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Chiyan Zhou, Suping Li, Qinhao Song, Xiaodan Liu, Zhengyou Miao
OBJECTIVE: To explore the molecular basis for an individual with postnatal deafness and provide genetic counseling for her family. METHODS: Following extraction of genomic DNA from peripheral blood samples, 127 genes associated with deafness were subjected to targeted capturing and next generation sequencing. Suspected mutation was verified by Sanger sequencing. RESULTS: The proband was found to carry a homozygous c.1893C>A mutation in the TECTA gene, which is located in the tectorial membrane of inner ear and may cause premature termination of translation of TECTA protein...
February 10, 2019: Zhonghua Yi Xue Yi Chuan Xue za Zhi, Zhonghua Yixue Yichuanxue Zazhi, Chinese Journal of Medical Genetics
Pu Wang, Yibei Wang, Xinmiao Fan, Yaping Liu, Yue Fan, Tao Liu, Chongjian Chen, Shuyang Zhang, Xiaowei Chen
BACKGROUND: Microtia-atresia is characterized by abnormalities of the auricle (microtia) and aplasia or hypoplasia of the external auditory canal, often associated with middle ear abnormalities. To date, no causal genetic mutations or genes have been identified in microtia-atresia patients. METHODS: We designed a panel of 131 genes associated with external/middle or inner ear deformity. Targeted genomic capturing combined with next-generation sequencing (NGS) was utilized to screen for mutations in 40 severe microtia-atresia patients...
January 28, 2019: BMC Medical Genomics
Marina Riera, Achchhe Patel, Borja Corcostegui, Stanley Chang, Barbara Corneo, Janet R Sparrow, Esther Pomares
A human induced pluripotent stem cell (iPSC) line was generated from a female patient affected by autosomal recessive retinitis pigmentosa with two mutations in the USH2A gene: c.2209C > T (p.Arg737Ter) and c.8693A > C (p.Tyr2898Ser). Skin fibroblasts were infected with Sendai virus containing the Yamanaka factors and the resulting cells were fully characterized to confirm successful reprogramming. The iPSC line expressed several pluripotency markers, could generate the three germ layers, had a normal karyotype, carried the two USH2A mutations and was free of Sendai virus...
January 17, 2019: Stem Cell Research
Guy P Richardson, Christine Petit
Up to five distinct cell-surface specializations interconnect the stereocilia and the kinocilium of the mature hair bundle in some species: kinocilial links, tip links, top connectors, shaft connectors, and ankle links. In developing hair bundles, transient lateral links are prominent. Mutations in genes encoding proteins associated with these links cause Usher deafness/blindness syndrome or nonsyndromic (isolated) forms of human hereditary deafness, and mice with constitutive or conditional alleles of these genes have provided considerable insight into the molecular composition and function of the different links...
January 7, 2019: Cold Spring Harbor Perspectives in Medicine
Johannes Birtel, Martin Gliem, Elisabeth Mangold, Philipp L Müller, Frank G Holz, Christine Neuhaus, Steffen Lenzner, Diana Zahnleiter, Christian Betz, Tobias Eisenberger, Hanno J Bolz, Peter Charbel Issa
Retinitis pigmentosa (RP) is an inherited degenerative disease causing severe retinal dystrophy and visual impairment mainly with onset in infancy or adolescence. Targeted next-generation sequencing (NGS) has become an efficient tool to encounter the enormous genetic heterogeneity of diverse retinal dystrophies, including RP. To identify disease-causing mutations in unselected, consecutive RP patients, we conducted Sanger sequencing of genes commonly involved in the suspected genetic RP subtype, followed by targeted large-panel NGS if no mutation was identified, or NGS as primary analysis...
2018: PloS One
Guillaume Jouret, Céline Poirsier, Marta Spodenkiewicz, Clémence Jaquin, Evan Gouy, Carl Arndt, Marc Labrousse, Dominique Gaillard, Martine Doco-Fenzy, Anne-Sophie Lebre
OBJECTIVE: To describe the genetic and phenotypic spectrum of Usher syndrome after 6 years of studies by next-generation sequencing, and propose an up-to-date classification of Usher genes in patients with both visual and hearing impairments suggesting Usher syndrome, and in patients with seemingly isolated deafness. STUDY DESIGN: The systematic review and meta-analysis protocol was based on Cochrane and Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines...
January 2019: Otology & Neurotology
Carla Sanjurjo-Soriano, Nejla Erkilic, Gaël Manes, Gregor Dubois, Christian P Hamel, Isabelle Meunier, Vasiliki Kalatzis
We generated an induced pluripotent stem cell (iPSC) line using dermal fibroblasts from a patient with Usher syndrome type 2 (USH2). This individual was homozygous for the most prevalent variant reported in the USH2A gene, c.2299delG localized in exon 13. Reprogramming was performed using the non-integrative Sendai virus reprogramming method and the human OSKM transcription factor cocktail under feeder-free culture conditions. This iPSC line will be an invaluable tool for studying the pathophysiology of USH2 and for testing the efficacy of novel treatments...
November 16, 2018: Stem Cell Research
Carla Fuster-García, Gema García-García, Teresa Jaijo, Neus Fornés, Carmen Ayuso, Miguel Fernández-Burriel, Ana Sánchez-De la Morena, Elena Aller, José M Millán
Usher syndrome is a rare disorder causing retinitis pigmentosa, together with sensorineural hearing loss. Due to the phenotypic and genetic heterogeneity of this disease, the best method to screen the causative mutations is by high-throughput sequencing. In this study, we tested a semiconductor chip based sequencing approach with 77 unrelated patients, as a molecular diagnosis routine. In addition, Multiplex Ligation-dependent Probe Amplification and microarray-based Comparative Genomic Hybridization techniques were applied to detect large rearrangements, and minigene assays were performed to confirm the mRNA processing aberrations caused by splice-site mutations...
November 20, 2018: Scientific Reports
Carla Sanjurjo-Soriano, Nejla Erkilic, Gaël Manes, Gregor Dubois, Christian P Hamel, Isabelle Meunier, Vasiliki Kalatzis
We generated an induced pluripotent stem cell (iPSC) line from a patient with non-syndromic retinitis pigmentosa who is a compound heterozygote for the two most frequent USH2A variants, c.2276G > T and c.2299delG localized in exon 13. Patient fibroblasts were reprogrammed using the non-integrative Sendai virus reprogramming method and the human OSKM transcription factor cocktail. The generated cells were pluripotent and genetically stable. This iPSC line will be an important tool for studying the pathogenesis of these USH2A mutations and for developing treatments that, due their high prevalence, will target a large patient population...
November 10, 2018: Stem Cell Research
Fabiana Louise Motta, Renan Paulo Martin, Rafael Filippelli-Silva, Mariana Vallim Salles, Juliana Maria Ferraz Sallum
Among the Brazilian population, the frequency rates of inherited retinal dystrophies and their causative genes are underreported. To increase the knowledge about these dystrophies in our population, we retrospectively studied the medical records of 1,246 Brazilian patients with hereditary retinopathies during 20 years of specialized outpatient clinic care. Of these patients, 559 had undergone at least one genetic test. In this cohort, the most prevalent dystrophies were non-syndromic retinitis pigmentosa (35%), Stargardt disease (21%), Leber congenital amaurosis (9%), and syndromic inherited retinal dystrophies (12%)...
October 29, 2018: Scientific Reports
Marianna E Ivanova, Vladimir N Trubilin, Dmitry S Atarshchikov, Andrey M Demchinsky, Vladimir V Strelnikov, Alexander S Tanas, Olga M Orlova, Anton S Machalov, Kira V Overchenko, Tatiana V Markova, Daria M Golenkova, Kirill I Anoshkin, Ilya V Volodin, Dmitry V Zaletaev, Andrey A Pulin, Irina I Nadelyaeva, Alexey I Kalinkin, Debmalya Barh
BACKGROUND: Usher syndrome (USH) is heterogeneous in nature and requires genetic test for diagnosis and management. Mutations in USH associated genes are reported in some populations except Russians. Here, we first time represented the mutation spectrum of a Russian USH cohort. METHODS: Twenty-eight patients with USH were selected from 3214 patients from Deaf-Blind Support Foundation "Con-nection" during 2014-2016 following the observational study NCT03319524...
December 2018: Ophthalmic Genetics
Stephanie J Valberg, Sudeep Perumbakkam, Erica C McKenzie, Carrie J Finno
Equine myofibrillar myopathy (MFM) causes exertional muscle pain and is characterized by myofibrillar disarray and ectopic desmin aggregates of unknown origin. To investigate the pathophysiology of MFM, we compared resting and 3 h post-exercise transcriptomes of gluteal muscle and the resting skeletal muscle proteome of MFM and control Arabian horses using RNA-sequencing and iTRAQ analyses. Three hours after exercise, 191 genes were identified as differentially expressed (DE) in MFM vs. control muscle with > 1 log2 fold change [FC] in genes involved in sulfur compound/ cysteine metabolism such as cystathionine-beta-synthase [CBS, ↓4...
October 5, 2018: Physiological Genomics
Ralph Slijkerman, Alexander Goloborodko, Sanne Broekman, Erik de Vrieze, Lisette Hetterschijt, Theo Peters, Milou Gerits, Hannie Kremer, Erwin van Wijk
The frequent deep-intronic c.7595-2144A>G mutation in intron 40 of USH2A generates a high-quality splice donor site, resulting in the incorporation of a pseudoexon (PE40) into the mature transcript that is predicted to prematurely terminate usherin translation. Aberrant USH2A pre-mRNA splicing could be corrected in patient-derived fibroblasts using antisense oligonucleotides. With the aim to study the effect of the c.7595-2144A>G mutation and USH2A splice redirection on retinal function, a humanized zebrafish knockin model was generated, in which 670 basepairs of ush2a intron 40 were exchanged for 557 basepairs of the corresponding human sequence using an optimized CRISPR/Cas9-based protocol...
December 2018: Zebrafish
Yue-Chuan Fu, Na Chen, Zi-Long Qiu, Lin Liu, Jie Shen
Retinitis pigmentosa (RP) is a common form of inherited retinal degeneration that causes progressive loss of vision or adult blindness, characterized by the impairment of rod and cone photoreceptors. At present, mutations in >60 pathogenic genes have been confirmed to cause RP. The predominant modes of inheritance are autosomal dominant, autosomal recessive and X‑linked. In addition, other modes of inheritance, including digenic or mitochondrial inheritance, have been reported. In previous decades, with the development of sequencing techniques, significant advances in identifying novel RP pathogenic genes and screening mutations have been made...
December 2018: Molecular Medicine Reports
Ling Wan, Boling Deng, Zhengzheng Wu, Xiaoming Chen
Background: High myopia is a common ocular disease worldwide. To expand our current understanding of the genetic basis of high myopia, we carried out a whole exome sequencing (WES) study to identify potential causal gene mutations. Methods: A total of 20 individuals with high myopia were exome sequenced. A novel filtering strategy combining phenotypes and functional impact of variants was applied to identify candidate genes by multi-step bioinformatics analyses...
2018: PeerJ
Shanshan Han, Xiliang Liu, Shanglun Xie, Meng Gao, Fei Liu, Shanshan Yu, Peng Sun, Changquan Wang, Stephen Archacki, Zhaojing Lu, Xuebin Hu, Yayun Qin, Zhen Qu, Yuwen Huang, Yuexia Lv, Jiayi Tu, Jingzhen Li, Tinsae Assefa Yimer, Tao Jiang, Zhaohui Tang, Daji Luo, Fangyi Chen, Mugen Liu
Most cases of Usher syndrome type II (USH2) are due to mutations in the USH2A gene. There are no effective treatments or ideal animal models for this disease, and the pathological mechanisms of USH2 caused by USH2A mutations are still unknown. Here, we constructed a ush2a knockout (ush2a-/- ) zebrafish model using TALEN technology to investigate the molecular pathology of USH2. An early onset auditory disorder and abnormal morphology of inner ear stereocilia were identified in the ush2a-/- zebrafish. Consequently, the disruption of Ush2a in zebrafish led to a hearing impairment, like that in mammals...
October 2018: Human Genetics
María González-Del Pozo, Marta Martín-Sánchez, Nereida Bravo-Gil, Cristina Méndez-Vidal, Ángel Chimenea, Enrique Rodríguez-de la Rúa, Salud Borrego, Guillermo Antiñolo
Inherited Retinal Dystrophies are clinically and genetically heterogeneous disorders affecting the photoreceptors. Although NGS has shown to be helpful for the molecular diagnosis of these conditions, some cases remain unsolved. Among these, several individuals harboured monoallelic variants in a recessive gene, suggesting that a comprehensive screening could improve the overall diagnosis. In order to assess the contribution of non-coding variations in a cohort of 29 patients, 25 of them with monoallelic mutations, we performed targeted NGS...
September 6, 2018: Scientific Reports
Francisco Zurita-Díaz, María Del Carmen Ortuño-Costela, Ana Moreno-Izquierdo, Liliana Galbis, José María Millán, Carmen Ayuso, Rafael Garesse, M Esther Gallardo
A human iPSC line, IISHDOi004-A, from fibroblasts obtained from a patient with Usher syndrome, harboring a homozygous mutation in the USH2A gene (c.2276G>T; p.Cys759Phe) has been generated. Reprogramming factors Oct3/4, Sox2, Klf4, and c-Myc were delivered using Sendai virus.
August 2018: Stem Cell Research
Weijing Cai, Dapeng Zhou, Weibo Wu, Wen Ling Tan, Jiaqian Wang, Caicun Zhou, Yanyan Lou
BACKGROUND: Mutant peptides presented by MHC (major histocompatibility complex) Class II in cancer are important targets for cancer immunotherapy. Both animal studies and clinical trials in cancer patients showed that CD4 T cells specific to tumor-derived mutant peptides are essential for the efficacy of immune checkpoint blockade therapy by PD1 antibody. RESULTS: In this study, we analyzed the next generation sequencing data of 147 lung adenocarcinoma patients from The Cancer Genome Atlas and predicted neoantigens presented by MHC Class I and Class II molecules...
August 3, 2018: BMC Genomics
Iikki Donner, Riku Katainen, Lauri J Sipilä, Mervi Aavikko, Eero Pukkala, Lauri A Aaltonen
OBJECTIVES: Although the primary cause of lung cancer is smoking, a considerable proportion of all lung cancers occur in never smokers. Gender influences the risk and characteristics of lung cancer and women are overrepresented among never smokers with the disease. Young age at onset and lack of established environmental risk factors suggest genetic predisposition. In this study, we used population-based sampling of young patients to discover candidate predisposition variants for lung adenocarcinoma in never-smoking women...
August 2018: Lung Cancer: Journal of the International Association for the Study of Lung Cancer
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