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https://www.readbyqxmd.com/read/30190494/searching-the-second-hit-in-patients-with-inherited-retinal-dystrophies-and-monoallelic-variants-in-abca4-ush2a-and-cep290-by-whole-gene-targeted-sequencing
#1
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
https://www.readbyqxmd.com/read/30096711/establishment-of-a-human-ipsc-line-iishdoi004-a-from-a-patient-with-usher-syndrome-associated-with-the-mutation-c-2276g-t-p-cys759phe-in-the-ush2a-gene
#2
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
https://www.readbyqxmd.com/read/30075702/mhc-class-ii-restricted-neoantigen-peptides-predicted-by-clonal-mutation-analysis-in-lung-adenocarcinoma-patients-implications-on-prognostic-immunological-biomarker-and-vaccine-design
#3
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
https://www.readbyqxmd.com/read/30032850/germline-mutations-in-young-non-smoking-women-with-lung-adenocarcinoma
#4
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
https://www.readbyqxmd.com/read/29986705/comprehensive-genomic-diagnosis-of-non-syndromic-and-syndromic-hereditary-hearing-loss-in-spanish-patients
#5
Rubén Cabanillas, Marta Diñeiro, Guadalupe A Cifuentes, David Castillo, Patricia C Pruneda, Rebeca Álvarez, Noelia Sánchez-Durán, Raquel Capín, Ana Plasencia, Mónica Viejo-Díaz, Noelia García-González, Inés Hernando, José L Llorente, Alfredo Repáraz-Andrade, Cristina Torreira-Banzas, Jordi Rosell, Nancy Govea, Justo Ramón Gómez-Martínez, Faustino Núñez-Batalla, José A Garrote, Ángel Mazón-Gutiérrez, María Costales, María Isidoro-García, Belén García-Berrocal, Gonzalo R Ordóñez, Juan Cadiñanos
BACKGROUND: Sensorineural hearing loss (SNHL) is the most common sensory impairment. Comprehensive next-generation sequencing (NGS) has become the standard for the etiological diagnosis of early-onset SNHL. However, accurate selection of target genomic regions (gene panel/exome/genome), analytical performance and variant interpretation remain relevant difficulties for its clinical implementation. METHODS: We developed a novel NGS panel with 199 genes associated with non-syndromic and/or syndromic SNHL...
July 9, 2018: BMC Medical Genomics
https://www.readbyqxmd.com/read/29953849/efficacy-outcome-measures-for-clinical-trials-of-ush2a-caused-by-the-common-c-2299delg-mutation
#6
Giacomo Calzetti, Richard A Levy, Artur V Cideciyan, Alexandra V Garafalo, Alejandro J Roman, Alexander Sumaroka, Jason Charng, Elise Heon, Samuel G Jacobson
PURPOSE: To determine the change in vision and retinal structure in patients with the common c.2299delG mutation in the USH2A gene in anticipation of clinical trials of therapy. DESIGN: Retrospective observational case series. METHODS: Eighteen patients, homozygotes or compound heterozygotes with the c.2299delG mutation in USH2A, were studied with regard to visual acuity, kinetic perimetry, dark- and light-adapted static perimetry, optical coherence tomography (OCT), and autofluorescence (AF) imaging...
September 2018: American Journal of Ophthalmology
https://www.readbyqxmd.com/read/29932521/association-of-common-candidate-variants-with-vascular-malformations-and-intracranial-hemorrhage-in-hereditary-hemorrhagic-telangiectasia
#7
Ludmila Pawlikowska, Jeffrey Nelson, Diana E Guo, Charles E McCulloch, Michael T Lawton, Helen Kim, Marie E Faughnan
BACKGROUND: Hereditary hemorrhagic telangiectasia (HHT) is caused by mutations in TGFβ/BMP9 pathway genes and characterized by vascular malformations (VM) including arteriovenous malformations (AVM) in lung, liver, and brain, which lead to severe complications including intracranial hemorrhage (ICH) from brain VM. The clinical heterogeneity of HHT suggests a role for genetic modifier effects. Common variants in loci that modify phenotype severity in Tgfb knockout mice were previously reported as associated with lung AVM in HHT...
May 2018: Molecular Genetics & Genomic Medicine
https://www.readbyqxmd.com/read/29921047/-application-of-next-generation-sequencing-in-congenital-sensorineural-deafness
#8
B Xu, Y Chen, A Jiang, C Chen, K Wang, J Zheng, Y Fu
Objective: The next-generation sequencing technology (NGS) was used to perform genetic testing on children diagnosed with sensorineural hearing loss in outpatient clinics.The information on the status and inheritance of disease causing genes in deafness was analyzed to provide a theoretical basis for genetic counseling, prenatal diagnosis, and birth defects prevention. Method: Ninety-four cases of sensorineural deafness diagnosed by medical history, audiological examination, and imaging examination were collected in our department...
June 5, 2018: Journal of Clinical Otorhinolaryngology, Head, and Neck Surgery
https://www.readbyqxmd.com/read/29912909/unravelling-the-pathogenic-role-and-genotype-phenotype-correlation-of-the-ush2a-p-cys759phe-variant-among-spanish-families
#9
Raquel Pérez-Carro, Fiona Blanco-Kelly, Lilián Galbis-Martínez, Gema García-García, Elena Aller, Blanca García-Sandoval, Pablo Mínguez, Marta Corton, Ignacio Mahíllo-Fernández, Inmaculada Martín-Mérida, Almudena Avila-Fernández, José M Millán, Carmen Ayuso
INTRODUCTION: Mutations in USH2A cause both isolated Retinitis Pigmentosa (RP) and Usher syndrome (that implies RP and hearing impairment). One of the most frequent variants identified in this gene and among these patients is the p.(Cys759Phe) change. However, the pathogenic role of this allele has been questioned since it was found in homozygosity in two healthy siblings of a Spanish family. To assess the causative role of USH2A p.(Cys759Phe) in autosomal recessive RP (ARRP) and Usher syndrome type II (USH2) and to establish possible genotype-phenotype correlations associated with p...
2018: PloS One
https://www.readbyqxmd.com/read/29899460/mutation-screening-of-the-ush2a-gene-in-retinitis-pigmentosa-and-usher-patients-in-a-han-chinese-population
#10
Lulin Huang, Yao Mao, Jiyun Yang, Yuanfeng Li, Yang Li, Zhenglin Yang
OBJECTIVES: USH2A encodes for usherin, a basement membrane protein in the inner ear and retina. USH2A can cause retinitis pigmentosa (RP) with or without hearing loss. The aim of this study was to detect USH2A mutations in a Chinese cohort of 75 small RP families and 10 Usher syndrome families. METHODS: We performed a direct Sanger sequencing analysis of the USH2A gene to identify mutations for this cohort. RESULTS: We identified a total of eight mutations in four of the 75 small RP families (5...
June 13, 2018: Eye
https://www.readbyqxmd.com/read/29777677/usherin-defects-lead-to-early-onset-retinal-dysfunction-in-zebrafish
#11
Margo Dona, Ralph Slijkerman, Kimberly Lerner, Sanne Broekman, Jeremy Wegner, Taylor Howat, Theo Peters, Lisette Hetterschijt, Nanda Boon, Erik de Vrieze, Nasrin Sorusch, Uwe Wolfrum, Hannie Kremer, Stephan Neuhauss, Jingjing Zang, Maarten Kamermans, Monte Westerfield, Jennifer Phillips, Erwin van Wijk
Mutations in USH2A are the most frequent cause of Usher syndrome and autosomal recessive nonsyndromic retinitis pigmentosa. To unravel the pathogenic mechanisms underlying USH2A-associated retinal degeneration and to evaluate future therapeutic strategies that could potentially halt the progression of this devastating disorder, an animal model is needed. The available Ush2a knock-out mouse model does not mimic the human phenotype, because it presents with only a mild and late-onset retinal degeneration. Using CRISPR/Cas9-technology, we introduced protein-truncating germline lesions into the zebrafish ush2a gene (ush2armc1 : c...
August 2018: Experimental Eye Research
https://www.readbyqxmd.com/read/29738887/transcriptome-analysis-reveals-enrichment-of-genes-associated-with-auditory-system-in-swimbladder-of-channel-catfish
#12
Yujia Yang, Xiaozhu Wang, Yang Liu, Qiang Fu, Changxu Tian, Chenglong Wu, Huitong Shi, Zihao Yuan, Suxu Tan, Shikai Liu, Dongya Gao, Rex Dunham, Zhanjiang Liu
In aquatic organisms, hearing is an important sense for acoustic communications and detection of sound-emitting predators and prey. Channel catfish is a dominant aquaculture species in the United States. As channel catfish can hear sounds of relatively high frequency, it serves as a good model for study auditory mechanisms. In catfishes, Weberian ossicles connect the swimbladder to the inner ear to transfer the forced vibrations and improve hearing ability. In this study, we examined the transcriptional profiles of channel catfish swimbladder and other four tissues (gill, liver, skin, and intestine)...
September 2018: Comparative Biochemistry and Physiology. Part D, Genomics & Proteomics
https://www.readbyqxmd.com/read/29668032/presence-of-meniscus-tear-alters-gene-expression-profile-of-anterior-cruciate-ligament-tears
#13
Robert H Brophy, Marcus A Rothermich, Eric D Tycksen, Lei Cai, Muhammad Farooq Rai
Anterior cruciate ligament (ACL) tears occur in isolation or in tandem with other intra-articular injuries such as meniscus tears. The impact of injury pattern on the molecular biology of the injured ACL is unknown. Here, we tested the hypothesis that the biological response of the ACL to injury varies based on the presence or absence of concomitant meniscus tear. We performed RNA-seq on 28 ACL tears remnants (12 isolated, 16 combined). In total, 16,654 transcripts were differentially expressed between isolated and combined injury groups at false discovery rate of 0...
April 18, 2018: Journal of Orthopaedic Research: Official Publication of the Orthopaedic Research Society
https://www.readbyqxmd.com/read/29660607/generation-of-an-ips-cell-line-via-a-non-integrative-method-using-urine-derived-cells-from-a-patient-with-ush2a-associated-retinitis-pigmentosa
#14
Yonglong Guo, Qiaolang Zeng, Shiwei Liu, Quan Yu, Peiyuan Wang, Hongjie Ma, Shanshan Shi, Xin Yan, Zekai Cui, Mengyuan Xie, Yunxia Xue, Qingbing Zha, Zhijie Li, Jun Zhang, Shibo Tang, Jiansu Chen
We have established an induced pluripotent stem (iPS) cell line using urine-derived cells from a 27-year-old male patient with retinitis pigmentosa associated with point mutations in the USH2A gene. Feeder-free culture conditions and the integration-free CytoTune™-iPS 2.0 Sendai Reprogramming Kit were used.
May 2018: Stem Cell Research
https://www.readbyqxmd.com/read/29655801/analysis-of-intragenic-ush2a-copy-number-variation-unveils-broad-spectrum-of-unique-and-recurrent-variants
#15
Christina A Austin-Tse, Diana L Mandelker, Andrea M Oza, Heather Mason-Suares, Heidi L Rehm, Sami S Amr
Given that all forms of Usher syndrome (USH) present with hearing loss in advance of retinal disease, the syndromic nature of the disorder is rarely appreciated when critical management decisions are being made. As a result, molecular diagnostics are crucial in guiding the management of USH patients. While 11 genes have been associated with USH, the USH2A gene is one of the largest contributors. Approximately 20% of suspected USH probands that undergo USH2A sequencing at our laboratory receive an inconclusive result due to the identification of a monoallelic disease-causing variant in USH2A...
October 2018: European Journal of Medical Genetics
https://www.readbyqxmd.com/read/29625443/comprehensive-molecular-screening-in-chinese-usher-syndrome-patients
#16
Tengyang Sun, Ke Xu, Yanfan Ren, Yue Xie, Xiaohui Zhang, Lu Tian, Yang Li
Purpose: Usher syndrome (USH) refers to a group of autosomal recessive disorders causing deafness and blindness. The objectives of this study were to determine the mutation spectrum in a cohort of Chinese patients with USH and to describe the clinical features of the patients with mutations. Methods: A total of 119 probands who were clinically diagnosed with USH were recruited for genetic analysis. All probands underwent ophthalmic examinations. A combination of molecular screening methods, including targeted next-generation sequencing, Sanger-DNA sequencing, and multiplex ligation probe amplification assay, was used to detect mutations...
March 1, 2018: Investigative Ophthalmology & Visual Science
https://www.readbyqxmd.com/read/29588463/combining-targeted-panel-based-resequencing-and-copy-number-variation-analysis-for-the-diagnosis-of-inherited-syndromic-retinopathies-and-associated-ciliopathies
#17
Iker Sanchez-Navarro, Luciana R J da Silva, Fiona Blanco-Kelly, Olga Zurita, Noelia Sanchez-Bolivar, Cristina Villaverde, Maria Isabel Lopez-Molina, Blanca Garcia-Sandoval, Saoud Tahsin-Swafiri, Pablo Minguez, Rosa Riveiro-Alvarez, Isabel Lorda, Rocío Sanchez-Alcudia, Raquel Perez-Carro, Diana Valverde, Yichuan Liu, Lifeng Tian, Hakon Hakonarson, Almudena Avila-Fernandez, Marta Corton, Carmen Ayuso
Inherited syndromic retinopathies are a highly heterogeneous group of diseases that involve retinal anomalies and systemic manifestations. They include retinal ciliopathies, other well-defined clinical syndromes presenting with retinal alterations and cases of non-specific multisystemic diseases. The heterogeneity of these conditions makes molecular and clinical characterization of patients challenging in daily clinical practice. We explored the capacity of targeted resequencing and copy-number variation analysis to improve diagnosis of a heterogeneous cohort of 47 patients mainly comprising atypical cases that did not clearly fit a specific clinical diagnosis...
March 27, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29490346/the-genetics-of-usher-syndrome-in-the-israeli-and-palestinian-populations
#18
Ayat Khalaileh, Alaa Abu-Diab, Tamar Ben-Yosef, Annick Raas-Rothschild, Israela Lerer, Yahya Alswaiti, Itay Chowers, Eyal Banin, Dror Sharon, Samer Khateb
Purpose: Usher syndrome (USH) is the most common cause for deaf-blindness. It is genetically and clinically heterogeneous and prevalent in populations with high consanguinity rate. We aim to characterize the set of genes and mutations that cause USH in the Israeli and Palestinian populations. Methods: Seventy-four families with USH were recruited (23 with USH type 1 [USH1], 33 with USH2, seven with USH3, four with atypical USH, and seven families with an undetermined USH type)...
February 1, 2018: Investigative Ophthalmology & Visual Science
https://www.readbyqxmd.com/read/29283788/investigating-the-disease-association-of-ush2a-p-c759f-variant-by-leveraging-large-retinitis-pigmentosa-cohort-data
#19
Mariana DuPont, Evan M Jones, Mingchu Xu, Rui Chen
No abstract text is available yet for this article.
April 2018: Ophthalmic Genetics
https://www.readbyqxmd.com/read/29196752/combined-genetic-approaches-yield-a-48-diagnostic-rate-in-a-large-cohort-of-french-hearing-impaired-patients
#20
D Baux, C Vaché, C Blanchet, M Willems, C Baudoin, M Moclyn, V Faugère, R Touraine, B Isidor, D Dupin-Deguine, M Nizon, M Vincent, S Mercier, C Calais, G García-García, Z Azher, L Lambert, Y Perdomo-Trujillo, F Giuliano, M Claustres, M Koenig, M Mondain, A F Roux
Hearing loss is the most common sensory disorder and because of its high genetic heterogeneity, implementation of Massively Parallel Sequencing (MPS) in diagnostic laboratories is greatly improving the possibilities of offering optimal care to patients. We present the results of a two-year period of molecular diagnosis that included 207 French families referred for non-syndromic hearing loss. Our multi-step strategy involved (i) DFNB1 locus analysis, (ii) MPS of 74 genes, and (iii) additional approaches including Copy Number Variations, in silico analyses, minigene studies coupled when appropriate with complete gene sequencing, and a specific assay for STRC...
December 1, 2017: Scientific Reports
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