1
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Scala M, Tomati V, Ferla M, Lena M, Cohen JS, Fatemi A, Brokamp E, Bican A, Phillips JA, Koziura ME, Nicouleau M, Rio M, Siquier K, Boddaert N, Musante I, Tamburro S, Baldassari S, Iacomino M, Scudieri P, Rosenfeld JA, Bellus G, Reed S, Al Saif H, Russo RS, Walsh MB, Cantagrel V, Crunk A, Gustincich S, Ruggiero SM, Fitzgerald MP, Helbig I, Striano P, Severino M, Salpietro V, Pedemonte N, Zara F. De novo variants in DENND5B cause a neurodevelopmental disorder. Am J Hum Genet 2024; 111:529-543. [PMID: 38387458 PMCID: PMC10940048 DOI: 10.1016/j.ajhg.2024.02.001] [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: 08/31/2023] [Revised: 01/30/2024] [Accepted: 02/01/2024] [Indexed: 02/24/2024] Open
Abstract
The Rab family of guanosine triphosphatases (GTPases) includes key regulators of intracellular transport and membrane trafficking targeting specific steps in exocytic, endocytic, and recycling pathways. DENND5B (Rab6-interacting Protein 1B-like protein, R6IP1B) is the longest isoform of DENND5, an evolutionarily conserved DENN domain-containing guanine nucleotide exchange factor (GEF) that is highly expressed in the brain. Through exome sequencing and international matchmaking platforms, we identified five de novo variants in DENND5B in a cohort of five unrelated individuals with neurodevelopmental phenotypes featuring cognitive impairment, dysmorphism, abnormal behavior, variable epilepsy, white matter abnormalities, and cortical gyration defects. We used biochemical assays and confocal microscopy to assess the impact of DENND5B variants on protein accumulation and distribution. Then, exploiting fluorescent lipid cargoes coupled to high-content imaging and analysis in living cells, we investigated whether DENND5B variants affected the dynamics of vesicle-mediated intracellular transport of specific cargoes. We further generated an in silico model to investigate the consequences of DENND5B variants on the DENND5B-RAB39A interaction. Biochemical analysis showed decreased protein levels of DENND5B mutants in various cell types. Functional investigation of DENND5B variants revealed defective intracellular vesicle trafficking, with significant impairment of lipid uptake and distribution. Although none of the variants affected the DENND5B-RAB39A interface, all were predicted to disrupt protein folding. Overall, our findings indicate that DENND5B variants perturb intracellular membrane trafficking pathways and cause a complex neurodevelopmental syndrome with variable epilepsy and white matter involvement.
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Affiliation(s)
- Marcello Scala
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health, University of Genoa, Genoa, Italy; Pediatric Neurology and Muscular Diseases Unit, IRCCS Istituto Giannina Gaslini, Genoa, Italy; UOC Genetica Medica, IRCCS Giannina Gaslini, Genoa, Italy
| | - Valeria Tomati
- UOC Genetica Medica, IRCCS Giannina Gaslini, Genoa, Italy
| | - Matteo Ferla
- Oxford Protein Informatics Group, Department of Statistics, University of Oxford, Oxford, UK
| | - Mariateresa Lena
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health, University of Genoa, Genoa, Italy
| | - Julie S Cohen
- Department of Neurology and Developmental Medicine, Kennedy Krieger Institute, Baltimore, MD, USA; Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Ali Fatemi
- Department of Neurology and Developmental Medicine, Kennedy Krieger Institute, Baltimore, MD, USA; Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Elly Brokamp
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Anna Bican
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - John A Phillips
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Mary E Koziura
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Michael Nicouleau
- Université Paris Cité, Imagine Institute, Developmental Brain Disorders Laboratory, INSERM UMR 1163, 75015 Paris, France
| | - Marlene Rio
- Université Paris Cité, Imagine Institute, Developmental Brain Disorders Laboratory, INSERM UMR 1163, 75015 Paris, France; Service de Génétique, Necker Enfants Malades University Hospital, Assistance Publique-Hôpitaux de Pairs, Paris, France
| | - Karine Siquier
- Université Paris Cité, Imagine Institute, Developmental Brain Disorders Laboratory, INSERM UMR 1163, 75015 Paris, France
| | - Nathalie Boddaert
- Département de Radiologie Pédiatrique, INSERM UMR 1163 and INSERM U1000, AP-HP, Hôpital Necker-Enfants Malades, Paris, France
| | - Ilaria Musante
- UOC Genetica Medica, IRCCS Giannina Gaslini, Genoa, Italy
| | | | | | | | - Paolo Scudieri
- UOC Genetica Medica, IRCCS Giannina Gaslini, Genoa, Italy
| | - Jill A Rosenfeld
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX, USA; Baylor Genetics Laboratories, Houston, TX, USA
| | - Gary Bellus
- Clinical Genetics, Geisinger Medical Center, Danville, PA 17822, USA
| | - Sara Reed
- Clinical Genetics, Geisinger Medical Center, Danville, PA 17822, USA
| | - Hind Al Saif
- Department of Human and Molecular Genetics, Division of Clinical Genetics, Virginia Commonwealth University School of Medicine, Richmond, VA, USA
| | | | - Matthew B Walsh
- Department of Human Genetics, Emory University, Atlanta, GA 30322, USA
| | - Vincent Cantagrel
- Université Paris Cité, Imagine Institute, Developmental Brain Disorders Laboratory, INSERM UMR 1163, 75015 Paris, France
| | | | - Stefano Gustincich
- Department of Neuroscience and Brain Technologies, Istituto Italiano di Tecnologia, 16163 Genoa, Italy
| | - Sarah M Ruggiero
- Division of Neurology, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; The Epilepsy NeuroGenetics Initiative (ENGIN), Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Mark P Fitzgerald
- Division of Neurology, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; The Epilepsy NeuroGenetics Initiative (ENGIN), Children's Hospital of Philadelphia, Philadelphia, PA, USA; Department of Neurology, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Ingo Helbig
- Division of Neurology, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; The Epilepsy NeuroGenetics Initiative (ENGIN), Children's Hospital of Philadelphia, Philadelphia, PA, USA; Department of Neurology, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA 19104, USA; Department of Biomedical and Health Informatics (DBHi), Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Pasquale Striano
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health, University of Genoa, Genoa, Italy; Pediatric Neurology and Muscular Diseases Unit, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | | | - Vincenzo Salpietro
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health, University of Genoa, Genoa, Italy; Pediatric Neurology and Muscular Diseases Unit, IRCCS Istituto Giannina Gaslini, Genoa, Italy.
| | | | - Federico Zara
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health, University of Genoa, Genoa, Italy; UOC Genetica Medica, IRCCS Giannina Gaslini, Genoa, Italy
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2
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Shuey MM, Stead WW, Aka I, Barnado AL, Bastarache JA, Brokamp E, Campbell M, Carroll RJ, Goldstein JA, Lewis A, Malow BA, Mosley JD, Osterman T, Padovani-Claudio DA, Ramirez A, Roden DM, Schuler BA, Siew E, Sucre J, Thomsen I, Tinker RJ, Van Driest S, Walsh C, Warner JL, Wells QS, Wheless L, Bastarache L. Next-generation phenotyping: introducing phecodeX for enhanced discovery research in medical phenomics. Bioinformatics 2023; 39:btad655. [PMID: 37930895 PMCID: PMC10627409 DOI: 10.1093/bioinformatics/btad655] [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: 06/09/2023] [Revised: 09/13/2023] [Indexed: 11/08/2023] Open
Abstract
MOTIVATION Phecodes are widely used and easily adapted phenotypes based on International Classification of Diseases codes. The current version of phecodes (v1.2) was designed primarily to study common/complex diseases diagnosed in adults; however, there are numerous limitations in the codes and their structure. RESULTS Here, we present phecodeX, an expanded version of phecodes with a revised structure and 1,761 new codes. PhecodeX adds granularity to phenotypes in key disease domains that are under-represented in the current phecode structure-including infectious disease, pregnancy, congenital anomalies, and neonatology-and is a more robust representation of the medical phenome for global use in discovery research. AVAILABILITY AND IMPLEMENTATION phecodeX is available at https://github.com/PheWAS/phecodeX.
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Affiliation(s)
- Megan M Shuey
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37203, United States
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN 37203, United States
| | - William W Stead
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN 37203, United States
| | - Ida Aka
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN 37203, United States
| | - April L Barnado
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN 37203, United States
| | - Julie A Bastarache
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37203, United States
| | - Elly Brokamp
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN 37203, United States
| | - Meredith Campbell
- Department of Pediatrics, Virginia Commonwealth University, Richmond, VA 23219, United States
| | - Robert J Carroll
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN 37203, United States
| | - Jeffrey A Goldstein
- Department of Pathology, Northwestern Feinberg School of Medicine, Chicago, IL 60611, United States
| | - Adam Lewis
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN 37203, United States
| | - Beth A Malow
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37203, United States
| | - Jonathan D Mosley
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37203, United States
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN 37203, United States
| | - Travis Osterman
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN 37203, United States
| | - Dolly A Padovani-Claudio
- Department of Ophthalmology, Vanderbilt University Medical Center, Nashville, TN 37232, United States
| | - Andrea Ramirez
- All of Us Research Program, National Institutes of Health, Bethesda, MD 20892, United States
| | - Dan M Roden
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37203, United States
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN 37203, United States
| | - Bryce A Schuler
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN 37203, United States
| | - Edward Siew
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37203, United States
| | - Jennifer Sucre
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN 37203, United States
| | - Isaac Thomsen
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN 37203, United States
| | - Rory J Tinker
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN 37203, United States
| | - Sara Van Driest
- All of Us Research Program, National Institutes of Health, Bethesda, MD 20892, United States
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN 37203, United States
| | - Colin Walsh
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN 37203, United States
| | - Jeremy L Warner
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN 37203, United States
| | - Quinn S Wells
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37203, United States
| | - Lee Wheless
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37203, United States
| | - Lisa Bastarache
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN 37203, United States
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3
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Ganapathi M, Matsuoka LS, March M, Li D, Brokamp E, Benito-Sanz S, White SM, Lachlan K, Ahimaz P, Sewda A, Bastarache L, Thomas-Wilson A, Stoler JM, Bramswig NC, Baptista J, Stals K, Demurger F, Cogne B, Isidor B, Bedeschi MF, Peron A, Amiel J, Zackai E, Schacht JP, Iglesias AD, Morton J, Schmetz A, Seidel V, Lucia S, Baskin SM, Thiffault I, Cogan JD, Gordon CT, Chung WK, Bowdin S, Bhoj E. Heterozygous rare variants in NR2F2 cause a recognizable multiple congenital anomaly syndrome with developmental delays. Eur J Hum Genet 2023; 31:1117-1124. [PMID: 37500725 PMCID: PMC10545729 DOI: 10.1038/s41431-023-01434-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [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: 02/08/2023] [Revised: 06/07/2023] [Accepted: 07/11/2023] [Indexed: 07/29/2023] Open
Abstract
Nuclear receptor subfamily 2 group F member 2 (NR2F2 or COUP-TF2) encodes a transcription factor which is expressed at high levels during mammalian development. Rare heterozygous Mendelian variants in NR2F2 were initially identified in individuals with congenital heart disease (CHD), then subsequently in cohorts of congenital diaphragmatic hernia (CDH) and 46,XX ovotesticular disorders/differences of sexual development (DSD); however, the phenotypic spectrum associated with pathogenic variants in NR2F2 remains poorly characterized. Currently, less than 40 individuals with heterozygous pathogenic variants in NR2F2 have been reported. Here, we review the clinical and molecular details of 17 previously unreported individuals with rare heterozygous NR2F2 variants, the majority of which were de novo. Clinical features were variable, including intrauterine growth restriction (IUGR), CHD, CDH, genital anomalies, DSD, developmental delays, hypotonia, feeding difficulties, failure to thrive, congenital and acquired microcephaly, dysmorphic facial features, renal failure, hearing loss, strabismus, asplenia, and vascular malformations, thus expanding the phenotypic spectrum associated with NR2F2 variants. The variants seen were predicted loss of function, including a nonsense variant inherited from a mildly affected mosaic mother, missense and a large deletion including the NR2F2 gene. Our study presents evidence for rare, heterozygous NR2F2 variants causing a highly variable syndrome of congenital anomalies, commonly associated with heart defects, developmental delays/intellectual disability, dysmorphic features, feeding difficulties, hypotonia, and genital anomalies. Based on the new and previous cases, we provide clinical recommendations for evaluating individuals diagnosed with an NR2F2-associated disorder.
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Affiliation(s)
- Mythily Ganapathi
- Department of Pathology & Cell Biology, Columbia University Irving Medical Center, New York, NY, USA
| | | | - Michael March
- Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Dong Li
- Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Elly Brokamp
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Sara Benito-Sanz
- CIBERER, ISCIII. Institute of Medical and Molecular Genetics (INGEMM), Disorder of Sex Development Multidisciplinary Unit, Hospital Universitario La Paz, Madrid, Spain
| | - Susan M White
- Victorian Clinical Genetics Service, Murdoch Children's Research Institute, Melbourne, VIC, Australia
- Department of Pediatrics, University of Melbourne, Melbourne, VIC, Australia
| | - Katherine Lachlan
- Wessex Clinical Genetics Service, University Hospital Southampton NHS Trust, Southampton, UK
- Department of Human Genetics and Genomic Medicine, Southampton University, Southampton, UK
| | - Priyanka Ahimaz
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY, USA
| | - Anshuman Sewda
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY, USA
| | - Lisa Bastarache
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Amanda Thomas-Wilson
- Department of Pathology & Cell Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Joan M Stoler
- Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Nuria C Bramswig
- Institute of Human Genetics, Medical Faculty and University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, 40225, Düsseldorf, Germany
| | - Julia Baptista
- Exeter Genomics Laboratory, Royal Devon & Exeter NHS Foundation Trust, Exeter, UK
- Peninsula Medical School, Faculty of Health, University of Plymouth, PL4 8AA, Plymouth, UK
| | - Karen Stals
- Exeter Genomics Laboratory, Royal Devon & Exeter NHS Foundation Trust, Exeter, UK
| | | | - Benjamin Cogne
- Nantes Université, CHU de Nantes, CNRS, INSERM, l'institut du thorax, F-44000, Nantes, France
- Nantes Université, CHU de Nantes, Service de Génétique médicale, F-44000, Nantes, France
| | - Bertrand Isidor
- Nantes Université, CHU de Nantes, CNRS, INSERM, l'institut du thorax, F-44000, Nantes, France
- Nantes Université, CHU de Nantes, Service de Génétique médicale, F-44000, Nantes, France
| | | | - Angela Peron
- Medical Genetics, ASST Santi Paolo e Carlo, San Paolo Hospital, Università degli Studi di Milano, Milan, Italy
- Division of Medical Genetics, Department of Pediatrics, University of Utah, Salt Lake City, UT, USA
| | - Jeanne Amiel
- INSERM UMR1163, Institut Imagine, Université Paris-Cité, Paris, France
- Service de Médecine Génomique des Maladies Rares, Hôpital Necker-Enfants Malades, AP-HP, Paris, France
| | - Elaine Zackai
- Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - John P Schacht
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY, USA
| | - Alejandro D Iglesias
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY, USA
| | - Jenny Morton
- West Midlands Regional Clinical Genetics Service and Birmingham Health Partners, Birmingham Women's and Children's Hospitals NHS Foundation Trust, Birmingham, UK
| | - Ariane Schmetz
- Institute of Human Genetics, Medical Faculty and University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, 40225, Düsseldorf, Germany
| | - Verónica Seidel
- Clinical Genetics, Department of Pediatrics, Gregorio Marañón General University Hospital, Madrid, Spain
| | - Stephanie Lucia
- Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Stephanie M Baskin
- Department of Pediatrics, Baylor College of Medicine, San Antonio, TX, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Isabelle Thiffault
- Genomic Medicine Center, Children's Mercy Hospital, Kansas City, MO, USA
| | - Joy D Cogan
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN, USA
| | | | - Wendy K Chung
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY, USA
| | - Sarah Bowdin
- Department of Clinical Genetics, Addenbrooke's Hospital, Cambridge University Hospitals NHS, Foundation Trust, Cambridge, UK
| | - Elizabeth Bhoj
- Children's Hospital of Philadelphia, Philadelphia, PA, USA.
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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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Appelbaum PS, Berger SM, Brokamp E, Brown HS, Burke W, Clayton EW, Evans BJ, Hamid R, Marchant GE, Martin DM, O'Connor BC, Pagán JA, Parens E, Roberts JL, Rowe J, Schneider J, Siegel K, Veenstra DL, Chung WK. Practical considerations for reinterpretation of individual genetic variants. Genet Med 2023; 25:100801. [PMID: 36748709 PMCID: PMC10408279 DOI: 10.1016/j.gim.2023.100801] [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: 08/29/2022] [Revised: 01/30/2023] [Accepted: 02/01/2023] [Indexed: 02/05/2023] Open
Abstract
With the growing use of genetic testing in medicine, the question of when genetic findings should be reinterpreted in light of new data has become inescapable. The generation of population and disease-specific data, development of computational tools, and new understandings of the relationship of specific genes to disorders can all trigger changes in variant classification that may have important implications for patients and the clinicians caring for them. This is a particular concern for patients from groups underrepresented in current reference datasets, since they have higher rates of uncertain findings. Here we identify the challenges to implementing a systematic approach to variant reinterpretation and propose solutions. In particular, we address (a) the infrastructure needed to support implementation of systematic variant reinterpretation, (b) the issues around obtaining consent from patients for reinterpretation, (c) the process for triggering reinterpretation, (d) pathways for the flow of reinterpreted data, (e) considerations for how to cover the costs of reinterpretation, and (f) practical issues related to implementation of processes and policies that address these issues, including the importance of a fixed duration during which there is an expectation that variants will be reinterpreted.
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Affiliation(s)
- Paul S Appelbaum
- Department of Psychiatry, Columbia University Irving Medical Center, New York, NY
| | - Sara M Berger
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY
| | - Elly Brokamp
- Vanderbilt Genomics Institute, Vanderbilt University Medical Center, Nashville, TN
| | - Henry Shelton Brown
- Management, Policy and Community Health, UT Health School of Public Health, University of Texas Health Science Center at Houston, Austin Regional Campus, Austin, TX
| | - Wylie Burke
- Department of Bioethics and Humanities, University of Washington, Seattle, WA
| | - Ellen Wright Clayton
- Center for Biomedical Ethics and Society, Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN; Center for Biomedical Ethics and Society, School of Law, Vanderbilt University, Nashville, TN
| | - Barbara J Evans
- Levin College of Law, University of Florida, Gainesville, FL; Wertheim College of Engineering, University of Florida, Gainesville, FL
| | - Rizwan Hamid
- Division of Medical Genetics and Genomic Medicine, Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN
| | - Gary E Marchant
- Center for Law, Science & Innovation, Sandra Day O'Connor School of Law, Arizona State University, Phoenix, AZ
| | - Donna M Martin
- Departments of Pediatrics and Human Genetics, University of Michigan Medical School, Ann Arbor, MI
| | | | - José A Pagán
- Department of Public Health Policy and Management, School of Global Public Health, New York University, New York, NY
| | - Erik Parens
- Hastings Center Initiative in Bioethics, The Hastings Center, Garrison, NY
| | - Jessica L Roberts
- Health Law & Policy Institute Humanities, University of Houston Law Center, Houston, TX; College of Medicine, University of Houston, Houston, TX
| | - John Rowe
- Department of Health Policy and Management, Mailman School of Public Health, Columbia University, New York, NY
| | | | - Karolynn Siegel
- Department of Sociomedical Sciences, Mailman School of Public Health, Columbia University Irving Medical Center, New York, NY
| | - David L Veenstra
- The Comparative Health Outcomes, Policy and Economics (CHOICE) Institute, School of Pharmacy, University of Washington, Seattle, WA
| | - Wendy K Chung
- Departments of Pediatrics and Medicine, Columbia University Irving Medical Center, New York, NY.
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6
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Srivastava S, Shaked HM, Gable K, Gupta SD, Pan X, Somashekarappa N, Han G, Mohassel P, Gotkine M, Doney E, Goldenberg P, Tan QKG, Gong Y, Kleinstiver B, Wishart B, Cope H, Pires CB, Stutzman H, Spillmann RC, Sadjadi R, Elpeleg O, Lee CH, Bellen HJ, Edvardson S, Eichler F, Dunn TM, Dai H, Dhar SU, Emrick LT, Goldman AM, Hanchard NA, Jamal F, Karaviti L, Lalani SR, Lee BH, Lewis RA, Marom R, Moretti PM, Murdock DR, Nicholas SK, Orengo JP, Posey JE, Potocki L, Rosenfeld JA, Samson SL, Scott DA, Tran AA, Vogel TP, Wangler MF, Yamamoto S, Eng CM, Liu P, Ward PA, Behrens E, Deardorff M, Falk M, Hassey K, Sullivan K, Vanderver A, Goldstein DB, Cope H, McConkie-Rosell A, Schoch K, Shashi V, Smith EC, Spillmann RC, Sullivan JA, Tan QKG, Walley NM, Agrawal PB, Beggs AH, Berry GT, Briere LC, Cobban LA, Coggins M, Cooper CM, Fieg EL, High F, Holm IA, Korrick S, Krier JB, Lincoln SA, Loscalzo J, Maas RL, MacRae CA, Pallais JC, Rao DA, Rodan LH, Silverman EK, Stoler JM, Sweetser DA, Walker M, Walsh CA, Esteves C, Kelley EG, Kohane IS, LeBlanc K, McCray AT, Nagy A, Dasari S, Lanpher BC, Lanza IR, Morava E, Oglesbee D, Bademci G, Barbouth D, Bivona S, Carrasquillo O, Chang TCP, Forghani I, Grajewski A, Isasi R, Lam B, Levitt R, Liu XZ, McCauley J, Sacco R, Saporta M, Schaechter J, Tekin M, Telischi F, Thorson W, Zuchner S, Colley HA, Dayal JG, Eckstein DJ, Findley LC, Krasnewich DM, Mamounas LA, Manolio TA, Mulvihill JJ, LaMoure GL, Goldrich MP, Urv TK, Doss AL, Acosta MT, Bonnenmann C, D’Souza P, Draper DD, Ferreira C, Godfrey RA, Groden CA, Macnamara EF, Maduro VV, Markello TC, Nath A, Novacic D, Pusey BN, Toro C, Wahl CE, Baker E, Burke EA, Adams DR, Gahl WA, Malicdan MCV, Tifft CJ, Wolfe LA, Yang J, Power B, Gochuico B, Huryn L, Latham L, Davis J, Mosbrook-Davis D, Rossignol F, Solomon B, MacDowall J, Thurm A, Zein W, Yousef M, Adam M, Amendola L, Bamshad M, Beck A, Bennett J, Berg-Rood B, Blue E, Boyd B, Byers P, Chanprasert S, Cunningham M, Dipple K, Doherty D, Earl D, Glass I, Golden-Grant K, Hahn S, Hing A, Hisama FM, Horike-Pyne M, Jarvik GP, Jarvik J, Jayadev S, Lam C, Maravilla K, Mefford H, Merritt JL, Mirzaa G, Nickerson D, Raskind W, Rosenwasser N, Scott CR, Sun A, Sybert V, Wallace S, Wener M, Wenger T, Ashley EA, Bejerano G, Bernstein JA, Bonner D, Coakley TR, Fernandez L, Fisher PG, Fresard L, Hom J, Huang Y, Kohler JN, Kravets E, Majcherska MM, Martin BA, Marwaha S, McCormack CE, Raja AN, Reuter CM, Ruzhnikov M, Sampson JB, Smith KS, Sutton S, Tabor HK, Tucker BM, Wheeler MT, Zastrow DB, Zhao C, Byrd WE, Crouse AB, Might M, Nakano-Okuno M, Whitlock J, Brown G, Butte MJ, Dell’Angelica EC, Dorrani N, Douine ED, Fogel BL, Gutierrez I, Huang A, Krakow D, Lee H, Loo SK, Mak BC, Martin MG, Martínez-Agosto JA, McGee E, Nelson SF, Nieves-Rodriguez S, Palmer CGS, Papp JC, Parker NH, Renteria G, Signer RH, Sinsheimer JS, Wan J, Wang LK, Perry KW, Woods JD, Alvey J, Andrews A, Bale J, Bohnsack J, Botto L, Carey J, Pace L, Longo N, Marth G, Moretti P, Quinlan A, Velinder M, Viskochi D, Bayrak-Toydemir P, Mao R, Westerfield M, Bican A, Brokamp E, Duncan L, Hamid R, Kennedy J, Kozuira M, Newman JH, PhillipsIII JA, Rives L, Robertson AK, Solem E, Cogan JD, Cole FS, Hayes N, Kiley D, Sisco K, Wambach J, Wegner D, Baldridge D, Pak S, Schedl T, Shin J, Solnica-Krezel L, Sadjadi R, Elpeleg O, Lee CH, Bellen HJ, Edvardson S, Eichler F, Dunn TM. SPTSSA variants alter sphingolipid synthesis and cause a complex hereditary spastic paraplegia. Brain 2023; 146:1420-1435. [PMID: 36718090 PMCID: PMC10319774 DOI: 10.1093/brain/awac460] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [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: 06/17/2022] [Revised: 11/03/2022] [Accepted: 11/19/2022] [Indexed: 02/01/2023] Open
Abstract
Sphingolipids are a diverse family of lipids with critical structural and signalling functions in the mammalian nervous system, where they are abundant in myelin membranes. Serine palmitoyltransferase, the enzyme that catalyses the rate-limiting reaction of sphingolipid synthesis, is composed of multiple subunits including an activating subunit, SPTSSA. Sphingolipids are both essential and cytotoxic and their synthesis must therefore be tightly regulated. Key to the homeostatic regulation are the ORMDL proteins that are bound to serine palmitoyltransferase and mediate feedback inhibition of enzymatic activity when sphingolipid levels become excessive. Exome sequencing identified potential disease-causing variants in SPTSSA in three children presenting with a complex form of hereditary spastic paraplegia. The effect of these variants on the catalytic activity and homeostatic regulation of serine palmitoyltransferase was investigated in human embryonic kidney cells, patient fibroblasts and Drosophila. Our results showed that two different pathogenic variants in SPTSSA caused a hereditary spastic paraplegia resulting in progressive motor disturbance with variable sensorineural hearing loss and language/cognitive dysfunction in three individuals. The variants in SPTSSA impaired the negative regulation of serine palmitoyltransferase by ORMDLs leading to excessive sphingolipid synthesis based on biochemical studies and in vivo studies in Drosophila. These findings support the pathogenicity of the SPTSSA variants and point to excessive sphingolipid synthesis due to impaired homeostatic regulation of serine palmitoyltransferase as responsible for defects in early brain development and function.
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Affiliation(s)
- Siddharth Srivastava
- Department of Neurology, Rosamund Stone Zander Translational Neuroscience Center, BostonChildren's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Hagar Mor Shaked
- Department of Genetics, Hadassah Medical Center and Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem 91120, Israel
| | - Kenneth Gable
- Department of Biochemistry and Molecular Biology, Uniformed Services University of the Health Sciences, Bethesda, MD 20814, USA
| | - Sita D Gupta
- Department of Biochemistry and Molecular Biology, Uniformed Services University of the Health Sciences, Bethesda, MD 20814, USA
| | - Xueyang Pan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.,Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX 77030, USA
| | - Niranjanakumari Somashekarappa
- Department of Biochemistry and Molecular Biology, Uniformed Services University of the Health Sciences, Bethesda, MD 20814, USA
| | - Gongshe Han
- Department of Biochemistry and Molecular Biology, Uniformed Services University of the Health Sciences, Bethesda, MD 20814, USA
| | - Payam Mohassel
- Neuromuscular and Neurogenetic Disorders of Childhood Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20814, USA
| | - Marc Gotkine
- Department of Genetics, Hadassah Medical Center and Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem 91120, Israel
| | | | - Paula Goldenberg
- Department of Pediatrics, Section on Medical Genetics, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Queenie K G Tan
- Department of Pediatrics, Division of Medical Genetics, Duke University School of Medicine, Durham, NC 27710, USA
| | - Yi Gong
- Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA.,Center for Genomic Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Benjamin Kleinstiver
- Center for Genomic Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA.,Department of Pathology, Massachusetts General Hospital, Boston, MA 02114, USA.,Department of Pathology, Harvard Medical School, Boston, MA 02115, USA
| | - Brian Wishart
- Physical Medicine and Rehabilitation, Spaulding Rehabilitation Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Heidi Cope
- Department of Pediatrics, Division of Medical Genetics, Duke University School of Medicine, Durham, NC 27710, USA
| | - Claudia Brito Pires
- Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA.,Center for Genomic Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Hannah Stutzman
- Center for Genomic Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA.,Department of Pathology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Rebecca C Spillmann
- Department of Pediatrics, Division of Medical Genetics, Duke University School of Medicine, Durham, NC 27710, USA
| | | | - Reza Sadjadi
- Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Orly Elpeleg
- Department of Genetics, Hadassah Medical Center and Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem 91120, Israel
| | - Chia-Hsueh Lee
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Hugo J Bellen
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.,Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX 77030, USA
| | - Simon Edvardson
- Pediatric Neurology Unit, Hadassah University Hospital, Mount Scopus, Jerusalem 91240, Israel
| | - Florian Eichler
- Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA.,Center for Genomic Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Teresa M Dunn
- Department of Biochemistry and Molecular Biology, Uniformed Services University of the Health Sciences, Bethesda, MD 20814, USA
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- Department of Neurology, Massachusetts General Hospital, Harvard Medical School , Boston, MA 02114 , USA
| | - Orly Elpeleg
- Department of Genetics, Hadassah Medical Center and Faculty of Medicine, Hebrew University of Jerusalem , Jerusalem 91120 , Israel
| | - Chia-Hsueh Lee
- Department of Structural Biology, St. Jude Children’s Research Hospital , Memphis, TN 38105 , USA
| | - Hugo J Bellen
- Department of Molecular and Human Genetics, Baylor College of Medicine , Houston, TX 77030 , USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital , Houston, TX 77030 , USA
| | - Simon Edvardson
- Pediatric Neurology Unit, Hadassah University Hospital, Mount Scopus , Jerusalem 91240 , Israel
| | - Florian Eichler
- Department of Neurology, Massachusetts General Hospital, Harvard Medical School , Boston, MA 02114 , USA
- Center for Genomic Medicine, Massachusetts General Hospital, Harvard Medical School , Boston, MA 02114 , USA
| | - Teresa M Dunn
- Department of Biochemistry and Molecular Biology, Uniformed Services University of the Health Sciences , Bethesda, MD 20814 , USA
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7
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Morimoto M, Bhambhani V, Gazzaz N, Davids M, Sathiyaseelan P, Macnamara EF, Lange J, Lehman A, Zerfas PM, Murphy JL, Acosta MT, Wang C, Alderman E, Reichert S, Thurm A, Adams DR, Introne WJ, Gorski SM, Boerkoel CF, Gahl WA, Tifft CJ, Malicdan MCV, Baldridge D, Bale J, Bamshad M, Barbouth D, Bayrak-Toydemir P, Beck A, Beggs AH, Behrens E, Bejerano G, Bellen HJ, Bennett J, Berg-Rood B, Bernstein JA, Berry GT, Bican A, Bivona S, Blue E, Bohnsack J, Bonner D, Botto L, Boyd B, Briere LC, Brokamp E, Brown G, Burke EA, Burrage LC, Butte MJ, Byers P, Byrd WE, Carey J, Carrasquillo O, Cassini T, Chang TCP, Chanprasert S, Chao HT, Clark GD, Coakley TR, Cobban LA, Cogan JD, Coggins M, Cole FS, Colley HA, Cooper CM, Cope H, Craigen WJ, Crouse AB, Cunningham M, D’Souza P, Dai H, Dasari S, Davis J, Dayal JG, Dell’Angelica EC, Dipple K, Doherty D, Dorrani N, Doss AL, Douine ED, Duncan L, Earl D, Eckstein DJ, Emrick LT, Eng CM, Esteves C, Falk M, Fieg EL, Fisher PG, Fogel BL, Forghani I, Glass I, Gochuico B, Goddard PC, Godfrey RA, Golden-Grant K, Grajewski A, Gutierrez I, Hadley D, Hahn S, Halley MC, Hamid R, Hassey K, Hayes N, High F, Hing A, Hisama FM, Holm IA, Hom J, Horike-Pyne M, Huang A, Hutchison S, Introne WJ, Isasi R, Izumi K, Jamal F, Jarvik GP, Jarvik J, Jayadev S, Jean-Marie O, Jobanputra V, Karaviti L, Kennedy J, Ketkar S, Kiley D, Kilich G, Kobren SN, Kohane IS, Kohler JN, Korrick S, Kozuira M, Krakow D, Krasnewich DM, Kravets E, Lalani SR, Lam B, Lam C, Lanpher BC, Lanza IR, LeBlanc K, Lee BH, Levitt R, Lewis RA, Liu P, Liu XZ, Longo N, Loo SK, Loscalzo J, Maas RL, MacRae CA, Maduro VV, Mahoney R, Mak BC, Mamounas LA, Manolio TA, Mao R, Maravilla K, Marom R, Marth G, Martin BA, Martin MG, Martínez-Agosto JA, Marwaha S, McCauley J, McConkie-Rosell A, McCray AT, McGee E, Mefford H, Merritt JL, Might M, Mirzaa G, Morava E, Moretti P, Nakano-Okuno M, Nelson SF, Newman JH, Nicholas SK, Nickerson D, Nieves-Rodriguez S, Novacic D, Oglesbee D, Orengo JP, Pace L, Pak S, Pallais JC, Palmer CGS, Papp JC, Parker NH, Phillips JA, Posey JE, Potocki L, Pusey Swerdzewski BN, Quinlan A, Rao DA, Raper A, Raskind W, Renteria G, Reuter CM, Rives L, Robertson AK, Rodan LH, Rosenfeld JA, Rosenwasser N, Rossignol F, Ruzhnikov M, Sacco R, Sampson JB, Saporta M, Schaechter J, Schedl T, Schoch K, Scott DA, Scott CR, Shashi V, Shin J, Silverman EK, Sinsheimer JS, Sisco K, Smith EC, Smith KS, Solem E, Solnica-Krezel L, Solomon B, Spillmann RC, Stoler JM, Sullivan K, Sullivan JA, Sun A, Sutton S, Sweetser DA, Sybert V, Tabor HK, Tan QKG, Tan ALM, Tekin M, Telischi F, Thorson W, Toro C, Tran AA, Ungar RA, Urv TK, Vanderver A, Velinder M, Viskochil D, Vogel TP, Wahl CE, Walker M, Wallace S, Walley NM, Wambach J, Wan J, Wang LK, Wangler MF, Ward PA, Wegner D, Weisz Hubshman M, Wener M, Wenger T, Wesseling Perry K, Westerfield M, Wheeler MT, Whitlock J, Wolfe LA, Worley K, Xiao C, Yamamoto S, Yang J, Zhang Z, Zuchner S, Reichert S, Thurm A, Adams DR, Introne WJ, Gorski SM, Boerkoel CF, Gahl WA, Tifft CJ, Malicdan MCV. Bi-allelic ATG4D variants are associated with a neurodevelopmental disorder characterized by speech and motor impairment. NPJ Genom Med 2023; 8:4. [PMID: 36765070 PMCID: PMC9918471 DOI: 10.1038/s41525-022-00343-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Accepted: 12/06/2022] [Indexed: 02/12/2023] Open
Abstract
Autophagy regulates the degradation of damaged organelles and protein aggregates, and is critical for neuronal development, homeostasis, and maintenance, yet few neurodevelopmental disorders have been associated with pathogenic variants in genes encoding autophagy-related proteins. We report three individuals from two unrelated families with a neurodevelopmental disorder characterized by speech and motor impairment, and similar facial characteristics. Rare, conserved, bi-allelic variants were identified in ATG4D, encoding one of four ATG4 cysteine proteases important for autophagosome biogenesis, a hallmark of autophagy. Autophagosome biogenesis and induction of autophagy were intact in cells from affected individuals. However, studies evaluating the predominant substrate of ATG4D, GABARAPL1, demonstrated that three of the four ATG4D patient variants functionally impair ATG4D activity. GABARAPL1 is cleaved or "primed" by ATG4D and an in vitro GABARAPL1 priming assay revealed decreased priming activity for three of the four ATG4D variants. Furthermore, a rescue experiment performed in an ATG4 tetra knockout cell line, in which all four ATG4 isoforms were knocked out by gene editing, showed decreased GABARAPL1 priming activity for the two ATG4D missense variants located in the cysteine protease domain required for priming, suggesting that these variants impair the function of ATG4D. The clinical, bioinformatic, and functional data suggest that bi-allelic loss-of-function variants in ATG4D contribute to the pathogenesis of this syndromic neurodevelopmental disorder.
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Affiliation(s)
- Marie Morimoto
- grid.94365.3d0000 0001 2297 5165National Institutes of Health Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, MD 20892 USA
| | - Vikas Bhambhani
- grid.418506.e0000 0004 0629 5022Department of Medical Genetics, Children’s Hospitals and Clinics of Minnesota, Minneapolis, MN 55404 USA
| | - Nour Gazzaz
- grid.17091.3e0000 0001 2288 9830Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, BC V6H 3N1 Canada ,grid.414137.40000 0001 0684 7788Provincial Medical Genetics Program, British Columbia Women’s and Children’s Hospital, Vancouver, BC V6H 3N1 Canada ,grid.412125.10000 0001 0619 1117Department of Pediatrics, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Mariska Davids
- grid.94365.3d0000 0001 2297 5165National Institutes of Health Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, MD 20892 USA
| | - Paalini Sathiyaseelan
- grid.434706.20000 0004 0410 5424Canada’s Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC V5Z 1L3 Canada ,grid.61971.380000 0004 1936 7494Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC V5A 1S6 Canada
| | - Ellen F. Macnamara
- grid.94365.3d0000 0001 2297 5165National Institutes of Health Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, MD 20892 USA
| | | | - Anna Lehman
- grid.17091.3e0000 0001 2288 9830Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, BC V6H 3N1 Canada
| | - Patricia M. Zerfas
- grid.94365.3d0000 0001 2297 5165Diagnostic and Research Services Branch, Office of Research Services, National Institutes of Health, Bethesda, MD 20892 USA
| | - Jennifer L. Murphy
- grid.94365.3d0000 0001 2297 5165National Institutes of Health Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, MD 20892 USA
| | - Maria T. Acosta
- grid.94365.3d0000 0001 2297 5165National Institutes of Health Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, MD 20892 USA
| | - Camille Wang
- grid.94365.3d0000 0001 2297 5165National Institutes of Health Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, MD 20892 USA
| | - Emily Alderman
- grid.17091.3e0000 0001 2288 9830Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, BC V6H 3N1 Canada ,grid.414137.40000 0001 0684 7788Provincial Medical Genetics Program, British Columbia Women’s and Children’s Hospital, Vancouver, BC V6H 3N1 Canada
| | | | - Sara Reichert
- grid.418506.e0000 0004 0629 5022Department of Medical Genetics, Children’s Hospitals and Clinics of Minnesota, Minneapolis, MN 55404 USA
| | - Audrey Thurm
- grid.94365.3d0000 0001 2297 5165Neurodevelopmental and Behavioral Phenotyping Service, Office of the Clinical Director, National Institute of Mental Health, National Institutes of Health, Bethesda, MD 20892 USA
| | - David R. Adams
- grid.94365.3d0000 0001 2297 5165National Institutes of Health Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, MD 20892 USA ,grid.94365.3d0000 0001 2297 5165Office of the Clinical Director, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892 USA
| | - Wendy J. Introne
- grid.94365.3d0000 0001 2297 5165National Institutes of Health Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, MD 20892 USA ,grid.94365.3d0000 0001 2297 5165Office of the Clinical Director, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892 USA ,grid.94365.3d0000 0001 2297 5165Human Biochemical Genetics Section, Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892 USA
| | - Sharon M. Gorski
- grid.17091.3e0000 0001 2288 9830Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, BC V6H 3N1 Canada ,grid.434706.20000 0004 0410 5424Canada’s Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC V5Z 1L3 Canada ,grid.61971.380000 0004 1936 7494Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC V5A 1S6 Canada
| | - Cornelius F. Boerkoel
- grid.17091.3e0000 0001 2288 9830Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, BC V6H 3N1 Canada ,grid.414137.40000 0001 0684 7788Provincial Medical Genetics Program, British Columbia Women’s and Children’s Hospital, Vancouver, BC V6H 3N1 Canada
| | - William A. Gahl
- grid.94365.3d0000 0001 2297 5165National Institutes of Health Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, MD 20892 USA ,grid.94365.3d0000 0001 2297 5165Human Biochemical Genetics Section, Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892 USA
| | - Cynthia J. Tifft
- grid.94365.3d0000 0001 2297 5165National Institutes of Health Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, MD 20892 USA ,grid.94365.3d0000 0001 2297 5165Office of the Clinical Director, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892 USA
| | - May Christine V. Malicdan
- grid.94365.3d0000 0001 2297 5165National Institutes of Health Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, MD 20892 USA ,grid.94365.3d0000 0001 2297 5165Human Biochemical Genetics Section, Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892 USA
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Miller IM, Yashar BM, Macnamara EF, Adams DR, Agrawal PB, Alvey J, Amendola L, Andrews A, Ashley EA, Azamian MS, Bacino CA, Bademci G, Baker E, Balasubramanyam A, Baldridge D, Bale J, Bamshad M, Barbouth D, Bayrak-Toydemir P, Beck A, Beggs AH, Behrens E, Bejerano G, Bellen HJ, Bennett J, Berg-Rood B, Bernstein JA, Berry GT, Bican A, Bivona S, Blue E, Bohnsack J, Bonnenmann C, Bonner D, Botto L, Boyd B, Briere LC, Brokamp E, Brown G, Burke EA, Burrage LC, Butte MJ, Byers P, Byrd WE, Carey J, Carrasquillo O, Chang TCP, Chanprasert S, Chao HT, Clark GD, Coakley TR, Cobban LA, Cogan JD, Coggins M, Cole FS, Colley HA, Cooper CM, Cope H, Craigen WJ, Crouse AB, Cunningham M, D’Souza P, Dai H, Dasari S, Davis J, Dayal JG, Dell’Angelica EC, Dipple K, Doherty D, Dorrani N, Doss AL, Douine ED, Draper DD, Duncan L, Earl D, Eckstein DJ, Emrick LT, Eng CM, Esteves C, Falk M, Fernandez L, Ferreira C, Fieg EL, Findley LC, Fisher PG, Fogel BL, Forghani I, Gahl WA, Glass I, Gochuico B, Godfrey RA, Golden-Grant K, Goldrich MP, Goldstein DB, Grajewski A, Groden CA, Gutierrez I, Hahn S, Hamid R, Hassey K, Hayes N, High F, Hing A, Hisama FM, Holm IA, Hom J, Horike-Pyne M, Huang Y, Huang A, Huryn L, Isasi R, Izumi K, Jamal F, Jarvik GP, Jarvik J, Jayadev S, Karaviti L, Kennedy J, Ketkar S, Kiley D, Kilich G, Kobren SN, Kohane IS, Kohler JN, Korrick S, Kozuira M, Krakow D, Krasnewich DM, Kravets E, Krier JB, Lalani SR, Lam B, Lam C, LaMoure GL, Lanpher BC, Lanza IR, Latham L, LeBlanc K, Lee BH, Lee H, Levitt R, Lewis RA, Lincoln SA, Liu P, Liu XZ, Longo N, Loo SK, Loscalzo J, Maas RL, MacDowall J, Macnamara EF, MacRae CA, Maduro VV, Mahoney R, Mak BC, Malicdan MCV, Mamounas LA, Manolio TA, Mao R, Maravilla K, Markello TC, Marom R, Marth G, Martin BA, Martin MG, Martfnez-Agosto JA, Marwaha S, McCauley J, McConkie-Rosell A, McCray AT, McGee E, Mefford H, Merritt JL, Might M, Mirzaa G, Morava E, Moretti PM, Moretti P, Mosbrook-Davis D, Mulvihill JJ, Nakano-Okuno M, Nath A, Nelson SF, Newman JH, Nicholas SK, Nickerson D, Nieves-Rodriguez S, Novacic D, Oglesbee D, Orengo JP, Pace L, Pak S, Pallais JC, Palmer CGS, Papp JC, Parker NH, Phillips JA, Posey JE, Potocki L, Power B, Pusey BN, Quinlan A, Raja AN, Rao DA, Raper A, Raskind W, Renteria G, Reuter CM, Rives L, Robertson AK, Rodan LH, Rosenfeld JA, Rosenwasser N, Rossignol F, Ruzhnikov M, Sacco R, Sampson JB, Saporta M, Schaechter J, Schedl T, Schoch K, Scott DA, Scott CR, Shashi V, Shin J, Signer RH, Silverman EK, Sinsheimer JS, Sisco K, Smith EC, Smith KS, Solem E, Solnica-Krezel L, Solomon B, Spillmann RC, Stoler JM, Sullivan K, Sullivan JA, Sun A, Sutton S, Sweetser DA, Sybert V, Tabor HK, Tan QKG, Tan ALM, Tekin M, Telischi F, Thorson W, Thurm A, Tifft CJ, Toro C, Tran AA, Tucker BM, Urv TK, Vanderver A, Velinder M, Viskochil D, Vogel TP, Wahl CE, Walker M, Wallace S, Walley NM, Walsh CA, Wambach J, Wan J, Wang LK, Wangler MF, Ward PA, Wegner D, Hubshman MW, Wener M, Wenger T, Perry KW, Westerfield M, Wheeler MT, Whitlock J, Wolfe LA, Woods JD, Worley K, Yamamoto S, Yang J, Yousef M, Zastrow DB, Zein W, Zhang Z, Zhao C, Zuchner S, Macnamara EF. Continuing a search for a diagnosis: the impact of adolescence and family dynamics. Orphanet J Rare Dis 2023; 18:6. [PMID: 36624503 PMCID: PMC9830697 DOI: 10.1186/s13023-022-02598-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Accepted: 12/14/2022] [Indexed: 01/11/2023] Open
Abstract
The "diagnostic odyssey" describes the process those with undiagnosed conditions undergo to identify a diagnosis. Throughout this process, families of children with undiagnosed conditions have multiple opportunities to decide whether to continue or stop their search for a diagnosis and accept the lack of a diagnostic label. Previous studies identified factors motivating a family to begin searching, but there is limited information about the decision-making process in a prolonged search and how the affected child impacts a family's decision. This study aimed to understand how families of children with undiagnosed diseases decide whether to continue to pursue a diagnosis after standard clinical testing has failed. Parents who applied to the Undiagnosed Disease Network (UDN) at the National Institutes of Health (NIH) were recruited to participate in semi-structured interviews. The 2015 Supportive Care Needs model by Pelenstov, which defines critical needs in families with rare/undiagnosed diseases, provided a framework for interview guide development and transcript analysis (Pelentsov et al in Disabil Health J 8(4):475-491, 2015. https://doi.org/10.1016/J.DHJO.2015.03.009 ). A deductive, iterative coding approach was used to identify common unifying themes. Fourteen parents from 13 families were interviewed. The average child's age was 11 years (range 3-18) and an average 63% of their life had been spent searching for a diagnosis. Our analysis found that alignment or misalignment of parent and child needs impact the trajectory of the diagnostic search. When needs and desires align, reevaluation of a decision to pursue a diagnosis is limited. However, when there is conflict between parent and child desires, there is reevaluation, and often a pause, in the search. This tension is exacerbated when children are adolescents and attempting to balance their dependence on parents for medical care with a natural desire for independence. Our results provide novel insights into the roles of adolescents in the diagnostic odyssey. The tension between desired and realistic developmental outcomes for parents and adolescents impacts if, and how, the search for a diagnosis progresses.
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Affiliation(s)
- Ilana M. Miller
- grid.239560.b0000 0004 0482 1586Children’s National Medical Center, Rare Disease Institute, 7125 13th Place NW, DC 20012 Washington, USA ,grid.214458.e0000000086837370Department of Human Genetics, University of Michigan, 4909 Buhl Building, Catherine St, Ann Arbor, MI 48109 USA
| | - Beverly M. Yashar
- grid.214458.e0000000086837370Department of Human Genetics, University of Michigan, 4909 Buhl Building, Catherine St, Ann Arbor, MI 48109 USA
| | | | - Ellen F. Macnamara
- grid.453125.40000 0004 0533 8641National Institutes of Health Undiagnosed Diseases Program, Common Fund, Office of the Director, NIH, Bethesda, MD USA
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9
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Berger SM, Appelbaum PS, Siegel K, Wynn J, Saami AM, Brokamp E, O'Connor BC, Hamid R, Martin DM, Chung WK. Challenges of variant reinterpretation: Opinions of stakeholders and need for guidelines. Genet Med 2022; 24:1878-1887. [PMID: 35767006 PMCID: PMC10407574 DOI: 10.1016/j.gim.2022.06.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [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: 01/27/2022] [Revised: 06/09/2022] [Accepted: 06/10/2022] [Indexed: 11/24/2022] Open
Abstract
PURPOSE The knowledge used to classify genetic variants is continually evolving, and the classification can change on the basis of newly available data. Although up-to-date variant classification is essential for clinical management, reproductive planning, and identifying at-risk family members, there is no consistent practice across laboratories or clinicians on how or under what circumstances to perform variant reinterpretation. METHODS We conducted exploratory focus groups (N = 142) and surveys (N = 1753) with stakeholders involved in the process of variant reinterpretation (laboratory directors, clinical geneticists, genetic counselors, nongenetic providers, and patients/parents) to assess opinions on key issues, including initiation of reinterpretation, variants to report, termination of the responsibility to reinterpret, and concerns about consent, cost, and liability. RESULTS Stakeholders widely agreed that there should be no fixed termination point to the responsibility to reinterpret a previously reported genetic variant. There were significant concerns about liability and lack of agreement about many logistical aspects of variant reinterpretation. CONCLUSION Our findings suggest a need to (1) develop consensus and (2) create transparency and awareness about the roles and responsibilities of parties involved in variant reinterpretation. These data provide a foundation for developing guidelines on variant reinterpretation that can aid in the development of a low-cost, scalable, and accessible approach.
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Affiliation(s)
- Sara M Berger
- Department of Pediatrics, Columbia University Irving Medical Center, Columbia University, New York, NY
| | - Paul S Appelbaum
- Department of Psychiatry, Columbia University Irving Medical Center, Columbia University, New York, NY
| | - Karolynn Siegel
- Department of Sociomedical Sciences, Mailman School of Public Health, Columbia University Irving Medical Center, New York, NY
| | - Julia Wynn
- Department of Pediatrics, Columbia University Irving Medical Center, Columbia University, New York, NY
| | - Akilan M Saami
- Department of Pediatrics, Columbia University Irving Medical Center, Columbia University, New York, NY
| | - Elly Brokamp
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN
| | | | - Rizwan Hamid
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN
| | - Donna M Martin
- Departments of Pediatrics and Human Genetics, University of Michigan Medical School, Michigan Medicine, Ann Arbor, MI
| | - Wendy K Chung
- Department of Pediatrics, Columbia University Irving Medical Center, Columbia University, New York, NY; Department of Medicine, Columbia University Irving Medical Center, Columbia University, New York, NY.
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10
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Ferdinandusse S, McWalter K, Te Brinke H, IJlst L, Mooijer PM, Ruiter JPN, van Lint AEM, Pras-Raves M, Wever E, Millan F, Guillen Sacoto MJ, Begtrup A, Tarnopolsky M, Brady L, Ladda RL, Sell SL, Nowak CB, Douglas J, Tian C, Ulm E, Perlman S, Drack AV, Chong K, Martin N, Brault J, Brokamp E, Toro C, Gahl WA, Macnamara EF, Wolfe L, Waisfisz Q, Zwijnenburg PJG, Ziegler A, Barth M, Smith R, Ellingwood S, Gaebler-Spira D, Bakhtiari S, Kruer MC, van Kampen AHC, Wanders RJA, Waterham HR, Cassiman D, Vaz FM. Correction to: An autosomal dominant neurological disorder caused by de novo variants in FAR1 resulting in uncontrolled synthesis of ether lipids. Genet Med 2021; 23:2467. [PMID: 34667295 PMCID: PMC8629751 DOI: 10.1038/s41436-021-01189-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Affiliation(s)
- Sacha Ferdinandusse
- Laboratory Genetic Metabolic Diseases, Amsterdam UMC, University of Amsterdam, Department of Clinical Chemistry, Amsterdam Gastroenterology Endocrinology Metabolism, Amsterdam, The Netherlands.
| | | | - Heleen Te Brinke
- Laboratory Genetic Metabolic Diseases, Amsterdam UMC, University of Amsterdam, Department of Clinical Chemistry, Amsterdam Gastroenterology Endocrinology Metabolism, Amsterdam, The Netherlands
| | - Lodewijk IJlst
- Laboratory Genetic Metabolic Diseases, Amsterdam UMC, University of Amsterdam, Department of Clinical Chemistry, Amsterdam Gastroenterology Endocrinology Metabolism, Amsterdam, The Netherlands
| | - Petra M Mooijer
- Laboratory Genetic Metabolic Diseases, Amsterdam UMC, University of Amsterdam, Department of Clinical Chemistry, Amsterdam Gastroenterology Endocrinology Metabolism, Amsterdam, The Netherlands
| | - Jos P N Ruiter
- Laboratory Genetic Metabolic Diseases, Amsterdam UMC, University of Amsterdam, Department of Clinical Chemistry, Amsterdam Gastroenterology Endocrinology Metabolism, Amsterdam, The Netherlands
| | - Alida E M van Lint
- Laboratory Genetic Metabolic Diseases, Amsterdam UMC, University of Amsterdam, Department of Clinical Chemistry, Amsterdam Gastroenterology Endocrinology Metabolism, Amsterdam, The Netherlands
| | - Mia Pras-Raves
- Laboratory Genetic Metabolic Diseases, Amsterdam UMC, University of Amsterdam, Department of Clinical Chemistry, Amsterdam Gastroenterology Endocrinology Metabolism, Amsterdam, The Netherlands
- Core Facility Metabolomics, Amsterdam UMC, Amsterdam, The Netherlands
- Bioinformatics Laboratory, Department of Epidemiology and Data Science, Amsterdam Public Health Research Institute, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Eric Wever
- Laboratory Genetic Metabolic Diseases, Amsterdam UMC, University of Amsterdam, Department of Clinical Chemistry, Amsterdam Gastroenterology Endocrinology Metabolism, Amsterdam, The Netherlands
- Core Facility Metabolomics, Amsterdam UMC, Amsterdam, The Netherlands
- Bioinformatics Laboratory, Department of Epidemiology and Data Science, Amsterdam Public Health Research Institute, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | | | | | | | - Mark Tarnopolsky
- Department of Pediatrics, McMaster University Children's Hospital, Hamilton, ON, Canada
| | - Lauren Brady
- Department of Pediatrics, McMaster University Children's Hospital, Hamilton, ON, Canada
| | - Roger L Ladda
- Department of Pediatrics, Penn State Children's Hospital, Hershey, PA, USA
| | - Susan L Sell
- Department of Pediatrics, Penn State Children's Hospital, Hershey, PA, USA
| | - Catherine B Nowak
- The Feingold Center for Children, Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA
| | - Jessica Douglas
- The Feingold Center for Children, Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA
| | - Cuixia Tian
- Division of Neurology, Cincinnati Children's Hospital Medical Center, Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Elizabeth Ulm
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Seth Perlman
- Department of Neurology, University of Iowa Hospitals and Clinics, Iowa City, IA, USA
| | - Arlene V Drack
- Department of Ophthalmology and Visual Sciences, University of Iowa, Iowa City, IA, USA
| | - Karen Chong
- Mount Sinai Hospital, Department of Obstetrics and Gynecology, Prenatal Diagnosis and Medical Genetics Program, Toronto, ON, Canada
| | - Nicole Martin
- Mount Sinai Hospital, Department of Obstetrics and Gynecology, Prenatal Diagnosis and Medical Genetics Program, Toronto, ON, Canada
| | - Jennifer Brault
- Vanderbilt University Medical Center, Department of Pediatrics, Nashville, TN, USA
| | - Elly Brokamp
- Vanderbilt University Medical Center, Department of Pediatrics, Nashville, TN, USA
| | - Camilo Toro
- NIH Undiagnosed Diseases Program, Office of the Clinical Director, National Human Genome Research Institute, NIH, Bethesda, MD, USA
| | - William A Gahl
- NIH Undiagnosed Diseases Program, Office of the Clinical Director, National Human Genome Research Institute, NIH, Bethesda, MD, USA
| | - Ellen F Macnamara
- NIH Undiagnosed Diseases Program, Office of the Clinical Director, National Human Genome Research Institute, NIH, Bethesda, MD, USA
| | - Lynne Wolfe
- NIH Undiagnosed Diseases Program, Office of the Clinical Director, National Human Genome Research Institute, NIH, Bethesda, MD, USA
| | - Quinten Waisfisz
- Department of Clinical Genetics, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Petra J G Zwijnenburg
- Department of Clinical Genetics, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Alban Ziegler
- Genetic department, University Hospital Angers, Angers, France
| | - Magalie Barth
- Genetic department, University Hospital Angers, Angers, France
| | - Rosemarie Smith
- Division of Genetics, Department of Pediatrics, Maine Medical Center, Portland, ME, USA
| | - Sara Ellingwood
- Division of Genetics, Department of Pediatrics, Maine Medical Center, Portland, ME, USA
| | - Deborah Gaebler-Spira
- Feinberg Northwestern University School of Medicine, Shirley Ryan Ability Lab, Chicago, IL, USA
| | - Somayeh Bakhtiari
- Barrow Neurological Institute, Phoenix Children's Hospital and University of Arizona College of Medicine, Phoenix, AZ, USA
| | - Michael C Kruer
- Barrow Neurological Institute, Phoenix Children's Hospital and University of Arizona College of Medicine, Phoenix, AZ, USA
| | - Antoine H C van Kampen
- Bioinformatics Laboratory, Department of Epidemiology and Data Science, Amsterdam Public Health Research Institute, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
- Biosystems Data Analysis, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands
| | - Ronald J A Wanders
- Laboratory Genetic Metabolic Diseases, Amsterdam UMC, University of Amsterdam, Department of Clinical Chemistry, Amsterdam Gastroenterology Endocrinology Metabolism, Amsterdam, The Netherlands
| | - Hans R Waterham
- Laboratory Genetic Metabolic Diseases, Amsterdam UMC, University of Amsterdam, Department of Clinical Chemistry, Amsterdam Gastroenterology Endocrinology Metabolism, Amsterdam, The Netherlands
| | - David Cassiman
- Department of Gastroenterology-Hepatology, Metabolic Center, University Hospitals Leuven, Leuven, Belgium
| | - Frédéric M Vaz
- Laboratory Genetic Metabolic Diseases, Amsterdam UMC, University of Amsterdam, Department of Clinical Chemistry, Amsterdam Gastroenterology Endocrinology Metabolism, Amsterdam, The Netherlands.
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11
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Brokamp E, Koziura ME, Phillips JA, Tang LA, Cogan JD, Rives LC, Robertson AK, Duncan L, Bican A, Peterson JF, Newman JH, Hamid R, Bastarache L. One is the loneliest number: genotypic matchmaking using the electronic health record. Genet Med 2021; 23:1830-1832. [PMID: 34230636 DOI: 10.1038/s41436-021-01179-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Accepted: 04/05/2021] [Indexed: 01/02/2023] Open
Affiliation(s)
- Elly Brokamp
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN, USA.
| | - Mary E Koziura
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - John A Phillips
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Leigh Anne Tang
- Center for Precision Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Joy D Cogan
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Lynette C Rives
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Amy K Robertson
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Laura Duncan
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Anna Bican
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Josh F Peterson
- Center for Precision Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - John H Newman
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Rizwan Hamid
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Lisa Bastarache
- Center for Precision Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
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12
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Briere LC, Walker MA, High FA, Cooper C, Rogers CA, Callahan CJ, Ishimura R, Ichimura Y, Caruso PA, Sharma N, Brokamp E, Koziura ME, Mohammad SS, Dale RC, Riley LG, Phillips JA, Komatsu M, Sweetser DA. A description of novel variants and review of phenotypic spectrum in UBA5-related early epileptic encephalopathy. Cold Spring Harb Mol Case Stud 2021; 7:a005827. [PMID: 33811063 PMCID: PMC8208045 DOI: 10.1101/mcs.a005827] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Accepted: 03/10/2021] [Indexed: 12/22/2022] Open
Abstract
Early infantile epileptic encephalopathy-44 (EIEE44, MIM: 617132) is a previously described condition resulting from biallelic variants in UBA5, a gene involved in a ubiquitin-like post-translational modification system called UFMylation. Here we report five children from four families with biallelic pathogenic variants in UBA5 All five children presented with global developmental delay, epilepsy, axial hypotonia, appendicular hypertonia, and a movement disorder, including dystonia in four. Affected individuals in all four families have compound heterozygous pathogenic variants in UBA5 All have the recurrent mild c.1111G > A (p.Ala371Thr) variant in trans with a second UBA5 variant. One patient has the previously described c.562C > T (p. Arg188*) variant, two other unrelated patients have a novel missense variant, c.907T > C (p.Cys303Arg), and the two siblings have a novel missense variant, c.761T > C (p.Leu254Pro). Functional analyses demonstrate that both the p.Cys303Arg variant and the p.Leu254Pro variants result in a significant decrease in protein function. We also review the phenotypes and genotypes of all 15 previously reported families with biallelic UBA5 variants, of which two families have presented with distinct phenotypes, and we describe evidence for some limited genotype-phenotype correlation. The overlap of motor and developmental phenotypes noted in our cohort and literature review adds to the increasing understanding of genetic syndromes with movement disorders-epilepsy.
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Affiliation(s)
- Lauren C Briere
- Department of Pediatrics, Division of Medical Genetics and Metabolism, and Center for Genomic Medicine, Massachusetts 02114, USA
| | - Melissa A Walker
- Department of Neurology, Division of Neurogenetics, Child Neurology, Massachusetts 02114, USA
| | - Frances A High
- Department of Pediatrics, Division of Medical Genetics and Metabolism, Massachusetts 02114, USA
| | - Cynthia Cooper
- Department of Internal Medicine, Massachusetts General Hospital, Boston, Massachusetts 02114, USA
| | - Cassandra A Rogers
- Department of Pediatrics, Division of Medical Genetics and Metabolism, and Center for Genomic Medicine, Massachusetts 02114, USA
| | - Christine J Callahan
- Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts 02115, USA
| | - Ryosuke Ishimura
- Department of Biochemistry, Niigata University School of Medical and Dental Sciences, Chuo-ku, Niigata 951-8510, Japan
| | - Yoshinobu Ichimura
- Department of Biochemistry, Niigata University School of Medical and Dental Sciences, Chuo-ku, Niigata 951-8510, Japan
| | - Paul A Caruso
- Department of Radiology, Massachusetts General Hospital, Boston, Massachusetts 02114, USA
| | - Nutan Sharma
- Department of Neurology, Massachusetts General Hospital, Boston, Massachusetts 02114, USA
| | - Elly Brokamp
- Division of Medical Genetics and Genomic Medicine, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, USA
| | - Mary E Koziura
- Division of Medical Genetics and Genomic Medicine, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, USA
| | - Shekeeb S Mohammad
- Kids Neuroscience Center & Children's Hospital at Westmead Clinical School, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Russell C Dale
- Kids Neuroscience Center & Children's Hospital at Westmead Clinical School, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Lisa G Riley
- Rare Diseases Functional Genomics, Kids Research, The Children's Hospital at Westmead and Children's Medical Research Institute, Westmead, New South Wales 2145, Australia
- Discipline of Child & Adolescent Health, University of Sydney, Sydney, New South Wales 2006, Australia
| | - John A Phillips
- Division of Medical Genetics and Genomic Medicine, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, USA
| | - Masaaki Komatsu
- Department of Biochemistry, Niigata University School of Medical and Dental Sciences, Chuo-ku, Niigata 951-8510, Japan
- Department of Physiology, Juntendo University School of Medicine, Tokyo 113-8421, Japan
| | - David A Sweetser
- Department of Pediatrics, Division of Medical Genetics and Metabolism, and Center for Genomic Medicine, Massachusetts 02114, USA
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13
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Ferdinandusse S, McWalter K, Te Brinke H, IJlst L, Mooijer PM, Ruiter JPN, van Lint AEM, Pras-Raves M, Wever E, Millan F, Guillen Sacoto MJ, Begtrup A, Tarnopolsky M, Brady L, Ladda RL, Sell SL, Nowak CB, Douglas J, Tian C, Ulm E, Perlman S, Drack AV, Chong K, Martin N, Brault J, Brokamp E, Toro C, Gahl WA, Macnamara EF, Wolfe L, Waisfisz Q, Zwijnenburg PJG, Ziegler A, Barth M, Smith R, Ellingwood S, Gaebler-Spira D, Bakhtiari S, Kruer MC, van Kampen AHC, Wanders RJA, Waterham HR, Cassiman D, Vaz FM. An autosomal dominant neurological disorder caused by de novo variants in FAR1 resulting in uncontrolled synthesis of ether lipids. Genet Med 2021; 23:740-750. [PMID: 33239752 PMCID: PMC8026396 DOI: 10.1038/s41436-020-01027-3] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [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: 07/24/2020] [Revised: 10/15/2020] [Accepted: 10/21/2020] [Indexed: 12/25/2022] Open
Abstract
PURPOSE In this study we investigate the disease etiology in 12 patients with de novo variants in FAR1 all resulting in an amino acid change at position 480 (p.Arg480Cys/His/Leu). METHODS Following next-generation sequencing and clinical phenotyping, functional characterization was performed in patients' fibroblasts using FAR1 enzyme analysis, FAR1 immunoblotting/immunofluorescence, and lipidomics. RESULTS All patients had spastic paraparesis and bilateral congenital/juvenile cataracts, in most combined with speech and gross motor developmental delay and truncal hypotonia. FAR1 deficiency caused by biallelic variants results in defective ether lipid synthesis and plasmalogen deficiency. In contrast, patients' fibroblasts with the de novo FAR1 variants showed elevated plasmalogen levels. Further functional studies in fibroblasts showed that these variants cause a disruption of the plasmalogen-dependent feedback regulation of FAR1 protein levels leading to uncontrolled ether lipid production. CONCLUSION Heterozygous de novo variants affecting the Arg480 residue of FAR1 lead to an autosomal dominant disorder with a different disease mechanism than that of recessive FAR1 deficiency and a diametrically opposed biochemical phenotype. Our findings show that for patients with spastic paraparesis and bilateral cataracts, FAR1 should be considered as a candidate gene and added to gene panels for hereditary spastic paraplegia, cerebral palsy, and juvenile cataracts.
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Affiliation(s)
- Sacha Ferdinandusse
- Laboratory Genetic Metabolic Diseases, Amsterdam UMC, University of Amsterdam, Department of Clinical Chemistry, Amsterdam Gastroenterology Endocrinology Metabolism, Amsterdam, The Netherlands.
| | | | - Heleen Te Brinke
- Laboratory Genetic Metabolic Diseases, Amsterdam UMC, University of Amsterdam, Department of Clinical Chemistry, Amsterdam Gastroenterology Endocrinology Metabolism, Amsterdam, The Netherlands
| | - Lodewijk IJlst
- Laboratory Genetic Metabolic Diseases, Amsterdam UMC, University of Amsterdam, Department of Clinical Chemistry, Amsterdam Gastroenterology Endocrinology Metabolism, Amsterdam, The Netherlands
| | - Petra M Mooijer
- Laboratory Genetic Metabolic Diseases, Amsterdam UMC, University of Amsterdam, Department of Clinical Chemistry, Amsterdam Gastroenterology Endocrinology Metabolism, Amsterdam, The Netherlands
| | - Jos P N Ruiter
- Laboratory Genetic Metabolic Diseases, Amsterdam UMC, University of Amsterdam, Department of Clinical Chemistry, Amsterdam Gastroenterology Endocrinology Metabolism, Amsterdam, The Netherlands
| | - Alida E M van Lint
- Laboratory Genetic Metabolic Diseases, Amsterdam UMC, University of Amsterdam, Department of Clinical Chemistry, Amsterdam Gastroenterology Endocrinology Metabolism, Amsterdam, The Netherlands
| | - Mia Pras-Raves
- Laboratory Genetic Metabolic Diseases, Amsterdam UMC, University of Amsterdam, Department of Clinical Chemistry, Amsterdam Gastroenterology Endocrinology Metabolism, Amsterdam, The Netherlands
- Core Facility Metabolomics, Amsterdam UMC, Amsterdam, The Netherlands
- Bioinformatics Laboratory, Department of Epidemiology and Data Science, Amsterdam Public Health Research Institute, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Eric Wever
- Laboratory Genetic Metabolic Diseases, Amsterdam UMC, University of Amsterdam, Department of Clinical Chemistry, Amsterdam Gastroenterology Endocrinology Metabolism, Amsterdam, The Netherlands
- Core Facility Metabolomics, Amsterdam UMC, Amsterdam, The Netherlands
- Bioinformatics Laboratory, Department of Epidemiology and Data Science, Amsterdam Public Health Research Institute, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | | | | | | | - Mark Tarnopolsky
- Department of Pediatrics, McMaster University Children's Hospital, Hamilton, ON, Canada
| | - Lauren Brady
- Department of Pediatrics, McMaster University Children's Hospital, Hamilton, ON, Canada
| | - Roger L Ladda
- Department of Pediatrics, Penn State Children's Hospital, Hershey, PA, USA
| | - Susan L Sell
- Department of Pediatrics, Penn State Children's Hospital, Hershey, PA, USA
| | - Catherine B Nowak
- The Feingold Center for Children, Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA
| | - Jessica Douglas
- The Feingold Center for Children, Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA
| | - Cuixia Tian
- Division of Neurology, Cincinnati Children's Hospital Medical Center, Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Elizabeth Ulm
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Seth Perlman
- Department of Neurology, University of Iowa Hospitals and Clinics, Iowa City, IA, USA
| | - Arlene V Drack
- Department of Ophthalmology and Visual Sciences, University of Iowa, Iowa City, IA, USA
| | - Karen Chong
- Mount Sinai Hospital, Department of Obstetrics and Gynecology, Prenatal Diagnosis and Medical Genetics Program, Toronto, ON, Canada
| | - Nicole Martin
- Mount Sinai Hospital, Department of Obstetrics and Gynecology, Prenatal Diagnosis and Medical Genetics Program, Toronto, ON, Canada
| | - Jennifer Brault
- Vanderbilt University Medical Center, Department of Pediatrics, Nashville, TN, USA
| | - Elly Brokamp
- Vanderbilt University Medical Center, Department of Pediatrics, Nashville, TN, USA
| | - Camilo Toro
- NIH Undiagnosed Diseases Program, Office of the Clinical Director, National Human Genome Research Institute, NIH, Bethesda, MD, USA
| | - William A Gahl
- NIH Undiagnosed Diseases Program, Office of the Clinical Director, National Human Genome Research Institute, NIH, Bethesda, MD, USA
| | - Ellen F Macnamara
- NIH Undiagnosed Diseases Program, Office of the Clinical Director, National Human Genome Research Institute, NIH, Bethesda, MD, USA
| | - Lynne Wolfe
- NIH Undiagnosed Diseases Program, Office of the Clinical Director, National Human Genome Research Institute, NIH, Bethesda, MD, USA
| | - Quinten Waisfisz
- Department of Clinical Genetics, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Petra J G Zwijnenburg
- Department of Clinical Genetics, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Alban Ziegler
- Genetic department, University Hospital Angers, Angers, France
| | - Magalie Barth
- Genetic department, University Hospital Angers, Angers, France
| | - Rosemarie Smith
- Division of Genetics, Department of Pediatrics, Maine Medical Center, Portland, ME, USA
| | - Sara Ellingwood
- Division of Genetics, Department of Pediatrics, Maine Medical Center, Portland, ME, USA
| | - Deborah Gaebler-Spira
- Feinberg Northwestern University School of Medicine, Shirley Ryan Ability Lab, Chicago, IL, USA
| | - Somayeh Bakhtiari
- Barrow Neurological Institute, Phoenix Children's Hospital and University of Arizona College of Medicine, Phoenix, AZ, USA
| | - Michael C Kruer
- Barrow Neurological Institute, Phoenix Children's Hospital and University of Arizona College of Medicine, Phoenix, AZ, USA
| | - Antoine H C van Kampen
- Bioinformatics Laboratory, Department of Epidemiology and Data Science, Amsterdam Public Health Research Institute, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
- Biosystems Data Analysis, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands
| | - Ronald J A Wanders
- Laboratory Genetic Metabolic Diseases, Amsterdam UMC, University of Amsterdam, Department of Clinical Chemistry, Amsterdam Gastroenterology Endocrinology Metabolism, Amsterdam, The Netherlands
| | - Hans R Waterham
- Laboratory Genetic Metabolic Diseases, Amsterdam UMC, University of Amsterdam, Department of Clinical Chemistry, Amsterdam Gastroenterology Endocrinology Metabolism, Amsterdam, The Netherlands
| | - David Cassiman
- Department of Gastroenterology-Hepatology, Metabolic Center, University Hospitals Leuven, Leuven, Belgium
| | - Frédéric M Vaz
- Laboratory Genetic Metabolic Diseases, Amsterdam UMC, University of Amsterdam, Department of Clinical Chemistry, Amsterdam Gastroenterology Endocrinology Metabolism, Amsterdam, The Netherlands.
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14
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Bryant L, Li D, Cox SG, Marchione D, Joiner EF, Wilson K, Janssen K, Lee P, March ME, Nair D, Sherr E, Fregeau B, Wierenga KJ, Wadley A, Mancini GMS, Powell-Hamilton N, van de Kamp J, Grebe T, Dean J, Ross A, Crawford HP, Powis Z, Cho MT, Willing MC, Manwaring L, Schot R, Nava C, Afenjar A, Lessel D, Wagner M, Klopstock T, Winkelmann J, Catarino CB, Retterer K, Schuette JL, Innis JW, Pizzino A, Lüttgen S, Denecke J, Strom TM, Monaghan KG, Yuan ZF, Dubbs H, Bend R, Lee JA, Lyons MJ, Hoefele J, Günthner R, Reutter H, Keren B, Radtke K, Sherbini O, Mrokse C, Helbig KL, Odent S, Cogne B, Mercier S, Bezieau S, Besnard T, Kury S, Redon R, Reinson K, Wojcik MH, Õunap K, Ilves P, Innes AM, Kernohan KD, Costain G, Meyn MS, Chitayat D, Zackai E, Lehman A, Kitson H, Martin MG, Martinez-Agosto JA, Nelson SF, Palmer CGS, Papp JC, Parker NH, Sinsheimer JS, Vilain E, Wan J, Yoon AJ, Zheng A, Brimble E, Ferrero GB, Radio FC, Carli D, Barresi S, Brusco A, Tartaglia M, Thomas JM, Umana L, Weiss MM, Gotway G, Stuurman KE, Thompson ML, McWalter K, Stumpel CTRM, Stevens SJC, Stegmann APA, Tveten K, Vøllo A, Prescott T, Fagerberg C, Laulund LW, Larsen MJ, Byler M, Lebel RR, Hurst AC, Dean J, Schrier Vergano SA, Norman J, Mercimek-Andrews S, Neira J, Van Allen MI, Longo N, Sellars E, Louie RJ, Cathey SS, Brokamp E, Heron D, Snyder M, Vanderver A, Simon C, de la Cruz X, Padilla N, Crump JG, Chung W, Garcia B, Hakonarson HH, Bhoj EJ. Histone H3.3 beyond cancer: Germline mutations in Histone 3 Family 3A and 3B cause a previously unidentified neurodegenerative disorder in 46 patients. Sci Adv 2020; 6:eabc9207. [PMID: 33268356 PMCID: PMC7821880 DOI: 10.1126/sciadv.abc9207] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Accepted: 10/19/2020] [Indexed: 05/07/2023]
Abstract
Although somatic mutations in Histone 3.3 (H3.3) are well-studied drivers of oncogenesis, the role of germline mutations remains unreported. We analyze 46 patients bearing de novo germline mutations in histone 3 family 3A (H3F3A) or H3F3B with progressive neurologic dysfunction and congenital anomalies without malignancies. Molecular modeling of all 37 variants demonstrated clear disruptions in interactions with DNA, other histones, and histone chaperone proteins. Patient histone posttranslational modifications (PTMs) analysis revealed notably aberrant local PTM patterns distinct from the somatic lysine mutations that cause global PTM dysregulation. RNA sequencing on patient cells demonstrated up-regulated gene expression related to mitosis and cell division, and cellular assays confirmed an increased proliferative capacity. A zebrafish model showed craniofacial anomalies and a defect in Foxd3-derived glia. These data suggest that the mechanism of germline mutations are distinct from cancer-associated somatic histone mutations but may converge on control of cell proliferation.
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Affiliation(s)
- Laura Bryant
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Dong Li
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Samuel G Cox
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine, University of Southern California, CA 90033, USA
| | - Dylan Marchione
- Epigenetics Institute, Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Evan F Joiner
- Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA
| | - Khadija Wilson
- Epigenetics Institute, Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Kevin Janssen
- Epigenetics Institute, Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Pearl Lee
- Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Michael E March
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Divya Nair
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Elliott Sherr
- Department of Neurology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Brieana Fregeau
- Department of Neurology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Klaas J Wierenga
- Department of Clinical Genomics, Mayo Clinic Florida, Jacksonville, FL 32224, USA
| | - Alexandrea Wadley
- Department of Clinical Genomics, Mayo Clinic Florida, Jacksonville, FL 32224, USA
| | - Grazia M S Mancini
- Department of Clinical Genetics, Erasmus University Medical Center, 3015 CN Rotterdam, Netherlands
| | - Nina Powell-Hamilton
- Department of Medical Genetics, Alfred I. duPont Hospital for Children, Wilmington, DE 19810, USA
| | | | - Theresa Grebe
- Division of Genetics and Metabolism, Phoenix Children's Hospital, Phoenix, AZ 85016, USA
| | - John Dean
- Department of Medical Genetics, Aberdeen Royal Infirmary, Aberdeen, Scotland, UK
| | - Alison Ross
- Department of Medical Genetics, Aberdeen Royal Infirmary, Aberdeen, Scotland, UK
| | - Heather P Crawford
- Clinical and Metabolic Genetics, Cook Children's Medical Center, Fort Worth, TX 76104, USA
| | - Zoe Powis
- Department of Emerging Genetic Medicine, Ambry Genetics, Aliso Viejo, CA 92656, USA
| | - Megan T Cho
- GeneDx, 207 Perry Parkway, Gaithersburg, MD 20877, USA
| | - Marcia C Willing
- Division of Genetics and Genomic Medicine, Department of Pediatrics, Washington University in St. Louis, School of Medicine, St. Louis, MO 63110, USA
| | - Linda Manwaring
- Division of Genetics and Genomic Medicine, Department of Pediatrics, Washington University in St. Louis, School of Medicine, St. Louis, MO 63110, USA
| | - Rachel Schot
- Department of Clinical Genetics, Erasmus University Medical Center, 3015 CN Rotterdam, Netherlands
| | - Caroline Nava
- Sorbonne Universités, UPMC Univ Paris 06, UMR S 1127, Inserm U 1127, CNRS UMR 7225, ICM, Paris, France
- AP-HP, Hôpital de la Pitié-Salpêtrière, Département de Génétique, F-75013 Paris, France
| | - Alexandra Afenjar
- Service de génétique, CRMR des malformations et maladies congénitales du cervelet et CRMR déficience intellectuelle, hôpital Trousseau, AP-HP, France
| | - Davor Lessel
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
- Undiagnosed Disease Program at the University Medical Center Hamburg-Eppendorf (UDP-UKE), Martinistrasse 52, 20246 Hamburg, Germany
| | - Matias Wagner
- Institut für Neurogenomik, Helmholtz Zentrum München, Munich, Germany
- Institut für Humangenetik, Helmholtz Zentrum München, Munich, Germany
- Institut für Humangenetik, Technische Universität München, Munich, Germany
| | - Thomas Klopstock
- Friedrich-Baur-Institute, Department of Neurology, Ludwig-Maximilians University, Ziemssenstr. 1a, 80336 Munich, Germany
- German Center for Neurodegenerative Diseases (DZNE), Munich, Germany
- Munich Cluster for Systems Neurology, SyNergy, Munich, Germany
| | - Juliane Winkelmann
- Institut für Neurogenomik, Helmholtz Zentrum München, Munich, Germany
- Institut für Humangenetik, Technische Universität München, Munich, Germany
- Munich Cluster for Systems Neurology, SyNergy, Munich, Germany
- Klinik und Poliklinik für Neurologie, Klinikum rechts der Isar, Technische Universität München, Munich, Germany
| | - Claudia B Catarino
- Friedrich-Baur-Institute, Department of Neurology, Ludwig-Maximilians University, Ziemssenstr. 1a, 80336 Munich, Germany
| | - Kyle Retterer
- GeneDx, 207 Perry Parkway, Gaithersburg, MD 20877, USA
| | - Jane L Schuette
- Division of Genetics, Metabolism, and Genomic Medicine, Department of Pediatrics and Communicable Diseases, University of Michigan, Ann Arbor, MI 48109, USA
| | - Jeffrey W Innis
- Division of Genetics, Metabolism, and Genomic Medicine, Department of Pediatrics and Communicable Diseases, University of Michigan, Ann Arbor, MI 48109, USA
| | - Amy Pizzino
- Division of Neurology, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19103, USA
| | - Sabine Lüttgen
- Department of Pediatrics, University Medical Center Eppendorf, 20246 Hamburg, Germany
| | - Jonas Denecke
- Department of Pediatrics, University Medical Center Eppendorf, 20246 Hamburg, Germany
| | - Tim M Strom
- Institut für Neurogenomik, Helmholtz Zentrum München, Munich, Germany
- Institut für Humangenetik, Technische Universität München, Munich, Germany
| | | | - Zuo-Fei Yuan
- Epigenetics Institute, Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Holly Dubbs
- Division of Neurology, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19103, USA
| | - Renee Bend
- Greenwood Genetic Center, Greenwood, SC 29646, USA
| | | | | | - Julia Hoefele
- Institut für Humangenetik, Technische Universität München, Munich, Germany
| | - Roman Günthner
- Department of Nephrology, Klinikum Rechts der Isar, Technical University Munich, Munich, Germany
- Institute of Human Genetics, Klinikum Rechts der Isar, Technical University Munich, Munich, Germany
| | - Heiko Reutter
- Department of Neonatology and Pediatric Intensive Care, Children's Hospital, University Hospital Bonn & Institute of Human Genetics, University Hospital Bonn, Bonn, Germany
| | - Boris Keren
- AP-HP, Hôpital de la Pitié-Salpêtrière, Département de Génétique, F-75013 Paris, France
| | - Kelly Radtke
- Department of Clinical Genomics, Ambry Genetics, Aliso Viejo, CA 92656, USA
| | - Omar Sherbini
- Division of Neurology, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19103, USA
| | - Cameron Mrokse
- Department of Clinical Genomics, Ambry Genetics, Aliso Viejo, CA 92656, USA
| | - Katherine L Helbig
- Department of Clinical Genomics, Ambry Genetics, Aliso Viejo, CA 92656, USA
| | - Sylvie Odent
- CHU Rennes, Service de Génétique Clinique, CNRS UMR6290, University Rennes1, Rennes, France
| | - Benjamin Cogne
- CHU Nantes, Service de Génétique Médicale, 9 quai Moncousu, 44093 Nantes, France
- INSERM, CNRS, UNIV Nantes, CHU Nantes, l'institut du thorax, 44007 Nantes, France
| | - Sandra Mercier
- CHU Nantes, Service de Génétique Médicale, 9 quai Moncousu, 44093 Nantes, France
- INSERM, CNRS, UNIV Nantes, CHU Nantes, l'institut du thorax, 44007 Nantes, France
| | - Stephane Bezieau
- CHU Nantes, Service de Génétique Médicale, 9 quai Moncousu, 44093 Nantes, France
- INSERM, CNRS, UNIV Nantes, CHU Nantes, l'institut du thorax, 44007 Nantes, France
| | - Thomas Besnard
- CHU Nantes, Service de Génétique Médicale, 9 quai Moncousu, 44093 Nantes, France
- INSERM, CNRS, UNIV Nantes, CHU Nantes, l'institut du thorax, 44007 Nantes, France
| | - Sebastien Kury
- CHU Nantes, Service de Génétique Médicale, 9 quai Moncousu, 44093 Nantes, France
- INSERM, CNRS, UNIV Nantes, CHU Nantes, l'institut du thorax, 44007 Nantes, France
| | - Richard Redon
- INSERM, CNRS, UNIV Nantes, CHU Nantes, l'institut du thorax, 44007 Nantes, France
| | - Karit Reinson
- Department of Clinical Genetics, United Laboratories, Tartu University Hospital, Tartu, Estonia
- Institute of Clinical Medicine, University of Tartu, Tartu, Estonia
| | - Monica H Wojcik
- Division of Genetics and Genomics and Division of Newborn Medicine, Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
- Broad Institute, Cambridge, MA 02142, USA
| | - Katrin Õunap
- Department of Clinical Genetics, United Laboratories, Tartu University Hospital, Tartu, Estonia
- Institute of Clinical Medicine, University of Tartu, Tartu, Estonia
| | - Pilvi Ilves
- Radiology Department of Tartu University Hospital and Institute of Clinical Medicine, University of Tartu, Tartu, Estonia
| | - A Micheil Innes
- Alberta Children's Hospital Research Institute, Department of Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Kristin D Kernohan
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, Ontario K1H8L1, Canada
- Newborn Screening Ontario (NSO), Children's Hospital of Eastern Ontario, Ottawa, Ontario, Canada
| | - Gregory Costain
- Division of Clinical and Metabolic Genetics, Department of Pediatrics, University of Toronto, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - M Stephen Meyn
- Division of Clinical and Metabolic Genetics, Department of Pediatrics, University of Toronto, The Hospital for Sick Children, Toronto, Ontario, Canada
- The Center for Human Genomics and Precision Medicine, School of Medicine and Public Health, University of Wisconsin - Madison, Madison, Wisconsin 53705, USA
| | - David Chitayat
- Division of Clinical and Metabolic Genetics, Department of Pediatrics, University of Toronto, The Hospital for Sick Children, Toronto, Ontario, Canada
- The Prenatal Diagnosis and Medical Genetics Program, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Elaine Zackai
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Anna Lehman
- Department of Medical Genetics, University of British Columbia, Vancouver, Canada
| | - Hilary Kitson
- Department of Pediatrics, University of British Columbia, Vancouver, Canada
| | - Martin G Martin
- Division of Gastroenterology and Nutrition, Department of Pediatrics, Mattel Children's Hospital, Los Angeles, CA 90095, USA
- Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research and the David Geffen School of Medicine, UCLA, Los Angeles, CA 90095, USA
| | - Julian A Martinez-Agosto
- Department of Human Genetics, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095, USA
- Division of Medical Genetics, Department of Pediatrics, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095, USA
| | - Stan F Nelson
- Department of Human Genetics, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095, USA
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095, USA
| | - Christina G S Palmer
- Department of Human Genetics, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095, USA
- Institute for Society and Genetics, Department of Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095, USA
| | - Jeanette C Papp
- Department of Human Genetics, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095, USA
| | - Neil H Parker
- David Geffen School of Medicine, Los Angeles, CA 90095, USA
| | - Janet S Sinsheimer
- Institute for Society and Genetics, Departments of Human Genetics, Biomathematics, and Biostatistics, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095, USA
| | - Eric Vilain
- Center for Genetic Medicine Research, Children's National Medical Center, Washington, DC 20010, USA
| | - Jijun Wan
- Department of Human Genetics, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095, USA
| | - Amanda J Yoon
- Department of Human Genetics, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095, USA
| | - Allison Zheng
- Department of Human Genetics, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095, USA
| | - Elise Brimble
- Department of Neurology and Neurological Sciences, Stanford Medicine, Stanford, CA 94305, USA
| | | | | | - Diana Carli
- Department of Public Health and Pediatrics, University of Torino, Turin, Italy
| | - Sabina Barresi
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, Rome, Italy
| | - Alfredo Brusco
- Department of Medical Sciences, University of Torino, Turin, Italy
| | - Marco Tartaglia
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, Rome, Italy
| | - Jennifer Muncy Thomas
- Pediatrics and Neurology and Neurotherapeutics, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Luis Umana
- Genetics and Metabolism, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Marjan M Weiss
- Department of Clinical Genetics, VU Medical Center, Amsterdam, Netherlands
| | - Garrett Gotway
- Genetics and Metabolism, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - K E Stuurman
- Department of Clinical Genetics, Erasmus University Medical Center, 3015 CN Rotterdam, Netherlands
| | | | | | - Constance T R M Stumpel
- Department of Clinical Genetics, Maastricht University Medical Center, Maastricht, Netherlands
| | - Servi J C Stevens
- Department of Clinical Genetics, Maastricht University Medical Center, Maastricht, Netherlands
| | - Alexander P A Stegmann
- Department of Clinical Genetics, Maastricht University Medical Center, Maastricht, Netherlands
| | - Kristian Tveten
- Department of Medical Genetics, Telemark Hospital Trust, 3710 Skien, Norway
| | - Arve Vøllo
- Department of Pediatrics, Hospital of Østfold, 1714 Grålum, Norway
| | - Trine Prescott
- Department of Medical Genetics, Telemark Hospital Trust, 3710 Skien, Norway
| | - Christina Fagerberg
- Department of Clinical Genetics, Odense University Hospital, Odense, Denmark
| | | | - Martin J Larsen
- Department of Clinical Genetics, Odense University Hospital, Odense, Denmark
| | - Melissa Byler
- SUNY Upstate Medical University, Syracuse, NY 13210, USA
| | | | - Anna C Hurst
- University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Joy Dean
- University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Samantha A Schrier Vergano
- Division of Medical Genetics and Metabolism, Children's Hospital of The King's Daughters, Norfolk VA 23507, USA
| | | | - Saadet Mercimek-Andrews
- Division of Clinical and Metabolic Genetics, Department of Pediatrics, University of Toronto, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Juanita Neira
- Department of Human Genetics, Emory University, Atlanta, GA 30322, USA
| | - Margot I Van Allen
- Department of Medical Genetics, University of British Columbia, Vancouver, Canada
- Medical Genetics Programs, Provincial Health Shared Services BC and Vancouver Island Health Shared Services BC, Canada
| | - Nicola Longo
- Division of Medical Genetics, Department of Pediatrics, University of Utah, Salt Lake City, UT 84112, USA
| | - Elizabeth Sellars
- University of Arkansas for Medical Sciences, Little Rock, AR 72701, USA
| | | | | | | | - Delphine Heron
- AP-HP, Hôpital de la Pitié-Salpêtrière, Département de Génétique, F-75013 Paris, France
| | - Molly Snyder
- Child Neurology, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Adeline Vanderver
- Division of Neurology, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19103, USA
| | - Celeste Simon
- Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA
| | - Xavier de la Cruz
- Vall d'Hebron Institute of Research (VHIR), Universitat Autònoma de Barcelona, Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Natália Padilla
- Vall d'Hebron Institute of Research (VHIR), Universitat Autònoma de Barcelona, Barcelona, Spain
| | - J Gage Crump
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine, University of Southern California, CA 90033, USA
| | - Wendy Chung
- Departments of Pediatrics and Medicine, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Benjamin Garcia
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine, University of Southern California, CA 90033, USA
- Epigenetics Institute, Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Hakon H Hakonarson
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Elizabeth J Bhoj
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA.
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15
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Cope H, Spillmann R, Rosenfeld JA, Brokamp E, Signer R, Schoch K, Kelley EG, Sullivan JA, Macnamara E, Lincoln S, Golden-Grant K, Orengo JP, Clark G, Burrage LC, Posey JE, Punetha J, Robertson A, Cogan J, Phillips JA, Martinez-Agosto J, Shashi V. Missed diagnoses: Clinically relevant lessons learned through medical mysteries solved by the Undiagnosed Diseases Network. Mol Genet Genomic Med 2020; 8:e1397. [PMID: 32730690 PMCID: PMC7549585 DOI: 10.1002/mgg3.1397] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [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: 05/14/2020] [Revised: 06/04/2020] [Accepted: 06/08/2020] [Indexed: 12/12/2022] Open
Abstract
Background Resources within the Undiagnosed Diseases Network (UDN), such as genome sequencing (GS) and model organisms aid in diagnosis and identification of new disease genes, but are currently difficult to access by clinical providers. While these resources do contribute to diagnoses in many cases, they are not always necessary to reach diagnostic resolution. The UDN experience has been that participants can also receive diagnoses through the thoughtful and customized application of approaches and resources that are readily available in clinical settings. Methods The UDN Genetic Counseling and Testing Working Group collected case vignettes that illustrated how clinically available methods resulted in diagnoses. The case vignettes were classified into three themes; phenotypic considerations, selection of genetic testing, and evaluating exome/GS variants and data. Results We present 12 participants that illustrate how clinical practices such as phenotype‐driven genomic investigations, consideration of variable expressivity, selecting the relevant tissue of interest for testing, utilizing updated testing platforms, and recognition of alternate transcript nomenclature resulted in diagnoses. Conclusion These examples demonstrate that when a diagnosis is elusive, an iterative patient‐specific approach utilizing assessment options available to clinical providers may solve a portion of cases. However, this does require increased provider time commitment, a particular challenge in the current practice of genomics.
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Affiliation(s)
- Heidi Cope
- Division of Medical Genetics, Department of Pediatrics, Duke University Medical Center, Durham, NC, USA
| | - Rebecca Spillmann
- Division of Medical Genetics, Department of Pediatrics, Duke University Medical Center, Durham, NC, USA
| | - Jill A Rosenfeld
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Elly Brokamp
- Division of Medical Genetics and Genomic Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Rebecca Signer
- Department of Human Genetics, University of California, Los Angeles, CA, USA
| | - Kelly Schoch
- Division of Medical Genetics, Department of Pediatrics, Duke University Medical Center, Durham, NC, USA
| | - Emily G Kelley
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Jennifer A Sullivan
- Division of Medical Genetics, Department of Pediatrics, Duke University Medical Center, Durham, NC, USA
| | - Ellen Macnamara
- Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, NIH, Bethesda, MD, USA
| | - Sharyn Lincoln
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital, Boston, MA, USA
| | - Katie Golden-Grant
- Division of Medical Genetics, University of Washington, Seattle, WA, USA
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- Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, NIH, Bethesda, MD, USA
| | - James P Orengo
- Department of Neurology, Baylor College of Medicine, Houston, TX, USA
| | - Gary Clark
- Department of Neurology, Baylor College of Medicine, Houston, TX, USA
| | - Lindsay C Burrage
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Jennifer E Posey
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Jaya Punetha
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Amy Robertson
- Division of Medical Genetics and Genomic Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Joy Cogan
- Division of Medical Genetics and Genomic Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - John A Phillips
- Division of Medical Genetics and Genomic Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | | | - Vandana Shashi
- Division of Medical Genetics, Department of Pediatrics, Duke University Medical Center, Durham, NC, USA
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16
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Mao D, Reuter CM, Ruzhnikov MR, Beck AE, Farrow EG, Emrick LT, Rosenfeld JA, Mackenzie KM, Robak L, Wheeler MT, Burrage LC, Jain M, Liu P, Calame D, Küry S, Sillesen M, Schmitz-Abe K, Tonduti D, Spaccini L, Iascone M, Genetti CA, Koenig MK, Graf M, Tran A, Alejandro M, Lee BH, Thiffault I, Agrawal PB, Bernstein JA, Bellen HJ, Chao HT, Acosta MT, Adam M, Adams DR, Agrawal PB, Alejandro ME, Allard P, Alvey J, Amendola L, Andrews A, Ashley EA, Azamian MS, Bacino CA, Bademci G, Baker E, Balasubramanyam A, Baldridge D, Bale J, Bamshad M, Barbouth D, Batzli GF, Bayrak-Toydemir P, Beck A, Beggs AH, Bejerano G, Bellen HJ, Bennet J, Berg-Rood B, Bernier R, Bernstein JA, Berry GT, Bican A, Bivona S, Blue E, Bohnsack J, Bonnenmann C, Bonner D, Botto L, Briere LC, Brokamp E, Burke EA, Burrage LC, Butte MJ, Byers P, Carey J, Carrasquillo O, Chang TCP, Chanprasert S, Chao HT, Clark GD, Coakley TR, Cobban LA, Cogan JD, Cole FS, Colley HA, Cooper CM, Cope H, Craigen WJ, Cunningham M, D’Souza P, Dai H, Dasari S, Davids M, Dayal JG, Dell’Angelica EC, Dhar SU, Dipple K, Doherty D, Dorrani N, Douine ED, Draper DD, Duncan L, Earl D, Eckstein DJ, Emrick LT, Eng CM, Esteves C, Estwick T, Fernandez L, Ferreira C, Fieg EL, Fisher PG, Fogel BL, Forghani I, Fresard L, Gahl WA, Glass I, Godfrey RA, Golden-Grant K, Goldman AM, Goldstein DB, Grajewski A, Groden CA, Gropman AL, Hahn S, Hamid R, Hanchard NA, Hayes N, High F, Hing A, Hisama FM, Holm IA, Hom J, Horike-Pyne M, Huang A, Huang Y, Isasi R, Jamal F, Jarvik GP, Jarvik J, Jayadev S, Jiang YH, Johnston JM, Karaviti L, Kelley EG, Kiley D, Kohane IS, Kohler JN, Krakow D, Krasnewich DM, Korrick S, Koziura M, Krier JB, Lalani SR, Lam B, Lam C, Lanpher BC, Lanza IR, Lau CC, LeBlanc K, Lee BH, Lee H, Levitt R, Lewis RA, Lincoln SA, Liu P, Liu XZ, Longo N, Loo SK, Loscalzo J, Maas RL, Macnamara EF, MacRae CA, Maduro VV, Majcherska MM, Malicdan MCV, Mamounas LA, Manolio TA, Mao R, Maravilla K, Markello TC, Marom R, Marth G, Martin BA, Martin MG, Martínez-Agosto JA, Marwaha S, McCauley J, McConkie-Rosell A, McCormack CE, McCray AT, Mefford H, Merritt JL, Might M, Mirzaa G, Morava-Kozicz E, Moretti PM, Morimoto M, Mulvihill JJ, Murdock DR, Nath A, Nelson SF, Newman JH, Nicholas SK, Nickerson D, Novacic D, Oglesbee D, Orengo JP, Pace L, Pak S, Pallais JC, Palmer CG, Papp JC, Parker NH, Phillips JA, Posey JE, Postlethwait JH, Potocki L, Pusey BN, Quinlan A, Raskind W, Raja AN, Renteria G, Reuter CM, Rives L, Robertson AK, Rodan LH, Rosenfeld JA, Rowley RK, Ruzhnikov M, Sacco R, Sampson JB, Samson SL, Saporta M, Scott CR, Schaechter J, Schedl T, Schoch K, Scott DA, Shakachite L, Sharma P, Shashi V, Shin J, Signer R, Sillari CH, Silverman EK, Sinsheimer JS, Sisco K, Smith KS, Solnica-Krezel L, Spillmann RC, Stoler JM, Stong N, Sullivan JA, Sun A, Sutton S, Sweetser DA, Sybert V, Tabor HK, Tamburro CP, Tan QKG, Tekin M, Telischi F, Thorson W, Tifft CJ, Toro C, Tran AA, Urv TK, Velinder M, Viskochil D, Vogel TP, Wahl CE, Wallace S, Walley NM, Walsh CA, Walker M, Wambach J, Wan J, Wang LK, Wangler MF, Ward PA, Wegner D, Wener M, Westerfield M, Wheeler MT, Wise AL, Wolfe LA, Woods JD, Yamamoto S, Yang J, Yoon AJ, Yu G, Zastrow DB, Zhao C, Zuchner S. De novo EIF2AK1 and EIF2AK2 Variants Are Associated with Developmental Delay, Leukoencephalopathy, and Neurologic Decompensation. Am J Hum Genet 2020; 106:570-583. [PMID: 32197074 PMCID: PMC7118694 DOI: 10.1016/j.ajhg.2020.02.016] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Accepted: 02/28/2020] [Indexed: 02/03/2023] Open
Abstract
EIF2AK1 and EIF2AK2 encode members of the eukaryotic translation initiation factor 2 alpha kinase (EIF2AK) family that inhibits protein synthesis in response to physiologic stress conditions. EIF2AK2 is also involved in innate immune response and the regulation of signal transduction, apoptosis, cell proliferation, and differentiation. Despite these findings, human disorders associated with deleterious variants in EIF2AK1 and EIF2AK2 have not been reported. Here, we describe the identification of nine unrelated individuals with heterozygous de novo missense variants in EIF2AK1 (1/9) or EIF2AK2 (8/9). Features seen in these nine individuals include white matter alterations (9/9), developmental delay (9/9), impaired language (9/9), cognitive impairment (8/9), ataxia (6/9), dysarthria in probands with verbal ability (6/9), hypotonia (7/9), hypertonia (6/9), and involuntary movements (3/9). Individuals with EIF2AK2 variants also exhibit neurological regression in the setting of febrile illness or infection. We use mammalian cell lines and proband-derived fibroblasts to further confirm the pathogenicity of variants in these genes and found reduced kinase activity. EIF2AKs phosphorylate eukaryotic translation initiation factor 2 subunit 1 (EIF2S1, also known as EIF2α), which then inhibits EIF2B activity. Deleterious variants in genes encoding EIF2B proteins cause childhood ataxia with central nervous system hypomyelination/vanishing white matter (CACH/VWM), a leukodystrophy characterized by neurologic regression in the setting of febrile illness and other stressors. Our findings indicate that EIF2AK2 missense variants cause a neurodevelopmental syndrome that may share phenotypic and pathogenic mechanisms with CACH/VWM.
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17
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Burdick KJ, Cogan JD, Rives LC, Robertson AK, Koziura ME, Brokamp E, Duncan L, Hannig V, Pfotenhauer J, Vanzo R, Paul MS, Bican A, Morgan T, Duis J, Newman JH, Hamid R, Phillips JA. Limitations of exome sequencing in detecting rare and undiagnosed diseases. Am J Med Genet A 2020; 182:1400-1406. [PMID: 32190976 DOI: 10.1002/ajmg.a.61558] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [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: 08/15/2019] [Revised: 01/28/2020] [Accepted: 03/03/2020] [Indexed: 12/21/2022]
Abstract
While exome sequencing (ES) is commonly the final diagnostic step in clinical genetics, it may miss diagnoses. To clarify the limitations of ES, we investigated the diagnostic yield of genetic tests beyond ES in our Undiagnosed Diseases Network (UDN) participants. We reviewed the yield of additional genetic testing including genome sequencing (GS), copy number variant (CNV), noncoding variant (NCV), repeat expansion (RE), or methylation testing in UDN cases with nondiagnostic ES results. Overall, 36/54 (67%) of total diagnoses were based on clinical findings and coding variants found by ES and 3/54 (6%) were based on clinical findings only. The remaining 15/54 (28%) required testing beyond ES. Of these, 7/15 (47%) had NCV, 6/15 (40%) CNV, and 2/15 (13%) had a RE or a DNA methylation disorder. Thus 18/54 (33%) of diagnoses were not solved exclusively by ES. Several methods were needed to detect and/or confirm the functional effects of the variants missed by ES, and in some cases by GS. These results indicate that tests to detect elusive variants should be considered after nondiagnostic preliminary steps. Further studies are needed to determine the cost-effectiveness of tests beyond ES that provide diagnoses and insights to possible treatment.
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Affiliation(s)
- Kendall J Burdick
- University of Massachusetts of Medical School, Worcester, Massachusetts, USA
| | - Joy D Cogan
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Lynette C Rives
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Amy K Robertson
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Mary E Koziura
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Elly Brokamp
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Laura Duncan
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Vickie Hannig
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Jean Pfotenhauer
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Rena Vanzo
- Lineagen Inc., Salt Lake City, Utah, USA
| | | | - Anna Bican
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Thomas Morgan
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Jessica Duis
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - John H Newman
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Rizwan Hamid
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - John A Phillips
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
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18
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Bhatia A, Mobley BC, Cogan J, Koziura ME, Brokamp E, Phillips J, Newman J, Moore SA, Hamid R. Magnetic Resonance Imaging characteristics in case of TOR1AIP1 muscular dystrophy. Clin Imaging 2019; 58:108-113. [PMID: 31299614 PMCID: PMC6893088 DOI: 10.1016/j.clinimag.2019.06.010] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2019] [Revised: 05/24/2019] [Accepted: 06/18/2019] [Indexed: 11/19/2022]
Abstract
Mutations in the torsinA-interacting protein 1 (TOR1AIP1) gene result in a severe muscular dystrophy with minimal literature in the pediatric population. We review a case of TOR1AIP1 gene mutation in a 16-year-old Caucasian female with a long history of muscle weakness. Extensive clinical workup was performed and MRI at time of initial presentation demonstrated no significant muscular atrophy with heterogenous STIR hyperintensity of the lower extremity muscles. MRI findings seven years later included extensive atrophy of the lower extremities, with severe progression, including the gluteal muscles, iliopsoas, rectus femoris, and obturator internus. There was also significant atrophy of the rectus abdominis and internal and external oblique muscles, and iliacus muscles. The MRI findings showed more proximal involvement of lower extremities and no atrophy of the tibialis anterior, making TOR1AIP1 the more likely genetic cause. Muscle biopsy findings supported TOR1AIP1 limb-girdle muscular dystrophy. Though rare, TOR1AIP1 gene mutation occurs in pediatric patients and MRI can aid in diagnosis and help differentiate from other types of muscular dystrophy. Genetic and pathology workup is also crucial to accurate diagnosis and possible treatment of these patients.
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Affiliation(s)
- Aashim Bhatia
- Department of Radiology, Vanderbilt University Medical Center, Nashville, TN, USA.
| | - Bret C Mobley
- Pathology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Joy Cogan
- Pediatrics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Mary E Koziura
- Pediatrics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Elly Brokamp
- Pediatrics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - John Phillips
- Pediatrics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - John Newman
- Internal Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Steven A Moore
- Department of Pathology, The University of Iowa, Iowa City, IA, USA
| | - Rizwan Hamid
- Pediatrics, Vanderbilt University Medical Center, Nashville, TN, USA
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19
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Reuter CM, Kohler JN, Bonner D, Zastrow D, Fernandez L, Dries A, Marwaha S, Davidson J, Brokamp E, Herzog M, Hong J, Macnamara E, Rosenfeld JA, Schoch K, Spillmann R, Loscalzo J, Krier J, Stoler J, Sweetser D, Palmer CGS, Phillips JA, Shashi V, Adams DA, Yang Y, Ashley EA, Fisher PG, Mulvihill JJ, Bernstein JA, Wheeler MT. Yield of whole exome sequencing in undiagnosed patients facing insurance coverage barriers to genetic testing. J Genet Couns 2019; 28:1107-1118. [PMID: 31478310 DOI: 10.1002/jgc4.1161] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [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: 03/13/2019] [Revised: 07/12/2019] [Accepted: 07/27/2019] [Indexed: 01/02/2023]
Abstract
BACKGROUND Despite growing evidence of diagnostic yield and clinical utility of whole exome sequencing (WES) in patients with undiagnosed diseases, there remain significant cost and reimbursement barriers limiting access to such testing. The diagnostic yield and resulting clinical actions of WES for patients who previously faced insurance coverage barriers have not yet been explored. METHODS We performed a retrospective descriptive analysis of clinical WES outcomes for patients facing insurance coverage barriers prior to clinical WES and who subsequently enrolled in the Undiagnosed Diseases Network (UDN). Clinical WES was completed as a result of participation in the UDN. Payer type, molecular diagnostic yield, and resulting clinical actions were evaluated. RESULTS Sixty-six patients in the UDN faced insurance coverage barriers to WES at the time of enrollment (67% public payer, 26% private payer). Forty-two of 66 (64%) received insurance denial for clinician-ordered WES, 19/66 (29%) had health insurance through a payer known not to cover WES, and 5/66 (8%) had previous payer denial of other genetic tests. Clinical WES results yielded a molecular diagnosis in 23 of 66 patients (35% [78% pediatric, 65% neurologic indication]). Molecular diagnosis resulted in clinical actions in 14 of 23 patients (61%). CONCLUSIONS These data demonstrate that a substantial proportion of patients who encountered insurance coverage barriers to WES had a clinically actionable molecular diagnosis, supporting the notion that WES has value as a covered benefit for patients who remain undiagnosed despite objective clinical findings.
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Affiliation(s)
- Chloe M Reuter
- Center for Undiagnosed Diseases, Stanford University School of Medicine, Stanford, CA.,Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA
| | - Jennefer N Kohler
- Center for Undiagnosed Diseases, Stanford University School of Medicine, Stanford, CA.,Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA
| | - Devon Bonner
- Center for Undiagnosed Diseases, Stanford University School of Medicine, Stanford, CA.,Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA
| | - Diane Zastrow
- Center for Undiagnosed Diseases, Stanford University School of Medicine, Stanford, CA.,Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA
| | - Liliana Fernandez
- Center for Undiagnosed Diseases, Stanford University School of Medicine, Stanford, CA.,Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA
| | - Annika Dries
- Center for Undiagnosed Diseases, Stanford University School of Medicine, Stanford, CA.,Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA
| | - Shruti Marwaha
- Center for Undiagnosed Diseases, Stanford University School of Medicine, Stanford, CA.,Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA
| | - Jean Davidson
- Center for Undiagnosed Diseases, Stanford University School of Medicine, Stanford, CA.,Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA
| | - Elly Brokamp
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN
| | - Matthew Herzog
- Department of Human Genetics, University of California Los Angeles, Los Angeles, CA
| | - Joyce Hong
- Department of Medicine, Brigham and Women's Hospital, Boston, MA
| | - Ellen Macnamara
- Undiagnosed Diseases Program, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD
| | - Jill A Rosenfeld
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX
| | - Kelly Schoch
- Department of Pediatrics, Duke University Medical Center, Durham, NC
| | - Rebecca Spillmann
- Department of Pediatrics, Duke University Medical Center, Durham, NC
| | | | - Joseph Loscalzo
- Department of Medicine, Brigham and Women's Hospital, Boston, MA
| | - Joel Krier
- Department of Medicine, Brigham and Women's Hospital, Boston, MA
| | - Joan Stoler
- Division of Genetics, Boston Children's Hospital, Boston, MA
| | - David Sweetser
- Division of Medical Genetics and Metabolism, Department of Pediatrics, Massachusetts General Hospital, Boston, MA
| | - Christina G S Palmer
- Department of Human Genetics, University of California Los Angeles, Los Angeles, CA.,Psychiatry & Biobehavioral Sciences, University of California Los Angeles, Los Angeles, CA.,Institute for Society & Genetics, University of California Los Angeles, Los Angeles, CA
| | - John A Phillips
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN
| | - Vandana Shashi
- Department of Pediatrics, Duke University Medical Center, Durham, NC
| | - David A Adams
- Undiagnosed Diseases Program, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD
| | - Yaping Yang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX
| | - Euan A Ashley
- Center for Undiagnosed Diseases, Stanford University School of Medicine, Stanford, CA.,Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA.,Department of Genetics, Stanford University School of Medicine, Stanford, CA
| | - Paul G Fisher
- Center for Undiagnosed Diseases, Stanford University School of Medicine, Stanford, CA.,Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA.,Department of Pediatrics, Stanford University School of Medicine, Stanford, CA
| | - John J Mulvihill
- Division of Genomic Medicine, National Human Genome Research Institute, Bethesda, MD
| | - Jonathan A Bernstein
- Center for Undiagnosed Diseases, Stanford University School of Medicine, Stanford, CA.,Department of Pediatrics, Stanford University School of Medicine, Stanford, CA
| | - Matthew T Wheeler
- Center for Undiagnosed Diseases, Stanford University School of Medicine, Stanford, CA.,Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA
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20
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Patrick AE, Wang W, Brokamp E, Graham TB, Aune TM, Duis JB. Juvenile idiopathic arthritis associated with a mutation in GATA3. Arthritis Res Ther 2019; 21:156. [PMID: 31238969 PMCID: PMC6593533 DOI: 10.1186/s13075-019-1946-3] [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] [Received: 01/04/2019] [Accepted: 06/17/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND GATA3 is a transcription factor that is important during development and plays a role in differentiation and activity of immune cells, particularly T cells. Abnormal T cell function is found in autoimmune arthritis. We present the first known case of autoimmune arthritis associated with a novel GATA3 mutation. METHODS Whole exome sequencing of the proband was performed on a clinical basis. Peripheral blood mononuclear cells (PBMCs) were collected from the proband, healthy sibling, and parent. cDNA prepared from RNA was analyzed with polymerase chain reaction and Sanger sequencing. Intracellular proteins were assessed by immunoblot of PBMC homogenates. GATA3 in vitro activity was measured in HeLa cell cultures expressing a mammalian expression vector containing GATA3 or mutants generated by site-directed mutagenesis. GATA3 transcriptional activity was examined using a luciferase reporter assay system. T helper cell ex vivo function was evaluated by stimulating PBMCs to differentiate into effector T cells along Th0, Th1, Th2, and Th17 lineages, and re-stimulating effector cells to secrete cytokines. Cytokine production was measured by enzyme-linked immunosorbent assay. RESULTS The proband is the first known case of autoimmune arthritis associated with a mutation in GATA3. The proband M401VfsX106 protein is expressed and has a dominant negative function on GATA3 transcriptional activity. The proband PBMCs have markedly increased differentiation along the Th1 and Th17 pathways, with decreased differentiation along the Th2 pathway. Unexpectedly, Th0 cells from the proband express high levels of IFNγ. CONCLUSIONS Our research presents the first known case of autoimmune arthritis associated with a mutation in GATA3. This work expands the phenotypic spectrum of GATA3 mutations. It reveals the novel insight that decreased and altered GATA3 activity coincides with autoimmune arthritis. This work suggests that modulation of GATA3 may be a therapeutic approach for patients with autoimmune arthritis.
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Affiliation(s)
- Anna E Patrick
- Division of Rheumatology, Department of Pediatrics, Vanderbilt University Medical Center, 1211 Medical Center Drive, Nashville, TN, 37232, USA
| | - Wei Wang
- GeneDx, Inc, 207 Perry Parkway, Gaithersburg, MD, 20877, USA
| | - Elly Brokamp
- Division of Medical Genetics and Genomic Medicine, Department of Pediatrics, Vanderbilt University Medical Center, 1211 Medical Center Drive, Nashville, TN, 37232, USA
| | - Thomas Brent Graham
- Division of Rheumatology, Department of Pediatrics, Vanderbilt University Medical Center, 1211 Medical Center Drive, Nashville, TN, 37232, USA
| | - Thomas M Aune
- Division of Rheumatology and Immunology, Department of Medicine, Vanderbilt University Medical Center, 1211 Medical Center Drive, Nashville, TN, 37232, USA.
| | - Jessica B Duis
- Division of Medical Genetics and Genomic Medicine, Department of Pediatrics, Vanderbilt University Medical Center, 1211 Medical Center Drive, Nashville, TN, 37232, USA
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21
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Duis J, van Wattum PJ, Scheimann A, Salehi P, Brokamp E, Fairbrother L, Childers A, Shelton AR, Bingham NC, Shoemaker AH, Miller JL. A multidisciplinary approach to the clinical management of Prader-Willi syndrome. Mol Genet Genomic Med 2019; 7:e514. [PMID: 30697974 PMCID: PMC6418440 DOI: 10.1002/mgg3.514] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [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: 04/23/2018] [Revised: 10/16/2018] [Accepted: 10/22/2018] [Indexed: 12/14/2022] Open
Abstract
Background Prader–Willi syndrome (PWS) is a complex neuroendocrine disorder affecting approximately 1/15,000–1/30,000 people. Unmet medical needs of individuals with PWS make it a rare disease that models the importance of multidisciplinary approaches to care with collaboration between academic centers, medical homes, industry, and parent organizations. Multidisciplinary clinics support comprehensive, patient‐centered care for individuals with complex genetic disorders and their families. Value comes from improved communication and focuses on quality family‐centered care. Methods Interviews with medical professionals, scientists, managed care experts, parents, and individuals with PWS were conducted from July 1 to December 1, 2016. Review of the literature was used to provide support. Results Data are presented based on consensus from these interviews by specialty focusing on unique aspects of care, research, and management. We have also defined the Center of Excellence beyond the multidisciplinary clinic. Conclusion Establishment of clinics motivates collaboration to provide evidence‐based new standards of care, increases the knowledge base including through randomized controlled trials, and offers an additional resource for the community. They have a role in global telemedicine, including to rural areas with few resources, and create opportunities for clinical work to inform basic and translational research. As a care team, we are currently charged with understanding the molecular basis of PWS beyond the known genetic cause; developing appropriate clinical outcome measures and biomarkers; bringing new therapies to change the natural history of disease; improving daily patient struggles, access to care, and caregiver burden; and decreasing healthcare load. Based on experience to date with a PWS multidisciplinary clinic, we propose a design for this approach and emphasize the development of “Centers of Excellence.” We highlight the dearth of evidence for management approaches creating huge gaps in care practices as a means to illustrate the importance of the collaborative environment and translational approaches.
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Affiliation(s)
- Jessica Duis
- Division of Medical Genetics and Genomic Medicine, Department of Pediatrics, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Pieter J van Wattum
- Department of Psychiatry, Child Study Center, Yale School of Medicine, New Haven, Connecticut.,Clifford Beers Clinic, New Haven, Connecticut
| | - Ann Scheimann
- Pediatric Gastroenterology, Johns Hopkins Children's Center, Baltimore, Maryland
| | - Parisa Salehi
- Division of Endocrinology and Diabetes, Seattle Children's, University of Washington, Seattle, Washington
| | - Elly Brokamp
- Division of Medical Genetics and Genomic Medicine, Department of Pediatrics, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Laura Fairbrother
- Division of Medical Genetics and Genomic Medicine, Department of Pediatrics, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Anna Childers
- Division of Medical Genetics and Genomic Medicine, Department of Pediatrics, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Althea Robinson Shelton
- Neuro-Sleep Division, Department of Neurology, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Nathan C Bingham
- Division of Pediatric Endocrinology, Department of Pediatrics, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Ashley H Shoemaker
- Division of Pediatric Endocrinology, Department of Pediatrics, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Jennifer L Miller
- Pediatric Endocrinology, University of Florida, Gainesville, Florida
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22
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Macnamara EF, Schoch K, Kelley EG, Fieg E, Brokamp E, Signer R, LeBlanc K, McConkie-Rosell A, Palmer CGS. Cases from the Undiagnosed Diseases Network: The continued value of counseling skills in a new genomic era. J Genet Couns 2019; 28:194-201. [PMID: 30680851 DOI: 10.1002/jgc4.1091] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [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: 09/10/2018] [Revised: 12/14/2018] [Accepted: 12/16/2018] [Indexed: 01/15/2023]
Abstract
The "diagnostic odyssey" is well known and described in genetic counseling literature. Studies addressing the psychological, emotional, and financial costs of not having a diagnosis have shown how it permeates the lives of patients and families. The Undiagnosed Diseases Network aims to end this odyssey by providing diagnoses to individuals with undiagnosed conditions through multidisciplinary evaluations, whole exome and genome sequencing, and basic science research. It also provides an opportunity to learn from patients and families and to better understand their journeys and the impact of receiving a diagnosis. Seven cases are presented that outline challenges that come from working with chronically undiagnosed and newly diagnosed patients in a time when sequencing for clinical diagnosis is rapidly increasing. They illuminate the emotional journey of patients and families searching for a diagnosis and the mental health problems, financial distress, and chaos that can accompany not having answers. They also illustrate the surprising reactions patients and families can have to receiving a diagnosis, including anger, grief, and disappointment. While the lessons learned from these families are not novel, new strategies are presented for handling these challenges in undiagnosed and ultra-rare populations, groups that will increase with the rise of clinical sequencing.
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Affiliation(s)
- Ellen F Macnamara
- National Institutes of Health, Undiagnosed Diseases Program, Common Fund, Office of the Director, NIH, Bethesda, Maryland
| | - Kelly Schoch
- Division of Medical Genetics, Duke University Medical Center, Durham, North Carolina
| | - Emily G Kelley
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts
| | - Elizabeth Fieg
- Division of Genetics, Brigham and Women's Hospital, Boston, Massachusetts
| | - Elly Brokamp
- Division of Genetics and Genomic Medicine, Vanderbilt University Medical Center, Nashville, Tennessee
| | | | - Rebecca Signer
- Department of Human Genetics, University of California, Los Angeles, California
| | - Kimberly LeBlanc
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts
| | - Allyn McConkie-Rosell
- Division of Medical Genetics, Duke University Medical Center, Durham, North Carolina
| | - Christina G S Palmer
- Department of Human Genetics, University of California, Los Angeles, California.,Department of Psychiatry & Biobehavioral Sciences, University of California, Los Angeles, California.,Institute for Society and Genetics, University of California, Los Angeles, California
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