1
|
Guner Yilmaz B, Akgun-Dogan O, Ozdemir O, Yuksel B, Hatirnaz Ng O, Bilguvar K, Ay B, Ozkose GS, Aydin E, Yigit A, Bulut A, Esen FN, Beken S, Aktas S, Demirel A, Arcagok BC, Kazanci E, Bingol İ, Umur O, Sik G, Isik U, Ersoy M, Korkmaz A, Citak A, Mardinoglu A, Ozbek U, Alanay Y. Rapid genome sequencing for critically ill infants: an inaugural pilot study from Turkey. Front Pediatr 2024; 12:1412880. [PMID: 39026936 PMCID: PMC11254770 DOI: 10.3389/fped.2024.1412880] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/05/2024] [Accepted: 06/12/2024] [Indexed: 07/20/2024] Open
Abstract
Introduction Rare and ultra-rare genetic conditions significantly contribute to infant morbidity and mortality, often presenting with atypical features and genetic heterogeneity that complicate management. Rapid genome sequencing (RGS) offers a timely and cost-effective approach to diagnosis, aiding in early clinical management and reducing unnecessary interventions. This pilot study represents the inaugural use of next-generation sequencing (NGS) as a diagnostic instrument for critically ill neonatal and pediatric ICU patients in a Turkish hospital setting. Methods Ten infants were enrolled based on predefined inclusion criteria, and trio RGS was performed. The mean age of the participants was 124 days, with congenital abnormalities being the most common indication for testing. Three patients had consanguineous parents. The mean turnaround time from enrollment to delivery of results was 169 h, with a diagnostic yield of 50%. Results Three patients received a definitive molecular diagnosis, impacting their clinical management. Two patients benefited from the exclusion of Mendelian conditions, leading to alternative diagnoses. Discussion This study demonstrates the feasibility and results of RGS in Turkish hospital settings, emphasizing the importance of timely genetic diagnosis in reducing the diagnostic odyssey for families and improving patient care. Further research is needed to evaluate the cost-effectiveness and applicability of RGS in the Turkish healthcare system for children with diseases of uncertain etiology.
Collapse
Affiliation(s)
- Bengisu Guner Yilmaz
- Department of Pediatrics, School of Medicine, Acibadem Mehmet Ali Aydinlar University, Istanbul, Turkey
| | - Ozlem Akgun-Dogan
- Division of Pediatric Genetics, Department of Pediatrics, School of Medicine, Acibadem Mehmet Ali Aydinlar University, Istanbul, Turkey
- Acibadem Mehmet Ali Aydinlar University Rare Diseases and Orphan Drugs Application and Research Center (ACURARE), Acibadem Mehmet Ali Aydinlar University, Istanbul, Turkey
- Department of Transitional Medicine, Health Sciences Institute, Acibadem Mehmet Ali Aydinlar University, Istanbul, Turkey
| | - Ozkan Ozdemir
- Acibadem Mehmet Ali Aydinlar University Rare Diseases and Orphan Drugs Application and Research Center (ACURARE), Acibadem Mehmet Ali Aydinlar University, Istanbul, Turkey
- Department of Genome Studies, Health Sciences Institute, Acibadem Mehmet Ali Aydinlar University, Istanbul, Turkey
- Division of Medical Biology, Department of Basic Sciences, School of Medicine, Acibadem Mehmet Ali Aydinlar University, Istanbul, Turkey
| | - Bayram Yuksel
- Genetic Diagnosis Center, SZA OMICS, Istanbul, Turkey
| | - Ozden Hatirnaz Ng
- Acibadem Mehmet Ali Aydinlar University Rare Diseases and Orphan Drugs Application and Research Center (ACURARE), Acibadem Mehmet Ali Aydinlar University, Istanbul, Turkey
- Division of Medical Biology, Department of Basic Sciences, School of Medicine, Acibadem Mehmet Ali Aydinlar University, Istanbul, Turkey
| | - Kaya Bilguvar
- Acibadem Mehmet Ali Aydinlar University Rare Diseases and Orphan Drugs Application and Research Center (ACURARE), Acibadem Mehmet Ali Aydinlar University, Istanbul, Turkey
- Department of Medical Genetics, School of Medicine, Acibadem Mehmet Ali Aydinlar University, Istanbul, Turkey
| | - Beril Ay
- School of Medicine, Acibadem Mehmet Ali Aydinlar University, Istanbul, Turkey
| | - Gulsah Sebnem Ozkose
- Department of Genome Studies, Health Sciences Institute, Acibadem Mehmet Ali Aydinlar University, Istanbul, Turkey
| | - Eylul Aydin
- Department of Genome Studies, Health Sciences Institute, Acibadem Mehmet Ali Aydinlar University, Istanbul, Turkey
| | - Ayca Yigit
- Department of Genome Studies, Health Sciences Institute, Acibadem Mehmet Ali Aydinlar University, Istanbul, Turkey
| | - Aybike Bulut
- Department of Genome Studies, Health Sciences Institute, Acibadem Mehmet Ali Aydinlar University, Istanbul, Turkey
| | | | - Serdar Beken
- Division of Neonatology, Department of Pediatrics, School of Medicine, Acibadem Mehmet Ali Aydinlar University, Istanbul, Turkey
| | - Selma Aktas
- Division of Neonatology, Department of Pediatrics, School of Medicine, Acibadem Mehmet Ali Aydinlar University, Istanbul, Turkey
| | - Atalay Demirel
- Division of Neonatology, Department of Pediatrics, School of Medicine, Acibadem Mehmet Ali Aydinlar University, Istanbul, Turkey
| | - Baran Cengiz Arcagok
- Division of Neonatology, Department of Pediatrics, School of Medicine, Acibadem Mehmet Ali Aydinlar University, Istanbul, Turkey
| | - Ebru Kazanci
- Division of Neonatology, Department of Pediatrics, School of Medicine, Acibadem Mehmet Ali Aydinlar University, Istanbul, Turkey
| | - İbrahim Bingol
- Division of Intensive Care, Department of Pediatrics, School of Medicine, Acibadem Mehmet Ali Aydinlar University, Istanbul, Turkey
| | - Ozge Umur
- Division of Intensive Care, Department of Pediatrics, School of Medicine, Acibadem Mehmet Ali Aydinlar University, Istanbul, Turkey
| | - Guntulu Sik
- Division of Intensive Care, Department of Pediatrics, School of Medicine, Acibadem Mehmet Ali Aydinlar University, Istanbul, Turkey
| | - Ugur Isik
- Division of Neurology, Department of Pediatrics, School of Medicine, Acibadem Mehmet Ali Aydinlar University, Istanbul, Turkey
| | - Melike Ersoy
- Division of Pediatric Metabolism, Department of Pediatrics, University of Health Sciences, Bakırkoy Dr. Sadi Konuk Training and Research, Istanbul, Turkey
| | - Ayse Korkmaz
- Division of Neonatology, Department of Pediatrics, School of Medicine, Acibadem Mehmet Ali Aydinlar University, Istanbul, Turkey
| | - Agop Citak
- Division of Intensive Care, Department of Pediatrics, School of Medicine, Acibadem Mehmet Ali Aydinlar University, Istanbul, Turkey
| | - Adil Mardinoglu
- Genetic Diagnosis Center, SZA OMICS, Istanbul, Turkey
- Faculty of Dentistry, Oral & Craniofacial Sciences, Centre for Host-Microbiome Interactions, King's College London, London, United Kingdom
- Science for Life Laboratory, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - Ugur Ozbek
- Acibadem Mehmet Ali Aydinlar University Rare Diseases and Orphan Drugs Application and Research Center (ACURARE), Acibadem Mehmet Ali Aydinlar University, Istanbul, Turkey
- Department of Genome Studies, Health Sciences Institute, Acibadem Mehmet Ali Aydinlar University, Istanbul, Turkey
- Department of Medical Genetics, School of Medicine, Acibadem Mehmet Ali Aydinlar University, Istanbul, Turkey
| | - Yasemin Alanay
- Division of Pediatric Genetics, Department of Pediatrics, School of Medicine, Acibadem Mehmet Ali Aydinlar University, Istanbul, Turkey
- Acibadem Mehmet Ali Aydinlar University Rare Diseases and Orphan Drugs Application and Research Center (ACURARE), Acibadem Mehmet Ali Aydinlar University, Istanbul, Turkey
- Department of Genome Studies, Health Sciences Institute, Acibadem Mehmet Ali Aydinlar University, Istanbul, Turkey
| |
Collapse
|
2
|
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.
Collapse
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
| |
Collapse
|
3
|
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.
Collapse
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
| |
Collapse
|