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https://www.readbyqxmd.com/read/29792937/a-reliable-targeted-next-generation-sequencing-strategy-for-diagnosis-of-myopathies-and-muscular-dystrophies-especially-for-the-giant-titin-and-nebulin-genes
#1
Reda Zenagui, Delphine Lacourt, Henri Pegeot, Kevin Yauy, Raul Juntas Morales, Corine Theze, François Rivier, Claude Cances, Guilhem Sole, Dimitri Renard, Ulrike Walther-Louvier, Xavier Ferrer-Monasterio, Caroline Espil, Marie-Christine Arné-Bes, Pascal Cintas, Emmanuelle Uro-Coste, Marie-Laure Martin Negrier, Valérie Rigau, Eric Bieth, Cyril Goizet, Mireille Claustres, Michel Koenig, Mireille Cossée
Myopathies and muscular dystrophies (M-MDs) are genetically heterogeneous diseases, with more than 100 identified genes, including the giant and complex titin (TTN) and nebulin (NEB) genes. Next-generation sequencing technology revolutionized M-MD diagnosis and revealed high frequency of TTN and NEB variants. We developed a next-generation sequencing diagnostic strategy targeted on the coding sequences of 135 M-MD genes. Comparison of two targeted capture technologies (SeqCap EZ Choice library capture kit (Roche-Nimblegen) and Nextera Rapid Capture Custom Enrichment kit (Illumina)) and of two whole exome sequencing kits (SureSelect V5 (Agilent) and TruSeq RapidExome capture (Illumina)) revealed best coverage with the SeqCap EZ Choice protocol...
May 21, 2018: Journal of Molecular Diagnostics: JMD
https://www.readbyqxmd.com/read/29791457/a-feasibility-study-of-colorectal-cancer-diagnosis-via-circulating-tumor-dna-derived-cnv-detection
#2
Bhuvan Molparia, Glenn Oliveira, Jennifer L Wagner, Emily G Spencer, Ali Torkamani
Circulating tumor DNA (ctDNA) has shown great promise as a biomarker for early detection of cancer. However, due to the low abundance of ctDNA, especially at early stages, it is hard to detect at high accuracies while keeping sequencing costs low. Here we present a pilot stage study to detect large scale somatic copy numbers variations (CNVs), which contribute more molecules to ctDNA signal compared to point mutations, via cell free DNA sequencing. We show that it is possible to detect somatic CNVs in early stage colorectal cancer (CRC) patients and subsequently discriminate them from normal patients...
2018: PloS One
https://www.readbyqxmd.com/read/29789371/identification-of-new-risk-factors-for-rolandic-epilepsy-cnv-at-xp22-31-and-alterations-at-cholinergic-synapses
#3
Laura Addis, William Sproviero, Sanjeev V Thomas, Roberto H Caraballo, Stephen J Newhouse, Kumudini Gomez, Elaine Hughes, Maria Kinali, David McCormick, Siobhan Hannan, Silvia Cossu, Jacqueline Taylor, Cigdem I Akman, Steven M Wolf, David E Mandelbaum, Rajesh Gupta, Rick A van der Spek, Dario Pruna, Deb K Pal
BACKGROUND: Rolandic epilepsy (RE) is the most common genetic childhood epilepsy, consisting of focal, nocturnal seizures and frequent neurodevelopmental impairments in speech, language, literacy and attention. A complex genetic aetiology is presumed in most, with monogenic mutations in GRIN2A accounting for >5% of cases. OBJECTIVE: To identify rare, causal CNV in patients with RE. METHODS: We used high-density SNP arrays to analyse the presence of rare CNVs in 186 patients with RE from the UK, the USA, Sardinia, Argentina and Kerala, India...
May 22, 2018: Journal of Medical Genetics
https://www.readbyqxmd.com/read/29788921/signatures-of-host-specialization-and-a-recent-transposable-element-burst-in-the-dynamic-one-speed-genome-of-the-fungal-barley-powdery-mildew-pathogen
#4
Lamprinos Frantzeskakis, Barbara Kracher, Stefan Kusch, Makoto Yoshikawa-Maekawa, Saskia Bauer, Carsten Pedersen, Pietro D Spanu, Takaki Maekawa, Paul Schulze-Lefert, Ralph Panstruga
BACKGROUND: Powdery mildews are biotrophic pathogenic fungi infecting a number of economically important plants. The grass powdery mildew, Blumeria graminis, has become a model organism to study host specialization of obligate biotrophic fungal pathogens. We resolved the large-scale genomic architecture of B. graminis forma specialis hordei (Bgh) to explore the potential influence of its genome organization on the co-evolutionary process with its host plant, barley (Hordeum vulgare). RESULTS: The near-chromosome level assemblies of the Bgh reference isolate DH14 and one of the most diversified isolates, RACE1, enabled a comparative analysis of these haploid genomes, which are highly enriched with transposable elements (TEs)...
May 22, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29783949/gene-copy-number-variation-in-natural-populations-of-plasmodium-falciparum-in-eastern-africa
#5
Joan Simam, Martin Rono, Joyce Ngoi, Mary Nyonda, Sachel Mok, Kevin Marsh, Zbynek Bozdech, Margaret Mackinnon
BACKGROUND: Gene copy number variants (CNVs), which consist of deletions and amplifications of single or sets of contiguous genes, contribute to the great diversity in the Plasmodium falciparum genome. In vitro studies in the laboratory have revealed their important role in parasite fitness phenotypes such as red cell invasion, transmissibility and cytoadherence. Studies of natural parasite populations indicate that CNVs are also common in the field and thus may facilitate adaptation of the parasite to its local environment...
May 21, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29783821/-clinical-and-genetic-analysis-of-eleven-pediatric-patients-with-alagille-syndrome
#6
L Guo, S T Zhao, Y Cheng, M Deng, H Li, Y Z Song, X R Cai, Q Zhou
Objective: To explore the clinical and molecular genetic features of patients with Alagille syndrome (AS). Methods: The clinical data of eleven pediatric patients, who were suspected to have AS at the Department of Pediatrics in the First Affiliated Hospital of Jinan University from August 2010 to March 2017, were collected and analyzed. Genomic DNA was extracted from peripheral blood leukocytes of the patients and their parents. For 5 patients collected before March 2006, all JAG1 exons and their flanking sequences were directly sequenced...
May 2, 2018: Zhonghua Er Ke za Zhi. Chinese Journal of Pediatrics
https://www.readbyqxmd.com/read/29780227/neurophysiologic-tests-screening-cognitive-impairment-in-idiopathic-intracranial-hypertension-patients
#7
Iman A Elbanhawy, Gihan M Ramzy, Mye A Basheer, Diana M Khedr
Background: Idiopathic intracranial hypertension (IIH) is a disorder with increased intracranial pressure of obscure cause. Patients with IIH may suffer from difficulty in thinking or concentrating. This work aimed at highlighting the neurophysiologic suggestions of cognitive impairment in IIH patients. Methods: Twenty patients with IIH-and a similar number of matched control subjects-were examined in this case-control study. The P300 and contingent negative variation (CNV) were performed...
2018: The Egyptian journal of neurology, psychiatry and neurosurgery
https://www.readbyqxmd.com/read/29778275/quantifying-the-effects-of-16p11-2-copy-number-variants-on-brain-structure-a-multisite-genetic-first-study
#8
Sandra Martin-Brevet, Borja Rodríguez-Herreros, Jared A Nielsen, Clara Moreau, Claudia Modenato, Anne M Maillard, Aurélie Pain, Sonia Richetin, Aia E Jønch, Abid Y Qureshi, Nicole R Zürcher, Philippe Conus, Wendy K Chung, Elliott H Sherr, John E Spiro, Ferath Kherif, Jacques S Beckmann, Nouchine Hadjikhani, Alexandre Reymond, Randy L Buckner, Bogdan Draganski, Sébastien Jacquemont
BACKGROUND: 16p11.2 breakpoint 4 to 5 copy number variants (CNVs) increase the risk for developing autism spectrum disorder, schizophrenia, and language and cognitive impairment. In this multisite study, we aimed to quantify the effect of 16p11.2 CNVs on brain structure. METHODS: Using voxel- and surface-based brain morphometric methods, we analyzed structural magnetic resonance imaging collected at seven sites from 78 individuals with a deletion, 71 individuals with a duplication, and 212 individuals without a CNV...
March 27, 2018: Biological Psychiatry
https://www.readbyqxmd.com/read/29776329/convaq-a-web-tool-for-copy-number-variation-based-association-studies
#9
Simon Jonas Larsen, Luisa Matos do Canto, Silvia Regina Rogatto, Jan Baumbach
BACKGROUND: Copy number variations (CNVs) are large segments of the genome that are duplicated or deleted. Structural variations in the genome have been linked to many complex diseases. Similar to how genome-wide association studies (GWAS) have helped discover single-nucleotide polymorphisms linked to disease phenotypes, the extension of GWAS to CNVs has aided the discovery of structural variants associated with human traits and diseases. RESULTS: We present CoNVaQ, an easy-to-use web-based tool for CNV-based association studies...
May 18, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29774977/a-novel-4q25-microdeletion-encompassing-pitx2-associated-with-rieger-syndrome
#10
Yi Yang, Xin Wang, Yuming Zhao, Man Qin
OBJECTIVE: Rieger syndrome (RS) is a genetic disorder characterized by abnormal development of the eyes, teeth, and umbilicus, and the paired like homeodomain 2 (PITX2) gene is often implicated in its pathogenesis. The present study aimed to identify the underlying genetic defect in a Chinese patient with RS. SUBJECTS AND METHODS: DNA samples were screened for PITX2 gene mutations and copy number variations (CNVs) using Sanger sequencing and quantitative genomic PCR analysis (qPCR)...
May 18, 2018: Oral Diseases
https://www.readbyqxmd.com/read/29772047/swept-source-oct-angiography-identifies-choroidal-neovascularization-arising-from-a-choroidal-nevus
#11
Abed Namavari, Fang Zheng, Elie H Motulsky, João R de Oliveira Dias, Giovanni Gregori, Philip J Rosenfeld
Swept-source optical coherence tomography angiography (SS-OCTA) was used to diagnose choroidal neovascularization (CNV) arising from a choroidal nevus. A 61-year-old woman initially presented with submacular hemorrhage. She was diagnosed with neovascular age-related macular degeneration (AMD) and received three injections of bevacizumab (Avastin; Genentech, South San Francisco, CA). At a follow-up visit, SS-OCTA showed that the CNV appeared to arise from an adjacent choroidal nevus. This is the first report of using SS-OCTA to diagnose CNV associated with a choroidal nevus masquerading as neovascular AMD...
May 1, 2018: Ophthalmic Surgery, Lasers & Imaging Retina
https://www.readbyqxmd.com/read/29772044/a-phase-1-open-label-dose-escalation-trial-to-investigate-safety-and-tolerability-of-single-intravitreous-injections-of-icon-1-targeting-tissue-factor-in-wet-amd
#12
John A Wells, Christine R Gonzales, Brian B Berger, Victor H Gonzalez, Brian D Sippy, Gabriela Burian
BACKGROUND AND OBJECTIVE: This phase 1 study evaluated the safety and tolerability of single intravitreous injections (IVIs) of ICON-1 (Iconic Therapeutics, South San Francisco, CA) in patients with neovascular age-related macular degeneration (nAMD). ICON-1 is a modified factor VIIa protein linked with the Fc portion of a human immunoglobulin G1. The molecule binds tissue factor overexpressed on choroidal neovascularization (CNV) in AMD. PATIENTS AND METHODS: Open-label, interventional, dose-escalation trial in 18 patients with CNV due to AMD, with six patients per dose cohort...
May 1, 2018: Ophthalmic Surgery, Lasers & Imaging Retina
https://www.readbyqxmd.com/read/29769284/dynamic-copy-number-evolution-of-x-and-y-linked-ampliconic-genes-in-human-populations
#13
Elise A Lucotte, Laurits Skov, Jacob Malte Jensen, Moisès Coll Macià, Kasper Munch, Mikkel H Schierup
Ampliconic genes are multicopy, in majority found on sex-chromosomes and enriched for testis-expressed genes. While ampliconic genes have been associated with the emergence of hybrid incompatibilities, we know little about their copy number distribution and their turnover in human populations. Here we explore the evolution of human X- and Y-linked ampliconic genes by investigating copy number variation (CNV) and coding variation between populations using the Simons Genome Diversity Project. We develop a method to assess CNVs using the read-depth on modified X and Y chromosome targets containing only one repetition of each ampliconic gene...
May 16, 2018: Genetics
https://www.readbyqxmd.com/read/29767721/bhd-associated-kidney-cancer-exhibits-unique-molecular-characteristics-and-a-wide-variety-of-variants-in-chromatin-remodeling-genes
#14
Hisashi Hasumi, Mitsuko Furuya, Kenji Tatsuno, Shogo Yamamoto, Masaya Baba, Yukiko Hasumi, Yasuhiro Isono, Kae Suzuki, Ryosuke Jikuya, Shinji Otake, Kentaro Muraoka, Kimito Osaka, Narihiko Hayashi, Kazuhide Makiyama, Yasuhide Miyoshi, Keiichi Kondo, Noboru Nakaigawa, Takashi Kawahara, Koji Izumi, Junichi Teranishi, Yasushi Yumura, Hiroji Uemura, Yoji Nagashima, Adam R Metwalli, Laura S Schmidt, Hiroyuki Aburatani, W Marston Linehan, Masahiro Yao
Birt-Hogg-Dubé (BHD) syndrome is a hereditary kidney cancer syndrome, which predisposes patients to develop kidney cancer, cutaneous fibrofolliculomas and pulmonary cysts. The responsible gene FLCN is a tumor suppressor for kidney cancer which plays an important role in energy homeostasis through the regulation of mitochondrial oxidative metabolism. However, the process by which FLCN-deficiency leads to renal tumorigenesis is unclear. In order to clarify molecular pathogenesis of BHD-associated kidney cancer, we conducted whole-exome sequencing analysis using next-generation sequencing technology as well as metabolite analysis using LC/MS and GC/MS...
May 14, 2018: Human Molecular Genetics
https://www.readbyqxmd.com/read/29767709/double-hits-in-schizophrenia
#15
Jacob A S Vorstman, Loes M Olde Loohuis, René S Kahn, Roel A Ophoff
The co-occurrence of a Copy Number Variant (CNV) and a functional variant on the other allele may be a relevant genetic mechanism in schizophrenia. We hypothesized that the cumulative burden of such double hits - in particular those composed of a deletion and a coding single nucleotide variation (SNV) - is increased in patients with schizophrenia.We combined CNV data with coding variants data in 795 patients with schizophrenia and 474 controls. To limit false CNV-detection, only CNVs called only by two algorithms we included...
May 14, 2018: Human Molecular Genetics
https://www.readbyqxmd.com/read/29766021/transduction-patterns-of-adeno-associated-viral-vectors-in-a-laser-induced-choroidal-neovascularization-mouse-model
#16
Si Hyung Lee, Ye Seul Kim, Seung Kwan Nah, Hee Jong Kim, Ha Yan Park, Jin Young Yang, Keerang Park, Tae Kwann Park
Adeno-associated virus (AAV) vector is a promising platform technology for ocular gene therapy. Recently clinical successes to treat choroidal neovascularization (CNV) in wet type age-related macular degeneration have been reported. However, because pathologic conditions of the retina may alter the tropism of viral vectors, it is necessary to evaluate the transduction efficiency of different serotypes of AAV vectors in the retinas with CNVs. Here, we show the patterns and efficacy of transduction of AAV2, -5, and -8 vectors in a laser-induced CNV mouse model...
June 15, 2018: Molecular Therapy. Methods & Clinical Development
https://www.readbyqxmd.com/read/29765959/outcome-of-5-year-treatment-of-neovascular-age-related-macular-degeneration-with-intravitreal-anti-vegf-using-treat-and-extend-regimen
#17
Polona Jaki Mekjavic, Polona Zaletel Benda
Objective: The aim of this study is twofold. First , to evaluate the long-term outcome of anti-vascular endothelial growth factor (anti-VEGF) treatment in a clinical setting using the "treat-and-extend regimen" (TER) in patients with neovascular age-related macular degeneration (nAMD). Second , to determine the proportion of patients treated with anti-VEGF with good visual acuity (VA), i.e., vision sufficient to maintain a high level of independence. Design: We conducted a single center retrospective review of patients with treatment-naive nAMD who were treated with anti-VEGF...
2018: Frontiers in Medicine
https://www.readbyqxmd.com/read/29765375/functional-alleles-of-chicken-bg-genes-members-of-the-butyrophilin-gene-family-in-peripheral-t-cells
#18
Lei Chen, Michaela Fakiola, Karen Staines, Colin Butter, Jim Kaufman
γδ T cells recognize a wide variety of ligands in mammals, among them members of the butyrophilin (BTN) family. Nothing is known about γδ T cell ligands in chickens, despite there being many such cells in blood and lymphoid tissues, as well as in mucosal surfaces. The major histocompatibility complex (MHC) of chickens was discovered because of polymorphic BG genes, part of the BTN family. All but two BG genes are located in the BG region, oriented head-to-tail so that unequal crossing-over has led to copy number variation (CNV) as well as hybrid (chimeric) genes, making it difficult to identify true alleles...
2018: Frontiers in Immunology
https://www.readbyqxmd.com/read/29765130/copy-number-variants-implicate-cardiac-function-and-development-pathways-in-earthquake-induced-stress-cardiomyopathy
#19
Cameron J Lacey, Kit Doudney, Paul G Bridgman, Peter M George, Roger T Mulder, Julie J Zarifeh, Bridget Kimber, Murray J Cadzow, Michael A Black, Tony R Merriman, Klaus Lehnert, Vivienne M Bickley, John F Pearson, Vicky A Cameron, Martin A Kennedy
The pathophysiology of stress cardiomyopathy (SCM), also known as takotsubo syndrome, is poorly understood. SCM usually occurs sporadically, often in association with a stressful event, but clusters of cases are reported after major natural disasters. There is some evidence that this is a familial condition. We have examined three possible models for an underlying genetic predisposition to SCM. Our primary study cohort consists of 28 women who suffered SCM as a result of two devastating earthquakes that struck the city of Christchurch, New Zealand, in 2010 and 2011...
May 15, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29763612/topographic-correspondence-of-macular-atrophy-with-choroidal-neovascularization-in-ranibizumab-treated-eyes-of-the-trex-amd-trial
#20
Nizar Saleh Abdelfattah, Amirhossein Hariri, Mayss Al-Sheikh, Sean Pitetta, Adel Ebraheem, Charles C Wykoff, SriniVas R Sadda
PURPOSE: To quantify the extent of topographic correspondence between baseline (BSL) CNV and macular atrophy (MA) at follow-up in eyes with NVAMD. DESIGN: Post hoc analysis of randomized, controlled clinical trial data. METHODS: Sixty treatment-naïve neovascular age-related macular degeneration (NVAMD) patients from TREX-AMD trial were followed for 18-months. Regions of month-18 macular atrophy (MA) were graded on fundus autofluorescence (FAF) with guidance of spectral domain optical coherence tomography (SD-OCT)...
May 12, 2018: American Journal of Ophthalmology
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