Montpellier, Univ Montpellier, Montpellier, France.
- Inserm U1298, INM, CHU Montpellier, Univ. Montpellier, Montpellier, France.
- Reference Centre AD SOOR, AnDDI-RARE, Competence Centre for Rare Skeletal Disorders, OSCAR Network, Montpellier, France.
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29
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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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30
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Lunke S, Stark Z. Can Rapid Nanopore Sequencing Bring Genomic Testing to the Bedside? Clin Chem 2022; 68:1484-1485. [PMID: 35848937 DOI: 10.1093/clinchem/hvac111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Accepted: 06/07/2022] [Indexed: 11/13/2022]
Affiliation(s)
- Sebastian Lunke
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Victoria, Australia.,University of Melbourne, Melbourne, Australia
| | - Zornitza Stark
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Victoria, Australia.,University of Melbourne, Melbourne, Australia.,Australian Genomics, Melbourne, Australia
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31
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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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32
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Forbes TA, Wallace J, Kumble S, Delatycki MB, Stark Z. Neonatal Bartter syndrome diagnosed by rapid genomics following low risk pre-conception carrier screening. J Paediatr Child Health 2022; 58:758-761. [PMID: 35348259 PMCID: PMC9313891 DOI: 10.1111/jpc.15955] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 01/28/2022] [Accepted: 03/02/2022] [Indexed: 11/29/2022]
Abstract
Advances in the speed and accessibility of genomic sequencing are broadening the application of this technology to rapid, acute care diagnostics and pre-conception carrier screening. In both circumstances, genetic counselling plays a critical role in preparing couples for the strengths and limitations of the testing. For pre-conception carrier screening in particular, it is important that parents and clinicians are aware that even in the absence of an identified risk for recessive disease, a baby with a genetic condition may still be conceived. As an example, we present the genomic journey of a couple who underwent pre-conception carrier screening and following a low-risk result, delivered a baby boy who was diagnosed with Type 1 Bartter syndrome. Ultra-rapid, post-natal, trio whole genome sequencing resolved both parents as carriers of pathogenic variants in SLC12A1, a gene not included in the original pre-conception screening panel. This family's story highlights (i) the intricacy of gene selection for pre-conception screening panels, (ii) the benefits of high-quality pre-test genetic counselling in supporting families through adverse genomic findings and (iii) the role rapid genomics can play in resolving uncertainty for families and clinicians in circumstances where suspicion of genetic disease exists. This article is accompanied by a Patient Voice perspective written by the child's parents, placing emphasis on the essential role genetic counselling played in their journey.
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Affiliation(s)
- Thomas A Forbes
- Department of NephrologyRoyal Children's HospitalMelbourneVictoriaAustralia,Department of PaediatricsUniversity of MelbourneMelbourneVictoriaAustralia,Kidney Regeneration GroupMurdoch Children's Research InstituteMelbourneVictoriaAustralia
| | - Jane Wallace
- Victorian Clinical Genetics ServicesMurdoch Children's Research InstituteMelbourneVictoriaAustralia
| | - Smitha Kumble
- Victorian Clinical Genetics ServicesMurdoch Children's Research InstituteMelbourneVictoriaAustralia
| | - Martin B Delatycki
- Department of PaediatricsUniversity of MelbourneMelbourneVictoriaAustralia,Victorian Clinical Genetics ServicesMurdoch Children's Research InstituteMelbourneVictoriaAustralia
| | - Zornitza Stark
- Department of PaediatricsUniversity of MelbourneMelbourneVictoriaAustralia,Victorian Clinical Genetics ServicesMurdoch Children's Research InstituteMelbourneVictoriaAustralia,Australian Genomics Health AllianceMelbourneVictoriaAustralia
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33
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Goranitis I, Wu Y, Lunke S, White SM, Tan TY, Yeung A, Hunter MF, Martyn M, Gaff C, Stark Z. Is faster better? An economic evaluation of rapid and ultra-rapid genomic testing in critically ill infants and children. Genet Med 2022; 24:1037-1044. [PMID: 35181209 DOI: 10.1016/j.gim.2022.01.013] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Revised: 01/17/2022] [Accepted: 01/19/2022] [Indexed: 01/02/2023] Open
Abstract
PURPOSE To evaluate whether the additional cost of providing increasingly faster genomic results in pediatric critical care is outweighed by reductions in health care costs and increases in personal utility. METHODS Hospital costs and medical files from a cohort of 40 children were analyzed. The health economic impact of rapid and ultra-rapid genomic testing, with and without early initiation, relative to standard genomic testing was evaluated. RESULTS Shortening the time to results led to substantial economic and personal benefits. Early initiation of ultra-rapid genomic testing was the most cost-beneficial strategy, leading to a cost saving of AU$26,600 per child tested relative to standard genomic testing and a welfare gain of AU$12,000 per child tested. Implementation of early ultra-rapid testing of critically ill children is expected to lead to an annual cost saving of AU$7.3 million for the Australian health system and an aggregate welfare gain of AU$3.3 million, corresponding to a total net benefit of AU$10.6 million. CONCLUSION Early initiation of ultra-rapid genomic testing can offer substantial economic and personal benefits. Future implementation of rapid genomic testing programs should focus not only on optimizing the laboratory workflow to achieve a fast turnaround time but also on changing clinical practice to expedite test initiation.
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Affiliation(s)
- Ilias Goranitis
- Health Economics Unit, Centre for Health Policy, Melbourne School of Population and Global Health, University of Melbourne, Melbourne, Victoria, Australia; Australian Genomics Health Alliance, Melbourne, Victoria, Australia; Murdoch Children's Research Institute, Melbourne, Victoria, Australia.
| | - You Wu
- Health Economics Unit, Centre for Health Policy, Melbourne School of Population and Global Health, University of Melbourne, Melbourne, Victoria, Australia; Australian Genomics Health Alliance, Melbourne, Victoria, Australia; Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Sebastian Lunke
- Australian Genomics Health Alliance, Melbourne, Victoria, Australia; Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Victoria, Australia; Department of Pediatrics, University of Melbourne, Melbourne, Victoria, Australia
| | - Susan M White
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Victoria, Australia; Department of Pediatrics, University of Melbourne, Melbourne, Victoria, Australia
| | - Tiong Y Tan
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Victoria, Australia; Department of Pediatrics, University of Melbourne, Melbourne, Victoria, Australia
| | - Alison Yeung
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Victoria, Australia; Department of Pediatrics, University of Melbourne, Melbourne, Victoria, Australia
| | - Matthew F Hunter
- Monash Genetics, Monash Health, Melbourne, Victoria, Australia; Department of Pediatrics, Monash University, Melbourne, Victoria, Australia
| | - Melissa Martyn
- Murdoch Children's Research Institute, Melbourne, Victoria, Australia; Melbourne Genomics Health Alliance, Melbourne, Victoria, Australia
| | - Clara Gaff
- Murdoch Children's Research Institute, Melbourne, Victoria, Australia; Department of Pediatrics, University of Melbourne, Melbourne, Victoria, Australia; Melbourne Genomics Health Alliance, Melbourne, Victoria, Australia
| | - Zornitza Stark
- Australian Genomics Health Alliance, Melbourne, Victoria, Australia; Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Victoria, Australia; Department of Pediatrics, University of Melbourne, Melbourne, Victoria, Australia.
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34
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French CE, Dolling H, Mégy K, Sanchis-Juan A, Kumar A, Delon I, Wakeling M, Mallin L, Agrawal S, Austin T, Walston F, Park SM, Parker A, Piyasena C, Bradbury K, Ellard S, Rowitch DH, Raymond FL. Refinements and considerations for trio whole genome sequence analysis when investigating Mendelian Diseases presenting in early childhood. HGG ADVANCES 2022; 3:100113. [PMID: 35586607 PMCID: PMC9108978 DOI: 10.1016/j.xhgg.2022.100113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Accepted: 04/19/2022] [Indexed: 11/30/2022] Open
Abstract
To facilitate early deployment of whole-genome sequencing (WGS) for severely ill children, a standardized pipeline for WGS analysis with timely turnaround and primary care pediatric uptake is needed. We developed a bioinformatics pipeline for comprehensive gene-agnostic trio WGS analysis of children suspected of having an undiagnosed monogenic disease that included detection and interpretation of primary genetic mechanisms of disease, including SNVs/indels, CNVs/SVs, uniparental disomy (UPD), imprinted genes, short tandem repeat expansions, mobile element insertions, SMN1/2 copy number calling, and mitochondrial genome variants. We assessed primary care practitioner experience and competence in a large cohort of 521 families (comprising 90% WGS trios). Children were identified by primary practitioners for recruitment, and we used the UK index of multiple deprivation to confirm lack of patient socio-economic status ascertainment bias. Of the 521 children sequenced, 176 (34%) received molecular diagnoses, with rates as high as 45% for neurology clinics. Twenty-three of the diagnosed cases (13%) required bespoke methods beyond routine SNV/CNV analysis. In our multidisciplinary clinician user experience assessment, both pediatricians and clinical geneticists expressed strong support for rapid WGS early in the care pathway, but requested further training in determining patient selection, consenting, and variant interpretation. Rapid trio WGS provides an efficacious single-pass screening test for children when deployed by primary practitioners in clinical settings that carry high a priori risk for rare pediatric disease presentations.
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Affiliation(s)
- Courtney E. French
- School of Clinical Medicine, University of Cambridge, Cambridge CB2 1TN, UK
- Boston Children’s Hospital, Boston, MA 02115, USA
| | - Helen Dolling
- School of Clinical Medicine, University of Cambridge, Cambridge CB2 1TN, UK
- Cambridge University Hospitals NHS Foundation Trust, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK
- NIHR Bioresource, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK
- Centre for Family Research, Department of Psychology, University of Cambridge, Cambridge CB2 3RQ, UK
| | - Karyn Mégy
- School of Clinical Medicine, University of Cambridge, Cambridge CB2 1TN, UK
- NIHR Bioresource, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK
| | - Alba Sanchis-Juan
- School of Clinical Medicine, University of Cambridge, Cambridge CB2 1TN, UK
- NIHR Bioresource, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK
| | - Ajay Kumar
- School of Clinical Medicine, University of Cambridge, Cambridge CB2 1TN, UK
| | - Isabelle Delon
- Cambridge University Hospitals NHS Foundation Trust, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK
| | - Matthew Wakeling
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, University of Exeter, Exeter EX4 4PY, UK
| | - Lucy Mallin
- Royal Devon and Exeter NHS Foundation Trust, Exeter EX2 5DW, UK
| | - Shruti Agrawal
- Cambridge University Hospitals NHS Foundation Trust, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK
| | - Topun Austin
- School of Clinical Medicine, University of Cambridge, Cambridge CB2 1TN, UK
- Cambridge University Hospitals NHS Foundation Trust, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK
| | - Florence Walston
- Norfolk and Norwich University Hospital NHS Foundation Trust, Norwich NR4 7UY, UK
| | - Soo-Mi Park
- Cambridge University Hospitals NHS Foundation Trust, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK
| | - Alasdair Parker
- Cambridge University Hospitals NHS Foundation Trust, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK
| | | | | | | | - Sian Ellard
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, University of Exeter, Exeter EX4 4PY, UK
- Royal Devon and Exeter NHS Foundation Trust, Exeter EX2 5DW, UK
| | - David H. Rowitch
- School of Clinical Medicine, University of Cambridge, Cambridge CB2 1TN, UK
- Cambridge University Hospitals NHS Foundation Trust, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK
- NIHR Bioresource, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK
| | - F. Lucy Raymond
- School of Clinical Medicine, University of Cambridge, Cambridge CB2 1TN, UK
- Cambridge University Hospitals NHS Foundation Trust, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK
- NIHR Bioresource, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK
- Corresponding author
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35
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P. Fishler K, Euteneuer JC, Brunelli L. Ethical Considerations for Equitable Access to Genomic Sequencing for Critically Ill Neonates in the United States. Int J Neonatal Screen 2022; 8:ijns8010022. [PMID: 35323201 PMCID: PMC8950005 DOI: 10.3390/ijns8010022] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Revised: 03/12/2022] [Accepted: 03/14/2022] [Indexed: 11/16/2022] Open
Abstract
Rare diseases impact all socio-economic, geographic, and racial groups indiscriminately. Newborn screening (NBS) is an exemplary international public health initiative that identifies infants with rare conditions early in life to reduce morbidity and mortality. NBS theoretically promotes equity through universal access, regardless of financial ability. There is however heterogeneity in access to newborn screening and conditions that are screened throughout the world. In the United States and some other developed countries, NBS is provided to all babies, subsidized by the local or federal government. Although NBS is an equitable test, infants admitted to neonatal intensive care units (NICUs) may not receive similar benefits to healthier infants. Newborns in the NICU may receive delayed and/or multiple newborn screens due to known limitations in interpreting the results with prematurity, total parenteral nutrition, blood transfusions, infection, and life support. Thus, genomic technologies might be needed in addition to NBS for equitable care of this vulnerable population. Whole exome (WES) and genome sequencing (WGS) have been recently studied in critically ill newborns across the world and have shown promising results in shortening diagnostic odysseys and providing clinical utility. However, in certain circumstances several barriers might limit access to these tests. Here, we discuss some of the existing barriers to genomic sequencing in NICUs in the United States, explore the ethical implications related to low access, consider ways to increase access to genomic testing, and offer some suggestions for future research in these areas.
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Affiliation(s)
- Kristen P. Fishler
- Munroe-Meyer Institute for Genetics and Rehabilitation, University of Nebraska Medical Center, Omaha, NE 68198, USA
- Correspondence:
| | | | - Luca Brunelli
- Division of Neonatology, University of Utah School of Medicine, Salt Lake City, UT 84132, USA;
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36
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A new system for variant classification? Eur J Hum Genet 2022; 30:137-138. [PMID: 35132196 PMCID: PMC8821601 DOI: 10.1038/s41431-021-01032-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
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37
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Van Bergen NJ, Hock DH, Spencer L, Massey S, Stait T, Stark Z, Lunke S, Roesley A, Peters H, Lee JY, Le Fevre A, Heath O, Mignone C, Yang JYM, Ryan MM, D’Arcy C, Nash M, Smith S, Caruana NJ, Thorburn DR, Stroud DA, White SM, Christodoulou J, Brown NJ. Biallelic Variants in PYROXD2 Cause a Severe Infantile Metabolic Disorder Affecting Mitochondrial Function. Int J Mol Sci 2022; 23:ijms23020986. [PMID: 35055180 PMCID: PMC8777681 DOI: 10.3390/ijms23020986] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 01/11/2022] [Accepted: 01/13/2022] [Indexed: 12/04/2022] Open
Abstract
Pyridine Nucleotide-Disulfide Oxidoreductase Domain 2 (PYROXD2; previously called YueF) is a mitochondrial inner membrane/matrix-residing protein and is reported to regulate mitochondrial function. The clinical importance of PYROXD2 has been unclear, and little is known of the protein’s precise biological function. In the present paper, we report biallelic variants in PYROXD2 identified by genome sequencing in a patient with suspected mitochondrial disease. The child presented with acute neurological deterioration, unresponsive episodes, and extreme metabolic acidosis, and received rapid genomic testing. He died shortly after. Magnetic resonance imaging (MRI) brain imaging showed changes resembling Leigh syndrome, one of the more common childhood mitochondrial neurological diseases. Functional studies in patient fibroblasts showed a heightened sensitivity to mitochondrial metabolic stress and increased mitochondrial superoxide levels. Quantitative proteomic analysis demonstrated decreased levels of subunits of the mitochondrial respiratory chain complex I, and both the small and large subunits of the mitochondrial ribosome, suggesting a mitoribosomal defect. Our findings support the critical role of PYROXD2 in human cells, and suggest that the biallelic PYROXD2 variants are associated with mitochondrial dysfunction, and can plausibly explain the child’s clinical presentation.
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Affiliation(s)
- Nicole J. Van Bergen
- Brain and Mitochondrial Research Group, Murdoch Children’s Research Institute, Royal Children’s Hospital, Parkville, VIC 3052, Australia; (L.S.); (S.M.); (T.S.); (D.R.T.); (D.A.S.)
- Department of Paediatrics, University of Melbourne, Parkville, VIC 3010, Australia; (Z.S.); (S.L.); (J.Y.L.); (J.Y.-M.Y.); (S.M.W.)
- Correspondence: (N.J.V.B.); (J.C.); (N.J.B.)
| | - Daniella H. Hock
- Department of Biochemistry and Pharmacology and Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, VIC 3010, Australia; (D.H.H.); (N.J.C.)
| | - Lucy Spencer
- Brain and Mitochondrial Research Group, Murdoch Children’s Research Institute, Royal Children’s Hospital, Parkville, VIC 3052, Australia; (L.S.); (S.M.); (T.S.); (D.R.T.); (D.A.S.)
| | - Sean Massey
- Brain and Mitochondrial Research Group, Murdoch Children’s Research Institute, Royal Children’s Hospital, Parkville, VIC 3052, Australia; (L.S.); (S.M.); (T.S.); (D.R.T.); (D.A.S.)
| | - Tegan Stait
- Brain and Mitochondrial Research Group, Murdoch Children’s Research Institute, Royal Children’s Hospital, Parkville, VIC 3052, Australia; (L.S.); (S.M.); (T.S.); (D.R.T.); (D.A.S.)
| | - Zornitza Stark
- Department of Paediatrics, University of Melbourne, Parkville, VIC 3010, Australia; (Z.S.); (S.L.); (J.Y.L.); (J.Y.-M.Y.); (S.M.W.)
- Victorian Clinical Genetics Services, Murdoch Children’s Research Institute, Parkville, VIC 3052, Australia; (A.R.); (A.L.F.)
- Australian Genomics Health Alliance, Parkville, VIC 3052, Australia
| | - Sebastian Lunke
- Department of Paediatrics, University of Melbourne, Parkville, VIC 3010, Australia; (Z.S.); (S.L.); (J.Y.L.); (J.Y.-M.Y.); (S.M.W.)
- Department of Pathology, University of Melbourne, Parkville, VIC 3010, Australia
| | - Ain Roesley
- Victorian Clinical Genetics Services, Murdoch Children’s Research Institute, Parkville, VIC 3052, Australia; (A.R.); (A.L.F.)
| | - Heidi Peters
- Department of Metabolic Medicine, Royal Children’s Hospital, Parkville, VIC 3052, Australia; (H.P.); (O.H.)
| | - Joy Yaplito Lee
- Department of Paediatrics, University of Melbourne, Parkville, VIC 3010, Australia; (Z.S.); (S.L.); (J.Y.L.); (J.Y.-M.Y.); (S.M.W.)
- Department of Metabolic Medicine, Royal Children’s Hospital, Parkville, VIC 3052, Australia; (H.P.); (O.H.)
| | - Anna Le Fevre
- Victorian Clinical Genetics Services, Murdoch Children’s Research Institute, Parkville, VIC 3052, Australia; (A.R.); (A.L.F.)
| | - Oliver Heath
- Department of Metabolic Medicine, Royal Children’s Hospital, Parkville, VIC 3052, Australia; (H.P.); (O.H.)
| | - Cristina Mignone
- Medical Imaging Department, Royal Children’s Hospital, Parkville, VIC 3052, Australia;
| | - Joseph Yuan-Mou Yang
- Department of Paediatrics, University of Melbourne, Parkville, VIC 3010, Australia; (Z.S.); (S.L.); (J.Y.L.); (J.Y.-M.Y.); (S.M.W.)
- Department of Neurosurgery, Neuroscience Advanced Clinical Imaging Service (NACIS), The Royal Children’s Hospital, Parkville, VIC 3052, Australia
- Developmental Imaging, Murdoch Children’s Research Institute, Parkville, VIC 3052, Australia
- Neuroscience Research, Murdoch Children’s Research Institute, Parkville, VIC 3052, Australia
| | - Monique M. Ryan
- Neurology Department, Royal Children’s Hospital, Parkville, VIC 3052, Australia;
| | - Colleen D’Arcy
- Anatomical Pathology Department, Royal Children’s Hospital, Parkville, VIC 3052, Australia;
| | - Margot Nash
- General Medicine, Royal Children’s Hospital, Parkville, VIC 3052, Australia;
| | - Sile Smith
- Paediatric Intensive Care Unit, Royal Children’s Hospital, Parkville, VIC 3052, Australia;
| | - Nikeisha J. Caruana
- Department of Biochemistry and Pharmacology and Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, VIC 3010, Australia; (D.H.H.); (N.J.C.)
- Institute for Health and Sport (iHeS), Victoria University, Footscray, VIC 3011, Australia
| | - David R. Thorburn
- Brain and Mitochondrial Research Group, Murdoch Children’s Research Institute, Royal Children’s Hospital, Parkville, VIC 3052, Australia; (L.S.); (S.M.); (T.S.); (D.R.T.); (D.A.S.)
- Department of Paediatrics, University of Melbourne, Parkville, VIC 3010, Australia; (Z.S.); (S.L.); (J.Y.L.); (J.Y.-M.Y.); (S.M.W.)
- Victorian Clinical Genetics Services, Murdoch Children’s Research Institute, Parkville, VIC 3052, Australia; (A.R.); (A.L.F.)
| | - David A. Stroud
- Brain and Mitochondrial Research Group, Murdoch Children’s Research Institute, Royal Children’s Hospital, Parkville, VIC 3052, Australia; (L.S.); (S.M.); (T.S.); (D.R.T.); (D.A.S.)
- Department of Biochemistry and Pharmacology and Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, VIC 3010, Australia; (D.H.H.); (N.J.C.)
| | - Susan M. White
- Department of Paediatrics, University of Melbourne, Parkville, VIC 3010, Australia; (Z.S.); (S.L.); (J.Y.L.); (J.Y.-M.Y.); (S.M.W.)
- Victorian Clinical Genetics Services, Murdoch Children’s Research Institute, Parkville, VIC 3052, Australia; (A.R.); (A.L.F.)
| | - John Christodoulou
- Brain and Mitochondrial Research Group, Murdoch Children’s Research Institute, Royal Children’s Hospital, Parkville, VIC 3052, Australia; (L.S.); (S.M.); (T.S.); (D.R.T.); (D.A.S.)
- Department of Paediatrics, University of Melbourne, Parkville, VIC 3010, Australia; (Z.S.); (S.L.); (J.Y.L.); (J.Y.-M.Y.); (S.M.W.)
- Victorian Clinical Genetics Services, Murdoch Children’s Research Institute, Parkville, VIC 3052, Australia; (A.R.); (A.L.F.)
- Discipline of Child and Adolescent Health, University of Sydney, Camperdown, NSW 2006, Australia
- Correspondence: (N.J.V.B.); (J.C.); (N.J.B.)
| | - Natasha J. Brown
- Department of Paediatrics, University of Melbourne, Parkville, VIC 3010, Australia; (Z.S.); (S.L.); (J.Y.L.); (J.Y.-M.Y.); (S.M.W.)
- Victorian Clinical Genetics Services, Murdoch Children’s Research Institute, Parkville, VIC 3052, Australia; (A.R.); (A.L.F.)
- Correspondence: (N.J.V.B.); (J.C.); (N.J.B.)
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Consent for rapid genomic sequencing for critically ill children: legal and ethical issues. Monash Bioeth Rev 2021; 39:117-129. [PMID: 34971444 DOI: 10.1007/s40592-021-00146-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/05/2021] [Indexed: 10/19/2022]
Abstract
Although rapid genomic sequencing (RGS) is improving care for critically ill children with rare disease, it also raises important ethical questions that need to be explored as its use becomes more widespread. Two such questions relate to the degree of consent that should be required for RGS to proceed and whether it might ever be appropriate to override parents' decisions not to allow RGS to be performed in their critically ill child. To explore these questions, we first examine the legal frameworks on securing consent for genomic sequencing and how they apply to the specific context of RGS for critically ill children. We then use a tool from clinical ethics, the Zone of Parental Discretion, to explore two case studies and identify under which circumstances it might be appropriate for parental refusal of RGS to be overridden. We argue that RGS may be a context where, in addition to assessing the complexity of the test offered, it is ethically appropriate to consider an effect on patient outcomes when deciding the degree of consent required. We also suggest that there are some contexts where it may be ethically justified to perform RGS, even when it is actively against the wishes of the parents. More work is needed to examine exactly how 'time-sensitive' exceptions to current guidance on consent for genomic sequencing could be formulated and operationalised for RGS for critically ill-children.
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