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Nikam V, Mohammad NS. Tissue-specific DNase I footprint analysis confirms the association of GATAD2B Q470* variant with intellectual disability. J Genet 2021. [DOI: 10.1007/s12041-021-01308-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Levchenko A, Kanapin A, Samsonova A, Fedorenko OY, Kornetova EG, Nurgaliev T, Mazo GE, Semke AV, Kibitov AO, Bokhan NA, Gainetdinov RR, Ivanova SA. A genome-wide association study identifies a gene network associated with paranoid schizophrenia and antipsychotics-induced tardive dyskinesia. Prog Neuropsychopharmacol Biol Psychiatry 2021; 105:110134. [PMID: 33065217 DOI: 10.1016/j.pnpbp.2020.110134] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Revised: 09/10/2020] [Accepted: 10/06/2020] [Indexed: 02/06/2023]
Abstract
In the present study we conducted a genome-wide association study (GWAS) in a cohort of 505 patients with paranoid schizophrenia (SCZ), of which 95 had tardive dyskinesia (TD), and 503 healthy controls. Using data generated by the PsychENCODE Consortium (PEC) and other bioinformatic databases, we revealed a gene network, implicated in neurodevelopment and brain function, associated with both these disorders. Almost all these genes are in gene or isoform co-expression PEC network modules important for the functioning of the brain; the activity of these networks is also altered in SCZ, bipolar disorder and autism spectrum disorders. The associated PEC network modules are enriched for gene ontology terms relevant to the brain development and function (CNS development, neuron development, axon ensheathment, synapse, synaptic vesicle cycle, and signaling receptor activity) and to the immune system (inflammatory response). Results of the present study suggest that orofacial and limbtruncal types of TD seem to share the molecular network with SCZ. Paranoid SCZ and abnormal involuntary movements that indicate the orofacial type of TD are associated with the same genomic loci on chromosomes 3p22.2, 8q21.13, and 13q14.2. The limbtruncal type of TD is associated with a locus on chromosome 3p13 where the best functional candidate is FOXP1, a high-confidence SCZ gene. The results of this study shed light on common pathogenic mechanisms for SCZ and TD, and indicate that the pathogenesis of the orofacial and limbtruncal types of TD might be driven by interacting genes implicated in neurodevelopment.
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Affiliation(s)
- Anastasia Levchenko
- Theodosius Dobzhansky Center for Genome Bioinformatics, Saint Petersburg State University, Saint Petersburg, Russia.
| | - Alexander Kanapin
- Theodosius Dobzhansky Center for Genome Bioinformatics, Saint Petersburg State University, Saint Petersburg, Russia
| | - Anastasia Samsonova
- Theodosius Dobzhansky Center for Genome Bioinformatics, Saint Petersburg State University, Saint Petersburg, Russia
| | - Olga Yu Fedorenko
- Mental Health Research Institute, Tomsk National Research Medical Center, Russian Academy of Sciences, Tomsk, Russia; National Research Tomsk Polytechnic University, Tomsk, Russia
| | - Elena G Kornetova
- Mental Health Research Institute, Tomsk National Research Medical Center, Russian Academy of Sciences, Tomsk, Russia; Siberian State Medical University, Tomsk, Russia
| | | | - Galina E Mazo
- Department of Endocrine Psychiatry, V.M. Bekhterev National Medical Research Center for Psychiatry and Neurology, Saint Petersburg, Russia
| | - Arkadiy V Semke
- Mental Health Research Institute, Tomsk National Research Medical Center, Russian Academy of Sciences, Tomsk, Russia
| | - Alexander O Kibitov
- Department of Endocrine Psychiatry, V.M. Bekhterev National Medical Research Center for Psychiatry and Neurology, Saint Petersburg, Russia; Laboratory of Molecular Genetics, Serbsky National Medical Research Center on Psychiatry and Addictions, Moscow, Russia
| | - Nikolay A Bokhan
- Mental Health Research Institute, Tomsk National Research Medical Center, Russian Academy of Sciences, Tomsk, Russia; Siberian State Medical University, Tomsk, Russia; National Research Tomsk State University, Tomsk, Russia
| | - Raul R Gainetdinov
- Institute of Translational Biomedicine, Saint Petersburg State University, Saint Petersburg, Russia
| | - Svetlana A Ivanova
- Mental Health Research Institute, Tomsk National Research Medical Center, Russian Academy of Sciences, Tomsk, Russia; National Research Tomsk Polytechnic University, Tomsk, Russia; Siberian State Medical University, Tomsk, Russia
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Vera G, Sorlin A, Delplancq G, Lecoquierre F, Brasseur-Daudruy M, Petit F, Smol T, Ziegler A, Bonneau D, Colin E, Mercier S, Cogné B, Bézieau S, Edery P, Lesca G, Chatron N, Sabatier I, Duban-Bedu B, Colson C, Piton A, Durand B, Capri Y, Perrin L, Wiesener A, Zweier C, Maroofian R, Carroll CJ, Galehdari H, Mazaheri N, Callewaert B, Giulianno F, Zaafrane-Khachnaoui K, Buchert-Lo R, Haack T, Magg J, Rieß A, Blandfort M, Waldmüller S, Horber V, Leonardi E, Polli R, Turolla L, Murgia A, Frebourg T, Lebre AS, Nicolas G, Saugier-Veber P, Guerrot AM. Clinical and molecular description of 19 patients with GATAD2B-Associated Neurodevelopmental Disorder (GAND). Eur J Med Genet 2020; 63:104004. [PMID: 32688057 DOI: 10.1016/j.ejmg.2020.104004] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Accepted: 07/07/2020] [Indexed: 12/16/2022]
Abstract
De novo pathogenic variants in the GATAD2B gene have been associated with a syndromic neurodevelopmental disorder (GAND) characterized by severe intellectual disability (ID), impaired speech, childhood hypotonia, and dysmorphic features. Since its first description in 2013, nine patients have been reported in case reports and a series of 50 patients was recently published, which is consistent with the relative frequency of GATAD2B pathogenic variants in public databases. We report the detailed phenotype of 19 patients from various ethnic backgrounds with confirmed pathogenic GATAD2B variants including intragenic deletions. All individuals presented developmental delay with a median age of 2.5 years for independent walking and of 3 years for first spoken words. GATAD2B variant carriers showed very little subsequent speech progress, two patients over 30 years of age remaining non-verbal. ID was mostly moderate to severe, with one profound and one mild case, which shows a wider spectrum of disease severity than previously reported. We confirm macrocephaly as a major feature in GAND (53%). Most common dysmorphic features included broad forehead, deeply set eyes, hypertelorism, wide nasal base, and pointed chin. Conversely, prenatal abnormalities, non-cerebral malformations, epilepsy, and autistic behavior were uncommon. Other features included feeding difficulties, behavioral abnormalities, and unspecific abnormalities on brain MRI. Improving our knowledge of the clinical phenotype is essential for correct interpretation of the molecular results and accurate patient management.
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Daum H, Mor-Shaked H, Ta-Shma A, Shaag A, Silverstein S, Shohat M, Elpeleg O, Meiner V, Harel T. Grandparental genotyping enhances exome variant interpretation. Am J Med Genet A 2020; 182:689-696. [PMID: 32027463 DOI: 10.1002/ajmg.a.61511] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Revised: 12/09/2019] [Accepted: 01/03/2020] [Indexed: 12/14/2022]
Abstract
Trio exome sequencing is a powerful tool in the molecular investigation of monogenic disorders and provides an incremental diagnostic yield over proband-only sequencing, mainly due to the rapid identification of de novo disease-causing variants. However, heterozygous variants inherited from unaffected parents may be inadvertently dismissed, although multiple explanations are available for such scenarios including mosaicism in the parent, incomplete penetrance, imprinting, or skewed X-inactivation. We report three probands, in which a pathogenic or likely pathogenic variant was identified upon exome sequencing, yet was inherited from an unaffected parent. Segregation of the variants (in NOTCH1, PHF6, and SOX10) in the grandparent generation revealed that the variant was de novo in each case. Additionally, one proband had skewed X-inactivation. We discuss the possible genetic mechanism in each case, and urge caution in data interpretation of exome sequencing data. We illustrate the utility of expanding segregation studies to the grandparent generation and demonstrate the impact on exome interpretation strategies, by showing that objective genotype data can overcome subjective parental report of lack of symptoms.
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Affiliation(s)
- Hagit Daum
- Department of Genetic and Metabolic Diseases, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Hagar Mor-Shaked
- Department of Genetic and Metabolic Diseases, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Asaf Ta-Shma
- Department of Pediatric Cardiology, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Avraham Shaag
- Department of Genetic and Metabolic Diseases, Hadassah-Hebrew University Medical Center, Jerusalem, Israel.,Monique and Jacques Roboh Department of Genetic Research, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Shira Silverstein
- Department of Genetic and Metabolic Diseases, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Mordechai Shohat
- Bioinformatics Unit - Sheba Cancer Research Center, Sheba Medical Center, Tel-Hashomer, Israel.,The Genetic Institute of Maccabi Health Medicinal Organization, Rehovot, Israel.,The Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Orly Elpeleg
- Department of Genetic and Metabolic Diseases, Hadassah-Hebrew University Medical Center, Jerusalem, Israel.,Monique and Jacques Roboh Department of Genetic Research, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Vardiella Meiner
- Department of Genetic and Metabolic Diseases, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Tamar Harel
- Department of Genetic and Metabolic Diseases, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
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Pierson TM, Otero MG, Grand K, Choi A, Graham JM, Young JI, Mackay JP. The NuRD complex and macrocephaly associated neurodevelopmental disorders. Am J Med Genet C Semin Med Genet 2019; 181:548-556. [PMID: 31737996 DOI: 10.1002/ajmg.c.31752] [Citation(s) in RCA: 20] [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] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Revised: 10/08/2019] [Accepted: 10/10/2019] [Indexed: 12/13/2022]
Abstract
The nucleosome remodeling and deacetylase (NuRD) complex is a major regulator of gene expression involved in pluripotency, lineage commitment, and corticogenesis. This important complex is composed of seven different proteins, with mutations in CHD3, CHD4, and GATAD2B being associated with neurodevelopmental disorders presenting with macrocephaly and intellectual disability similar to other overgrowth and intellectual disability (OGID) syndromes. Pathogenic variants in CHD3 and CHD4 primarily involve disruption of enzymatic function. GATAD2B variants include loss-of-function mutations that alter protein dosage and missense variants that involve either of two conserved domains (CR1 and CR2) known to interact with other NuRD proteins. In addition to macrocephaly and intellectual disability, CHD3 variants are associated with inguinal hernias and apraxia of speech; whereas CHD4 variants are associated with skeletal anomalies, deafness, and cardiac defects. GATAD2B-associated neurodevelopmental disorder (GAND) has phenotypic overlap with both of these disorders. Of note, structural models of NuRD indicate that CHD3 and CHD4 require direct contact with the GATAD2B-CR2 domain to interact with the rest of the complex. Therefore, the phenotypic overlaps of CHD3- and CHD4-related disorders with GAND are consistent with a loss in the ability of GATAD2B to recruit CHD3 or CHD4 to the complex. The shared features of these neurodevelopmental disorders may represent a new class of OGID syndrome: the NuRDopathies.
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Affiliation(s)
- Tyler Mark Pierson
- Department of Pediatrics, Cedars-Sinai Medical Center, Los Angeles, California.,Department of Neurology, Cedars-Sinai Medical Center, Los Angeles, California.,Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, California
| | - Maria G Otero
- Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, California
| | - Katheryn Grand
- Department of Pediatrics, Medical Genetics, Cedars-Sinai Medical Center, Los Angeles, California
| | - Andrew Choi
- Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, California
| | - John M Graham
- Department of Pediatrics, Medical Genetics, Cedars-Sinai Medical Center, Los Angeles, California
| | - Juan I Young
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, Florida
| | - Joel P Mackay
- School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales, Australia
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Kaur P, Mishra S, Rajesh SM, Girisha KM, Shukla A. GATAD2B-related intellectual disability due to parental mosaicism and review of literature. Clin Dysmorphol 2019; 28:190-4. [DOI: 10.1097/mcd.0000000000000288] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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