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Ma A, Newing TP, O'Shea R, Gokoolparsadh A, Murdoch E, Hayward J, Shannon G, Kevin L, Bennetts B, Ho G, Smith J, Shah M, Jones KJ, Josephi-Taylor S, Sandaradura SA, Adès L, Jamieson R, Rankin NM. Genomic multidisciplinary teams: A model for navigating genetic mainstreaming and precision medicine. J Paediatr Child Health 2024; 60:118-124. [PMID: 38605555 DOI: 10.1111/jpc.16547] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Revised: 03/27/2024] [Accepted: 04/04/2024] [Indexed: 04/13/2024]
Abstract
AIM Recent rapid advances in genomics are revolutionising patient diagnosis and management of genetic conditions. However, this has led to many challenges in service provision, education and upskilling requirements for non-genetics health-care professionals and remuneration for genomic testing. In Australia, Medicare funding with a Paediatric genomic testing item for patients with intellectual disability or syndromic features has attempted to address this latter issue. The Sydney Children's Hospitals Network - Westmead (SCHN-W) Clinical Genetics Department established Paediatric and Neurology genomic multidisciplinary team (MDT) meetings to address the Medicare-specified requirement for discussion with clinical genetics, and increasing genomic testing advice requests. METHODS This SCHN-W genomic MDT was evaluated with two implementation science frameworks - the RE-AIM (Reach, Effectiveness, Adoption, Implementation, Maintenance) and GMIR - Genomic Medicine Integrative Research frameworks. Data from June 2020 to July 2022 were synthesised and evaluated, as well as process mapping of the MDT service. RESULTS A total of 205 patients were discussed in 34 MDT meetings, facilitating 148 genomic tests, of which 73 were Medicare eligible. This was equivalent to 26% of SCHN-W genetics outpatient activity, and 13% of all Medicare-funded paediatric genomic testing in NSW. 39% of patients received a genetic diagnosis. CONCLUSION The genomic MDT facilitated increased genomic testing at a tertiary paediatric centre and is an effective model for mainstreaming and facilitating precision medicine. However, significant implementation issues were identified including cost and sustainability, as well as the high level of resourcing that will be required to scale up this approach to other areas of medicine.
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Affiliation(s)
- Alan Ma
- Department of Clinical Genetics, Sydney Children's Hospitals Network - Westmead, Sydney, New South Wales, Australia
- Specialty of Genomic Medicine, University of Sydney, Sydney, New South Wales, Australia
| | - Timothy P Newing
- Sydney Medical School, University of Sydney, Sydney, New South Wales, Australia
| | - Rosie O'Shea
- Specialty of Genomic Medicine, University of Sydney, Sydney, New South Wales, Australia
| | - Akira Gokoolparsadh
- Department of Clinical Genetics, Sydney Children's Hospitals Network - Westmead, Sydney, New South Wales, Australia
| | - Emma Murdoch
- Department of Clinical Genetics, Sydney Children's Hospitals Network - Westmead, Sydney, New South Wales, Australia
| | - Janette Hayward
- Department of Clinical Genetics, Sydney Children's Hospitals Network - Westmead, Sydney, New South Wales, Australia
| | - Gillian Shannon
- Western NSW Local Health District, Dubbo, New South Wales, Australia
| | - Lucy Kevin
- Department of Clinical Genetics, Sydney Children's Hospitals Network - Westmead, Sydney, New South Wales, Australia
| | - Bruce Bennetts
- Specialty of Genomic Medicine, University of Sydney, Sydney, New South Wales, Australia
- Department of Molecular Genetics, Sydney Genome Diagnostics, Sydney Children's Hospitals Network - Westmead, Sydney, New South Wales, Australia
| | - Gladys Ho
- Specialty of Genomic Medicine, University of Sydney, Sydney, New South Wales, Australia
- Department of Molecular Genetics, Sydney Genome Diagnostics, Sydney Children's Hospitals Network - Westmead, Sydney, New South Wales, Australia
| | - Janine Smith
- Department of Clinical Genetics, Sydney Children's Hospitals Network - Westmead, Sydney, New South Wales, Australia
- Specialty of Genomic Medicine, University of Sydney, Sydney, New South Wales, Australia
| | - Margit Shah
- Department of Clinical Genetics, Sydney Children's Hospitals Network - Westmead, Sydney, New South Wales, Australia
- Specialty of Genomic Medicine, University of Sydney, Sydney, New South Wales, Australia
| | - Kristi J Jones
- Department of Clinical Genetics, Sydney Children's Hospitals Network - Westmead, Sydney, New South Wales, Australia
- Specialty of Genomic Medicine, University of Sydney, Sydney, New South Wales, Australia
| | - Sarah Josephi-Taylor
- Department of Clinical Genetics, Sydney Children's Hospitals Network - Westmead, Sydney, New South Wales, Australia
- Specialty of Genomic Medicine, University of Sydney, Sydney, New South Wales, Australia
| | - Sarah A Sandaradura
- Department of Clinical Genetics, Sydney Children's Hospitals Network - Westmead, Sydney, New South Wales, Australia
- Specialty of Genomic Medicine, University of Sydney, Sydney, New South Wales, Australia
| | - Lesley Adès
- Department of Clinical Genetics, Sydney Children's Hospitals Network - Westmead, Sydney, New South Wales, Australia
- Specialty of Genomic Medicine, University of Sydney, Sydney, New South Wales, Australia
| | - Robyn Jamieson
- Department of Clinical Genetics, Sydney Children's Hospitals Network - Westmead, Sydney, New South Wales, Australia
- Specialty of Genomic Medicine, University of Sydney, Sydney, New South Wales, Australia
- Eye Genetics Research Unit, Children's Medical Research Institute, Sydney, New South Wales, Australia
| | - Nicole M Rankin
- Evaluation and Implementation Science Unit, Melbourne School of Population and Global Health, University of Melbourne, Melbourne, Victoria, Australia
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Hudson R, Abeysekera N, Wolski P, Simons C, Francis L, Farnsworth E, Bennetts B, Patel C, Spijker S, Mallett A. De novo HNF4A-associated atypical Fanconi renal tubulopathy syndrome. J Nephrol 2024; 37:191-197. [PMID: 37308774 PMCID: PMC10920409 DOI: 10.1007/s40620-023-01666-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2023] [Accepted: 04/29/2023] [Indexed: 06/14/2023]
Affiliation(s)
- Rebecca Hudson
- Department of Renal Medicine, Royal Brisbane and Women's Hospital, Herston, QLD, Australia
| | - Natasha Abeysekera
- Department of Renal Medicine, Royal Brisbane and Women's Hospital, Herston, QLD, Australia
- Department of General Surgery, Royal Brisbane and Women's Hospital, Herston, QLD, Australia
| | - Penny Wolski
- Department of Diabetes and Endocrinology, Royal Brisbane and Women's Hospital, Herston, QLD, Australia
| | - Cas Simons
- Centre for Population Genomics, Garvan Institute of Medical Research, and University of New South Wales, Sydney, NSW, Australia
- Centre for Population Genomics, Murdoch Children's Research Institute, Melbourne, VIC, Australia
| | - Leo Francis
- Anatomical Pathology, Pathology Queensland, Royal Brisbane and Women's Hospital, Herston, QLD, Australia
| | - Elizabeth Farnsworth
- Sydney Genome Diagnostics, Western Sydney Genetics Program, Children's Hospital Westmead, Westmead, NSW, Australia
| | - Bruce Bennetts
- Sydney Genome Diagnostics, Western Sydney Genetics Program, Children's Hospital Westmead, Westmead, NSW, Australia
- Specialty of Genomic Medicine, Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia
| | - Chirag Patel
- Genetic Health Queensland, Royal Brisbane and Women's Hospital, Herston, QLD, Australia
| | - Siebe Spijker
- Department of Nephrology, Leiden University Medical Centre, Leiden, The Netherlands
| | - Andrew Mallett
- Department of Renal Medicine, Townsville Hospital and Health Service, Townsville University Hospital, 100 Angus Smith Drive, Douglas, QLD, 4814, Australia.
- Faculty of Medicine, James Cook University, Townsville, QLD, Australia.
- Faculty of Medicine, The University of Queensland, Herston, QLD, Australia.
- Institute for Molecular Bioscience, The University of Queensland, St Lucia, QLD, Australia.
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Ngo C, Baluyot M, Bennetts B, Carmichael J, Clark A, Darmanian A, Gayagay T, Jones L, Nash B, Clark M, Jose N, Robinson S, St Heaps L, Wright D. SNP chromosome microarray genotyping for detection of uniparental disomy in the clinical diagnostic laboratory. Pathology 2023; 55:818-826. [PMID: 37414616 DOI: 10.1016/j.pathol.2023.04.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2022] [Revised: 01/21/2023] [Accepted: 04/17/2023] [Indexed: 07/08/2023]
Abstract
Single nucleotide polymorphism (SNP) chromosome microarray is well established for investigation of children with intellectual deficit/development delay and prenatal diagnosis of fetal malformation but has also emerged for uniparental disomy (UPD) genotyping. Despite published guidelines on clinical indications for testing there are no laboratory guidelines published for performing SNP microarray UPD genotyping. We evaluated SNP microarray UPD genotyping using Illumina beadchips on family trios/duos within a clinical cohort (n=98) and then explored our findings in a post-study audit (n=123). UPD occurred in 18.6% and 19.5% cases, respectively, with chromosome 15 most frequent (62.5% and 25.0%). UPD was predominantly maternal in origin (87.5% and 79.2%), highest in suspected genomic imprinting disorder cases (56.3% and 41.7%) but absent amongst children of translocation carriers. We assessed regions of homozygosity among UPD cases. The smallest interstitial and terminal regions were 2.5 Mb and 9.3 Mb, respectively. We found regions of homozygosity confounded genotyping in a consanguineous case with UPD15 and another with segmental UPD due to non-informative probes. In a unique case with chromosome 15q UPD mosaicism, we established the detection limit of mosaicism as ∼5%. From the benefits and pitfalls identified in this study, we propose a testing model and recommendations for UPD genotyping by SNP microarray.
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Affiliation(s)
- Con Ngo
- Sydney Genome Diagnostics, Cytogenetics, The Children's Hospital at Westmead, Westmead, NSW, Australia.
| | - Maria Baluyot
- Sydney Genome Diagnostics, Cytogenetics, The Children's Hospital at Westmead, Westmead, NSW, Australia
| | - Bruce Bennetts
- Specialty of Genomic Medicine, Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia; Sydney Genome Diagnostics, Molecular Genetics, The Children's Hospital at Westmead, Westmead, NSW, Australia
| | - Johanna Carmichael
- Sydney Genome Diagnostics, Cytogenetics, The Children's Hospital at Westmead, Westmead, NSW, Australia
| | - Alissa Clark
- Sydney Genome Diagnostics, Cytogenetics, The Children's Hospital at Westmead, Westmead, NSW, Australia
| | - Artur Darmanian
- Sydney Genome Diagnostics, Cytogenetics, The Children's Hospital at Westmead, Westmead, NSW, Australia
| | - Thet Gayagay
- Sydney Genome Diagnostics, Molecular Genetics, The Children's Hospital at Westmead, Westmead, NSW, Australia
| | - Luke Jones
- Sydney Genome Diagnostics, Cytogenetics, The Children's Hospital at Westmead, Westmead, NSW, Australia
| | - Benjamin Nash
- Sydney Genome Diagnostics, Cytogenetics, The Children's Hospital at Westmead, Westmead, NSW, Australia; Specialty of Genomic Medicine, Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia
| | - Melanie Clark
- Sydney Genome Diagnostics, Cytogenetics, The Children's Hospital at Westmead, Westmead, NSW, Australia
| | - Ngaire Jose
- Sydney Genome Diagnostics, Cytogenetics, The Children's Hospital at Westmead, Westmead, NSW, Australia
| | - Samantha Robinson
- Sydney Genome Diagnostics, Cytogenetics, The Children's Hospital at Westmead, Westmead, NSW, Australia
| | - Luke St Heaps
- Sydney Genome Diagnostics, Cytogenetics, The Children's Hospital at Westmead, Westmead, NSW, Australia; Specialty of Genomic Medicine, Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia
| | - Dale Wright
- Sydney Genome Diagnostics, Cytogenetics, The Children's Hospital at Westmead, Westmead, NSW, Australia; Specialty of Genomic Medicine, Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia
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4
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Musto E, Liao VWY, Johannesen KM, Fenger CD, Lederer D, Kothur K, Fisk K, Bennetts B, Vrielynck P, Delaby D, Ceulemans B, Weckhuysen S, Sparber P, Bouman A, Ardern-Holmes S, Troedson C, Battaglia DI, Goel H, Feyma T, Bakhtiari S, Tjoa L, Boxill M, Demina N, Shchagina O, Dadali E, Kruer M, Cantalupo G, Contaldo I, Polster T, Isidor B, Bova SM, Fazeli W, Wouters L, Miranda MJ, Darra F, Pede E, Le Duc D, Jamra RA, Küry S, Proietti J, McSweeney N, Brokamp E, Andrews PI, Gouray Garcia M, Chebib M, Møller RS, Ahring PK, Gardella E. GABRA1-Related Disorders: From Genetic to Functional Pathways. Ann Neurol 2023; 95:27-41. [PMID: 37606373 DOI: 10.1002/ana.26774] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 08/18/2023] [Accepted: 08/18/2023] [Indexed: 08/23/2023]
Abstract
OBJECTIVE Variants in GABRA1 have been associated with a broad epilepsy spectrum, ranging from genetic generalized epilepsies to developmental and epileptic encephalopathies. However, our understanding of what determines the phenotype severity and best treatment options remains inadequate. We therefore aimed to analyze the electroclinical features and the functional effects of GABRA1 variants to establish genotype-phenotype correlations. METHODS Genetic and electroclinical data of 27 individuals (22 unrelated and 2 families) harboring 20 different GABRA1 variants were collected and accompanied by functional analysis of 19 variants. RESULTS Individuals in this cohort could be assigned into different clinical subgroups based on the functional effect of their variant and its structural position within the GABRA1 subunit. A homogenous phenotype with mild cognitive impairment and infantile onset epilepsy (focal seizures, fever sensitivity, and electroencephalographic posterior epileptiform discharges) was described for variants in the extracellular domain and the small transmembrane loops. These variants displayed loss-of-function (LoF) effects, and the patients generally had a favorable outcome. A more severe phenotype was associated with variants in the pore-forming transmembrane helices. These variants displayed either gain-of-function (GoF) or LoF effects. GoF variants were associated with severe early onset neurodevelopmental disorders, including early infantile developmental and epileptic encephalopathy. INTERPRETATION Our data expand the genetic and phenotypic spectrum of GABRA1 epilepsies and permit delineation of specific subphenotypes for LoF and GoF variants, through the heterogeneity of phenotypes and variants. Generally, variants in the transmembrane helices cause more severe phenotypes, in particular GoF variants. These findings establish the basis for a better understanding of the pathomechanism and a precision medicine approach in GABRA1-related disorders. Further studies in larger populations are needed to provide a conclusive genotype-phenotype correlation. ANN NEUROL 2023.
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Affiliation(s)
- Elisa Musto
- Department of Epilepsy Genetics and Personalized Medicine, Danish Epilepsy Center, Dianalund, Denmark
- Pediatric Neurology, Department of Woman and Child Health and Public Health, Child Health Area, Catholic University UCSC, Rome, Italy
- Epilepsy and Movement Disorder Neurology, Ospedale Pediatrico Bambino Gesù IRCCS, Rome, Italy
| | - Vivian W Y Liao
- Brain and Mind Centre, School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia
| | - Katrine M Johannesen
- Department of Epilepsy Genetics and Personalized Medicine, Danish Epilepsy Center, Dianalund, Denmark
- Department of Genetics, University Hospital of Copenhagen, Copenhagen, Denmark
| | - Christina D Fenger
- Department of Epilepsy Genetics and Personalized Medicine, Danish Epilepsy Center, Dianalund, Denmark
- Amplexa Genetics, Odense, Denmark
| | - Damien Lederer
- Center for Human Genetics, Institut de Pathologie et de Génétique, Gosselies, Belgium
| | - Kavitha Kothur
- Kids Neuroscience Centre, Children's Hospital at Westmead, University of Sydney, Sydney, New South Wales, Australia
| | - Katrina Fisk
- Sydney Genome Diagnostics, Western Sydney Genetics Program, Children's Hospital at Westmead, Sydney, New South Wales, Australia
| | - Bruce Bennetts
- Sydney Genome Diagnostics, Western Sydney Genetics Program, Children's Hospital at Westmead, Sydney, New South Wales, Australia
- Specialty of Genomic Medicine, Children's Hospital at Westmead Clinical School, Faculty of Medicine and Health, University of Sydney, Sydney, New South Wales, Australia
| | - Pascal Vrielynck
- Reference Center for Refractory Epilepsy, Catholic University of Louvain, William Lennox Neurological Hospital, Ottignies, Belgium
| | - Delphine Delaby
- Reference Center for Refractory Epilepsy, Catholic University of Louvain, William Lennox Neurological Hospital, Ottignies, Belgium
| | - Berten Ceulemans
- Department of Pediatric Neurology, Antwerp University Hospital, University of Antwerp, Antwerp, Belgium
| | - Sarah Weckhuysen
- Applied & Translational Neurogenomics Group, VIB-Department of Molecular Genetics, University of Antwerp, Antwerp, Belgium
- Department of Neurology, Antwerp University Hospital, Antwerp, Belgium
- Translational Neurosciences, Faculty of Medicine and Health Science, University of Antwerp, Antwerp, Belgium
| | - Peter Sparber
- Research Center for Medical Genetics Moskvorechie 1, Moscow, Russia
| | - Arjan Bouman
- Department of Clinical Genetics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Simone Ardern-Holmes
- Kids Neuroscience Centre, Children's Hospital at Westmead, University of Sydney, Sydney, New South Wales, Australia
- T. Y. Nelson Department of Neurology and Neurosurgery, Children's Hospital at Westmead, Westmead, New South Wales, Australia
| | - Christopher Troedson
- T. Y. Nelson Department of Neurology and Neurosurgery, Children's Hospital at Westmead, Westmead, New South Wales, Australia
| | - Domenica I Battaglia
- Pediatric Neurology, Department of Woman and Child Health and Public Health, Child Health Area, Catholic University UCSC, Rome, Italy
| | - Himanshu Goel
- Hunter Genetics, Newcastle, New South Wales, Australia
| | - Timothy Feyma
- Gillette Children's Specialty Healthcare, Saint Paul, MN, USA
| | - Somayeh Bakhtiari
- Pediatric Movement Disorders Program, Division of Pediatric Neurology, Barrow Neurological Institute, Phoenix Children's Hospital, Phoenix, AZ, USA
- Departments of Child Health, Neurology, and Cellular & Molecular Medicine and Program in Genetics, University of Arizona College of Medicine, Phoenix, AZ, USA
| | - Linda Tjoa
- Townsville University Hospital, Douglas, Queensland, Australia
| | - Martin Boxill
- Department of Pediatrics, Viborg Regional Hospital, Viborg, Denmark
| | - Nina Demina
- Research Center for Medical Genetics Moskvorechie 1, Moscow, Russia
| | - Olga Shchagina
- Research Center for Medical Genetics Moskvorechie 1, Moscow, Russia
| | - Elena Dadali
- Research Center for Medical Genetics Moskvorechie 1, Moscow, Russia
| | - Michael Kruer
- Pediatric Movement Disorders Program, Division of Pediatric Neurology, Barrow Neurological Institute, Phoenix Children's Hospital, Phoenix, AZ, USA
- Departments of Child Health, Neurology, and Cellular & Molecular Medicine and Program in Genetics, University of Arizona College of Medicine, Phoenix, AZ, USA
| | - Gaetano Cantalupo
- Child Neuropsychiatry Section, Department of Surgical Sciences, Dentistry, Gynecology and Paediatrics, University of Verona, Verona, Italy
- UOC Neuropsichiatria Infantile, Dipartimento Materno-Infantile, Azienda Ospedaliero-Universitaria Integrata (full member of the ERN EpiCare), Verona, Italy
- Center for Research on Epilepsies in Pediatric age (CREP), Verona, Italy
| | - Ilaria Contaldo
- Pediatric Neurology, Department of Woman and Child Health and Public Health, Child Health Area, Catholic University UCSC, Rome, Italy
| | - Tilman Polster
- Department of Epileptology (Krankenhaus Mara), Bielefeld University Medical School, Bielefeld, Germany
| | | | - Stefania M Bova
- Pediatric Neurology Unit, V. Buzzi Children's Hospital, Milan, Italy
| | - Walid Fazeli
- Department of Neuropediatrics, Children's Hospital, University of Bonn, Bonn, Germany
| | - Leen Wouters
- Department of Pediatrics, Ziekenhuis Oost-Limburg, Genk, Belgium
| | - Maria J Miranda
- Department of Pediatrics, Pediatric Neurology, Herlev University Hospital, Copenhagen University, Herlev, Denmark
| | - Francesca Darra
- Child Neuropsychiatry Section, Department of Surgical Sciences, Dentistry, Gynecology and Paediatrics, University of Verona, Verona, Italy
- UOC Neuropsichiatria Infantile, Dipartimento Materno-Infantile, Azienda Ospedaliero-Universitaria Integrata (full member of the ERN EpiCare), Verona, Italy
- Center for Research on Epilepsies in Pediatric age (CREP), Verona, Italy
| | - Elisa Pede
- Pediatric Neurology, Department of Woman and Child Health and Public Health, Child Health Area, Catholic University UCSC, Rome, Italy
| | - Diana Le Duc
- Department of Human Genetics, University of Leipzig Faculty of Medicine, Leipzig, Germany
| | - Rami Abou Jamra
- Department of Human Genetics, University of Leipzig Faculty of Medicine, Leipzig, Germany
| | - Sébastien Küry
- Service de Génétique Médicale, CHU Nantes, Nantes, France
- l'Institut du Thorax, INSERM, CNRS, Université de Nantes, Nantes, France
| | - Jacopo Proietti
- Child Neuropsychiatry Section, Department of Surgical Sciences, Dentistry, Gynecology and Paediatrics, University of Verona, Verona, Italy
- Irish Centre for Fetal and Neonatal Translational Research, Child Neuropsychiatry, Cork, Ireland
| | - Niamh McSweeney
- Department of Paediatrics, Cork University Hospital, Cork, Ireland
| | - Elly Brokamp
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Peter Ian Andrews
- Department of Neurology, Sydney Children's Hospital, Randwick, New South Wales, Australia
| | | | - Mary Chebib
- Brain and Mind Centre, School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia
| | - Rikke S Møller
- Department of Epilepsy Genetics and Personalized Medicine, Danish Epilepsy Center, Dianalund, Denmark
- Department of Regional Health Research, Faculty of Health Sciences, University of Southern Denmark, Odense, Denmark
| | - Philip K Ahring
- Brain and Mind Centre, School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia
| | - Elena Gardella
- Department of Epilepsy Genetics and Personalized Medicine, Danish Epilepsy Center, Dianalund, Denmark
- Department of Regional Health Research, Faculty of Health Sciences, University of Southern Denmark, Odense, Denmark
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5
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Ebstein F, Küry S, Most V, Rosenfelt C, Scott-Boyer MP, van Woerden GM, Besnard T, Papendorf JJ, Studencka-Turski M, Wang T, Hsieh TC, Golnik R, Baldridge D, Forster C, de Konink C, Teurlings SM, Vignard V, van Jaarsveld RH, Ades L, Cogné B, Mignot C, Deb W, Jongmans MC, Sessions Cole F, van den Boogaard MJH, Wambach JA, Wegner DJ, Yang S, Hannig V, Brault JA, Zadeh N, Bennetts B, Keren B, Gélineau AC, Powis Z, Towne M, Bachman K, Seeley A, Beck AE, Morrison J, Westman R, Averill K, Brunet T, Haasters J, Carter MT, Osmond M, Wheeler PG, Forzano F, Mohammed S, Trakadis Y, Accogli A, Harrison R, Guo Y, Hakonarson H, Rondeau S, Baujat G, Barcia G, Feichtinger RG, Mayr JA, Preisel M, Laumonnier F, Kallinich T, Knaus A, Isidor B, Krawitz P, Völker U, Hammer E, Droit A, Eichler EE, Elgersma Y, Hildebrand PW, Bolduc F, Krüger E, Bézieau S. PSMC3 proteasome subunit variants are associated with neurodevelopmental delay and type I interferon production. Sci Transl Med 2023; 15:eabo3189. [PMID: 37256937 PMCID: PMC10506367 DOI: 10.1126/scitranslmed.abo3189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 05/10/2023] [Indexed: 06/02/2023]
Abstract
A critical step in preserving protein homeostasis is the recognition, binding, unfolding, and translocation of protein substrates by six AAA-ATPase proteasome subunits (ATPase-associated with various cellular activities) termed PSMC1-6, which are required for degradation of proteins by 26S proteasomes. Here, we identified 15 de novo missense variants in the PSMC3 gene encoding the AAA-ATPase proteasome subunit PSMC3/Rpt5 in 23 unrelated heterozygous patients with an autosomal dominant form of neurodevelopmental delay and intellectual disability. Expression of PSMC3 variants in mouse neuronal cultures led to altered dendrite development, and deletion of the PSMC3 fly ortholog Rpt5 impaired reversal learning capabilities in fruit flies. Structural modeling as well as proteomic and transcriptomic analyses of T cells derived from patients with PSMC3 variants implicated the PSMC3 variants in proteasome dysfunction through disruption of substrate translocation, induction of proteotoxic stress, and alterations in proteins controlling developmental and innate immune programs. The proteostatic perturbations in T cells from patients with PSMC3 variants correlated with a dysregulation in type I interferon (IFN) signaling in these T cells, which could be blocked by inhibition of the intracellular stress sensor protein kinase R (PKR). These results suggest that proteotoxic stress activated PKR in patient-derived T cells, resulting in a type I IFN response. The potential relationship among proteosome dysfunction, type I IFN production, and neurodevelopment suggests new directions in our understanding of pathogenesis in some neurodevelopmental disorders.
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Affiliation(s)
- Frédéric Ebstein
- Institut für Medizinische Biochemie und Molekularbiologie (IMBM), Universitätsmedizin Greifswald, Ferdinand-Sauerbruch-Straße, 17475 Greifswald, Germany
| | - Sébastien Küry
- Nantes Université, CHU Nantes, Service de Génétique Médicale, 44000 Nantes, France
- Nantes Université, CHU Nantes, CNRS, INSERM, l’institut du thorax, 44000 Nantes, France
| | - Victoria Most
- Institut für Medizinische Physik und Biophysik, Universität Leipzig, Medizinische Fakultät, Härtelstr. 16-18, 04107 Leipzig, Germany
| | - Cory Rosenfelt
- Department of Pediatrics, University of Alberta, Edmonton, AB CT6G 1C9, Canada
| | | | - Geeske M. van Woerden
- Department of Neuroscience, Erasmus University Medical Center, 3015 CN, Rotterdam, The Netherlands
- ENCORE Expertise Center for Neurodevelopmental Disorders, Erasmus University Medical Center, 3015 CN, Rotterdam, The Netherlands
- Department of Clinical Genetics, Erasmus University Medical Center, 3015 CN, Rotterdam, The Netherlands
| | - Thomas Besnard
- Nantes Université, CHU Nantes, Service de Génétique Médicale, 44000 Nantes, France
- Nantes Université, CHU Nantes, CNRS, INSERM, l’institut du thorax, 44000 Nantes, France
| | - Jonas Johannes Papendorf
- Institut für Medizinische Biochemie und Molekularbiologie (IMBM), Universitätsmedizin Greifswald, Ferdinand-Sauerbruch-Straße, 17475 Greifswald, Germany
| | - Maja Studencka-Turski
- Institut für Medizinische Biochemie und Molekularbiologie (IMBM), Universitätsmedizin Greifswald, Ferdinand-Sauerbruch-Straße, 17475 Greifswald, Germany
| | - Tianyun Wang
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
- Department of Medical Genetics, Center for Medical Genetics, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
- Neuroscience Research Institute, Peking University; Key Laboratory for Neuroscience, Ministry of Education of China & National Health Commission of China, Beijing 100191, China
| | - Tzung-Chien Hsieh
- Institute for Genomic Statistics and Bioinformatics, University Hospital Bonn, Rheinische Friedrich-Wilhelms-Universität Bonn, 53127 Bonn, Germany
| | - Richard Golnik
- Klinik für Pädiatrie I, Universitätsklinikum Halle (Saale), 06120 Halle (Saale)
| | - Dustin Baldridge
- The Edward Mallinckrodt Department of Pediatrics, Washington University School of Medicine, St. Louis, MO 63130-4899, USA
| | - Cara Forster
- GeneDx, 207 Perry Parkway, Gaithersburg, MD 20877, USA
| | - Charlotte de Konink
- Department of Neuroscience, Erasmus University Medical Center, 3015 CN, Rotterdam, The Netherlands
- ENCORE Expertise Center for Neurodevelopmental Disorders, Erasmus University Medical Center, 3015 CN, Rotterdam, The Netherlands
| | - Selina M.W. Teurlings
- Department of Neuroscience, Erasmus University Medical Center, 3015 CN, Rotterdam, The Netherlands
- ENCORE Expertise Center for Neurodevelopmental Disorders, Erasmus University Medical Center, 3015 CN, Rotterdam, The Netherlands
| | - Virginie Vignard
- Nantes Université, CHU Nantes, Service de Génétique Médicale, 44000 Nantes, France
- Nantes Université, CHU Nantes, CNRS, INSERM, l’institut du thorax, 44000 Nantes, France
| | | | - Lesley Ades
- Department of Clinical Genetics, The Children’s Hospital at Westmead, Locked Bag 4001, Westmead, NSW, 2145, Australia
- Disciplines of Genomic Medicine & Child and Adolescent Health, Faculty of Medicine and Health, University of Sydney, Sydney, NSW, 2145, Australia
| | - Benjamin Cogné
- Nantes Université, CHU Nantes, Service de Génétique Médicale, 44000 Nantes, France
- Nantes Université, CHU Nantes, CNRS, INSERM, l’institut du thorax, 44000 Nantes, France
| | - Cyril Mignot
- APHP, Hôpital Pitié-Salpêtrière, Département de Génétique, Centre de Reference Déficience Intellectuelle de Causes Rares, GRC UPMC «Déficience Intellectuelle et Autisme», 75013 Paris, France
- Sorbonne Universités, Institut du Cerveau et de la Moelle épinière, ICM, Inserm U1127, CNRS UMR 7225, 75013, Paris, France
| | - Wallid Deb
- Nantes Université, CHU Nantes, Service de Génétique Médicale, 44000 Nantes, France
- Nantes Université, CHU Nantes, CNRS, INSERM, l’institut du thorax, 44000 Nantes, France
| | - Marjolijn C.J. Jongmans
- Department of Genetics, University Medical Center Utrecht, 3508 AB, Utrecht, The Netherlands
- Princess Máxima Center for Pediatric Oncology, 3584 CS, Utrecht, The Netherlands
| | - F. Sessions Cole
- The Edward Mallinckrodt Department of Pediatrics, Washington University School of Medicine, St. Louis, MO 63130-4899, USA
| | | | - Jennifer A. Wambach
- The Edward Mallinckrodt Department of Pediatrics, Washington University School of Medicine, St. Louis, MO 63130-4899, USA
| | - Daniel J. Wegner
- The Edward Mallinckrodt Department of Pediatrics, Washington University School of Medicine, St. Louis, MO 63130-4899, USA
| | - Sandra Yang
- GeneDx, 207 Perry Parkway, Gaithersburg, MD 20877, USA
| | - Vickie Hannig
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Jennifer Ann Brault
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Neda Zadeh
- Genetics Center, Orange, CA 92868, USA; Division of Medical Genetics, Children’s Hospital of Orange County, Orange, CA 92868, USA
| | - Bruce Bennetts
- Disciplines of Genomic Medicine & Child and Adolescent Health, Faculty of Medicine and Health, University of Sydney, Sydney, NSW, 2145, Australia
- Sydney Genome Diagnostics, Western Sydney Genetics Program, The Children’s Hospital at Westmead, Sydney, NSW, 2145, Australia
| | - Boris Keren
- Département de Génétique, Centre de Référence des Déficiences Intellectuelles de Causes Rares, Groupe Hospitalier Pitié-Salpêtrière, Assistance Publique-Hôpitaux de Paris, 75013 Paris
| | - Anne-Claire Gélineau
- Département de Génétique, Centre de Référence des Déficiences Intellectuelles de Causes Rares, Groupe Hospitalier Pitié-Salpêtrière, Assistance Publique-Hôpitaux de Paris, 75013 Paris
| | - Zöe Powis
- Department of Clinical Research, Ambry Genetics, Aliso Viejo, CA 92656, USA
| | - Meghan Towne
- Department of Clinical Research, Ambry Genetics, Aliso Viejo, CA 92656, USA
| | | | - Andrea Seeley
- Genomic Medicine Institute, Geisinger, Danville, PA 17822, USA
| | - Anita E. Beck
- Department of Pediatrics, Division of Genetic Medicine, University of Washington & Seattle Children’s Hospital, Seattle, WA 98195-6320, USA
| | - Jennifer Morrison
- Division of Genetics, Arnold Palmer Hospital for Children, Orlando Health, Orlando, FL 32806, USA
| | - Rachel Westman
- Division of Genetics, St. Luke’s Clinic, Boise, ID 83712, USA
| | - Kelly Averill
- Department of Pediatrics, Division of Pediatric Neurology, UT Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Theresa Brunet
- Institute of Human Genetics, Technical University of Munich, School of Medicine, 81675 Munich, Germany
- Institute of Neurogenomics (ING), Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany
| | - Judith Haasters
- Klinikum der Universität München, Integriertes Sozial- pädiatrisches Zentrum, 80337 Munich, Germany
| | - Melissa T. Carter
- Children’s Hospital of Eastern Ontario Research Institute, University of Ottawa, ON K1H 8L1, Canada
- Department of Genetics, Children’s Hospital of Eastern Ontario, Ottawa, ON K1H 8L1, Canada
| | - Matthew Osmond
- Children’s Hospital of Eastern Ontario Research Institute, University of Ottawa, ON K1H 8L1, Canada
| | - Patricia G. Wheeler
- Division of Genetics, Arnold Palmer Hospital for Children, Orlando Health, Orlando, FL 32806, USA
| | - Francesca Forzano
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
- Clinical Genetics Department, Guy’s & St Thomas’ NHS Foundation Trust, London SE1 9RT, UK
| | - Shehla Mohammed
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
- Clinical Genetics Department, Guy’s & St Thomas’ NHS Foundation Trust, London SE1 9RT, UK
| | - Yannis Trakadis
- Division of Medical Genetics, McGill University Health Centre, Montreal, QC H4A 3J1, Canada
| | - Andrea Accogli
- Division of Medical Genetics, McGill University Health Centre, Montreal, QC H4A 3J1, Canada
| | - Rachel Harrison
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
- Department of Clinical Genetics, Nottingham University Hospitals NHS Trust, City Hospital Campus, The Gables, Gate 3, Hucknall Road, Nottingham NG5 1PB, UK
| | - Yiran Guo
- Center for Applied Genomics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Center for Data Driven Discovery in Biomedicine, Children’s Hospital of Philadelphia, Philadelphia, PA 19146, USA
| | - Hakon Hakonarson
- Center for Applied Genomics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Sophie Rondeau
- Service de Médecine Génomique des Maladies Rares, Hôpital Universitaire Necker-Enfants Malades, 75743 Paris, France
| | - Geneviève Baujat
- Service de Médecine Génomique des Maladies Rares, Hôpital Universitaire Necker-Enfants Malades, 75743 Paris, France
| | - Giulia Barcia
- Service de Médecine Génomique des Maladies Rares, Hôpital Universitaire Necker-Enfants Malades, 75743 Paris, France
| | - René Günther Feichtinger
- University Children’s Hospital, Salzburger Landeskliniken (SALK) and Paracelsus Medical University (PMU), 5020 Salzburg, Austria
| | - Johannes Adalbert Mayr
- University Children’s Hospital, Salzburger Landeskliniken (SALK) and Paracelsus Medical University (PMU), 5020 Salzburg, Austria
| | - Martin Preisel
- University Children’s Hospital, Salzburger Landeskliniken (SALK) and Paracelsus Medical University (PMU), 5020 Salzburg, Austria
| | - Frédéric Laumonnier
- UMR 1253, iBrain, Université de Tours, Inserm, 37032 Tours, France
- Service de Génétique, Centre Hospitalier Régional Universitaire, 37032 Tours, France
| | - Tilmann Kallinich
- Department of Pediatric Respiratory Medicine, Immunology and Critical Care Medicine, Charité Universitätsmedizin Berlin; 13353 Berlin, Germany
- Deutsches Rheumaforschungszentrum, An Institute of the Leibniz Association, Berlin and Berlin Institute of Health, 10117 Berlin, Germany
| | - Alexej Knaus
- Institute for Genomic Statistics and Bioinformatics, University Hospital Bonn, Rheinische Friedrich-Wilhelms-Universität Bonn, 53127 Bonn, Germany
| | - Bertrand Isidor
- Nantes Université, CHU Nantes, Service de Génétique Médicale, 44000 Nantes, France
- Nantes Université, CHU Nantes, CNRS, INSERM, l’institut du thorax, 44000 Nantes, France
| | - Peter Krawitz
- Institute for Genomic Statistics and Bioinformatics, University Hospital Bonn, Rheinische Friedrich-Wilhelms-Universität Bonn, 53127 Bonn, Germany
| | - Uwe Völker
- Universitätsmedizin Greifswald, Interfakultäres Institut für Genetik und Funktionelle Genomforschung, Abteilung für Funktionelle Genomforschung, 17487 Greifswald, Germany
| | - Elke Hammer
- Universitätsmedizin Greifswald, Interfakultäres Institut für Genetik und Funktionelle Genomforschung, Abteilung für Funktionelle Genomforschung, 17487 Greifswald, Germany
| | - Arnaud Droit
- Research Center of Quebec CHU-Université Laval, Québec, QC PQ G1E6W2, Canada
| | - Evan E. Eichler
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, 98195, USA
| | - Ype Elgersma
- ENCORE Expertise Center for Neurodevelopmental Disorders, Erasmus University Medical Center, 3015 CN, Rotterdam, The Netherlands
- Department of Clinical Genetics, Erasmus University Medical Center, 3015 CN, Rotterdam, The Netherlands
| | - Peter W. Hildebrand
- Institut für Medizinische Physik und Biophysik, Universität Leipzig, Medizinische Fakultät, Härtelstr. 16-18, 04107 Leipzig, Germany
- Charité Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Medical Physics and Biophysics, Berlin, Germany
- Berlin Institute of Health, 10178 Berlin, Germany
| | - François Bolduc
- Department of Pediatrics, University of Alberta, Edmonton, AB CT6G 1C9, Canada
- Neuroscience and Mental Health Institute, University of Alberta, Edmonton, AB T6G 2E1, Canada
- Department of Medical Genetics, University of Alberta, Edmonton, AB T6G 2H7, Canada
| | - Elke Krüger
- Institut für Medizinische Biochemie und Molekularbiologie (IMBM), Universitätsmedizin Greifswald, Ferdinand-Sauerbruch-Straße, 17475 Greifswald, Germany
| | - Stéphane Bézieau
- Nantes Université, CHU Nantes, Service de Génétique Médicale, 44000 Nantes, France
- Nantes Université, CHU Nantes, CNRS, INSERM, l’institut du thorax, 44000 Nantes, France
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6
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Leffler M, Christie L, Hackett A, Bennetts B, Goel H, Amor DJ, Peters GB, Field M, Dudding-Byth T. Further delineation of dosage-sensitive K/L mediated Xq28 duplication syndrome includes incomplete penetrance. Clin Genet 2023; 103:681-687. [PMID: 36688272 DOI: 10.1111/cge.14303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 01/07/2023] [Accepted: 01/17/2023] [Indexed: 01/24/2023]
Abstract
The low copy tandem repeat area at Xq28 is prone to recurrent copy number gains, including the K/L mediated duplications of 300 kb size (herein described as the K/L mediated Xq28 duplication syndrome). We describe five families, including nine males with K/L mediated Xq28 duplications, some with regions of greater copy number variation (CNV). We summarise findings in 25 affected males reported to date. Within the five families, males were variably affected by seizures, intellectual disability, and neurological features; however, one male with a familial K/L mediated Xq28 duplication has normal intelligence, suggesting that this CNV is not 100% penetrant. Including our five families, 13 carrier females have been identified, with nine presenting phenotypically normal. Three carrier females reported mild learning difficulties, and all of them had duplications containing regions with at least four copies. Delineation of the spectrum of K/L mediated Xq28 duplication syndrome highlights GDI1 as the most likely candidate gene contributing to the phenotype. For patients identified with CNVs in this region, high-resolution microarray is required to define copy number gains and provide families with accurate information.
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Affiliation(s)
- Melanie Leffler
- NSW Genetics of Learning Disability (GOLD) Service, Hunter New England Local Health District, Waratah, New South Wales, Australia
| | - Louise Christie
- NSW Genetics of Learning Disability (GOLD) Service, Hunter New England Local Health District, Waratah, New South Wales, Australia
| | - Anna Hackett
- NSW Genetics of Learning Disability (GOLD) Service, Hunter New England Local Health District, Waratah, New South Wales, Australia
| | - Bruce Bennetts
- Department of Molecular Genetics, Sydney Genome Diagnostics, Western Sydney Genetics Program, The Children's Hospital at Westmead, Sydney, New South Wales, Australia.,Specialty of Genomic Medicine, Faculty of Medicine and Health, University of Sydney, Sydney, New South Wales, Australia
| | - Himanshu Goel
- Hunter Genetics, Hunter New England Local Health District, Waratah, New South Wales, Australia.,University of Newcastle, Callaghan, New South Wales, Australia
| | - David J Amor
- Murdoch Children's Research Institute, Parkville, Victoria, Australia.,Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, Victoria, Australia.,Department of Paediatrics, Royal Children's Hospital, Parkville, Victoria, Australia
| | - Greg B Peters
- Formerly of Sydney Genome Diagnostics, The Children's Hospital at Westmead, Sydney, New South Wales, Australia
| | - Michael Field
- NSW Genetics of Learning Disability (GOLD) Service, Hunter New England Local Health District, Waratah, New South Wales, Australia
| | - Tracy Dudding-Byth
- NSW Genetics of Learning Disability (GOLD) Service, Hunter New England Local Health District, Waratah, New South Wales, Australia.,Hunter Genetics, Hunter New England Local Health District, Waratah, New South Wales, Australia.,University of Newcastle, Callaghan, New South Wales, Australia
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7
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Hertzog A, Selvanathan A, Farnsworth E, Tchan M, Adams L, Lewis K, Tolun AA, Bennetts B, Ho G, Bhattacharya K. Intronic variants in inborn errors of metabolism: Beyond the exome. Front Genet 2022; 13:1031495. [PMID: 36561316 PMCID: PMC9763607 DOI: 10.3389/fgene.2022.1031495] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Accepted: 11/15/2022] [Indexed: 12/12/2022] Open
Abstract
Non-coding regions are areas of the genome that do not directly encode protein and were initially thought to be of little biological relevance. However, subsequent identification of pathogenic variants in these regions indicates there are exceptions to this assertion. With the increasing availability of next generation sequencing, variants in non-coding regions are often considered when no causative exonic changes have been identified. There is still a lack of understanding of normal human variation in non-coding areas. As a result, potentially pathogenic non-coding variants are initially classified as variants of uncertain significance or are even overlooked during genomic analysis. In most cases where the phenotype is non-specific, clinical suspicion is not sufficient to warrant further exploration of these changes, partly due to the magnitude of non-coding variants identified. In contrast, inborn errors of metabolism (IEMs) are one group of genetic disorders where there is often high phenotypic specificity. The clinical and biochemical features seen often result in a narrow list of diagnostic possibilities. In this context, there have been numerous cases in which suspicion of a particular IEM led to the discovery of a variant in a non-coding region. We present four patients with IEMs where the molecular aetiology was identified within non-coding regions. Confirmation of the molecular diagnosis is often aided by the clinical and biochemical specificity associated with IEMs. Whilst the clinical severity associated with a non-coding variant can be difficult to predict, obtaining a molecular diagnosis is crucial as it ends diagnostic odysseys and assists in management.
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Affiliation(s)
- Ashley Hertzog
- NSW Biochemical Genetics Service, Western Sydney Genetics Program, The Children’s Hospital at Westmead, Sydney, NSW, Australia,Disciplines of Genetic Medicine and Child and Adolescent Health, Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia,*Correspondence: Ashley Hertzog,
| | - Arthavan Selvanathan
- Genetic Metabolic Disorders Service, Sydney Children’s Hospitals Network, Sydney, NSW, Australia
| | - Elizabeth Farnsworth
- Department of Molecular Genetics, Sydney Genome Diagnostics, Western Sydney Genetics Program, The Children’s Hospital at Westmead, Sydney, NSW, Australia
| | - Michel Tchan
- Department of Genetic Medicine, Westmead Hospital, Sydney, NSW, Australia
| | - Louisa Adams
- Genetic Metabolic Disorders Service, Sydney Children’s Hospitals Network, Sydney, NSW, Australia
| | - Katherine Lewis
- Genetic Metabolic Disorders Service, Sydney Children’s Hospitals Network, Sydney, NSW, Australia
| | - Adviye Ayper Tolun
- NSW Biochemical Genetics Service, Western Sydney Genetics Program, The Children’s Hospital at Westmead, Sydney, NSW, Australia,Disciplines of Genetic Medicine and Child and Adolescent Health, Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia
| | - Bruce Bennetts
- Disciplines of Genetic Medicine and Child and Adolescent Health, Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia,Department of Molecular Genetics, Sydney Genome Diagnostics, Western Sydney Genetics Program, The Children’s Hospital at Westmead, Sydney, NSW, Australia
| | - Gladys Ho
- Disciplines of Genetic Medicine and Child and Adolescent Health, Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia,Department of Molecular Genetics, Sydney Genome Diagnostics, Western Sydney Genetics Program, The Children’s Hospital at Westmead, Sydney, NSW, Australia
| | - Kaustuv Bhattacharya
- Disciplines of Genetic Medicine and Child and Adolescent Health, Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia,Genetic Metabolic Disorders Service, Sydney Children’s Hospitals Network, Sydney, NSW, Australia
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8
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Tudini E, Andrews J, Lawrence DM, King-Smith SL, Baker N, Baxter L, Beilby J, Bennetts B, Beshay V, Black M, Boughtwood TF, Brion K, Cheong PL, Christie M, Christodoulou J, Chong B, Cox K, Davis MR, Dejong L, Dinger ME, Doig KD, Douglas E, Dubowsky A, Ellul M, Fellowes A, Fisk K, Fortuno C, Friend K, Gallagher RL, Gao S, Hackett E, Hadler J, Hipwell M, Ho G, Hollway G, Hooper AJ, Kassahn KS, Krishnaraj R, Lau C, Le H, San Leong H, Lundie B, Lunke S, Marty A, McPhillips M, Nguyen LT, Nones K, Palmer K, Pearson JV, Quinn MC, Rawlings LH, Sadedin S, Sanchez L, Schreiber AW, Sigalas E, Simsek A, Soubrier J, Stark Z, Thompson BA, U J, Vakulin CG, Wells AV, Wise CA, Woods R, Ziolkowski A, Brion MJ, Scott HS, Thorne NP, Spurdle AB. Shariant platform: Enabling evidence sharing across Australian clinical genetic-testing laboratories to support variant interpretation. Am J Hum Genet 2022; 109:1960-1973. [PMID: 36332611 PMCID: PMC9674965 DOI: 10.1016/j.ajhg.2022.10.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 10/10/2022] [Indexed: 11/06/2022] Open
Abstract
Sharing genomic variant interpretations across laboratories promotes consistency in variant assertions. A landscape analysis of Australian clinical genetic-testing laboratories in 2017 identified that, despite the national-accreditation-body recommendations encouraging laboratories to submit genotypic data to clinical databases, fewer than 300 variants had been shared to the ClinVar public database. Consultations with Australian laboratories identified resource constraints limiting routine application of manual processes, consent issues, and differences in interpretation systems as barriers to sharing. This information was used to define key needs and solutions required to enable national sharing of variant interpretations. The Shariant platform, using both the GRCh37 and GRCh38 genome builds, was developed to enable ongoing sharing of variant interpretations and associated evidence between Australian clinical genetic-testing laboratories. Where possible, two-way automated sharing was implemented so that disruption to laboratory workflows would be minimized. Terms of use were developed through consultation and currently restrict access to Australian clinical genetic-testing laboratories. Shariant was designed to store and compare structured evidence, to promote and record resolution of inter-laboratory classification discrepancies, and to streamline the submission of variant assertions to ClinVar. As of December 2021, more than 14,000 largely prospectively curated variant records from 11 participating laboratories have been shared. Discrepant classifications have been identified for 11% (28/260) of variants submitted by more than one laboratory. We have demonstrated that co-design with clinical laboratories is vital to developing and implementing a national variant-interpretation sharing effort. This approach has improved inter-laboratory concordance and enabled opportunities to standardize interpretation practices.
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Affiliation(s)
- Emma Tudini
- Australian Genomics, Melbourne, VIC 3052, Australia,Population Health, QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia
| | - James Andrews
- Australian Genomics, Melbourne, VIC 3052, Australia,Australian Cancer Research Foundation Cancer Genomics Facility, Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, SA 5000, Australia
| | - David M. Lawrence
- Australian Cancer Research Foundation Cancer Genomics Facility, Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, SA 5000, Australia
| | - Sarah L. King-Smith
- Australian Genomics, Melbourne, VIC 3052, Australia,Genetics and Molecular Pathology, SA Pathology, Adelaide, SA 5000, Australia
| | - Naomi Baker
- Victorian Clinical Genetics Services, Murdoch Children’s Research Institute, Melbourne, VIC 3052, Australia,University of Melbourne, Melbourne, VIC 3052, Australia
| | | | - John Beilby
- PathWest Laboratory Medicine Western Australia, Perth, WA 6009, Australia,School of Biomedical Sciences, The University of Western Australia, Perth, WA 6009, Australia
| | - Bruce Bennetts
- Sydney Genome Diagnostics, Western Sydney Genetics Program, The Children’s Hospital at Westmead, Sydney, NSW 2145, Australia,Disciplines of Child and Adolescent Health and Genomic Medicine, University of Sydney, Sydney, NSW 2145, Australia
| | - Victoria Beshay
- Department of Pathology, Peter MacCallum Cancer Centre, Melbourne, VIC 3052, Australia
| | - Michael Black
- Department of Diagnostic Genomics, PathWest Laboratory Medicine Western Australia, Perth, WA 6009, Australia
| | - Tiffany F. Boughtwood
- Australian Genomics, Melbourne, VIC 3052, Australia,Murdoch Children’s Research Institute, Melbourne, VIC 3052, Australia
| | | | - Pak Leng Cheong
- Department of Medical Genomics, Royal Prince Alfred Hospital, NSW Health Pathology, Sydney, NSW 2050, Australia,University of Sydney, Sydney, NSW 2006, Australia
| | - Michael Christie
- Department of Pathology, Royal Melbourne Hospital, Melbourne, VIC 3050, Australia
| | - John Christodoulou
- Australian Genomics, Melbourne, VIC 3052, Australia,Disciplines of Child and Adolescent Health and Genomic Medicine, University of Sydney, Sydney, NSW 2145, Australia,Murdoch Children’s Research Institute, Melbourne, VIC 3052, Australia,Department of Paediatrics, University of Melbourne, Melbourne, VIC 3052, Australia
| | - Belinda Chong
- Victorian Clinical Genetics Services, Murdoch Children’s Research Institute, Melbourne, VIC 3052, Australia
| | - Kathy Cox
- Genetics and Molecular Pathology, SA Pathology, Adelaide, SA 5000, Australia
| | - Mark R. Davis
- Department of Diagnostic Genomics, PathWest Laboratory Medicine Western Australia, Perth, WA 6009, Australia,Centre for Medical Research, The University of Western Australia, Perth, WA 6009, Australia
| | - Lucas Dejong
- Genetics and Molecular Pathology, SA Pathology, Adelaide, SA 5000, Australia
| | - Marcel E. Dinger
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - Kenneth D. Doig
- Department of Pathology, Peter MacCallum Cancer Centre, Melbourne, VIC 3052, Australia,Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC 3052, Australia
| | - Evelyn Douglas
- Genetics and Molecular Pathology, SA Pathology, Adelaide, SA 5000, Australia
| | - Andrew Dubowsky
- Genetics and Molecular Pathology, SA Pathology, Adelaide, SA 5000, Australia
| | - Melissa Ellul
- Genetics and Molecular Pathology, SA Pathology, Adelaide, SA 5000, Australia
| | - Andrew Fellowes
- Department of Pathology, Peter MacCallum Cancer Centre, Melbourne, VIC 3052, Australia
| | - Katrina Fisk
- Sydney Genome Diagnostics, Western Sydney Genetics Program, The Children’s Hospital at Westmead, Sydney, NSW 2145, Australia
| | - Cristina Fortuno
- Population Health, QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia
| | - Kathryn Friend
- Genetics and Molecular Pathology, SA Pathology, Adelaide, SA 5000, Australia
| | | | - Song Gao
- Genetics and Molecular Pathology, SA Pathology, Adelaide, SA 5000, Australia
| | - Emma Hackett
- Sydney Genome Diagnostics, Western Sydney Genetics Program, The Children’s Hospital at Westmead, Sydney, NSW 2145, Australia
| | - Johanna Hadler
- Genetics and Molecular Pathology, SA Pathology, Adelaide, SA 5000, Australia
| | - Michael Hipwell
- Division of Molecular Medicine, NSW Health Pathology North, Newcastle, NSW 2305, Australia
| | - Gladys Ho
- Sydney Genome Diagnostics, Western Sydney Genetics Program, The Children’s Hospital at Westmead, Sydney, NSW 2145, Australia,Disciplines of Child and Adolescent Health and Genomic Medicine, University of Sydney, Sydney, NSW 2145, Australia
| | - Georgina Hollway
- Garvan Institute of Medical Research, Sydney, NSW 2010, Australia,Cancer Research, QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia
| | - Amanda J. Hooper
- Department of Clinical Biochemistry, PathWest Laboratory Medicine Western Australia, Fiona Stanley Hospital Network, Perth, WA 6150, Australia,School of Medicine, The University of Western Australia, Perth, WA 6009, Australia
| | - Karin S. Kassahn
- Genetics and Molecular Pathology, SA Pathology, Adelaide, SA 5000, Australia,Adelaide Medical School, The University of Adelaide, Adelaide, SA 5000, Australia
| | - Rahul Krishnaraj
- Sydney Genome Diagnostics, Western Sydney Genetics Program, The Children’s Hospital at Westmead, Sydney, NSW 2145, Australia
| | - Chiyan Lau
- Pathology Queensland, Brisbane, QLD 4006, Australia,The University of Queensland, Brisbane, QLD 4072, Australia
| | - Huong Le
- Department of Medical Genomics, Royal Prince Alfred Hospital, NSW Health Pathology, Sydney, NSW 2050, Australia
| | - Huei San Leong
- Department of Pathology, Peter MacCallum Cancer Centre, Melbourne, VIC 3052, Australia
| | - Ben Lundie
- Pathology Queensland, Brisbane, QLD 4006, Australia
| | - Sebastian Lunke
- Victorian Clinical Genetics Services, Murdoch Children’s Research Institute, Melbourne, VIC 3052, Australia,University of Melbourne, Melbourne, VIC 3052, Australia
| | - Anthony Marty
- Melbourne Genomics Health Alliance, Melbourne, VIC 3052, Australia
| | - Mary McPhillips
- Division of Molecular Medicine, NSW Health Pathology North, Newcastle, NSW 2305, Australia
| | - Lan T. Nguyen
- Department of Clinical Biochemistry, PathWest Laboratory Medicine Western Australia, Fiona Stanley Hospital Network, Perth, WA 6150, Australia
| | - Katia Nones
- Cancer Research, QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia
| | - Kristen Palmer
- Genomics Statewide Services, New South Wales Health Pathology, Newcastle, NSW 2300, Australia
| | - John V. Pearson
- Genome Informatics, QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia
| | - Michael C.J. Quinn
- Australian Genomics, Melbourne, VIC 3052, Australia,Genetic Health Queensland, Royal Brisbane and Women’s Hospital, Brisbane, QLD 4006, Australia
| | - Lesley H. Rawlings
- Genetics and Molecular Pathology, SA Pathology, Adelaide, SA 5000, Australia
| | - Simon Sadedin
- Victorian Clinical Genetics Services, Murdoch Children’s Research Institute, Melbourne, VIC 3052, Australia,University of Melbourne, Melbourne, VIC 3052, Australia,Murdoch Children’s Research Institute, Melbourne, VIC 3052, Australia
| | - Louisa Sanchez
- Genetics and Molecular Pathology, SA Pathology, Adelaide, SA 5000, Australia
| | - Andreas W. Schreiber
- Australian Cancer Research Foundation Cancer Genomics Facility, Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, SA 5000, Australia,School of Biological Sciences, The University of Adelaide, Adelaide, SA 5005, Australia
| | - Emanouil Sigalas
- Department of Pathology, Royal Melbourne Hospital, Melbourne, VIC 3050, Australia
| | - Aygul Simsek
- Genetics and Molecular Pathology, SA Pathology, Adelaide, SA 5000, Australia
| | - Julien Soubrier
- Genetics and Molecular Pathology, SA Pathology, Adelaide, SA 5000, Australia,School of Biological Sciences, The University of Adelaide, Adelaide, SA 5005, Australia
| | - Zornitza Stark
- Australian Genomics, Melbourne, VIC 3052, Australia,Victorian Clinical Genetics Services, Murdoch Children’s Research Institute, Melbourne, VIC 3052, Australia,University of Melbourne, Melbourne, VIC 3052, Australia
| | - Bryony A. Thompson
- Department of Pathology, Royal Melbourne Hospital, Melbourne, VIC 3050, Australia
| | - James U
- Melbourne Genomics Health Alliance, Melbourne, VIC 3052, Australia
| | | | - Amanda V. Wells
- Genetics and Molecular Pathology, SA Pathology, Adelaide, SA 5000, Australia
| | - Cheryl A. Wise
- Department of Diagnostic Genomics, PathWest Laboratory Medicine Western Australia, Perth, WA 6009, Australia
| | - Rick Woods
- Pathology Queensland, Brisbane, QLD 4006, Australia
| | - Andrew Ziolkowski
- Division of Molecular Medicine, NSW Health Pathology North, Newcastle, NSW 2305, Australia
| | - Marie-Jo Brion
- Australian Genomics, Melbourne, VIC 3052, Australia,Population Health, QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia
| | - Hamish S. Scott
- Australian Genomics, Melbourne, VIC 3052, Australia,Australian Cancer Research Foundation Cancer Genomics Facility, Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, SA 5000, Australia,Genetics and Molecular Pathology, SA Pathology, Adelaide, SA 5000, Australia,Adelaide Medical School, The University of Adelaide, Adelaide, SA 5000, Australia
| | - Natalie P. Thorne
- Australian Genomics, Melbourne, VIC 3052, Australia,University of Melbourne, Melbourne, VIC 3052, Australia,Murdoch Children’s Research Institute, Melbourne, VIC 3052, Australia,Melbourne Genomics Health Alliance, Melbourne, VIC 3052, Australia,Walter and Eliza Hall Institute, Melbourne, VIC 3052, Australia
| | - Amanda B. Spurdle
- Australian Genomics, Melbourne, VIC 3052, Australia,Population Health, QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia,Corresponding author
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9
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Temple SEL, Ho G, Bennetts B, Boggs K, Vidic N, Mowat D, Christodoulou J, Schultz A, Gayagay T, Roscioli T, Zhu Y, Lunke S, Armstrong D, Harrison J, Kapur N, McDonald T, Selvadurai H, Tai A, Stark Z, Jaffe A. The role of exome sequencing in childhood interstitial or diffuse lung disease. Orphanet J Rare Dis 2022; 17:350. [PMID: 36085161 PMCID: PMC9463757 DOI: 10.1186/s13023-022-02508-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 09/04/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Children's interstitial and diffuse lung disease (chILD) is a complex heterogeneous group of lung disorders. Gene panel approaches have a reported diagnostic yield of ~ 12%. No data currently exist using trio exome sequencing as the standard diagnostic modality. We assessed the diagnostic utility of using trio exome sequencing in chILD. We prospectively enrolled children meeting specified clinical criteria between 2016 and 2020 from 16 Australian hospitals. Exome sequencing was performed with analysis of an initial gene panel followed by trio exome analysis. A subset of critically ill infants underwent ultra-rapid trio exome sequencing as first-line test. RESULTS 36 patients [median (range) age 0.34 years (0.02-11.46); 11F] were recruited from multiple States and Territories. Five patients had clinically significant likely pathogenic/pathogenic variants (RARB, RPL15, CTCF, RFXANK, TBX4) and one patient had a variant of uncertain significance (VIP) suspected to contribute to their clinical phenotype, with VIP being a novel gene candidate. CONCLUSIONS Trio exomes (6/36; 16.7%) had a better diagnostic rate than gene panel (1/36; 2.8%), due to the ability to consider a broader range of underlying conditions. However, the aetiology of chILD in most cases remained undetermined, likely reflecting the interplay between low penetrant genetic and environmental factors.
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Affiliation(s)
- Suzanna E L Temple
- Department of Clinical Genetics, Liverpool Hospital, Sydney, NSW, Australia. .,School of Women's and Children's Health, Faculty of Medicine and Health, UNSW, Sydney, NSW, Australia.
| | - Gladys Ho
- Sydney Genome Diagnostics, Western Sydney Genetics Program, The Children's Hospital at Westmead, Sydney, NSW, Australia.,Disciplines of Child and Adolescent Health and Genomic Medicine, University of Sydney, Sydney, NSW, Australia
| | - Bruce Bennetts
- Sydney Genome Diagnostics, Western Sydney Genetics Program, The Children's Hospital at Westmead, Sydney, NSW, Australia.,Disciplines of Child and Adolescent Health and Genomic Medicine, University of Sydney, Sydney, NSW, Australia
| | - Kirsten Boggs
- Australian Genomics Health Alliance, Melbourne, VIC, Australia.,Department of Clinical Genetics, Children's Hospital Westmead, Sydney, NSW, Australia.,Centre for Clinical Genetics, Sydney Children's Hospital Randwick, Sydney, NSW, Australia
| | - Nada Vidic
- School of Women's and Children's Health, Faculty of Medicine and Health, UNSW, Sydney, NSW, Australia.,Australian Genomics Health Alliance, Melbourne, VIC, Australia
| | - David Mowat
- School of Women's and Children's Health, Faculty of Medicine and Health, UNSW, Sydney, NSW, Australia.,Centre for Clinical Genetics, Sydney Children's Hospital Randwick, Sydney, NSW, Australia
| | - John Christodoulou
- Disciplines of Child and Adolescent Health and Genomic Medicine, University of Sydney, Sydney, NSW, Australia.,Australian Genomics Health Alliance, Melbourne, VIC, Australia.,University of Melbourne, Melbourne, VIC, Australia.,Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, VIC, Australia
| | - André Schultz
- Wal-Yan Respiratory Research Centre, Telethon Kids Institute, University of Western Australia, Perth, Australia.,Department of Respiratory Medicine, Perth Children's Hospital, Nedlands, WA, Australia.,Division of Paediatrics, Faculty of Medicine, University of Western Australia, Perth, Australia
| | - Thet Gayagay
- Sydney Genome Diagnostics, Western Sydney Genetics Program, The Children's Hospital at Westmead, Sydney, NSW, Australia
| | - Tony Roscioli
- Centre for Clinical Genetics, Sydney Children's Hospital Randwick, Sydney, NSW, Australia.,Randwick Genomics Laboratory, NSW Health Pathology, Prince of Wales Hospital, Sydney, NSW, Australia.,Neuroscience Research Australia (NeuRA), Sydney, NSW, Australia
| | - Ying Zhu
- Randwick Genomics Laboratory, NSW Health Pathology, Prince of Wales Hospital, Sydney, NSW, Australia
| | - Sebastian Lunke
- Australian Genomics Health Alliance, Melbourne, VIC, Australia.,University of Melbourne, Melbourne, VIC, Australia.,Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, VIC, Australia
| | - David Armstrong
- Department of Paediatrics, Monash University, Clayton Rd, Clayton, VIC, Australia.,Department of Respiratory and Sleep Medicine, Monash Children's Hospital, Clayton Rd, Clayton, VIC, Australia
| | - Joanne Harrison
- University of Melbourne, Melbourne, VIC, Australia.,Department of Respiratory and Sleep Medicine, The Royal Children's Hospital, Melbourne, VIC, Australia
| | - Nitin Kapur
- Department of Respiratory and Sleep Medicine, Queensland Children's Hospital, Brisbane, QLD, Australia.,School of Medicine, University of Queensland, Brisbane, QLD, Australia
| | | | - Hiran Selvadurai
- Disciplines of Child and Adolescent Health and Genomic Medicine, University of Sydney, Sydney, NSW, Australia.,Children's Hospital Westmead, Sydney, NSW, Australia
| | - Andrew Tai
- Paediatric Respiratory and Sleep Department, Women's and Children's Hospital, Adelaide, SA, Australia.,Robinson Research Institute, University of Adelaide, Adelaide, SA, Australia
| | - Zornitza Stark
- Australian Genomics Health Alliance, Melbourne, VIC, Australia.,University of Melbourne, Melbourne, VIC, Australia.,Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, VIC, Australia
| | - Adam Jaffe
- School of Women's and Children's Health, Faculty of Medicine and Health, UNSW, Sydney, NSW, Australia.,Department Respiratory and Sleep Medicine, Sydney Children's Hospital, Randwick, NSW, Australia
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10
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Hertzog A, Selvanathan A, Halligan R, Fazio T, Jong G, Bratkovic D, Bhattacharya K, Tolun AA, Bennetts B, Fisk K. A serendipitous journey to a promoter variant: The c.‐
106C
>A variant and its role in late‐onset ornithine transcarbamylase deficiency. JIMD Rep 2022; 63:271-275. [PMID: 35822098 PMCID: PMC9259394 DOI: 10.1002/jmd2.12289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 03/15/2022] [Accepted: 04/01/2022] [Indexed: 11/19/2022] Open
Abstract
Ornithine transcarbamylase deficiency (OTCD) is an X‐linked urea cycle disorder characterised by reduced or absent OTC enzyme activity, resulting in the accumulation of neurotoxic ammonia. Approximately 80%–90% of the causative variants are identified by Sanger sequencing or multiplex ligation‐dependent probe amplification (MLPA) of the OTC gene. A 23‐year‐old male with biochemical evidence of OTCD was referred for molecular analysis. Initial Sanger sequencing yielded no pathogenic variants. MLPA testing raised suspicion of a mosaic deletion of exon 1; however, high‐resolution microarray did not identify a copy number variant on the X chromosome. Sequencing over the suspected breakpoint detected a hemizygous likely pathogenic promoter variant, c.‐106C > A, which was located within the MLPA probe binding site. Subsequently, historical patients referred to our centre, without a molecular aetiology for their OTCD, were re‐sequenced with these primers and this variant was also identified in two additional unrelated males. All three patients described in this case series have the late‐onset disease. Two presented at 5 years of age with vomiting, whilst the other was managed from birth based on a family history of late‐onset OTCD. One patient required liver transplantation due to recurrent decompensations; the other two are managed with a protein‐restricted diet. All three patients have not sustained any significant neurological insults and are functioning well as adults. These cases support screening of the promoter region within the OTC gene, particularly if a molecular basis has not been elucidated by MLPA or sequencing of the coding regions.
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Affiliation(s)
- Ashley Hertzog
- NSW Biochemical Genetics Service The Children's Hospital at Westmead Westmead New South Wales Australia
| | - Arthavan Selvanathan
- Genetic Metabolic Disorders Service The Children's Hospital at Westmead Westmead New South Wales Australia
| | - Rebecca Halligan
- Metabolic Unit Women's and Children's Hospital Adelaide South Australia Australia
| | - Timothy Fazio
- Metabolic Diseases Unit Royal Melbourne Hospital Parkville Victoria Australia
- Melbourne Medical School University of Melbourne Parkville Victoria Australia
| | - Gerard Jong
- Metabolic Diseases Unit Royal Melbourne Hospital Parkville Victoria Australia
- Melbourne Medical School University of Melbourne Parkville Victoria Australia
| | - Drago Bratkovic
- Metabolic Unit Women's and Children's Hospital Adelaide South Australia Australia
| | - Kaustuv Bhattacharya
- Genetic Metabolic Disorders Service The Children's Hospital at Westmead Westmead New South Wales Australia
- Disciplines of Genomic Medicine and Child and Adolescent Health Faculty of Medicine and Health, University of Sydney Sydney New South Wales Australia
| | - Adviye Ayper Tolun
- NSW Biochemical Genetics Service The Children's Hospital at Westmead Westmead New South Wales Australia
- Disciplines of Genomic Medicine and Child and Adolescent Health Faculty of Medicine and Health, University of Sydney Sydney New South Wales Australia
| | - Bruce Bennetts
- Disciplines of Genomic Medicine and Child and Adolescent Health Faculty of Medicine and Health, University of Sydney Sydney New South Wales Australia
- Department of Molecular Genetics Western Sydney Genetics Program, The Children's Hospital at Westmead Westmead New South Wales Australia
| | - Katrina Fisk
- Department of Molecular Genetics Western Sydney Genetics Program, The Children's Hospital at Westmead Westmead New South Wales Australia
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11
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Chahine Karam F, Loi TH, Ma A, Nash BM, Grigg JR, Parekh D, Riley LG, Farnsworth E, Bennetts B, Gonzalez-Cordero A, Jamieson RV. Human iPSC-Derived Retinal Organoids and Retinal Pigment Epithelium for Novel Intronic RPGR Variant Assessment for Therapy Suitability. J Pers Med 2022; 12:jpm12030502. [PMID: 35330501 PMCID: PMC8951517 DOI: 10.3390/jpm12030502] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 03/16/2022] [Accepted: 03/17/2022] [Indexed: 02/04/2023] Open
Abstract
The RPGR gene encodes Retinitis Pigmentosa GTPase Regulator, a known interactor with ciliary proteins, which is involved in maintaining healthy photoreceptor cells. Variants in RPGR are the main contributor to X-linked rod-cone dystrophy (RCD), and RPGR gene therapy approaches are in clinical trials. Hence, elucidation of the pathogenicity of novel RPGR variants is important for a patient therapy opportunity. Here, we describe a novel intronic RPGR variant, c.1415 − 9A>G, in a patient with RCD, which was classified as a variant of uncertain significance according to current clinical diagnostic criteria. The variant lay several base pairs intronic to the canonical splice acceptor site, raising suspicion of an RPGR RNA splicing abnormality and consequent protein dysfunction. To investigate disease causation in an appropriate disease model, induced pluripotent stem cells were generated from patient fibroblasts and differentiated to retinal pigment epithelium (iPSC-RPE) and retinal organoids (iPSC-RO). Abnormal RNA splicing of RPGR was demonstrated in patient fibroblasts, iPSC-RPE and iPSC-ROs, leading to a predicted frameshift and premature stop codon. Decreased RPGR expression was demonstrated in these cell types, with a striking loss of RPGR localization at the ciliary transitional zone, critically in the photoreceptor cilium of the patient iPSC-ROs. Mislocalisation of rhodopsin staining was present in the patient’s iPSC-RO rod photoreceptor cells, along with an abnormality of L/M opsin staining affecting cone photoreceptor cells and increased photoreceptor apoptosis. Additionally, patient iPSC-ROs displayed an increase in F-actin expression that was consistent with an abnormal actin regulation phenotype. Collectively, these studies indicate that the splicing abnormality caused by the c.1415 − 9A>G variant has an impact on RPGR function. This work has enabled the reclassification of this variant to pathogenic, allowing the consideration of patients with this variant having access to gene therapy clinical trials. In addition, we have identified biomarkers of disease suitable for the interrogation of other RPGR variants of uncertain significance.
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Affiliation(s)
- Fidelle Chahine Karam
- Eye Genetics Research Unit, Children’s Medical Research Institute, Sydney Children’s Hospitals Network, Save Sight Institute, University of Sydney, Westmead, Sydney 2145, Australia; (F.C.K.); (T.H.L.); (A.M.); (B.M.N.); (J.R.G.)
| | - To Ha Loi
- Eye Genetics Research Unit, Children’s Medical Research Institute, Sydney Children’s Hospitals Network, Save Sight Institute, University of Sydney, Westmead, Sydney 2145, Australia; (F.C.K.); (T.H.L.); (A.M.); (B.M.N.); (J.R.G.)
| | - Alan Ma
- Eye Genetics Research Unit, Children’s Medical Research Institute, Sydney Children’s Hospitals Network, Save Sight Institute, University of Sydney, Westmead, Sydney 2145, Australia; (F.C.K.); (T.H.L.); (A.M.); (B.M.N.); (J.R.G.)
- Department of Clinical Genetics, Western Sydney Genetics Program, Sydney Children’s Hospitals Network, Westmead, Sydney 2145, Australia
- Specialty of Genomic Medicine, Faculty of Medicine and Health, University of Sydney, Westmead, Sydney 2145, Australia; (E.F.); (B.B.)
| | - Benjamin M. Nash
- Eye Genetics Research Unit, Children’s Medical Research Institute, Sydney Children’s Hospitals Network, Save Sight Institute, University of Sydney, Westmead, Sydney 2145, Australia; (F.C.K.); (T.H.L.); (A.M.); (B.M.N.); (J.R.G.)
- Specialty of Genomic Medicine, Faculty of Medicine and Health, University of Sydney, Westmead, Sydney 2145, Australia; (E.F.); (B.B.)
- Sydney Genome Diagnostics, Western Sydney Genetics Program, Sydney Children’s Hospitals Network, Westmead, Sydney 2145, Australia
| | - John R. Grigg
- Eye Genetics Research Unit, Children’s Medical Research Institute, Sydney Children’s Hospitals Network, Save Sight Institute, University of Sydney, Westmead, Sydney 2145, Australia; (F.C.K.); (T.H.L.); (A.M.); (B.M.N.); (J.R.G.)
- Specialty of Ophthalmology, Faculty of Medicine and Health, University of Sydney, Sydney 2006, Australia
| | - Darshan Parekh
- Rare Diseases Functional Genomics Laboratory, Sydney Children’s Hospitals Network and Children’s Medical Research Institute, Westmead, Sydney 2145, Australia; (D.P.); (L.G.R.)
| | - Lisa G. Riley
- Rare Diseases Functional Genomics Laboratory, Sydney Children’s Hospitals Network and Children’s Medical Research Institute, Westmead, Sydney 2145, Australia; (D.P.); (L.G.R.)
- Specialty of Child and Adolescent Health, University of Sydney, Westmead, Sydney 2145, Australia
| | - Elizabeth Farnsworth
- Specialty of Genomic Medicine, Faculty of Medicine and Health, University of Sydney, Westmead, Sydney 2145, Australia; (E.F.); (B.B.)
- Sydney Genome Diagnostics, Western Sydney Genetics Program, Sydney Children’s Hospitals Network, Westmead, Sydney 2145, Australia
| | - Bruce Bennetts
- Specialty of Genomic Medicine, Faculty of Medicine and Health, University of Sydney, Westmead, Sydney 2145, Australia; (E.F.); (B.B.)
- Sydney Genome Diagnostics, Western Sydney Genetics Program, Sydney Children’s Hospitals Network, Westmead, Sydney 2145, Australia
| | - Anai Gonzalez-Cordero
- Stem Cell Medicine Group, Children’s Medical Research Institute, University of Sydney, Westmead, Sydney 2145, Australia;
- School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, Sydney 2006, Australia
| | - Robyn V. Jamieson
- Eye Genetics Research Unit, Children’s Medical Research Institute, Sydney Children’s Hospitals Network, Save Sight Institute, University of Sydney, Westmead, Sydney 2145, Australia; (F.C.K.); (T.H.L.); (A.M.); (B.M.N.); (J.R.G.)
- Department of Clinical Genetics, Western Sydney Genetics Program, Sydney Children’s Hospitals Network, Westmead, Sydney 2145, Australia
- Specialty of Genomic Medicine, Faculty of Medicine and Health, University of Sydney, Westmead, Sydney 2145, Australia; (E.F.); (B.B.)
- Correspondence: ; Tel.: +61-2-9687-2800; Fax: +61-2-9687-2120
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12
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Chai SY, Munusamy N, Bennetts B, Badrick T. Using EQA data to determine risk in molecular diagnostic tests. Pathology 2022. [DOI: 10.1016/j.pathol.2021.12.059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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13
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Kelada L, Wakefield C, Vidic N, Armstrong DS, Bennetts B, Boggs K, Christodoulou J, Harrison J, Ho G, Kapur N, Lindsey-Temple S, McDonald T, Mowat D, Schultz A, Selvadurai H, Tai A, Jaffe A. Genomic testing for children with interstitial and diffuse lung disease (chILD): parent satisfaction, understanding and health-related quality of life. BMJ Open Respir Res 2022; 9:9/1/e001139. [PMID: 35190460 PMCID: PMC8862491 DOI: 10.1136/bmjresp-2021-001139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 02/02/2022] [Indexed: 12/02/2022] Open
Abstract
Objective Research is needed to determine best practice for genomic testing in the context of child interstitial or diffuse lung disease (chILD). We explored parent’s and child’s health-related quality of life (HRQoL), parents’ perceived understanding of a genomic testing study, satisfaction with information and the study and decisional regret to undertake genomic testing. Methods Parents of children with diagnosed or suspected chILD who were enrolled in a genomic sequencing study were invited to complete questionnaires pretesting (T1) and after receiving the result (T2). Results Parents’ (T1, n=19; T2, n=17) HRQoL was lower than population norms. Study satisfaction (T1) and perceived understanding (T2) were positively correlated (rs=0.68, p=0.014). Satisfaction with information (T1 and T2) and decisional regret (T2) were negatively correlated (T1 rs=−0.71, p=0.01; T2 rs=−0.56, p=0.03). Parents reported wanting more frequent communication with staff throughout the genomic sequencing study, and greater information about the confidentiality of test results. Conclusions Understanding of genomic testing, satisfaction with information and participation and decisional regret are inter-related. Pretest consultations are important and can allow researchers to explain confidentiality of data and the variable turnaround times for receiving a test result. Staff can also update parents when there will be delays to receiving a result.
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Affiliation(s)
- Lauren Kelada
- Behavioural Sciences Unit, Kids Cancer Centre, Sydney Children's Hospital Randwick, Randwick, New South Wales, Australia
- School of Clinical Medicine, UNSW Medicine & Health, UNSW, Sydney, New South Wales, Australia
| | - Claire Wakefield
- Behavioural Sciences Unit, Kids Cancer Centre, Sydney Children's Hospital Randwick, Randwick, New South Wales, Australia
- School of Clinical Medicine, UNSW Medicine & Health, UNSW, Sydney, New South Wales, Australia
| | - Nada Vidic
- School of Clinical Medicine, UNSW Medicine & Health, UNSW, Sydney, New South Wales, Australia
| | - David S Armstrong
- Department of Respiratory Medicine, Monash Children's Hospital, Melbourne, Victoria, Australia
- Department of Paediatrics, Monash University, Melbourne, Victoria, Australia
| | - Bruce Bennetts
- Discipline of Genetic Medicine and Discipline of Child & Adolescent Health, Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia
- Sydney Genome Diagnostics, Western Sydney Genetics Program, The Children's Hospital at Westmead, Sydney, New South Wales, Australia
- KidGen Collaborative, Australian Genomics Health Alliance, Parkville, Victoria, Australia
| | - Kirsten Boggs
- Department of Clinical Genetics, Sydney Children's Hospital Network, Westmead, New South Wales, Australia
- Mackenzie's Mission, Australian Genomics Health Alliance, Melbourne, Victoria, Australia
- Centre for Clinical Genetics, Sydney Children's Hospital Randwick, Randwick, New South Wales, Australia
| | - John Christodoulou
- Discipline of Genetic Medicine and Discipline of Child & Adolescent Health, Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia
- Brain and Mitochondrial, Murdoch Children's Research Institute, University of Melbourne, Melbourne, Victoria, Australia
- Department of Paediatrics, University of Melbourne, Melbourne, Victoria, Australia
| | - Joanne Harrison
- Department of Paediatrics, University of Melbourne, Melbourne, Victoria, Australia
- Department of Respiratory and Sleep Medicine, The Royal Children's Hospital Melbourne, Melbourne, Victoria, Australia
- Division of Infection and Immunity, Murdoch Children's Research Institute, University of Melbourne, Melbourne, Victoria, Australia
| | - Gladys Ho
- Discipline of Genetic Medicine and Discipline of Child & Adolescent Health, Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia
- Sydney Genome Diagnostics, Western Sydney Genetics Program, The Children's Hospital at Westmead, Sydney, New South Wales, Australia
| | - Nitin Kapur
- Department of Respiratory and Sleep Medicine, Queensland Children's Hospital, South Brisbane, Queensland, Australia
- School of Medicine, University of Queensland, Brisbane, Queensland, Australia
| | - Suzanna Lindsey-Temple
- School of Clinical Medicine, UNSW Medicine & Health, UNSW, Sydney, New South Wales, Australia
- Department of Clinical Genetics, Liverpool Hospital, Liverpool, New South Wales, Australia
| | - Tim McDonald
- Paediatrics, Canberra Hospital, Canberra, Australian Capital Territory, Australia
| | - David Mowat
- School of Clinical Medicine, UNSW Medicine & Health, UNSW, Sydney, New South Wales, Australia
- Centre for Clinical Genetics, Sydney Children's Hospital Randwick, Randwick, New South Wales, Australia
| | - André Schultz
- Department of Respiratory and Sleep Medicine, Perth Children's Hospital, Perth, Western Australia, Australia
- Faculty of Medicine, Dentistry and Health Sciences, The University of Western Australia, Perth, Western Australia, Australia
- Wal-yan Respiratory Research Centre, Telethon Kids Institute, University of Western Australia, Nedlands, Western Australia, Australia
| | - Hiran Selvadurai
- Department of Respiratory Medicine, The Children's Hospital at Westmead, Sydney, New South Wales, Australia
- Discipline of Paediatrics and Child Health, Sydney Medical School, The University of Sydney, Sydney, New South Wales, Australia
| | - Andrew Tai
- Respiratory and Sleep Medicine, Women's and Children's Hospital Adelaide, North Adelaide, South Australia, Australia
- Robinson Research Institute, The University of Adelaide, Adelaide, South Australia, Australia
| | - Adam Jaffe
- School of Clinical Medicine, UNSW Medicine & Health, UNSW, Sydney, New South Wales, Australia
- Respiratory Department, Sydney Children's Hospital Randwick, Randwick, New South Wales, Australia
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14
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Morrish A, O'Malley B, Hilton D, Sholler G, Bennetts B, Smith J, Blue G. Outcomes of Clinical Genetic Testing in Congenital Heart Disease – A Single-Site Audit Study. Heart Lung Circ 2022. [DOI: 10.1016/j.hlc.2022.04.029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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15
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Morrish A, O’Malley B, Hilton D, Sholler G, Bennetts B, Smith J, Blue G. Outcomes of Clinical Genetic Testing in Congenital Heart Disease – A Single-Site Audit Study. Heart Lung Circ 2022. [DOI: 10.1016/j.hlc.2022.06.685] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
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16
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Nash BM, Loi TH, Fernando M, Sabri A, Robinson J, Cheng A, Eamegdool SS, Farnsworth E, Bennetts B, Grigg JR, Chung SK, Gonzalez-Cordero A, Jamieson RV. Evaluation for Retinal Therapy for RPE65 Variation Assessed in hiPSC Retinal Pigment Epithelial Cells. Stem Cells Int 2021; 2021:4536382. [PMID: 34938339 PMCID: PMC8687838 DOI: 10.1155/2021/4536382] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2021] [Accepted: 11/02/2021] [Indexed: 12/14/2022] Open
Abstract
Human induced pluripotent stem cells (hiPSCs) generated from patients and the derivative retinal cells enable the investigation of pathological and novel variants in relevant cell populations. Biallelic pathogenic variants in RPE65 cause early-onset severe retinal dystrophy (EOSRD) or Leber congenital amaurosis (LCA). Increasingly, regulatory-approved in vivo RPE65 retinal gene replacement therapy is available for patients with these clinical features, but only if they have biallelic pathological variants and sufficient viable retinal cells. In our cohort of patients, we identified siblings with early-onset severe retinal degeneration where genomic studies revealed compound heterozygous variants in RPE65, one a known pathogenic missense variant and the other a novel synonymous variant of uncertain significance. The synonymous variant was suspected to affect RNA splicing. Since RPE65 is very poorly expressed in all tissues except the retinal pigment epithelium (RPE), we generated hiPSC-derived RPE cells from the parental carrier of the synonymous variant. Sequencing of RNA obtained from hiPSC-RPE cells demonstrated heterozygous skipping of RPE65 exon 2 and the introduction of a premature stop codon in the mRNA. Minigene studies confirmed the splicing aberration. Results from this study led to reclassification of the synonymous variant to a pathogenic variant, providing the affected patients with access to RPE65 gene replacement therapy.
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Affiliation(s)
- Benjamin M. Nash
- Eye Genetics Research Unit, Sydney Children's Hospitals Network-Westmead, Save Sight Institute, Children's Medical Research Institute, University of Sydney, Sydney, New South Wales, Australia
- Specialty of Genomic Medicine, Faculty of Medicine and Health, University of Sydney, New South Wales, Australia
- Sydney Genome Diagnostics, Western Sydney Genetics Program, Sydney Children's Hospitals Network-Westmead, Sydney, New South Wales, Australia
| | - To Ha Loi
- Eye Genetics Research Unit, Sydney Children's Hospitals Network-Westmead, Save Sight Institute, Children's Medical Research Institute, University of Sydney, Sydney, New South Wales, Australia
| | - Milan Fernando
- Stem Cell Medicine Group and Stem Cell and Organoid Facility, Children's Medical Research Institute, University of Sydney, Faculty of Medicine & Health, Sydney NSW, Australia
| | - Amin Sabri
- Eye Genetics Research Unit, Sydney Children's Hospitals Network-Westmead, Save Sight Institute, Children's Medical Research Institute, University of Sydney, Sydney, New South Wales, Australia
| | - James Robinson
- Department of Ophthalmology, Sydney Children's Hospitals Network-Westmead, Sydney, New South Wales, Australia
- Specialty of Ophthalmology, Faculty of Medicine and Health, University of Sydney, Sydney, New South Wales, Australia
| | - Anson Cheng
- Eye Genetics Research Unit, Sydney Children's Hospitals Network-Westmead, Save Sight Institute, Children's Medical Research Institute, University of Sydney, Sydney, New South Wales, Australia
| | - Steven S. Eamegdool
- Eye Genetics Research Unit, Sydney Children's Hospitals Network-Westmead, Save Sight Institute, Children's Medical Research Institute, University of Sydney, Sydney, New South Wales, Australia
| | - Elizabeth Farnsworth
- Sydney Genome Diagnostics, Western Sydney Genetics Program, Sydney Children's Hospitals Network-Westmead, Sydney, New South Wales, Australia
| | - Bruce Bennetts
- Specialty of Genomic Medicine, Faculty of Medicine and Health, University of Sydney, New South Wales, Australia
- Sydney Genome Diagnostics, Western Sydney Genetics Program, Sydney Children's Hospitals Network-Westmead, Sydney, New South Wales, Australia
| | - John R. Grigg
- Eye Genetics Research Unit, Sydney Children's Hospitals Network-Westmead, Save Sight Institute, Children's Medical Research Institute, University of Sydney, Sydney, New South Wales, Australia
- Department of Ophthalmology, Sydney Children's Hospitals Network-Westmead, Sydney, New South Wales, Australia
- Specialty of Ophthalmology, Faculty of Medicine and Health, University of Sydney, Sydney, New South Wales, Australia
| | - Seo-Kyung Chung
- Translational Neurogenomics Group, Kids Research, Sydney Children's Hospitals Network-Westmead, Sydney NSW, Australia
- Brain and Mind Centre, Faculty of Medicine & Health, University of Sydney, Sydney NSW, Australia
| | - Anai Gonzalez-Cordero
- Stem Cell Medicine Group and Stem Cell and Organoid Facility, Children's Medical Research Institute, University of Sydney, Faculty of Medicine & Health, Sydney NSW, Australia
| | - Robyn V. Jamieson
- Eye Genetics Research Unit, Sydney Children's Hospitals Network-Westmead, Save Sight Institute, Children's Medical Research Institute, University of Sydney, Sydney, New South Wales, Australia
- Specialty of Genomic Medicine, Faculty of Medicine and Health, University of Sydney, New South Wales, Australia
- Department of Clinical Genetics, Western Sydney Genetics Program, Sydney Children's Hospitals Network-Westmead, Sydney, New South Wales, Australia
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17
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Bournazos AM, Riley LG, Bommireddipalli S, Ades L, Akesson LS, Al-Shinnag M, Alexander SI, Archibald AD, Balasubramaniam S, Berman Y, Beshay V, Boggs K, Bojadzieva J, Brown NJ, Bryen SJ, Buckley MF, Chong B, Davis MR, Dawes R, Delatycki M, Donaldson L, Downie L, Edwards C, Edwards M, Engel A, Ewans LJ, Faiz F, Fennell A, Field M, Freckmann ML, Gallacher L, Gear R, Goel H, Goh S, Goodwin L, Hanna B, Harraway J, Higgins M, Ho G, Hopper BK, Horton AE, Hunter MF, Huq AJ, Josephi-Taylor S, Joshi H, Kirk E, Krzesinski E, Kumar KR, Lemckert F, Leventer RJ, Lindsey-Temple SE, Lunke S, Ma A, Macaskill S, Mallawaarachchi A, Marty M, Marum JE, McCarthy HJ, Menezes MP, McLean A, Milnes D, Mohammad S, Mowat D, Niaz A, Palmer EE, Patel C, Patel SG, Phelan D, Pinner JR, Rajagopalan S, Regan M, Rodgers J, Rodrigues M, Roxburgh RH, Sachdev R, Roscioli T, Samarasekera R, Sandaradura SA, Savva E, Schindler T, Shah M, Sinnerbrink IB, Smith JM, Smith RJ, Springer A, Stark Z, Strom SP, Sue CM, Tan K, Tan TY, Tantsis E, Tchan MC, Thompson BA, Trainer AH, van Spaendonck-Zwarts K, Walsh R, Warwick L, White S, White SM, Williams MG, Wilson MJ, Wong WK, Wright DC, Yap P, Yeung A, Young H, Jones KJ, Bennetts B, Cooper ST. Standardized practices for RNA diagnostics using clinically accessible specimens reclassifies 75% of putative splicing variants. Genet Med 2021; 24:130-145. [PMID: 34906502 DOI: 10.1016/j.gim.2021.09.001] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 06/18/2021] [Accepted: 09/10/2021] [Indexed: 02/06/2023] Open
Abstract
PURPOSE Genetic variants causing aberrant premessenger RNA splicing are increasingly being recognized as causal variants in genetic disorders. In this study, we devise standardized practices for polymerase chain reaction (PCR)-based RNA diagnostics using clinically accessible specimens (blood, fibroblasts, urothelia, biopsy). METHODS A total of 74 families with diverse monogenic conditions (31% prenatal-congenital onset, 47% early childhood, and 22% teenage-adult onset) were triaged into PCR-based RNA testing, with comparative RNA sequencing for 19 cases. RESULTS Informative RNA assay data were obtained for 96% of cases, enabling variant reclassification for 75% variants that can be used for genetic counseling (71%), to inform clinical care (32%) and prenatal counseling (41%). Variant-associated mis-splicing was highly reproducible for 28 cases with samples from ≥2 affected individuals or heterozygotes and 10 cases with ≥2 biospecimens. PCR amplicons encompassing another segregated heterozygous variant was vital for clinical interpretation of 22 of 79 variants to phase RNA splicing events and discern complete from partial mis-splicing. CONCLUSION RNA diagnostics enabled provision of a genetic diagnosis for 64% of recruited cases. PCR-based RNA diagnostics has capacity to analyze 81.3% of clinically significant genes, with long amplicons providing an advantage over RNA sequencing to phase RNA splicing events. The Australasian Consortium for RNA Diagnostics (SpliceACORD) provide clinically-endorsed, standardized protocols and recommendations for interpreting RNA assay data.
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Affiliation(s)
- Adam M Bournazos
- Kids Neuroscience Centre, Kids Research, The Children's Hospital at Westmead, Westmead, New South Wales, Australia; Department of Child and Adolescent Health, Faculty of Medicine and Health, The University of Sydney, Westmead, New South Wales, Australia
| | - Lisa G Riley
- Department of Child and Adolescent Health, Faculty of Medicine and Health, The University of Sydney, Westmead, New South Wales, Australia; Rare Diseases Functional Genomics, Kids Research, Sydney Children's Hospital Network and Children's Medical Research Institute, Westmead, New South Wales, Australia
| | - Shobhana Bommireddipalli
- Kids Neuroscience Centre, Kids Research, The Children's Hospital at Westmead, Westmead, New South Wales, Australia
| | - Lesley Ades
- Department of Child and Adolescent Health, Faculty of Medicine and Health, The University of Sydney, Westmead, New South Wales, Australia; Department of Clinical Genetics, The Children's Hospital at Westmead, Westmead, New South Wales, Australia
| | - Lauren S Akesson
- Department of Paediatrics, University of Melbourne, Parkville, Victoria, Australia; Department of Medicine, University of Melbourne, Parkville, Victoria, Australia; Department of Pathology, University of Melbourne, Parkville, Victoria, Australia; Department of Genomic Medicine, The Royal Melbourne Hospital, Parkville, Victoria, Australia; Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Parkville, Victoria, Australia; Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Mohammad Al-Shinnag
- Genetic Health Queensland, Royal Brisbane and Women's Hospital, Herston, Queensland, Australia; The University of Queensland, Herston, Queensland, Australia
| | - Stephen I Alexander
- Department of Child and Adolescent Health, Faculty of Medicine and Health, The University of Sydney, Westmead, New South Wales, Australia; Department of Pediatric Nephrology, The Children's Hospital at Westmead, Westmead, New South Wales, Australia
| | - Alison D Archibald
- Department of Paediatrics, University of Melbourne, Parkville, Victoria, Australia; Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Parkville, Victoria, Australia
| | - Shanti Balasubramaniam
- Genetic Metabolic Disorders Service, The Children's Hospital at Westmead, Westmead, New South Wales, Australia; Western Sydney Genetics Program, The Children's Hospital at Westmead, Westmead, New South Wales, Australia; Specialty of Genomic Medicine, Faculty of Medicine and Health, The University of Sydney, Westmead, New South Wales, Australia
| | - Yemima Berman
- Department of Clinical Genetics, Royal North Shore Hospital, St Leonards, New South Wales, Australia; Northern Clinical School, Royal North Shore Hospital, St Leonards, New South Wales, Australia
| | - Victoria Beshay
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Kirsten Boggs
- Department of Clinical Genetics, The Children's Hospital at Westmead, Westmead, New South Wales, Australia; Australian Genomics Health Alliance, Parkville, Victoria, Australia; Centre for Clinical Genetics, Sydney Children's Hospital Randwick, Randwick, New South Wales, Australia
| | - Jasmina Bojadzieva
- Department of Clinical Genetics, Austin Health, Heidelberg, Victoria, Australia
| | - Natasha J Brown
- Department of Paediatrics, University of Melbourne, Parkville, Victoria, Australia; Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Parkville, Victoria, Australia
| | - Samantha J Bryen
- Kids Neuroscience Centre, Kids Research, The Children's Hospital at Westmead, Westmead, New South Wales, Australia; Department of Child and Adolescent Health, Faculty of Medicine and Health, The University of Sydney, Westmead, New South Wales, Australia
| | | | - Belinda Chong
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Parkville, Victoria, Australia
| | - Mark R Davis
- Department of Diagnostic Genomics, PathWest Laboratory Medicine, QEII Medical Centre, Nedlands, Western Australia, Australia
| | - Ruebena Dawes
- Kids Neuroscience Centre, Kids Research, The Children's Hospital at Westmead, Westmead, New South Wales, Australia; Department of Child and Adolescent Health, Faculty of Medicine and Health, The University of Sydney, Westmead, New South Wales, Australia
| | - Martin Delatycki
- Department of Paediatrics, University of Melbourne, Parkville, Victoria, Australia; Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Parkville, Victoria, Australia
| | - Liz Donaldson
- The Royal Melbourne Hospital, Parkville, Victoria, Australia
| | - Lilian Downie
- Department of Paediatrics, University of Melbourne, Parkville, Victoria, Australia; The Royal Melbourne Hospital, Parkville, Victoria, Australia; Murdoch Children's Research Institute, Parkville, Victoria, Australia
| | - Caitlin Edwards
- Department of Diagnostic Genomics, PathWest Laboratory Medicine, QEII Medical Centre, Nedlands, Western Australia, Australia
| | - Matthew Edwards
- Department of Paediatrics, School of Medicine, Western Sydney University, Penrith South, New South Wales, Australia
| | - Amanda Engel
- ACT Genetic Service, ACT Health, The Canberra Hospital, Garran, ACT, Australia
| | - Lisa J Ewans
- Department of Medical Genomics, Royal Prince Alfred Hospital, Camperdown, New South Wales, Australia; Central Clinical School, The University of Sydney, Camperdown, New South Wales, Australia
| | - Fathimath Faiz
- Department of Diagnostic Genomics, PathWest Laboratory Medicine, QEII Medical Centre, Nedlands, Western Australia, Australia
| | - Andrew Fennell
- Department of Paediatrics, University of Melbourne, Parkville, Victoria, Australia; Monash Genetics, Monash Health, Clayton, Victoria, Australia
| | - Michael Field
- Genetics of Learning Disability Service, Hunter Genetics, Waratah, New South Wales, Australia
| | | | - Lyndon Gallacher
- Department of Paediatrics, University of Melbourne, Parkville, Victoria, Australia; Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Parkville, Victoria, Australia
| | - Russell Gear
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Parkville, Victoria, Australia
| | - Himanshu Goel
- Genetics of Learning Disability Service, Hunter Genetics, Waratah, New South Wales, Australia; The University of Newcastle, Callaghan, New South Wales, Australia
| | - Shuxiang Goh
- Department of Clinical Genetics, Liverpool Hospital, Liverpool, New South Wales, Australia
| | - Linda Goodwin
- Department of Clinical Genetics, Nepean Hospital, Kingswood, New South Wales, Australia
| | - Bernadette Hanna
- Department of Genomic Medicine, Westmead Hospital, Westmead, New South Wales, Australia
| | - James Harraway
- Sullivan Nicolaides Pathology, Bowen Hills, Queensland, Australia
| | - Megan Higgins
- Genetic Health Queensland, Royal Brisbane and Women's Hospital, Herston, Queensland, Australia
| | - Gladys Ho
- Department of Child and Adolescent Health, Faculty of Medicine and Health, The University of Sydney, Westmead, New South Wales, Australia; Department of Molecular Genetics, The Children's Hospital at Westmead, Westmead, New South Wales, Australia
| | | | - Ari E Horton
- Department of Paediatrics, University of Melbourne, Parkville, Victoria, Australia; Monash Genetics, Monash Health, Clayton, Victoria, Australia; Monash Heart and Monash Children's Hospital, Monash Health, Clayton, Victoria, Australia; Monash Cardiovascular Research Centre, Clayton, Victoria, Australia
| | - Matthew F Hunter
- Monash Genetics, Monash Health, Clayton, Victoria, Australia; Department of Paediatrics, Monash University, Clayton, Victoria, Australia
| | - Aamira J Huq
- Department of Medicine, University of Melbourne, Parkville, Victoria, Australia; The Royal Melbourne Hospital, Parkville, Victoria, Australia
| | - Sarah Josephi-Taylor
- Department of Clinical Genetics, The Children's Hospital at Westmead, Westmead, New South Wales, Australia; Department of Genomic Medicine, Westmead Hospital, Westmead, New South Wales, Australia
| | - Himanshu Joshi
- Kids Neuroscience Centre, Kids Research, The Children's Hospital at Westmead, Westmead, New South Wales, Australia
| | - Edwin Kirk
- NSW Health Pathology, Randwick, New South Wales, Australia; Center for Clinical Genetics, Sydney Children's Hospital, Randwick, New South Wales, Australia
| | - Emma Krzesinski
- Monash Genetics, Monash Health, Clayton, Victoria, Australia; Department of Paediatrics, Monash University, Clayton, Victoria, Australia
| | - Kishore R Kumar
- Department of Neurogenetics, Kolling Institute, Faculty of Medicine and Health, University of Sydney, Royal North Shore Hospital, St Leonards, New South Wales, Australia; Translational Genomics, Kinghorn Centre for Clinical Genomics, Garvan Institute for Medical Research, Darlinghurst, New South Wales, Australia
| | - Frances Lemckert
- Kids Neuroscience Centre, Kids Research, The Children's Hospital at Westmead, Westmead, New South Wales, Australia; Department of Child and Adolescent Health, Faculty of Medicine and Health, The University of Sydney, Westmead, New South Wales, Australia
| | - Richard J Leventer
- Department of Paediatrics, University of Melbourne, Parkville, Victoria, Australia; Murdoch Children's Research Institute, Parkville, Victoria, Australia; Department of Neurology, The Royal Children's Hospital, Parkville, Victoria, Australia
| | - Suzanna E Lindsey-Temple
- Department of Clinical Genetics, Liverpool Hospital, Liverpool, New South Wales, Australia; School of Women's and Children's Health, Faculty of Medicine and Health, University of New South Wales, Kensington, NSW, Australia
| | - Sebastian Lunke
- Department of Pathology, University of Melbourne, Parkville, Victoria, Australia; Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Parkville, Victoria, Australia
| | - Alan Ma
- Department of Child and Adolescent Health, Faculty of Medicine and Health, The University of Sydney, Westmead, New South Wales, Australia; Department of Clinical Genetics, The Children's Hospital at Westmead, Westmead, New South Wales, Australia
| | | | - Amali Mallawaarachchi
- Department of Medical Genomics, Royal Prince Alfred Hospital, Camperdown, New South Wales, Australia; Division of Genomics and Epigenetics, Garvan Institute of Medical Research, Darlinghurst, New South Wales, Australia
| | - Melanie Marty
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Parkville, Victoria, Australia
| | - Justine E Marum
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Parkville, Victoria, Australia
| | - Hugh J McCarthy
- Department of Child and Adolescent Health, Faculty of Medicine and Health, The University of Sydney, Westmead, New South Wales, Australia; Department of Pediatric Nephrology, The Children's Hospital at Westmead, Westmead, New South Wales, Australia
| | - Manoj P Menezes
- Department of Child and Adolescent Health, Faculty of Medicine and Health, The University of Sydney, Westmead, New South Wales, Australia; The TY Nelson Department of Neurology and Neurosurgery, The Children's Hospital at Westmead, Westmead, New South Wales, Australia
| | - Alison McLean
- Department of Clinical Genetics, Liverpool Hospital, Liverpool, New South Wales, Australia
| | - Di Milnes
- Genetic Health Queensland, Royal Brisbane and Women's Hospital, Herston, Queensland, Australia
| | - Shekeeb Mohammad
- Department of Child and Adolescent Health, Faculty of Medicine and Health, The University of Sydney, Westmead, New South Wales, Australia; The TY Nelson Department of Neurology and Neurosurgery, The Children's Hospital at Westmead, Westmead, New South Wales, Australia
| | - David Mowat
- Center for Clinical Genetics, Sydney Children's Hospital, Randwick, New South Wales, Australia; School of Women's and Children's Health, Faculty of Medicine and Health, University of New South Wales, Kensington, NSW, Australia
| | - Aram Niaz
- Rare Diseases Functional Genomics, Kids Research, Sydney Children's Hospital Network and Children's Medical Research Institute, Westmead, New South Wales, Australia
| | - Elizabeth E Palmer
- Center for Clinical Genetics, Sydney Children's Hospital, Randwick, New South Wales, Australia; School of Women's and Children's Health, Faculty of Medicine and Health, University of New South Wales, Kensington, NSW, Australia
| | - Chirag Patel
- Genetic Health Queensland, Royal Brisbane and Women's Hospital, Herston, Queensland, Australia
| | - Shilpan G Patel
- School of Medicine, The University of Auckland, Auckland, New Zealand
| | - Dean Phelan
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Parkville, Victoria, Australia
| | - Jason R Pinner
- Center for Clinical Genetics, Sydney Children's Hospital, Randwick, New South Wales, Australia; School of Women's and Children's Health, Faculty of Medicine and Health, University of New South Wales, Kensington, NSW, Australia
| | - Sulekha Rajagopalan
- Department of Clinical Genetics, Liverpool Hospital, Liverpool, New South Wales, Australia
| | - Matthew Regan
- Monash Genetics, Monash Health, Clayton, Victoria, Australia; Department of Paediatrics, Monash University, Clayton, Victoria, Australia
| | - Jonathan Rodgers
- Genetic Health Queensland, Royal Brisbane and Women's Hospital, Herston, Queensland, Australia
| | - Miriam Rodrigues
- Department of Neurology, Auckland City Hospital, Auckland, New Zealand
| | | | - Rani Sachdev
- Center for Clinical Genetics, Sydney Children's Hospital, Randwick, New South Wales, Australia
| | - Tony Roscioli
- NSW Health Pathology, Randwick, New South Wales, Australia; Center for Clinical Genetics, Sydney Children's Hospital, Randwick, New South Wales, Australia; Neuroscience Research Australia, University of New South Wales, Randwick, New South Wales, Australia
| | - Ruvishani Samarasekera
- Department of Clinical Genetics, The Children's Hospital at Westmead, Westmead, New South Wales, Australia
| | - Sarah A Sandaradura
- Kids Neuroscience Centre, Kids Research, The Children's Hospital at Westmead, Westmead, New South Wales, Australia; Department of Child and Adolescent Health, Faculty of Medicine and Health, The University of Sydney, Westmead, New South Wales, Australia; Department of Clinical Genetics, The Children's Hospital at Westmead, Westmead, New South Wales, Australia
| | - Elena Savva
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Parkville, Victoria, Australia
| | - Tim Schindler
- School of Women's and Children's Health, Faculty of Medicine and Health, University of New South Wales, Kensington, NSW, Australia; Newborn Care, Royal Hospital for Women, Randwick, New South Wales, Australia
| | - Margit Shah
- Department of Clinical Genetics, The Children's Hospital at Westmead, Westmead, New South Wales, Australia
| | - Ingrid B Sinnerbrink
- Specialty of Genomic Medicine, Faculty of Medicine and Health, The University of Sydney, Westmead, New South Wales, Australia; Department of Clinical Genetics, Nepean Hospital, Kingswood, New South Wales, Australia
| | - Janine M Smith
- Department of Clinical Genetics, The Children's Hospital at Westmead, Westmead, New South Wales, Australia; Specialty of Genomic Medicine, Faculty of Medicine and Health, The University of Sydney, Westmead, New South Wales, Australia
| | - Richard J Smith
- Molecular Otolaryngology and Renal Research Laboratories, Carver College of Medicine, University of Iowa, Iowa City, IA, United States
| | - Amanda Springer
- Department of Paediatrics, Monash University, Clayton, Victoria, Australia
| | - Zornitza Stark
- Department of Paediatrics, University of Melbourne, Parkville, Victoria, Australia; Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Parkville, Victoria, Australia
| | | | - Carolyn M Sue
- Department of Neurogenetics, Kolling Institute, Faculty of Medicine and Health, University of Sydney, Royal North Shore Hospital, St Leonards, New South Wales, Australia
| | - Kenneth Tan
- Department of Paediatrics, Monash University, Clayton, Victoria, Australia; Monash Newborn, Monash Children's Hospital, Clayton, Victoria, Australia
| | - Tiong Y Tan
- Department of Paediatrics, University of Melbourne, Parkville, Victoria, Australia; Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Parkville, Victoria, Australia
| | - Esther Tantsis
- Department of Child and Adolescent Health, Faculty of Medicine and Health, The University of Sydney, Westmead, New South Wales, Australia; The TY Nelson Department of Neurology and Neurosurgery, The Children's Hospital at Westmead, Westmead, New South Wales, Australia
| | - Michel C Tchan
- Specialty of Genomic Medicine, Faculty of Medicine and Health, The University of Sydney, Westmead, New South Wales, Australia; Department of Genomic Medicine, Westmead Hospital, Westmead, New South Wales, Australia
| | - Bryony A Thompson
- Department of Pathology, The Royal Melbourne Hospital, Parkville, Victoria, Australia; Department of Clinical Pathology, University of Melbourne, Parkville, Victoria, Australia
| | - Alison H Trainer
- Department of Medicine, University of Melbourne, Parkville, Victoria, Australia; Department of Genomic Medicine, The Royal Melbourne Hospital, Parkville, Victoria, Australia
| | | | - Rebecca Walsh
- NSW Health Pathology, Randwick, New South Wales, Australia
| | - Linda Warwick
- ACT Genetic Service, ACT Health, The Canberra Hospital, Garran, ACT, Australia
| | - Stephanie White
- Department of Clinical Genetics, Royal North Shore Hospital, St Leonards, New South Wales, Australia
| | - Susan M White
- Department of Paediatrics, University of Melbourne, Parkville, Victoria, Australia; Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Parkville, Victoria, Australia
| | - Mark G Williams
- Mater Research Institute, The University of Queensland, South Brisbane, Queensland, Australia
| | - Meredith J Wilson
- Department of Clinical Genetics, The Children's Hospital at Westmead, Westmead, New South Wales, Australia; Specialty of Genomic Medicine, Faculty of Medicine and Health, The University of Sydney, Westmead, New South Wales, Australia
| | - Wui Kwan Wong
- Kids Neuroscience Centre, Kids Research, The Children's Hospital at Westmead, Westmead, New South Wales, Australia; Department of Child and Adolescent Health, Faculty of Medicine and Health, The University of Sydney, Westmead, New South Wales, Australia; The TY Nelson Department of Neurology and Neurosurgery, The Children's Hospital at Westmead, Westmead, New South Wales, Australia
| | - Dale C Wright
- Department of Child and Adolescent Health, Faculty of Medicine and Health, The University of Sydney, Westmead, New South Wales, Australia; Specialty of Genomic Medicine, Faculty of Medicine and Health, The University of Sydney, Westmead, New South Wales, Australia; Department of Cytogenetics, The Children's Hospital at Westmead, Westmead, New South Wales, Australia
| | - Patrick Yap
- Northern Hub, Genetic Health Service NZ, Auckland, New Zealand
| | - Alison Yeung
- Department of Paediatrics, University of Melbourne, Parkville, Victoria, Australia; Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Parkville, Victoria, Australia
| | - Helen Young
- Department of Intensive Care, Austin Hospital, Heidelberg, Victoria, Australia
| | - Kristi J Jones
- Kids Neuroscience Centre, Kids Research, The Children's Hospital at Westmead, Westmead, New South Wales, Australia; Department of Child and Adolescent Health, Faculty of Medicine and Health, The University of Sydney, Westmead, New South Wales, Australia; Department of Clinical Genetics, The Children's Hospital at Westmead, Westmead, New South Wales, Australia
| | - Bruce Bennetts
- Department of Child and Adolescent Health, Faculty of Medicine and Health, The University of Sydney, Westmead, New South Wales, Australia; Department of Molecular Genetics, The Children's Hospital at Westmead, Westmead, New South Wales, Australia
| | - Sandra T Cooper
- Kids Neuroscience Centre, Kids Research, The Children's Hospital at Westmead, Westmead, New South Wales, Australia; Department of Child and Adolescent Health, Faculty of Medicine and Health, The University of Sydney, Westmead, New South Wales, Australia; The Children's Medical Research Institute, Westmead, New South Wales, Australia.
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18
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Sylvester DE, Chen Y, Grima N, Saletta F, Padhye B, Bennetts B, Wright D, Krivanek M, Graf N, Zhou L, Catchpoole D, Kirk J, Latchoumanin O, Qiao L, Ballinger M, Thomas D, Jamieson R, Dalla-Pozza L, Byrne JA. Rare germline variants in childhood cancer patients suspected of genetic predisposition to cancer. Genes Chromosomes Cancer 2021; 61:81-93. [PMID: 34687117 DOI: 10.1002/gcc.23006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 10/11/2021] [Accepted: 10/13/2021] [Indexed: 11/11/2022] Open
Abstract
Identification of cancer-predisposing germline variants in childhood cancer patients is important for therapeutic decisions, disease surveillance and risk assessment for patients, and potentially, also for family members. We investigated the spectrum and prevalence of pathogenic germline variants in selected childhood cancer patients with features suggestive of genetic predisposition to cancer. Germline DNA was subjected to exome sequencing to filter variants in 1048 genes of interest including 176 known cancer predisposition genes (CPGs). An enrichment burden analysis compared rare deleterious germline CPG variants in the patient cohort with those in a healthy aged control population. A subset of predicted deleterious variants in novel candidate CPGs was investigated further by examining matched tumor samples, and the functional impact of AXIN1 variants was analyzed in cultured cells. Twenty-two pathogenic/likely pathogenic (P/LP) germline variants detected in 13 CPGs were identified in 19 of 76 patients (25.0%). Unclear association with the diagnosed cancer types was observed in 11 of 19 patients carrying P/LP CPG variants. The burden of rare deleterious germline variants in autosomal dominant CPGs was significantly higher in study patients versus healthy aged controls. A novel AXIN1 frameshift variant (Ser321fs) may impact the regulation of β-catenin levels. Selection of childhood cancer patients for germline testing based on features suggestive of an underlying genetic predisposition could help to identify carriers of clinically relevant germline CPG variants, and streamline the integration of germline genomic testing in the pediatric oncology clinic.
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Affiliation(s)
- Dianne E Sylvester
- Molecular Oncology Laboratory, Children's Cancer Research Unit, Kids Research, The Children's Hospital at Westmead, Westmead, New South Wales, Australia.,Children's Hospital at Westmead Clinical School, Faculty of Medicine and Health, University of Sydney, The Children's Hospital at Westmead, Westmead, New South Wales, Australia
| | - Yuyan Chen
- Molecular Oncology Laboratory, Children's Cancer Research Unit, Kids Research, The Children's Hospital at Westmead, Westmead, New South Wales, Australia.,Children's Hospital at Westmead Clinical School, Faculty of Medicine and Health, University of Sydney, The Children's Hospital at Westmead, Westmead, New South Wales, Australia
| | - Natalie Grima
- Molecular Oncology Laboratory, Children's Cancer Research Unit, Kids Research, The Children's Hospital at Westmead, Westmead, New South Wales, Australia.,Children's Hospital at Westmead Clinical School, Faculty of Medicine and Health, University of Sydney, The Children's Hospital at Westmead, Westmead, New South Wales, Australia
| | - Federica Saletta
- Molecular Oncology Laboratory, Children's Cancer Research Unit, Kids Research, The Children's Hospital at Westmead, Westmead, New South Wales, Australia.,Children's Hospital at Westmead Clinical School, Faculty of Medicine and Health, University of Sydney, The Children's Hospital at Westmead, Westmead, New South Wales, Australia
| | - Bhavna Padhye
- The Cancer Centre for Children, The Children's Hospital at Westmead, Westmead, New South Wales, Australia
| | - Bruce Bennetts
- Sydney Genome Diagnostics, The Children's Hospital at Westmead, Westmead, New South Wales, Australia
| | - Dale Wright
- Sydney Genome Diagnostics, The Children's Hospital at Westmead, Westmead, New South Wales, Australia
| | - Michael Krivanek
- Histopathology Department, The Children's Hospital at Westmead, Westmead, New South Wales, Australia
| | - Nicole Graf
- Histopathology Department, The Children's Hospital at Westmead, Westmead, New South Wales, Australia
| | - Li Zhou
- Sydney Children's Tumour Bank Network, Children's Cancer Research Unit, Kids Research, The Children's Hospital at Westmead, Westmead, New South Wales, Australia
| | - Daniel Catchpoole
- Sydney Children's Tumour Bank Network, Children's Cancer Research Unit, Kids Research, The Children's Hospital at Westmead, Westmead, New South Wales, Australia
| | - Judy Kirk
- Familial Cancer Service, Westmead Hospital, Westmead Institute for Medical Research, University of Sydney, Westmead, New South Wales, Australia
| | - Olivier Latchoumanin
- Storr Liver Centre, Westmead Institute for Medical Research, University of Sydney & Westmead Hospital, Westmead, New South Wales, Australia
| | - Liang Qiao
- Storr Liver Centre, Westmead Institute for Medical Research, University of Sydney & Westmead Hospital, Westmead, New South Wales, Australia
| | - Mandy Ballinger
- The Kinghorn Cancer Centre & Genomic Cancer Medicine, Garvan Institute of Medical Research, Darlinghurst, New South Wales, Australia
| | - David Thomas
- The Kinghorn Cancer Centre & Genomic Cancer Medicine, Garvan Institute of Medical Research, Darlinghurst, New South Wales, Australia
| | - Robyn Jamieson
- Children's Hospital at Westmead Clinical School, Faculty of Medicine and Health, University of Sydney, The Children's Hospital at Westmead, Westmead, New South Wales, Australia.,Eye and Developmental Genetics Research Group, The Children's Hospital at Westmead and Children's Medical Research Institute, and Disciplines of Genetic Medicine, Sydney Medical School, University of Sydney, Sydney, New South Wales, Australia
| | - Luciano Dalla-Pozza
- The Cancer Centre for Children, The Children's Hospital at Westmead, Westmead, New South Wales, Australia
| | - Jennifer A Byrne
- Molecular Oncology Laboratory, Children's Cancer Research Unit, Kids Research, The Children's Hospital at Westmead, Westmead, New South Wales, Australia.,Children's Hospital at Westmead Clinical School, Faculty of Medicine and Health, University of Sydney, The Children's Hospital at Westmead, Westmead, New South Wales, Australia.,NSW Health Statewide Biobank, NSW Health Pathology, Camperdown, New South Wales, Australia
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19
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Graves LE, Wall CL, Briody JN, Bennetts B, Wong K, Onikul E, Biggin A, Munns CF. High Bone Mineral Density Osteogenesis Imperfecta in a Family with a Novel Pathogenic Variant in COL1A2. Horm Res Paediatr 2021; 93:263-271. [PMID: 32920552 DOI: 10.1159/000510463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Accepted: 07/27/2020] [Indexed: 11/19/2022] Open
Abstract
Osteogenesis imperfecta (OI) is a heterogenous group of heritable bone dysplasias characterized by bone fragility, typically low bone mass, joint laxity, easy bruising, and variable short stature. Classical OI is caused by autosomal dominant pathogenic variants in COL1A1 or COL1A2 that result in either reduced production of normal type 1 collagen or structurally abnormal collagen molecules. Pathogenic variants in these genes generally result in low bone mass. Here, we report a family that had 2 affected individuals who presented with minimal trauma fractures and were found to have elevated bone mineral density (BMD) and a previously unreported variant in COL1A2 c.3356C>T p.(Ala1119Val). We report the change in BMD using dual-energy X-ray and peripheral quantitative computed tomography over a 2.3-year period in the proband. This case report highlights the importance of BMD studies and genetic testing in the diagnostic process for brittle bone disorders.
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Affiliation(s)
- Lara E Graves
- Institute of Endocrinology and Diabetes, The Children's Hospital at Westmead, Westmead, New South Wales, Australia,
| | - Christie-Lee Wall
- Institute of Endocrinology and Diabetes, The Children's Hospital at Westmead, Westmead, New South Wales, Australia
| | - Julie N Briody
- Department of Nuclear Medicine, The Children's Hospital at Westmead, Westmead, New South Wales, Australia
| | - Bruce Bennetts
- Molecular Genetics Department, Western Sydney Genetics Program, The Children's Hospital at Westmead, Westmead, New South Wales, Australia.,Discipline of Genomic Medicine, Children's Hospital at Westmead Clinical School, Westmead, New South Wales, Australia.,Discipline of Child and Adolescent Health, Children's Hospital at Westmead Clinical School, Westmead, New South Wales, Australia
| | - Karen Wong
- Molecular Genetics Department, Western Sydney Genetics Program, The Children's Hospital at Westmead, Westmead, New South Wales, Australia
| | - Ella Onikul
- Department of Medical Imaging, The Children's Hospital at Westmead, Westmead, New South Wales, Australia
| | - Andrew Biggin
- Institute of Endocrinology and Diabetes, The Children's Hospital at Westmead, Westmead, New South Wales, Australia.,Discipline of Child and Adolescent Health, Children's Hospital at Westmead Clinical School, Westmead, New South Wales, Australia
| | - Craig F Munns
- Institute of Endocrinology and Diabetes, The Children's Hospital at Westmead, Westmead, New South Wales, Australia.,Discipline of Child and Adolescent Health, Children's Hospital at Westmead Clinical School, Westmead, New South Wales, Australia
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20
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Ma A, Grigg JR, Flaherty M, Smith J, Minoche AE, Cowley MJ, Nash BM, Ho G, Gayagay T, Lai T, Farnsworth E, Hackett EL, Slater K, Wong K, Holman KJ, Jenkins G, Cheng A, Martin F, Brown NJ, Leighton SE, Amor DJ, Goel H, Dinger ME, Bennetts B, Jamieson RV. Genome sequencing in congenital cataracts improves diagnostic yield. Hum Mutat 2021; 42:1173-1183. [PMID: 34101287 DOI: 10.1002/humu.24240] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 05/31/2021] [Accepted: 06/03/2021] [Indexed: 01/11/2023]
Abstract
Congenital cataracts are one of the major causes of childhood-onset blindness around the world. Genetic diagnosis provides benefits through avoidance of unnecessary tests, surveillance of extraocular features, and genetic family information. In this study, we demonstrate the value of genome sequencing in improving diagnostic yield in congenital cataract patients and families. We applied genome sequencing to investigate 20 probands with congenital cataracts. We examined the added value of genome sequencing across a total cohort of 52 probands, including 14 unable to be diagnosed using previous microarray and exome or panel-based approaches. Although exome or genome sequencing would have detected the variants in 35/52 (67%) of the cases, specific advantages of genome sequencing led to additional diagnoses in 10% (5/52) of the overall cohort, and we achieved an overall diagnostic rate of 77% (40/52). Specific benefits of genome sequencing were due to detection of small copy number variants (2), indels in repetitive regions (2) or single-nucleotide variants (SNVs) in GC-rich regions (1), not detectable on the previous microarray, exome sequencing, or panel-based approaches. In other cases, SNVs were identified in cataract disease genes, including those newly identified since our previous study. This study highlights the additional yield of genome sequencing in congenital cataracts.
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Affiliation(s)
- Alan Ma
- Eye Genetics Research Unit, The Children's Hospital at Westmead, Save Sight Institute, Children's Medical Research Institute, University of Sydney, Sydney, New South Wales, Australia.,Department of Clinical Genetics, Western Sydney Genetics Program, The Children's Hospital at Westmead, Sydney, New South Wales, Australia.,Specialties of Genomic Medicine & Child and Adolescent Health, Faculty of Medicine and Health, University of Sydney, Sydney, New South Wales, Australia
| | - John R Grigg
- Eye Genetics Research Unit, The Children's Hospital at Westmead, Save Sight Institute, Children's Medical Research Institute, University of Sydney, Sydney, New South Wales, Australia.,Department of Ophthalmology, The Children's Hospital at Westmead, Sydney, New South Wales, Australia.,Specialty of Ophthalmology, University of Sydney, Sydney, New South Wales, Australia.,Save Sight Institute, Sydney Eye Hospital, Sydney, New South Wales, Australia
| | - Maree Flaherty
- Department of Ophthalmology, The Children's Hospital at Westmead, Sydney, New South Wales, Australia.,Specialty of Ophthalmology, University of Sydney, Sydney, New South Wales, Australia
| | - James Smith
- Department of Ophthalmology, The Children's Hospital at Westmead, Sydney, New South Wales, Australia.,Specialty of Ophthalmology, University of Sydney, Sydney, New South Wales, Australia
| | - Andre E Minoche
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Darlinghurst, New South Wales, Australia
| | - Mark J Cowley
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Darlinghurst, New South Wales, Australia.,Children's Cancer Institute, Lowy Cancer Research Centre, University of New South Wales, Randwick, New South Wales, Australia.,St Vincent's Clinical School, Faculty of Medicine, UNSW Australia, Sydney, New South Wales, Australia
| | - Benjamin M Nash
- Eye Genetics Research Unit, The Children's Hospital at Westmead, Save Sight Institute, Children's Medical Research Institute, University of Sydney, Sydney, New South Wales, Australia.,Specialties of Genomic Medicine & Child and Adolescent Health, Faculty of Medicine and Health, University of Sydney, Sydney, New South Wales, Australia.,Sydney Genome Diagnostics, Western Sydney Genetics Program, The Children's Hospital at Westmead, Sydney, New South Wales, Australia
| | - Gladys Ho
- Specialties of Genomic Medicine & Child and Adolescent Health, Faculty of Medicine and Health, University of Sydney, Sydney, New South Wales, Australia.,Sydney Genome Diagnostics, Western Sydney Genetics Program, The Children's Hospital at Westmead, Sydney, New South Wales, Australia
| | - Thet Gayagay
- Sydney Genome Diagnostics, Western Sydney Genetics Program, The Children's Hospital at Westmead, Sydney, New South Wales, Australia
| | - Tiffany Lai
- Sydney Genome Diagnostics, Western Sydney Genetics Program, The Children's Hospital at Westmead, Sydney, New South Wales, Australia
| | - Elizabeth Farnsworth
- Sydney Genome Diagnostics, Western Sydney Genetics Program, The Children's Hospital at Westmead, Sydney, New South Wales, Australia
| | - Emma L Hackett
- Sydney Genome Diagnostics, Western Sydney Genetics Program, The Children's Hospital at Westmead, Sydney, New South Wales, Australia
| | - Katrina Slater
- Sydney Genome Diagnostics, Western Sydney Genetics Program, The Children's Hospital at Westmead, Sydney, New South Wales, Australia
| | - Karen Wong
- Sydney Genome Diagnostics, Western Sydney Genetics Program, The Children's Hospital at Westmead, Sydney, New South Wales, Australia
| | - Katherine J Holman
- Sydney Genome Diagnostics, Western Sydney Genetics Program, The Children's Hospital at Westmead, Sydney, New South Wales, Australia
| | - Gemma Jenkins
- Sydney Genome Diagnostics, Western Sydney Genetics Program, The Children's Hospital at Westmead, Sydney, New South Wales, Australia
| | - Anson Cheng
- Eye Genetics Research Unit, The Children's Hospital at Westmead, Save Sight Institute, Children's Medical Research Institute, University of Sydney, Sydney, New South Wales, Australia
| | - Frank Martin
- Department of Ophthalmology, The Children's Hospital at Westmead, Sydney, New South Wales, Australia.,Specialty of Ophthalmology, University of Sydney, Sydney, New South Wales, Australia
| | - Natasha J Brown
- Department of Paediatrics, University of Melbourne, Parkville, Victoria, Australia.,Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Australia
| | | | - David J Amor
- Department of Paediatrics, University of Melbourne, Parkville, Victoria, Australia.,Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Australia
| | - Himanshu Goel
- Hunter Genetics, Newcastle, New South Wales, Australia
| | - Marcel E Dinger
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Darlinghurst, New South Wales, Australia.,School of Biotechnology and Biomolecular Sciences, Faculty of Science, UNSW, Sydney, New South Wales, Australia
| | - Bruce Bennetts
- Specialties of Genomic Medicine & Child and Adolescent Health, Faculty of Medicine and Health, University of Sydney, Sydney, New South Wales, Australia.,Sydney Genome Diagnostics, Western Sydney Genetics Program, The Children's Hospital at Westmead, Sydney, New South Wales, Australia
| | - Robyn V Jamieson
- Eye Genetics Research Unit, The Children's Hospital at Westmead, Save Sight Institute, Children's Medical Research Institute, University of Sydney, Sydney, New South Wales, Australia.,Department of Clinical Genetics, Western Sydney Genetics Program, The Children's Hospital at Westmead, Sydney, New South Wales, Australia.,Specialties of Genomic Medicine & Child and Adolescent Health, Faculty of Medicine and Health, University of Sydney, Sydney, New South Wales, Australia
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21
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Sajeev M, Chin S, Ho G, Bennetts B, Sankaran BP, Gutierrez B, Devanapalli B, Tolun AA, Wiley V, Fletcher J, Fuller M, Balasubramaniam S. Challenges in Diagnosing Intermediate Maple Syrup Urine Disease by Newborn Screening and Functional Validation of Genomic Results Imperative for Reproductive Family Planning. Int J Neonatal Screen 2021; 7:ijns7020025. [PMID: 34069211 PMCID: PMC8162326 DOI: 10.3390/ijns7020025] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/27/2021] [Revised: 05/08/2021] [Accepted: 05/12/2021] [Indexed: 11/16/2022] Open
Abstract
Maple syrup urine disease is caused by a deficiency of branched-chain alpha-ketoacid dehydrogenase, responsible for degradation of leucine, isoleucine, and valine. Biallelic pathogenic variants in BCKDHA, BCKDHB, or DBT genes result in enzyme deficiency. We report the case of a female infant who presented with mild gross motor delay at 4 months, and seizures with hypoglycaemia at 5 months. Newborn screening returned total leucine/isoleucine at the 99.5th centile of the population; however, as second-tier testing reported minimal alloisoleucine, the results were considered inconsistent with MSUD. Plasma amino acid and urine organic acid analyses at 5 months were, however, consistent with a diagnosis of MSUD. A brain MRI showed bilateral symmetrical T2 hyperintense signal abnormalities involving white matter, globus pallidus, thalamus, brainstem, and dentate nuclei with restricted diffusion. A repeat MRI 10 months post-dietary-intervention showed the resolution of these changes and progression in myelination. Her clinical phenotype, including protein tolerance, correlated with intermediate MSUD. Molecular analysis of all three genes identified two variants of uncertain significance, c.434-15_434-4del and c.365A>G (p. Tyr122Cys) in the DBT gene. The rate of leucine decarboxylation in fibroblasts was reduced, but not to the extent observed in classical MSUD patients, supporting an intermediate form of MSUD. Previously reported mRNA splicing studies supported a deleterious effect of the c.434-15_434-4del variant. This functional evidence and confirmation that the variants were in trans, permitted their reclassification as pathogenic and likely pathogenic, respectively, facilitating subsequent prenatal testing. This report highlights the challenges in identifying intermediate MSUD by newborn screening, reinforcing the importance of functional studies to confirm variant pathogenicity in this era of molecular diagnostics.
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Affiliation(s)
- Mona Sajeev
- Genetic Metabolic Disorders Service, Western Sydney Genetics Program, The Children’s Hospital at Westmead, Sydney, NSW 2145, Australia; (M.S.); (B.P.S.)
| | - Sharon Chin
- Genetics and Molecular Pathology, SA Pathology at Women’s and Children’s Hospital, North Adelaide, SA 5006, Australia; (S.C.); (J.F.); (M.F.)
| | - Gladys Ho
- Department of Molecular Genetics, Western Sydney Genetics Program, The Children’s Hospital at Westmead, Sydney, NSW 2145, Australia; (G.H.); (B.B.)
- Discipline of Genetic Medicine, Sydney Medical School, The University of Sydney, Sydney, NSW 2006, Australia; (A.A.T.); (V.W.)
| | - Bruce Bennetts
- Department of Molecular Genetics, Western Sydney Genetics Program, The Children’s Hospital at Westmead, Sydney, NSW 2145, Australia; (G.H.); (B.B.)
- Discipline of Genetic Medicine, Sydney Medical School, The University of Sydney, Sydney, NSW 2006, Australia; (A.A.T.); (V.W.)
| | - Bindu Parayil Sankaran
- Genetic Metabolic Disorders Service, Western Sydney Genetics Program, The Children’s Hospital at Westmead, Sydney, NSW 2145, Australia; (M.S.); (B.P.S.)
- The Children’s Hospital at Westmead Clinical School, Faculty of Medicine & Health, Sydney Medical School, The University of Sydney, Sydney, NSW 2006, Australia
| | - Bea Gutierrez
- NSW Biochemical Genetics Service, Western Sydney Genetics Program, The Children’s Hospital at Westmead, Sydney, NSW 2145, Australia; (B.G.); (B.D.)
| | - Beena Devanapalli
- NSW Biochemical Genetics Service, Western Sydney Genetics Program, The Children’s Hospital at Westmead, Sydney, NSW 2145, Australia; (B.G.); (B.D.)
| | - Adviye Ayper Tolun
- Discipline of Genetic Medicine, Sydney Medical School, The University of Sydney, Sydney, NSW 2006, Australia; (A.A.T.); (V.W.)
- NSW Biochemical Genetics Service, Western Sydney Genetics Program, The Children’s Hospital at Westmead, Sydney, NSW 2145, Australia; (B.G.); (B.D.)
| | - Veronica Wiley
- Discipline of Genetic Medicine, Sydney Medical School, The University of Sydney, Sydney, NSW 2006, Australia; (A.A.T.); (V.W.)
- NSW Newborn Screening Programme, Western Sydney Genetics Program, The Children’s Hospital at Westmead, Sydney, NSW 2145, Australia
| | - Janice Fletcher
- Genetics and Molecular Pathology, SA Pathology at Women’s and Children’s Hospital, North Adelaide, SA 5006, Australia; (S.C.); (J.F.); (M.F.)
| | - Maria Fuller
- Genetics and Molecular Pathology, SA Pathology at Women’s and Children’s Hospital, North Adelaide, SA 5006, Australia; (S.C.); (J.F.); (M.F.)
- Adelaide Medical School, University of Adelaide, Adelaide, SA 5005, Australia
| | - Shanti Balasubramaniam
- Genetic Metabolic Disorders Service, Western Sydney Genetics Program, The Children’s Hospital at Westmead, Sydney, NSW 2145, Australia; (M.S.); (B.P.S.)
- Discipline of Genetic Medicine, Sydney Medical School, The University of Sydney, Sydney, NSW 2006, Australia; (A.A.T.); (V.W.)
- Correspondence: ; Tel.: +61-2-9845-0201; Fax: +61-2-9845-3121
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22
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Arthur JW, Pickett HA, Barbaro PM, Kilo T, Vasireddy RS, Beilharz TH, Powell DR, Hackett EL, Bennetts B, Curtin JA, Jones K, Christodoulou J, Reddel RR, Teo J, Bryan TM. A novel cause of DKC1-related bone marrow failure: Partial deletion of the 3' untranslated region. EJHaem 2021; 2:157-166. [PMID: 35845273 PMCID: PMC9175968 DOI: 10.1002/jha2.165] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/22/2020] [Revised: 01/03/2021] [Accepted: 01/07/2021] [Indexed: 12/11/2022]
Abstract
Telomere biology disorders (TBDs), including dyskeratosis congenita (DC), are a group of rare inherited diseases characterized by very short telomeres. Mutations in the components of the enzyme telomerase can lead to insufficient telomere maintenance in hematopoietic stem cells, resulting in the bone marrow failure that is characteristic of these disorders. While an increasing number of genes are being linked to TBDs, the causative mutation remains unidentified in 30‐40% of patients with DC. There is therefore a need for whole genome sequencing (WGS) in these families to identify novel genes, or mutations in regulatory regions of known disease‐causing genes. Here we describe a family in which a partial deletion of the 3′ untranslated region (3′ UTR) of DKC1, encoding the protein dyskerin, was identified by WGS, despite being missed by whole exome sequencing. The deletion segregated with disease across the family and resulted in reduced levels of DKC1 mRNA in the proband. We demonstrate that the DKC1 3′ UTR contains two polyadenylation signals, both of which were removed by this deletion, likely causing mRNA instability. Consistent with the major function of dyskerin in stabilization of the RNA subunit of telomerase, hTR, the level of hTR was also reduced in the proband, providing a molecular basis for his very short telomeres. This study demonstrates that the terminal region of the 3′ UTR of the DKC1 gene is essential for gene function and illustrates the importance of analyzing regulatory regions of the genome for molecular diagnosis of inherited disease.
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Affiliation(s)
- Jonathan W Arthur
- Children's Medical Research Institute Faculty of Medicine and Health, University of Sydney Westmead New South Wales Australia
| | - Hilda A Pickett
- Children's Medical Research Institute Faculty of Medicine and Health, University of Sydney Westmead New South Wales Australia
| | - Pasquale M Barbaro
- Children's Medical Research Institute Faculty of Medicine and Health, University of Sydney Westmead New South Wales Australia
| | - Tatjana Kilo
- Haematology Department Children's Hospital at Westmead Westmead New South Wales Australia
| | - Raja S Vasireddy
- Haematology Department Children's Hospital at Westmead Westmead New South Wales Australia
| | - Traude H Beilharz
- Monash Biomedicine Discovery Institute Department of Biochemistry and Molecular Biology, Monash University Clayton Victoria Australia
| | - David R Powell
- Monash Bioinformatics Platform Monash University Clayton Victoria Australia
| | - Emma L Hackett
- Department of Molecular Genetics Children's Hospital Westmead Westmead New South Wales Australia
| | - Bruce Bennetts
- Department of Molecular Genetics Children's Hospital Westmead Westmead New South Wales Australia.,Disciplines of Genetic Medicine and Child and Adolescent Health, Faculty of Medicine and Health University of Sydney Westmead New South Wales Australia
| | - Julie A Curtin
- Haematology Department Children's Hospital at Westmead Westmead New South Wales Australia
| | - Kristi Jones
- Disciplines of Genetic Medicine and Child and Adolescent Health, Faculty of Medicine and Health University of Sydney Westmead New South Wales Australia.,Department of Clinical Genetics Children's Hospital Westmead Westmead New South Wales Australia
| | - John Christodoulou
- Disciplines of Genetic Medicine and Child and Adolescent Health, Faculty of Medicine and Health University of Sydney Westmead New South Wales Australia.,Murdoch Children's Research Institute and Department of Paediatrics Melbourne Medical School Parkville Victoria Australia
| | - Roger R Reddel
- Children's Medical Research Institute Faculty of Medicine and Health, University of Sydney Westmead New South Wales Australia
| | - Juliana Teo
- Haematology Department Children's Hospital at Westmead Westmead New South Wales Australia
| | - Tracy M Bryan
- Children's Medical Research Institute Faculty of Medicine and Health, University of Sydney Westmead New South Wales Australia
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23
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Nash BM, Watson CJG, Hughes E, Hou AL, Loi TH, Bennetts B, Jelovic D, Polkinghorne PJ, Gorbatov M, Grigg JR, Vincent AL, Jamieson RV. Heterozygous COL9A3 variants cause severe peripheral vitreoretinal degeneration and retinal detachment. Eur J Hum Genet 2021; 29:881-886. [PMID: 33633367 PMCID: PMC8110976 DOI: 10.1038/s41431-021-00820-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Revised: 01/11/2021] [Accepted: 01/26/2021] [Indexed: 01/31/2023] Open
Abstract
The COL9A3 gene encodes one of the three alpha chains of Type IX collagen, with heterozygous variants reported to cause multiple epiphyseal dysplasia, and suggested as contributory in some cases of sensorineural hearing loss. Patients with homozygous variants have midface hypoplasia, myopia, sensorineural hearing loss, epiphyseal changes and carry a diagnosis of Stickler syndrome. Variants in COL9A3 have not previously been reported to cause vitreoretinal degeneration and/or retinal detachments. This report describes two families with autosomal dominant inheritance and predominant features of peripheral vitreoretinal lattice degeneration and retinal detachment. Genomic sequencing revealed a heterozygous splice variant in COL9A3 [NG_016353.1(NM_001853.4):c.1107 + 1G>C, NC_000020.10(NM_001853.4):c.1107 + 1G>C, LRG1253t1] in Family 1, and a heterozygous missense variant [NG_016353.1(NM_001853.4):c.388G>A p.(Gly130Ser)] in Family 2, each segregating with disease. cDNA studies of the splice variant demonstrated an in-frame deletion in the COL2 domain, and the missense variant occurred in the COL3 domain, both indicating the critical role of Type IX collagen in the vitreous base of the eye.
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Affiliation(s)
- Benjamin M. Nash
- Eye Genetics Research Unit, The Children’s Hospital at Westmead, Save Sight Institute, Children’s Medical Research Institute, University of Sydney, Sydney, NSW Australia ,Disciplines of Genomic Medicine and Child and Adolescent Health, Faculty of Medicine and Health, University of Sydney, Sydney, NSW Australia ,Sydney Genome Diagnostics, Western Sydney Genetics Program, The Children’s Hospital at Westmead, Sydney, NSW Australia
| | - Christopher J. G. Watson
- Eye Genetics Research Unit, The Children’s Hospital at Westmead, Save Sight Institute, Children’s Medical Research Institute, University of Sydney, Sydney, NSW Australia ,Disciplines of Genomic Medicine and Child and Adolescent Health, Faculty of Medicine and Health, University of Sydney, Sydney, NSW Australia
| | - Edward Hughes
- Sydney Eye Hospital, Sydney, NSW Australia ,Department of Ophthalmology, Sussex Eye Hospital, Brighton and Sussex University Hospitals NHS Trust, Brighton, United Kingdom
| | - Alec L. Hou
- Department of Ophthalmology, New Zealand National Eye Centre, Faculty of Health and Medical Science, University of Auckland, Auckland, New Zealand
| | - To Ha Loi
- Eye Genetics Research Unit, The Children’s Hospital at Westmead, Save Sight Institute, Children’s Medical Research Institute, University of Sydney, Sydney, NSW Australia
| | - Bruce Bennetts
- Disciplines of Genomic Medicine and Child and Adolescent Health, Faculty of Medicine and Health, University of Sydney, Sydney, NSW Australia ,Sydney Genome Diagnostics, Western Sydney Genetics Program, The Children’s Hospital at Westmead, Sydney, NSW Australia
| | - Diana Jelovic
- Eye Genetics Research Unit, The Children’s Hospital at Westmead, Save Sight Institute, Children’s Medical Research Institute, University of Sydney, Sydney, NSW Australia ,Disciplines of Genomic Medicine and Child and Adolescent Health, Faculty of Medicine and Health, University of Sydney, Sydney, NSW Australia
| | - Philip J. Polkinghorne
- Department of Ophthalmology, New Zealand National Eye Centre, Faculty of Health and Medical Science, University of Auckland, Auckland, New Zealand ,Eye Department, Greenlane Clinical Centre, Auckland District Health Board, Auckland, New Zealand
| | | | - John R. Grigg
- Eye Genetics Research Unit, The Children’s Hospital at Westmead, Save Sight Institute, Children’s Medical Research Institute, University of Sydney, Sydney, NSW Australia ,Sydney Eye Hospital, Sydney, NSW Australia ,Discipline of Ophthalmology, Faculty of Medicine and Health, University of Sydney, Sydney, NSW Australia
| | - Andrea L. Vincent
- Department of Ophthalmology, New Zealand National Eye Centre, Faculty of Health and Medical Science, University of Auckland, Auckland, New Zealand ,Eye Department, Greenlane Clinical Centre, Auckland District Health Board, Auckland, New Zealand
| | - Robyn V. Jamieson
- Eye Genetics Research Unit, The Children’s Hospital at Westmead, Save Sight Institute, Children’s Medical Research Institute, University of Sydney, Sydney, NSW Australia ,Disciplines of Genomic Medicine and Child and Adolescent Health, Faculty of Medicine and Health, University of Sydney, Sydney, NSW Australia ,Department of Clinical Genetics, Western Sydney Genetics Program, The Children’s Hospital at Westmead, Sydney, NSW Australia
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24
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Absalom NL, Liao VWY, Kothur K, Indurthi DC, Bennetts B, Troedson C, Mohammad SS, Gupta S, McGregor IS, Bowen MT, Lederer D, Mary S, De Waele L, Jansen K, Gill D, Kurian MA, McTague A, Møller RS, Ahring PK, Dale RC, Chebib M. Gain-of-function GABRB3 variants identified in vigabatrin-hypersensitive epileptic encephalopathies. Brain Commun 2020; 2:fcaa162. [PMID: 33585817 PMCID: PMC7869430 DOI: 10.1093/braincomms/fcaa162] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Revised: 07/31/2020] [Accepted: 08/28/2020] [Indexed: 01/06/2023] Open
Abstract
Variants in the GABRB3 gene encoding the β3-subunit of the γ-aminobutyric acid type A ( receptor are associated with various developmental and epileptic encephalopathies. Typically, these variants cause a loss-of-function molecular phenotype whereby γ-aminobutyric acid has reduced inhibitory effectiveness leading to seizures. Drugs that potentiate inhibitory GABAergic activity, such as nitrazepam, phenobarbital or vigabatrin, are expected to compensate for this and thereby reduce seizure frequency. However, vigabatrin, a drug that inhibits γ-aminobutyric acid transaminase to increase tonic γ-aminobutyric acid currents, has mixed success in treating seizures in patients with GABRB3 variants: some patients experience seizure cessation, but there is hypersensitivity in some patients associated with hypotonia, sedation and respiratory suppression. A GABRB3 variant that responds well to vigabatrin involves a truncation variant (p.Arg194*) resulting in a clear loss-of-function. We hypothesized that patients with a hypersensitive response to vigabatrin may exhibit a different γ-aminobutyric acid A receptor phenotype. To test this hypothesis, we evaluated the phenotype of de novo variants in GABRB3 (p.Glu77Lys and p.Thr287Ile) associated with patients who are clinically hypersensitive to vigabatrin. We introduced the GABRB3 p.Glu77Lys and p.Thr287Ile variants into a concatenated synaptic and extrasynaptic γ-aminobutyric acid A receptor construct, to resemble the γ-aminobutyric acid A receptor expression by a patient heterozygous for the GABRB3 variant. The mRNA of these constructs was injected into Xenopus oocytes and activation properties of each receptor measured by two-electrode voltage clamp electrophysiology. Results showed an atypical gain-of-function molecular phenotype in the GABRB3 p.Glu77Lys and p.Thr287Ile variants characterized by increased potency of γ-aminobutyric acid A without change to the estimated maximum open channel probability, deactivation kinetics or absolute currents. Modelling of the activation properties of the receptors indicated that either variant caused increased chloride flux in response to low concentrations of γ-aminobutyric acid that mediate tonic currents. We therefore propose that the hypersensitivity reaction to vigabatrin is a result of GABRB3 variants that exacerbate GABAergic tonic currents and caution is required when prescribing vigabatrin. In contrast, drug strategies increasing tonic currents in loss-of-function variants are likely to be a safe and effective therapy. This study demonstrates that functional genomics can explain beneficial and adverse anti-epileptic drug effects, and propose that vigabatrin should be considered in patients with clear loss-of-function GABRB3 variants.
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Affiliation(s)
- Nathan L Absalom
- Faculty of Medicine and Health, School of Pharmacy, Brain and Mind Centre, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Vivian W Y Liao
- Faculty of Medicine and Health, School of Pharmacy, Brain and Mind Centre, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Kavitha Kothur
- Kids Neuroscience Centre at The Children’s Hospital at Westmead, Westmead, New South Wales 2145, Australia
| | - Dinesh C Indurthi
- Faculty of Medicine and Health, School of Pharmacy, Brain and Mind Centre, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Bruce Bennetts
- Department of Molecular Genetics, The Children’s Hospital at Westmead, Westmead, New South Wales 2145, Australia
- Discipline of Paediatrics and Adolescent Health, The Children's Hospital at Westmead Clinical School, The University of Sydney, 2145, Australia
| | - Christopher Troedson
- T.Y. Nelson Department of Neurology and Neurosurgery, The Children's Hospital at Westmead, Westmead, New South Wales 2145, Australia
| | - Shekeeb S Mohammad
- Kids Neuroscience Centre at The Children’s Hospital at Westmead, Westmead, New South Wales 2145, Australia
| | - Sachin Gupta
- T.Y. Nelson Department of Neurology and Neurosurgery, The Children's Hospital at Westmead, Westmead, New South Wales 2145, Australia
| | - Iain S McGregor
- Faculty of Science, Lambert Initiative for Cannabinoid Therapeutics, Brain and Mind Centre, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Michael T Bowen
- Faculty of Science, Lambert Initiative for Cannabinoid Therapeutics, Brain and Mind Centre, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Damien Lederer
- Institute of Pathology and Genetics, Center for Human Genetics, Gosselies 6041, Belgium
| | - Sandrine Mary
- Institute of Pathology and Genetics, Center for Human Genetics, Gosselies 6041, Belgium
| | - Liesbeth De Waele
- Department of Development and Regeneration, KULeuven, Leuven 3000, Belgium
| | - Katrien Jansen
- Department of Development and Regeneration, KULeuven, Leuven 3000, Belgium
| | - Deepak Gill
- Kids Neuroscience Centre at The Children’s Hospital at Westmead, Westmead, New South Wales 2145, Australia
| | - Manju A Kurian
- Molecular Neurosciences, UCL Great Ormond Street Institute of Child Health, London WC1E 6BT, UK
- Department of Neurology, Great Ormond Street Hospital for Children, London WC1N 3JH, UK
| | - Amy McTague
- Molecular Neurosciences, UCL Great Ormond Street Institute of Child Health, London WC1E 6BT, UK
- Department of Neurology, Great Ormond Street Hospital for Children, London WC1N 3JH, UK
| | - Rikke S Møller
- Department of Epilepsy Genetics and Personalized Medicine, Danish Epilepsy Centre, Dianalund 4293, Denmark
- Department of Regional Health Research, University of Southern Denmark, Odense 5230, Denmark
| | - Philip K Ahring
- Faculty of Medicine and Health, School of Pharmacy, Brain and Mind Centre, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Russell C Dale
- Kids Neuroscience Centre at The Children’s Hospital at Westmead, Westmead, New South Wales 2145, Australia
| | - Mary Chebib
- Faculty of Medicine and Health, School of Pharmacy, Brain and Mind Centre, The University of Sydney, Sydney, New South Wales 2006, Australia
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Bhadada SK, Sridhar S, Dhiman V, Wong K, Bennetts B, Naot D, Jayaraman S, Cundy T. HYPOPHOSPHATEMIC RICKETS WITH HYPERCALCIURIA: A NOVEL HOMOZYGOUS MUTATION IN SLC34A3 AND LITERATURE REVIEW. AACE Clin Case Rep 2020; 6:e105-e112. [PMID: 32524022 PMCID: PMC7282280 DOI: 10.4158/accr-2019-0456] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Accepted: 12/30/2019] [Indexed: 11/21/2023] Open
Abstract
OBJECTIVE Hypophosphatemic rickets with hypercalciuria (HHRH) is a rare, recessively-inherited form of rickets caused by homozygous or compound heterozygous mutations in the SLC34A3 gene that encodes the renal tubular phosphate transporter protein NaPi2c. The bone phenotype varies from severe rickets to no disease. Accurate diagnosis is important as the treatment differs from other forms of rickets. METHODS The patient was a 12-year-old boy from the Indian subcontinent with florid hypophosphatemic rickets. A targeted gene panel to search for mutations in genes associated with inherited forms of rickets was performed. We also completed a literature search of published cases of HHRH. RESULTS The targeted gene panel demonstrated a novel homozygous SLC34A3 mutation: c.1339 G>A (p.Ala447Thr). His parents were heterozygous for the mutation. In our literature review we found that people with homozygous SLC34A3 mutations were more likely to have rickets than those with compound heterozygous mutations (85% versus 45%, p<0.002) and that serum phosphate z scores were lower in those with rickets than those without (-3.3 with a standard deviation of 1.5 versus -2.1 with a standard deviation of 1.5, p<0.005). CONCLUSION The bone phenotype of HHRH is related to the nature of the mutation and serum phosphate levels. Targeted gene panels can aid in the accurate diagnosis of inherited forms of rickets, and facilitate correct treatment.
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Bennetts B. Recommendations from the maternal cell contamination working party. Pathology 2020. [DOI: 10.1016/j.pathol.2020.01.116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Klinken EM, Gray PE, Pillay B, Worley L, Edwards ESJ, Payne K, Bennetts B, Hung D, Wood BA, Chan JJ, Marshall GM, Mitchell R, Uzel G, Ma CS, Tangye SG, McLean-Tooke A. Diversity of XMEN Disease: Description of 2 Novel Variants and Analysis of the Lymphocyte Phenotype. J Clin Immunol 2019; 40:299-309. [DOI: 10.1007/s10875-019-00732-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Accepted: 12/04/2019] [Indexed: 01/22/2023]
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Hudson R, Patel C, Hawley CM, O'Shea S, Snelling P, Ho G, Holman K, Bennetts B, Crawford J, Francis L, Simons C, Mallett A. Adult-Diagnosed Nonsyndromic Nephronophthisis in Australian Families Caused by Biallelic NPHP4 Variants. Am J Kidney Dis 2019; 76:282-287. [PMID: 31810733 DOI: 10.1053/j.ajkd.2019.08.031] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Accepted: 08/29/2019] [Indexed: 11/11/2022]
Abstract
There is increasing appreciation of nephronophthisis (NPHP) as an autosomal recessive cause of kidney failure and earlier stages of chronic kidney disease among adults. We identified 2 families with presumed adult-diagnosed nonsyndromic NPHP and negative diagnostic genetic testing results from our Renal Genetics Clinic. Both had 2 affected siblings without extrarenal phenotypes. After informed consent, research whole-genome sequencing was undertaken. Biallelic NPHP4 variants were identified in trans and clinically confirmed in all 4 affected individuals, confirming a genetic diagnosis. Participant 1 of the first family (F1P1) had kidney failure diagnosed at 19 years of age. An affected younger sibling (F1P2) reached kidney failure at age 15 years after kidney biopsy suggested NPHP. Pathogenic variants detected in NPHP4 in this family were NM_015102.4:c.3766C>T (p.Gln1256*) and a 31-kb deletion affecting exons 12 to 16. In the second family, F2P3 reached kidney failure at age 27 years having undergone kidney biopsy suggesting NPHP. An affected younger sibling (F2P4) has chronic kidney disease stage 4 at age 39 years. The NPHP4 variants detected were NM_015102.4:c.1998_1999del (p.Tyr667Phefs*23) and c.3646G>T (p.Asp1216Tyr). The latter variant was initially missed in diagnostic sequencing due to inadequate NPHP4 coverage (94.3% exonic coverage). With these reports, we identify NPHP4 as an appreciable genetic cause for adult-diagnosed nonsyndromic NPHP that should be considered by adult nephrologists.
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Affiliation(s)
- Rebecca Hudson
- Department of Renal Medicine, Royal Brisbane and Women's Hospital, Herston, QLD
| | - Chirag Patel
- Genetic Health Queensland, Royal Brisbane and Women's Hospital, Herston, QLD; KidGen Collaborative, Australian Genomics Health Alliance, Parkville, VIC
| | - Carmel M Hawley
- Department of Nephrology, Princess Alexandra Hospital, Woolloongabba, QLD; Translational Research Institute, Brisbane, Queensland; Australasian Kidney Trials Network, The University of Queensland, Queensland
| | | | - Paul Snelling
- KidGen Collaborative, Australian Genomics Health Alliance, Parkville, VIC; Department of Nephrology, Royal Prince Alfred Hospital, Camperdown, NSW
| | - Gladys Ho
- KidGen Collaborative, Australian Genomics Health Alliance, Parkville, VIC; Department of Molecular Genetics, Children's Hospital at Westmead, Westmead, NSW; Discipline of Genetic Medicine and Discipline of Child & Adolescent Health, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW
| | - Katherine Holman
- KidGen Collaborative, Australian Genomics Health Alliance, Parkville, VIC; Department of Molecular Genetics, Children's Hospital at Westmead, Westmead, NSW
| | - Bruce Bennetts
- KidGen Collaborative, Australian Genomics Health Alliance, Parkville, VIC; Department of Molecular Genetics, Children's Hospital at Westmead, Westmead, NSW; Discipline of Genetic Medicine and Discipline of Child & Adolescent Health, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW
| | - Joanna Crawford
- KidGen Collaborative, Australian Genomics Health Alliance, Parkville, VIC; Institute for Molecular Bioscience, The University of Queensland, St Lucia, QLD
| | - Leo Francis
- Department of Anatomical Pathology, Pathology Queensland, Herston, QLD
| | - Cas Simons
- KidGen Collaborative, Australian Genomics Health Alliance, Parkville, VIC; Institute for Molecular Bioscience, The University of Queensland, St Lucia, QLD; Murdoch Children's Research Institute, The Royal Children's Hospital Melbourne, Parkville, Melbourne, VIC
| | - Andrew Mallett
- Department of Renal Medicine, Royal Brisbane and Women's Hospital, Herston, QLD; KidGen Collaborative, Australian Genomics Health Alliance, Parkville, VIC; Institute for Molecular Bioscience, The University of Queensland, St Lucia, QLD; Department of Anatomical Pathology, Pathology Queensland, Herston, QLD; Faculty of Medicine, The University of Queensland, Herston, QLD, Australia.
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29
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Mallett AJ, Quinlan C, Patel C, Fowles L, Crawford J, Gattas M, Baer R, Bennetts B, Ho G, Holman K, Simons C. Precision Medicine Diagnostics for Rare Kidney Disease: Twitter as a Tool in Clinical Genomic Translation. Kidney Med 2019; 1:315-318. [PMID: 32734212 PMCID: PMC7380393 DOI: 10.1016/j.xkme.2019.06.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
New technologies such as genomics present opportunities to deliver precision medicine, including in the diagnosis of rare kidney disorders. Simultaneously, social media platforms such as Twitter can provide rapid and wide-reaching information dissemination in health care and science. We present 2 cases in which the reporting of a novel genetic cause for human kidney disease was communicated through Twitter and then subsequently noted by treating clinicians, thereby resulting in rapid clinical diagnostic translation. In 1 family, this involved the reporting of heterozygous variants in GREB1L relating to autosomal dominant unilateral or bilateral renal agenesis, and in the other family, this involved biallelic variants in CLDN10 relating to autosomal recessive hypokalemic renal tubular phenotypes. The times from Twitter notification to clinical diagnostic genetic report for these families were 111 and 200 days, respectively. Although caution is required, these cases show that social media platforms can contribute to rapid and accessible academic communication that may benefit clinicians, genomics-based researchers, and patients and families affected by rare kidney diseases.
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Affiliation(s)
- Andrew J Mallett
- Department of Renal Medicine, Royal Brisbane and Women's Hospital, Herston, QLD, Australia.,KidGen Collaborative, Australian Genomics Health Alliance, Parkville, VIC, Australia.,Institute for Molecular Bioscience, The University of Queensland, St Lucia, QLD, Australia.,Murdoch Children's Research Institute, The Royal Children's Hospital Melbourne, Parkville, Melbourne, VIC, Australia.,Faculty of Medicine, The University of Queensland, Herston, QLD, Australia
| | - Catherine Quinlan
- KidGen Collaborative, Australian Genomics Health Alliance, Parkville, VIC, Australia.,Murdoch Children's Research Institute, The Royal Children's Hospital Melbourne, Parkville, Melbourne, VIC, Australia.,Department of Paediatric Nephrology, Royal Children's Hospital, Parkville, VIC, Australia.,Department of Paediatrics, University of Melbourne, VIC, Australia
| | - Chirag Patel
- KidGen Collaborative, Australian Genomics Health Alliance, Parkville, VIC, Australia.,Genetic Health Queensland, Royal Brisbane and Women's Hospital, Herston, QLD, Australia
| | - Lindsay Fowles
- KidGen Collaborative, Australian Genomics Health Alliance, Parkville, VIC, Australia.,Genetic Health Queensland, Royal Brisbane and Women's Hospital, Herston, QLD, Australia
| | - Joanna Crawford
- KidGen Collaborative, Australian Genomics Health Alliance, Parkville, VIC, Australia.,Institute for Molecular Bioscience, The University of Queensland, St Lucia, QLD, Australia
| | - Michael Gattas
- Genetic Health Queensland, Royal Brisbane and Women's Hospital, Herston, QLD, Australia
| | - Richard Baer
- Department of Nephrology, Mater Public Hospital, South Brisbane, QLD, Australia
| | - Bruce Bennetts
- KidGen Collaborative, Australian Genomics Health Alliance, Parkville, VIC, Australia.,Department of Molecular Genetics, Children's Hospital at Westmead, Westmead, NSW, Australia.,Discipline of Genetic Medicine and Discipline of Child & Adolescent Health, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
| | - Gladys Ho
- KidGen Collaborative, Australian Genomics Health Alliance, Parkville, VIC, Australia.,Department of Molecular Genetics, Children's Hospital at Westmead, Westmead, NSW, Australia.,Discipline of Genetic Medicine and Discipline of Child & Adolescent Health, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
| | - Katherine Holman
- KidGen Collaborative, Australian Genomics Health Alliance, Parkville, VIC, Australia.,Department of Molecular Genetics, Children's Hospital at Westmead, Westmead, NSW, Australia.,Discipline of Genetic Medicine and Discipline of Child & Adolescent Health, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
| | - Cas Simons
- KidGen Collaborative, Australian Genomics Health Alliance, Parkville, VIC, Australia.,Institute for Molecular Bioscience, The University of Queensland, St Lucia, QLD, Australia.,Murdoch Children's Research Institute, The Royal Children's Hospital Melbourne, Parkville, Melbourne, VIC, Australia
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30
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Karolak JA, Vincent M, Deutsch G, Gambin T, Cogné B, Pichon O, Vetrini F, Mefford HC, Dines JN, Golden-Grant K, Dipple K, Freed AS, Leppig KA, Dishop M, Mowat D, Bennetts B, Gifford AJ, Weber MA, Lee AF, Boerkoel CF, Bartell TM, Ward-Melver C, Besnard T, Petit F, Bache I, Tümer Z, Denis-Musquer M, Joubert M, Martinovic J, Bénéteau C, Molin A, Carles D, André G, Bieth E, Chassaing N, Devisme L, Chalabreysse L, Pasquier L, Secq V, Don M, Orsaria M, Missirian C, Mortreux J, Sanlaville D, Pons L, Küry S, Bézieau S, Liet JM, Joram N, Bihouée T, Scott DA, Brown CW, Scaglia F, Tsai ACH, Grange DK, Phillips JA, Pfotenhauer JP, Jhangiani SN, Gonzaga-Jauregui CG, Chung WK, Schauer GM, Lipson MH, Mercer CL, van Haeringen A, Liu Q, Popek E, Coban Akdemir ZH, Lupski JR, Szafranski P, Isidor B, Le Caignec C, Stankiewicz P. Complex Compound Inheritance of Lethal Lung Developmental Disorders Due to Disruption of the TBX-FGF Pathway. Am J Hum Genet 2019; 104:213-228. [PMID: 30639323 DOI: 10.1016/j.ajhg.2018.12.010] [Citation(s) in RCA: 65] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Accepted: 12/13/2018] [Indexed: 12/24/2022] Open
Abstract
Primary defects in lung branching morphogenesis, resulting in neonatal lethal pulmonary hypoplasias, are incompletely understood. To elucidate the pathogenetics of human lung development, we studied a unique collection of samples obtained from deceased individuals with clinically and histopathologically diagnosed interstitial neonatal lung disorders: acinar dysplasia (n = 14), congenital alveolar dysplasia (n = 2), and other lethal lung hypoplasias (n = 10). We identified rare heterozygous copy-number variant deletions or single-nucleotide variants (SNVs) involving TBX4 (n = 8 and n = 2, respectively) or FGF10 (n = 2 and n = 2, respectively) in 16/26 (61%) individuals. In addition to TBX4, the overlapping ∼2 Mb recurrent and nonrecurrent deletions at 17q23.1q23.2 identified in seven individuals with lung hypoplasia also remove a lung-specific enhancer region. Individuals with coding variants involving either TBX4 or FGF10 also harbored at least one non-coding SNV in the predicted lung-specific enhancer region, which was absent in 13 control individuals with the overlapping deletions but without any structural lung anomalies. The occurrence of rare coding variants involving TBX4 or FGF10 with the putative hypomorphic non-coding SNVs implies a complex compound inheritance of these pulmonary hypoplasias. Moreover, they support the importance of TBX4-FGF10-FGFR2 epithelial-mesenchymal signaling in human lung organogenesis and help to explain the histopathological continuum observed in these rare lethal developmental disorders of the lung.
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MESH Headings
- DNA Copy Number Variations/genetics
- Female
- Fibroblast Growth Factor 10/genetics
- Fibroblast Growth Factor 10/metabolism
- Gene Expression Regulation
- Gestational Age
- Humans
- Infant, Newborn
- Infant, Newborn, Diseases/genetics
- Infant, Newborn, Diseases/metabolism
- Infant, Newborn, Diseases/mortality
- Infant, Newborn, Diseases/pathology
- Lung/embryology
- Lung/growth & development
- Lung Diseases/genetics
- Lung Diseases/metabolism
- Lung Diseases/mortality
- Lung Diseases/pathology
- Male
- Maternal Inheritance
- Organogenesis
- Paternal Inheritance
- Pedigree
- Polymorphism, Single Nucleotide/genetics
- Receptor, Fibroblast Growth Factor, Type 2/metabolism
- Signal Transduction/genetics
- T-Box Domain Proteins/genetics
- T-Box Domain Proteins/metabolism
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Affiliation(s)
- Justyna A Karolak
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Department of Genetics and Pharmaceutical Microbiology, Poznan University of Medical Sciences, 60-781 Poznan, Poland
| | - Marie Vincent
- Service de Génétique Médicale, CHU de Nantes, 44000 Nantes, France; Inserm, CNRS, Univ Nantes, l'institut du thorax, 44000 Nantes, France
| | - Gail Deutsch
- Department of Pathology, Seattle Children's Hospital, Seattle, WA 98105, USA
| | - Tomasz Gambin
- Department of Medical Genetics, Institute of Mother and Child, 01-211 Warsaw, Poland; Institute of Computer Science, Warsaw University of Technology, 00-665 Warsaw, Poland
| | - Benjamin Cogné
- Service de Génétique Médicale, CHU de Nantes, 44000 Nantes, France; Inserm, CNRS, Univ Nantes, l'institut du thorax, 44000 Nantes, France
| | - Olivier Pichon
- Service de Génétique Médicale, CHU de Nantes, 44000 Nantes, France
| | | | - Heather C Mefford
- Department of Pediatrics, Division of Genetic Medicine, University of Washington, Seattle, WA 98195, USA
| | - Jennifer N Dines
- Department of Pediatrics, Division of Genetic Medicine, University of Washington, Seattle, WA 98195, USA; Department of Medicine, Division of Medical Genetics, University of Washington, Seattle, WA 98195, USA
| | - Katie Golden-Grant
- Division of Genetic Medicine, Seattle Children's Hospital, Seattle, WA 98105, USA
| | - Katrina Dipple
- Department of Pediatrics, Division of Genetic Medicine, University of Washington, Seattle, WA 98195, USA; Division of Genetic Medicine, Seattle Children's Hospital, Seattle, WA 98105, USA
| | - Amanda S Freed
- Department of Pediatrics, Division of Genetic Medicine, University of Washington, Seattle, WA 98195, USA; Department of Medicine, Division of Medical Genetics, University of Washington, Seattle, WA 98195, USA
| | - Kathleen A Leppig
- Genetic Services Kaiser Permanente of Washington, Seattle, WA 98112, USA
| | - Megan Dishop
- Pathology and Laboratory Medicine, Phoenix Children's Hospital, Phoenix, AZ 85016, USA
| | - David Mowat
- Centre for Clinical Genetics, Sydney Children's Hospital, Randwick Sydney, NSW 2031 Australia; School of Women's and Children's Health, The University of New South Wales, Sydney, NSW 2052, Australia
| | - Bruce Bennetts
- Discipline of Child & Adolescent Health, Sydney Medical School, University of Sydney, Sydney, NSW 2006, Australia; Molecular Genetics Department, Western Sydney Genetics Program, The Children's Hospital at Westmead, Sydney, NSW 2145, Australia; Discipline of Genetic Medicine, Sydney Medical School, University of Sydney, Sydney, NSW 2006, Australia
| | - Andrew J Gifford
- School of Women's and Children's Health, The University of New South Wales, Sydney, NSW 2052, Australia; Department of Anatomical Pathology, Prince of Wales Hospital, Randwick, NSW 2031, Australia
| | - Martin A Weber
- Department of Anatomical Pathology, Prince of Wales Hospital, Randwick, NSW 2031, Australia; School of Medical Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - Anna F Lee
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC V6T 2B5, Canada
| | - Cornelius F Boerkoel
- Department of Medical Genetics, University of British Columbia, Vancouver, BC V6H 3N1, Canada
| | - Tina M Bartell
- Department of Genetics, Kaiser Permanente Sacramento Medical Center, Sacramento, CA 95815, USA
| | | | - Thomas Besnard
- Service de Génétique Médicale, CHU de Nantes, 44000 Nantes, France; Inserm, CNRS, Univ Nantes, l'institut du thorax, 44000 Nantes, France
| | - Florence Petit
- Service de Génétique Clinique, CHU Lille, 59000 Lille, France
| | - Iben Bache
- Department of Cellular and Molecular Medicine, University of Copenhagen, 2200 N Copenhagen, Denmark; Department of Clinical Genetics, Copenhagen University Hospital, Rigshospitalet, 2100 Ø Copenhagen, Denmark
| | - Zeynep Tümer
- Kennedy Center, Department of Clinical Genetics, Copenhagen University Hospital, Rigshospitalet, 2600 Glostrup, Copenhagen, Denmark; Deparment of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 N, Copenhagen, Denmark
| | | | | | - Jelena Martinovic
- Unit of Fetal Pathology, AP-HP, Antoine Beclere Hospital, 75000 Paris, France
| | - Claire Bénéteau
- Service de Génétique Médicale, CHU de Nantes, 44000 Nantes, France; Inserm, CNRS, Univ Nantes, l'institut du thorax, 44000 Nantes, France
| | - Arnaud Molin
- Service de Génétique Médicale, CHU Caen, 14000 Caen, France
| | - Dominique Carles
- Service d'anatomo-pathologie, CHU Bordeaux, 33000 Bordeaux, France
| | - Gwenaelle André
- Service d'anatomo-pathologie, CHU Bordeaux, 33000 Bordeaux, France
| | - Eric Bieth
- Service de génétique médicale, CHU Toulouse, France and UDEAR, UMR 1056 Inserm - Université de Toulouse, 31000 Toulouse, France
| | - Nicolas Chassaing
- Service de génétique médicale, CHU Toulouse, France and UDEAR, UMR 1056 Inserm - Université de Toulouse, 31000 Toulouse, France
| | | | | | | | - Véronique Secq
- Aix Marseille Univ, APHM, Hôpital Nord, Service d'anatomo-pathologie, 13000 Marseille, France
| | - Massimiliano Don
- Sant'Antonio General Hospital, Pediatric Care Unit, San Daniele del Friuli, 33100 Udine, Italy
| | - Maria Orsaria
- Department of Medical and Biological Sciences, Pathology Unit, University of Udine, Udine, Italy
| | - Chantal Missirian
- Aix Marseille Univ, APHM, INSERM, MMG, Marseille, Timone Hospital, 13000 Marseille, France
| | - Jérémie Mortreux
- Aix Marseille Univ, APHM, INSERM, MMG, Marseille, Timone Hospital, 13000 Marseille, France
| | - Damien Sanlaville
- Hospices Civils de Lyon, GHE, Genetics department, and Lyon University, 69000 Lyon, France
| | - Linda Pons
- Hospices Civils de Lyon, GHE, Genetics department, and Lyon University, 69000 Lyon, France
| | - Sébastien Küry
- Service de Génétique Médicale, CHU de Nantes, 44000 Nantes, France; Inserm, CNRS, Univ Nantes, l'institut du thorax, 44000 Nantes, France
| | - Stéphane Bézieau
- Service de Génétique Médicale, CHU de Nantes, 44000 Nantes, France; Inserm, CNRS, Univ Nantes, l'institut du thorax, 44000 Nantes, France
| | - Jean-Michel Liet
- Service de réanimation pédiatrique, CHU Nantes, 44000 Nantes, France
| | - Nicolas Joram
- Service de réanimation pédiatrique, CHU Nantes, 44000 Nantes, France
| | | | - Daryl A Scott
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Texas Children's Hospital, Houston, TX 77030, USA; Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Chester W Brown
- Department of Pediatrics, Genetics Division, University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Fernando Scaglia
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Texas Children's Hospital, Houston, TX 77030, USA; Joint BCM-CUHK Center of Medical Genetics, Prince of Wales Hospital, ShaTin, New Territories, Hong Kong SAR
| | - Anne Chun-Hui Tsai
- Department of Pediatrics, The Children's Hospital, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Dorothy K Grange
- Department of Pediatrics, Division of Genetics and Genomic Medicine, Washington University School of Medicine, St. Louis Children's Hospital, St. Louis, MO 63110, USA
| | - John A Phillips
- Department of Pediatrics, Division of Medical Genetics and Genomic Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Jean P Pfotenhauer
- Department of Pediatrics, Division of Medical Genetics and Genomic Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Shalini N Jhangiani
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | | | - Wendy K Chung
- Departments of Pediatrics and Medicine, Columbia University, New York, NY 10032, USA
| | - Galen M Schauer
- Department of Pathology, Kaiser Permanente Oakland Medical Center, Oakland, CA 94611, USA
| | - Mark H Lipson
- Department of Genetics, Kaiser Permanente Sacramento Medical Center, Sacramento, CA 95815, USA
| | - Catherine L Mercer
- Wessex Clinical Genetics Service, University Hospital Southampton NHS Foundation Trust, Princess Anne Hospital, Southampton SO16 5YA, UK
| | - Arie van Haeringen
- Department of Clinical Genetics, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands
| | - Qian Liu
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Edwina Popek
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Zeynep H Coban Akdemir
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - James R Lupski
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Texas Children's Hospital, Houston, TX 77030, USA; Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Przemyslaw Szafranski
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Bertrand Isidor
- Service de Génétique Médicale, CHU de Nantes, 44000 Nantes, France; Inserm, CNRS, Univ Nantes, l'institut du thorax, 44000 Nantes, France
| | | | - Paweł Stankiewicz
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Baylor Genetics, Houston, TX 77021, USA; Institute of Mother and Child, 01-211 Warsaw, Poland.
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31
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Ng MSY, McClymont K, McCallum N, Dua R, Holman K, Bennetts B, Ho G, Patel C, Mallett AJ. CFHR5 Nephropathy in a Greek-Cypriot Australian Family: Ancestry-Informed Precision Medicine. Kidney Int Rep 2018; 3:1222-1228. [PMID: 30197990 PMCID: PMC6127413 DOI: 10.1016/j.ekir.2018.04.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Affiliation(s)
- Monica S Y Ng
- Kidney Health Service, Royal Brisbane and Women's Hospital, Brisbane, Australia.,Faculty of Medicine, The University of Queensland, Brisbane, Australia
| | - Kelly McClymont
- Department of Histopathology, Sullivan Nicolaides Pathology, Brisbane, Australia
| | - Naomi McCallum
- Electron Microscopy Unit, Pathology Queensland, Royal Brisbane & Women's Hospital, Brisbane, Australia
| | - Rahul Dua
- Mater Private Hospital, Townsville, Australia
| | - Katherine Holman
- Department of Molecular Genetics, The Children's Hospital at Westmead, Sydney, Australia
| | - Bruce Bennetts
- Department of Molecular Genetics, The Children's Hospital at Westmead, Sydney, Australia.,Disciplines of Genetic Medicine and Paediatrics and Child Health, The University of Sydney, Sydney, Australia
| | - Gladys Ho
- Department of Molecular Genetics, The Children's Hospital at Westmead, Sydney, Australia
| | - Chirag Patel
- Genetic Health Queensland, Royal Brisbane and Women's Hospital, Brisbane, Australia
| | - Andrew J Mallett
- Kidney Health Service, Royal Brisbane and Women's Hospital, Brisbane, Australia.,Faculty of Medicine, The University of Queensland, Brisbane, Australia
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Kothur K, Holman K, Farnsworth E, Ho G, Lorentzos M, Troedson C, Gupta S, Webster R, Procopis PG, Menezes MP, Antony J, Ardern-Holmes S, Dale RC, Christodoulou J, Gill D, Bennetts B. Diagnostic yield of targeted massively parallel sequencing in children with epileptic encephalopathy. Seizure 2018; 59:132-140. [DOI: 10.1016/j.seizure.2018.05.005] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Revised: 02/20/2018] [Accepted: 05/08/2018] [Indexed: 12/28/2022] Open
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Forbes TA, Howden SE, Lawlor K, Phipson B, Maksimovic J, Hale L, Wilson S, Quinlan C, Ho G, Holman K, Bennetts B, Crawford J, Trnka P, Oshlack A, Patel C, Mallett A, Simons C, Little MH. Patient-iPSC-Derived Kidney Organoids Show Functional Validation of a Ciliopathic Renal Phenotype and Reveal Underlying Pathogenetic Mechanisms. Am J Hum Genet 2018; 102:816-831. [PMID: 29706353 DOI: 10.1016/j.ajhg.2018.03.014] [Citation(s) in RCA: 134] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Accepted: 03/05/2018] [Indexed: 02/07/2023] Open
Abstract
Despite the increasing diagnostic rate of genomic sequencing, the genetic basis of more than 50% of heritable kidney disease remains unresolved. Kidney organoids differentiated from induced pluripotent stem cells (iPSCs) of individuals affected by inherited renal disease represent a potential, but unvalidated, platform for the functional validation of novel gene variants and investigation of underlying pathogenetic mechanisms. In this study, trio whole-exome sequencing of a prospectively identified nephronophthisis (NPHP) proband and her parents identified compound-heterozygous variants in IFT140, a gene previously associated with NPHP-related ciliopathies. IFT140 plays a key role in retrograde intraflagellar transport, but the precise downstream cellular mechanisms responsible for disease presentation remain unknown. A one-step reprogramming and gene-editing protocol was used to derive both uncorrected proband iPSCs and isogenic gene-corrected iPSCs, which were differentiated to kidney organoids. Proband organoid tubules demonstrated shortened, club-shaped primary cilia, whereas gene correction rescued this phenotype. Differential expression analysis of epithelial cells isolated from organoids suggested downregulation of genes associated with apicobasal polarity, cell-cell junctions, and dynein motor assembly in proband epithelial cells. Matrigel cyst cultures confirmed a polarization defect in proband versus gene-corrected renal epithelium. As such, this study represents a "proof of concept" for using proband-derived iPSCs to model renal disease and illustrates dysfunctional cellular pathways beyond the primary cilium in the setting of IFT140 mutations, which are established for other NPHP genotypes.
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Fiscaletti M, Biggin A, Bennetts B, Wong K, Briody J, Pacey V, Birman C, Munns CF. Novel variant in Sp7/Osx associated with recessive osteogenesis imperfecta with bone fragility and hearing impairment. Bone 2018; 110:66-75. [PMID: 29382611 DOI: 10.1016/j.bone.2018.01.031] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Revised: 01/24/2018] [Accepted: 01/25/2018] [Indexed: 01/26/2023]
Abstract
Osteogenesis imperfecta (OI) is a connective tissue disorder characterized by low bone density and recurrent fractures with a wide genotypic and phenotypic spectrum. Common features include short stature, opalescent teeth, blue sclerae and hearing impairment. The majority (>90%) of patients with OI have autosomal dominant variants in COL1A1/COL1A2, which lead to defects in type 1 collagen. More recently, numerous recessive variants involving other genes have also been identified. Sp7/Osx gene, is a protein coding gene that encodes a zinc finger transcription factor, osterix, which is a member of the Sp subfamily of sequence-specific DNA-binding proteins. Osterix is expressed primarily by osteoblasts and has been shown to be vital for bone formation and bone homeostasis by promoting osteoblast differentiation and maturation. In animal models, Sp7/Osx has also been shown to regulate biomineralization of otoliths, calcium carbonate structures found in the inner ear of vertebrates. Until recently, only one report of a boy with an Sp7/Osx pathogenic variant presenting with bone fragility, limb deformities and normal hearing has been described in the literature. We have identified a novel Sp7/Osx variant in another sibship that presented with osteoporosis, low-trauma fractures and short stature. Progressive moderate-to-severe and severe-to-profound hearing loss secondary to otospongiosis and poor mineralization of ossicles and petrous temporal bone was also noted in two of the siblings. A homozygous pathogenic variant in exon 2 of the Sp7/Osx gene was found in all affected relatives; c.946C>T (p.Arg316Cys). Bone biopsies in the proband and his male sibling revealed significant cortical porosity and high trabecular bone turnover. This is the second report to describe children with OI associated with an Sp7/Osx variant. However, it is the first to describe the bone histomorphometry associated with this disorder and identifies a significant hearing loss as a potential feature in this OI subtype. Early audiology screening in these children is therefore warranted.
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Affiliation(s)
- Melissa Fiscaletti
- Institute of Endocrinology and Diabetes, The Children's Hospital at Westmead, Sydney, NSW, Australia.
| | - Andrew Biggin
- Institute of Endocrinology and Diabetes, The Children's Hospital at Westmead, Sydney, NSW, Australia; Discipline of Child & Adolescent Health, Sydney Medical School, University of Sydney, Sydney, NSW, Australia
| | - Bruce Bennetts
- Discipline of Child & Adolescent Health, Sydney Medical School, University of Sydney, Sydney, NSW, Australia; Molecular Genetics Department, Western Sydney Genetics Program, The Children's Hospital at Westmead, Sydney, NSW, Australia; Discipline of Genetic Medicine, Sydney Medical School, University of Sydney, Sydney, NSW, Australia
| | - Karen Wong
- Molecular Genetics Department, Western Sydney Genetics Program, The Children's Hospital at Westmead, Sydney, NSW, Australia; Discipline of Genetic Medicine, Sydney Medical School, University of Sydney, Sydney, NSW, Australia
| | - Julie Briody
- Department of Nuclear Medicine, The Children's Hospital at Westmead, Sydney, NSW, Australia
| | - Verity Pacey
- Institute of Endocrinology and Diabetes, The Children's Hospital at Westmead, Sydney, NSW, Australia; Department of Health Professions, Macquarie University, Sydney, NSW, Australia
| | - Catherine Birman
- Department of ENT and Discipline of Paediatrics and Child health, The Children's Hospital at Westmead, Sydney, NSW, Australia
| | - Craig F Munns
- Institute of Endocrinology and Diabetes, The Children's Hospital at Westmead, Sydney, NSW, Australia; Discipline of Child & Adolescent Health, Sydney Medical School, University of Sydney, Sydney, NSW, Australia
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Biggin A, Enriquez A, Wong M, Bennetts B, Lau C, Chan CY, Pinner J, Adelstein S, Adès LC. Hemophagocytic Lymphohistiocytosis in Loeys-Dietz Syndrome. J Clin Immunol 2018. [PMID: 29524015 DOI: 10.1007/s10875-018-0484-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Andrew Biggin
- The Children's Hospital at Westmead Clinical School, University of Sydney, Westmead, NSW, 2145, Australia.,Discipline of Child and Adolescent Health, University of Sydney, Westmead, NSW, 2145, Australia
| | - Annabelle Enriquez
- Discipline of Child and Adolescent Health, University of Sydney, Westmead, NSW, 2145, Australia.,Department of Clinical Genetics, The Children's Hospital at Westmead, Locked Bag 4001, Westmead, NSW, 2145, Australia.,Discipline of Genetic Medicine, University of Sydney, Westmead, NSW, 2145, Australia
| | - Melanie Wong
- Discipline of Child and Adolescent Health, University of Sydney, Westmead, NSW, 2145, Australia.,Department of Allergy and Immunology, The Children's Hospital at Westmead, Locked Bag 4001, Westmead, NSW, 2145, Australia
| | - Bruce Bennetts
- Department of Molecular Genetics, The Children's Hospital at Westmead, Locked Bag 4001, Westmead, NSW, 2145, Australia
| | - Chiyan Lau
- NSW Health Pathology Randwick Genetics Laboratory, Randwick, Australia
| | - Cheng Yee Chan
- NSW Health Pathology Randwick Genetics Laboratory, Randwick, Australia
| | - Jason Pinner
- Centre for Clinical Genetics, Sydney Children's Hospital, Randwick, Australia.,Department of Medical Genomics, Royal Prince Alfred Hospital, 50 Missenden Rd, Camperdown, NSW, 2050, Australia
| | - Stephen Adelstein
- Department of Clinical Immunology and Allergy, Royal Prince Alfred Hospital, 50 Missenden Rd, Camperdown, NSW, 2050, Australia
| | - Lesley C Adès
- Discipline of Child and Adolescent Health, University of Sydney, Westmead, NSW, 2145, Australia. .,Department of Clinical Genetics, The Children's Hospital at Westmead, Locked Bag 4001, Westmead, NSW, 2145, Australia. .,Discipline of Genetic Medicine, University of Sydney, Westmead, NSW, 2145, Australia.
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Wotton T, Wiley V, Bennetts B, Christie L, Wilcken B, Jenkins G, Rogers C, Boyle J, Field M. Are We Ready for Fragile X Newborn Screening Testing?-Lessons Learnt from a Feasibility Study. Int J Neonatal Screen 2018; 4:9. [PMID: 33072935 PMCID: PMC7548904 DOI: 10.3390/ijns4010009] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Accepted: 01/23/2018] [Indexed: 12/17/2022] Open
Abstract
Fragile X syndrome (FXS) is the most prevalent heritable cause of cognitive impairment but is not yet included in a newborn screening (NBS) program within Australia. This paper aims to assess the feasibility and reliability of population screening for FXS using a pilot study in one hospital. A total of 1971 mothers consented for 2000 newborns to be tested using routine NBS dried blood spot samples. DNA was extracted and a modified PCR assay with a chimeric CGG primer was used to detect fragile X alleles in both males and females in the normal, premutation, and full mutation ranges. A routine PCR-based fragile X assay was run in parallel to validate the chimeric primer assay. Babies with CGG repeat number ≥59 were referred for family studies. One thousand nine hundred and ninety NBS samples had a CGG repeat number less than 55 (1986 < 50); 10 had premutation alleles >54 CGG repeats (1/123 females and 1/507 males). There was complete concordance between the two PCR-based assays. A recent review revealed no clinically identified cases in the cohort up to 5 years later. The cost per test was $AUD19. Fragile X status can be determined on routine NBS samples using the chimeric primer assay. However, whilst this assay may not be considered cost-effective for population screening, it could be considered as a second-tier assay to a developed immunoassay for fragile X mental retardation protein (FMRP).
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Affiliation(s)
- Tiffany Wotton
- The NSW Newborn Screening Programme, The Children’s Hospital at Westmead, Westmead, NSW 2145, Australia
- Correspondence:
| | - Veronica Wiley
- The NSW Newborn Screening Programme, The Children’s Hospital at Westmead, Westmead, NSW 2145, Australia
- Disciplines of Paediatrics & Child Health and Genetic Medicine, The University of Sydney, Sydney, NSW 2006, Australia
| | - Bruce Bennetts
- Disciplines of Paediatrics & Child Health and Genetic Medicine, The University of Sydney, Sydney, NSW 2006, Australia
- Sydney Genome Diagnostics—Department of Molecular Genetics, The Children’s Hospital at Westmead, Westmead, NSW 2145, Australia
| | - Louise Christie
- Genetics of Learning Disability, Hunter Genetics, Waratah, NSW 2298, Australia
| | - Bridget Wilcken
- The NSW Newborn Screening Programme, The Children’s Hospital at Westmead, Westmead, NSW 2145, Australia
- Disciplines of Paediatrics & Child Health and Genetic Medicine, The University of Sydney, Sydney, NSW 2006, Australia
| | - Gemma Jenkins
- Sydney Genome Diagnostics—Department of Molecular Genetics, The Children’s Hospital at Westmead, Westmead, NSW 2145, Australia
| | - Carolyn Rogers
- Genetics of Learning Disability, Hunter Genetics, Waratah, NSW 2298, Australia
| | - Jackie Boyle
- Genetics of Learning Disability, Hunter Genetics, Waratah, NSW 2298, Australia
| | - Michael Field
- Genetics of Learning Disability, Hunter Genetics, Waratah, NSW 2298, Australia
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Chai SY, Pillay N, Badrick T, Bennetts B, Horan M. Developing quality assurance program for total DNA extraction. Pathology 2018. [DOI: 10.1016/j.pathol.2017.12.067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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38
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Pillay N, Horan M, Chai SY, Badrick T, Branford S, Bennetts B. Developing a quantitative external quality assurance (EQA) module to monitor BCR-ABL1 levels in chronic myeloid leukaemia (CML) and acute lymphoblastic leukaemia (ALL) using the international scale (IS) to determine a patient's molecular response. Pathology 2018. [DOI: 10.1016/j.pathol.2017.12.281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Nash BM, Symes R, Goel H, Dinger ME, Bennetts B, Grigg JR, Jamieson RV. NMNAT1 variants cause cone and cone-rod dystrophy. Eur J Hum Genet 2017; 26:428-433. [PMID: 29184169 DOI: 10.1038/s41431-017-0029-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Revised: 09/13/2017] [Accepted: 10/10/2017] [Indexed: 11/09/2022] Open
Abstract
Cone and cone-rod dystrophies (CD and CRD, respectively) are degenerative retinal diseases that predominantly affect the cone photoreceptors. The underlying disease gene is not known in approximately 75% of autosomal recessive cases. Variants in NMNAT1 cause a severe, early-onset retinal dystrophy called Leber congenital amaurosis (LCA). We report two patients where clinical phenotyping indicated diagnoses of CD and CRD, respectively. NMNAT1 variants were identified, with Case 1 showing an extremely rare homozygous variant c.[271G > A] p.(Glu91Lys) and Case 2 compound heterozygous variants c.[53 A > G];[769G > A] p.(Asn18Ser);(Glu257Lys). The detailed variant analysis, in combination with the observation of an associated macular atrophy phenotype, indicated that these variants were disease-causing. This report demonstrates that the variants in NMNAT1 may cause CD or CRD associated with macular atrophy. Genetic investigations of the patients with CD or CRD should include NMNAT1 in the genes examined.
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Affiliation(s)
- Benjamin M Nash
- Eye Genetics Research, The Children's Hospital at Westmead, Save Sight Institute, Children's Medical Research Institute, University of Sydney, Sydney, NSW, Australia.,Disciplines of Genetic Medicine, and Child and Adolescent Health, Sydney Medical School, University of Sydney, Sydney, NSW, Australia.,Sydney Genome Diagnostics, Western Sydney Genetics Program, The Children's Hospital at Westmead, Sydney, NSW, Australia
| | - Richard Symes
- Discipline of Ophthalmology, Sydney Medical School, University of Sydney, Sydney, NSW, Australia
| | | | - Marcel E Dinger
- Kinghorn Centre for Clinical Genomics, Garvan Institute for Medical Research, Sydney, NSW, Australia.,St Vincent's Clinical School, University of New South Wales, Sydney, NSW, Australia
| | - Bruce Bennetts
- Sydney Genome Diagnostics, Western Sydney Genetics Program, The Children's Hospital at Westmead, Sydney, NSW, Australia
| | - John R Grigg
- Eye Genetics Research, The Children's Hospital at Westmead, Save Sight Institute, Children's Medical Research Institute, University of Sydney, Sydney, NSW, Australia.,Discipline of Ophthalmology, Sydney Medical School, University of Sydney, Sydney, NSW, Australia
| | - Robyn V Jamieson
- Eye Genetics Research, The Children's Hospital at Westmead, Save Sight Institute, Children's Medical Research Institute, University of Sydney, Sydney, NSW, Australia. .,Disciplines of Genetic Medicine, and Child and Adolescent Health, Sydney Medical School, University of Sydney, Sydney, NSW, Australia. .,Department of Clinical Genetics, Western Sydney Genetics Program, The Children's Hospital at Westmead, Sydney, NSW, Australia.
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40
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Ma AS, Grigg JR, Prokudin I, Flaherty M, Bennetts B, Jamieson RV. New mutations in GJA8 expand the phenotype to include total sclerocornea. Clin Genet 2017; 93:155-159. [PMID: 28455998 DOI: 10.1111/cge.13045] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2017] [Revised: 04/12/2017] [Accepted: 04/19/2017] [Indexed: 01/05/2023]
Abstract
This project expands the disease spectrum for mutations in GJA8 to include total sclerocornea, rudimentary lenses and microphthalmia, in addition to this gene's previously known role in isolated congenital cataracts. Ophthalmic findings revealed bilateral total sclerocornea in 3 probands, with small abnormal lenses in 2 of the cases, and cataracts and microphthalmia in 1 case. Next-generation sequencing revealed de novo heterozygous mutations affecting the same codon of GJA8 : (c.281G>A; p.(Gly94Glu) and c.280G>C; p.(Gly94Arg)) in 2 of the probands, in addition to the c.151G>A; p.(Asp51Asn) mutation we had previously identified in the third case. In silico analysis predicted all of the mutations to be pathogenic. These cases show that deleterious, heterozygous mutations in GJA8 can lead to a severe ocular phenotype of total sclerocornea, abnormal lenses, and/or cataracts with or without microphthalmia, broadening the phenotype associated with this gene. GJA8 should be included when investigating patients with the severe anterior segment abnormality of total sclerocornea.
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Affiliation(s)
- A S Ma
- Eye Genetics Research Unit, The Children's Hospital at Westmead, Save Sight Institute, Children's Medical Research Institute, University of Sydney, Sydney, Australia.,Department of Clinical Genetics, Western Sydney Genetics Program, The Children's Hospital at Westmead, Sydney, Australia.,Disciplines of Genetic Medicine & Child and Adolescent Health, Sydney Medical School, University of Sydney, Sydney, Australia
| | - J R Grigg
- Eye Genetics Research Unit, The Children's Hospital at Westmead, Save Sight Institute, Children's Medical Research Institute, University of Sydney, Sydney, Australia.,Department of Ophthalmology, The Children's Hospital at Westmead, Sydney, Australia.,Discipline of Ophthalmology, Sydney Medical School, University of Sydney, Sydney, Australia
| | - I Prokudin
- Eye Genetics Research Unit, The Children's Hospital at Westmead, Save Sight Institute, Children's Medical Research Institute, University of Sydney, Sydney, Australia
| | - M Flaherty
- Eye Genetics Research Unit, The Children's Hospital at Westmead, Save Sight Institute, Children's Medical Research Institute, University of Sydney, Sydney, Australia.,Department of Ophthalmology, The Children's Hospital at Westmead, Sydney, Australia.,Discipline of Ophthalmology, Sydney Medical School, University of Sydney, Sydney, Australia
| | - B Bennetts
- Disciplines of Genetic Medicine & Child and Adolescent Health, Sydney Medical School, University of Sydney, Sydney, Australia.,Department of Molecular Genetics, Western Sydney Genetics Program, The Children's Hospital at Westmead, Sydney, Australia
| | - R V Jamieson
- Eye Genetics Research Unit, The Children's Hospital at Westmead, Save Sight Institute, Children's Medical Research Institute, University of Sydney, Sydney, Australia.,Department of Clinical Genetics, Western Sydney Genetics Program, The Children's Hospital at Westmead, Sydney, Australia.,Disciplines of Genetic Medicine & Child and Adolescent Health, Sydney Medical School, University of Sydney, Sydney, Australia.,Discipline of Ophthalmology, Sydney Medical School, University of Sydney, Sydney, Australia
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Mallett AJ, McCarthy HJ, Ho G, Holman K, Farnsworth E, Patel C, Fletcher JT, Mallawaarachchi A, Quinlan C, Bennetts B, Alexander SI. Massively parallel sequencing and targeted exomes in familial kidney disease can diagnose underlying genetic disorders. Kidney Int 2017; 92:1493-1506. [PMID: 28844315 DOI: 10.1016/j.kint.2017.06.013] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Revised: 06/06/2017] [Accepted: 06/08/2017] [Indexed: 10/19/2022]
Abstract
Inherited kidney disease encompasses a broad range of disorders, with both multiple genes contributing to specific phenotypes and single gene defects having multiple clinical presentations. Advances in sequencing capacity may allow a genetic diagnosis for familial renal disease, by testing the increasing number of known causative genes. However, there has been limited translation of research findings of causative genes into clinical settings. Here, we report the results of a national accredited diagnostic genetic service for familial renal disease. An expert multidisciplinary team developed a targeted exomic sequencing approach with ten curated multigene panels (207 genes) and variant assessment individualized to the patient's phenotype. A genetic diagnosis (pathogenic genetic variant[s]) was identified in 58 of 135 families referred in two years. The genetic diagnosis rate was similar between families with a pediatric versus adult proband (46% vs 40%), although significant differences were found in certain panels such as atypical hemolytic uremic syndrome (88% vs 17%). High diagnostic rates were found for Alport syndrome (22 of 27) and tubular disorders (8 of 10), whereas the monogenic diagnostic rate for congenital anomalies of the kidney and urinary tract was one of 13. Quality reporting was aided by a strong clinical renal and genetic multidisciplinary committee review. Importantly, for a diagnostic service, few variants of uncertain significance were found with this targeted, phenotype-based approach. Thus, use of targeted massively parallel sequencing approaches in inherited kidney disease has a significant capacity to diagnose the underlying genetic disorder across most renal phenotypes.
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Affiliation(s)
- Andrew J Mallett
- Kidney Health Service and Conjoint Renal Research Laboratory, Royal Brisbane and Women's Hospital, Brisbane, Australia; Faculty of Medicine, University of Queensland, Brisbane, Australia; KidGen Renal Genetics Flagship, Australian Genomics Health Alliance, Australia.
| | - Hugh J McCarthy
- KidGen Renal Genetics Flagship, Australian Genomics Health Alliance, Australia; Department of Pediatric Nephrology, The Children's Hospital at Westmead, Sydney, Australia; Discipline of Pediatrics and Child Health, University of Sydney, Sydney, Australia
| | - Gladys Ho
- KidGen Renal Genetics Flagship, Australian Genomics Health Alliance, Australia; Department of Molecular Genetics, The Children's Hospital at Westmead, Sydney, Australia
| | - Katherine Holman
- KidGen Renal Genetics Flagship, Australian Genomics Health Alliance, Australia; Department of Molecular Genetics, The Children's Hospital at Westmead, Sydney, Australia
| | - Elizabeth Farnsworth
- KidGen Renal Genetics Flagship, Australian Genomics Health Alliance, Australia; Department of Molecular Genetics, The Children's Hospital at Westmead, Sydney, Australia
| | - Chirag Patel
- KidGen Renal Genetics Flagship, Australian Genomics Health Alliance, Australia; Genetic Health Queensland, Royal Brisbane and Women's Hospital, Brisbane, Australia
| | - Jeffery T Fletcher
- KidGen Renal Genetics Flagship, Australian Genomics Health Alliance, Australia; Department of Pediatrics, The Canberra Hospital, Canberra, Australia
| | - Amali Mallawaarachchi
- KidGen Renal Genetics Flagship, Australian Genomics Health Alliance, Australia; Department of Clinical Genetics, Liverpool Hospital, Sydney, Australia; Discipline of Genetic Medicine, University of Sydney, Sydney, Australia
| | - Catherine Quinlan
- KidGen Renal Genetics Flagship, Australian Genomics Health Alliance, Australia; Murdoch Children's Research Institute, Melbourne, Australia; Department of Pediatric Nephrology, Royal Children's Hospital, Melbourne, Australia
| | - Bruce Bennetts
- KidGen Renal Genetics Flagship, Australian Genomics Health Alliance, Australia; Department of Molecular Genetics, The Children's Hospital at Westmead, Sydney, Australia; Discipline of Genetic Medicine, University of Sydney, Sydney, Australia
| | - Stephen I Alexander
- KidGen Renal Genetics Flagship, Australian Genomics Health Alliance, Australia; Department of Pediatric Nephrology, The Children's Hospital at Westmead, Sydney, Australia; Discipline of Pediatrics and Child Health, University of Sydney, Sydney, Australia; Centre for Kidney Research, University of Sydney, Sydney, Australia.
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42
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Saddi V, Beggs S, Bennetts B, Harrison J, Hime N, Kapur N, Lipsett J, Nogee LM, Phu A, Suresh S, Schultz A, Selvadurai H, Sherrard S, Strachan R, Vyas J, Zurynski Y, Jaffé A. Childhood interstitial lung diseases in immunocompetent children in Australia and New Zealand: a decade's experience. Orphanet J Rare Dis 2017; 12:133. [PMID: 28743279 PMCID: PMC5526310 DOI: 10.1186/s13023-017-0637-x] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Accepted: 04/19/2017] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND Childhood interstitial lung disease (chILD) represents a rare heterogeneous group of respiratory disorders. In the absence of randomized controlled clinical trials, global collaborations have utilized case series with an aim to standardising approaches to diagnosis and management. Australasian data are lacking. The aim of this study was to calculate prevalence and report the experience of chILD in Australasia over a decade. METHODS Paediatric pulmonologists in Australia and New Zealand involved in the care of patients aged 0-18 years with chILD completed a questionnaire on demographics, clinical features and outcomes, over a 10 year period. These data, together with data from the 2 reference genetics laboratories, were used to calculate prevalence. RESULTS One hundred fifteen cases were identified equating to a period prevalence (range) of 1.5 (0.8-2.1) cases/million for children aged 0-18years. Clinical data were provided on 106 patients: the <2 year group comprised 66 children, median age (range) 0.50 years (0.01-1.92); the ≥2 year group comprised 40 children, median age 8.2 years (2.0-18.0). Management approach was heterogeneous. Overall, 79% of patients had a good clinical outcome. Mortality rate was 7% in the study population. CONCLUSION chILD is rare in Australasia. This study demonstrates variation in the investigations and management of chILD cases across Australasia, however the general outcome is favorable. Further international collaboration will help finesse the understanding of these disorders.
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Affiliation(s)
- Vishal Saddi
- Department of Respiratory Medicine, Discipline of Paediatrics, Sydney Children’s Hospital, Randwick, Sydney, NSW 2031 Australia
| | - Sean Beggs
- Department of Paediatrics, Royal Hobart Hospital, Hobart, TAS 7000 Australia
| | - Bruce Bennetts
- Department of Molecular Genetics, The Children’s Hospital at Westmead, Sydney, NSW 2145 Australia
- Discipline of Paediatrics and Child Health, Sydney Medical School, The University of Sydney, Sydney, Australia
| | - Joanne Harrison
- Department of Respiratory Medicine, The Children’s Hospital, Melbourne, VIC 3052 Australia
| | - Neil Hime
- Discipline of Paediatrics and Child Health, Sydney Medical School, The University of Sydney, Sydney, Australia
- Australian Paediatric Surveillance Unit, Kids Research Institute, Sydney, NSW 2145 Australia
| | - Nitin Kapur
- Department of Respiratory Medicine, Lady Cilento Children’s Hospital, Brisbane, QLD 4101 Australia
| | - Jill Lipsett
- Anatomical Pathology, S.A. Pathology, Women’s and Children’s Hospital, Adelaide, South Australia 5154 Australia
| | - Lawrence M. Nogee
- Eudowood Neonatal Pulmonary Division, Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, MD 21287 USA
| | - Amy Phu
- Discipline of Paediatrics and Child Health, Sydney Medical School, The University of Sydney, Sydney, Australia
- Australian Paediatric Surveillance Unit, Kids Research Institute, Sydney, NSW 2145 Australia
| | - Sadasivam Suresh
- Department of Respiratory Medicine, Lady Cilento Children’s Hospital, Brisbane, QLD 4101 Australia
| | - André Schultz
- Department of Respiratory Medicine, Princess Margaret Hospital for Children, Perth, WA 6008 Australia
| | - Hiran Selvadurai
- Discipline of Paediatrics and Child Health, Sydney Medical School, The University of Sydney, Sydney, Australia
- Department of Respiratory Medicine, The Children’s Hospital at Westmead, Sydney, NSW 2145 Australia
| | - Stephanie Sherrard
- Department of Respiratory Medicine, Princess Margaret Hospital for Children, Perth, WA 6008 Australia
| | - Roxanne Strachan
- Department of Respiratory Medicine, Discipline of Paediatrics, Sydney Children’s Hospital, Randwick, Sydney, NSW 2031 Australia
| | - Julian Vyas
- Department of Respiratory Paediatrics, Starship Children’s Hospital, Auckland, 1023 New Zealand
| | - Yvonne Zurynski
- Australian Paediatric Surveillance Unit, Kids Research Institute, Sydney, NSW 2145 Australia
| | - Adam Jaffé
- School of Women’s and Children’s Health, Faculty of Medicine, University of New South Wales, Sydney, NSW 2031 Australia
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Wright DC, Mohammad S, Dale R, Bennetts B. Evaluation of a gene panel for movement disorders in a small cohort of dystonia patients. Pathology 2017. [DOI: 10.1016/j.pathol.2016.12.140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Ma AS, Grigg JR, Ho G, Prokudin I, Farnsworth E, Holman K, Cheng A, Billson FA, Martin F, Fraser C, Mowat D, Smith J, Christodoulou J, Flaherty M, Bennetts B, Jamieson RV. Sporadic and Familial Congenital Cataracts: Mutational Spectrum and New Diagnoses Using Next-Generation Sequencing. Hum Mutat 2016; 37:371-84. [PMID: 26694549 PMCID: PMC4787201 DOI: 10.1002/humu.22948] [Citation(s) in RCA: 94] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2015] [Accepted: 12/14/2015] [Indexed: 12/13/2022]
Abstract
Congenital cataracts are a significant cause of lifelong visual loss. They may be isolated or associated with microcornea, microphthalmia, anterior segment dysgenesis (ASD) and glaucoma, and there can be syndromic associations. Genetic diagnosis is challenging due to marked genetic heterogeneity. In this study, next-generation sequencing (NGS) of 32 cataract-associated genes was undertaken in 46 apparently nonsyndromic congenital cataract probands, around half sporadic and half familial cases. We identified pathogenic variants in 70% of cases, and over 68% of these were novel. In almost two-thirds (20/33) of these cases, this resulted in new information about the diagnosis and/or inheritance pattern. This included identification of: new syndromic diagnoses due to NHS or BCOR mutations; complex ocular phenotypes due to PAX6 mutations; de novo autosomal-dominant or X-linked mutations in sporadic cases; and mutations in two separate cataract genes in one family. Variants were found in the crystallin and gap junction genes, including the first report of severe microphthalmia and sclerocornea associated with a novel GJA8 mutation. Mutations were also found in rarely reported genes including MAF, VIM, MIP, and BFSP1. Targeted NGS in presumed nonsyndromic congenital cataract patients provided significant diagnostic information in both familial and sporadic cases.
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Affiliation(s)
- Alan S. Ma
- Eye Genetics ResearchThe Children's Hospital at WestmeadSave Sight InstituteChildren's Medical Research InstituteUniversity of SydneySydneyNew South WalesAustralia
- Department of Clinical GeneticsThe Children's Hospital at WestmeadSydneyNew South WalesAustralia
- Western Sydney Genetics ProgramThe Children's Hospital at WestmeadSydneyNew South WalesAustralia
- Discipline of Paediatrics and Child Healthand Discipline of Genetic MedicineSydney Medical SchoolUniversity of SydneyNew South WalesAustralia
| | - John R. Grigg
- Eye Genetics ResearchThe Children's Hospital at WestmeadSave Sight InstituteChildren's Medical Research InstituteUniversity of SydneySydneyNew South WalesAustralia
- Department of OphthalmologyThe Children's Hospital at WestmeadSydneyNew South WalesAustralia
- Discipline of OphthalmologySydney Medical SchoolUniversity of SydneyNew South WalesAustralia
| | - Gladys Ho
- Western Sydney Genetics ProgramThe Children's Hospital at WestmeadSydneyNew South WalesAustralia
- Department of Molecular GeneticsThe Children's Hospital at WestmeadSydneyNew South WalesAustralia
| | - Ivan Prokudin
- Eye Genetics ResearchThe Children's Hospital at WestmeadSave Sight InstituteChildren's Medical Research InstituteUniversity of SydneySydneyNew South WalesAustralia
| | - Elizabeth Farnsworth
- Western Sydney Genetics ProgramThe Children's Hospital at WestmeadSydneyNew South WalesAustralia
- Department of Molecular GeneticsThe Children's Hospital at WestmeadSydneyNew South WalesAustralia
| | - Katherine Holman
- Western Sydney Genetics ProgramThe Children's Hospital at WestmeadSydneyNew South WalesAustralia
- Department of Molecular GeneticsThe Children's Hospital at WestmeadSydneyNew South WalesAustralia
| | - Anson Cheng
- Eye Genetics ResearchThe Children's Hospital at WestmeadSave Sight InstituteChildren's Medical Research InstituteUniversity of SydneySydneyNew South WalesAustralia
| | - Frank A. Billson
- Eye Genetics ResearchThe Children's Hospital at WestmeadSave Sight InstituteChildren's Medical Research InstituteUniversity of SydneySydneyNew South WalesAustralia
- Department of OphthalmologyThe Children's Hospital at WestmeadSydneyNew South WalesAustralia
- Discipline of OphthalmologySydney Medical SchoolUniversity of SydneyNew South WalesAustralia
| | - Frank Martin
- Department of OphthalmologyThe Children's Hospital at WestmeadSydneyNew South WalesAustralia
- Discipline of OphthalmologySydney Medical SchoolUniversity of SydneyNew South WalesAustralia
| | - Clare Fraser
- Discipline of OphthalmologySydney Medical SchoolUniversity of SydneyNew South WalesAustralia
| | - David Mowat
- Department of Medical GeneticsSydney Children's HospitalSydneyNew South WalesAustralia
| | - James Smith
- Department of OphthalmologyThe Children's Hospital at WestmeadSydneyNew South WalesAustralia
| | - John Christodoulou
- Western Sydney Genetics ProgramThe Children's Hospital at WestmeadSydneyNew South WalesAustralia
- Discipline of Paediatrics and Child Healthand Discipline of Genetic MedicineSydney Medical SchoolUniversity of SydneyNew South WalesAustralia
| | - Maree Flaherty
- Eye Genetics ResearchThe Children's Hospital at WestmeadSave Sight InstituteChildren's Medical Research InstituteUniversity of SydneySydneyNew South WalesAustralia
- Department of OphthalmologyThe Children's Hospital at WestmeadSydneyNew South WalesAustralia
- Discipline of OphthalmologySydney Medical SchoolUniversity of SydneyNew South WalesAustralia
| | - Bruce Bennetts
- Western Sydney Genetics ProgramThe Children's Hospital at WestmeadSydneyNew South WalesAustralia
- Discipline of Paediatrics and Child Healthand Discipline of Genetic MedicineSydney Medical SchoolUniversity of SydneyNew South WalesAustralia
- Department of Molecular GeneticsThe Children's Hospital at WestmeadSydneyNew South WalesAustralia
| | - Robyn V. Jamieson
- Eye Genetics ResearchThe Children's Hospital at WestmeadSave Sight InstituteChildren's Medical Research InstituteUniversity of SydneySydneyNew South WalesAustralia
- Department of Clinical GeneticsThe Children's Hospital at WestmeadSydneyNew South WalesAustralia
- Western Sydney Genetics ProgramThe Children's Hospital at WestmeadSydneyNew South WalesAustralia
- Discipline of Paediatrics and Child Healthand Discipline of Genetic MedicineSydney Medical SchoolUniversity of SydneyNew South WalesAustralia
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Wong KKY, Jackson J, Whidborne R, Mallon D, Bennetts B, D’Orsogna LJ. Autosomal recessive transmission of TRAPS in a family with a novel TNFRSF1Amutation. Scand J Rheumatol Suppl 2015; 44:255-6. [DOI: 10.3109/03009742.2015.1005663] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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Abstract
Retinal dystrophies (RDs) are degenerative diseases of the retina which have marked clinical and genetic heterogeneity. Common presentations among these disorders include night or colour blindness, tunnel vision and subsequent progression to complete blindness. The known causative disease genes have a variety of developmental and functional roles with mutations in more than 120 genes shown to be responsible for the phenotypes. In addition, mutations within the same gene have been shown to cause different disease phenotypes, even amongst affected individuals within the same family highlighting further levels of complexity. The known disease genes encode proteins involved in retinal cellular structures, phototransduction, the visual cycle, and photoreceptor structure or gene regulation. This review aims to demonstrate the high degree of genetic complexity in both the causative disease genes and their associated phenotypes, highlighting the more common clinical manifestation of retinitis pigmentosa (RP). The review also provides insight to recent advances in genomic molecular diagnosis and gene and cell-based therapies for the RDs.
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Affiliation(s)
- Benjamin M Nash
- 1 Eye Genetics Research Group, Children's Medical Research Institute, University of Sydney, The Children's Hospital at Westmead and Save Sight Institute, Sydney, NSW, Australia ; 2 Sydney Genome Diagnostics, The Children's Hospital at Westmead, Sydney, NSW, Australia ; 3 Discipline of Paediatrics and Child Health, Sydney Medical School, University of Sydney, NSW, Australia
| | - Dale C Wright
- 1 Eye Genetics Research Group, Children's Medical Research Institute, University of Sydney, The Children's Hospital at Westmead and Save Sight Institute, Sydney, NSW, Australia ; 2 Sydney Genome Diagnostics, The Children's Hospital at Westmead, Sydney, NSW, Australia ; 3 Discipline of Paediatrics and Child Health, Sydney Medical School, University of Sydney, NSW, Australia
| | - John R Grigg
- 1 Eye Genetics Research Group, Children's Medical Research Institute, University of Sydney, The Children's Hospital at Westmead and Save Sight Institute, Sydney, NSW, Australia ; 2 Sydney Genome Diagnostics, The Children's Hospital at Westmead, Sydney, NSW, Australia ; 3 Discipline of Paediatrics and Child Health, Sydney Medical School, University of Sydney, NSW, Australia
| | - Bruce Bennetts
- 1 Eye Genetics Research Group, Children's Medical Research Institute, University of Sydney, The Children's Hospital at Westmead and Save Sight Institute, Sydney, NSW, Australia ; 2 Sydney Genome Diagnostics, The Children's Hospital at Westmead, Sydney, NSW, Australia ; 3 Discipline of Paediatrics and Child Health, Sydney Medical School, University of Sydney, NSW, Australia
| | - Robyn V Jamieson
- 1 Eye Genetics Research Group, Children's Medical Research Institute, University of Sydney, The Children's Hospital at Westmead and Save Sight Institute, Sydney, NSW, Australia ; 2 Sydney Genome Diagnostics, The Children's Hospital at Westmead, Sydney, NSW, Australia ; 3 Discipline of Paediatrics and Child Health, Sydney Medical School, University of Sydney, NSW, Australia
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Bennetts B, Caramins M, Hsu A, Lau C, Mead S, Meldrum C, Smith T, Suthers G, Taylor G, Cotton R, Tyrrell V. Quality standards for DNA sequence variation databases to improve clinical management under development in Australia. Appl Transl Genom 2014; 3:54-57. [PMID: 27294016 PMCID: PMC4888016 DOI: 10.1016/j.atg.2014.07.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2014] [Revised: 06/30/2014] [Accepted: 07/04/2014] [Indexed: 06/06/2023]
Abstract
Despite the routine nature of comparing sequence variations identified during clinical testing to database records, few databases meet quality requirements for clinical diagnostics. To address this issue, The Royal College of Pathologists of Australasia (RCPA) in collaboration with the Human Genetics Society of Australasia (HGSA), and the Human Variome Project (HVP) is developing standards for DNA sequence variation databases intended for use in the Australian clinical environment. The outputs of this project will be promoted to other health systems and accreditation bodies by the Human Variome Project to support the development of similar frameworks in other jurisdictions.
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Affiliation(s)
- B. Bennetts
- Western Sydney Genetics Program, The Children's Hospital at Westmead, Westmead, NSW 2145, Australia
| | - M. Caramins
- SDS Pathology, North Ryde, NSW 2113, Australia
| | - A. Hsu
- Genomic Medicine, Department of Pathology, University of Melbourne, Melbourne, VIC 3010, Australia
| | - C. Lau
- Royal College of Pathologists of Australasia, 207 Albion Street, Surry Hills, NSW 2010, Australia
| | - S. Mead
- South Eastern Sydney Laboratory Services, Prince of Wales Hospital, Randwick, NSW 2031, Australia
| | - C. Meldrum
- Hunter Area Pathology Service, John Hunter Hospital, New Lambton Heights, NSW 2305, Australia
| | - T.D. Smith
- Genomic Medicine, Department of Pathology, University of Melbourne, Melbourne, VIC 3010, Australia
- Human Variome Project International, Level 5, 234 Queensberry Street, University of Melbourne, VIC 3010, Australia
| | - G. Suthers
- SA Clinical Genetics Service, SA Pathology, Adelaide, SA 5000, Australia
- Department of Paediatrics, University of Adelaide, SA 5008, Australia
| | - G.R. Taylor
- Genomic Medicine, Department of Pathology, University of Melbourne, Melbourne, VIC 3010, Australia
| | - R.G.H. Cotton
- Genomic Medicine, Department of Pathology, University of Melbourne, Melbourne, VIC 3010, Australia
- Human Variome Project International, Level 5, 234 Queensberry Street, University of Melbourne, VIC 3010, Australia
| | - V. Tyrrell
- Royal College of Pathologists of Australasia, 207 Albion Street, Surry Hills, NSW 2010, Australia
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Christie L, Wotton T, Bennetts B, Wiley V, Wilcken B, Rogers C, Boyle J, Turner C, Hansen J, Hunter M, Goel H, Field M. Maternal attitudes to newborn screening for fragile X syndrome. Am J Med Genet A 2013; 161A:301-11. [DOI: 10.1002/ajmg.a.35752] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2012] [Accepted: 10/11/2012] [Indexed: 01/19/2023]
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Shinar Y, Obici L, Aksentijevich I, Bennetts B, Austrup F, Ceccherini I, Costa JM, De Leener A, Gattorno M, Kania U, Kone-Paut I, Lezer S, Livneh A, Moix I, Nishikomori R, Ozen S, Phylactou L, Risom L, Rowczenio D, Sarkisian T, van Gijn ME, Witsch-Baumgartner M, Morris M, Hoffman HM, Touitou I. Guidelines for the genetic diagnosis of hereditary recurrent fevers. Ann Rheum Dis 2012; 71:1599-605. [PMID: 22661645 PMCID: PMC3500529 DOI: 10.1136/annrheumdis-2011-201271] [Citation(s) in RCA: 119] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Hereditary recurrent fevers (HRFs) are a group of monogenic autoinflammatory diseases characterised by recurrent bouts of fever and serosal inflammation that are caused by pathogenic variants in genes important for the regulation of innate immunity. Discovery of the molecular defects responsible for these diseases has initiated genetic diagnostics in many countries around the world, including the Middle East, Europe, USA, Japan and Australia. However, diverse testing methods and reporting practices are employed and there is a clear need for consensus guidelines for HRF genetic testing. Draft guidelines were prepared based on current practice deduced from previous HRF external quality assurance schemes and data from the literature. The draft document was disseminated through the European Molecular Genetics Quality Network for broader consultation and amendment. A workshop was held in Bruges (Belgium) on 18 and 19 September 2011 to ratify the draft and obtain a final consensus document. An agreed set of best practice guidelines was proposed for genetic diagnostic testing of HRFs, for reporting the genetic results and for defining their clinical significance.
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Affiliation(s)
- Y Shinar
- Unité médicale des maladies autoinflammatoires, CHRU Montpellier, INSERM U844, Université UM1, Montpellier, France
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White R, Ho G, Schmidt S, Scheffer IE, Fischer A, Yendle SC, Bienvenu T, Nectoux J, Ellaway CJ, Darmanian A, Tong X, Cloosterman D, Bennetts B, Kalra V, Fullston T, Gecz J, Cox TC, Christodoulou J. Cyclin-Dependent Kinase-Like 5 (CDKL5) Mutation Screening in Rett Syndrome and Related Disorders. Twin Res Hum Genet 2012; 13:168-78. [DOI: 10.1375/twin.13.2.168] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
AbstractRett syndrome (RTT) is a severe neurodevelopmental disorder affecting females almost exclusively and is characterized by a wide spectrum of clinical manifestations. Mutations in the X-linked methyl-CpG-binding protein 2 (MECP2) gene have been found in up to 95% of classical RTT cases and a lesser proportion of atypical cases. Recently, mutations in another X-linked gene, CDKL5 (cyclin-dependent kinase-like 5) have been found to cause atypical RTT, in particular the early onset seizure (Hanefeld variant) and one female with autism. In this study we screened several cohorts of children for CDKL5 mutations, totaling 316 patients, including individuals with a clinical diagnosis of RTT but who were negative for MECP2 mutations (n = 102), males with X-linked mental retardation (n = 9), patients with West syndrome (n = 52), patients with autism (n = 59), patients with epileptic encephalopathy (n = 33), patients with Aicardi syndrome (n = 7) and other patients with intellectual disability with or without seizures (n = 54). In all, seven polymorphic variations and four de novo mutations (c.586C>T [p.S196L]; c.58G>C [p.G20R]; c.2504delC [p.P835fs]; deletion of exons 1 - 3) were identified, and in all instances of the latter the clinical phenotype was that of an epileptic encephalopathy. These results suggest that pathogenic CDKL5 mutations are unlikely to be identified in the absence of severe early-onset seizures and highlight the importance of screening for large intragenic and whole gene deletions.
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