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Tolezano GC, Bastos GC, da Costa SS, Freire BL, Homma TK, Honjo RS, Yamamoto GL, Passos-Bueno MR, Koiffmann CP, Kim CA, Vianna-Morgante AM, de Lima Jorge AA, Bertola DR, Rosenberg C, Krepischi ACV. Burden of Rare Copy Number Variants in Microcephaly: A Brazilian Cohort of 185 Microcephalic Patients and Review of the Literature. J Autism Dev Disord 2024; 54:1181-1212. [PMID: 36502452 DOI: 10.1007/s10803-022-05853-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/26/2022] [Indexed: 12/14/2022]
Abstract
Microcephaly presents heterogeneous genetic etiology linked to several neurodevelopmental disorders (NDD). Copy number variants (CNVs) are a causal mechanism of microcephaly whose investigation is a crucial step for unraveling its molecular basis. Our purpose was to investigate the burden of rare CNVs in microcephalic individuals and to review genes and CNV syndromes associated with microcephaly. We performed chromosomal microarray analysis (CMA) in 185 Brazilian patients with microcephaly and evaluated microcephalic patients carrying < 200 kb CNVs documented in the DECIPHER database. Additionally, we reviewed known genes and CNV syndromes causally linked to microcephaly through the PubMed, OMIM, DECIPHER, and ClinGen databases. Rare clinically relevant CNVs were detected in 39 out of the 185 Brazilian patients investigated by CMA (21%). In 31 among the 60 DECIPHER patients carrying < 200 kb CNVs, at least one known microcephaly gene was observed. Overall, four gene sets implicated in microcephaly were disclosed: known microcephaly genes; genes with supporting evidence of association with microcephaly; known macrocephaly genes; and novel candidates, including OTUD7A, BBC3, CNTN6, and NAA15. In the review, we compiled 957 known microcephaly genes and 58 genomic CNV loci, comprising 13 duplications and 50 deletions, which have already been associated with clinical findings including microcephaly. We reviewed genes and CNV syndromes previously associated with microcephaly, reinforced the high CMA diagnostic yield for this condition, pinpointed novel candidate loci linked to microcephaly deserving further evaluation, and provided a useful resource for future research on the field of neurodevelopment.
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Affiliation(s)
- Giovanna Cantini Tolezano
- Department of Genetics and Evolutionary Biology, Human Genome and Stem-Cell Research Center, Institute of Biosciences, University of São Paulo, 106 Rua do Matão, São Paulo, SP, 05508-090, Brazil
| | - Giovanna Civitate Bastos
- Department of Genetics and Evolutionary Biology, Human Genome and Stem-Cell Research Center, Institute of Biosciences, University of São Paulo, 106 Rua do Matão, São Paulo, SP, 05508-090, Brazil
| | - Silvia Souza da Costa
- Department of Genetics and Evolutionary Biology, Human Genome and Stem-Cell Research Center, Institute of Biosciences, University of São Paulo, 106 Rua do Matão, São Paulo, SP, 05508-090, Brazil
| | - Bruna Lucheze Freire
- Unidade de Endocrinologia Genética (LIM25), Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, 455 Avenida Doutor Arnaldo, São Paulo, SP, 01246-903, Brazil
| | - Thais Kataoka Homma
- Unidade de Endocrinologia Genética (LIM25), Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, 455 Avenida Doutor Arnaldo, São Paulo, SP, 01246-903, Brazil
| | - Rachel Sayuri Honjo
- Unidade de Genética do Instituto da Criança, Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, 647 Avenida Doutor Enéas Carvalho de Aguiar, São Paulo, SP, 05403-900, Brazil
| | - Guilherme Lopes Yamamoto
- Department of Genetics and Evolutionary Biology, Human Genome and Stem-Cell Research Center, Institute of Biosciences, University of São Paulo, 106 Rua do Matão, São Paulo, SP, 05508-090, Brazil
- Unidade de Genética do Instituto da Criança, Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, 647 Avenida Doutor Enéas Carvalho de Aguiar, São Paulo, SP, 05403-900, Brazil
| | - Maria Rita Passos-Bueno
- Department of Genetics and Evolutionary Biology, Human Genome and Stem-Cell Research Center, Institute of Biosciences, University of São Paulo, 106 Rua do Matão, São Paulo, SP, 05508-090, Brazil
| | - Celia Priszkulnik Koiffmann
- Department of Genetics and Evolutionary Biology, Human Genome and Stem-Cell Research Center, Institute of Biosciences, University of São Paulo, 106 Rua do Matão, São Paulo, SP, 05508-090, Brazil
| | - Chong Ae Kim
- Unidade de Genética do Instituto da Criança, Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, 647 Avenida Doutor Enéas Carvalho de Aguiar, São Paulo, SP, 05403-900, Brazil
| | - Angela Maria Vianna-Morgante
- Department of Genetics and Evolutionary Biology, Human Genome and Stem-Cell Research Center, Institute of Biosciences, University of São Paulo, 106 Rua do Matão, São Paulo, SP, 05508-090, Brazil
| | - Alexander Augusto de Lima Jorge
- Unidade de Endocrinologia Genética (LIM25), Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, 455 Avenida Doutor Arnaldo, São Paulo, SP, 01246-903, Brazil
| | - Débora Romeo Bertola
- Department of Genetics and Evolutionary Biology, Human Genome and Stem-Cell Research Center, Institute of Biosciences, University of São Paulo, 106 Rua do Matão, São Paulo, SP, 05508-090, Brazil
- Unidade de Genética do Instituto da Criança, Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, 647 Avenida Doutor Enéas Carvalho de Aguiar, São Paulo, SP, 05403-900, Brazil
| | - Carla Rosenberg
- Department of Genetics and Evolutionary Biology, Human Genome and Stem-Cell Research Center, Institute of Biosciences, University of São Paulo, 106 Rua do Matão, São Paulo, SP, 05508-090, Brazil
| | - Ana Cristina Victorino Krepischi
- Department of Genetics and Evolutionary Biology, Human Genome and Stem-Cell Research Center, Institute of Biosciences, University of São Paulo, 106 Rua do Matão, São Paulo, SP, 05508-090, Brazil.
- Institute of Biosciences, University of São Paulo, 277 Rua do Matão, São Paulo, SP, 05508-090, Brazil.
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Liu J, Yan J, Qu F, Mo W, Yu H, Hu P, Zhang Z. A pilot study on glutamate receptor and carrier gene variants and risk of childhood autism spectrum. Metab Brain Dis 2023; 38:2477-2488. [PMID: 37578654 DOI: 10.1007/s11011-023-01272-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/25/2023] [Accepted: 07/26/2023] [Indexed: 08/15/2023]
Abstract
Imbalanced glutamate signaling has been implicated in the development of autism spectrum disorder (ASD). This case-control study was to examine single nucleotide polymorphisms (SNPs) in glutamate receptor and carrier genes and determine their association with childhood ASD in a Chinese Han population. A total of 12 SNPs in genes encoding glutamate receptors (GRM7 and GRM8) and carriers (SLC1A1 and SLC25A12) were examined in 249 autistic children and 353 healthy controls. The Childhood Autism Rating Scale (CARS) and its verbal communication domain were applied to evaluate the severity of the disease and language impairment, respectively. The T allele of rs2292813 in the SLC25A12 gene was significantly associated with an increased risk of ASD (odds ratio (OD) = 1.7, 95% confidence interval (CI): 1.1-2.6, P = 0.0107). Neither the genotypes nor allele distributions of other SNPs were associated with the risk of ASD. Notably, rs1800656 and rs2237731 in the GRM8 gene, but not other SNPs, were related to the severity of language impairment. All SNPs were not correlated with the overall severity of ASD. Our findings support associations between the SLC25A12 gene variant and the risk of childhood ASD, and between the GRM8 gene variant and the severity of language impairment in the Chinese Han population.
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Affiliation(s)
- Jun Liu
- Department of Clinical Laboratory, Affiliated Xiaoshan Hospital of Hangzhou Normal University, No. 728, Yucai North Road, Xiaoshan District, Hangzhou, 311202, China.
| | - Jing Yan
- Department of Clinical Laboratory, Affiliated Xiaoshan Hospital of Hangzhou Normal University, No. 728, Yucai North Road, Xiaoshan District, Hangzhou, 311202, China
| | - Fei Qu
- Department of Clinical Laboratory, Affiliated Xiaoshan Hospital of Hangzhou Normal University, No. 728, Yucai North Road, Xiaoshan District, Hangzhou, 311202, China
| | - Weiming Mo
- Department of Clinical Laboratory, Affiliated Xiaoshan Hospital of Hangzhou Normal University, No. 728, Yucai North Road, Xiaoshan District, Hangzhou, 311202, China
| | - Hong Yu
- Department of Clinical Psychology, Xiaoshan First Affiliated Hospital of Hangzhou Normal University, Hangzhou, China
| | - Pingfang Hu
- Department of Clinical Laboratory, Affiliated Xiaoshan Hospital of Hangzhou Normal University, No. 728, Yucai North Road, Xiaoshan District, Hangzhou, 311202, China
| | - Zengyu Zhang
- Department of Pediatrics, Xiaoshan First Affiliated Hospital of Hangzhou Normal University, Hangzhou, China
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3
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Mollon J, Schultz LM, Huguet G, Knowles EEM, Mathias SR, Rodrigue A, Alexander-Bloch A, Saci Z, Jean-Louis M, Kumar K, Douard E, Almasy L, Jacquemont S, Glahn DC. Impact of Copy Number Variants and Polygenic Risk Scores on Psychopathology in the UK Biobank. Biol Psychiatry 2023; 94:591-600. [PMID: 36764568 PMCID: PMC10409883 DOI: 10.1016/j.biopsych.2023.01.028] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 01/31/2023] [Accepted: 01/31/2023] [Indexed: 02/11/2023]
Abstract
BACKGROUND Our understanding of the impact of copy number variants (CNVs) on psychopathology and their joint influence with polygenic risk scores (PRSs) remains limited. METHODS The UK Biobank recruited 502,534 individuals ages 37 to 73 years living in the United Kingdom between 2006 and 2010. After quality control, genotype data from 459,855 individuals were available for CNV calling. A total of 61 commonly studied recurrent neuropsychiatric CNVs were selected for analyses and examined individually and in aggregate (any CNV, deletion, or duplication). CNV risk scores were used to quantify intolerance of CNVs to haploinsufficiency. Major depressive disorder and generalized anxiety disorder PRSs were generated for White British individuals (N = 408,870). Mood/anxiety factor scores were generated using item-level questionnaire data (N = 501,289). RESULTS CNV carriers showed higher mood/anxiety scores than noncarriers, with the largest effects seen for intolerant deletions. A total of 11 individual deletions and 8 duplications were associated with higher mood/anxiety. Carriers of the 9p24.3 (DMRT1) duplication showed lower mood/anxiety. Associations remained significant for most CNVs when excluding individuals with psychiatric diagnoses. Nominally significant CNV × PRS interactions provided preliminary evidence that associations between select individual CNVs, but not CNVs in aggregate, and mood/anxiety may be modulated by PRSs. CONCLUSIONS CNVs associated with risk for psychiatric disorders showed small to large effects on dimensional mood/anxiety scores in a general population cohort, even when excluding individuals with psychiatric diagnoses. CNV × PRS interactions showed that associations between select CNVs and mood/anxiety may be modulated by PRSs.
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Affiliation(s)
- Josephine Mollon
- Department of Psychiatry, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts.
| | - Laura M Schultz
- Department of Biomedical and Health Informatics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Guillaume Huguet
- Department of Pediatrics, Université de Montréal, Montreal, Quebec, Canada; Department of Pediatrics, Center Hospitalier Universitaire Sainte-Justine Research Center, Montreal, Quebec, Canada
| | - Emma E M Knowles
- Department of Psychiatry, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Samuel R Mathias
- Department of Psychiatry, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Amanda Rodrigue
- Department of Psychiatry, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Aaron Alexander-Bloch
- Department of Child and Adolescent Psychiatry and Behavioral Science, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania; Lifespan Brain Institute, The Children's Hospital of Philadelphia and Penn Medicine, University of Pennsylvania, Philadelphia, Pennsylvania; Neurodevelopment and Psychosis Section, Department of Psychiatry, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Zohra Saci
- Department of Pediatrics, Center Hospitalier Universitaire Sainte-Justine Research Center, Montreal, Quebec, Canada
| | - Martineau Jean-Louis
- Department of Pediatrics, Center Hospitalier Universitaire Sainte-Justine Research Center, Montreal, Quebec, Canada
| | - Kuldeep Kumar
- Department of Pediatrics, Center Hospitalier Universitaire Sainte-Justine Research Center, Montreal, Quebec, Canada
| | - Elise Douard
- Department of Pediatrics, Université de Montréal, Montreal, Quebec, Canada; Department of Pediatrics, Center Hospitalier Universitaire Sainte-Justine Research Center, Montreal, Quebec, Canada
| | - Laura Almasy
- Department of Biomedical and Health Informatics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania; Department of Genetics, Perelman School of Medicine, Penn-CHOP Lifespan Brain Institute, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Sebastien Jacquemont
- Department of Pediatrics, Université de Montréal, Montreal, Quebec, Canada; Department of Pediatrics, Center Hospitalier Universitaire Sainte-Justine Research Center, Montreal, Quebec, Canada
| | - David C Glahn
- Department of Psychiatry, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts; Olin Neuropsychiatry Research Center, Institute of Living, Hartford, Connecticut
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Kubota N, Takeda R, Kobayashi J, Hidaka E, Nishi E, Takano K, Wakui K. Reanalysis of Chromosomal Microarray Data Using a Smaller Copy Number Variant Call Threshold Identifies Four Cases with Heterozygous Multiexon Deletions of ARID1B, EHMT1, and FOXP1 Genes. Mol Syndromol 2023; 14:394-404. [PMID: 37901861 PMCID: PMC10601822 DOI: 10.1159/000530252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Accepted: 03/16/2023] [Indexed: 10/31/2023] Open
Abstract
Introduction Chromosomal microarray (CMA) is a highly accurate and established method for detecting copy number variations (CNVs) in clinical genetic testing. CNVs are important etiological factors for disorders such as intellectual disability, developmental delay, and multiple congenital anomalies. Recently developed analytical methods have facilitated the identification of smaller CNVs. Therefore, reanalyzing CMA data using a smaller CNV calling threshold may yield useful information. However, this method was left to the discretion of each institution. Methods We reanalyzed the CMA data of 131 patients using a smaller CNV call threshold: 50 kb 50 probes for gain and 25 kb 25 probes for loss. We interpreted the reanalyzed CNVs based on the most recently available information. In the reanalysis, we filtered the data using the Clinical Genome Resource dosage sensitivity gene list as an index to quickly and efficiently check morbid genes. Results The number of copy number loss was approximately 20 times greater, and copy number gain was approximately three times greater compared to those in the previous analysis. We detected new likely pathogenic CNVs in four participants: a 236.5 kb loss within ARID1B, a 50.6 kb loss including EHMT1, a 46.5 kb loss including EHMT1, and an 89.1 kb loss within the FOXP1 gene. Conclusion The method employed in this study is simple and effective for CMA data reanalysis using a smaller CNV call threshold. Thus, this method is efficient for both ongoing and repeated analyses. This study may stimulate further discussion of reanalysis methodology in clinical laboratories.
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Affiliation(s)
- Noriko Kubota
- Life Science Research Center, Nagano Children’s Hospital, Azumino, Japan
| | - Ryojun Takeda
- Life Science Research Center, Nagano Children’s Hospital, Azumino, Japan
- Division of Medical Genetics, Nagano Children’s Hospital, Azumino, Japan
| | - Jun Kobayashi
- Life Science Research Center, Nagano Children’s Hospital, Azumino, Japan
| | - Eiko Hidaka
- Life Science Research Center, Nagano Children’s Hospital, Azumino, Japan
| | - Eriko Nishi
- Division of Medical Genetics, Nagano Children’s Hospital, Azumino, Japan
| | - Kyoko Takano
- Division of Medical Genetics, Nagano Children’s Hospital, Azumino, Japan
- Department of Medical Genetics, Shinshu University School of Medicine, Matsumoto, Japan
- Center for Medical Genetics, Shinshu University Hospital, Matsumoto, Japan
| | - Keiko Wakui
- Life Science Research Center, Nagano Children’s Hospital, Azumino, Japan
- Department of Medical Genetics, Shinshu University School of Medicine, Matsumoto, Japan
- Center for Medical Genetics, Shinshu University Hospital, Matsumoto, Japan
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5
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Vaz R, Edwards S, Dueñas-Rey A, Hofmeister W, Lindstrand A. Loss of ctnnd2b affects neuronal differentiation and behavior in zebrafish. Front Neurosci 2023; 17:1205653. [PMID: 37465584 PMCID: PMC10351287 DOI: 10.3389/fnins.2023.1205653] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Accepted: 06/15/2023] [Indexed: 07/20/2023] Open
Abstract
Delta-catenin (CTNND2) is an adhesive junction associated protein belonging to the family of p120 catenins. The human gene is located on the short arm of chromosome 5, the region deleted in Cri-du-chat syndrome (OMIM #123450). Heterozygous loss of CTNND2 has been linked to a wide spectrum of neurodevelopmental disorders such as autism, schizophrenia, and intellectual disability. Here we studied how heterozygous loss of ctnnd2b affects zebrafish embryonic development, and larvae and adult behavior. First, we observed a disorganization of neuronal subtypes in the developing forebrain, namely the presence of ectopic isl1-expressing cells and a local reduction of GABA-positive neurons in the optic recess region. Next, using time-lapse analysis, we found that the disorganized distribution of is1l-expressing forebrain neurons resulted from an increased specification of Isl1:GFP neurons. Finally, we studied the swimming patterns of both larval and adult heterozygous zebrafish and observed an increased activity compared to wildtype animals. Overall, this data suggests a role for ctnnd2b in the differentiation cascade of neuronal subtypes in specific regions of the vertebrate brain, with repercussions in the animal's behavior.
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Affiliation(s)
- Raquel Vaz
- Department of Molecular Medicine and Surgery and Centre of Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Steven Edwards
- Department of Applied Physics and Science for Life Laboratory, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Alfredo Dueñas-Rey
- Department of Molecular Medicine and Surgery and Centre of Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Wolfgang Hofmeister
- Department of Molecular Medicine and Surgery and Centre of Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Anna Lindstrand
- Department of Molecular Medicine and Surgery and Centre of Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
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6
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Muhie S, Gautam A, Yang R, Misganaw B, Daigle BJ, Mellon SH, Flory JD, Abu-Amara D, Lee I, Wang K, Rampersaud R, Hood L, Yehuda R, Marmar CR, Wolkowitz OM, Ressler KJ, Doyle FJ, Hammamieh R, Jett M. Molecular signatures of post-traumatic stress disorder in war-zone-exposed veteran and active-duty soldiers. Cell Rep Med 2023; 4:101045. [PMID: 37196634 DOI: 10.1016/j.xcrm.2023.101045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 11/23/2022] [Accepted: 04/18/2023] [Indexed: 05/19/2023]
Abstract
Post-traumatic stress disorder (PTSD) is a multisystem syndrome. Integration of systems-level multi-modal datasets can provide a molecular understanding of PTSD. Proteomic, metabolomic, and epigenomic assays are conducted on blood samples of two cohorts of well-characterized PTSD cases and controls: 340 veterans and 180 active-duty soldiers. All participants had been deployed to Iraq and/or Afghanistan and exposed to military-service-related criterion A trauma. Molecular signatures are identified from a discovery cohort of 218 veterans (109/109 PTSD+/-). Identified molecular signatures are tested in 122 separate veterans (62/60 PTSD+/-) and in 180 active-duty soldiers (PTSD+/-). Molecular profiles are computationally integrated with upstream regulators (genetic/methylation/microRNAs) and functional units (mRNAs/proteins/metabolites). Reproducible molecular features of PTSD are identified, including activated inflammation, oxidative stress, metabolic dysregulation, and impaired angiogenesis. These processes may play a role in psychiatric and physical comorbidities, including impaired repair/wound healing mechanisms and cardiovascular, metabolic, and psychiatric diseases.
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Affiliation(s)
- Seid Muhie
- Medical Readiness Systems Biology, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA; The Geneva Foundation, Silver Spring, MD 20910, USA.
| | - Aarti Gautam
- Medical Readiness Systems Biology, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
| | - Ruoting Yang
- Medical Readiness Systems Biology, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
| | - Burook Misganaw
- Medical Readiness Systems Biology, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA; Vysnova Inc., Landover, MD 20785, USA
| | - Bernie J Daigle
- Departments of Biological Sciences and Computer Science, The University of Memphis, Memphis, TN 38152, USA
| | - Synthia H Mellon
- Department of Obstetrics, Gynecology & Reproductive Sciences, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Janine D Flory
- Office of Mental Health, James J. Peters VA Medical Center, Bronx, NY 10468, USA; Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10468, USA
| | - Duna Abu-Amara
- Department of Psychiatry, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Inyoul Lee
- Institute for Systems Biology, Seattle, WA 98109, USA
| | - Kai Wang
- Institute for Systems Biology, Seattle, WA 98109, USA
| | - Ryan Rampersaud
- Department of Psychiatry and Behavioral Sciences, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Leroy Hood
- Institute for Systems Biology, Seattle, WA 98109, USA
| | - Rachel Yehuda
- Office of Mental Health, James J. Peters VA Medical Center, Bronx, NY 10468, USA; Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10468, USA
| | - Charles R Marmar
- Department of Psychiatry, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Owen M Wolkowitz
- Department of Psychiatry and Behavioral Sciences, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Kerry J Ressler
- McLean Hospital, Belmont, MA 02478, USA; Harvard Medical School, Boston, MA 02115, USA
| | - Francis J Doyle
- Harvard John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02134, USA
| | - Rasha Hammamieh
- Medical Readiness Systems Biology, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
| | - Marti Jett
- US Army Medical Research and Development Command, HQ, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA.
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7
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Rieger M, Moutton S, Verheyen S, Steindl K, Popp B, Leheup B, Bonnet C, Oneda B, Rauch A, Reis A, Krumbiegel M, Hüffmeier U. Microdeletions at 19p13.11p12 in five individuals with neurodevelopmental delay. Eur J Med Genet 2023; 66:104669. [PMID: 36379434 DOI: 10.1016/j.ejmg.2022.104669] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 10/11/2022] [Accepted: 11/11/2022] [Indexed: 11/15/2022]
Abstract
Only few copy number variants at chromosome 19p13.11 have been reported, thus associated clinical information is scarce. Proximal to these copy number losses, we now identified deletions in five unrelated individuals with neurodevelopmental disorders. They presented with psychomotor delay as well as behavioral and sleeping disorders, while complex cardiovascular, skeletal, and various other malformations were more variable. Dysmorphic features were rather unspecific and not considered as a recognizable gestalt. Neither of the analyzed parents carried their offsprings' deletions, indicating de novo occurrence. The deletion sizes ranged between 0.7 and 5.2 Mb, were located between 18 and 24 megabases from the telomere, and contained a variable number of protein-coding genes (n = 25-68). Although not all microdeletions shared a common region, the smallest common overlap of some of the deletions provided interesting insights in the chromosomal region 19p13.11p12. Diligent literature review using OMIM and Pubmed did not identify a satisfying candidate gene for neurodevelopmental disorders. In the literature, a de novo in-frame deletion in MAU2 was considered pathogenic in an individual with Cornelia de Lange syndrome. Therefore, the clinical differential diagnosis of this latter syndrome in one individual and the encompassment of MAU2 in three individuals' deletions suggest clinical and genetic overlap with this specific syndrome. Three of the four here reported individuals with deletion encompassing GDF1 had different congenital heart defects, suggesting that this gene's haploinsufficiency might contribute to the cardiovascular phenotype, however, with reduced penetrance. Our findings indicate an association of microdeletions at 19p13.11/ 19p13.11p12 with neurodevelopmental disorders, variable symptoms, and malformations, and delineate the phenotypic spectrum of deletions within this genomic region.
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Affiliation(s)
- Melissa Rieger
- Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Universitätsklinikum Erlangen, Institute of Human Genetics, 91054 Erlangen, Germany
| | | | - Sarah Verheyen
- Institute of Human Genetics, Diagnostic and Research Center for MolecularBioMedicine, Medical University of Graz, Austria
| | - Katharina Steindl
- Institute of Medical Genetics, University of Zurich, Schlieren, Zurich, Switzerland
| | - Bernt Popp
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig 04103, Germany; Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Center of Functional Genomics, Hessische Straße 4A, 10115 Berlin, Germany
| | - Bruno Leheup
- Service de génétique médicale, CHU de Nancy, Nancy, France
| | - Céline Bonnet
- Laboratoire de génétique médicale, CHRU Nancy, Nancy, France
| | - Beatrice Oneda
- Institute of Medical Genetics, University of Zurich, Schlieren, Zurich, Switzerland
| | - Anita Rauch
- Institute of Medical Genetics, University of Zurich, Schlieren, Zurich, Switzerland
| | - André Reis
- Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Universitätsklinikum Erlangen, Institute of Human Genetics, 91054 Erlangen, Germany
| | - Mandy Krumbiegel
- Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Universitätsklinikum Erlangen, Institute of Human Genetics, 91054 Erlangen, Germany
| | - Ulrike Hüffmeier
- Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Universitätsklinikum Erlangen, Institute of Human Genetics, 91054 Erlangen, Germany.
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8
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Gibitova EA, Dobrynin PV, Pomerantseva EA, Musatova EV, Kostareva A, Evsyukov I, Rychkov SY, Zhukova OV, Naumova OY, Grigorenko EL. A Study of the Genomic Variations Associated with Autistic Spectrum Disorders in a Russian Cohort of Patients Using Whole-Exome Sequencing. Genes (Basel) 2022; 13:genes13050920. [PMID: 35627305 PMCID: PMC9141003 DOI: 10.3390/genes13050920] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 04/30/2022] [Accepted: 05/16/2022] [Indexed: 12/10/2022] Open
Abstract
This study provides new data on the whole-exome sequencing of a cohort of children with autistic spectrum disorders (ASD) from an underexplored Russian population. Using both a cross-sectional approach involving a control cohort of the same ancestry and an annotation-based approach involving relevant public databases, we explored exonic single nucleotide variants and copy-number variation potentially involved in the manifestation of ASD. The study results reveal new potential ASD candidate-variants found in the studied Russian cohort and show a high prevalence of common ASD-associated genomic variants, especially those in the genes known to be associated with the manifestation of intellectual disabilities. Our screening of an ASD cohort from a previously understudied population allowed us to flag at least a few novel genes (IGLJ2, FAM21A, OR11H12, HIP1, PRAMEF10, and ZNF717) regarding their potential involvement in ASD.
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Affiliation(s)
- Ekaterina A. Gibitova
- Computer Technologies Laboratory, University of Information Technologies, Mechanics and Optics, Saint Petersburg 197101, Russia; (E.A.G.); (P.V.D.); (I.E.)
| | - Pavel V. Dobrynin
- Computer Technologies Laboratory, University of Information Technologies, Mechanics and Optics, Saint Petersburg 197101, Russia; (E.A.G.); (P.V.D.); (I.E.)
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Human Genetics Laboratory, Vavilov Institute of General Genetics RAS, Moscow 119991, Russia; (S.Y.R.); (O.V.Z.)
| | - Ekaterina A. Pomerantseva
- The ‘Genetico’ Center for Genetics and Reproductive Medicine, Moscow 119333, Russia; (E.A.P.); (E.V.M.)
| | - Elizaveta V. Musatova
- The ‘Genetico’ Center for Genetics and Reproductive Medicine, Moscow 119333, Russia; (E.A.P.); (E.V.M.)
| | - Anna Kostareva
- Almazov National Medical Research Centre, Saint Petersburg 197341, Russia;
- Department of Women’s and Children’s Health, Karolinska Institute, Stockholm 17177, Sweden
| | - Igor Evsyukov
- Computer Technologies Laboratory, University of Information Technologies, Mechanics and Optics, Saint Petersburg 197101, Russia; (E.A.G.); (P.V.D.); (I.E.)
| | - Sergey Y. Rychkov
- Human Genetics Laboratory, Vavilov Institute of General Genetics RAS, Moscow 119991, Russia; (S.Y.R.); (O.V.Z.)
| | - Olga V. Zhukova
- Human Genetics Laboratory, Vavilov Institute of General Genetics RAS, Moscow 119991, Russia; (S.Y.R.); (O.V.Z.)
| | - Oxana Y. Naumova
- Human Genetics Laboratory, Vavilov Institute of General Genetics RAS, Moscow 119991, Russia; (S.Y.R.); (O.V.Z.)
- Department of Psychology, University of Houston, Houston, TX 77204, USA
- Department of Psychology, Saint-Petersburg State University, Saint Petersburg 199034, Russia
- Correspondence: (O.Y.N.); (E.L.G.)
| | - Elena L. Grigorenko
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Psychology, University of Houston, Houston, TX 77204, USA
- Department of Psychology, Saint-Petersburg State University, Saint Petersburg 199034, Russia
- Center of Cognitive Research, Sirius University of Science and Technology, Sochi 354340, Russia
- Correspondence: (O.Y.N.); (E.L.G.)
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9
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Chau MHK, Qian J, Chen Z, Li Y, Zheng Y, Tse WT, Kwok YK, Leung TY, Dong Z, Choy KW. Trio-Based Low-Pass Genome Sequencing Reveals Characteristics and Significance of Rare Copy Number Variants in Prenatal Diagnosis. Front Genet 2021; 12:742325. [PMID: 34616436 PMCID: PMC8488434 DOI: 10.3389/fgene.2021.742325] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 08/25/2021] [Indexed: 01/22/2023] Open
Abstract
Background: Low-pass genome sequencing (GS) detects clinically significant copy number variants (CNVs) in prenatal diagnosis. However, detection at improved resolutions leads to an increase in the number of CNVs identified, increasing the difficulty of clinical interpretation and management. Methods: Trio-based low-pass GS was performed in 315 pregnancies undergoing invasive testing. Rare CNVs detected in the fetuses were investigated. The characteristics of rare CNVs were described and compared to curated CNVs in other studies. Results: A total of 603 rare CNVs, namely, 597 constitutional and 6 mosaic CNVs, were detected in 272 fetuses (272/315, 86.3%), providing 1.9 rare CNVs per fetus (603/315). Most CNVs were smaller than 1 Mb (562/603, 93.2%), while 1% (6/603) were mosaic. Forty-six de novo (7.6%, 46/603) CNVs were detected in 11.4% (36/315) of the cases. Eighty-four CNVs (74 fetuses, 23.5%) involved disease-causing genes of which the mode of inheritance was crucial for interpretation and assessment of recurrence risk. Overall, 31 pathogenic/likely pathogenic CNVs were detected, among which 25.8% (8/31) were small (<100 kb; n = 3) or mosaic CNVs (n = 5). Conclusion: We examined the landscape of rare CNVs with parental inheritance assignment and demonstrated that they occur frequently in prenatal diagnosis. This information has clinical implications regarding genetic counseling and consideration for trio-based CNV analysis.
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Affiliation(s)
- Matthew Hoi Kin Chau
- Department of Obstetrics and Gynecology, The Chinese University of Hong Kong, Shatin, Hong Kong, SAR China.,Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, Hong Kong, SAR China.,Hong Kong Hub of Pediatric Excellence, The Chinese University of Hong Kong, Shatin, Hong Kong, SAR China
| | - Jicheng Qian
- Department of Obstetrics and Gynecology, The Chinese University of Hong Kong, Shatin, Hong Kong, SAR China.,Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, Hong Kong, SAR China
| | - Zihan Chen
- Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, Hong Kong, SAR China
| | - Ying Li
- Department of Obstetrics and Gynecology, The Chinese University of Hong Kong, Shatin, Hong Kong, SAR China.,Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, Hong Kong, SAR China.,Hong Kong Hub of Pediatric Excellence, The Chinese University of Hong Kong, Shatin, Hong Kong, SAR China
| | - Yu Zheng
- Department of Obstetrics and Gynecology, The Chinese University of Hong Kong, Shatin, Hong Kong, SAR China.,Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, Hong Kong, SAR China
| | - Wing Ting Tse
- Department of Obstetrics and Gynecology, The Chinese University of Hong Kong, Shatin, Hong Kong, SAR China
| | - Yvonne K Kwok
- Department of Obstetrics and Gynecology, The Chinese University of Hong Kong, Shatin, Hong Kong, SAR China.,Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, Hong Kong, SAR China
| | - Tak Yeung Leung
- Department of Obstetrics and Gynecology, The Chinese University of Hong Kong, Shatin, Hong Kong, SAR China.,Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, Hong Kong, SAR China.,The Chinese University of Hong Kong-Baylor College of Medicine Joint Center For Medical Genetics, Shatin, Hong Kong, SAR China
| | - Zirui Dong
- Department of Obstetrics and Gynecology, The Chinese University of Hong Kong, Shatin, Hong Kong, SAR China.,Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, Hong Kong, SAR China.,Hong Kong Hub of Pediatric Excellence, The Chinese University of Hong Kong, Shatin, Hong Kong, SAR China
| | - Kwong Wai Choy
- Department of Obstetrics and Gynecology, The Chinese University of Hong Kong, Shatin, Hong Kong, SAR China.,Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, Hong Kong, SAR China.,Hong Kong Hub of Pediatric Excellence, The Chinese University of Hong Kong, Shatin, Hong Kong, SAR China.,The Chinese University of Hong Kong-Baylor College of Medicine Joint Center For Medical Genetics, Shatin, Hong Kong, SAR China
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10
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Sanchez-Jimeno C, Blanco-Kelly F, López-Grondona F, Losada-Del Pozo R, Moreno B, Rodrigo-Moreno M, Martinez-Cayuelas E, Riveiro-Alvarez R, Fenollar-Cortés M, Ayuso C, Rodríguez de Alba M, Lorda-Sanchez I, Almoguera B. Attention Deficit Hyperactivity and Autism Spectrum Disorders as the Core Symptoms of AUTS2 Syndrome: Description of Five New Patients and Update of the Frequency of Manifestations and Genotype-Phenotype Correlation. Genes (Basel) 2021; 12:genes12091360. [PMID: 34573342 PMCID: PMC8471078 DOI: 10.3390/genes12091360] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 08/23/2021] [Accepted: 08/27/2021] [Indexed: 12/14/2022] Open
Abstract
Haploinsufficiency of AUTS2 has been associated with a syndromic form of neurodevelopmental delay characterized by intellectual disability, autistic features, and microcephaly, also known as AUTS2 syndrome. While the phenotype associated with large deletions and duplications of AUTS2 is well established, clinical features of patients harboring AUTS2 sequence variants have not been extensively described. In this study, we describe the phenotype of five new patients with AUTS2 pathogenic variants, three of them harboring loss-of-function sequence variants. The phenotype of the patients was characterized by attention deficit/hyperactivity disorder (ADHD) and autism spectrum disorder (ASD) or autistic features and mild global developmental delay (GDD) or intellectual disability (ID), all in 4/5 patients (80%), a frequency higher than previously reported for ADHD and autistic features. Microcephaly and short stature were found in 60% of the patients; and feeding difficulties, generalized hypotonia, and ptosis, were each found in 40%. We also provide the aggregated frequency of the 32 items included in the AUTS2 syndrome severity score (ASSS) in patients currently reported in the literature. The main characteristics of the syndrome are GDD/ID in 98% of patients, microcephaly in 65%, feeding difficulties in 62%, ADHD or hyperactivity in 54%, and autistic traits in 52%. Finally, using the location of 31 variants from the literature together with variants from the five patients, we found significantly higher ASSS values in patients with pathogenic variants affecting the 3′ end of the gene, confirming the genotype-phenotype correlation initially described.
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Affiliation(s)
- Carolina Sanchez-Jimeno
- Department of Genetics and Genomics, IIS–Fundación Jiménez Díaz University Hospital, 28040 Madrid, Spain; (C.S.-J.); (F.B.-K.); (F.L.-G.); (R.R.-A.); (C.A.); (M.R.d.A.); (I.L.-S.)
- Center for Biomedical Network Research on Rare Diseases (CIBERER), ISCIII, 28040 Madrid, Spain
| | - Fiona Blanco-Kelly
- Department of Genetics and Genomics, IIS–Fundación Jiménez Díaz University Hospital, 28040 Madrid, Spain; (C.S.-J.); (F.B.-K.); (F.L.-G.); (R.R.-A.); (C.A.); (M.R.d.A.); (I.L.-S.)
- Center for Biomedical Network Research on Rare Diseases (CIBERER), ISCIII, 28040 Madrid, Spain
| | - Fermina López-Grondona
- Department of Genetics and Genomics, IIS–Fundación Jiménez Díaz University Hospital, 28040 Madrid, Spain; (C.S.-J.); (F.B.-K.); (F.L.-G.); (R.R.-A.); (C.A.); (M.R.d.A.); (I.L.-S.)
- Center for Biomedical Network Research on Rare Diseases (CIBERER), ISCIII, 28040 Madrid, Spain
| | - Rebeca Losada-Del Pozo
- Department of Pediatrics, IIS–Fundación Jiménez Díaz University Hospital, 28040 Madrid, Spain; (R.L.-D.P.); (B.M.); (M.R.-M.); (E.M.-C.)
| | - Beatriz Moreno
- Department of Pediatrics, IIS–Fundación Jiménez Díaz University Hospital, 28040 Madrid, Spain; (R.L.-D.P.); (B.M.); (M.R.-M.); (E.M.-C.)
| | - María Rodrigo-Moreno
- Department of Pediatrics, IIS–Fundación Jiménez Díaz University Hospital, 28040 Madrid, Spain; (R.L.-D.P.); (B.M.); (M.R.-M.); (E.M.-C.)
| | - Elena Martinez-Cayuelas
- Department of Pediatrics, IIS–Fundación Jiménez Díaz University Hospital, 28040 Madrid, Spain; (R.L.-D.P.); (B.M.); (M.R.-M.); (E.M.-C.)
| | - Rosa Riveiro-Alvarez
- Department of Genetics and Genomics, IIS–Fundación Jiménez Díaz University Hospital, 28040 Madrid, Spain; (C.S.-J.); (F.B.-K.); (F.L.-G.); (R.R.-A.); (C.A.); (M.R.d.A.); (I.L.-S.)
- Center for Biomedical Network Research on Rare Diseases (CIBERER), ISCIII, 28040 Madrid, Spain
| | - María Fenollar-Cortés
- Clinical Genetics Unit, Department of Clinical Analysis, Clínico San Carlos University Hospital, 28040 Madrid, Spain;
- IIS-Clínico San Carlos University Hospital (IsISSC), 28040 Madrid, Spain
| | - Carmen Ayuso
- Department of Genetics and Genomics, IIS–Fundación Jiménez Díaz University Hospital, 28040 Madrid, Spain; (C.S.-J.); (F.B.-K.); (F.L.-G.); (R.R.-A.); (C.A.); (M.R.d.A.); (I.L.-S.)
- Center for Biomedical Network Research on Rare Diseases (CIBERER), ISCIII, 28040 Madrid, Spain
| | - Marta Rodríguez de Alba
- Department of Genetics and Genomics, IIS–Fundación Jiménez Díaz University Hospital, 28040 Madrid, Spain; (C.S.-J.); (F.B.-K.); (F.L.-G.); (R.R.-A.); (C.A.); (M.R.d.A.); (I.L.-S.)
- Center for Biomedical Network Research on Rare Diseases (CIBERER), ISCIII, 28040 Madrid, Spain
| | - Isabel Lorda-Sanchez
- Department of Genetics and Genomics, IIS–Fundación Jiménez Díaz University Hospital, 28040 Madrid, Spain; (C.S.-J.); (F.B.-K.); (F.L.-G.); (R.R.-A.); (C.A.); (M.R.d.A.); (I.L.-S.)
- Center for Biomedical Network Research on Rare Diseases (CIBERER), ISCIII, 28040 Madrid, Spain
| | - Berta Almoguera
- Department of Genetics and Genomics, IIS–Fundación Jiménez Díaz University Hospital, 28040 Madrid, Spain; (C.S.-J.); (F.B.-K.); (F.L.-G.); (R.R.-A.); (C.A.); (M.R.d.A.); (I.L.-S.)
- Center for Biomedical Network Research on Rare Diseases (CIBERER), ISCIII, 28040 Madrid, Spain
- Correspondence:
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11
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Erotomania and phenotypic continuum in a family frameshift variant of AUTS2: a case report and review. BMC Psychiatry 2021; 21:360. [PMID: 34273950 PMCID: PMC8285776 DOI: 10.1186/s12888-021-03342-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Accepted: 06/25/2021] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND Pathogenic variants of the AUTS2 (Autism Susceptibility candidate 2) gene predispose to intellectual disability, autism spectrum disorder, attention deficit hyperactivity disorder, facial dysmorphism and short stature. This phenotype is therefore associated with neurocognitive disturbances and social cognition, indicating potential functional maladjustment in the affected subjects, and a potentially significant impact on quality of life. Although many isolated cases have been reported in the literature, to date no families have been described. This case reports on a family (three generations) with a frameshift variant in the AUTS2 gene. CASE PRESENTATION The proband is 13 years old with short stature, dysmorphic features, moderate intellectual disability and autism spectrum disorder. His mother is 49 years old and also has short stature and similar dysmorphic features. She does not have autism disorder but presents an erotomaniac delusion. Her cognitive performance is heterogeneous. The two aunts are also of short stature. The 50-year-old aunt has isolated social cognition disorders. The 45-year-old aunt has severe cognitive impairment and autism spectrum disorder. The molecular analysis of the three sisters and the proband shows the same AUTS2 heterozygous duplication leading to a frame shift expected to produce a premature stop codon, p.(Met593Tyrfs*85). Previously reported isolated cases revealed phenotypic and cognitive impairment variability. In this case report, these variabilities are present within the same family, presenting the same variant. CONCLUSIONS The possibility of a phenotypic spectrum within the same family highlights the need for joint psychiatry and genetics research.
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12
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Qin F, Luo X, Cai G, Xiao F. Shall genomic correlation structure be considered in copy number variants detection? Brief Bioinform 2021; 22:6295811. [PMID: 34114005 DOI: 10.1093/bib/bbab215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 04/16/2021] [Accepted: 05/17/2021] [Indexed: 11/14/2022] Open
Abstract
Copy number variation has been identified as a major source of genomic variation associated with disease susceptibility. With the advent of whole-exome sequencing (WES) technology, massive WES data have been generated, allowing for the identification of copy number variants (CNVs) in the protein-coding regions with direct functional interpretation. We have previously shown evidence of the genomic correlation structure in array data and developed a novel chromosomal breakpoint detection algorithm, LDcnv, which showed significantly improved detection power through integrating the correlation structure in a systematic modeling manner. However, it remains unexplored whether the genomic correlation exists in WES data and how such correlation structure integration can improve the CNV detection accuracy. In this study, we first explored the correlation structure of the WES data using the 1000 Genomes Project data. Both real raw read depth and median-normalized data showed strong evidence of the correlation structure. Motivated by this fact, we proposed a correlation-based method, CORRseq, as a novel release of the LDcnv algorithm in profiling WES data. The performance of CORRseq was evaluated in extensive simulation studies and real data analysis from the 1000 Genomes Project. CORRseq outperformed the existing methods in detecting medium and large CNVs. In conclusion, it would be more advantageous to model genomic correlation structure in detecting relatively long CNVs. This study provides great insights for methodology development of CNV detection with NGS data.
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Affiliation(s)
- Fei Qin
- Department of Epidemiology and Biostatistics, Arnold School of Public Health, University of South Carolina (USC), Discovery 449, 915 Greene St, Columbia, SC 29208, USA
| | - Xizhi Luo
- Department of Epidemiology and Biostatistics, Arnold School of Public Health, USC, Discovery 449, 915 Greene St, Columbia, SC 29208, USA
| | - Guoshuai Cai
- Department of Environmental Health Science, Arnold School of Public Health, USC, Discovery 449, 915 Greene St, Columbia, SC 29208, USA
| | - Feifei Xiao
- Department of Epidemiology and Biostatistics, Arnold School of Public Health, USC, Discovery 449, 915 Greene St, Columbia, SC 29208, USA
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13
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Luo X, Qin F, Cai G, Xiao F. Integrating genomic correlation structure improves copy number variations detection. Bioinformatics 2021; 37:312-317. [PMID: 32805016 DOI: 10.1093/bioinformatics/btaa737] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 07/23/2020] [Accepted: 08/12/2020] [Indexed: 12/16/2022] Open
Abstract
MOTIVATION Copy number variation plays important roles in human complex diseases. The detection of copy number variants (CNVs) is identifying mean shift in genetic intensities to locate chromosomal breakpoints, the step of which is referred to as chromosomal segmentation. Many segmentation algorithms have been developed with a strong assumption of independent observations in the genetic loci, and they assume each locus has an equal chance to be a breakpoint (i.e. boundary of CNVs). However, this assumption is violated in the genetics perspective due to the existence of correlation among genomic positions, such as linkage disequilibrium (LD). Our study showed that the LD structure is related to the location distribution of CNVs, which indeed presents a non-random pattern on the genome. To generate more accurate CNVs, we proposed a novel algorithm, LDcnv, that models the CNV data with its biological characteristics relating to genetic dependence structure (i.e. LD). RESULTS We theoretically demonstrated the correlation structure of CNV data in SNP array, which further supports the necessity of integrating biological structure in statistical methods for CNV detection. Therefore, we developed the LDcnv that integrated the genomic correlation structure with a local search strategy into statistical modeling of the CNV intensities. To evaluate the performance of LDcnv, we conducted extensive simulations and analyzed large-scale HapMap datasets. We showed that LDcnv presented high accuracy, stability and robustness in CNV detection and higher precision in detecting short CNVs compared to existing methods. This new segmentation algorithm has a wide scope of potential application with data from various high-throughput technology platforms. AVAILABILITY AND IMPLEMENTATION https://github.com/FeifeiXiaoUSC/LDcnv. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Xizhi Luo
- Department of Epidemiology and Biostatistics, Arnold School of Public Health, University of South Carolina, Columbia, SC 29208, USA
| | - Fei Qin
- Department of Epidemiology and Biostatistics, Arnold School of Public Health, University of South Carolina, Columbia, SC 29208, USA
| | - Guoshuai Cai
- Department of Environmental Health Science, Arnold School of Public Health, University of South Carolina, Columbia, SC 29208, USA
| | - Feifei Xiao
- Department of Epidemiology and Biostatistics, Arnold School of Public Health, University of South Carolina, Columbia, SC 29208, USA
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14
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Hiatt SM, Lawlor JM, Handley LH, Ramaker RC, Rogers BB, Partridge EC, Boston LB, Williams M, Plott CB, Jenkins J, Gray DE, Holt JM, Bowling KM, Bebin EM, Grimwood J, Schmutz J, Cooper GM. Long-read genome sequencing for the molecular diagnosis of neurodevelopmental disorders. HGG ADVANCES 2021; 2:100023. [PMID: 33937879 PMCID: PMC8087252 DOI: 10.1016/j.xhgg.2021.100023] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Accepted: 01/07/2021] [Indexed: 02/07/2023] Open
Abstract
Exome and genome sequencing have proven to be effective tools for the diagnosis of neurodevelopmental disorders (NDDs), but large fractions of NDDs cannot be attributed to currently detectable genetic variation. This is likely, at least in part, a result of the fact that many genetic variants are difficult or impossible to detect through typical short-read sequencing approaches. Here, we describe a genomic analysis using Pacific Biosciences circular consensus sequencing (CCS) reads, which are both long (>10 kb) and accurate (>99% bp accuracy). We used CCS on six proband-parent trios with NDDs that were unexplained despite extensive testing, including genome sequencing with short reads. We identified variants and created de novo assemblies in each trio, with global metrics indicating these datasets are more accurate and comprehensive than those provided by short-read data. In one proband, we identified a likely pathogenic (LP), de novo L1-mediated insertion in CDKL5 that results in duplication of exon 3, leading to a frameshift. In a second proband, we identified multiple large de novo structural variants, including insertion-translocations affecting DGKB and MLLT3, which we show disrupt MLLT3 transcript levels. We consider this extensive structural variation likely pathogenic. The breadth and quality of variant detection, coupled to finding variants of clinical and research interest in two of six probands with unexplained NDDs, support the hypothesis that long-read genome sequencing can substantially improve rare disease genetic discovery rates.
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Affiliation(s)
- Susan M. Hiatt
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | | | - Lori H. Handley
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - Ryne C. Ramaker
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - Brianne B. Rogers
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL 35924, USA
| | | | - Lori Beth Boston
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - Melissa Williams
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | | | - Jerry Jenkins
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - David E. Gray
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - James M. Holt
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - Kevin M. Bowling
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - E. Martina Bebin
- Department of Neurology, University of Alabama at Birmingham, Birmingham, AL 35924, USA
| | - Jane Grimwood
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - Jeremy Schmutz
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
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15
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Wang H, Avillach P. Diagnostic Classification and Prognostic Prediction Using Common Genetic Variants in Autism Spectrum Disorder: Genotype-Based Deep Learning. JMIR Med Inform 2021; 9:e24754. [PMID: 33714937 PMCID: PMC8060867 DOI: 10.2196/24754] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2020] [Revised: 02/18/2021] [Accepted: 03/14/2021] [Indexed: 02/07/2023] Open
Abstract
Background In the United States, about 3 million people have autism spectrum disorder (ASD), and around 1 out of 59 children are diagnosed with ASD. People with ASD have characteristic social communication deficits and repetitive behaviors. The causes of this disorder remain unknown; however, in up to 25% of cases, a genetic cause can be identified. Detecting ASD as early as possible is desirable because early detection of ASD enables timely interventions in children with ASD. Identification of ASD based on objective pathogenic mutation screening is the major first step toward early intervention and effective treatment of affected children. Objective Recent investigation interrogated genomics data for detecting and treating autism disorders, in addition to the conventional clinical interview as a diagnostic test. Since deep neural networks perform better than shallow machine learning models on complex and high-dimensional data, in this study, we sought to apply deep learning to genetic data obtained across thousands of simplex families at risk for ASD to identify contributory mutations and to create an advanced diagnostic classifier for autism screening. Methods After preprocessing the genomics data from the Simons Simplex Collection, we extracted top ranking common variants that may be protective or pathogenic for autism based on a chi-square test. A convolutional neural network–based diagnostic classifier was then designed using the identified significant common variants to predict autism. The performance was then compared with shallow machine learning–based classifiers and randomly selected common variants. Results The selected contributory common variants were significantly enriched in chromosome X while chromosome Y was also discriminatory in determining the identification of autistic individuals from nonautistic individuals. The ARSD, MAGEB16, and MXRA5 genes had the largest effect in the contributory variants. Thus, screening algorithms were adapted to include these common variants. The deep learning model yielded an area under the receiver operating characteristic curve of 0.955 and an accuracy of 88% for identifying autistic individuals from nonautistic individuals. Our classifier demonstrated a considerable improvement of ~13% in terms of classification accuracy compared to standard autism screening tools. Conclusions Common variants are informative for autism identification. Our findings also suggest that the deep learning process is a reliable method for distinguishing the diseased group from the control group based on the common variants of autism.
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Affiliation(s)
- Haishuai Wang
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, United States.,Department of Computer Science and Engineering, Fairfield University, Fairfield, CT, United States
| | - Paul Avillach
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, United States
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16
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Mezinska S, Gallagher L, Verbrugge M, Bunnik EM. Ethical issues in genomics research on neurodevelopmental disorders: a critical interpretive review. Hum Genomics 2021; 15:16. [PMID: 33712057 PMCID: PMC7953558 DOI: 10.1186/s40246-021-00317-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Accepted: 03/04/2021] [Indexed: 11/16/2022] Open
Abstract
Background Genomic research on neurodevelopmental disorders (NDDs), particularly involving minors, combines and amplifies existing research ethics issues for biomedical research. We performed a review of the literature on the ethical issues associated with genomic research involving children affected by NDDs as an aid to researchers to better anticipate and address ethical concerns. Results Qualitative thematic analysis of the included articles revealed themes in three main areas: research design and ethics review, inclusion of research participants, and communication of research results. Ethical issues known to be associated with genomic research in general, such as privacy risks and informed consent/assent, seem especially pressing for NDD participants because of their potentially decreased cognitive abilities, increased vulnerability, and stigma associated with mental health problems. Additionally, there are informational risks: learning genetic information about NDD may have psychological and social impact, not only for the research participant but also for family members. However, there are potential benefits associated with research participation, too: by enrolling in research, the participants may access genetic testing and thus increase their chances of receiving a (genetic) diagnosis for their neurodevelopmental symptoms, prognostic or predictive information about disease progression or the risk of concurrent future disorders. Based on the results of our review, we developed an ethics checklist for genomic research involving children affected by NDDs. Conclusions In setting up and designing genomic research efforts in NDD, researchers should partner with communities of persons with NDDs. Particular attention should be paid to preventing disproportional burdens of research participation of children with NDDs and their siblings, parents and other family members. Researchers should carefully tailor the information and informed consent procedures to avoid therapeutic and diagnostic misconception in NDD research. To better anticipate and address ethical issues in specific NDD studies, we suggest researchers to use the ethics checklist for genomic research involving children affected by NDDs presented in this paper. Supplementary Information The online version contains supplementary material available at 10.1186/s40246-021-00317-4.
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Affiliation(s)
- S Mezinska
- Faculty of Medicine and Institute of Clinical and Preventive Medicine, University of Latvia, Jelgavas Str.3, Riga, LV-1004, Latvia.
| | - L Gallagher
- Discipline of Psychiatry, School of Medicine, Trinity College Dublin, Dublin, Ireland.,Trinity Translational Medicine Institute, St. James Hospital, Dublin 8, Ireland
| | - M Verbrugge
- Department of Medical Ethics, Philosophy and History of Medicine, Erasmus MC, University Medical Centre Rotterdam, PO Box 2400, Rotterdam, 3000, CA, The Netherlands
| | - E M Bunnik
- Department of Medical Ethics, Philosophy and History of Medicine, Erasmus MC, University Medical Centre Rotterdam, PO Box 2400, Rotterdam, 3000, CA, The Netherlands
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17
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Minoche AE, Lundie B, Peters GB, Ohnesorg T, Pinese M, Thomas DM, Zankl A, Roscioli T, Schonrock N, Kummerfeld S, Burnett L, Dinger ME, Cowley MJ. ClinSV: clinical grade structural and copy number variant detection from whole genome sequencing data. Genome Med 2021; 13:32. [PMID: 33632298 PMCID: PMC7908648 DOI: 10.1186/s13073-021-00841-x] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 02/02/2021] [Indexed: 01/09/2023] Open
Abstract
Whole genome sequencing (WGS) has the potential to outperform clinical microarrays for the detection of structural variants (SV) including copy number variants (CNVs), but has been challenged by high false positive rates. Here we present ClinSV, a WGS based SV integration, annotation, prioritization, and visualization framework, which identified 99.8% of simulated pathogenic ClinVar CNVs > 10 kb and 11/11 pathogenic variants from matched microarrays. The false positive rate was low (1.5-4.5%) and reproducibility high (95-99%). In clinical practice, ClinSV identified reportable variants in 22 of 485 patients (4.7%) of which 35-63% were not detectable by current clinical microarray designs. ClinSV is available at https://github.com/KCCG/ClinSV .
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Affiliation(s)
- Andre E Minoche
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, 370 Victoria Street, Darlinghurst, NSW, Australia.
- St Vincent's Clinical School, UNSW, Sydney, NSW, Australia.
| | - Ben Lundie
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, 370 Victoria Street, Darlinghurst, NSW, Australia
| | - Greg B Peters
- Sydney Genome Diagnostics, The Children's Hospital at Westmead, Hawkesbury Road & Hainsworth Street, Westmead, NSW, Australia
| | - Thomas Ohnesorg
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, 370 Victoria Street, Darlinghurst, NSW, Australia
- Genome.One, Darlinghurst, NSW, Australia
| | - Mark Pinese
- Children's Cancer Institute, University of New South Wales, Randwick, Sydney, NSW, Australia
- School of Women's and Children's Health, UNSW, Sydney, NSW, Australia
| | - David M Thomas
- St Vincent's Clinical School, UNSW, Sydney, NSW, Australia
- The Kinghorn Cancer Centre and Cancer Division, Garvan Institute of Medical Research, 370 Victoria Street, Darlinghurst, NSW, Australia
| | - Andreas Zankl
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, 370 Victoria Street, Darlinghurst, NSW, Australia
- Department of Clinical Genetics, The Children's Hospital at Westmead, Hawkesbury Road, Westmead, NSW, Australia
- Sydney Medical School, The University of Sydney, Camperdown, NSW, Australia
| | - Tony Roscioli
- NSW Health Pathology Randwick, Sydney, NSW, Australia
- Centre for Clinical Genetics, Sydney Children's Hospital, Randwick, NSW, Australia
- Prince of Wales Clinical School, University of New South Wales, Sydney, NSW, Australia
- Neuroscience Research Australia, University of New South Wales, Randwick, Sydney, NSW, Australia
| | - Nicole Schonrock
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, 370 Victoria Street, Darlinghurst, NSW, Australia
- Genome.One, Darlinghurst, NSW, Australia
| | - Sarah Kummerfeld
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, 370 Victoria Street, Darlinghurst, NSW, Australia
- St Vincent's Clinical School, UNSW, Sydney, NSW, Australia
| | - Leslie Burnett
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, 370 Victoria Street, Darlinghurst, NSW, Australia
- St Vincent's Clinical School, UNSW, Sydney, NSW, Australia
- Genome.One, Darlinghurst, NSW, Australia
- Sydney Medical School, The University of Sydney, Camperdown, NSW, Australia
| | - Marcel E Dinger
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, 370 Victoria Street, Darlinghurst, NSW, Australia
- School of Biotechnology and Biomolecular Sciences, UNSW, Sydney, NSW, Australia
| | - Mark J Cowley
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, 370 Victoria Street, Darlinghurst, NSW, Australia.
- St Vincent's Clinical School, UNSW, Sydney, NSW, Australia.
- Children's Cancer Institute, University of New South Wales, Randwick, Sydney, NSW, Australia.
- School of Women's and Children's Health, UNSW, Sydney, NSW, Australia.
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18
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Gieldon L, Jauch A, Obeid K, Kaufmann L, Hinderhofer K, Haug U, Moog U. Germ cell mosaicism for AUTS2 exon 6 deletion. Am J Med Genet A 2021; 185:1261-1265. [PMID: 33577136 DOI: 10.1002/ajmg.a.62091] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 01/07/2021] [Accepted: 01/09/2021] [Indexed: 11/11/2022]
Abstract
Haploinsufficiency of AUTS2 has been associated with neurodevelopmental disorders and dysmorphic features (MIM # 615834). More than 50 patients have been described, mostly carrying de novo deletions of one or more exons, including eight patients with exon 6 deletions. We report on two siblings, a girl and a boy aged 11 and 13 years, in whom the same pathogenic 85 kb deletion on 7q11.22 encompassing exon 6 of AUTS2 by SNP array analysis was identified. Both children had typical symptoms of AUTS2 syndrome such as intellectual impairment and behavioral problems, but with markedly different expression. SNP array analysis excluded the deletion in blood samples of both parents and a healthy brother. Conventional karyotyping of both parents and additional FISH analyses, marking the flanking regions of the deletion, did not show any structural rearrangements involving 7q11.22. A germ cell mosaicism was suggested as the most probable explanation for occurrence of the same deletion in these two siblings. To our knowledge this is the first report of germ cell mosaicism for AUTS2 syndrome. It additionally provides further evidence of intrafamilial phenotypic variability in AUTS2 syndrome and adds clinical information to the phenotypic spectrum of patients with AUTS2 exon 6 deletions.
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Affiliation(s)
- Laura Gieldon
- Institute of Human Genetics, Heidelberg University, Heidelberg, Germany
| | - Anna Jauch
- Institute of Human Genetics, Heidelberg University, Heidelberg, Germany
| | - Katharina Obeid
- Institute of Human Genetics, Heidelberg University, Heidelberg, Germany
| | - Lilian Kaufmann
- Institute of Human Genetics, Heidelberg University, Heidelberg, Germany
| | | | - Ulrich Haug
- Center for Child Neurology and Social Pediatrics Maulbronn, Maulbronn, Germany
| | - Ute Moog
- Institute of Human Genetics, Heidelberg University, Heidelberg, Germany
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19
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Fernandez RF, Ellis JM. Acyl-CoA synthetases as regulators of brain phospholipid acyl-chain diversity. Prostaglandins Leukot Essent Fatty Acids 2020; 161:102175. [PMID: 33031993 PMCID: PMC8693597 DOI: 10.1016/j.plefa.2020.102175] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 07/22/2020] [Accepted: 09/09/2020] [Indexed: 12/20/2022]
Abstract
Each individual cell-type is defined by its distinct morphology, phenotype, molecular and lipidomic profile. The importance of maintaining cell-specific lipidomic profiles is exemplified by the numerous diseases, disorders, and dysfunctional outcomes that occur as a direct result of altered lipidome. Therefore, the mechanisms regulating cellular lipidome diversity play a role in maintaining essential biological functions. The brain is an organ particularly rich in phospholipids, the main constituents of cellular membranes. The phospholipid acyl-chain profile of membranes in the brain is rather diverse due in part to the high degree of cellular heterogeneity. These membranes and the acyl-chain composition of their phospholipids are highly regulated, but the mechanisms that confer this tight regulation are incompletely understood. A family of enzymes called acyl-CoA synthetases (ACSs) stands at a pinnacle step allowing influence over cellular acyl-chain selection and subsequent metabolic flux. ACSs perform the initial reaction for cellular fatty acid metabolism by ligating a Coenzyme A to a fatty acid which both traps a fatty acid within a cell and activates it for metabolism. The ACS family of enzymes is large and diverse consisting of 25-26 family members that are nonredundant, each with unique distribution across and within cell types, and differential fatty acid substrate preferences. Thus, ACSs confer a critical intracellular fatty acid selecting step in a cell-type dependent manner providing acyl-CoA moieties that serve as essential precursors for phospholipid synthesis and remodeling, and therefore serve as a key regulator of cellular membrane acyl-chain compositional diversity. Here we will discuss how the contribution of individual ACSs towards brain lipid metabolism has only just begun to be elucidated and discuss the possibilities for how ACSs may differentially regulate brain lipidomic diversity.
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Affiliation(s)
- Regina F Fernandez
- Department of Physiology and East Carolina Diabetes and Obesity Institute, East Carolina University, Brody School of Medicine, NC, United States
| | - Jessica M Ellis
- Department of Physiology and East Carolina Diabetes and Obesity Institute, East Carolina University, Brody School of Medicine, NC, United States.
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20
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Jagannath V, Grünblatt E, Theodoridou A, Oneda B, Roth A, Gerstenberg M, Franscini M, Traber-Walker N, Correll CU, Heekeren K, Rössler W, Rauch A, Walitza S. Rare copy number variants in individuals at clinical high risk for psychosis: Enrichment of synaptic/brain-related functional pathways. Am J Med Genet B Neuropsychiatr Genet 2020; 183:140-151. [PMID: 31742845 DOI: 10.1002/ajmg.b.32770] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/23/2019] [Revised: 10/08/2019] [Accepted: 10/23/2019] [Indexed: 11/07/2022]
Abstract
Schizophrenia is a complex and chronic neuropsychiatric disorder, with a heritability of around 60-80%. Large (>100 kb) rare (<1%) copy number variants (CNVs) occur more frequently in schizophrenia patients compared to controls. Currently, there are no studies reporting genome-wide CNVs in clinical high risk for psychosis (CHR-P) individuals. The aim of this study was to investigate the role of rare genome-wide CNVs in 84 CHR-P individuals and 124 presumably healthy controls. There were no significant differences in all rare CNV frequencies and sizes between CHR-P individuals and controls. However, brain-related CNVs and brain-related deletions were significantly more frequent in CHR-P individuals than controls. In CHR-P individuals, significant associations were found between brain-related CNV carriers and attenuated positive symptoms syndrome or cognitive disturbances (OR = 3.07, p = .0286). Brain-related CNV carriers experienced significantly higher negative symptoms (p = .0047), higher depressive symptoms (p = .0175), and higher disturbances of self and surroundings (p = .0029) than noncarriers. Furthermore, enrichment analysis of genes was performed in the regions of rare CNVs using three independent methods, which confirmed significant clustering of predefined genes involved in synaptic/brain-related functional pathways in CHR-P individuals. These results suggest that rare CNVs might affect synaptic/brain-related functional pathways in CHR-P individuals.
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Affiliation(s)
- Vinita Jagannath
- Department of Child and Adolescent Psychiatry and Psychotherapy, University Hospital of Psychiatry, University of Zurich, Zurich, Switzerland
| | - Edna Grünblatt
- Department of Child and Adolescent Psychiatry and Psychotherapy, University Hospital of Psychiatry, University of Zurich, Zurich, Switzerland.,Neuroscience Center Zurich, University of Zurich and ETH Zurich, Zurich, Switzerland.,Zurich Center for Integrative Human Physiology, University of Zurich, Zurich, Switzerland
| | - Anastasia Theodoridou
- The Zurich Program for Sustainable Development of Mental Health Services (ZInEP), University Hospital of Psychiatry Zurich, Zurich, Switzerland.,Department of Psychiatry, Psychotherapy and Psychosomatics, University Hospital of Psychiatry, University of Zurich, Zurich, Switzerland
| | - Beatrice Oneda
- Institute of Medical Genetics, University of Zurich, Schlieren, Switzerland
| | - Alexander Roth
- Department of Child and Adolescent Psychiatry and Psychotherapy, University Hospital of Psychiatry, University of Zurich, Zurich, Switzerland
| | - Miriam Gerstenberg
- Department of Child and Adolescent Psychiatry and Psychotherapy, University Hospital of Psychiatry, University of Zurich, Zurich, Switzerland
| | - Maurizia Franscini
- Department of Child and Adolescent Psychiatry and Psychotherapy, University Hospital of Psychiatry, University of Zurich, Zurich, Switzerland
| | - Nina Traber-Walker
- Department of Child and Adolescent Psychiatry and Psychotherapy, University Hospital of Psychiatry, University of Zurich, Zurich, Switzerland
| | - Christoph U Correll
- Department of Psychiatry, The Zucker Hillside Hospital, Northwell Health, Glen Oaks, New York.,Department of Psychiatry and Molecular Medicine, Zucker School of Medicine at Hofstra/Northwell, Hempstead, New York.,The Feinstein Institute for Medical Research, Manhasset, New York.,Department of Child and Adolescent Psychiatry, Charité Universitätsmedizin, Berlin, Germany
| | - Karsten Heekeren
- The Zurich Program for Sustainable Development of Mental Health Services (ZInEP), University Hospital of Psychiatry Zurich, Zurich, Switzerland.,Department of Psychiatry, Psychotherapy and Psychosomatics, University Hospital of Psychiatry, University of Zurich, Zurich, Switzerland
| | - Wulf Rössler
- The Zurich Program for Sustainable Development of Mental Health Services (ZInEP), University Hospital of Psychiatry Zurich, Zurich, Switzerland.,Department of Psychiatry and Psychotherapy, Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Anita Rauch
- Neuroscience Center Zurich, University of Zurich and ETH Zurich, Zurich, Switzerland.,Zurich Center for Integrative Human Physiology, University of Zurich, Zurich, Switzerland.,Institute of Medical Genetics, University of Zurich, Schlieren, Switzerland
| | - Susanne Walitza
- Department of Child and Adolescent Psychiatry and Psychotherapy, University Hospital of Psychiatry, University of Zurich, Zurich, Switzerland.,Neuroscience Center Zurich, University of Zurich and ETH Zurich, Zurich, Switzerland.,Zurich Center for Integrative Human Physiology, University of Zurich, Zurich, Switzerland.,The Zurich Program for Sustainable Development of Mental Health Services (ZInEP), University Hospital of Psychiatry Zurich, Zurich, Switzerland
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21
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High-resolution chromosomal microarray analysis for copy-number variations in high-functioning autism reveals large aberration typical for intellectual disability. J Neural Transm (Vienna) 2019; 127:81-94. [PMID: 31838600 DOI: 10.1007/s00702-019-02114-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Accepted: 12/03/2019] [Indexed: 10/25/2022]
Abstract
Copy-number variants (CNVs), in particular rare, small and large ones (< 1% frequency) and those encompassing brain-related genes, have been shown to be associated with neurodevelopmental disorders like autism spectrum disorders (ASDs), attention deficit hyperactivity disorder (ADHD), and intellectual disability (ID). However, the vast majority of CNV findings lack specificity with respect to autistic or developmental-delay phenotypes. Therefore, the aim of the study was to investigate the size and frequency of CNVs in high-functioning ASD (HFA) without ID compared with a random population sample and with published findings in ASD and ID. To investigate the role of CNVs for the "core symptoms" of high-functioning autism, we included in the present exploratory study only patients with HFA without ID. The aim was to test whether HFA have similar large rare (> 1 Mb) CNVs as reported in ASD and ID. We performed high-resolution chromosomal microarray analysis in 108 children and adolescents with HFA without ID. There was no significant difference in the overall number of rare CNVs compared to 124 random population samples. However, patients with HFA carried significantly more frequently CNVs containing brain-related genes. Surprisingly, six HFA patients carried very large CNVs known to be typically present in ID. Our findings provide new evidence that not only small, but also large CNVs affecting several key genes contribute to the genetic etiology/risk of HFA without affecting their intellectual ability.
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22
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Bowman CE, Selen Alpergin ES, Ellis JM, Wolfgang MJ. Loss of ACOT7 potentiates seizures and metabolic dysfunction. Am J Physiol Endocrinol Metab 2019; 317:E941-E951. [PMID: 31039008 PMCID: PMC6879868 DOI: 10.1152/ajpendo.00537.2018] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Revised: 04/24/2019] [Accepted: 04/24/2019] [Indexed: 01/02/2023]
Abstract
Neurons uniquely antagonize fatty acid utilization by hydrolyzing the activated form of fatty acids, long chain acyl-CoAs, via the enzyme acyl-CoA thioesterase 7, Acot7. The loss of Acot7 results in increased fatty acid utilization in neurons and exaggerated stimulus-evoked behavior such as an increased startle response. To understand the contribution of Acot7 to seizure susceptibility, we generated Acot7 knockout (KO) mice and assayed their response to kainate-induced seizures. Acot7 KO mice exhibited potentiated behavioral and molecular indices of seizure severity following kainic acid administration, suggesting that fatty acid metabolism in neurons can be a critical regulator of neuronal activity. These data are consistent with the presentation of seizures in a human with genomic deletion of ACOT7 demonstrating the conservation of function across species. To further understand the metabolic complications arising from a deletion in Acot7, we subjected Acot7 KO mice to a high-fat diet. While the loss of Acot7 did not result in metabolic complications following a normal chow diet, a high-fat diet induced greater body weight gain, adiposity, and glucose intolerance in Acot7 KO mice. These data demonstrate that Acot7, a fatty acid metabolic enzyme highly enriched in neurons, regulates both brain-specific metabolic processes related to seizure susceptibility and the whole body response to dietary lipid.
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Affiliation(s)
- Caitlyn E Bowman
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Ebru S Selen Alpergin
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Jessica M Ellis
- Department of Physiology, East Carolina Diabetes and Obesity Institute, East Carolina University, Greenville, North Carolina
| | - Michael J Wolfgang
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland
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23
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24
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Challenges in the clinical interpretation of small de novo copy number variants in neurodevelopmental disorders. Gene 2019; 706:162-171. [PMID: 31085274 DOI: 10.1016/j.gene.2019.05.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Revised: 03/27/2019] [Accepted: 05/03/2019] [Indexed: 12/17/2022]
Abstract
In clinical genetics, the need to discriminate between benign and pathogenic variants identified in patients with neurodevelopmental disorders is an absolute necessity. Copy number variants (CNVs) of small size can enable the identification of genes that are critical for neurologic development. However, assigning a definite association with a specific disorder is a difficult task. Among 328 trios analyzed over seven years of activity in a single laboratory, we identified 19 unrelated patients (5.8%) who carried a small (<500 kb) de novo CNV. Four patients had an additional independent de novo CNV. Nine had a variant that could be assigned as definitely pathogenic, whereas the remaining CNVs were considered as variants of unknown significance (VUS). We report clinical and molecular findings of patients harboring VUS. We reviewed the medical literature available for genes impacted by CNVs, obtained the probability of truncating loss-of-function intolerance, and compared overlapping CNVs reported in databases. The classification of small non-recurrent CNVs remains difficult but, among our findings, we provide support for a role of SND1 in the susceptibility of autism, describe a new case of the rare 17p13.1 microduplication syndrome, and report an X-linked duplication involving KIF4A and DLG3 as a likely cause of epilepsy.
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25
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Corrêa T, Feltes BC, Riegel M. Integrated analysis of the critical region 5p15.3-p15.2 associated with cri-du-chat syndrome. Genet Mol Biol 2019; 42:186-196. [PMID: 30985858 PMCID: PMC6687350 DOI: 10.1590/1678-4685-gmb-2018-0173] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Accepted: 07/29/2018] [Indexed: 11/21/2022] Open
Abstract
Cri-du-chat syndrome (CdCs) is one of the most common contiguous gene syndromes,
with an incidence of 1:15,000 to 1:50,000 live births. To better understand the
etiology of CdCs at the molecular level, we investigated theprotein–protein
interaction (PPI) network within the critical chromosomal region 5p15.3–p15.2
associated with CdCs using systemsbiology. Data were extracted from cytogenomic
findings from patients with CdCs. Based on clinical findings, molecular
characterization of chromosomal rearrangements, and systems biology data, we
explored possible genotype–phenotype correlations involving biological processes
connected with CdCs candidate genes. We identified biological processes
involving genes previously found to be associated with CdCs, such as
TERT, SLC6A3, and
CTDNND2, as well as novel candidate proteins with potential
contributions to CdCs phenotypes, including CCT5, TPPP, MED10, ADCY2, MTRR,
CEP72, NDUFS6, and MRPL36. Although further functional analyses of these
proteins are required, we identified candidate proteins for the development of
new multi-target genetic editing tools to study CdCs. Further research may
confirm those that are directly involved in the development of CdCs phenotypes
and improve our understanding of CdCs-associated molecular mechanisms.
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Affiliation(s)
- Thiago Corrêa
- Post-Graduate Program in Genetics and Molecular Biology, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Bruno César Feltes
- Institute of Informatics, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Mariluce Riegel
- Post-Graduate Program in Genetics and Molecular Biology, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil.,Medical Genetics Service, Hospital de Clínicas de Porto Alegre, Porto Alegre, RS, Brazil
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26
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Ghani SMA, Goon JA, Azman NHEN, Zakaria SNA, Hamid Z, Ngah WZW. Comparing the effects of vitamin E tocotrienol-rich fraction supplementation and α-tocopherol supplementation on gene expression in healthy older adults. Clinics (Sao Paulo) 2019; 74:e688. [PMID: 30864639 PMCID: PMC6438703 DOI: 10.6061/clinics/2019/e688] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Accepted: 10/02/2018] [Indexed: 01/06/2023] Open
Abstract
OBJECTIVES This study aims to compare the differential gene expression resulting from tocotrienol-rich fraction and α-tocopherol supplementation in healthy older adults. METHODS A total of 71 eligible subjects aged 50 to 55 years from Gombak and Kuala Lumpur, Malaysia, were divided into three groups and supplemented with placebo (n=23), α-tocopherol (n=24) or tocotrienol-rich fraction (n=24). Blood samples were collected at baseline and at 3 and 6 months of supplementation for microarray analysis. RESULTS The number of genes altered by α-tocopherol was higher after 6 months (1,410) than after 3 months (273) of supplementation. α-Tocopherol altered the expression of more genes in males (952) than in females (731). Similarly, tocotrienol-rich fraction modulated the expression of more genes after 6 months (1,084) than after 3 months (596) and affected more genes in males (899) than in females (781). α-Tocopherol supplementation modulated pathways involving the response to stress and stimuli, the immune response, the response to hypoxia and bacteria, the metabolism of toxins and xenobiotics, mitosis, and synaptic transmission as well as activated the mitogen-activated protein kinase and complement pathways after 6 months. However, tocotrienol-rich fraction supplementation affected pathways such as the signal transduction, apoptosis, nuclear factor kappa B kinase, cascade extracellular signal-regulated kinase-1 and extracellular signal-regulated kinase-2, immune response, response to drug, cell adhesion, multicellular organismal development and G protein signaling pathways. CONCLUSION Supplementation with either α-tocopherol or tocotrienol-rich fraction affected the immune and drug response and the cell adhesion and signal transduction pathways but modulated other pathways differently after 6 months of supplementation, with sex-specific responses.
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Affiliation(s)
- Siti Madiani Abdul Ghani
- Department of Biochemistry, Faculty of Medicine, Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia
| | - Jo Aan Goon
- Department of Biochemistry, Faculty of Medicine, Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia
- Corresponding author. E-mail:
| | - Nor Helwa Ezzah Nor Azman
- Department of Biochemistry, Faculty of Medicine, Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia
| | - Siti Nor Asyikin Zakaria
- Department of Biochemistry, Faculty of Medicine, Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia
| | - Zalina Hamid
- Sime Darby Foods & Beverages Marketing Sdn Bhd, Petaling Jaya, Selangor, Malaysia
| | - Wan Zurinah Wan Ngah
- Department of Biochemistry, Faculty of Medicine, Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia
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27
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Elucidation of the phenotypic spectrum and genetic landscape in primary and secondary microcephaly. Genet Med 2019; 21:2043-2058. [PMID: 30842647 PMCID: PMC6752480 DOI: 10.1038/s41436-019-0464-7] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Accepted: 02/11/2019] [Indexed: 01/28/2023] Open
Abstract
Purpose Microcephaly is a sign of many genetic conditions but has been rarely systematically evaluated. We therefore comprehensively studied the clinical and genetic landscape of an unselected cohort of patients with microcephaly. Methods We performed clinical assessment, high-resolution chromosomal microarray analysis, exome sequencing, and functional studies in 62 patients (58% with primary microcephaly [PM], 27% with secondary microcephaly [SM], and 15% of unknown onset). Results We found severity of developmental delay/intellectual disability correlating with severity of microcephaly in PM, but not SM. We detected causative variants in 48.4% of patients and found divergent inheritance and variant pattern for PM (mainly recessive and likely gene-disrupting [LGD]) versus SM (all dominant de novo and evenly LGD or missense). While centrosome-related pathways were solely identified in PM, transcriptional regulation was the most frequently affected pathway in both SM and PM. Unexpectedly, we found causative variants in different mitochondria-related genes accounting for ~5% of patients, which emphasizes their role even in syndromic PM. Additionally, we delineated novel candidate genes involved in centrosome-related pathway (SPAG5, TEDC1), Wnt signaling (VPS26A, ZNRF3), and RNA trafficking (DDX1). Conclusion Our findings enable improved evaluation and genetic counseling of PM and SM patients and further elucidate microcephaly pathways.
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28
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Neurodevelopmental disease genes implicated by de novo mutation and copy number variation morbidity. Nat Genet 2018; 51:106-116. [PMID: 30559488 PMCID: PMC6309590 DOI: 10.1038/s41588-018-0288-4] [Citation(s) in RCA: 181] [Impact Index Per Article: 30.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Accepted: 10/23/2018] [Indexed: 12/11/2022]
Abstract
We combined de novo mutation (DNM) data from 10,927 individuals with developmental delay and autism to identify 253 candidate neurodevelopmental disease genes with an excess of missense and/or likely gene-disruptive (LGD) mutations. Of these genes, 124 reach exome-wide significance (P < 5 × 10-7) for DNM. Intersecting these results with copy number variation (CNV) morbidity data shows an enrichment for genomic disorder regions (30/253, likelihood ratio (LR) +1.85, P = 0.0017). We identify genes with an excess of missense DNMs overlapping deletion syndromes (for example, KIF1A and the 2q37 deletion) as well as duplication syndromes, such as recurrent MAPK3 missense mutations within the chromosome 16p11.2 duplication, recurrent CHD4 missense DNMs in the 12p13 duplication region, and recurrent WDFY4 missense DNMs in the 10q11.23 duplication region. Network analyses of genes showing an excess of DNMs highlights functional networks, including cell-specific enrichments in the D1+ and D2+ spiny neurons of the striatum.
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Papuc SM, Abela L, Steindl K, Begemann A, Simmons TL, Schmitt B, Zweier M, Oneda B, Socher E, Crowther LM, Wohlrab G, Gogoll L, Poms M, Seiler M, Papik M, Baldinger R, Baumer A, Asadollahi R, Kroell-Seger J, Schmid R, Iff T, Schmitt-Mechelke T, Otten K, Hackenberg A, Addor MC, Klein A, Azzarello-Burri S, Sticht H, Joset P, Plecko B, Rauch A. The role of recessive inheritance in early-onset epileptic encephalopathies: a combined whole-exome sequencing and copy number study. Eur J Hum Genet 2018; 27:408-421. [PMID: 30552426 PMCID: PMC6460568 DOI: 10.1038/s41431-018-0299-8] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Revised: 10/05/2018] [Accepted: 10/25/2018] [Indexed: 11/16/2022] Open
Abstract
Early-onset epileptic encephalopathy (EE) and combined developmental and epileptic encephalopathies (DEE) are clinically and genetically heterogeneous severely devastating conditions. Recent studies emphasized de novo variants as major underlying cause suggesting a generally low-recurrence risk. In order to better understand the full genetic landscape of EE and DEE, we performed high-resolution chromosomal microarray analysis in combination with whole-exome sequencing in 63 deeply phenotyped independent patients. After bioinformatic filtering for rare variants, diagnostic yield was improved for recessive disorders by manual data curation as well as molecular modeling of missense variants and untargeted plasma-metabolomics in selected patients. In total, we yielded a diagnosis in ∼42% of cases with causative copy number variants in 6 patients (∼10%) and causative sequence variants in 16 established disease genes in 20 patients (∼32%), including compound heterozygosity for causative sequence and copy number variants in one patient. In total, 38% of diagnosed cases were caused by recessive genes, of which two cases escaped automatic calling due to one allele occurring de novo. Notably, we found the recessive gene SPATA5 causative in as much as 3% of our cohort, indicating that it may have been underdiagnosed in previous studies. We further support candidacy for neurodevelopmental disorders of four previously described genes (PIK3AP1, GTF3C3, UFC1, and WRAP53), three of which also followed a recessive inheritance pattern. Our results therefore confirm the importance of de novo causative gene variants in EE/DEE, but additionally illustrate the major role of mostly compound heterozygous or hemizygous recessive inheritance and consequently high-recurrence risk.
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Affiliation(s)
- Sorina M Papuc
- Institute of Medical Genetics, University of Zurich, Schlieren-Zurich, 8952, Switzerland.,Victor Babes National Institute of Pathology, Bucharest, 050096, Romania
| | - Lucia Abela
- Division of Child Neurology, University Children's Hospital Zurich, Zurich, 8032, Switzerland.,CRC Clinical Research Center University, Children's Hospital Zurich, Zurich, 8032, Switzerland.,radiz-Rare Disease Initiative Zürich, Clinical Research Priority Program for Rare Diseases University of Zurich, Zurich, 8032, Switzerland
| | - Katharina Steindl
- Institute of Medical Genetics, University of Zurich, Schlieren-Zurich, 8952, Switzerland
| | - Anaïs Begemann
- Institute of Medical Genetics, University of Zurich, Schlieren-Zurich, 8952, Switzerland
| | - Thomas L Simmons
- Division of Child Neurology, University Children's Hospital Zurich, Zurich, 8032, Switzerland
| | - Bernhard Schmitt
- Division of Child Neurology, University Children's Hospital Zurich, Zurich, 8032, Switzerland.,CRC Clinical Research Center University, Children's Hospital Zurich, Zurich, 8032, Switzerland
| | - Markus Zweier
- Institute of Medical Genetics, University of Zurich, Schlieren-Zurich, 8952, Switzerland
| | - Beatrice Oneda
- Institute of Medical Genetics, University of Zurich, Schlieren-Zurich, 8952, Switzerland
| | - Eileen Socher
- Institute of Biochemistry, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, 91054, Germany
| | - Lisa M Crowther
- Division of Child Neurology, University Children's Hospital Zurich, Zurich, 8032, Switzerland
| | - Gabriele Wohlrab
- Division of Child Neurology, University Children's Hospital Zurich, Zurich, 8032, Switzerland
| | - Laura Gogoll
- Institute of Medical Genetics, University of Zurich, Schlieren-Zurich, 8952, Switzerland
| | - Martin Poms
- Division of Child Neurology, University Children's Hospital Zurich, Zurich, 8032, Switzerland
| | - Michelle Seiler
- Pediatric Emergency Department, University Children's Hospital Zurich, Zurich, 8032, Switzerland
| | - Michael Papik
- Institute of Medical Genetics, University of Zurich, Schlieren-Zurich, 8952, Switzerland
| | - Rosa Baldinger
- Institute of Medical Genetics, University of Zurich, Schlieren-Zurich, 8952, Switzerland
| | - Alessandra Baumer
- Institute of Medical Genetics, University of Zurich, Schlieren-Zurich, 8952, Switzerland
| | - Reza Asadollahi
- Institute of Medical Genetics, University of Zurich, Schlieren-Zurich, 8952, Switzerland
| | - Judith Kroell-Seger
- Children's department, Swiss Epilepsy Centre, Clinic Lengg, Zurich, 8000, Switzerland
| | - Regula Schmid
- Division of Child Neurology, Kantonsspital Winterthur, Winterthur, 8401, Switzerland
| | - Tobias Iff
- Municipal Hospital of Zurich Triemli, Zurich, 8063, Switzerland
| | | | - Karoline Otten
- Children's department, Swiss Epilepsy Centre, Clinic Lengg, Zurich, 8000, Switzerland
| | - Annette Hackenberg
- Division of Child Neurology, University Children's Hospital Zurich, Zurich, 8032, Switzerland
| | - Marie-Claude Addor
- Department of Woman-Mother-Child, University Medical Center CHUV, Lausanne, 1015, Switzerland
| | - Andrea Klein
- Division of Paediatric Neurology, University Childerns Hospital Basel, UKBB, 4031, Basel, Switzerland.,Division of Paediatric Neurology, Development and Rehabilitation, University Children's Hospital, 3010, Bern, Switzerland
| | - Silvia Azzarello-Burri
- Institute of Medical Genetics, University of Zurich, Schlieren-Zurich, 8952, Switzerland
| | - Heinrich Sticht
- Institute of Biochemistry, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, 91054, Germany
| | - Pascal Joset
- Institute of Medical Genetics, University of Zurich, Schlieren-Zurich, 8952, Switzerland
| | - Barbara Plecko
- Division of Child Neurology, University Children's Hospital Zurich, Zurich, 8032, Switzerland.,CRC Clinical Research Center University, Children's Hospital Zurich, Zurich, 8032, Switzerland.,radiz-Rare Disease Initiative Zürich, Clinical Research Priority Program for Rare Diseases University of Zurich, Zurich, 8032, Switzerland.,Neuroscience Center Zurich, University of Zurich and ETH Zurich, Zurich, 8057, Switzerland.,Division of General Pediatrics, Department of Pediatrics, Medical University of Graz, 8036, Graz, Austria
| | - Anita Rauch
- Institute of Medical Genetics, University of Zurich, Schlieren-Zurich, 8952, Switzerland. .,radiz-Rare Disease Initiative Zürich, Clinical Research Priority Program for Rare Diseases University of Zurich, Zurich, 8032, Switzerland. .,Neuroscience Center Zurich, University of Zurich and ETH Zurich, Zurich, 8057, Switzerland. .,Zurich Center for Integrative Human Physiology, University of Zurich, Zurich, 8057, Switzerland.
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30
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Guo W, Zhu X, Yan L, Qiao J. The present and future of whole-exome sequencing in studying and treating human reproductive disorders. J Genet Genomics 2018; 45:517-525. [DOI: 10.1016/j.jgg.2018.08.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Revised: 08/23/2018] [Accepted: 08/24/2018] [Indexed: 12/16/2022]
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31
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The Cytoscan HD Array in the Diagnosis of Neurodevelopmental Disorders. High Throughput 2018; 7:ht7030028. [PMID: 30223503 PMCID: PMC6164295 DOI: 10.3390/ht7030028] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Revised: 09/06/2018] [Accepted: 09/06/2018] [Indexed: 12/14/2022] Open
Abstract
Submicroscopic chromosomal copy number variations (CNVs), such as deletions and duplications, account for about 15–20% of patients affected with developmental delay, intellectual disability, multiple congenital anomalies, and autism spectrum disorder. Most of CNVs are de novo or inherited rearrangements with clinical relevance, but there are also rare inherited imbalances with unknown significance that make difficult the clinical management and genetic counselling. Chromosomal microarrays analysis (CMA) are recognized as the first-line test for CNV detection and are now routinely used in the clinical diagnostic laboratory. The recent use of CMA platforms that combine classic copy number analysis with single-nucleotide polymorphism (SNP) genotyping has increased the diagnostic yields. Here we discuss the application of the Cytoscan high-density (HD) SNP-array for the detection of CNVs. We provide an overview of molecular analyses involved in identifying pathogenic CNVs and highlight important guidelines to establish pathogenicity of CNV.
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Cosemans N, Claes P, Brison N, Vermeesch JR, Peeters H. Noise-robust assessment of SNP array based CNV calls through local noise estimation of log R ratios. Stat Appl Genet Mol Biol 2018; 17:sagmb-2017-0026. [PMID: 29708886 DOI: 10.1515/sagmb-2017-0026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Arrays based on single nucleotide polymorphisms (SNPs) have been successful for the large scale discovery of copy number variants (CNVs). However, current CNV calling algorithms still have limitations in detecting CNVs with high specificity and sensitivity, especially in case of small (<100 kb) CNVs. Therefore, this study presents a simple statistical analysis to evaluate CNV calls from SNP arrays in order to improve the noise-robustness of existing CNV calling algorithms. The proposed approach estimates local noise of log R ratios and returns the probability that a certain observation is different from this log R ratio noise level. This probability can be triggered at different thresholds to tailor specificity and/or sensitivity in a flexible way. Moreover, a comparison based on qPCR experiments showed that the proposed noise-robust CNV calls outperformed original ones for multiple threshold values.
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Affiliation(s)
- Nele Cosemans
- Center for Human Genetics, University Hospital Leuven, KU Leuven, Leuven, Belgium
| | - Peter Claes
- Medical Image Computing, ESAT/PSI, Department of Electrical Engineering, KU Leuven, Leuven, Belgium
- Medical Imaging Research Center, UZ Leuven, Leuven, Belgium
| | - Nathalie Brison
- Center for Human Genetics, University Hospital Leuven, KU Leuven, Leuven, Belgium
| | | | - Hilde Peeters
- Center for Human Genetics, University Hospital Leuven, KU Leuven, Leuven, Belgium
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Schöneberg T, Meister J, Knierim AB, Schulz A. The G protein-coupled receptor GPR34 - The past 20 years of a grownup. Pharmacol Ther 2018; 189:71-88. [PMID: 29684466 DOI: 10.1016/j.pharmthera.2018.04.008] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Research on GPR34, which was discovered in 1999 as an orphan G protein-coupled receptor of the rhodopsin-like class, disclosed its physiologic relevance only piece by piece. Being present in all recent vertebrate genomes analyzed so far it seems to improve the fitness of species although it is not essential for life and reproduction as GPR34-deficient mice demonstrate. However, closer inspection of macrophages and microglia, where it is mainly expressed, revealed its relevance in immune cell function. Recent data clearly demonstrate that GPR34 function is required to arrest microglia in the M0 homeostatic non-phagocytic phenotype. Herein, we summarize the current knowledge on its evolution, genomic and structural organization, physiology, pharmacology and relevance in human diseases including neurodegenerative diseases and cancer, which accumulated over the last 20 years.
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Affiliation(s)
- Torsten Schöneberg
- Rudolf Schönheimer Institute of Biochemistry, Molecular Biochemistry, Medical Faculty, University of Leipzig, 04103 Leipzig, Germany.
| | - Jaroslawna Meister
- Molecular Signaling Section, Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, United States
| | - Alexander Bernd Knierim
- Rudolf Schönheimer Institute of Biochemistry, Molecular Biochemistry, Medical Faculty, University of Leipzig, 04103 Leipzig, Germany; Leipzig University Medical Center, IFB AdiposityDiseases, 04103 Leipzig, Germany
| | - Angela Schulz
- Rudolf Schönheimer Institute of Biochemistry, Molecular Biochemistry, Medical Faculty, University of Leipzig, 04103 Leipzig, Germany
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Gupta A, Yo J, Huang G, Soong L, Dong J. Developmental Defects Associated With DNA Copy Number Gain of Chromosome 2q33.1: A Case Report and Review of Literature. Lab Med 2018; 49:160-164. [PMID: 29301000 DOI: 10.1093/labmed/lmx086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Caspases play a vital role during apoptosis. In addition to apoptosis, caspases play a role in cytokine gene induction and work to inhibit apoptosis. In order for individuals to thrive with useful tissue growth, the rate of cell growth and division must surpass the rate of cell division. It is well established that excessive cell death of embryonic cells is a vital process occurring before structural abnormalities, regardless of their nature. Here we describe a 13-month-old male patient with a 4.7Mb interstitial duplication of chromosome 2q33.1. This duplication was identified by chromosomal microarray (CMA) which is the first-tier clinical diagnostic test to identify copy number variants (CNVs) for patients with unexplained developmental delay or intellectual disability. This patient presents with global developmental delay, especially in speech, language, hypotonia, and bilateral simian creases. The duplicated region contains several disease-causing genes. We believe that the phenotype in this patient's case was likely related to the gain of caspase 8 and 10 genes.
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Affiliation(s)
- Akshaya Gupta
- School of Medicine, University of Texas Medical Branch, Galveston, TX, USA
| | - Jacob Yo
- Department of Pathology, University of Texas Medical Branch, Galveston, TX, USA
| | - Gengming Huang
- Department of Pathology, University of Texas Medical Branch, Galveston, TX, USA
| | - Lynn Soong
- Departments of Microbiology & Immunology and Pathology, University of Texas Medical Branch, Galveston, TX, USA
| | - Jianli Dong
- Department of Pathology, University of Texas Medical Branch, Galveston, TX, USA
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35
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da Silva HPV, Oliveira GHDM, Ururahy MAG, Bezerra JF, de Souza KSC, Bortolin RH, Luchessi AD, Silbiger VN, Lima VMGDM, Leite GCP, Brito MEF, Ribeiro EM, Gil-da-Silva-Lopes VL, de Rezende AA. Application of high-resolution array platform for genome-wide copy number variation analysis in patients with nonsyndromic cleft lip and palate. J Clin Lab Anal 2018; 32:e22428. [PMID: 29512191 DOI: 10.1002/jcla.22428] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Accepted: 02/09/2018] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND Although more than 14 loci may be involved in the development of nonsyndromic cleft lip and palate (NSCLP), the etiology has not been fully elucidated due to genetic and environmental risk factor interactions. Despite advances in identifying genes associated with the NSCLP development using traditional genetic mapping strategies of candidate genes, genome-wide studies, and epidemiologic and linkage analysis, microarray techniques have become important complementary tools in the search for potential causative oral clefts genes in genetic studies. Microarray hybridization enables scanning of the whole genome and detecting copy number variants (CNVs). Although common benign CNVs are often smaller, with sizes smaller than 20 kb, here we reveal small exonic CNVs based on the importance of the encompassed genes in cleft lip and palate phenotype. METHODS Microarray hybridization analysis was performed in 15 individuals with NSCLP. RESULTS We identified 11 exonic CNVs affecting at least one exon of the candidate genes. Thirteen candidate genes (COL11A1-1p21; IRF6-1q32.3; MSX1-4p16.2; TERT-5p15.33; MIR4457-5p15.33; CLPTM1L-5p15.33; ESR1-6q25.1; GLI3-7p13; FGFR-8p11.23; TBX1-22q11.21; OFD-Xp22; PHF8-Xp11.22; and FLNA-Xq28) overlapped with the CNVs identified. CONCLUSIONS Considering the importance to NSCLP, the microdeletions that encompass MSX1, microduplications over TERT, MIR4457, CLPTM1L, and microduplication of PHF8 have been identified as small CNVs related to sequence variants associated with oral clefts susceptibility. Our findings represent a preliminary study on the clinical significance of small CNVs and their relationship with genes implicated in NSCLP.
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Affiliation(s)
| | | | | | - João Felipe Bezerra
- Department of Clinical and Toxicological Analyses, Federal University of Rio Grande do Norte, Natal, Brazil
| | | | - Raul Hernandes Bortolin
- Department of Clinical and Toxicological Analyses, Federal University of Rio Grande do Norte, Natal, Brazil
| | - André Ducati Luchessi
- Department of Clinical and Toxicological Analyses, Federal University of Rio Grande do Norte, Natal, Brazil
| | - Vivian Nogueira Silbiger
- Department of Clinical and Toxicological Analyses, Federal University of Rio Grande do Norte, Natal, Brazil
| | | | | | | | | | | | - Adriana Augusto de Rezende
- Department of Clinical and Toxicological Analyses, Federal University of Rio Grande do Norte, Natal, Brazil
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36
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Clinical and experimental evidence suggest a link between KIF7 and C5orf42-related ciliopathies through Sonic Hedgehog signaling. Eur J Hum Genet 2018; 26:197-209. [PMID: 29321670 PMCID: PMC5839020 DOI: 10.1038/s41431-017-0019-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2017] [Revised: 09/11/2017] [Accepted: 09/19/2017] [Indexed: 01/03/2023] Open
Abstract
Acrocallosal syndrome (ACLS) is an autosomal recessive neurodevelopmental disorder caused by KIF7 defects and belongs to the heterogeneous group of ciliopathies related to Joubert syndrome (JBTS). While ACLS is characterized by macrocephaly, prominent forehead, depressed nasal bridge, and hypertelorism, facial dysmorphism has not been emphasized in JBTS cohorts with molecular diagnosis. To evaluate the specificity and etiology of ACLS craniofacial features, we performed whole exome or targeted Sanger sequencing in patients with the aforementioned overlapping craniofacial appearance but variable additional ciliopathy features followed by functional studies. We found (likely) pathogenic variants of KIF7 in 5 out of 9 families, including the original ACLS patients, and delineated 1000 to 4000-year-old Swiss founder alleles. Three of the remaining families had (likely) pathogenic variants in the JBTS gene C5orf42, and one patient had a novel de novo frameshift variant in SHH known to cause autosomal dominant holoprosencephaly. In accordance with the patients' craniofacial anomalies, we showed facial midline widening after silencing of C5orf42 in chicken embryos. We further supported the link between KIF7, SHH, and C5orf42 by demonstrating abnormal primary cilia and diminished response to a SHH agonist in fibroblasts of C5orf42-mutated patients, as well as axonal pathfinding errors in C5orf42-silenced chicken embryos similar to those observed after perturbation of Shh signaling. Our findings, therefore, suggest that beside the neurodevelopmental features, macrocephaly and facial widening are likely more general signs of disturbed SHH signaling. Nevertheless, long-term follow-up revealed that C5orf42-mutated patients showed catch-up development and fainting of facial features contrary to KIF7-mutated patients.
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37
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Grünblatt E, Oneda B, Ekici AB, Ball J, Geissler J, Uebe S, Romanos M, Rauch A, Walitza S. High resolution chromosomal microarray analysis in paediatric obsessive-compulsive disorder. BMC Med Genomics 2017; 10:68. [PMID: 29179725 PMCID: PMC5704537 DOI: 10.1186/s12920-017-0299-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Accepted: 11/06/2017] [Indexed: 02/16/2023] Open
Abstract
Background Obsessive-Compulsive Disorder (OCD) is a common and chronic disorder in which a person has uncontrollable, reoccurring thoughts and behaviours. It is a complex genetic condition and, in case of early onset (EO), the patients manifest a more severe phenotype, and an increased heritability. Large (>500 kb) copy number variations (CNVs) previously associated with autism and schizophrenia have been reported in OCD. Recently, rare CNVs smaller than 500 kb overlapping risk loci for other neurodevelopmental conditions have also been reported in OCD, stressing the importance of examining CNVs of any size range. The aim of this study was to further investigate the role of rare and small CNVs in the aetiology of EO-OCD. Methods We performed high-resolution chromosomal microarray analysis in 121 paediatric OCD patients and in 124 random controls to identify rare CNVs (>50 kb) which might contribute to EO-OCD. Results The frequencies and the size of the observed rare CNVs in the patients did not differ from the controls. However, we observed a significantly higher frequency of rare CNVs affecting brain related genes, especially deletions, in the patients (OR = 1.98, 95% CI 1.02–3.84; OR = 3.61, 95% CI 1.14–11.41, respectively). Similarly, enrichment-analysis of CNVs gene content, performed with three independent methods, confirmed significant clustering of predefined genes involved in synaptic/brain related functional pathways in the patients but not in the controls. In two patients we detected de-novo CNVs encompassing genes previously associated with different neurodevelopmental disorders (NRXN1, ANKS1B, UHRF1BP1). Conclusions Our results further strengthen the role of small rare CNVs, particularly deletions, as susceptibility factors for paediatric OCD. Electronic supplementary material The online version of this article (10.1186/s12920-017-0299-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Edna Grünblatt
- Department of Child and Adolescent Psychiatry and Psychotherapy, University Hospital of Psychiatry Zurich, University of Zurich, Neumünsterallee 9, 8032, Zürich, Switzerland. .,Neuroscience Center Zurich, University of Zurich and ETH Zurich, Zurich, Switzerland. .,Department of Psychiatry, Psychosomatic and Psychotherapy, University Hospital of Würzburg, Würzburg, Germany. .,Zurich Center for Integrative Human Physiology, University of Zurich, Zurich, Switzerland. .,Department of Child and Adolescent Psychiatry and Psychotherapy, University Hospital of Psychiatry Zurich, University of Zurich, Wagistrasse 12, 8952, Schlieren, Switzerland.
| | - Beatrice Oneda
- Institute of Medical Genetics, University of Zurich, Zurich-Schlieren, Switzerland
| | - Arif B Ekici
- Institute of Human Genetics, University Hospital Erlangen, Erlangen, Germany
| | - Juliane Ball
- Department of Child and Adolescent Psychiatry and Psychotherapy, University Hospital of Psychiatry Zurich, University of Zurich, Neumünsterallee 9, 8032, Zürich, Switzerland
| | - Julia Geissler
- Center of Mental Health, Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy, University Hospital of Würzburg, Würzburg, Germany
| | - Steffen Uebe
- Institute of Human Genetics, University Hospital Erlangen, Erlangen, Germany
| | - Marcel Romanos
- Center of Mental Health, Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy, University Hospital of Würzburg, Würzburg, Germany
| | - Anita Rauch
- Neuroscience Center Zurich, University of Zurich and ETH Zurich, Zurich, Switzerland.,Zurich Center for Integrative Human Physiology, University of Zurich, Zurich, Switzerland.,Institute of Medical Genetics, University of Zurich, Zurich-Schlieren, Switzerland
| | - Susanne Walitza
- Department of Child and Adolescent Psychiatry and Psychotherapy, University Hospital of Psychiatry Zurich, University of Zurich, Neumünsterallee 9, 8032, Zürich, Switzerland. .,Neuroscience Center Zurich, University of Zurich and ETH Zurich, Zurich, Switzerland. .,Zurich Center for Integrative Human Physiology, University of Zurich, Zurich, Switzerland.
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38
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Uebe S, Ehrlicher M, Ekici AB, Behrens F, Böhm B, Homuth G, Schurmann C, Völker U, Jünger M, Nauck M, Völzke H, Traupe H, Krawczak M, Burkhardt H, Reis A, Hüffmeier U. Genome-wide association and targeted analysis of copy number variants with psoriatic arthritis in German patients. BMC MEDICAL GENETICS 2017; 18:92. [PMID: 28835222 PMCID: PMC5569473 DOI: 10.1186/s12881-017-0447-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/04/2016] [Accepted: 07/31/2017] [Indexed: 01/16/2023]
Abstract
Background Psoriatic Arthritis (PsA) is a chronic inflammatory disease of the joints. PsA is etiologically complex, and 11 susceptibility loci have been identified so far. Most of these overlap with loci associated with psoriasis vulgaris (PsV), the most common psoriatic skin manifestation which is also frequently seen in PsA patients. In addition, two copy number variants (CNVs) are associated with PsV, one of which, located within the LCE3 gene cluster, is also associated with PsA. Finally, an intergenic deletion has been reported as a PsA-specific CNV. Methods We performed a genome-wide association study (GWAS) of CNVs in PsA and assessed the contribution to disease risk by CNVs at known psoriasis susceptibility loci. Results After stringent quality assessment and validation of CNVs of the GWAS with an alternative quantitative method, two significantly associated CNVs remained, one near UXS1, the other one at the TRB locus. However, MLPA analysis did not confirm the CN state in ~1/3 of individuals, and an analysis of an independent case-control-study failed to confirm the initial associations. Furthermore, detailed PCR-based analysis of the sequence at TRB revealed the existence of a more complex genomic sequence most accurately represented by freeze hg18 which accordingly failed to confirm the hg19 sequence. Only rare CNVs were detected at psoriasis susceptibility loci. At three of 12 susceptibility loci with CNVs (CSMD1, IL12B, RYR2), CN variability was confirmed independently by MLPA. Overall, the rate of CNV confirmation by MLPA was strongly dependent upon CNV type, CNV size and the number of array markers involved in a CNV. Conclusion Although we identified PsA associations at several loci and confirmed that the common CNVs at these sites were real, ~1/3 of the common CNV states could not be reproduced. Furthermore, replication analysis failed to confirm the original association. Furthermore, SNP array-based analyses of CNVs were found to be more reliable for deletions than duplications, independent of the respective CNV allele frequency. CNVs are thus good candidate disease variants, while the methods to detect them should be applied cautiously and reproduced by an independent method. Electronic supplementary material The online version of this article (doi:10.1186/s12881-017-0447-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Steffen Uebe
- Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Schwabachanlage 10, 91054, Erlangen, Germany
| | - Maria Ehrlicher
- Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Schwabachanlage 10, 91054, Erlangen, Germany
| | - Arif Bülent Ekici
- Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Schwabachanlage 10, 91054, Erlangen, Germany
| | - Frank Behrens
- Division of Rheumatology and IME Fraunhofer Project Group Translational Medicine & Pharmacology, Goethe University, Frankfurt/Main, Germany
| | - Beate Böhm
- Division of Rheumatology and IME Fraunhofer Project Group Translational Medicine & Pharmacology, Goethe University, Frankfurt/Main, Germany
| | - Georg Homuth
- Interfaculty Institute for Genetics and Functional Genomics, University Medicine and Ernst-Moritz-Arndt University Greifswald, Greifswald, Germany
| | - Claudia Schurmann
- Interfaculty Institute for Genetics and Functional Genomics, University Medicine and Ernst-Moritz-Arndt University Greifswald, Greifswald, Germany
| | - Uwe Völker
- Interfaculty Institute for Genetics and Functional Genomics, University Medicine and Ernst-Moritz-Arndt University Greifswald, Greifswald, Germany
| | - Michael Jünger
- Clinic of Dermatology, University of Greifswald, Greifswald, Germany
| | - Matthias Nauck
- Institute of Clinical Chemistry and Laboratory Medicine, University of Greifswald, Greifswald, Germany
| | - Henry Völzke
- Institute for Community Medicine, University of Greifswald, Greifswald, Germany
| | - Heiko Traupe
- Department of Dermatology, University of Münster, Münster, Germany
| | - Michael Krawczak
- Institute for Medical Informatics and Statistics, Christian-Albrechts University Kiel, Kiel, Germany
| | - Harald Burkhardt
- Division of Rheumatology and IME Fraunhofer Project Group Translational Medicine & Pharmacology, Goethe University, Frankfurt/Main, Germany
| | - André Reis
- Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Schwabachanlage 10, 91054, Erlangen, Germany
| | - Ulrike Hüffmeier
- Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Schwabachanlage 10, 91054, Erlangen, Germany.
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39
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Tillander V, Alexson SEH, Cohen DE. Deactivating Fatty Acids: Acyl-CoA Thioesterase-Mediated Control of Lipid Metabolism. Trends Endocrinol Metab 2017; 28:473-484. [PMID: 28385385 PMCID: PMC5474144 DOI: 10.1016/j.tem.2017.03.001] [Citation(s) in RCA: 93] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/09/2017] [Accepted: 03/01/2017] [Indexed: 12/28/2022]
Abstract
The cellular uptake of free fatty acids (FFA) is followed by esterification to coenzyme A (CoA), generating fatty acyl-CoAs that are substrates for oxidation or incorporation into complex lipids. Acyl-CoA thioesterases (ACOTs) constitute a family of enzymes that hydrolyze fatty acyl-CoAs to form FFA and CoA. Although biochemically and biophysically well characterized, the metabolic functions of these enzymes remain incompletely understood. Existing evidence suggests regulatory roles in controlling rates of peroxisomal and mitochondrial fatty acyl-CoA oxidation, as well as in the subcellular trafficking of fatty acids. Emerging data implicate ACOTs in the pathogenesis of metabolic diseases, suggesting that better understanding their pathobiology could reveal unique targets in the management of obesity, diabetes, and nonalcoholic fatty liver disease.
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Affiliation(s)
- Veronika Tillander
- Division of Clinical Chemistry, Department of Laboratory Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, 14186, Sweden
| | - Stefan E H Alexson
- Division of Clinical Chemistry, Department of Laboratory Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, 14186, Sweden
| | - David E Cohen
- Division of Gastroenterology and Hepatology, Joan & Sanford I. Weill Department of Medicine, Weill Cornell Medical College, New York, NY 10021, USA.
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40
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Han YJ, Kwak DW. Prenatal diagnosis of 5p deletion syndrome: A case series report. ACTA ACUST UNITED AC 2017. [DOI: 10.5734/jgm.2017.14.1.34] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- You Jung Han
- Department of Obstetrics and Gynecology, Cheil General Hospital and Women’s Healthcare Center, Dankook University College of Medicine, Seoul, Korea
| | - Dong Wook Kwak
- Department of Obstetrics and Gynecology, Cheil General Hospital and Women’s Healthcare Center, Dankook University College of Medicine, Seoul, Korea
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41
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Asadollahi R, Zweier M, Gogoll L, Schiffmann R, Sticht H, Steindl K, Rauch A. Genotype-phenotype evaluation of MED13L defects in the light of a novel truncating and a recurrent missense mutation. Eur J Med Genet 2017. [PMID: 28645799 DOI: 10.1016/j.ejmg.2017.06.004] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
A decade after the designation of MED13L as a gene and its link to intellectual disability (ID) and dextro-looped transposition of great arteries in 2003, we previously described a recognizable syndrome due to MED13L haploinsufficiency. Subsequent reports of 22 further patients diagnosed by genome-wide testing further delineated the syndrome with expansion of the phenotypic spectrum and showed reduced penetrance for congenital heart defects. We now report two novel patients identified by whole exome sequencing, one with a de novo MED13L truncating mutation and the other with a de novo missense mutation. The first patient indicates some facial resemblance to Kleefstra syndrome as a novel differential diagnosis, and the second patient shows, for the first time, recurrence of a MED13L missense mutation (p.(Asp860Gly)). Notably, our in silico modelling predicted this missense mutation to decrease the stability of an alpha-helix and thereby affecting the MED13L secondary structure, while the majority of published missense mutations remain variants of uncertain significance. Review of the reported patients with MED13L haploinsufficiency indicates moderate to severe ID and facial anomalies in all patients, as well as severe speech delay and muscular hypotonia in the majority. Further common signs include abnormal MRI findings of myelination defects and abnormal corpus callosum, ataxia and coordination problems, autistic features, seizures/abnormal EEG, or congenital heart defects, present in about 20-50% of the patients. With reference to facial anomalies, the majority of patients were reported to show broad/prominent forehead, low set ears, bitemporal narrowing, upslanting palpebral fissures, depressed/flat nasal bridge, bulbous nose, and abnormal chin, but macroglossia and horizontal eyebrows were also observed in ∼30%. The latter are especially important in the differential diagnosis of 1p36 deletion and Kleefstra syndromes, while the more common facial gestalt shows some resemblance to 22q11.2 deletion syndrome. Despite the fact that MED13L was found to be one of the most common ID genes in the Deciphering Developmental Disorders Study, further detailed patient descriptions are needed to explore the full clinical spectrum, potential genotype-phenotype correlations, as well as the role of missense mutations and potential mutational hotspots along the gene.
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Affiliation(s)
- Reza Asadollahi
- Institute of Medical Genetics, University of Zurich, Schlieren-Zurich, Switzerland
| | - Markus Zweier
- Institute of Medical Genetics, University of Zurich, Schlieren-Zurich, Switzerland
| | - Laura Gogoll
- Institute of Medical Genetics, University of Zurich, Schlieren-Zurich, Switzerland
| | - Raphael Schiffmann
- Institute of Metabolic Disease, Baylor Scott & White Research Institute, Dallas, TX, USA
| | - Heinrich Sticht
- Institute of Biochemistry, University of Erlangen-Nuremberg, Erlangen, Germany
| | - Katharina Steindl
- Institute of Medical Genetics, University of Zurich, Schlieren-Zurich, Switzerland
| | - Anita Rauch
- Institute of Medical Genetics, University of Zurich, Schlieren-Zurich, Switzerland; Neuroscience Center Zurich, University of Zurich, Zurich, Switzerland; Zurich Center of Integrative Human Physiology, University of Zurich, Zurich, Switzerland.
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42
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Oneda B, Asadollahi R, Azzarello-Burri S, Niedrist D, Baldinger R, Masood R, Schinzel A, Latal B, Jenni OG, Rauch A. Low-Level Chromosomal Mosaicism in Neurodevelopmental Disorders. Mol Syndromol 2017; 8:266-271. [PMID: 28878611 DOI: 10.1159/000477189] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/29/2017] [Indexed: 11/19/2022] Open
Abstract
Chromosomal mosaicism, which represents a diagnostic challenge for detection and interpretation, has been described in several genetic conditions. It can contribute to a large phenotypic variation in diseases. At analysis of a well-characterized cohort of 714 patients with neurodevelopmental disorders (NDDs) of unknown etiology using a high-resolution chromosomal microarray platform, we found 2 cases (0.28%) of low-level mosaicism and defined a previously detected extra chromosome in a third patient. Two of the cases were mosaics for segmental imbalances (a partial trisomy 3q26.1q27.3 and a partial monosomy 18q21.2qter with 14.6 and 20% mosaic ratios in lymphocytes, respectively), and 1 was a mosaic for an entire chromosome (trisomy 14, mosaic ratio 20%). Our diagnostic yield is in line with the ratios previously published in patients with intellectual disability. Notably, the partial trisomy 3q26.1q27.3 case is an example of a rare and unusual class of a rearranged neocentric ring chromosome, which can neither be categorized in class I, nor in class II of such rearrangements. Our cases further elucidate the phenotypes related to the aberrations of the specific chromosome segments observed and underline the important role of low-level mosaics in the pathogenesis of NDDs of unknown etiology even in the absence of clinical signs of mosaicism.
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Affiliation(s)
- Beatrice Oneda
- Institute of Medical Genetics, University of Zurich, Zurich, Switzerland
| | - Reza Asadollahi
- Institute of Medical Genetics, University of Zurich, Zurich, Switzerland
| | | | - Dunja Niedrist
- Institute of Medical Genetics, University of Zurich, Zurich, Switzerland
| | - Rosa Baldinger
- Institute of Medical Genetics, University of Zurich, Zurich, Switzerland
| | - Rahim Masood
- Institute of Medical Genetics, University of Zurich, Zurich, Switzerland
| | - Albert Schinzel
- Institute of Medical Genetics, University of Zurich, Zurich, Switzerland
| | - Bea Latal
- Child Development Center, University Children's Hospital Zurich, Zurich, Switzerland
| | - Oskar G Jenni
- Child Development Center, University Children's Hospital Zurich, Zurich, Switzerland
| | - Anita Rauch
- Institute of Medical Genetics, University of Zurich, Zurich, Switzerland
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43
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Yuan L, Arikkath J. Functional roles of p120ctn family of proteins in central neurons. Semin Cell Dev Biol 2017; 69:70-82. [PMID: 28603076 DOI: 10.1016/j.semcdb.2017.05.027] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Revised: 05/16/2017] [Accepted: 05/30/2017] [Indexed: 02/06/2023]
Abstract
The cadherin-catenin complex in central neurons is associated with a variety of cytosolic partners, collectively called catenins. The p120ctn members are a family of catenins that are distinct from the more ubiquitously expressed α- and β-catenins. It is becoming increasingly clear that the functional roles of the p120ctn family of catenins in central neurons extend well beyond their functional roles in non-neuronal cells in partnering with cadherin to regulate adhesion. In this review, we will provide an overview of the p120ctn family in neurons and their varied functional roles in central neurons. Finally, we will examine the emerging roles of this family of proteins in neurodevelopmental disorders.
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Affiliation(s)
- Li Yuan
- Department of Pharmacology and Experimental Neuroscience, Munroe-Meyer Institute, University of Nebraska Medical Center, Omaha, NE 68198, United States; Developmental Neuroscience, Munroe-Meyer Institute, Durham Research Center II, Room 3031, University of Nebraska Medical Center, 985960 Nebraska Medical Center, Omaha, NE 68198-5960, United States.
| | - Jyothi Arikkath
- Developmental Neuroscience, Munroe-Meyer Institute, Durham Research Center II, Room 3031, University of Nebraska Medical Center, 985960 Nebraska Medical Center, Omaha, NE 68198-5960, United States.
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44
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The Mammalian Malonyl-CoA Synthetase ACSF3 Is Required for Mitochondrial Protein Malonylation and Metabolic Efficiency. Cell Chem Biol 2017; 24:673-684.e4. [PMID: 28479296 DOI: 10.1016/j.chembiol.2017.04.009] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2016] [Revised: 03/08/2017] [Accepted: 04/07/2017] [Indexed: 12/13/2022]
Abstract
Malonyl-coenzyme A (malonyl-CoA) is a central metabolite in mammalian fatty acid biochemistry generated and utilized in the cytoplasm; however, little is known about noncanonical organelle-specific malonyl-CoA metabolism. Intramitochondrial malonyl-CoA is generated by a malonyl-CoA synthetase, ACSF3, which produces malonyl-CoA from malonate, an endogenous competitive inhibitor of succinate dehydrogenase. To determine the metabolic requirement for mitochondrial malonyl-CoA, ACSF3 knockout (KO) cells were generated by CRISPR/Cas-mediated genome editing. ACSF3 KO cells exhibited elevated malonate and impaired mitochondrial metabolism. Unbiased and targeted metabolomics analysis of KO and control cells in the presence or absence of exogenous malonate revealed metabolic changes dependent on either malonate or malonyl-CoA. While ACSF3 was required for the metabolism and therefore detoxification of malonate, ACSF3-derived malonyl-CoA was specifically required for lysine malonylation of mitochondrial proteins. Together, these data describe an essential role for ACSF3 in dictating the metabolic fate of mitochondrial malonate and malonyl-CoA in mammalian metabolism.
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45
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Mullegama SV, Jensik P, Li C, Dorrani N, Kantarci S, Blumberg B, Grody WW, Strom SP. Coupling clinical exome sequencing with functional characterization studies to diagnose a patient with familial Mediterranean fever and MED13L haploinsufficiency syndromes. Clin Case Rep 2017; 5:833-840. [PMID: 28588821 PMCID: PMC5458005 DOI: 10.1002/ccr3.904] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Revised: 01/28/2017] [Accepted: 02/11/2017] [Indexed: 02/06/2023] Open
Abstract
Clinicians should consider that clinical exome sequencing provides the unique potential to disentangle complex phenotypes into multiple genetic etiologies. Further, functional studies on variants of uncertain significance are necessary to arrive at an accurate diagnosis for the patient.
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Affiliation(s)
- Sureni V Mullegama
- UCLA Department of Pathology and Laboratory Medicine David Geffen School of Medicine University of California, Los Angeles Los Angeles California.,UCLA Clinical Genomics Center David Geffen School of Medicine University of California, Los Angeles Los Angeles California
| | - Phillip Jensik
- Department of Physiology Southern Illinois University School of Medicine Carbondale Illinois
| | - Chen Li
- Department of Cellular and Genetic Medicine School of Basic Medical Sciences Fudan University Shanghai China
| | - Naghmeh Dorrani
- UCLA Department of Pathology and Laboratory Medicine David Geffen School of Medicine University of California, Los Angeles Los Angeles California.,UCLA Clinical Genomics Center David Geffen School of Medicine University of California, Los Angeles Los Angeles California.,Department of Human Genetics David Geffen School of Medicine University of California, Los Angeles Los Angeles California.,Department of Pediatrics David Geffen School of Medicine University of California, Los Angeles Los Angeles California
| | | | - Sibel Kantarci
- UCLA Department of Pathology and Laboratory Medicine David Geffen School of Medicine University of California, Los Angeles Los Angeles California.,UCLA Clinical Genomics Center David Geffen School of Medicine University of California, Los Angeles Los Angeles California
| | | | - Wayne W Grody
- UCLA Department of Pathology and Laboratory Medicine David Geffen School of Medicine University of California, Los Angeles Los Angeles California.,UCLA Clinical Genomics Center David Geffen School of Medicine University of California, Los Angeles Los Angeles California.,Department of Human Genetics David Geffen School of Medicine University of California, Los Angeles Los Angeles California.,Department of Pediatrics David Geffen School of Medicine University of California, Los Angeles Los Angeles California
| | - Samuel P Strom
- UCLA Department of Pathology and Laboratory Medicine David Geffen School of Medicine University of California, Los Angeles Los Angeles California.,UCLA Clinical Genomics Center David Geffen School of Medicine University of California, Los Angeles Los Angeles California
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46
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Sangu N, Shimojima K, Takahashi Y, Ohashi T, Tohyama J, Yamamoto T. A 7q31.33q32.1 microdeletion including LRRC4 and GRM8 is associated with severe intellectual disability and characteristics of autism. Hum Genome Var 2017; 4:17001. [PMID: 28224041 PMCID: PMC5298938 DOI: 10.1038/hgv.2017.1] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Revised: 10/21/2016] [Accepted: 11/17/2016] [Indexed: 12/28/2022] Open
Abstract
A 4-year-old boy with severe intellectual disability (ID) and characteristics of autism was found to have a de novo 1.9-Mb microdeletion in 7q31.33q32.1, in which LRRC4, GRM8, and 11 other genes were included. GRM8 is associated with attention deficit hyperactivity disorder. LRRC4 is related to synaptic cell adhesion molecules, some of which are associated with autism. The deletion of LRRC4 may be responsible for the severe ID and characteristics of autism observed in the present patient.
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Affiliation(s)
- Noriko Sangu
- Institute of Medical Genetics, Tokyo Women’s Medical University, Tokyo, Japan
- Department of Oral and Maxillofacial Surgery, Tokyo Women’s Medical University, Tokyo, Japan
| | - Keiko Shimojima
- Institute of Medical Genetics, Tokyo Women’s Medical University, Tokyo, Japan
| | - Yuya Takahashi
- Department of Pediatrics, Nagaoka Red Cross Hospital, Nagaoka, Japan
| | - Tsukasa Ohashi
- Department of Pediatrics, Niigata University Medical and Dental Hospital, Niigata, Japan
| | - Jun Tohyama
- Department of Child Neurology, Epilepsy Center, Nishi-Niigata Chuo National Hospital, Niigata, Japan
| | - Toshiyuki Yamamoto
- Institute of Medical Genetics, Tokyo Women’s Medical University, Tokyo, Japan
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47
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Zarate YA, Fish JL. SATB2-associated syndrome: Mechanisms, phenotype, and practical recommendations. Am J Med Genet A 2016; 173:327-337. [PMID: 27774744 PMCID: PMC5297989 DOI: 10.1002/ajmg.a.38022] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2016] [Accepted: 09/29/2016] [Indexed: 12/11/2022]
Abstract
The SATB2‐associated syndrome is a recently described syndrome characterized by developmental delay/intellectual disability with absent or limited speech development, craniofacial abnormalities, behavioral problems, dysmorphic features, and palatal and dental abnormalities. Alterations of the SATB2 gene can result from a variety of different mechanisms that include contiguous deletions, intragenic deletions and duplications, translocations with secondary gene disruption, and point mutations. The multisystemic nature of this syndrome demands a multisystemic approach and we propose evaluation and management guidelines. The SATB2‐associated syndrome registry has now been started and that will allow gathering further clinical information and refining the provided surveillance recommendations. © 2016 The Authors. American Journal of Medical Genetics Part A Published by Wiley Periodicals, Inc.
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Affiliation(s)
- Yuri A Zarate
- Section of Genetics and Metabolism, University of Arkansas for Medical Sciences, Little Rock, Arkansas
| | - Jennifer L Fish
- Department of Biological Sciences, University of Massachusetts Lowell, Lowell, Massachusetts
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48
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Hollenbeck D, Williams CL, Drazba K, Descartes M, Korf BR, Rutledge SL, Lose EJ, Robin NH, Carroll AJ, Mikhail FM. Clinical relevance of small copy-number variants in chromosomal microarray clinical testing. Genet Med 2016; 19:377-385. [PMID: 27632688 DOI: 10.1038/gim.2016.132] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Accepted: 07/21/2016] [Indexed: 11/09/2022] Open
Abstract
PURPOSE The 2010 consensus statement on diagnostic chromosomal microarray (CMA) testing recommended an array resolution ≥400 kb throughout the genome as a balance of analytical and clinical sensitivity. In spite of the clear evidence for pathogenicity of large copy-number variants (CNVs) in neurodevelopmental disorders and/or congenital anomalies, the significance of small, nonrecurrent CNVs (<500 kb) has not been well established in a clinical setting. METHODS We investigated the clinical significance of all nonpolymorphic small, nonrecurrent CNVs (<500 kb) in patients referred for CMA clinical testing over a period of 6 years, from 2009 to 2014 (a total of 4,417 patients). We excluded from our study patients with benign or likely benign CNVs and patients with only recurrent microdeletions/microduplications <500 kb. RESULTS In total, 383 patients (8.67%) were found to carry at least one small, nonrecurrent CNV, of whom 176 patients (3.98%) had one small CNV classified as a variant of uncertain significance (VUS), 45 (1.02%) had two or more small VUS CNVs, 20 (0.45%) had one small VUS CNV and a recurrent CNV, 113 (2.56%) had one small pathogenic or likely pathogenic CNV, 17 (0.38%) had two or more small pathogenic or likely pathogenic CNVs, and 12 (0.27%) had one small pathogenic or likely pathogenic CNV and a recurrent CNV. Within the pathogenic group, 80 of 142 patients (56% of all small pathogenic CNV cases) were found to have a single whole-gene or exonic deletion. The themes that emerged from our study are presented in the Discussion section. CONCLUSIONS Our study demonstrates the diagnostic clinical relevance of small, nonrecurrent CNVs <500 kb during CMA clinical testing and underscores the need for careful clinical interpretation of these CNVs.Genet Med 19 4, 377-385.
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Affiliation(s)
- Dana Hollenbeck
- Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Crescenda L Williams
- Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama, USA.,Current address: Children's Health Hospital, Dallas, Texas, USA
| | - Kathryn Drazba
- Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Maria Descartes
- Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama, USA.,Department of Pediatrics, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Bruce R Korf
- Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama, USA.,Department of Pediatrics, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - S Lane Rutledge
- Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama, USA.,Department of Pediatrics, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Edward J Lose
- Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama, USA.,Department of Pediatrics, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Nathaniel H Robin
- Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama, USA.,Department of Pediatrics, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Andrew J Carroll
- Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Fady M Mikhail
- Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama, USA
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49
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Amarillo IE, Nievera I, Hagan A, Huchthagowder V, Heeley J, Hollander A, Koenig J, Austin P, Wang T. Integrated small copy number variations and epigenome maps of disorders of sex development. Hum Genome Var 2016; 3:16012. [PMID: 27340555 PMCID: PMC4899613 DOI: 10.1038/hgv.2016.12] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2016] [Revised: 03/24/2016] [Accepted: 03/26/2016] [Indexed: 02/03/2023] Open
Abstract
Small copy number variations (CNVs) have typically not been analyzed or reported in clinical settings and hence have remained underrepresented in databases and the literature. Here, we focused our investigations on these small CNVs using chromosome microarray analysis (CMA) data previously obtained from patients with atypical characteristics or disorders of sex development (DSD). Using our customized CMA track targeting 334 genes involved in the development of urogenital and reproductive structures and a less stringent analysis filter, we uncovered small genes with recurrent and overlapping CNVs as small as 1 kb, and small regions of homozygosity (ROHs), imprinting and position effects. Detailed analysis of these high-resolution data revealed CNVs and ROHs involving structural and functional domains, repeat elements, active transcription sites and regulatory regions. Integration of these genomic data with DNA methylation, histone modification and predicted RNA expression profiles in normal testes and ovaries suggested spatiotemporal and tissue-specific gene regulation. This study emphasized a DSD-specific and gene-targeted CMA approach that uncovered previously unanalyzed or unreported small genes and CNVs, contributing to the growing resources on small CNVs and facilitating the narrowing of the genomic gap for identifying candidate genes or regions. This high-resolution analysis tool could improve the diagnostic utility of CMA, not only in patients with DSD but also in other clinical populations. These integrated data provided a better genomic-epigenomic landscape of DSD and greater opportunities for downstream research.
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Affiliation(s)
- Ina E Amarillo
- Cytogenomics and Molecular Pathology Laboratory, Division of Laboratory and Genomic Medicine, Department of Pathology and Immunology, Washington University in St Louis School of Medicine, St Louis, MO, USA; Washington University in St Louis School of Medicine DSD Team, St Louis, MO, USA
| | - Isabelle Nievera
- Washington University in St Louis School of Medicine DSD Team , St Louis, MO, USA
| | - Andrew Hagan
- Division of Biology and Biomedical Sciences, Washington University in St Louis , St Louis, MO, USA
| | - Vishwa Huchthagowder
- Cytogenomics and Molecular Pathology Laboratory, Division of Laboratory and Genomic Medicine, Department of Pathology and Immunology, Washington University in St Louis School of Medicine , St Louis, MO, USA
| | - Jennifer Heeley
- Washington University in St Louis School of Medicine DSD Team, St Louis, MO, USA; Department of Pediatrics, Washington University in St Louis School of Medicine, St Louis, MO, USA
| | - Abby Hollander
- Washington University in St Louis School of Medicine DSD Team, St Louis, MO, USA; Department of Pediatrics, Washington University in St Louis School of Medicine, St Louis, MO, USA
| | - Joel Koenig
- Washington University in St Louis School of Medicine DSD Team, St Louis, MO, USA; Department of Surgery, Washington University in St Louis School of Medicine, St Louis, MO, USA
| | - Paul Austin
- Washington University in St Louis School of Medicine DSD Team, St Louis, MO, USA; Department of Surgery, Washington University in St Louis School of Medicine, St Louis, MO, USA
| | - Ting Wang
- Department of Genetics, Washington University in St Louis School of Medicine , St Louis, MO, USA
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50
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Hyman SE. Enlisting hESCs to Interrogate Genetic Variants Associated with Neuropsychiatric Disorders. Cell Stem Cell 2016; 17:253-4. [PMID: 26340523 DOI: 10.1016/j.stem.2015.08.013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Connecting rare genetic variants to neuropsychiatric disease mechanisms remains a significant challenge. In this issue of Cell Stem Cell, Pak et al. (2015) combine gene targeting and stem cell technologies to identify a significant cellular effect of rare penetrant NRXN1 mutations in human neurons, which was found to cause a defect in neurotransmitter release.
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Affiliation(s)
- Steven E Hyman
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA.
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