1
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McFadden JR, Tolete CDP, Huang Y, Macnamara E, Sept D, Nesterova G, Gahl WA, Sackett DL, Malicdan MCV. Clinical, genetic, and structural characterization of a novel TUBB4B tubulinopathy. Mol Genet Metab Rep 2023; 36:100990. [PMID: 37448631 PMCID: PMC10336574 DOI: 10.1016/j.ymgmr.2023.100990] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2023] [Accepted: 06/25/2023] [Indexed: 07/15/2023] Open
Abstract
Microtubules are cytoskeletal polymers of ⍺/β-tubulin heterodimers essential for a wide range of cellular processes. Pathogenic variations in microtubule-encoding genes (e.g., TUBB4B, which encodes the β-4B tubulin isotype) are responsible for a wide spectrum of cerebral malformations, collectively referred to as "tubulinopathies." The phenotypic manifestation of TUBB4B-associated tubulinopathy is Leber congenital amaurosis with early-onset deafness (LCAEOD), an autosomal dominant syndrome characterized by photoreceptor and cochlear cell loss; all known patients have pathogenic variations in amino acid R391. We present the clinical and molecular genetics findings of a 16-year-old female with a de novo missense variant in exon 1 of TUBB4B, c.32 A > G (p.Gln11Arg; Q11R). In addition to hearing loss and hyperopia without retinal abnormalities, our proband presented with two phenotypes of unknown genetic etiology, i.e., renal tubular Fanconi Syndrome (FS) and hypophosphatemic rickets (HR). The Q11R variant expands the genetic basis of early sensory hearing loss; its consequences with respect to microtubule structure are described. A mechanistic explanation for the FS and rickets, involving microtubule-mediated translocation of transporter proteins to and from the apical membrane of renal proximal tubular cells, is proposed.
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Affiliation(s)
- Jason R. McFadden
- NIH Undiagnosed Diseases Program, National Human Genome Research Institute, NIH, Bethesda, MD 20892, USA
| | - Christina Deanne P. Tolete
- NIH Undiagnosed Diseases Program, National Human Genome Research Institute, NIH, Bethesda, MD 20892, USA
| | - Yan Huang
- NIH Undiagnosed Diseases Program, National Human Genome Research Institute, NIH, Bethesda, MD 20892, USA
| | - Ellen Macnamara
- NIH Undiagnosed Diseases Program, National Human Genome Research Institute, NIH, Bethesda, MD 20892, USA
| | - David Sept
- Departments of Biomedical Engineering and Biophysics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Galina Nesterova
- NIH Undiagnosed Diseases Program, National Human Genome Research Institute, NIH, Bethesda, MD 20892, USA
| | - William A. Gahl
- NIH Undiagnosed Diseases Program, National Human Genome Research Institute, NIH, Bethesda, MD 20892, USA
- Medical Genetics Branch, National Human Genome Research Institute, NIH, Bethesda, MD 20892-1851, USA
| | - Dan L. Sackett
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD 20892, USA
| | - May Christine V. Malicdan
- NIH Undiagnosed Diseases Program, National Human Genome Research Institute, NIH, Bethesda, MD 20892, USA
- Medical Genetics Branch, National Human Genome Research Institute, NIH, Bethesda, MD 20892-1851, USA
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2
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Burke EA, Sturgeon M, Zastrow DB, Fernandez L, Prybol C, Marwaha S, Frothingham EP, Ward PA, Eng CM, Fresard L, Montgomery SB, Enns GM, Fisher PG, Wolfe LA, Harding B, Carrington B, Bishop K, Sood R, Huang Y, Elkahloun A, Toro C, Bassuk AG, Wheeler MT, Markello TC, Gahl WA, Malicdan MCV. Compound heterozygous KCTD7 variants in progressive myoclonus epilepsy. J Neurogenet 2021; 35:74-83. [PMID: 33970744 DOI: 10.1080/01677063.2021.1892095] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
KCTD7 is a member of the potassium channel tetramerization domain-containing protein family and has been associated with progressive myoclonic epilepsy (PME), characterized by myoclonus, epilepsy, and neurological deterioration. Here we report four affected individuals from two unrelated families in which we identified KCTD7 compound heterozygous single nucleotide variants through exome sequencing. RNAseq was used to detect a non-annotated splicing junction created by a synonymous variant in the second family. Whole-cell patch-clamp analysis of neuroblastoma cells overexpressing the patients' variant alleles demonstrated aberrant potassium regulation. While all four patients experienced many of the common clinical features of PME, they also showed variable phenotypes not previously reported, including dysautonomia, brain pathology findings including a significantly reduced thalamus, and the lack of myoclonic seizures. To gain further insight into the pathogenesis of the disorder, zinc finger nucleases were used to generate kctd7 knockout zebrafish. Kctd7 homozygous mutants showed global dysregulation of gene expression and increased transcription of c-fos, which has previously been correlated with seizure activity in animal models. Together these findings expand the known phenotypic spectrum of KCTD7-associated PME, report a new animal model for future studies, and contribute valuable insights into the disease.
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Affiliation(s)
- Elizabeth A Burke
- NIH Undiagnosed Diseases Program, Common Fund, Office of the Director, NIH and National Human Genome Research Institute, NIH, Bethesda, MD, USA
| | - Morgan Sturgeon
- Department of Pediatrics, University of Iowa, Iowa City, IA, USA
| | - Diane B Zastrow
- Center for Undiagnosed Diseases, Stanford University School of Medicine, Stanford, CA, USA
| | - Liliana Fernandez
- Center for Undiagnosed Diseases, Stanford University School of Medicine, Stanford, CA, USA
| | - Cameron Prybol
- Center for Undiagnosed Diseases, Stanford University School of Medicine, Stanford, CA, USA
| | - Shruti Marwaha
- Center for Undiagnosed Diseases, Stanford University School of Medicine, Stanford, CA, USA
| | | | - Patricia A Ward
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Christine M Eng
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Laure Fresard
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Stephen B Montgomery
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA.,Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Gregory M Enns
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
| | - Paul G Fisher
- Center for Undiagnosed Diseases, Stanford University School of Medicine, Stanford, CA, USA.,Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA.,Department of Neurology, Stanford University School of Medicine, Stanford, CA, USA
| | - Lynne A Wolfe
- NIH Undiagnosed Diseases Program, Common Fund, Office of the Director, NIH and National Human Genome Research Institute, NIH, Bethesda, MD, USA
| | - Brian Harding
- Departments of Pathology and Lab Medicine (Neuropathology), Children's Hospital of Philadelphia and the Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Blake Carrington
- Zebrafish Core, Translational and Functional Genomics Branch, National Human Genome Research Institute, NIH, Bethesda, MD, USA
| | - Kevin Bishop
- Zebrafish Core, Translational and Functional Genomics Branch, National Human Genome Research Institute, NIH, Bethesda, MD, USA
| | - Raman Sood
- Zebrafish Core, Translational and Functional Genomics Branch, National Human Genome Research Institute, NIH, Bethesda, MD, USA
| | - Yan Huang
- NIH Undiagnosed Diseases Program, Common Fund, Office of the Director, NIH and National Human Genome Research Institute, NIH, Bethesda, MD, USA
| | - Abdel Elkahloun
- Microarray Core, Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, NIH, Bethesda, MD, USA
| | - Camilo Toro
- NIH Undiagnosed Diseases Program, Common Fund, Office of the Director, NIH and National Human Genome Research Institute, NIH, Bethesda, MD, USA
| | | | - Matthew T Wheeler
- Center for Undiagnosed Diseases, Stanford University School of Medicine, Stanford, CA, USA
| | - Thomas C Markello
- NIH Undiagnosed Diseases Program, Common Fund, Office of the Director, NIH and National Human Genome Research Institute, NIH, Bethesda, MD, USA
| | - William A Gahl
- NIH Undiagnosed Diseases Program, Common Fund, Office of the Director, NIH and National Human Genome Research Institute, NIH, Bethesda, MD, USA.,Medical Genetics Branch, National Human Genome Research Institute, NIH, Bethesda, MD, USA
| | - May Christine V Malicdan
- NIH Undiagnosed Diseases Program, Common Fund, Office of the Director, NIH and National Human Genome Research Institute, NIH, Bethesda, MD, USA
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3
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Macnamara EF, D’Souza P, Tifft CJ. The undiagnosed diseases program: Approach to diagnosis. TRANSLATIONAL SCIENCE OF RARE DISEASES 2020; 4:179-188. [PMID: 32477883 PMCID: PMC7250153 DOI: 10.3233/trd-190045] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Undiagnosed and rare conditions are collectively common and affect millions of people worldwide. The NIH Undiagnosed Diseases Program (UDP) strives to achieve both a comprehensive diagnosis and a better understanding of the mechanisms of disease for many of these individuals. Through the careful review of records, a well-orchestrated inpatient evaluation, genomic sequencing and testing, and with the use of emerging strategies such as matchmaking programs, the UDP succeeds nearly 30 percent of the time for these highly selective cases. Although the UDP process is built on a unique set of resources, case examples demonstrate steps genetic professionals can take, in both clinical and research settings, to arrive at a diagnosis for their most challenging cases.
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Affiliation(s)
- Ellen F. Macnamara
- National Institutes of Health, Undiagnosed Diseases Program, Common Fund, Office of the Director, Bethesda, MD, USA
| | - Precilla D’Souza
- National Institutes of Health, Undiagnosed Diseases Program, Common Fund, Office of the Director, Bethesda, MD, USA
| | - Undiagnosed Diseases Network
- National Institutes of Health, Undiagnosed Diseases Program, Common Fund, Office of the Director, Bethesda, MD, USA
- Office of the Clinical Director, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Cynthia J. Tifft
- National Institutes of Health, Undiagnosed Diseases Program, Common Fund, Office of the Director, Bethesda, MD, USA
- Office of the Clinical Director, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
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4
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Kuo ME, Theil AF, Kievit A, Malicdan MC, Introne WJ, Christian T, Verheijen FW, Smith DEC, Mendes MI, Hussaarts-Odijk L, van der Meijden E, van Slegtenhorst M, Wilke M, Vermeulen W, Raams A, Groden C, Shimada S, Meyer-Schuman R, Hou YM, Gahl WA, Antonellis A, Salomons GS, Mancini GMS. Cysteinyl-tRNA Synthetase Mutations Cause a Multi-System, Recessive Disease That Includes Microcephaly, Developmental Delay, and Brittle Hair and Nails. Am J Hum Genet 2019; 104:520-529. [PMID: 30824121 DOI: 10.1016/j.ajhg.2019.01.006] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Accepted: 01/15/2019] [Indexed: 02/06/2023] Open
Abstract
Aminoacyl-tRNA synthetases (ARSs) are essential enzymes responsible for charging tRNA molecules with cognate amino acids. Consistent with the essential function and ubiquitous expression of ARSs, mutations in 32 of the 37 ARS-encoding loci cause severe, early-onset recessive phenotypes. Previous genetic and functional data suggest a loss-of-function mechanism; however, our understanding of the allelic and locus heterogeneity of ARS-related disease is incomplete. Cysteinyl-tRNA synthetase (CARS) encodes the enzyme that charges tRNACys with cysteine in the cytoplasm. To date, CARS variants have not been implicated in any human disease phenotype. Here, we report on four subjects from three families with complex syndromes that include microcephaly, developmental delay, and brittle hair and nails. Each affected person carries bi-allelic CARS variants: one individual is compound heterozygous for c.1138C>T (p.Gln380∗) and c.1022G>A (p.Arg341His), two related individuals are compound heterozygous for c.1076C>T (p.Ser359Leu) and c.1199T>A (p.Leu400Gln), and one individual is homozygous for c.2061dup (p.Ser688Glnfs∗2). Measurement of protein abundance, yeast complementation assays, and assessments of tRNA charging indicate that each CARS variant causes a loss-of-function effect. Compared to subjects with previously reported ARS-related diseases, individuals with bi-allelic CARS variants are unique in presenting with a brittle-hair-and-nail phenotype, which most likely reflects the high cysteine content in human keratins. In sum, our efforts implicate CARS variants in human inherited disease, expand the locus and clinical heterogeneity of ARS-related clinical phenotypes, and further support impaired tRNA charging as the primary mechanism of recessive ARS-related disease.
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Affiliation(s)
- Molly E Kuo
- Cellular and Molecular Biology Program, University of Michigan Medical School, Ann Arbor, MI 48109, USA; Medical Scientist Training Program, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Arjan F Theil
- Department of Molecular Genetics, Oncode Institute, Erasmus Medical Center, University Medical Center Rotterdam, Dr. Molewaterplein 40, 3015 CN Rotterdam, the Netherlands
| | - Anneke Kievit
- Department of Clinical Genetics, Erasmus Medical Center, University Medical Center, 3015 GD Rotterdam, the Netherlands
| | - May Christine Malicdan
- Undiagnosed Diseases Program and Office of the Clinical Director, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Wendy J Introne
- Undiagnosed Diseases Program and Office of the Clinical Director, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Thomas Christian
- Department of Biochemistry and Molecular Biochemistry, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Frans W Verheijen
- Department of Clinical Genetics, Erasmus Medical Center, University Medical Center, 3015 GD Rotterdam, the Netherlands
| | - Desiree E C Smith
- Metabolic Unit, Department of Clinical Chemistry, Amsterdam University Medical Center and Amsterdam Gastroenterology and Metabolism, Vrije Universiteit Amsterdam, Amsterdam Neuroscience, 1081 HZ Amsterdam, the Netherlands
| | - Marisa I Mendes
- Metabolic Unit, Department of Clinical Chemistry, Amsterdam University Medical Center and Amsterdam Gastroenterology and Metabolism, Vrije Universiteit Amsterdam, Amsterdam Neuroscience, 1081 HZ Amsterdam, the Netherlands
| | - Lidia Hussaarts-Odijk
- Department of Clinical Genetics, Erasmus Medical Center, University Medical Center, 3015 GD Rotterdam, the Netherlands
| | - Eric van der Meijden
- Department of Clinical Genetics, Erasmus Medical Center, University Medical Center, 3015 GD Rotterdam, the Netherlands
| | - Marjon van Slegtenhorst
- Department of Clinical Genetics, Erasmus Medical Center, University Medical Center, 3015 GD Rotterdam, the Netherlands
| | - Martina Wilke
- Department of Clinical Genetics, Erasmus Medical Center, University Medical Center, 3015 GD Rotterdam, the Netherlands
| | - Wim Vermeulen
- Department of Molecular Genetics, Oncode Institute, Erasmus Medical Center, University Medical Center Rotterdam, Dr. Molewaterplein 40, 3015 CN Rotterdam, the Netherlands
| | - Anja Raams
- Department of Molecular Genetics, Oncode Institute, Erasmus Medical Center, University Medical Center Rotterdam, Dr. Molewaterplein 40, 3015 CN Rotterdam, the Netherlands
| | - Catherine Groden
- Undiagnosed Diseases Program and Office of the Clinical Director, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Shino Shimada
- Undiagnosed Diseases Program and Office of the Clinical Director, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Rebecca Meyer-Schuman
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Ya Ming Hou
- Department of Biochemistry and Molecular Biochemistry, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - William A Gahl
- Undiagnosed Diseases Program and Office of the Clinical Director, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Anthony Antonellis
- Cellular and Molecular Biology Program, University of Michigan Medical School, Ann Arbor, MI 48109, USA; Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI 48109, USA; Department of Neurology, University of Michigan Medical School, Ann Arbor, MI 48109, USA.
| | - Gajja S Salomons
- Metabolic Unit, Department of Clinical Chemistry, Amsterdam University Medical Center and Amsterdam Gastroenterology and Metabolism, Vrije Universiteit Amsterdam, Amsterdam Neuroscience, 1081 HZ Amsterdam, the Netherlands; Genetic Metabolic Diseases, Amsterdam University Medical Center, University of Amsterdam, 1081 HZ Amsterdam, the Netherlands.
| | - Grazia M S Mancini
- Department of Clinical Genetics, Erasmus Medical Center, University Medical Center, 3015 GD Rotterdam, the Netherlands
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5
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Chin JJ, Behnam B, Davids M, Sharma P, Zein WM, Wang C, Chepa-Lotrea X, Gallantine WB, Toro C, Adams DR, Tifft CJ, Gahl WA, Malicdan MCV. Novel mutations in CLN6 cause late-infantile neuronal ceroid lipofuscinosis without visual impairment in two unrelated patients. Mol Genet Metab 2019; 126:188-195. [PMID: 30528883 DOI: 10.1016/j.ymgme.2018.12.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Revised: 12/02/2018] [Accepted: 12/02/2018] [Indexed: 12/25/2022]
Abstract
CLN6 is a transmembrane protein located in the endoplasmic reticulum that is involved in lysosomal acidification. Mutations in CLN6 cause late-infantile neuronal ceroid lipofuscinosis (LINCL), and teenage and adult onset NCL without visual impairment. Here we describe two pediatric patients with LINCL from unrelated families who were evaluated at the National Institutes of Health. Both children exhibited typical phenotypes associated with LINCL except that they lacked the expected visual impairment. Whole exome sequencing identified novel biallelic mutations in CLN6, i.e., c.218-220dupGGT (p.Trp73dup) and c.296A > G (p.Lys99Arg) in Proband 1 and homozygous c.723G > T (p.Met241Ile) in Proband 2. Expression analysis in dermal fibroblasts showed a small increase in CLN6 protein levels. Electron micrographs of these fibroblasts demonstrated large numbers of small membrane-bound vesicles, in addition to lipofuscin deposits. LysoTracker™ Red intensity was increased in fibroblasts from both patients. This study supports a role for CLN6 in lysosomal homeostasis, and highlights the importance of considering CLN6 mutations in the diagnosis of Batten Disease even in patients with normal vision.
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Affiliation(s)
- Joseph J Chin
- NIH Undiagnosed Diseases Program, Common Fund, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, United States
| | - Babak Behnam
- NIH Undiagnosed Diseases Program, Common Fund, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, United States
| | - Mariska Davids
- NIH Undiagnosed Diseases Program, Common Fund, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, United States
| | - Prashant Sharma
- NIH Undiagnosed Diseases Program, Common Fund, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, United States
| | - Wadih M Zein
- National Eye Institute, National Institute of Health, Bethesda, MD, United States
| | - Camille Wang
- NIH Undiagnosed Diseases Program, Common Fund, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, United States
| | - Xenia Chepa-Lotrea
- NIH Undiagnosed Diseases Program, Common Fund, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, United States
| | | | - Camilo Toro
- NIH Undiagnosed Diseases Program, Common Fund, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, United States; Office of the Clinical Director, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, United States
| | - David R Adams
- NIH Undiagnosed Diseases Program, Common Fund, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, United States; Office of the Clinical Director, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, United States
| | - Cynthia J Tifft
- NIH Undiagnosed Diseases Program, Common Fund, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, United States; Office of the Clinical Director, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, United States
| | - William A Gahl
- NIH Undiagnosed Diseases Program, Common Fund, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, United States; Office of the Clinical Director, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, United States
| | - May Christine V Malicdan
- NIH Undiagnosed Diseases Program, Common Fund, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, United States; Office of the Clinical Director, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, United States.
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6
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Gartner V, Markello TC, Macnamara E, De Biase A, Thurm A, Joseph L, Beggs A, Schmahmann JD, Berry GT, Anselm I, Boslet E, Tifft CJ, Gahl WA, Lee PR. Novel variants in SPTAN1 without epilepsy: An expansion of the phenotype. Am J Med Genet A 2018; 176:2768-2776. [PMID: 30548380 PMCID: PMC11157598 DOI: 10.1002/ajmg.a.40628] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Revised: 07/19/2018] [Accepted: 08/13/2018] [Indexed: 11/11/2022]
Abstract
We describe two unrelated children with de novo variants in the non-erythrocytic alpha-II-spectrin (SPTAN1) gene who have hypoplastic brain structures, intellectual disability, and both fine and gross motor impairments. Using agnostic exome sequencing, we identified a nonsense variant creating a premature stop codon in exon 21 of SPTAN1, and in a second patient we identified an intronic substitution in SPTAN1 prior to exon 50 creating a new donor acceptor site. Neither of these variants has been described previously. Although some of these patients' features are consistent with the known SPTAN1 encephalopathy phenotype, these two children do not have epilepsy, in contrast to reports about nearly every other patient with heterozygous SPTAN1 variants and in all patients with a variant near the C-terminal coding region. Moreover, both children have abnormal thyroid function, which has not been previously reported in association with SPTAN1 variant. We present a detailed discussion of the clinical manifestations of these two unique SPTAN1 variants and provide evidence that both variants result in reduced mRNA expression despite different locations within the gene and clinical phenotypes. These findings expand the motor, cognitive, and behavioral spectrum of the SPTAN1-associated phenotype and invite speculation about underlying pathophysiologies.
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Affiliation(s)
- Valerie Gartner
- Office of the Clinical Director, NHGRI, and NIH Undiagnosed Diseases Program, Office of the Director, National Institutes of Health, Bethesda, Maryland
| | - Thomas C. Markello
- Office of the Clinical Director, NHGRI, and NIH Undiagnosed Diseases Program, Office of the Director, National Institutes of Health, Bethesda, Maryland
| | - Ellen Macnamara
- Office of the Clinical Director, NHGRI, and NIH Undiagnosed Diseases Program, Office of the Director, National Institutes of Health, Bethesda, Maryland
| | | | - Audrey Thurm
- Neurodevelopmental and Behavioral Phenotyping Service, Office of the Clinical Director, National Institute of Mental Health, National Institutes of Health, Bethesda, Maryland
| | - Lisa Joseph
- Neurodevelopmental and Behavioral Phenotyping Service, Office of the Clinical Director, National Institute of Mental Health, National Institutes of Health, Bethesda, Maryland
| | - Alan Beggs
- Division of Genetics and Genomics, The Manton Center for Orphan Disease Research, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts
| | - Jeremy D. Schmahmann
- Ataxia Unit, Cognitive Behavioral Neurology Unit, Laboratory for Neuroanatomy and Cerebellar Neurobiology, Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - Gerard T. Berry
- Division of Genetics and Genomics, The Manton Center for Orphan Disease Research, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts
| | - Irina Anselm
- Department of Neurology, Boston Children’s Hospital and Harvard Medical School, Boston, Massachusetts
| | - Emma Boslet
- Office of the Clinical Director, NHGRI, and NIH Undiagnosed Diseases Program, Office of the Director, National Institutes of Health, Bethesda, Maryland
| | - Cynthia J. Tifft
- Office of the Clinical Director, NHGRI, and NIH Undiagnosed Diseases Program, Office of the Director, National Institutes of Health, Bethesda, Maryland
| | - William A. Gahl
- Office of the Clinical Director, NHGRI, and NIH Undiagnosed Diseases Program, Office of the Director, National Institutes of Health, Bethesda, Maryland
| | - Paul R. Lee
- Office of the Clinical Director, NHGRI, and NIH Undiagnosed Diseases Program, Office of the Director, National Institutes of Health, Bethesda, Maryland
- Division of Neurology Products, Center for Drug Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland
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7
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Oprescu SN, Chepa-Lotrea X, Takase R, Golas G, Markello TC, Adams DR, Toro C, Gropman AL, Hou YM, Malicdan MCV, Gahl WA, Tifft CJ, Antonellis A. Compound heterozygosity for loss-of-function GARS variants results in a multisystem developmental syndrome that includes severe growth retardation. Hum Mutat 2017; 38:1412-1420. [PMID: 28675565 DOI: 10.1002/humu.23287] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Revised: 05/17/2017] [Accepted: 06/16/2017] [Indexed: 01/25/2023]
Abstract
Aminoacyl-tRNA synthetases (ARSs) are ubiquitously expressed enzymes that ligate amino acids onto tRNA molecules. Genes encoding ARSs have been implicated in myriad dominant and recessive disease phenotypes. Glycyl-tRNA synthetase (GARS) is a bifunctional ARS that charges tRNAGly in the cytoplasm and mitochondria. GARS variants have been associated with dominant Charcot-Marie-Tooth disease but have not been convincingly implicated in recessive phenotypes. Here, we describe a patient from the NIH Undiagnosed Diseases Program with a multisystem, developmental phenotype. Whole-exome sequence analysis revealed that the patient is compound heterozygous for one frameshift (p.Glu83Ilefs*6) and one missense (p.Arg310Gln) GARS variant. Using in vitro and in vivo functional studies, we show that both GARS variants cause a loss-of-function effect: the frameshift variant results in depleted protein levels and the missense variant reduces GARS tRNA charging activity. In support of GARS variant pathogenicity, our patient shows striking phenotypic overlap with other patients having ARS-related recessive diseases, including features associated with variants in both cytoplasmic and mitochondrial ARSs; this observation is consistent with the essential function of GARS in both cellular locations. In summary, our clinical, genetic, and functional analyses expand the phenotypic spectrum associated with GARS variants.
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Affiliation(s)
| | - Xenia Chepa-Lotrea
- NIH, Undiagnosed Diseases Program and Office of the Clinical Director, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland
| | - Ryuichi Takase
- Department of Biochemistry and Molecular Biochemistry, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Gretchen Golas
- NIH, Undiagnosed Diseases Program and Office of the Clinical Director, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland
| | - Thomas C Markello
- NIH, Undiagnosed Diseases Program and Office of the Clinical Director, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland
| | - David R Adams
- NIH, Undiagnosed Diseases Program and Office of the Clinical Director, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland
| | - Camilo Toro
- NIH, Undiagnosed Diseases Program and Office of the Clinical Director, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland
| | - Andrea L Gropman
- Division of Neurogenetics and Developmental Pediatrics, Children's National Medical Center, Washington, District of Columbia
| | - Ya-Ming Hou
- Department of Biochemistry and Molecular Biochemistry, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - May Christine V Malicdan
- NIH, Undiagnosed Diseases Program and Office of the Clinical Director, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland
| | - William A Gahl
- NIH, Undiagnosed Diseases Program and Office of the Clinical Director, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland
| | - Cynthia J Tifft
- NIH, Undiagnosed Diseases Program and Office of the Clinical Director, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland
| | - Anthony Antonellis
- Department of Human Genetics, University of Michigan, Ann Arbor, Michigan.,Department of Neurology, University of Michigan, Ann Arbor, Michigan
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8
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Du C, Pusey BN, Adams CJ, Lau CC, Bone WP, Gahl WA, Markello TC, Adams DR. Explorations to improve the completeness of exome sequencing. BMC Med Genomics 2016; 9:56. [PMID: 27568008 PMCID: PMC5002202 DOI: 10.1186/s12920-016-0216-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Accepted: 08/05/2016] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Exome sequencing has advanced to clinical practice and proven useful for obtaining molecular diagnoses in rare diseases. In approximately 75 % of cases, however, a clinical exome study does not produce a definitive molecular diagnosis. These residual cases comprise a new diagnostic challenge for the genetics community. The Undiagnosed Diseases Program of the National Institutes of Health routinely utilizes exome sequencing for refractory clinical cases. Our preliminary data suggest that disease-causing variants may be missed by current standard-of-care clinical exome analysis. Such false negatives reflect limitations in experimental design, technical performance, and data analysis. RESULTS We present examples from our datasets to quantify the analytical performance associated with current practices, and explore strategies to improve the completeness of data analysis. In particular, we focus on patient ascertainment, exome capture, inclusion of intronic variants, and evaluation of medium-sized structural variants. CONCLUSIONS The strategies we present may recover previously-missed, disease causing variants in second-pass exome analysis. Understanding the limitations of the current clinical exome search space provides a rational basis to improve methods for disease variant detection using genome-scale sequencing techniques.
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Affiliation(s)
- Chen Du
- NIH Undiagnosed Diseases Program, Common Fund, National Institutes of Health, National Human Genome Research Institute, Bethesda, MD, USA
| | - Barbara N Pusey
- NIH Undiagnosed Diseases Program, Common Fund, National Institutes of Health, National Human Genome Research Institute, Bethesda, MD, USA
| | - Christopher J Adams
- NIH Undiagnosed Diseases Program, Common Fund, National Institutes of Health, National Human Genome Research Institute, Bethesda, MD, USA
| | - C Christopher Lau
- NIH Undiagnosed Diseases Program, Common Fund, National Institutes of Health, National Human Genome Research Institute, Bethesda, MD, USA
| | - William P Bone
- NIH Undiagnosed Diseases Program, Common Fund, National Institutes of Health, National Human Genome Research Institute, Bethesda, MD, USA
| | - William A Gahl
- NIH Undiagnosed Diseases Program, Common Fund, National Institutes of Health, National Human Genome Research Institute, Bethesda, MD, USA
| | - Thomas C Markello
- NIH Undiagnosed Diseases Program, Common Fund, National Institutes of Health, National Human Genome Research Institute, Bethesda, MD, USA
| | - David R Adams
- NIH Undiagnosed Diseases Program, Common Fund, National Institutes of Health, National Human Genome Research Institute, Bethesda, MD, USA.
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9
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Valkanas E, Schaffer K, Dunham C, Maduro V, du Souich C, Rupps R, Adams DR, Baradaran-Heravi A, Flynn E, Malicdan MC, Gahl WA, Toro C, Boerkoel CF. Phenotypic evolution of UNC80 loss of function. Am J Med Genet A 2016; 170:3106-3114. [PMID: 27513830 DOI: 10.1002/ajmg.a.37929] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Accepted: 08/03/2016] [Indexed: 12/27/2022]
Abstract
Failure to thrive arises as a complication of a heterogeneous group of disorders. We describe two female siblings with spastic paraplegia and global developmental delay but also, atypically for the HSPs, poor weight gain classified as failure to thrive. After extensive clinical and biochemical investigations failed to identify the etiology, we used exome sequencing to identify biallelic UNC80 mutations (NM_032504.1:c.[3983-3_3994delinsA];[2431C>T]. The paternally inherited NM_032504.1:c.3983-3_3994delinsA is predicted to encode p.Ser1328Argfs*19 and the maternally inherited NM_032504.1:c.2431C>T is predicted to encode p.Arg811*. No UNC80 mRNA was detectable in patient cultured skin fibroblasts, suggesting UNC80 loss of function by nonsense mediated mRNA decay. Further supporting the UNC80 mutations as causative of these siblings' disorder, biallelic mutations in UNC80 have recently been described among individuals with an overlapping phenotype. This report expands the disease spectrum associated with UNC80 mutations. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Elise Valkanas
- NIH Undiagnosed Diseases Program, Common Fund, Office of the Director, NIH, National Institutes of Health, Bethesda, Maryland
| | - Katherine Schaffer
- NIH Undiagnosed Diseases Program, Common Fund, Office of the Director, NIH, National Institutes of Health, Bethesda, Maryland
| | - Christopher Dunham
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Valerie Maduro
- NIH Undiagnosed Diseases Program, Common Fund, Office of the Director, NIH, National Institutes of Health, Bethesda, Maryland
| | - Christèle du Souich
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada.,Child and Family Research Institute, University of British Columbia, Vancouver, BC, Canada
| | - Rosemarie Rupps
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada.,Child and Family Research Institute, University of British Columbia, Vancouver, BC, Canada
| | - David R Adams
- NIH Undiagnosed Diseases Program, Common Fund, Office of the Director, NIH, National Institutes of Health, Bethesda, Maryland
| | - Alireza Baradaran-Heravi
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada.,Child and Family Research Institute, University of British Columbia, Vancouver, BC, Canada
| | - Elise Flynn
- NIH Undiagnosed Diseases Program, Common Fund, Office of the Director, NIH, National Institutes of Health, Bethesda, Maryland
| | - May C Malicdan
- NIH Undiagnosed Diseases Program, Common Fund, Office of the Director, NIH, National Institutes of Health, Bethesda, Maryland
| | - William A Gahl
- NIH Undiagnosed Diseases Program, Common Fund, Office of the Director, NIH, National Institutes of Health, Bethesda, Maryland.,NHGRI, National Institutes of Health, Bethesda, Maryland
| | - Camilo Toro
- NIH Undiagnosed Diseases Program, Common Fund, Office of the Director, NIH, National Institutes of Health, Bethesda, Maryland
| | - Cornelius F Boerkoel
- NIH Undiagnosed Diseases Program, Common Fund, Office of the Director, NIH, National Institutes of Health, Bethesda, Maryland.,Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada.,Child and Family Research Institute, University of British Columbia, Vancouver, BC, Canada
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10
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Marchegiani S, Davis T, Tessadori F, van Haaften G, Brancati F, Hoischen A, Huang H, Valkanas E, Pusey B, Schanze D, Venselaar H, Vulto-van Silfhout AT, Wolfe LA, Tifft CJ, Zerfas PM, Zambruno G, Kariminejad A, Sabbagh-Kermani F, Lee J, Tsokos MG, Lee CCR, Ferraz V, da Silva EM, Stevens CA, Roche N, Bartsch O, Farndon P, Bermejo-Sanchez E, Brooks BP, Maduro V, Dallapiccola B, Ramos FJ, Chung HYB, Le Caignec C, Martins F, Jacyk WK, Mazzanti L, Brunner HG, Bakkers J, Lin S, Malicdan MCV, Boerkoel CF, Gahl WA, de Vries BBA, van Haelst MM, Zenker M, Markello TC. Recurrent Mutations in the Basic Domain of TWIST2 Cause Ablepharon Macrostomia and Barber-Say Syndromes. Am J Hum Genet 2015; 97:99-110. [PMID: 26119818 DOI: 10.1016/j.ajhg.2015.05.017] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2015] [Accepted: 05/21/2015] [Indexed: 11/29/2022] Open
Abstract
Ablepharon macrostomia syndrome (AMS) and Barber-Say syndrome (BSS) are rare congenital ectodermal dysplasias characterized by similar clinical features. To establish the genetic basis of AMS and BSS, we performed extensive clinical phenotyping, whole exome and candidate gene sequencing, and functional validations. We identified a recurrent de novo mutation in TWIST2 in seven independent AMS-affected families, as well as another recurrent de novo mutation affecting the same amino acid in ten independent BSS-affected families. Moreover, a genotype-phenotype correlation was observed, because the two syndromes differed based solely upon the nature of the substituting amino acid: a lysine at TWIST2 residue 75 resulted in AMS, whereas a glutamine or alanine yielded BSS. TWIST2 encodes a basic helix-loop-helix transcription factor that regulates the development of mesenchymal tissues. All identified mutations fell in the basic domain of TWIST2 and altered the DNA-binding pattern of Flag-TWIST2 in HeLa cells. Comparison of wild-type and mutant TWIST2 expressed in zebrafish identified abnormal developmental phenotypes and widespread transcriptome changes. Our results suggest that autosomal-dominant TWIST2 mutations cause AMS or BSS by inducing protean effects on the transcription factor's DNA binding.
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Affiliation(s)
- Shannon Marchegiani
- NIH Undiagnosed Diseases Program, Common Fund, Office of the Director, NIH and National Human Genome Research Institute, NIH, Bethesda, MD 20892, USA; Department of Pediatrics, Walter Reed National Military Medical Center, Bethesda, MD 20892, USA
| | - Taylor Davis
- NIH Undiagnosed Diseases Program, Common Fund, Office of the Director, NIH and National Human Genome Research Institute, NIH, Bethesda, MD 20892, USA
| | - Federico Tessadori
- Hubrecht Institute-KNAW and University Medical Centre Utrecht, 3584 CT Utrecht, the Netherlands
| | - Gijs van Haaften
- Department of Medical Genetics, University Medical Center Utrecht, 3508 AB Utrecht, the Netherlands
| | - Francesco Brancati
- Department of Medical, Oral, and Biotechnological Sciences, University of G. d' Annunzio Chieti and Pescara, Chieti 66100, Italy
| | - Alexander Hoischen
- Department of Human Genetics, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands
| | - Haigen Huang
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Elise Valkanas
- NIH Undiagnosed Diseases Program, Common Fund, Office of the Director, NIH and National Human Genome Research Institute, NIH, Bethesda, MD 20892, USA
| | - Barbara Pusey
- NIH Undiagnosed Diseases Program, Common Fund, Office of the Director, NIH and National Human Genome Research Institute, NIH, Bethesda, MD 20892, USA
| | - Denny Schanze
- Medizinische Fakultät und Universitätsklinikum Magdeburg, Institute of Human Genetics, 39120 Magdeburg, Germany
| | - Hanka Venselaar
- Department of Human Genetics, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands
| | | | - Lynne A Wolfe
- NIH Undiagnosed Diseases Program, Common Fund, Office of the Director, NIH and National Human Genome Research Institute, NIH, Bethesda, MD 20892, USA; Office of the Clinical Director, National Human Genome Research Institute/NIH, Bethesda, MD 20892, USA
| | - Cynthia J Tifft
- NIH Undiagnosed Diseases Program, Common Fund, Office of the Director, NIH and National Human Genome Research Institute, NIH, Bethesda, MD 20892, USA; Office of the Clinical Director, National Human Genome Research Institute/NIH, Bethesda, MD 20892, USA
| | - Patricia M Zerfas
- Office of Research Services, Division of Veterinary Resources, NIH, Bethesda, MD 20892, USA
| | - Giovanna Zambruno
- Laboratory of Molecular and Cell Biology, Istituto Dermopatico dell'Immacolata IDI-IRCCS, Rome 00167, Italy
| | | | | | - Janice Lee
- National Institute of Dental and Craniofacial Research, NIH, Bethesda, MD 20892, USA
| | - Maria G Tsokos
- Laboratory of Pathology, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Chyi-Chia R Lee
- Laboratory of Pathology, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Victor Ferraz
- Departamento de Genetica, Faculdade de Medicina de Ribeirao Preto, Universidade de Sao Paulo, Sao Paulo 14049, Brazil
| | - Eduarda Morgana da Silva
- Departamento de Genetica, Faculdade de Medicina de Ribeirao Preto, Universidade de Sao Paulo, Sao Paulo 14049, Brazil
| | - Cathy A Stevens
- Department of Medical Genetics, T.C. Thompson Children's Hospital, Chattanooga, TN 37403, USA
| | - Nathalie Roche
- Department of Plastic and Reconstructive Surgery, University Hospital of Ghent, Ghent 9000, Belgium
| | - Oliver Bartsch
- Institute of Human Genetics, Johannes Gutenberg University, Mainz 55131, Germany
| | - Peter Farndon
- Clinical Genetics Unit, Birmingham Women's Healthcare Trust, Birmingham B15 2TG, UK
| | - Eva Bermejo-Sanchez
- ECEMC (Spanish Collaborative Study of Congenital Malformations), CIAC, Instituto de Investigación de Enfermedades Raras (IIER), Instituto de Salud Carlos III; and CIBER de Enfermedades Raras (CIBERER)-U724, Madrid 28029, Spain
| | - Brian P Brooks
- Unit on Pediatric, Developmental, and Genetic Eye Disease, National Eye Institute, NIH, Bethesda, MD 20892, USA
| | - Valerie Maduro
- NIH Undiagnosed Diseases Program, Common Fund, Office of the Director, NIH and National Human Genome Research Institute, NIH, Bethesda, MD 20892, USA
| | - Bruno Dallapiccola
- Department of Medical Genetics, Bambino Gesù Children's Hospital, IRCCS, Rome 00165, Italy
| | - Feliciano J Ramos
- Unidad de Genética Médica, Servicio de Pediatría, GCV-CIBERER Hospital Clínico Universitario "Lozano Blesa," Facultad de Medicina, Universidad de Zaragoza, 50009 Zaragoza, Spain
| | - Hon-Yin Brian Chung
- Department of Paediatrics and Adolescent Medicine, Centre for Genomic Sciences, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Cédric Le Caignec
- Service de genetique medicale, CHU Nantes, 44093 Nantes, France and Inserm, UMR957, Faculté de Médecine, 44093 Nantes, France
| | - Fabiana Martins
- Special Care Dentistry Center, Department of Stomatology, School of Dentistry, University of São Paulo, São Paulo 05508-070, Brazil
| | - Witold K Jacyk
- Department of Dermatology, University of Pretoria, Pretoria 0028, Republic of South Africa
| | - Laura Mazzanti
- Department of Pediatrics, S. Orsola-Malpighi Hospital University of Bologna, 40138 Bologna, Italy
| | - Han G Brunner
- Department of Human Genetics, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands; Department of Clinical Genetics, Maastricht University Medical Center, PO Box 5800, 6202AZ Maastricht, the Netherlands
| | - Jeroen Bakkers
- Hubrecht Institute-KNAW and University Medical Centre Utrecht, 3584 CT Utrecht, the Netherlands
| | - Shuo Lin
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - May Christine V Malicdan
- NIH Undiagnosed Diseases Program, Common Fund, Office of the Director, NIH and National Human Genome Research Institute, NIH, Bethesda, MD 20892, USA; Office of the Clinical Director, National Human Genome Research Institute/NIH, Bethesda, MD 20892, USA.
| | - Cornelius F Boerkoel
- NIH Undiagnosed Diseases Program, Common Fund, Office of the Director, NIH and National Human Genome Research Institute, NIH, Bethesda, MD 20892, USA
| | - William A Gahl
- NIH Undiagnosed Diseases Program, Common Fund, Office of the Director, NIH and National Human Genome Research Institute, NIH, Bethesda, MD 20892, USA; Office of the Clinical Director, National Human Genome Research Institute/NIH, Bethesda, MD 20892, USA.
| | - Bert B A de Vries
- Department of Human Genetics, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands
| | - Mieke M van Haelst
- Department of Medical Genetics, University Medical Center Utrecht, 3508 AB Utrecht, the Netherlands
| | - Martin Zenker
- Medizinische Fakultät und Universitätsklinikum Magdeburg, Institute of Human Genetics, 39120 Magdeburg, Germany
| | - Thomas C Markello
- NIH Undiagnosed Diseases Program, Common Fund, Office of the Director, NIH and National Human Genome Research Institute, NIH, Bethesda, MD 20892, USA
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11
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Trehan A, Brady JM, Maduro V, Bone W, Huang Y, Golas GA, Kane M, Lee PR, Thurm A, Gropman AL, Paul SM, Vezina G, Markello TC, Gahl WA, Boerkoel CF, Tifft CJ. MED23-associated intellectual disability in a non-consanguineous family. Am J Med Genet A 2015; 167:1374-80. [PMID: 25845469 PMCID: PMC5671761 DOI: 10.1002/ajmg.a.37047] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2014] [Accepted: 02/18/2015] [Indexed: 11/10/2022]
Abstract
Intellectual disability (ID) is a heterogeneous condition arising from a variety of environmental and genetic factors. Among these causes are defects in transcriptional regulators. Herein, we report on two brothers in a nonconsanguineous family with novel compound heterozygous, disease-segregating mutations (NM_015979.3: [3656A > G];[4006C > T], NP_057063.2: [H1219R];[R1336X]) in MED23. This gene encodes a subunit of the Mediator complex that modulates the expression of RNA polymerase II-dependent genes. These brothers, who had profound ID, spasticity, congenital heart disease, brain abnormalities, and atypical electroencephalography, represent the first case of MED23-associated ID in a non-consanguineous family. They also expand upon the clinical features previously reported for mutations in this gene.
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Affiliation(s)
- Aditi Trehan
- Office of the Clinical Director, NHGRI/NIH, Bethesda, Maryland, USA
- NIH Undiagnosed Diseases Program, NIH Office of Rare Diseases Research and NHGRI, Bethesda, Maryland, USA
| | - Jacqueline M. Brady
- Office of the Clinical Director, NHGRI/NIH, Bethesda, Maryland, USA
- NIH Undiagnosed Diseases Program, NIH Office of Rare Diseases Research and NHGRI, Bethesda, Maryland, USA
| | - Valerie Maduro
- Office of the Clinical Director, NHGRI/NIH, Bethesda, Maryland, USA
- NIH Undiagnosed Diseases Program, NIH Office of Rare Diseases Research and NHGRI, Bethesda, Maryland, USA
| | - William Bone
- Office of the Clinical Director, NHGRI/NIH, Bethesda, Maryland, USA
- NIH Undiagnosed Diseases Program, NIH Office of Rare Diseases Research and NHGRI, Bethesda, Maryland, USA
| | - Yan Huang
- Office of the Clinical Director, NHGRI/NIH, Bethesda, Maryland, USA
- NIH Undiagnosed Diseases Program, NIH Office of Rare Diseases Research and NHGRI, Bethesda, Maryland, USA
| | - Gretchen A. Golas
- Office of the Clinical Director, NHGRI/NIH, Bethesda, Maryland, USA
- NIH Undiagnosed Diseases Program, NIH Office of Rare Diseases Research and NHGRI, Bethesda, Maryland, USA
| | - Megan Kane
- NIH Undiagnosed Diseases Program, NIH Office of Rare Diseases Research and NHGRI, Bethesda, Maryland, USA
| | - Paul R. Lee
- National Institute of Neurological Disorder and Stroke, NIH, Bethesda, Maryland, USA
| | - Audrey Thurm
- Pediatrics and Developmental Neuroscience, NIMH/NIH, Bethesda, Maryland, USA
| | - Andrea L. Gropman
- Office of the Clinical Director, NHGRI/NIH, Bethesda, Maryland, USA
- George Washington University School of Medicine and Health Sciences and Children’s National Medical Center, Washington D.C., USA
| | - Scott M. Paul
- Rehabilitation Medicine Department, Clinical Center, NIH, Bethesda, Maryland, USA
| | - Gilbert Vezina
- George Washington University School of Medicine and Health Sciences and Children’s National Medical Center, Washington D.C., USA
| | - Thomas C. Markello
- NIH Undiagnosed Diseases Program, NIH Office of Rare Diseases Research and NHGRI, Bethesda, Maryland, USA
| | - William A. Gahl
- Office of the Clinical Director, NHGRI/NIH, Bethesda, Maryland, USA
- NIH Undiagnosed Diseases Program, NIH Office of Rare Diseases Research and NHGRI, Bethesda, Maryland, USA
| | - Cornelius F. Boerkoel
- NIH Undiagnosed Diseases Program, NIH Office of Rare Diseases Research and NHGRI, Bethesda, Maryland, USA
| | - Cynthia J. Tifft
- Office of the Clinical Director, NHGRI/NIH, Bethesda, Maryland, USA
- NIH Undiagnosed Diseases Program, NIH Office of Rare Diseases Research and NHGRI, Bethesda, Maryland, USA
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12
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Albert JS, Bhattacharyya N, Wolfe LA, Bone WP, Maduro V, Accardi J, Adams DR, Schwartz CE, Norris J, Wood T, Gafni RI, Collins MT, Tosi LL, Markello TC, Gahl WA, Boerkoel CF. Impaired osteoblast and osteoclast function characterize the osteoporosis of Snyder - Robinson syndrome. Orphanet J Rare Dis 2015; 10:27. [PMID: 25888122 PMCID: PMC4428506 DOI: 10.1186/s13023-015-0235-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2014] [Accepted: 01/28/2015] [Indexed: 11/25/2022] Open
Abstract
Background Snyder-Robinson Syndrome (SRS) is an X-linked intellectual disability disorder also characterized by osteoporosis, scoliosis, and dysmorphic facial features. It is caused by mutations in SMS, a ubiquitously expressed gene encoding the polyamine biosynthetic enzyme spermine synthase. We hypothesized that the tissue specificity of SRS arises from differential sensitivity to spermidine toxicity or spermine deficiency. Methods We performed detailed clinical, endocrine, histopathologic, and morphometric studies on two affected brothers with a spermine synthase loss of function mutation (NM_004595.4:c.443A > G, p.Gln148Arg). We also measured spermine and spermidine levels in cultured human bone marrow stromal cells (hBMSCs) and fibroblasts using the Biochrom 30 polyamine protocol and assessed the osteogenic potential of hBMSCs. Results In addition to the known tissue-specific features of SRS, the propositi manifested retinal pigmentary changes, recurrent episodes of hyper- and hypoglycemia, nephrocalcinosis, renal cysts, and frequent respiratory infections. Bone histopathology and morphometry identified a profound depletion of osteoblasts and osteoclasts, absence of a trabecular meshwork, a low bone volume and a thin cortex. Comparison of cultured fibroblasts from affected and unaffected individuals showed relatively small changes in polyamine content, whereas comparison of cultured osteoblasts identified marked differences in spermidine and spermine content. Osteogenic differentiation of the SRS-derived hBMSCs identified a severe deficiency of calcium phosphate mineralization. Conclusions Our findings support the hypothesis that cell specific alterations in polyamine metabolism contribute to the tissue specificity of SRS features, and that the low bone density arises from a failure of mineralization. Electronic supplementary material The online version of this article (doi:10.1186/s13023-015-0235-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jessica S Albert
- Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, MD, 20814, USA. .,Medical Genetics Branch, National Human Genome Research Institute, Bethesda, MD, USA.
| | - Nisan Bhattacharyya
- Skeletal Clinical Studies Unit, Craniofacial and Skeletal Disease Branch, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD, 20892, USA.
| | - Lynne A Wolfe
- Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, MD, 20814, USA. .,Medical Genetics Branch, National Human Genome Research Institute, Bethesda, MD, USA.
| | - William P Bone
- Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, MD, 20814, USA.
| | - Valerie Maduro
- Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, MD, 20814, USA.
| | - John Accardi
- Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, MD, 20814, USA.
| | - David R Adams
- Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, MD, 20814, USA. .,Medical Genetics Branch, National Human Genome Research Institute, Bethesda, MD, USA.
| | - Charles E Schwartz
- J.C. Self Research Institute, Greenwood Genetics Centre, Greenwood, SC, 29646, USA.
| | - Joy Norris
- Skeletal Clinical Studies Unit, Craniofacial and Skeletal Disease Branch, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD, 20892, USA.
| | - Tim Wood
- J.C. Self Research Institute, Greenwood Genetics Centre, Greenwood, SC, 29646, USA.
| | - Rachel I Gafni
- Skeletal Clinical Studies Unit, Craniofacial and Skeletal Disease Branch, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD, 20892, USA.
| | - Michael T Collins
- Skeletal Clinical Studies Unit, Craniofacial and Skeletal Disease Branch, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD, 20892, USA.
| | - Laura L Tosi
- George Washington University School of Medicine, Washington, DC, USA. .,Children's National Medical Center, Washington, DC, USA.
| | - Thomas C Markello
- Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, MD, 20814, USA. .,Medical Genetics Branch, National Human Genome Research Institute, Bethesda, MD, USA.
| | - William A Gahl
- Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, MD, 20814, USA. .,Medical Genetics Branch, National Human Genome Research Institute, Bethesda, MD, USA.
| | - Cornelius F Boerkoel
- Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, MD, 20814, USA.
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13
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Adams DR, Yuan H, Holyoak T, Arajs KH, Hakimi P, Markello TC, Wolfe LA, Vilboux T, Burton BK, Fajardo KF, Grahame G, Holloman C, Sincan M, Smith ACM, Wells GA, Huang Y, Vega H, Snyder JP, Golas GA, Tifft CJ, Boerkoel CF, Hanson RW, Traynelis SF, Kerr DS, Gahl WA. Three rare diseases in one Sib pair: RAI1, PCK1, GRIN2B mutations associated with Smith-Magenis Syndrome, cytosolic PEPCK deficiency and NMDA receptor glutamate insensitivity. Mol Genet Metab 2014; 113:161-70. [PMID: 24863970 PMCID: PMC4219933 DOI: 10.1016/j.ymgme.2014.04.001] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/28/2014] [Revised: 04/05/2014] [Accepted: 04/06/2014] [Indexed: 01/28/2023]
Abstract
The National Institutes of Health Undiagnosed Diseases Program evaluates patients for whom no diagnosis has been discovered despite a comprehensive diagnostic workup. Failure to diagnose a condition may arise from the mutation of genes previously unassociated with disease. However, we hypothesized that this could also co-occur with multiple genetic disorders. Demonstrating a complex syndrome caused by multiple disorders, we report two siblings manifesting both similar and disparate signs and symptoms. They shared a history of episodes of hypoglycemia and lactic acidosis, but had differing exam findings and developmental courses. Clinical acumen and exome sequencing combined with biochemical and functional studies identified three genetic conditions. One sibling had Smith-Magenis Syndrome and a nonsense mutation in the RAI1 gene. The second sibling had a de novo mutation in GRIN2B, which resulted in markedly reduced glutamate potency of the encoded receptor. Both siblings had a protein-destabilizing homozygous mutation in PCK1, which encodes the cytosolic isoform of phosphoenolpyruvate carboxykinase (PEPCK-C). In summary, we present the first clinically-characterized mutation of PCK1 and demonstrate that complex medical disorders can represent the co-occurrence of multiple diseases.
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Affiliation(s)
- David R Adams
- Undiagnosed Diseases Program, Office of the Director, National Institutes of Health, Bethesda, MD, USA; Medical Genetics Branch, National Human Genome Research Institute, Bethesda, MD, USA.
| | - Hongjie Yuan
- Department of Pharmacology, Emory University School of Medicine, Rollins Research Center, Atlanta, GA, USA
| | - Todd Holyoak
- Department of Biology, University of Waterloo, Waterloo, ON, Canada
| | - Katrina H Arajs
- Department of Biology, University of Waterloo, Waterloo, ON, Canada
| | - Parvin Hakimi
- Department of Biochemistry, Case Western Reserve University, USA; Department of Pediatrics, Case Western Reserve University, USA
| | - Thomas C Markello
- Undiagnosed Diseases Program, Office of the Director, National Institutes of Health, Bethesda, MD, USA
| | - Lynne A Wolfe
- Undiagnosed Diseases Program, Office of the Director, National Institutes of Health, Bethesda, MD, USA
| | - Thierry Vilboux
- Medical Genetics Branch, National Human Genome Research Institute, Bethesda, MD, USA
| | - Barbara K Burton
- Ann and Robert H. Lurie Children's Hospital, Northwestern University, Chicago, IL, USA; Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Karin Fuentes Fajardo
- Undiagnosed Diseases Program, Office of the Director, National Institutes of Health, Bethesda, MD, USA
| | - George Grahame
- Center for Inherited Disorders of Energy Metabolism, University Hospitals Case Medical Center, Cleveland, OH, USA
| | - Conisha Holloman
- University of Rochester School of Medicine and Dentistry, Rochester, NY, USA
| | - Murat Sincan
- Undiagnosed Diseases Program, Office of the Director, National Institutes of Health, Bethesda, MD, USA
| | - Ann C M Smith
- Undiagnosed Diseases Program, Office of the Director, National Institutes of Health, Bethesda, MD, USA
| | - Gordon A Wells
- Department of Chemistry, Emory University, Atlanta, GA, USA; Department of Biochemistry, University of Stellenbosch, South Africa
| | - Yan Huang
- Undiagnosed Diseases Program, Office of the Director, National Institutes of Health, Bethesda, MD, USA
| | - Hugo Vega
- Undiagnosed Diseases Program, Office of the Director, National Institutes of Health, Bethesda, MD, USA
| | - James P Snyder
- Department of Chemistry, Emory University, Atlanta, GA, USA
| | - Gretchen A Golas
- Undiagnosed Diseases Program, Office of the Director, National Institutes of Health, Bethesda, MD, USA
| | - Cynthia J Tifft
- Undiagnosed Diseases Program, Office of the Director, National Institutes of Health, Bethesda, MD, USA
| | - Cornelius F Boerkoel
- Undiagnosed Diseases Program, Office of the Director, National Institutes of Health, Bethesda, MD, USA
| | - Richard W Hanson
- Department of Biochemistry, Case Western Reserve University, USA
| | - Stephen F Traynelis
- Department of Pharmacology, Emory University School of Medicine, Rollins Research Center, Atlanta, GA, USA
| | - Douglas S Kerr
- Department of Biochemistry, Case Western Reserve University, USA; Department of Pediatrics, Case Western Reserve University, USA; Center for Inherited Disorders of Energy Metabolism, University Hospitals Case Medical Center, Cleveland, OH, USA
| | - William A Gahl
- Undiagnosed Diseases Program, Office of the Director, National Institutes of Health, Bethesda, MD, USA; Medical Genetics Branch, National Human Genome Research Institute, Bethesda, MD, USA
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14
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Eccleston J, Koh C, Markello TC, Gahl WA, Heller T. An apparent homozygous deletion in maltase-glucoamylase, a lesson in the evolution of SNP arrays. Mol Genet Metab 2012; 107:674-8. [PMID: 23137569 PMCID: PMC3520432 DOI: 10.1016/j.ymgme.2012.10.013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/21/2012] [Revised: 10/15/2012] [Accepted: 10/15/2012] [Indexed: 10/27/2022]
Abstract
Single nucleotide polymorphism (SNP) arrays possess clinical potential due to their high throughput capacity, sensitivity and versatility. We used such an array to perform a genome-wide SNP analysis of a patient with a multi-system undiagnosed disease involving peripheral neuropathies and food intolerances. The patient had a homozygous deletion within the gene encoding maltase-glucoamylase (MGAM), an intestinal starch digestion enzyme, predicting absence of enzyme activity and potential starch indigestion. We then performed validation testing using a functional MGAM analysis that involved starch ingestion followed by measuring blood glucose and insulin levels as well as hydrogen breath levels. Gastrointestinal tissue was also obtained via endoscopy and immunohistochemical staining for intestinal MGAM was performed. Our results strongly suggest the presence and functioning of MGAM which disproved deficiency predictions based on SNP array analysis findings, classifying the deletion as a functional polymorphism. This study highlights a current clinical limitation of SNP arrays, i.e., distinguishing deleterious genomic alterations from misleading functional polymorphisms. We conclude that novel findings from SNP arrays should be clinically validated and published.
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Affiliation(s)
- Jason Eccleston
- Liver Diseases Branch, National Institute of Diabetes & Digestive & Kidney Diseases, National Institutes of Health, Bethesda, Maryland
| | - Christopher Koh
- Liver Diseases Branch, National Institute of Diabetes & Digestive & Kidney Diseases, National Institutes of Health, Bethesda, Maryland
| | - Thomas C. Markello
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland
- National Institutes of Health Undiagnosed Diseases Program, National Institutes of Health, Bethesda, Maryland
| | - William A. Gahl
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland
- National Institutes of Health Undiagnosed Diseases Program, National Institutes of Health, Bethesda, Maryland
- Office of the Clinical Director, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland
| | - Theo Heller
- Liver Diseases Branch, National Institute of Diabetes & Digestive & Kidney Diseases, National Institutes of Health, Bethesda, Maryland
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15
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Adams DR, Sincan M, Fuentes Fajardo K, Mullikin JC, Pierson TM, Toro C, Boerkoel CF, Tifft CJ, Gahl WA, Markello TC. Analysis of DNA sequence variants detected by high-throughput sequencing. Hum Mutat 2012; 33:599-608. [PMID: 22290882 DOI: 10.1002/humu.22035] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2011] [Accepted: 12/02/2011] [Indexed: 12/18/2022]
Abstract
The Undiagnosed Diseases Program at the National Institutes of Health uses high-throughput sequencing (HTS) to diagnose rare and novel diseases. HTS techniques generate large numbers of DNA sequence variants, which must be analyzed and filtered to find candidates for disease causation. Despite the publication of an increasing number of successful exome-based projects, there has been little formal discussion of the analytic steps applied to HTS variant lists. We present the results of our experience with over 30 families for whom HTS sequencing was used in an attempt to find clinical diagnoses. For each family, exome sequence was augmented with high-density SNP-array data. We present a discussion of the theory and practical application of each analytic step and provide example data to illustrate our approach. The article is designed to provide an analytic roadmap for variant analysis, thereby enabling a wide range of researchers and clinical genetics practitioners to perform direct analysis of HTS data for their patients and projects.
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Affiliation(s)
- David R Adams
- NIH Undiagnosed Diseases Program, NIH, Bethesda, Maryland, USA.
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