1
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Ikeri K, Quinones Cardona V, Joshi S, Menkiti O. Extracorporeal Membrane Oxygenation (ECMO) for suspected neonatal genetic diagnoses with cardiorespiratory failure. THE JOURNAL OF EXTRA-CORPOREAL TECHNOLOGY 2023; 55:147-152. [PMID: 37682215 PMCID: PMC10487301 DOI: 10.1051/ject/2023016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Accepted: 04/24/2023] [Indexed: 09/09/2023]
Abstract
Recent data describe an increasing use of extracorporeal membrane oxygenation (ECMO) in neonates with various clinical conditions besides primary respiratory or cardiac diagnoses. Infants with underlying genetic disorders characterized by cardiopulmonary failure pose unique management challenges. When pathognomonic dysmorphic features for common genetic diagnoses are not present, the prognosis is uncertain at best when determining ECMO candidacy. Lengthy turnaround times of genetic testing often delay definitive diagnosis during the ECMO course. Clinical management pathways to guide practice and evidence to support the use of ECMO in rare genetic conditions are lacking. The decision to initiate ECMO is daunting but may be of benefit if the subsequent genetic diagnosis is non-lethal. In lethal genetic cases warranting discontinuation of care, the time spent on ECMO may still be advantageous as a bridge to diagnosis while allowing for parental bonding with the terminally ill infant. Diagnostic confirmation may also facilitate the attainment of closure for these parents. Here, we report our experience providing ECMO to three neonates presenting with cardiorespiratory failure and later diagnosed with rare genetic syndromes. We share the challenges faced, lessons learned, and outcomes of these critically ill neonates.
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Affiliation(s)
- Kelechi Ikeri
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Division of Neonatology, Department of Pediatrics, St. Christopher’s Hospital for Children Philadelphia PA 19134 USA
| | - Vilmaris Quinones Cardona
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Division of Neonatology, Department of Pediatrics, St. Christopher’s Hospital for Children Philadelphia PA 19134 USA
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Drexel University College of Medicine Philadelphia PA USA
| | - Swosti Joshi
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Division of Neonatology, Department of Pediatrics, St. Christopher’s Hospital for Children Philadelphia PA 19134 USA
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Drexel University College of Medicine Philadelphia PA USA
| | - Ogechukwu Menkiti
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Division of Neonatology, Department of Pediatrics, St. Christopher’s Hospital for Children Philadelphia PA 19134 USA
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Drexel University College of Medicine Philadelphia PA USA
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2
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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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3
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Rimoldi M, Rinaldi B, Villa R, Cerasani J, Beltrami B, Iascone M, Silipigni R, Boito S, Gangi S, Colombo L, Porro M, Cesaretti C, Bedeschi MF. Congenital diaphragmatic hernia in Coffin Siris syndrome: Further evidence from two cases. Am J Med Genet A 2023; 191:605-611. [PMID: 36416235 DOI: 10.1002/ajmg.a.63054] [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: 05/03/2022] [Revised: 08/08/2022] [Accepted: 11/08/2022] [Indexed: 11/24/2022]
Abstract
Coffin-Siris Syndrome (CSS) is a rare multi-system dominant condition with a variable clinical presentation mainly characterized by hypoplasia/aplasia of the nail and/or distal phalanx of the fifth digit, coarse facies, hirsutism/hypertrichosis, developmental delay and intellectual disability of variable degree and growth impairment. Congenital anomalies may include cardiac, genitourinary and central nervous system malformations whereas congenital diaphragmatic hernia (CDH) is rarely reported. The genes usually involved in CSS pathogenesis are ARID1B (most frequently), SMARCA4, SMARCB1, ARID1A, SMARCE1, DPF2, and PHF6. Here, we present two cases of CSS presenting with CDH, for whom Whole Exome Sequencing (WES) identified two distinct de novo heterozygous causative variants, one in ARID1B (case 1) and one in SMARCA4 (case 2). Due to the rarity of CDH in CSS, in both cases the occurrence of CDH did not represent a predictive sign of CSS but, on the other hand, prompted genetic testing before (case 1) or independently (case 2) from the clinical hypothesis of CSS. We provide further evidence of the association between CSS and CDH, reviewed previous cases from literature and discuss possible functional links to related conditions.
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Affiliation(s)
- Martina Rimoldi
- Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Medical Genetics Unit, Milan, Italy
| | - Berardo Rinaldi
- Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Medical Genetics Unit, Milan, Italy
| | - Roberta Villa
- Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Medical Genetics Unit, Milan, Italy
| | - Jacopo Cerasani
- Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Neonatal Intensive Care Unit (NICU), Department of Clinical Science and Community Health, Università degli Studi di Milano, Milan, Italy
| | - Benedetta Beltrami
- Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Medical Genetics Unit, Milan, Italy
| | - Maria Iascone
- Ospedale Papa Giovanni XXIII, Laboratory of Medical Genetics, Bergamo, Italy
| | - Rosamaria Silipigni
- Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Laboratory of Medical Genetics, Milan, Italy
| | - Simona Boito
- Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Fetal Medicine and Surgery Service, Milan, Italy
| | - Silvana Gangi
- Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Neonatal Intensive Care Unit (NICU), Department of Clinical Science and Community Health, Università degli Studi di Milano, Milan, Italy
| | - Lorenzo Colombo
- Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Neonatal Intensive Care Unit (NICU), Department of Clinical Science and Community Health, Università degli Studi di Milano, Milan, Italy
| | - Matteo Porro
- Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Pediatric Physical Medicine and Rehabilitation Unit, Milan, Italy
| | - Claudia Cesaretti
- Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Medical Genetics Unit, Milan, Italy
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4
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Asegaonkar P, Kotecha U, Dongre M, Mistri M, Sharda S. Expanding the spectrum of ADNP-related disorder-Antenatally diagnosed congenital diaphragmatic hernia and a novel de novo mutation in ADNP gene. Am J Med Genet A 2023; 191:275-279. [PMID: 36321748 DOI: 10.1002/ajmg.a.63017] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2022] [Revised: 09/07/2022] [Accepted: 09/24/2022] [Indexed: 12/13/2022]
Abstract
De novo heterozygous ADNP variants have been associated with a complex neurological phenotype characterized primarily by neurodevelopmental delay. Cardiac and renal anomalies have additionally been observed in a few patients. All reported cases to date have been ascertained postnatally. Congenital diaphragmatic hernia (CDH) has been previously observed in one child diagnosed with a de novo ADNP-related neurodevelopmental disorder. We report a fetus who presented with syndromic CDH associated with a de novo heterozygous ADNP variant.
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Affiliation(s)
| | | | | | - Mehul Mistri
- Neuberg Centre for Genomic Medicine, Ahmedabad, India
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5
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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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6
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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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7
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Hardcastle A, Berry AM, Campbell IM, Zhao X, Liu P, Gerard AE, Rosenfeld JA, Sisoudiya SD, Hernandez-Garcia A, Loddo S, Di Tommaso S, Novelli A, Dentici ML, Capolino R, Digilio MC, Graziani L, Rustad CF, Neas K, Ferrero GB, Brusco A, Di Gregorio E, Wellesley D, Beneteau C, Joubert M, Van Den Bogaert K, Boogaerts A, McMullan DJ, Dean J, Giuffrida MG, Bernardini L, Varghese V, Shannon NL, Harrison RE, Lam WWK, McKee S, Turnpenny PD, Cole T, Morton J, Eason J, Jones MC, Hall R, Wright M, Horridge K, Shaw CA, Chung WK, Scott DA. Identifying phenotypic expansions for congenital diaphragmatic hernia plus (CDH+) using DECIPHER data. Am J Med Genet A 2022; 188:2958-2968. [PMID: 35904974 PMCID: PMC9474674 DOI: 10.1002/ajmg.a.62919] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 06/28/2022] [Accepted: 07/10/2022] [Indexed: 01/31/2023]
Abstract
Congenital diaphragmatic hernia (CDH) can occur in isolation or in conjunction with other birth defects (CDH+). A molecular etiology can only be identified in a subset of CDH cases. This is due, in part, to an incomplete understanding of the genes that contribute to diaphragm development. Here, we used clinical and molecular data from 36 individuals with CDH+ who are cataloged in the DECIPHER database to identify genes that may play a role in diaphragm development and to discover new phenotypic expansions. Among this group, we identified individuals who carried putatively deleterious sequence or copy number variants affecting CREBBP, SMARCA4, UBA2, and USP9X. The role of these genes in diaphragm development was supported by their expression in the developing mouse diaphragm, their similarity to known CDH genes using data from a previously published and validated machine learning algorithm, and/or the presence of CDH in other individuals with their associated genetic disorders. Our results demonstrate how data from DECIPHER, and other public databases, can be used to identify new phenotypic expansions and suggest that CREBBP, SMARCA4, UBA2, and USP9X play a role in diaphragm development.
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Affiliation(s)
- Amy Hardcastle
- Department of Microbiology and Molecular Biology, College of Life Sciences, Brigham Young University, Provo, UT, USA
| | - Aliska M. Berry
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Ian M. Campbell
- Division of Human Genetics, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Xiaonan Zhao
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Baylor Genetics, Houston, TX, USA
| | - Pengfei Liu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Baylor Genetics, Houston, TX, USA
| | - Amanda E. Gerard
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Texas Children’s Hospital, Houston, TX, USA
| | - Jill A. Rosenfeld
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Saumya D. Sisoudiya
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | | | - Sara Loddo
- Translational Cytogenomics Research Unit, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy
| | - Silvia Di Tommaso
- Translational Cytogenomics Research Unit, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy
| | - Antonio Novelli
- Translational Cytogenomics Research Unit, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy
| | - Maria L. Dentici
- Medical Genetics Unit, Academic Department of Pediatrics, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy
- Genetics and Rare Disease Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, Rome, Italy
| | - Rossella Capolino
- Medical Genetics Unit, Academic Department of Pediatrics, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy
- Genetics and Rare Disease Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, Rome, Italy
| | - Maria C. Digilio
- Medical Genetics Unit, Academic Department of Pediatrics, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy
- Genetics and Rare Disease Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, Rome, Italy
| | - Ludovico Graziani
- Genetics and Rare Disease Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, Rome, Italy
- Medical Genetics Unit, Tor Vergata Hospital, Rome, Italy
| | - Cecilie F. Rustad
- Department of Medical Genetics, Oslo University Hospital, Oslo, Norway
| | | | - Giovanni B. Ferrero
- Department of Clinical and Biological Sciences, University of Torino, Orbassano, Italy
| | - Alfredo Brusco
- Department of Medical Sciences, University of Torino, Torino, Italy
- Città della Salute e della Scienza University Hospital, Torino, Italy
| | | | - Diana Wellesley
- Wessex Clinical Genetics Service, Princess Anne Hospital, Southampton, Hampshire, UK
- University Hospital Southampton, Southampton, Hampshire, UK
| | - Claire Beneteau
- Nantes Université, CHU de Nantes, UF 9321 de Fœtopathologie et Génétique, Nantes, France
| | - Madeleine Joubert
- Nantes Université, CHU de Nantes, UF 9321 de Fœtopathologie et Génétique, Nantes, France
| | - Kris Van Den Bogaert
- Center for Human Genetics, University Hospitals Leuven–KU Leuven, Leuven, Belgium
| | - Anneleen Boogaerts
- Center for Human Genetics, University Hospitals Leuven–KU Leuven, Leuven, Belgium
| | - Dominic J. McMullan
- West Midlands Regional Genetics Laboratory, Birmingham Women’s and Children’s NHS Foundation Trust, UK
| | - John Dean
- Clinical Genetics Service, Ashgrove House, NHS Grampian, Aberdeen, UK
| | - Maria G. Giuffrida
- Medical Genetics Unit, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Laura Bernardini
- Medical Genetics Unit, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | | | - Nora L Shannon
- Clinical Genetics Service, Nottingham University Hospitals NHS Trust, Nottingham, UK
| | - Rachel E. Harrison
- Clinical Genetics Service, Nottingham University Hospitals NHS Trust, Nottingham, UK
| | - Wayne W. K. Lam
- South East of Scotland Clinical Genetics Service, Western General Hospital, Edinburgh, Scotland
| | - Shane McKee
- Northern Ireland Regional Genetics Service, Belfast City Hospital, Belfast, UK
| | - Peter D. Turnpenny
- Clinical Genetics Department, Royal Devon and Exeter Hospital, Exeter, UK
| | - Trevor Cole
- Clinical Genetics Unit, Birmingham Women’s Hospital, Birmingham, UK
| | - Jenny Morton
- Clinical Genetics Unit, Birmingham Women’s Hospital, Birmingham, UK
| | - Jacqueline Eason
- Clinical Genetics Service, Nottingham University Hospitals NHS Trust, Nottingham, UK
| | - Marilyn C. Jones
- University of California, San Diego and Rady Children’s Hospital, San Diego, CA, USA
| | - Rebecca Hall
- The Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Michael Wright
- The Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Karen Horridge
- South Tyneside and Sunderland NHS Foundation Trust, Sunderland, UK
| | - Chad A. Shaw
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Wendy K. Chung
- Department of Pediatrics, Columbia University, New York, NY, USA
- Department of Medicine, Columbia University, New York, NY, USA
| | - Daryl A. Scott
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Texas Children’s Hospital, Houston, TX, USA
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX, USA
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8
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Gofin Y, Zhao X, Gerard A, Scaglia F, Wangler MF, Vergano SAS, Scott DA. Evidence for an association between Coffin-Siris syndrome and congenital diaphragmatic hernia. Am J Med Genet A 2022; 188:2718-2723. [PMID: 35796094 PMCID: PMC9378577 DOI: 10.1002/ajmg.a.62889] [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: 04/29/2022] [Revised: 06/15/2022] [Accepted: 06/21/2022] [Indexed: 01/25/2023]
Abstract
Coffin-Siris syndrome (CSS) is an autosomal dominant neurodevelopmental syndrome that can present with a variety of structural birth defects. Pathogenic variants in 12 genes have been shown to cause CSS. Most of these genes encode proteins that are a part of the mammalian switch/sucrose non-fermentable (mSWI/SNF; BAF) complex. An association between genes that cause CSS and congenital diaphragmatic hernia (CDH) has been suggested based on case reports and the analysis of CSS and CDH cohorts. Here, we describe an unpublished individual with CSS and CDH, and we report additional clinical information on four published cases. Data from these individuals, and a review of the literature, provide evidence that deleterious variants in ARID1B, ARID1A, SMARCB1, SMARCA4, SMARCE1, ARID2, DPF2, and SMARCC2, which are associated with CSS types 1-8, respectively, are associated with the development of CDH. This suggests that additional genetic testing to identify a separate cause of CDH in an individual with CSS may be unwarranted, and that comprehensive genetic testing for individuals with non-isolated CDH should include an evaluation of CSS-related genes. These data also suggest that the mSWI/SNF (BAF) complex may play an important role in diaphragm development.
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MESH Headings
- Abnormalities, Multiple/diagnosis
- Abnormalities, Multiple/genetics
- Chromosomal Proteins, Non-Histone
- DNA Helicases/genetics
- DNA-Binding Proteins/genetics
- Face/abnormalities
- Hand Deformities, Congenital/complications
- Hand Deformities, Congenital/diagnosis
- Hand Deformities, Congenital/genetics
- Hernias, Diaphragmatic, Congenital/genetics
- Hernias, Diaphragmatic, Congenital/pathology
- Humans
- Intellectual Disability/pathology
- Micrognathism/genetics
- Micrognathism/pathology
- Neck/abnormalities
- Nuclear Proteins/genetics
- Transcription Factors/genetics
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Affiliation(s)
- Yoel Gofin
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Texas Children’s Hospital, Houston, TX 77030
| | - Xiaonan Zhao
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Baylor Genetics, Houston, TX 77021, USA
| | - Amanda Gerard
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Texas Children’s Hospital, Houston, TX 77030
| | - Fernando Scaglia
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Texas Children’s Hospital, Houston, TX 77030
- Joint BCM-CUHK Center of Medical Genetics, Prince of Wales Hospital, ShaTin, Hong Kong SAR
| | - Michael F. Wangler
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Texas Children’s Hospital, Houston, TX 77030
| | - Samantha A. Schrier Vergano
- Division of Medical Genetics and Metabolism, Children’s Hospital of The King’s Daughters, Norfolk, VA 23507, USA
- Department of Pediatrics, Eastern Virginia Medical School, Norfolk, VA 23501, USA
| | - Daryl A. Scott
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Texas Children’s Hospital, Houston, TX 77030
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX 77030, USA
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9
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van der Sluijs PJ, Joosten M, Alby C, Attié-Bitach T, Gilmore K, Dubourg C, Fradin M, Wang T, Kurtz-Nelson EC, Ahlers KP, Arts P, Barnett CP, Ashfaq M, Baban A, van den Born M, Borrie S, Busa T, Byrne A, Carriero M, Cesario C, Chong K, Cueto-González AM, Dempsey JC, Diderich KEM, Doherty D, Farholt S, Gerkes EH, Gorokhova S, Govaerts LCP, Gregersen PA, Hickey SE, Lefebvre M, Mari F, Martinovic J, Northrup H, O'Leary M, Parbhoo K, Patrier S, Popp B, Santos-Simarro F, Stoltenburg C, Thauvin-Robinet C, Thompson E, Vulto-van Silfhout AT, Zahir FR, Scott HS, Earl RK, Eichler EE, Vora NL, Wilnai Y, Giordano JL, Wapner RJ, Rosenfeld JA, Haak MC, Santen GWE. Discovering a new part of the phenotypic spectrum of Coffin-Siris syndrome in a fetal cohort. Genet Med 2022; 24:1753-1760. [PMID: 35579625 PMCID: PMC9378544 DOI: 10.1016/j.gim.2022.04.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Revised: 04/04/2022] [Accepted: 04/04/2022] [Indexed: 02/07/2023] Open
Abstract
PURPOSE Genome-wide sequencing is increasingly being performed during pregnancy to identify the genetic cause of congenital anomalies. The interpretation of prenatally identified variants can be challenging and is hampered by our often limited knowledge of prenatal phenotypes. To better delineate the prenatal phenotype of Coffin-Siris syndrome (CSS), we collected clinical data from patients with a prenatal phenotype and a pathogenic variant in one of the CSS-associated genes. METHODS Clinical data was collected through an extensive web-based survey. RESULTS We included 44 patients with a variant in a CSS-associated gene and a prenatal phenotype; 9 of these patients have been reported before. Prenatal anomalies that were frequently observed in our cohort include hydrocephalus, agenesis of the corpus callosum, hypoplastic left heart syndrome, persistent left vena cava, diaphragmatic hernia, renal agenesis, and intrauterine growth restriction. Anal anomalies were frequently identified after birth in patients with ARID1A variants (6/14, 43%). Interestingly, pathogenic ARID1A variants were much more frequently identified in the current prenatal cohort (16/44, 36%) than in postnatal CSS cohorts (5%-9%). CONCLUSION Our data shed new light on the prenatal phenotype of patients with pathogenic variants in CSS genes.
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Affiliation(s)
| | - Marieke Joosten
- Department of Clinical Genetics, Erasmus MC, University Medical Center Rotterdam, The Netherlands
| | - Caroline Alby
- Department of Histo-Embryology and Cytogenetics, Necker-Enfants Malades Hospital, AP-HP, Paris, France; National Institute of Health and Medical Research (INSERM), University of Paris, Imagine Institute, Paris, France
| | - Tania Attié-Bitach
- Department of Histo-Embryology and Cytogenetics, Necker-Enfants Malades Hospital, AP-HP, Paris, France; National Institute of Health and Medical Research (INSERM), University of Paris, Imagine Institute, Paris, France
| | - Kelly Gilmore
- Department of Obstetrics and Gynecology, Division of Maternal-Fetal Medicine, University of North Carolina School of Medicine, Chapel Hill, NC
| | - Christele Dubourg
- Department of Molecular Genetics and Genomics, Rennes University Hospital Center (CHU), Rennes, France
| | - Mélanie Fradin
- Department of Clinical Genetics, Centre de Référence Maladies Rares Anomalies du Développement, CHU de Rennes, Rennes, France
| | - Tianyun Wang
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA
| | | | - Kaitlyn P Ahlers
- Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle, WA
| | - Peer Arts
- Department of Genetics and Molecular Pathology, Centre for Cancer Biology, An Alliance Between SA Pathology and the University of South Australia, Adelaide, South Australia, Australia
| | - Christopher P Barnett
- Paediatric and Reproductive Genetics Unit, Women's and Children's Hospital, North Adelaide, South Australia, Australia; School of Medicine, University of Adelaide, Adelaide, South Australia, Australia
| | - Myla Ashfaq
- Department of Pediatrics, Division of Medical Genetics, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX
| | - Anwar Baban
- Department of Pediatric Cardiology and Cardiac Surgery, Bambino Gesù Children's Hospital and Research Institute, Scientific Institute for Research, Hospitalization and Healthcare, Rome, Italy
| | - Myrthe van den Born
- Department of Clinical Genetics, Erasmus MC, University Medical Center Rotterdam, The Netherlands
| | - Sarah Borrie
- Department of Pediatrics, Division of Medical Genetics, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX
| | - Tiffany Busa
- Service de Génétique Médicale, Hôpital de la Timone, APHM, Marseille, France; Department of Medical Genetics, Timone Hospital, APHM, Marseille, France
| | - Alicia Byrne
- Department of Genetics and Molecular Pathology, Centre for Cancer Biology, An Alliance Between SA Pathology and the University of South Australia, Adelaide, South Australia, Australia; Australian Genomics, Parkville, Victoria, Australia
| | | | - Claudia Cesario
- Medical Genetics Lab, Bambino Gesù Children's Hospital and Research Institute, Scientific Institute for Research, Hospitalization and Healthcare, Rome, Italy
| | - Karen Chong
- The Prenatal Diagnosis and Medical Genetics Program, Department of Obstetrics and Gynecology, Mount Sinai Hospital, University of Toronto, Toronto, Ontario, Canada; Division of Clinical and Metabolic Genetics, Department of Pediatrics, The Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada
| | - Anna Maria Cueto-González
- Department of Clinical and Molecular Genetics, Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain
| | | | - Karin E M Diderich
- Department of Clinical Genetics, Erasmus MC, University Medical Center Rotterdam, The Netherlands
| | - Dan Doherty
- Department of Pediatrics, University of Washington, Seattle, WA; Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA
| | - Stense Farholt
- Department of Children and Adolescents, University Hospital Rigshospitalet, Copenhagen, Denmark
| | - Erica H Gerkes
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Svetlana Gorokhova
- Service de Génétique Médicale, Hôpital de la Timone, APHM, Marseille, France; Department of Medical Genetics, Timone Hospital, APHM, Marseille, France; Aix Marseille University, INSERM, Marseille Medical Genetics, U 1251, Marseille, France
| | - Lutgarde C P Govaerts
- Department of Clinical Genetics, Erasmus MC, University Medical Center Rotterdam, The Netherlands
| | - Pernille A Gregersen
- Department of Clinical Genetics, Aarhus University Hospital, Aarhus, Denmark; Pediatrics and Adolescent Medicine, Centre for Rare Diseases, Aarhus University Hospital, Aarhus, Denmark
| | - Scott E Hickey
- Division of Genetic & Genomic Medicine, Nationwide Children's Hospital, Columbus, OH; Department of Pediatrics, The Ohio State University College of Medicine, Columbus, OH
| | - Mathilde Lefebvre
- Inserm UMR 1231 GAD, Genetics of Developmental Anomalies, F21000 Dijon, France; Functional Unit of Fœtal Pathology, Pathological Anatomy Department, CHR Orleans, Orleans, France
| | | | - Jelena Martinovic
- Department of Histo-Embryology and Cytogenetics, Necker-Enfants Malades Hospital, AP-HP, Paris, France; Unit of Fetal Pathology, Antoine Beclere Hospital, AP-HP, Clamart, France
| | - Hope Northrup
- Department of Pediatrics, Division of Medical Genetics, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX
| | - Melanie O'Leary
- Broad Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, MA
| | - Kareesma Parbhoo
- Division of Genetic & Genomic Medicine, Nationwide Children's Hospital, Columbus, OH
| | - Sophie Patrier
- Department of Pathology, CHU Charles Nicolle, Rouen, France
| | - Bernt Popp
- Institute of Human Genetics, University Hospital Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Fernando Santos-Simarro
- Institute of Medical and Molecular Genetics, Hospital Universitario La Paz, Hospital La Paz Institute for Health Research, Centre for Biomedical Network Research on Rare Diseases, Instituto de Salud Carlos III, Madrid, Spain
| | - Corinna Stoltenburg
- Department of Neuropaediatrics, Charité - Berlin University of Medicine, Berlin, Germany
| | - Christel Thauvin-Robinet
- Inserm UMR 1231 GAD, Genetics of Developmental Anomalies, F21000 Dijon, France; Reference Center for Rare Diseases, « Intellectual Disabilities from rare causes », CHU Dijon Bourgogne, F21000 Dijon, France
| | - Elisabeth Thompson
- Paediatric and Reproductive Genetics Unit, Women's and Children's Hospital, North Adelaide, South Australia, Australia; School of Medicine, University of Adelaide, Adelaide, South Australia, Australia
| | - Anneke T Vulto-van Silfhout
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Farah R Zahir
- Department of Medical Genetics, University of British Columbia, Children's and Women's Hospital, Vancouver, British Columbia, Canada
| | - Hamish S Scott
- Department of Genetics and Molecular Pathology, Centre for Cancer Biology, An Alliance Between SA Pathology and the University of South Australia, Adelaide, South Australia, Australia; School of Medicine, University of Adelaide, Adelaide, South Australia, Australia; Australian Genomics, Parkville, Victoria, Australia; ACRF Cancer Genomics Facility, Centre for Cancer Biology, An Alliance Between SA Pathology and the University of South Australia, Adelaide, South Australia, Australia
| | - Rachel K Earl
- Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle, WA
| | - Evan E Eichler
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA; Howard Hughes Medical Institute, University of Washington, Seattle, WA
| | - Neeta L Vora
- Department of Obstetrics and Gynecology, Division of Maternal-Fetal Medicine, University of North Carolina School of Medicine, Chapel Hill, NC
| | - Yael Wilnai
- Genetic Institute, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel
| | - Jessica L Giordano
- Institute for Genomic Medicine, Columbia University Medical Center, New York, NY; Division of Maternal-Fetal Medicine, Department of Obstetrics and Gynecology, Columbia University Vagelos Medical Center, New York, NY
| | - Ronald J Wapner
- Institute for Genomic Medicine, Columbia University Medical Center, New York, NY; Division of Maternal-Fetal Medicine, Department of Obstetrics and Gynecology, Columbia University Vagelos Medical Center, New York, NY
| | - Jill A Rosenfeld
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX; Baylor Genetics Laboratories, Houston, TX
| | - Monique C Haak
- Department of Obstetrics and Fetal Medicine, Leiden University Medical Center, Leiden, Netherlands
| | - Gijs W E Santen
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands.
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10
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Yu QX, Jing XY, Lin XM, Zhen L, Li DZ. Prenatal diagnosis of Coffin-Siris syndrome: WHAT ARE THE FETAL FEATURES? Prenat Diagn 2022; 42:1488-1492. [PMID: 35801292 DOI: 10.1002/pd.6213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Revised: 06/28/2022] [Accepted: 07/05/2022] [Indexed: 11/05/2022]
Abstract
OBJECTIVE To present both our center's and previously reported experience of prenatal diagnosis of Coffin-Siris syndrome (CSS) with regard to the laboratory testing and fetal features of this syndrome. METHODS This was a retrospective study of eight pregnancies with fetal CSS identified by prenatal or postnatal genetic testing. Clinical and laboratory data were collected and reviewed for these cases, including maternal demographics, prenatal sonographic findings, chromosomal microarray and exome sequencing (ES) results, and pregnancy outcomes. RESULTS A total of eight cases of fetal CSS based on molecular testing were detected. Two cases presented with an increased nuchal translucency (NT) in the first trimester. The remaining six were identified at the second trimester scan. Agenesis of the corpus callosum (ACC) was the most common sonographic finding, accounting for 5/7 (71.4%) cases in which a second trimester sonogram was performed: four had ACC as an isolated finding, and one had additional features of cerebellar hypoplasia and left congenital diaphragmatic hernia. CONCLUSION CSS should be included in the differential diagnosis when ACC is found by prenatal ultrasound. Both chromosomal microarray and ES should be options when counseling patients with a structurally anomalous fetus. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Qiu-Xia Yu
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center affiliated to Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Xiang-Yi Jing
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center affiliated to Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Xiao-Mei Lin
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center affiliated to Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Li Zhen
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center affiliated to Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Dong-Zhi Li
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center affiliated to Guangzhou Medical University, Guangzhou, Guangdong, China
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11
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Molecular Mechanisms Contributing to the Etiology of Congenital Diaphragmatic Hernia: A Review and Novel Cases. J Pediatr 2022; 246:251-265.e2. [PMID: 35314152 DOI: 10.1016/j.jpeds.2022.03.023] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Revised: 03/01/2022] [Accepted: 03/15/2022] [Indexed: 12/25/2022]
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12
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ZHANG-RUTLEDGE K, OWEN M, SWEENEY NM, DIMMOCK D, KINGSMORE SF, LAURENT LC. Retrospective identification of prenatal fetal anomalies associated with diagnostic neonatal genomic sequencing results. Prenat Diagn 2022; 42:705-716. [PMID: 35141907 PMCID: PMC9886440 DOI: 10.1002/pd.6111] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2021] [Revised: 01/04/2022] [Accepted: 02/03/2022] [Indexed: 02/01/2023]
Abstract
OBJECTIVE To determine which types of fetal anomalies are associated with postnatal diagnoses of genetic diseases by genomic sequencing and to assess how prenatal genomic sequencing could affect clinical management. METHOD This was a secondary analysis of the second Newborn Sequencing in Genomic Medicine and Public Health study that compared fetal imaging results in critically ill infants who had actionable versus negative postnatal genomic sequencing results. RESULTS Of 213 infants who received genomic sequencing, 80 had available prenatal ultrasounds. Twenty-one (26%) of these were found to have genetic diseases by genomic sequencing. Fourteen (67%) of the 21 with genetic diseases had suspected anomalies prenatally, compared with 33 (56%) of 59 with negative results. Among fetuses with suspected anomalies, genetic diseases were 4.5 times more common in those with multiple anomalies and 6.7 times more common in those with anomalies of the extremities compared to those with negative results. Had the genetic diseases been diagnosed prenatally, clinical management would have been altered in 13 of 14. CONCLUSION Critically ill infants with diagnostic genomic sequencing were more likely to have multiple anomalies and anomalies of the extremities on fetal imaging. Among almost all infants with suspected fetal anomalies and diagnostic genomic sequencing results, prenatal diagnosis would have likely altered clinical management.
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Affiliation(s)
- Kathy ZHANG-RUTLEDGE
- Department of Obstetrics, Gynecology, and Reproductive Sciences; University of California, San Diego, CA
| | - Mallory OWEN
- Rady Children’s Institute of Genomic Medicine, San Diego, CA
| | - Nathaly M. SWEENEY
- Rady Children’s Institute of Genomic Medicine, San Diego, CA, Department of Pediatrics; University of California, San Diego, CA
| | - David DIMMOCK
- Rady Children’s Institute of Genomic Medicine, San Diego, CA
| | | | - Louise C. LAURENT
- Department of Obstetrics, Gynecology, and Reproductive Sciences; University of California, San Diego, CA
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13
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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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14
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Nicholas TJ, Al‐Sweel N, Farrell A, Mao R, Bayrak‐Toydemir P, Miller CE, Bentley D, Palmquist R, Moore B, Hernandez EJ, Cormier MJ, Fredrickson E, Noble K, Rynearson S, Holt C, Karren M, Bonkowsky JL, Tristani‐Firouzi M, Yandell M, Marth G, Quinlan AR, Brunelli L, Toydemir R, Shayota BJ, Carey JC, Boyden SE, Malone Jenkins S. Comprehensive variant calling from whole-genome sequencing identifies a complex inversion that disrupts ZFPM2 in familial congenital diaphragmatic hernia. Mol Genet Genomic Med 2022; 10:e1888. [PMID: 35119225 PMCID: PMC9000945 DOI: 10.1002/mgg3.1888] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 01/14/2022] [Accepted: 01/18/2022] [Indexed: 01/03/2023] Open
Abstract
BACKGROUND Genetic disorders contribute to significant morbidity and mortality in critically ill newborns. Despite advances in genome sequencing technologies, a majority of neonatal cases remain unsolved. Complex structural variants (SVs) often elude conventional genome sequencing variant calling pipelines and will explain a portion of these unsolved cases. METHODS As part of the Utah NeoSeq project, we used a research-based, rapid whole-genome sequencing (WGS) protocol to investigate the genomic etiology for a newborn with a left-sided congenital diaphragmatic hernia (CDH) and cardiac malformations, whose mother also had a history of CDH and atrial septal defect. RESULTS Using both a novel, alignment-free and traditional alignment-based variant callers, we identified a maternally inherited complex SV on chromosome 8, consisting of an inversion flanked by deletions. This complex inversion, further confirmed using orthogonal molecular techniques, disrupts the ZFPM2 gene, which is associated with both CDH and various congenital heart defects. CONCLUSIONS Our results demonstrate that complex structural events, which often are unidentifiable or not reported by clinically validated testing procedures, can be discovered and accurately characterized with conventional, short-read sequencing and underscore the utility of WGS as a first-line diagnostic tool.
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Affiliation(s)
- Thomas J. Nicholas
- Department of Human Genetics, Utah Center for Genetic DiscoveryUniversity of UtahSalt Lake CityUSA
| | - Najla Al‐Sweel
- ARUP LaboratoriesSalt Lake CityUSA
- Department of PathologyUniversity of UtahSalt Lake CityUSA
| | - Andrew Farrell
- Department of Human Genetics, Utah Center for Genetic DiscoveryUniversity of UtahSalt Lake CityUSA
| | - Rong Mao
- ARUP LaboratoriesSalt Lake CityUSA
- Department of PathologyUniversity of UtahSalt Lake CityUSA
| | - Pinar Bayrak‐Toydemir
- ARUP LaboratoriesSalt Lake CityUSA
- Department of PathologyUniversity of UtahSalt Lake CityUSA
| | | | - Dawn Bentley
- Division of Neonatology, Department of PediatricsUniversity of Utah School of MedicineSalt Lake CityUSA
| | - Rachel Palmquist
- Division of Pediatric Neurology, Department of PediatricsUniversity of Utah School of MedicineSalt Lake CityUSA
- Primary Children's Center for Personalized MedicineSalt Lake CityUSA
| | - Barry Moore
- Department of Human Genetics, Utah Center for Genetic DiscoveryUniversity of UtahSalt Lake CityUSA
| | - Edgar J. Hernandez
- Department of Human Genetics, Utah Center for Genetic DiscoveryUniversity of UtahSalt Lake CityUSA
| | - Michael J. Cormier
- Department of Human Genetics, Utah Center for Genetic DiscoveryUniversity of UtahSalt Lake CityUSA
| | | | | | - Shawn Rynearson
- Department of Human Genetics, Utah Center for Genetic DiscoveryUniversity of UtahSalt Lake CityUSA
| | - Carson Holt
- Department of Human Genetics, Utah Center for Genetic DiscoveryUniversity of UtahSalt Lake CityUSA
| | - Mary Anne Karren
- Department of Human Genetics, Utah Center for Genetic DiscoveryUniversity of UtahSalt Lake CityUSA
| | - Joshua L. Bonkowsky
- Division of Pediatric Neurology, Department of PediatricsUniversity of Utah School of MedicineSalt Lake CityUSA
- Primary Children's Center for Personalized MedicineSalt Lake CityUSA
| | - Martin Tristani‐Firouzi
- Division of Pediatric Cardiology, Department of PediatricsUniversity of Utah School of MedicineSalt Lake CityUSA
| | - Mark Yandell
- Department of Human Genetics, Utah Center for Genetic DiscoveryUniversity of UtahSalt Lake CityUSA
| | - Gabor Marth
- Department of Human Genetics, Utah Center for Genetic DiscoveryUniversity of UtahSalt Lake CityUSA
| | - Aaron R. Quinlan
- Department of Human Genetics, Utah Center for Genetic DiscoveryUniversity of UtahSalt Lake CityUSA
- Department of Biomedical InformaticsUniversity of UtahSalt Lake CityUSA
| | - Luca Brunelli
- Division of Neonatology, Department of PediatricsUniversity of Utah School of MedicineSalt Lake CityUSA
| | - Reha M. Toydemir
- ARUP LaboratoriesSalt Lake CityUSA
- Department of PathologyUniversity of UtahSalt Lake CityUSA
| | - Brian J. Shayota
- Division of Medical Genetics, Department of PediatricsUniversity of Utah School of MedicineSalt Lake CityUSA
| | - John C. Carey
- Division of Medical Genetics, Department of PediatricsUniversity of Utah School of MedicineSalt Lake CityUSA
| | - Steven E. Boyden
- Department of Human Genetics, Utah Center for Genetic DiscoveryUniversity of UtahSalt Lake CityUSA
| | - Sabrina Malone Jenkins
- Division of Neonatology, Department of PediatricsUniversity of Utah School of MedicineSalt Lake CityUSA
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15
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Scott DA, Gofin Y, Berry AM, Adams AD. Underlying genetic etiologies of congenital diaphragmatic hernia. Prenat Diagn 2022; 42:373-386. [PMID: 35037267 PMCID: PMC8924940 DOI: 10.1002/pd.6099] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 01/11/2022] [Accepted: 01/12/2022] [Indexed: 11/09/2022]
Abstract
Congenital diaphragmatic hernia (CDH) is often detectable prenatally. Advances in genetic testing have made it possible to obtain a molecular diagnosis in many fetuses with CDH. Here, we review the aneuploidies, copy number variants (CNVs), and single genes that have been clearly associated with CDH. We suggest that array-based CNV analysis, with or without a chromosome analysis, is the optimal test for identifying chromosomal abnormalities and CNVs in fetuses with CDH. To identify causative sequence variants, whole exome sequencing (WES) is the most comprehensive strategy currently available. Whole genome sequencing (WGS) with CNV analysis has the potential to become the most efficient and effective means of identifying an underlying diagnosis but is not yet routinely available for prenatal diagnosis. We describe how to overcome and address the diagnostic and clinical uncertainty that may remain after genetic testing, and review how a molecular diagnosis may impact recurrence risk estimations, mortality rates, and the availability and outcomes of fetal therapy. We conclude that after the prenatal detection of CDH, patients should be counseled about the possible genetic causes of the CDH, and the genetic testing modalities available to them, in accordance with generally accepted guidelines for pretest counseling in the prenatal setting.
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Affiliation(s)
- Daryl A. Scott
- Texas Children’s Hospital, Houston, TX, 77030,
USA,Department of Molecular and Human Genetics, Baylor College
of Medicine, Houston, TX, 77030, USA,Department of Molecular Physiology and Biophysics, Baylor
College of Medicine, Houston, TX, 77030, USA,Correspondence: Daryl A. Scott, R813, One Baylor
Plaza. BCM225, Houston, TX 77030, USA, Phone: +1 713-203-7242,
| | - Yoel Gofin
- Texas Children’s Hospital, Houston, TX, 77030,
USA,Department of Molecular and Human Genetics, Baylor College
of Medicine, Houston, TX, 77030, USA
| | - Aliska M. Berry
- Department of Molecular and Human Genetics, Baylor College
of Medicine, Houston, TX, 77030, USA
| | - April D. Adams
- Department of Molecular and Human Genetics, Baylor College
of Medicine, Houston, TX, 77030, USA,Department of Obstetrics and Gynecology, Division of
Maternal Fetal Medicine, Baylor College of Medicine, Houston, TX, 77030, USA
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16
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Scott TM, Campbell IM, Hernandez-Garcia A, Lalani SR, Liu P, Shaw CA, Rosenfeld JA, Scott DA. Clinical exome sequencing data reveal high diagnostic yields for congenital diaphragmatic hernia plus (CDH+) and new phenotypic expansions involving CDH. J Med Genet 2022; 59:270-278. [PMID: 33461977 PMCID: PMC8286264 DOI: 10.1136/jmedgenet-2020-107317] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2020] [Revised: 11/17/2020] [Accepted: 12/26/2020] [Indexed: 01/10/2023]
Abstract
BACKGROUND Congenital diaphragmatic hernia (CDH) is a life-threatening birth defect that often co-occurs with non-hernia-related anomalies (CDH+). While copy number variant (CNV) analysis is often employed as a diagnostic test for CDH+, clinical exome sequencing (ES) has not been universally adopted. METHODS We analysed a clinical database of ~12 000 test results to determine the diagnostic yields of ES in CDH+ and to identify new phenotypic expansions. RESULTS Among the 76 cases with an indication of CDH+, a molecular diagnosis was made in 28 cases for a diagnostic yield of 37% (28/76). A provisional diagnosis was made in seven other cases (9%; 7/76). Four individuals had a diagnosis of Kabuki syndrome caused by frameshift variants in KMT2D. Putatively deleterious variants in ALG12 and EP300 were each found in two individuals, supporting their role in CDH development. We also identified individuals with de novo pathogenic variants in FOXP1 and SMARCA4, and compound heterozygous pathogenic variants in BRCA2. The role of these genes in CDH development is supported by the expression of their mouse homologs in the developing diaphragm, their high CDH-specific pathogenicity scores generated using a previously validated algorithm for genome-scale knowledge synthesis and previously published case reports. CONCLUSION We conclude that ES should be ordered in cases of CDH+ when a specific diagnosis is not suspected and CNV analyses are negative. Our results also provide evidence in favour of phenotypic expansions involving CDH for genes associated with ALG12-congenital disorder of glycosylation, Rubinstein-Taybi syndrome, Fanconi anaemia, Coffin-Siris syndrome and FOXP1-related disorders.
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Affiliation(s)
- Tiana M. Scott
- Department of Microbiology and Molecular Biology, College of Life Sciences, Brigham Young University, Provo, UT, 84602, USA,Texas Children’s Hospital, Houston, TX, 77030, USA
| | - Ian M. Campbell
- Division of Human Genetics, Children’s Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Andres Hernandez-Garcia
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Seema R. Lalani
- Texas Children’s Hospital, Houston, TX, 77030, USA,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Pengfei Liu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA,Baylor Genetics, Houston, TX, 77021, USA
| | - Chad A. Shaw
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Jill A. Rosenfeld
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Daryl A. Scott
- Texas Children’s Hospital, Houston, TX, 77030, USA,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA,Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX, 77030, USA,Correspondence Daryl A. Scott, R813, One Baylor Plaza. BCM225, Houston, TX 77030, USA, , Phone: +1 713-203-7242
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17
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Slavotinek A, Lefebvre M, Brehin AC, Thauvin C, Patrier S, Sparks TN, Norton M, Yu J, Huang E. Prenatal presentation of multiple anomalies associated with haploinsufficiency for ARID1A. Eur J Med Genet 2022; 65:104407. [PMID: 34942405 PMCID: PMC9162882 DOI: 10.1016/j.ejmg.2021.104407] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2021] [Revised: 11/04/2021] [Accepted: 12/14/2021] [Indexed: 02/03/2023]
Abstract
The ARID1A gene is an infrequent cause of Coffin-Siris syndrome (CSS) and has been associated with severe to profound developmental delays and hypotonia in addition to characteristic craniofacial and digital findings. We present three fetuses and a male neonate with ventriculomegaly/hydrocephalus, absence of the corpus callosum (ACC), cerebellar hypoplasia, retinal dysplasia, lung lobulation defects, renal dysplasia, imperforate or anteriorly placed anus, thymus hypoplasia and a single umbilical artery. Facial anomalies included downslanting palpebral fissures, wide-spaced eyes, low-set and posteriorly rotated ears, a small jaw, widely spaced nipples and hypoplastic nails. All fetuses had heterozygous variants predicting premature protein truncation in ARID1A (c.4886dup:p.Val1630Cysfs*18; c.4860dup:p.Pro1621Thrfs*27; and c.175G>T:p.Glu59*) and the baby's microarray demonstrated mosaicism for a deletion at chromosome 1p36.11 (arr[GRCh37] 1p36.11(26,797,508_27,052,080)×1∼2), that contained the first exon of ARID1A. Although malformations, in particular ACC, have been described with CSS caused by pathogenic variants in ARID1A, prenatal presentations associated with this gene are rare. Retinal dysplasia, lung lobulation defects and absent thymus were novel findings in association with ARID1A variants. Studies in cancer have demonstrated that pathogenic ARID1A variants hamper nuclear import of the protein and/or affect interaction with the subunits of SWI/SNF complex, resulting in dysregulation of the PI3K/AKT pathway and perturbed PTEN and PIKC3A signaling. As haploinsufficiency for PTEN and PIKC3A can be associated with ventriculomegaly/hydrocephalus, aberrant expression of these genes is a putative mechanism for the brain malformations demonstrated in patients with ARID1A variants.
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Affiliation(s)
- Anne Slavotinek
- Dept. Pediatrics, University of California San Francisco, San Francisco, CA, 94143, USA, Corresponding author. (A. Slavotinek)
| | - Mathilde Lefebvre
- UFR Des Sciences de Santé, INSERM-Université de Bourgogne UMR1231, Génétique des Anomalies du Développement, Dijon, France
| | | | - Christel Thauvin
- UFR Des Sciences de Santé, INSERM-Université de Bourgogne UMR1231, Génétique des Anomalies du Développement, Dijon, France
| | - Sophie Patrier
- Department of Pathology, CHU Rouen, F-76000, Rouen, France
| | - Teresa N. Sparks
- Department of Obstetrics, Gynecology, & Reproductive Sciences, University of California San Francisco, San Francisco, CA, 94143, USA
| | - Mary Norton
- Department of Obstetrics, Gynecology, & Reproductive Sciences, University of California San Francisco, San Francisco, CA, 94143, USA
| | - Jingwei Yu
- Dept. Cytogenetics, University of California San Francisco, San Francisco, CA, 94143, USA
| | - Eric Huang
- Dept. Pathology, University of California San Francisco, San Francisco, CA, 94143, USA
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18
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Stark Z, Ellard S. Rapid genomic testing for critically ill children: time to become standard of care? Eur J Hum Genet 2022; 30:142-149. [PMID: 34744166 PMCID: PMC8821543 DOI: 10.1038/s41431-021-00990-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2021] [Accepted: 10/17/2021] [Indexed: 02/03/2023] Open
Abstract
Rapid genomic testing in critically ill neonatal and paediatric patients has transformed the paradigm of rare disease diagnosis, delivering results in real time to inform patient management. More than 20 studies totalling over 1500 patients from diverse healthcare settings worldwide have now been published, forming a compelling evidence base for healthcare system implementation. We review the reported diagnostic and clinical outcomes, as well as broader evaluations of family and professional experiences, cost effectiveness, implementation challenges and bioethical issues arising from rapid testing. As rapid genomic testing transitions from the research to the healthcare setting to become a 'standard of care' test, there is a need to develop effective service delivery models to support scalability at both the laboratory and clinical level and promote equity of access, prompt test initiation, integrated multidisciplinary input and holistic family support. Harnessing the high level of professional engagement with rapid genomic testing programmes will continue to drive innovation and adoption, while close integration with emerging precision medicine approaches will be necessary to deliver on the promise of reduced infant and child mortality.
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Affiliation(s)
- Zornitza Stark
- Australian Genomics, Melbourne, VIC Australia ,grid.1058.c0000 0000 9442 535XVictorian Clinical Genetics Services, Murdoch Children’s Research Institute, Melbourne, VIC Australia ,grid.1008.90000 0001 2179 088XDepartment of Paediatrics, University of Melbourne, Melbourne, VIC Australia
| | - Sian Ellard
- grid.419309.60000 0004 0495 6261Exeter Genomics Laboratory, South West Genomic Laboratory Hub, Royal Devon & Exeter NHS Foundation Trust, Exeter, UK ,grid.8391.30000 0004 1936 8024Institute of Biomedical and Clinical Science, University of Exeter Medical School, Exeter, UK
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19
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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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20
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Bendixen C, Reutter H. The Role of De Novo Variants in Patients with Congenital Diaphragmatic Hernia. Genes (Basel) 2021; 12:genes12091405. [PMID: 34573387 PMCID: PMC8466043 DOI: 10.3390/genes12091405] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Revised: 09/03/2021] [Accepted: 09/08/2021] [Indexed: 01/21/2023] Open
Abstract
The genetic etiology of congenital diaphragmatic hernia (CDH), a common and severe birth defect, is still incompletely understood. Chromosomal aneuploidies, copy number variations (CNVs), and variants in a large panel of CDH-associated genes, both de novo and inherited, have been described. Due to impaired reproductive fitness, especially of syndromic CDH patients, and still significant mortality rates, the contribution of de novo variants to the genetic background of CDH is assumed to be high. This assumption is supported by the relatively low recurrence rate among siblings. Advantages in high-throughput genome-wide genotyping and sequencing methods have recently facilitated the detection of de novo variants in CDH. This review gives an overview of the known de novo disease-causing variants in CDH patients.
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Affiliation(s)
- Charlotte Bendixen
- Unit of Paediatric Surgery, Department of General, Visceral, Vascular and Thoracic Surgery, University Hospital Bonn, 53127 Bonn, Germany
- Correspondence:
| | - Heiko Reutter
- Institute of Human Genetics, University Hospital of Bonn, 53127 Bonn, Germany;
- Division of Neonatology and Paediatric Intensive Care, Department of Pediatrics and Adolescent Medicine, University Hospital Erlangen, 91054 Erlangen, Germany
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21
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Sweeney NM, Nahas SA, Chowdhury S, Batalov S, Clark M, Caylor S, Cakici J, Nigro JJ, Ding Y, Veeraraghavan N, Hobbs C, Dimmock D, Kingsmore SF. Rapid whole genome sequencing impacts care and resource utilization in infants with congenital heart disease. NPJ Genom Med 2021; 6:29. [PMID: 33888711 PMCID: PMC8062477 DOI: 10.1038/s41525-021-00192-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 03/19/2021] [Indexed: 11/09/2022] Open
Abstract
Congenital heart disease (CHD) is the most common congenital anomaly and a major cause of infant morbidity and mortality. While morbidity and mortality are highest in infants with underlying genetic conditions, molecular diagnoses are ascertained in only ~20% of cases using widely adopted genetic tests. Furthermore, cost of care for children and adults with CHD has increased dramatically. Rapid whole genome sequencing (rWGS) of newborns in intensive care units with suspected genetic diseases has been associated with increased rate of diagnosis and a net reduction in cost of care. In this study, we explored whether the clinical utility of rWGS extends to critically ill infants with structural CHD through a retrospective review of rWGS study data obtained from inpatient infants < 1 year with structural CHD at a regional children's hospital. rWGS diagnosed genetic disease in 46% of the enrolled infants. Moreover, genetic disease was identified five times more frequently with rWGS than microarray ± gene panel testing in 21 of these infants (rWGS diagnosed 43% versus 10% with microarray ± gene panels, p = 0.02). Molecular diagnoses ranged from syndromes affecting multiple organ systems to disorders limited to the cardiovascular system. The average daily hospital spending was lower in the time period post blood collection for rWGS compared to prior (p = 0.003) and further decreased after rWGS results (p = 0.000). The cost was not prohibitive to rWGS implementation in the care of this cohort of infants. rWGS provided timely actionable information that impacted care and there was evidence of decreased hospital spending around rWGS implementation.
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Affiliation(s)
- Nathaly M Sweeney
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA.
- Rady Children's Hospital, San Diego, CA, USA.
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA.
| | - Shareef A Nahas
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
| | - Shimul Chowdhury
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
| | - Sergey Batalov
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
| | - Michelle Clark
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
| | - Sara Caylor
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
| | - Julie Cakici
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
- Department of Family Medicine and Public Health, University of California San Diego, La Jolla, CA, USA
| | - John J Nigro
- Rady Children's Hospital, San Diego, CA, USA
- Department of Surgery, University of California San Diego, La Jolla, CA, USA
| | - Yan Ding
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
| | | | - Charlotte Hobbs
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
| | - David Dimmock
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
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22
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Zhao M, Havrilla JM, Fang L, Chen Y, Peng J, Liu C, Wu C, Sarmady M, Botas P, Isla J, Lyon GJ, Weng C, Wang K. Phen2Gene: rapid phenotype-driven gene prioritization for rare diseases. NAR Genom Bioinform 2020; 2:lqaa032. [PMID: 32500119 PMCID: PMC7252576 DOI: 10.1093/nargab/lqaa032] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Revised: 04/10/2020] [Accepted: 04/28/2020] [Indexed: 02/07/2023] Open
Abstract
Human Phenotype Ontology (HPO) terms are increasingly used in diagnostic settings to aid in the characterization of patient phenotypes. The HPO annotation database is updated frequently and can provide detailed phenotype knowledge on various human diseases, and many HPO terms are now mapped to candidate causal genes with binary relationships. To further improve the genetic diagnosis of rare diseases, we incorporated these HPO annotations, gene-disease databases and gene-gene databases in a probabilistic model to build a novel HPO-driven gene prioritization tool, Phen2Gene. Phen2Gene accesses a database built upon this information called the HPO2Gene Knowledgebase (H2GKB), which provides weighted and ranked gene lists for every HPO term. Phen2Gene is then able to access the H2GKB for patient-specific lists of HPO terms or PhenoPacket descriptions supported by GA4GH (http://phenopackets.org/), calculate a prioritized gene list based on a probabilistic model and output gene-disease relationships with great accuracy. Phen2Gene outperforms existing gene prioritization tools in speed and acts as a real-time phenotype-driven gene prioritization tool to aid the clinical diagnosis of rare undiagnosed diseases. In addition to a command line tool released under the MIT license (https://github.com/WGLab/Phen2Gene), we also developed a web server and web service (https://phen2gene.wglab.org/) for running the tool via web interface or RESTful API queries. Finally, we have curated a large amount of benchmarking data for phenotype-to-gene tools involving 197 patients across 76 scientific articles and 85 patients' de-identified HPO term data from the Children's Hospital of Philadelphia.
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Affiliation(s)
- Mengge Zhao
- Center for Cellular and Molecular Therapeutics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - James M Havrilla
- Center for Cellular and Molecular Therapeutics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Li Fang
- Center for Cellular and Molecular Therapeutics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Ying Chen
- Center for Cellular and Molecular Therapeutics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Jacqueline Peng
- Center for Cellular and Molecular Therapeutics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA.,Department of Bioengineering, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Cong Liu
- Department of Biomedical Informatics, Columbia University Medical Center, New York, NY 10032, USA
| | - Chao Wu
- Division of Genomic Diagnostics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Mahdi Sarmady
- Division of Genomic Diagnostics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA.,Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Pablo Botas
- Foundation 29, Pozuelo de Alarcon, 28223 Madrid, Spain
| | - Julián Isla
- Foundation 29, Pozuelo de Alarcon, 28223 Madrid, Spain.,Dravet Syndrome European Federation, 29200 Brest, France
| | - Gholson J Lyon
- Institute for Basic Research in Developmental Disabilities (IBR), Staten Island, NY 10314, USA
| | - Chunhua Weng
- Department of Biomedical Informatics, Columbia University Medical Center, New York, NY 10032, USA
| | - Kai Wang
- Center for Cellular and Molecular Therapeutics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA.,Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
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23
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Shillington A, Pedapati E, Hopkin R, Suhrie K. Early behavioral and developmental interventions in ADNP-syndrome: A case report of SWI/SNF-related neurodevelopmental syndrome. Mol Genet Genomic Med 2020; 8:e1230. [PMID: 32275126 PMCID: PMC7284036 DOI: 10.1002/mgg3.1230] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Revised: 03/06/2020] [Accepted: 03/12/2020] [Indexed: 11/30/2022] Open
Abstract
Background Autism spectrum disorder (ASD) affects approximately one in 59 children. Variants in the activity‐dependent neuroprotector homeobox ADNP (OMIM #611386) gene may be one of the most common single‐gene causes of syndromic ASD. Most patients diagnosed with ADNP syndrome have ASD as a comorbidity, and all patients have mild‐to‐severe intellectual disability. Methods/Case Report We present a case report of a patient diagnosed with ADNP syndrome at 2.5 years of age. The patient has many of the key features of the syndrome, including ASD, global developmental delay, behavioral problems, congenital heart defect, early tooth eruption, and vision problems. The patient's initial presentation included congenital diaphragmatic hernia (CDH), which has not been previously reported in this condition. Results The patient exhibited frequent behavioral outbursts and was initiated on antipsychotic medication with near‐complete resolution of symptoms allowing her to engage more fully in early intervention therapies leading to progress in language acquisition. Conclusion This short report provides guidance for antipsychotic medication dosing to improve early intervention outcomes. This is the first report of CDH in this syndrome.
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Affiliation(s)
| | - Ernest Pedapati
- Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Robert Hopkin
- Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Kristen Suhrie
- Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
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24
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Information Is the Resolution of Uncertainty: Whole Genome Approaches to Genetic Diagnosis on the PICU. Pediatr Crit Care Med 2019; 20:1087-1088. [PMID: 31688678 DOI: 10.1097/pcc.0000000000002091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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25
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Holt JM, Wilk B, Birch CL, Brown DM, Gajapathy M, Moss AC, Sosonkina N, Wilk MA, Anderson JA, Harris JM, Kelly JM, Shaterferdosian F, Uno-Antonison AE, Weborg A, Worthey EA. VarSight: prioritizing clinically reported variants with binary classification algorithms. BMC Bioinformatics 2019; 20:496. [PMID: 31615419 PMCID: PMC6792253 DOI: 10.1186/s12859-019-3026-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Accepted: 08/12/2019] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND When applying genomic medicine to a rare disease patient, the primary goal is to identify one or more genomic variants that may explain the patient's phenotypes. Typically, this is done through annotation, filtering, and then prioritization of variants for manual curation. However, prioritization of variants in rare disease patients remains a challenging task due to the high degree of variability in phenotype presentation and molecular source of disease. Thus, methods that can identify and/or prioritize variants to be clinically reported in the presence of such variability are of critical importance. METHODS We tested the application of classification algorithms that ingest variant annotations along with phenotype information for predicting whether a variant will ultimately be clinically reported and returned to a patient. To test the classifiers, we performed a retrospective study on variants that were clinically reported to 237 patients in the Undiagnosed Diseases Network. RESULTS We treated the classifiers as variant prioritization systems and compared them to four variant prioritization algorithms and two single-measure controls. We showed that the trained classifiers outperformed all other tested methods with the best classifiers ranking 72% of all reported variants and 94% of reported pathogenic variants in the top 20. CONCLUSIONS We demonstrated how freely available binary classification algorithms can be used to prioritize variants even in the presence of real-world variability. Furthermore, these classifiers outperformed all other tested methods, suggesting that they may be well suited for working with real rare disease patient datasets.
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Affiliation(s)
- James M. Holt
- HudsonAlpha Institute for Biotechnology, Software Development and Informatics, 601 Genome Way, Huntsville, 35806 USA
| | - Brandon Wilk
- HudsonAlpha Institute for Biotechnology, Software Development and Informatics, 601 Genome Way, Huntsville, 35806 USA
| | - Camille L. Birch
- HudsonAlpha Institute for Biotechnology, Software Development and Informatics, 601 Genome Way, Huntsville, 35806 USA
| | - Donna M. Brown
- HudsonAlpha Institute for Biotechnology, Software Development and Informatics, 601 Genome Way, Huntsville, 35806 USA
| | - Manavalan Gajapathy
- HudsonAlpha Institute for Biotechnology, Software Development and Informatics, 601 Genome Way, Huntsville, 35806 USA
| | - Alexander C. Moss
- HudsonAlpha Institute for Biotechnology, Software Development and Informatics, 601 Genome Way, Huntsville, 35806 USA
| | - Nadiya Sosonkina
- HudsonAlpha Institute for Biotechnology, Software Development and Informatics, 601 Genome Way, Huntsville, 35806 USA
- University of Alabama at Birmingham, Department of Genetics, 720 20th Street South, Birmingham, 35294 USA
| | - Melissa A. Wilk
- HudsonAlpha Institute for Biotechnology, Software Development and Informatics, 601 Genome Way, Huntsville, 35806 USA
| | - Julie A. Anderson
- HudsonAlpha Institute for Biotechnology, Software Development and Informatics, 601 Genome Way, Huntsville, 35806 USA
| | - Jeremy M. Harris
- HudsonAlpha Institute for Biotechnology, Software Development and Informatics, 601 Genome Way, Huntsville, 35806 USA
| | - Jacob M. Kelly
- HudsonAlpha Institute for Biotechnology, Software Development and Informatics, 601 Genome Way, Huntsville, 35806 USA
| | - Fariba Shaterferdosian
- HudsonAlpha Institute for Biotechnology, Software Development and Informatics, 601 Genome Way, Huntsville, 35806 USA
| | - Angelina E. Uno-Antonison
- HudsonAlpha Institute for Biotechnology, Software Development and Informatics, 601 Genome Way, Huntsville, 35806 USA
| | - Arthur Weborg
- HudsonAlpha Institute for Biotechnology, Software Development and Informatics, 601 Genome Way, Huntsville, 35806 USA
| | - Elizabeth A. Worthey
- HudsonAlpha Institute for Biotechnology, Software Development and Informatics, 601 Genome Way, Huntsville, 35806 USA
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26
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Grosse SD, Farnaes L. Genomic sequencing in acutely ill infants: what will it take to demonstrate clinical value? Genet Med 2018; 21:269-271. [PMID: 30100610 DOI: 10.1038/s41436-018-0124-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Accepted: 06/25/2018] [Indexed: 11/09/2022] Open
Affiliation(s)
- Scott D Grosse
- National Center on Birth Defects and Developmental Disabilities, Centers for Disease Control and Prevention, Atlanta, Georgia, USA.
| | - Lauge Farnaes
- Rady Children's Institute for Genomic Medicine, San Diego, California, USA.,Department of Pediatrics, University of California at San Diego, San Diego, California, USA
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