Association of Clinical Features with Mutation of TECTA in a Family with Autosomal Dominant Hearing Loss
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Porichthys Notatus), a Teleost with Divergent Sexual Phenotypes
Portland State University PDXScholar Biology Faculty Publications and Presentations Biology 11-11-2015 Saccular Transcriptome Profiles of the Seasonal Breeding Plainfin Midshipman Fish (Porichthys notatus), a Teleost with Divergent Sexual Phenotypes Joshua J. Faber-Hammond Portland State University Manoj P. Samanta Systemix Institute Elizabeth A. Whitchurch Humboldt State University Dustin Manning Oregon Health & Science University Joseph A. Sisneros University of Washington Follow this and additional works at: https://pdxscholar.library.pdx.edu/bio_fac Part of the Biology Commons LetSee next us page know for additional how authors access to this document benefits ou.y Citation Details Faber-Hammond, J., Samanta, M. P., Whitchurch, E. A., Manning, D., Sisneros, J. A., & Coffin, A. B. (2015). Saccular Transcriptome Profiles of the Seasonal Breeding Plainfin Midshipman Fish (Porichthys notatus), a Teleost with Divergent Sexual Phenotypes. PloS One, 10(11), e0142814. This Article is brought to you for free and open access. It has been accepted for inclusion in Biology Faculty Publications and Presentations by an authorized administrator of PDXScholar. Please contact us if we can make this document more accessible: [email protected]. Authors Joshua J. Faber-Hammond, Manoj P. Samanta, Elizabeth A. Whitchurch, Dustin Manning, Joseph A. Sisneros, and Allison B. Coffin This article is available at PDXScholar: https://pdxscholar.library.pdx.edu/bio_fac/108 RESEARCH ARTICLE Saccular Transcriptome Profiles of the Seasonal Breeding Plainfin Midshipman -
Identification of Inherited Retinal Disease-Associated Genetic Variants in 11 Candidate Genes
G C A T T A C G G C A T genes Article Identification of Inherited Retinal Disease-Associated Genetic Variants in 11 Candidate Genes Galuh D. N. Astuti 1,2, L. Ingeborgh van den Born 3, M. Imran Khan 1,4, Christian P. Hamel 5,6,7,†, Béatrice Bocquet 5,6,7, Gaël Manes 5,6, Mathieu Quinodoz 8, Manir Ali 9 ID , Carmel Toomes 9, Martin McKibbin 10 ID , Mohammed E. El-Asrag 9,11, Lonneke Haer-Wigman 1, Chris F. Inglehearn 9 ID , Graeme C. M. Black 12, Carel B. Hoyng 13, Frans P. M. Cremers 1,4 and Susanne Roosing 1,4,* ID 1 Department of Human Genetics, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands; [email protected] (G.D.N.A.); [email protected] (M.I.K.); [email protected] (L.H.-W.); [email protected] (F.P.M.C.) 2 Radboud Institute for Molecular Life Sciences, Radboud University, 6525 GA Nijmegen, The Netherlands 3 The Rotterdam Eye Hospital, 3011 BH Rotterdam, The Netherlands; [email protected] 4 Donders Institute for Brain, Cognition and Behaviour, Radboud University Nijmegen, 6525 EN Nijmegen, The Netherlands 5 Institut National de la Santé et de la Recherche Médicale, Institute for Neurosciences of Montpellier, 34080 Montpellier, France; [email protected] (B.B.); [email protected] (G.M.) 6 University of Montpellier, 34090 Montpellier, France 7 CHRU, Genetics of Sensory Diseases, 34295 Montpellier, France 8 Department of Computational Biology, Unit of Medical Genetics, University of Lausanne, 1015 Lausanne, Switzerland; [email protected] 9 Section of Ophthalmology & Neuroscience, Leeds Institute of Biomedical & Clinical Sciences, University of Leeds, St. -
Novel Candidate Genes for 46,XY Gonadal Dysgenesis Identified by a Customized 1 M Array-CGH Platformq
European Journal of Medical Genetics 56 (2013) 661e668 Contents lists available at ScienceDirect European Journal of Medical Genetics journal homepage: http://www.elsevier.com/locate/ejmg Clinical research Novel candidate genes for 46,XY gonadal dysgenesis identified by a customized 1 M array-CGH platformq Ameli Norling a, b, Angelica Lindén Hirschberg b, Erik Iwarsson a, Bengt Persson c, d, Anna Wedell a, e, Michela Barbaro a, e, * a Department of Molecular Medicine and Surgery, Karolinska Institutet, Karolinska University Hospital, 171 76 Stockholm, Sweden b Department of Women’s and Children’s Health, Karolinska Institutet, Karolinska University Hospital, 171 76 Stockholm, Sweden c Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, 751 24 Uppsala, Sweden d Science for Life Laboratory, Department of Cell and Molecular Biology, Karolinska Institutet, 171 77 Stockholm, Sweden e Center for Inherited Metabolic Diseases (CMMS), Karolinska University Hospital, 171 76 Stockholm, Sweden article info abstract Article history: Half of all patients with a disorder of sex development (DSD) do not receive a specific molecular diag- Received 18 June 2013 nosis. Comparative genomic hybridization (CGH) can detect copy number changes causing gene hap- Accepted 3 September 2013 loinsufficiency or over-expression that can lead to impaired gonadal development and gonadal DSD. The Available online 18 September 2013 purpose of this study was to identify novel candidate genes for 46,XY gonadal dysgenesis (GD) using a customized 1 M array-CGH platform with whole-genome coverage and probe enrichment targeting 78 Keywords: genes involved in sex development. Fourteen patients with 46,XY gonadal DSD were enrolled in the Array-CGH study. -
Downloaded at Were Examined by Indirect Ophthalmoscopy (Heine Genome.Ucsc.Edu, Accession 21/10/2015)
Michot et al. Genet Sel Evol (2016) 48:56 DOI 10.1186/s12711-016-0232-y Genetics Selection Evolution RESEARCH ARTICLE Open Access A reverse genetic approach identifies an ancestral frameshift mutation in RP1 causing recessive progressive retinal degeneration in European cattle breeds Pauline Michot1,2, Sabine Chahory3, Andrew Marete1,4, Cécile Grohs1, Dimitri Dagios3, Elise Donzel3, Abdelhak Aboukadiri1, Marie‑Christine Deloche1,2, Aurélie Allais‑Bonnet2,5, Matthieu Chambrial6, Sarah Barbey7, Lucie Genestout8, Mekki Boussaha1, Coralie Danchin‑Burge9, Sébastien Fritz1,2, Didier Boichard1 and Aurélien Capitan1,2* Abstract Background: Domestication and artificial selection have resulted in strong genetic drift, relaxation of purifying selection and accumulation of deleterious mutations. As a consequence, bovine breeds experience regular outbreaks of recessive genetic defects which might represent only the tip of the iceberg since their detection depends on the observation of affected animals with distinctive symptoms. Thus, recessive mutations resulting in embryonic mor‑ tality or in non-specific symptoms are likely to be missed. The increasing availability of whole-genome sequences has opened new research avenues such as reverse genetics for their investigation. Our aim was to characterize the genetic load of 15 European breeds using data from the 1000 bull genomes consortium and prove that widespread harmful mutations remain to be detected. Results: We listed 2489 putative deleterious variants (in 1923 genes) segregating at a minimal frequency of 5 % in at least one of the breeds studied. Gene enrichment analysis showed major enrichment for genes related to nerv‑ ous, visual and auditory systems, and moderate enrichment for genes related to cardiovascular and musculoskeletal systems. -
A New Otogelin ENU Mouse Model for Autosomal-Recessive Nonsyndromic Moderate Hearing Impairment Carole El Hakam, Laetitia Magnol, Véronique Blanquet
A new otogelin ENU mouse model for autosomal-recessive nonsyndromic moderate hearing impairment Carole El Hakam, Laetitia Magnol, Véronique Blanquet To cite this version: Carole El Hakam, Laetitia Magnol, Véronique Blanquet. A new otogelin ENU mouse model for autosomal-recessive nonsyndromic moderate hearing impairment. SpringerPlus, SpringerOpen, 2015, 4 (1), pp.2-8. 10.1186/s40064-015-1537-y. hal-02634509 HAL Id: hal-02634509 https://hal.inrae.fr/hal-02634509 Submitted on 27 May 2020 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. El Hakam Kamareddin et al. SpringerPlus (2015) 4:730 DOI 10.1186/s40064-015-1537-y RESEARCH Open Access A new Otogelin ENU mouse model for autosomal‑recessive nonsyndromic moderate hearing impairment Carole El Hakam Kamareddin, Laetitia Magnol and Veronique Blanquet* Abstract Approximately 10 % of the population worldwide suffers from hearing loss (HL) and about 60 % of persons with early onset HL have hereditary hearing loss due to genetic mutations. Highly efficient mutagenesis in mice with the chemical mutagen, ethylnitrosourea (ENU), associated with relevant phenotypic tools represents a powerful approach in producing mouse models for hearing impairment. A benefit of this strategy is to generate alleles to form a series revealing the full spectrum of gene function in vivo. -
Quantitative Trait Loci Mapping of Macrophage Atherogenic Phenotypes
QUANTITATIVE TRAIT LOCI MAPPING OF MACROPHAGE ATHEROGENIC PHENOTYPES BRIAN RITCHEY Bachelor of Science Biochemistry John Carroll University May 2009 submitted in partial fulfillment of requirements for the degree DOCTOR OF PHILOSOPHY IN CLINICAL AND BIOANALYTICAL CHEMISTRY at the CLEVELAND STATE UNIVERSITY December 2017 We hereby approve this thesis/dissertation for Brian Ritchey Candidate for the Doctor of Philosophy in Clinical-Bioanalytical Chemistry degree for the Department of Chemistry and the CLEVELAND STATE UNIVERSITY College of Graduate Studies by ______________________________ Date: _________ Dissertation Chairperson, Johnathan D. Smith, PhD Department of Cellular and Molecular Medicine, Cleveland Clinic ______________________________ Date: _________ Dissertation Committee member, David J. Anderson, PhD Department of Chemistry, Cleveland State University ______________________________ Date: _________ Dissertation Committee member, Baochuan Guo, PhD Department of Chemistry, Cleveland State University ______________________________ Date: _________ Dissertation Committee member, Stanley L. Hazen, MD PhD Department of Cellular and Molecular Medicine, Cleveland Clinic ______________________________ Date: _________ Dissertation Committee member, Renliang Zhang, MD PhD Department of Cellular and Molecular Medicine, Cleveland Clinic ______________________________ Date: _________ Dissertation Committee member, Aimin Zhou, PhD Department of Chemistry, Cleveland State University Date of Defense: October 23, 2017 DEDICATION I dedicate this work to my entire family. In particular, my brother Greg Ritchey, and most especially my father Dr. Michael Ritchey, without whose support none of this work would be possible. I am forever grateful to you for your devotion to me and our family. You are an eternal inspiration that will fuel me for the remainder of my life. I am extraordinarily lucky to have grown up in the family I did, which I will never forget. -
Novel Cell Types and Developmental Lineages Revealed by Single-Cell
RESEARCH ARTICLE Novel cell types and developmental lineages revealed by single-cell RNA-seq analysis of the mouse crista ampullaris Brent A Wilkerson1,2†, Heather L Zebroski1,2, Connor R Finkbeiner1,2, Alex D Chitsazan1,2,3‡, Kylie E Beach1,2, Nilasha Sen1, Renee C Zhang1, Olivia Bermingham-McDonogh1,2* 1Department of Biological Structure, University of Washington, Seattle, United States; 2Institute for Stem Cells and Regenerative Medicine, University of Washington, Seattle, United States; 3Department of Biochemistry, University of Washington, Seattle, United States Abstract This study provides transcriptomic characterization of the cells of the crista ampullaris, sensory structures at the base of the semicircular canals that are critical for vestibular function. We performed single-cell RNA-seq on ampullae microdissected from E16, E18, P3, and P7 mice. Cluster analysis identified the hair cells, support cells and glia of the crista as well as dark cells and other nonsensory epithelial cells of the ampulla, mesenchymal cells, vascular cells, macrophages, and melanocytes. Cluster-specific expression of genes predicted their spatially restricted domains of *For correspondence: gene expression in the crista and ampulla. Analysis of cellular proportions across developmental [email protected] time showed dynamics in cellular composition. The new cell types revealed by single-cell RNA-seq Present address: †Department could be important for understanding crista function and the markers identified in this study will of Otolaryngology-Head and enable the examination of their dynamics during development and disease. Neck Surgery, Medical University of South Carolina, Charleston, United States; ‡CEDAR, OHSU Knight Cancer Institute, School Introduction of Medicine, Portland, United States The vertebrate inner ear contains mechanosensory organs that sense sound and balance. -
Clinical Characteristics with Long-Term Follow-Up of Four Okinawan Families
Ganaha et al. Human Genome Variation (2019) 6:37 https://doi.org/10.1038/s41439-019-0068-4 Human Genome Variation ARTICLE Open Access Clinical characteristics with long-term follow-up of four Okinawan families with moderate hearing loss caused by an OTOG variant Akira Ganaha1,TadashiKaname 2,KumikoYanagi2, Tetsuya Tono1,TeruyukiHiga3 and Mikio Suzuki3 Abstract We describe the clinical features of four Japanese families with moderate sensorineural hearing loss due to the OTOG gene variant. We analyzed 98 hearing loss-related genes in patients with hearing loss originally from the Okinawa Islands using next-generation sequencing. We identified a homozygous variant of the gene encoding otogelin NM_001277269(OTOG): c.330C>G, p.Tyr110* in four families. All patients had moderate hearing loss with a slightly downsloping audiogram, including low frequency hearing loss without equilibrium dysfunction. Progressive hearing loss was not observed over the long-term in any patient. Among the three patients who underwent newborn hearing screening, two patients passed the test. OTOG-associated hearing loss was considered to progress early after birth, leading to moderate hearing loss and the later stable phase of hearing loss. Therefore, there are patients whose hearing loss cannot be detected by NHS, making genetic diagnosis of OTOG variants highly useful for complementing NHS in the clinical setting. Based on the allele frequency results, hearing loss caused by the p.Tyr110* variant in OTOG fi 1234567890():,; 1234567890():,; 1234567890():,; 1234567890():,; might be more common than we identi ed. The p.Tyr110* variant was reported in South Korea, suggesting that this variant is a common cause of moderate hearing loss in Japanese and Korean populations. -
Integrative Meta-Analysis of Differentially Expressed Genes in Osteoarthritis Using Microarray Technology
MOLECULAR MEDICINE REPORTS 12: 3439-3445, 2015 Integrative meta-analysis of differentially expressed genes in osteoarthritis using microarray technology XI WANG, YUJIE NING and XIONG GUO School of Public Health, Xi'an Jiaotong University Health Science Center, Key Laboratory of Trace Elements and Endemic Diseases, National Health and Family Planning Commission, Xi'an, Shaanxi 710061, P.R. China Received August 17, 2014; Accepted April 22, 2015 DOI: 10.3892/mmr.2015.3790 Abstract. The aim of the present study was to identify differ- Introduction entially expressed (DE) genes in patients with osteoarthritis (OA), and biological processes associated with changes in Osteoarthritis (OA) is the most prevalent joint disease and gene expression that occur in this disease. Using the INMEX is characterized by an abnormal remodeling of joint tissues, (integrative meta-analysis of expression data) software which is predominantly driven by inflammatory mediators tool, a meta-analysis of publicly available microarray Gene within the affected joint (1,2). The pathological changes of Expression Omnibus (GEO) datasets of OA was performed. OA primarily take place in the articular cartilage, and include Gene ontology (GO) enrichment analysis was performed cartilage degeneration, matrix degradation and synovial in order to detect enriched functional attributes based on inflammation (3‑5). Clinically, features of OA include pain, gene-associated GO terms. Three GEO datasets, containing stiffness, limitation of motion, swelling and deformity (6). 137 patients with OA and 52 healthy controls, were included Synovial inflammation is hypothesized to be the primary in the meta‑analysis. The analysis identified 85 genes that underlying etiology in OA (3). However, the biological mecha- were consistently differentially expressed in OA (30 genes nisms associated with OA remain to be elucidated. -
Mutations of the Gene Encoding Otogelin Are a Cause of Autosomal-Recessive Nonsyndromic Moderate Hearing Impairment
View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Elsevier - Publisher Connector REPORT Mutations of the Gene Encoding Otogelin Are a Cause of Autosomal-Recessive Nonsyndromic Moderate Hearing Impairment Margit Schraders,1,2,3 Laura Ruiz-Palmero,5,6 Ersan Kalay,7 Jaap Oostrik,1,2,3 Francisco J. del Castillo,5,6 Orhan Sezgin,8 Andy J. Beynon,1,3 Tim M. Strom,9 Ronald J.E. Pennings,1,3 Celia Zazo Seco,1,2,3 Anne M.M. Oonk,1,3 Henricus P.M. Kunst,1,3 Marı´a Domı´nguez-Ruiz,5,6 Ana M. Garcı´a-Arumi,10 Miguel del Campo,11 Manuela Villamar,5,6 Lies H. Hoefsloot,4 Felipe Moreno,5,6 Ronald J.C. Admiraal,1,3 Ignacio del Castillo,5,6 and Hannie Kremer1,2,3,4,* Already 40 genes have been identified for autosomal-recessive nonsyndromic hearing impairment (arNSHI); however, many more genes are still to be identified. In a Dutch family segregating arNSHI, homozygosity mapping revealed a 2.4 Mb homozygous region on chro- mosome 11 in p15.1-15.2, which partially overlapped with the previously described DFNB18 locus. However, no putative pathogenic variants were found in USH1C, the gene mutated in DFNB18 hearing impairment. The homozygous region contained 12 additional annotated genes including OTOG, the gene encoding otogelin, a component of the tectorial membrane. It is thought that otogelin contributes to the stability and strength of this membrane through interaction or stabilization of its constituent fibers. The murine orthologous gene was already known to cause hearing loss when defective. -
Enriched Genes FLX07
enriched genes FLX07 Entrez Symbols Name TermID TermDesc 24950 MGC156498,S5AR 1,Srd5a1 steroid-5-alpha-reductase, alpha polypeptide 1 (3-oxo-5 alpha-steroid delta 4-dehydrogenase alpha 1) GO:0003865 3-oxo-5-alpha-steroid 4-dehydrogenase activity 361191 Nsun2,RGD1311954 NOL1/NOP2/Sun domain family, member 2 GO:0003865 3-oxo-5-alpha-steroid 4-dehydrogenase activity 305291 RGD1308828,S5AR 3,Srd5a3 steroid 5 alpha-reductase 3 GO:0003865 3-oxo-5-alpha-steroid 4-dehydrogenase activity 311569 Acas2,Acss2 acyl-CoA synthetase short-chain family member 2 GO:0003987 acetate-CoA ligase activity 296259 Acas2l,Acss1 acyl-CoA synthetase short-chain family member 1 GO:0003987 acetate-CoA ligase activity 25288 ACS,Acas,Acsl1,COAA,Facl2 acyl-CoA synthetase long-chain family member 1 GO:0003987 acetate-CoA ligase activity 114024 Acs3,Acsl3,Facl3 acyl-CoA synthetase long-chain family member 3 GO:0003987 acetate-CoA ligase activity 299002 G2e3,RGD1310263 G2/M-phase specific E3 ubiquitin ligase GO:0016881 acid-amino acid ligase activity 361866 Hace1 HECT domain and ankyrin repeat containing, E3 ubiquitin protein ligase 1 GO:0016881 acid-amino acid ligase activity 316395 Hecw2 HECT, C2 and WW domain containing E3 ubiquitin protein ligase 2 GO:0016881 acid-amino acid ligase activity 309758 Herc4 hect domain and RLD 4 GO:0016881 acid-amino acid ligase activity 361815 MGC116114,Rnf8 ring finger protein 8 GO:0016881 acid-amino acid ligase activity 298576 Mul1,RGD1309944 mitochondrial ubiquitin ligase activator of NFKB 1 GO:0016881 acid-amino acid ligase activity -
Target Sequencing of 307 Deafness Genes Identifies Candidate Genes Implicated in Microtia
www.impactjournals.com/oncotarget/ Oncotarget, 2017, Vol. 8, (No. 38), pp: 63324-63332 Research Paper Target sequencing of 307 deafness genes identifies candidate genes implicated in microtia Pu Wang1, Xinmiao Fan1, Yibei Wang1, Yue Fan1, Yaping Liu2, Shuyang Zhang3 and Xiaowei Chen1 1Department of Otolaryngology, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China 2Department of Medical Genetics, School of Basic Medicine, Peking Union Medical College, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China 3Department of Cardiology, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China Correspondence to: Xiaowei Chen, email: [email protected] Shuyang Zhang, email: [email protected] Keywords: microtia, deafness genes, next-generation sequencing, SKAT Received: April 23, 2017 Accepted: May 29, 2017 Published: June 28, 2017 Copyright: Wang et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License 3.0 (CC BY 3.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. ABSTRACT Microtia is a congenital malformation of the external ear caused by genetic and/or environmental factors. However, no causal genetic mutations have been identified in isolated microtia patients. In this study, we utilized targeted genomic capturing combined with next-generation sequencing to screen for mutations in 307 deafness genes in 32 microtia patients. Forty-two rare heterozygous mutations in 25 genes, including 22 novel mutations in 24 isolated unilateral microtia cases were identified. Pathway analysis found five pathways especially focal adhesion pathway and ECM-receptor interaction pathway were significantly associated with microtia.