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https://www.readbyqxmd.com/read/28327206/lessons-learned-from-additional-research-analyses-of-unsolved-clinical-exome-cases
#1
Mohammad K Eldomery, Zeynep Coban-Akdemir, Tamar Harel, Jill A Rosenfeld, Tomasz Gambin, Asbjørg Stray-Pedersen, Sébastien Küry, Sandra Mercier, Davor Lessel, Jonas Denecke, Wojciech Wiszniewski, Samantha Penney, Pengfei Liu, Weimin Bi, Seema R Lalani, Christian P Schaaf, Michael F Wangler, Carlos A Bacino, Richard Alan Lewis, Lorraine Potocki, Brett H Graham, John W Belmont, Fernando Scaglia, Jordan S Orange, Shalini N Jhangiani, Theodore Chiang, Harsha Doddapaneni, Jianhong Hu, Donna M Muzny, Fan Xia, Arthur L Beaudet, Eric Boerwinkle, Christine M Eng, Sharon E Plon, V Reid Sutton, Richard A Gibbs, Jennifer E Posey, Yaping Yang, James R Lupski
BACKGROUND: Given the rarity of most single-gene Mendelian disorders, concerted efforts of data exchange between clinical and scientific communities are critical to optimize molecular diagnosis and novel disease gene discovery. METHODS: We designed and implemented protocols for the study of cases for which a plausible molecular diagnosis was not achieved in a clinical genomics diagnostic laboratory (i.e. unsolved clinical exomes). Such cases were recruited to a research laboratory for further analyses, in order to potentially: (1) accelerate novel disease gene discovery; (2) increase the molecular diagnostic yield of whole exome sequencing (WES); and (3) gain insight into the genetic mechanisms of disease...
March 21, 2017: Genome Medicine
https://www.readbyqxmd.com/read/28324114/novel-25-kb-deletion-of-mertk-causes-retinitis-pigmentosa-with-severe-progression
#2
Daniel R Evans, Jane S Green, Gordon J Johnson, Jeremy Schwartzentruber, Jacek Majewski, Chandree L Beaulieu, Wen Qin, Christian R Marshall, Tara A Paton, Nicole M Roslin, Andrew D Paterson, Somayyeh Fahiminiya, Justin French, Kym M Boycott, Michael O Woods
Purpose: Retinitis pigmentosa (RP) describes a complex group of inherited retinal dystrophies with almost 300 reported genes and loci. We investigated the genetic etiology of autosomal recessive RP (arRP) in a large kindred with 5 affected family members, who reside on the island of Newfoundland, Canada. Methods: Genetic linkage analysis was performed on 12 family members (Infinium HumanOmni2.5-8 BeadChip). Whole exome sequencing analysis (Illumina HiSeq) was performed on one affected individual...
March 1, 2017: Investigative Ophthalmology & Visual Science
https://www.readbyqxmd.com/read/28322986/differentiating-motivational-from-affective-influence-of-performance-contingent-reward-on-cognitive-control-the-wanting-component-enhances-both-proactive-and-reactive-control
#3
Anne-Clémence Chaillou, Anne Giersch, Marc Hoonakker, Rémi L Capa, Anne Bonnefond
Positive affect strongly modulates goal-directed behaviors and cognitive control mechanisms. It often results from the presence of a pleasant stimulus in the environment, whether that stimulus appears unpredictably or as a consequence of a particular behavior. The influence of positive affect linked to a random pleasant stimulus differs from the influence of positive affect resulting from performance-contingent pleasant stimuli. However, the mechanisms by which the performance contingency of pleasant stimuli modulates the influence of positive affect on cognitive control mechanisms have not been elucidated...
March 18, 2017: Biological Psychology
https://www.readbyqxmd.com/read/28322228/a-clear-bias-in-parental-origin-of-de-novo-pathogenic-cnvs-related-to-intellectual-disability-developmental-delay-and-multiple-congenital-anomalies
#4
Ruiyu Ma, Linbei Deng, Yan Xia, Xianda Wei, Yingxi Cao, Ruolan Guo, Rui Zhang, Jing Guo, Desheng Liang, Lingqian Wu
Copy number variation (CNV) is of great significance in human evolution and disorders. Through tracing the parent-of-origin of de novo pathogenic CNVs, we are expected to investigate the relative contributions of germline genomic stability on reproductive health. In our study, short tandem repeat (STR) and single nucleotide polymorphism (SNP) were used to determine the parent-of-origin of 87 de novo pathogenic CNVs found in unrelated patients with intellectual disability (ID), developmental delay (DD) and multiple congenital anomalies (MCA)...
March 21, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28320174/etiological-agents-of-viral-meningitis-in-children-from-a-dengue-endemic-area-southeast-region-of-brazil
#5
Danilo B de Oliveira, Talitah M Candiani, Ana Paula M Franco-Luiz, Gabriel M F Almeida, Jônatas S Abrahão, Maria Rios, Roney S Coimbra, Erna G Kroon
Meningitis is a disease with a global distribution that constitutes a worldwide burden, with viruses as the primary etiologic agents. The range of viral meningitis severity depends mainly on age, immune status and etiological agent. The aim of this work was to investigate the suspected cases of viral meningitis using molecular techniques to confirm the viral infection. The diagnosed virus was correlated with clinical findings and cytochemical parameters in cerebrospinal liquid (CSF) of patients. CSF of 70 children with the presumptive diagnosis of viral meningitis was analyzed by real time PCR (qPCR)...
April 15, 2017: Journal of the Neurological Sciences
https://www.readbyqxmd.com/read/28315434/identifying-the-clonal-relationship-model-of-multifocal-papillary-thyroid-carcinoma-by-whole-genome-sequencing
#6
Mao Xia, Hengyu Li, Qian Ma, Dong Yu, Jing Li, Yi Zhang, Yuan Sheng, Yingjun Guo
PURPOSE: To evaluate the application of whole genome sequencing (WGS) in determining the inter-foci clonal relationship of multifocal papillary thyroid carcinoma (mPTC). METHODS: After reviewing PTC patient profiles, 8 cancer foci and germline control samples from 3 mPTC patients were analyzed by WGS. Single nucleotide variations (SNVs), copy number variation (CNV), structural variation and mutational signature were examined. RESULTS: The multifocality rate of PTC was 35...
March 14, 2017: Cancer Letters
https://www.readbyqxmd.com/read/28304377/establishment-of-a-novel-cellular-model-for-myxofibrosarcoma-heterogeneity
#7
Birgit Lohberger, Nicole Stuendl, Andreas Leithner, Beate Rinner, Stefan Sauer, Karl Kashofer, Bernadette Liegl-Atzwanger
Human cancers frequently display substantial intra-tumoural heterogeneity in virtually all distinguishable phenotypic features, such as cellular morphology, gene expression, and metastatic potential. In order to investigate tumour heterogeneity in myxofibrosarcoma, we established a novel myxofibrosarcoma cell line with two well defined sub-clones named MUG-Myx2a and MUG-Myx2b. The parental tumour tissue and both MUG-Myx2 cell lines showed the same STR profile. The fact that MUG-Myx2a showed higher proliferation activity, faster migration and enhanced tumourigenicity was of particular interest...
March 17, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28304131/copy-number-variation-in-19-italian-multiplex-families-with-autism-spectrum-disorder-importance-of-synaptic-and-neurite-elongation-genes
#8
Carla Lintas, Chiara Picinelli, Ignazio Stefano Piras, Roberto Sacco, Claudia Brogna, Antonio M Persico
Autism Spectrum Disorder (ASD) is endowed with impressive heritability estimates and high recurrence rates. Its genetic underpinnings are nonetheless very heterogeneous, with common, and rare contributing variants located in hundreds of different loci, each characterized by variable levels of penetrance. Multiplex families from single ethnic groups represent a useful means to reduce heterogeneity and enhance genetic load. We screened 19 Italian ASD multiplex families (3 triplets and 16 duplets, total N = 41 ASD subjects), using array-CGH (Agilent 180 K)...
March 17, 2017: American Journal of Medical Genetics. Part B, Neuropsychiatric Genetics
https://www.readbyqxmd.com/read/28302160/increased-genomic-burden-of-germline-copy-number-variants-is-associated-with-early-onset-breast-cancer-australian-breast-cancer-family-registry
#9
Logan C Walker, John F Pearson, George A R Wiggins, Graham G Giles, John L Hopper, Melissa C Southey
BACKGROUND: Women with breast cancer who have multiple affected relatives are more likely to have inherited genetic risk factors for the disease. All the currently known genetic risk factors for breast cancer account for less than half of the average familial risk. Furthermore, the genetic factor(s) underlying an increased cancer risk for many women from multiple-case families remain unknown. Rare genomic duplications and deletions, known as copy number variants (CNVs), cover more than 10% of a human genome, are often not assessed in studies of genetic predisposition, and could account for some of the so-called "missing heritability"...
March 16, 2017: Breast Cancer Research: BCR
https://www.readbyqxmd.com/read/28299000/chorioretinal-coloboma-complications-retinal-detachment-and-choroidal-neovascular-membrane
#10
Rehan M Hussain, Ashkan M Abbey, Ankoor R Shah, Kimberly A Drenser, Michael T Trese, Antonio Capone
PURPOSE: To report the chorioretinal coloboma, and its association with increased risk of retinal detachment (RD) and choroidal neovascularization (CNV). METHODS: This retrospective case series included eyes with chorioretinal coloboma diagnosed between 1995 and 2014 with a focus on RD and CNV as related complications. Cases of CNV were managed with laser photocoagulation or intravitreal injection of bevacizumab. For eyes with CNV, therapeutic success was defined as resolution of the subretinal hemorrhage on fundus examination and resolution of the subretinal and intraretinal fluid on optical coherence tomography (OCT)...
January 2017: Journal of Ophthalmic & Vision Research
https://www.readbyqxmd.com/read/28298866/choroidal-neovascularization-secondary-to-ocular-penetration-during-retrobulbar-anesthesia-and-its-treatment
#11
Seyhan Dikci, Turgut Yılmaz, Zarife Ekici Gök, Soner Demirel, Oğuzhan Genç
Retrobulbar anesthesia is still used before ocular surgery; however, it has various complications including ocular penetration. The penetration/perforation of the globe can cause complications such as endophthalmitis, retinal detachment, and scotoma. Choroidal neovascularization (CNV) is rarely seen, following choroidal rupture in penetrating eye injuries. Here, we present a patient who underwent a pars plana vitrectomy for vitreous hemorrhage secondary to ocular penetration during a retrobulbar injection for cataract surgery...
January 2017: Oman Journal of Ophthalmology
https://www.readbyqxmd.com/read/28291231/targeted-deep-sequencing-of-flowering-regulators-in-brassica-napus-reveals-extensive-copy-number-variation
#12
Sarah Schiessl, Bruno Huettel, Diana Kuehn, Richard Reinhardt, Rod J Snowdon
Gene copy number variation (CNV) is increasingly implicated in control of complex trait networks, particularly in polyploid plants like rapeseed (Brassica napus L.) with an evolutionary history of genome restructuring. Here we performed sequence capture to assay nucleotide variation and CNV in a panel of central flowering time regulatory genes across a species-wide diversity set of 280 B. napus accessions. The genes were chosen based on prior knowledge from Arabidopsis thaliana and related Brassica species...
March 14, 2017: Scientific Data
https://www.readbyqxmd.com/read/28290094/evaluating-the-calling-performance-of-a-rare-disease-ngs-panel-for-single-nucleotide-and-copy-number-variants
#13
P Cacheiro, A Ordóñez-Ugalde, B Quintáns, S Piñeiro-Hermida, J Amigo, M García-Murias, S I Pascual-Pascual, F Grandas, J Arpa, A Carracedo, M J Sobrido
INTRODUCTION: Variant detection protocols for clinical next-generation sequencing (NGS) need application-specific optimization. Our aim was to analyze the performance of single nucleotide variant (SNV) and copy number (CNV) detection programs on an NGS panel for a rare disease. METHODS: Thirty genes were sequenced in 83 patients with hereditary spastic paraplegia. The variant calls obtained with LifeScope, GATK UnifiedGenotyper and GATK HaplotypeCaller were compared with Sanger sequencing...
March 13, 2017: Molecular Diagnosis & Therapy
https://www.readbyqxmd.com/read/28289850/neurophysiological-correlates-of-attentional-fluctuation-in-attention-deficit-hyperactivity-disorder
#14
Celeste H M Cheung, Gráinne McLoughlin, Daniel Brandeis, Tobias Banaschewski, Philip Asherson, Jonna Kuntsi
Cognitive performance in attention-deficit/hyperactivity disorder (ADHD) is characterised, in part, by frequent fluctuations in response speed, resulting in high reaction time variability (RTV). RTV captures a large proportion of the genetic risk in ADHD but, importantly, is malleable, improving significantly in a fast-paced, rewarded task condition. Using the temporal precision offered by event-related potentials (ERPs), we aimed to examine the neurophysiological measures of attention allocation (P3 amplitudes) and preparation (contingent negative variation, CNV), and their associations with the fluctuating RT performance and its improvement in ADHD...
March 14, 2017: Brain Topography
https://www.readbyqxmd.com/read/28285357/alternative-outcomes-of-pathogenic-complex-somatic-structural-variations-in-the-genomes-of-nf1-and-nf2-patients
#15
Meng-Chang Hsiao, Arkadiusz Piotrowski, Andrzej Brunon Poplawski, Tom Callens, Chuanhua Fu, Ludwine Messiaen
Multiplex ligation-dependent probe amplification (MLPA) has been widely used to identify copy-number variations (CNVs), but MLPA's sensitivity and specificity in mosaic CNV detection are largely unknown. Here, we present two mosaic deletions identified by MLPA as NF1 deletion of exons 17-21 and NF2 deletion of exons 9-10. Through cDNA analysis, genomic breakpoint-spanning PCR and Sanger sequencing, we found however both NF1 and NF2 deletions are each composed of two consecutive deletions, which cannot be differentiated by MLPA...
March 11, 2017: Neurogenetics
https://www.readbyqxmd.com/read/28284480/copy-number-variations-found-in-patients-with-a-corpus-callosum-abnormality-and-intellectual-disability
#16
Solveig Heide, Boris Keren, Thierry Billette de Villemeur, Sandra Chantot-Bastaraud, Christel Depienne, Caroline Nava, Cyril Mignot, Aurélia Jacquette, Eric Fonteneau, Elodie Lejeune, Corinne Mach, Isabelle Marey, Sandra Whalen, Didier Lacombe, Sophie Naudion, Caroline Rooryck, Annick Toutain, Cédric Le Caignec, Damien Haye, Laurence Olivier-Faivre, Alice Masurel-Paulet, Christel Thauvin-Robinet, Fabien Lesne, Anne Faudet, Dorothée Ville, Vincent des Portes, Damien Sanlaville, Jean-Pierre Siffroi, Marie-Laure Moutard, Delphine Héron
OBJECTIVE: To evaluate the role that chromosomal micro-rearrangements play in patients with both corpus callosum abnormality and intellectual disability, we analyzed copy number variations (CNVs) in patients with corpus callosum abnormality/intellectual disability STUDY DESIGN: We screened 149 patients with corpus callosum abnormality/intellectual disability using Illumina SNP arrays. RESULTS: In 20 patients (13%), we have identified at least 1 CNV that likely contributes to corpus callosum abnormality/intellectual disability phenotype...
March 8, 2017: Journal of Pediatrics
https://www.readbyqxmd.com/read/28282700/-choroidal-neovascularisation-other-than-typical-neovascular-age-related-macular-degeneration
#17
D Sandner
Choroidal neovascularisation (CNV) in the context of exsudative age-related macular degeneration (nAMD) can be divided into type 1 (occult) and type 2 (classical) membranes. Retinal angiomatous proliferation (RAP) or polypoidal choroidal vasculopathy (PCV) are "rare subtypes" of chorioretinal neovascularisation and are distinguished by their distinct morphology and the sometimes worse response to therapy. Chorioretinal anastomosis, severe exsudates with serosanguinous pigment epithelial detachment and, in PCV, orange-red lesions in the papillomacular bundle can be diagnostic...
March 10, 2017: Klinische Monatsblätter Für Augenheilkunde
https://www.readbyqxmd.com/read/28279756/analysis-of-ccr5-gene-polymorphisms-in-321-healthy-saudis-using-next-generation-sequencing
#18
Mohammed A Al Balwi, Ali I Hadadi, Wardah Alharbi, Mariam Ballow, Abdulrahman AlAsiri, Abdulkareem AlAbdulrahman, Udayaraja G K, Mohammed Aldrees, Ibrahim AlAbdulkareem, Ali H Hajeer
AIMS: To investigate the extent of CCR5 polymorphism in the healthy Saudi population. METHOD: A total of 321 healthy Saudi individuals were sequenced using the ion Ampliseq™ Exome kit (Life Technologies, USA) on genomic DNA following manufacturer's protocol. Whole Exome Sequencing (WES) reads were aligned to the human reference genome (hg19 build) with Torrent Suite Software (v5.0.2) and the variants were called using the Torrent Variant Caller plugin (v5.0) and imported into Ion Reporter Server (v5...
March 7, 2017: Human Immunology
https://www.readbyqxmd.com/read/28278507/improved-visual-outcome-and-low-recurrence-with-early-treatment-with-intravitreal-anti-vascular-endothelial-growth-factor-in-myopic-choroidal-neovascularization
#19
Byung Gil Moon, Ah Ran Cho, Junyeop Lee, Yoon Jeon Kim, Joo Yong Lee, June-Gone Kim, Young Hee Yoon
PURPOSE: The aim of this study was to determine the correlation between the duration of myopic choroidal neovascularization (CNV) and treatment outcome after anti-vascular endothelial growth factor (VEGF) injections. METHODS: We performed a retrospective review of treatment-naïve myopic CNV patients who were treated with anti-VEGF and followed for at least 24 months to identify factors predicting final outcome and recurrence. RESULTS: Among 106 eyes, a shorter duration of CNV was a significant predictor of a better final best-corrected visual acuity, even after controlling for other factors (p = 0...
March 10, 2017: Ophthalmologica. Journal International D'ophtalmologie
https://www.readbyqxmd.com/read/28273317/automated-quantitation-of-choroidal-neovascularization-a-comparison-study-between-spectral-domain-and-swept-source-oct-angiograms
#20
Qinqin Zhang, Chieh-Li Chen, Zhongdi Chu, Fang Zheng, Andrew Miller, Luiz Roisman, Joao Rafael de Oliveira Dias, Zohar Yehoshua, Karen B Schaal, William Feuer, Giovanni Gregori, Sophie Kubach, Lin An, Paul F Stetson, Mary K Durbin, Philip J Rosenfeld, Ruikang K Wang
Purpose: To compare the lesion sizes of choroidal neovascularization (CNV) imaged with spectral-domain (SD) and swept-source (SS) optical coherence tomography angiography (OCTA) and measured using an automated detection algorithm. Methods: Patients diagnosed with CNV were imaged by SD-OCTA and SS-OCTA systems using 3 × 3-mm and 6 × 6-mm scans. The complex optical microangiography (OMAGC) algorithm was used to generate the OCTA images. Optical coherence tomography A datasets for imaging CNV were derived by segmenting from the outer retina to 8 μm below Bruch's membrane...
March 1, 2017: Investigative Ophthalmology & Visual Science
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