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https://www.readbyqxmd.com/read/29351916/pathways-impacted-by-genomic-alterations-in-pulmonary-carcinoid-tumors
#1
Michael K Asiedu, Charles F Thomas, Jie Dong, Sandra C Schulte Tomaszek, Prasidda Khadka, Zhifu Sun, Farhad Kosari, Jin Jen, Julian R Molina, George Vasmatzis, Rui Kuang, Marie Christine Aubry, Ping Yang, Dennis A Wigle
PURPOSE: Pulmonary carcinoid tumors account for up to 5% of all lung malignancies in adults, comprise 30% of all carcinoid malignancies, and are defined histologically as typical carcinoid (TC) and atypical carcinoid (AC) tumors. The role of specific genomic alterations in the pathogenesis of pulmonary carcinoid tumors remains poorly understood. We sought to identify genomic alterations and pathways that are deregulated in these tumors to find novel therapeutic targets for pulmonary carcinoid tumors...
January 19, 2018: Clinical Cancer Research: An Official Journal of the American Association for Cancer Research
https://www.readbyqxmd.com/read/29351407/pedf-expression-affects-the-oxidative-and-inflammatory-state-of-choroidal-endothelial-cells
#2
Mitra Farnoodian, Christine M Sorenson, Nader Sheibani
Age related macular degeneration (AMD) is the leading cause of vision loss among the elderly population, and is associated with severe macular degeneration and choroidal neovascularization (CNV). Although the pathogenesis of AMD is associated with choroidal dysfunction and CNV, the detailed underlying mechanisms remain unresolved. Altered production of pigment epithelium derived factor (PEDF), a neuroprotective and anti-angiogenic factor, contributes to CNV. Furthermore, exogenous PEDF mitigates angiogenesis in preclinical CNV models...
January 10, 2018: American Journal of Physiology. Cell Physiology
https://www.readbyqxmd.com/read/29350689/safety-of-intravitreal-injection-of-ranibizumab-in-early-pregnancy-a-series-of-three-cases
#3
P Fossum, C Couret, B Briend, M Weber, L Lagarce
PurposeRanibizumab is used in the treatment of choroidal neovascularization (CNV). Although systemic exposure to ranibizumab is low after ocular administration, its mechanism of action must be regarded as potentially teratogenic and embryo-fetotoxic. Women are advised to wait 3 months after the last dose of treatment with ranibizumab before conceiving. Little is known about the fetal side-effects of this drug.MethodsThree pregnant women were treated with ranibizumab. One patient had idiopathic CNV.ResultsAfter receiving injections at 10 and 21 weeks after her last menstrual period (LMP), she gave birth to a healthy child...
January 19, 2018: Eye
https://www.readbyqxmd.com/read/29346644/genome-wide-analysis-of-disease-progression-in-age-related-macular-degeneration
#4
Qi Yan, Ying Ding, Yi Liu, Tao Sun, Lars G Fritsche, Traci Clemons, Rinki Ratnapriya, Michael L Klein, Richard J Cook, Yu Liu, Ruzong Fan, Lai Wei, Gonçalo R Abecasis, Anand Swaroop, Emily Y Chew, Daniel E Weeks, Wei Chen
Family- and population-based genetic studies have successfully identified multiple disease-susceptibility loci for Age-related Macular Degeneration (AMD), one of the first batch and most successful examples of genome-wide association study (GWAS). However, most genetic studies to date have focused on case-control studies of late AMD (choroidal neovascularization [CNV] or geographic atrophy [GA]). The genetic influences on disease progression are largely unexplored. We assembled unique resources to perform a genome-wide bivariate time-to-event analysis to test for association of time-to-late-AMD with ∼9 million variants on 2,721 Caucasians from a large multi-center randomized clinical trial, the Age-Related Eye Disease Study...
January 15, 2018: Human Molecular Genetics
https://www.readbyqxmd.com/read/29346103/wavedec-a-wavelet-approach-to-identify-both-shared-and-individual-patterns-of-copy-number-variations
#5
Hongmin Cai, Peihua Chen, Jiazhou Chen, Jiulun Cai, Yan Song, Guoqiang Han
Copy-number variations (CNVs) are associated with complex diseases and particular tumor types. Array-based comparative genomic hybridization (aCGH) is a common approach for the detection of CNVs. Traditional CNV detection methods for multiple aCGH samples mainly use batch samples to find common variations, not accounting for the individual characteristics of each sample. Accurately differentiating both the commonly shared and the individual CNV patterns is pivotal to identify cell populations, or to distinguish cell growth (as in cancer) from invasion of new cells...
February 2018: IEEE Transactions on Bio-medical Engineering
https://www.readbyqxmd.com/read/29342086/copy-number-variation-in-sox6-contributes-to-chicken-muscle-development
#6
Shudai Lin, Xiran Lin, Zihao Zhang, Mingya Jiang, Yousheng Rao, Qinghua Nie, Xiquan Zhang
Copy number variations (CNVs), which cover many functional genes, are associated with complex diseases, phenotypic diversity and traits that are economically important to raising chickens. The sex-determining region Y-box 6 (Sox6) plays a key role in fast-twitch muscle fiber differentiation of zebrafish and mice, but it is still unknown whether SOX6 plays a role in chicken skeletal muscle development. We identified two copy number polymorphisms (CNPs) which were significantly related to different traits on the genome level in chickens by AccuCopy® and CNVplex® analyses...
January 17, 2018: Genes
https://www.readbyqxmd.com/read/29339441/allele-specific-droplet-digital-pcr-combined-with-a-next-generation-sequencing-based-algorithm-for-diagnostic-copy-number-analysis-in-genes-with-high-homology-proof-of-concept-using-stereocilin
#7
Sami S Amr, Elissa Murphy, Elizabeth Duffy, Rojeen Niazi, Jorune Balciuniene, Minjie Luo, Heidi L Rehm, Ahmad N Abou Tayoun
BACKGROUND: Copy number variants (CNVs) can substantially contribute to the pathogenic variant spectrum in several disease genes. The detection of this type of variant is complicated in genes with high homology to other genomic sequences, yet such genomics regions are more likely to lead to CNVs, making it critical to address detection in these settings. METHODS: We developed a copy number analysis approach for high homology genes/regions that consisted of next-generation sequencing (NGS)-based dosage analysis accompanied by allele-specific droplet digital PCR (ddPCR) confirmatory testing...
January 16, 2018: Clinical Chemistry
https://www.readbyqxmd.com/read/29339063/evolution-of-intravitreal-therapy-for-retinal-diseases-from-cmv-to-cnv-the-lxxiv-edward-jackson-memorial-lecture
#8
Daniel F Martin
PURPOSE: To present the evolution of intravitreal therapy for retinal diseases and its impact on clinical practice. DESIGN: Retrospective literature review and personal perspective. METHODS: Retrospective literature review and personal perspective. RESULTS: Pharmacotherapeutic advances in retinal disease have been remarkable over the last 25 years. Almost all of the new drugs developed have required intravitreal administration to be highly effective, leading to an exponential increase in the annual number of intravitreal injections given...
January 12, 2018: American Journal of Ophthalmology
https://www.readbyqxmd.com/read/29331932/cnv-biology-in-neurodevelopmental-disorders
#9
REVIEW
Toru Takumi, Kota Tamada
Copy number variants (CNVs), characterized in recent years by cutting-edge technology, add complexity to our knowledge of the human genome. CNVs contribute not only to human diversity but also to different kinds of diseases including neurodevelopmental delay, autism spectrum disorder and neuropsychiatric diseases. Interestingly, many pathogenic CNVs are shared among these diseases. Studies suggest that pathophysiology of disease may not be simply attributed to a single driver gene within a CNV but also that multifactorial effects may be important...
January 10, 2018: Current Opinion in Neurobiology
https://www.readbyqxmd.com/read/29325733/associations-of-gbp2-gene-copy-number-variations-with-growth-traits-and-transcriptional-expression-in-chinese-cattle
#10
REVIEW
Gui-Min Zhang, Li Zheng, Hua He, Cheng-Chuang Song, Zi-Jing Zhang, Xiu-Kai Cao, Chu-Zhao Lei, Xian-Yong Lan, Xing-Lei Qi, Hong Chen, Yong-Zhen Huang
Copy number variations (CNVs) recently have been recognized as another important genetic variability followed single nucleotide polymorphisms (SNPs). The guanylate binding protein 2 (GBP2) gene plays an important role in cell proliferation. This study was performed to determine the presence of GBP2 CNV (relative to Angus cattle) in 466 individuals representing six main cattle breeds from China, identify its relationship with growth, and explore the biological effects of gene expression. There were two CNV regions in the GBP2 gene, for three types, CNV1 loss type (relative to Angus cattle) was more frequent in XN than other breeds, and CNV2 loss type (relative to Angus cattle) was more frequent in XN and CDM than other breeds...
January 8, 2018: Gene
https://www.readbyqxmd.com/read/29315303/genome-wide-comparison-of-ethiopian-leishmania-donovani-strains-reveals-differences-potentially-related-to-parasite-survival
#11
Arie Zackay, James A Cotton, Mandy Sanders, Asrat Hailu, Abedelmajeed Nasereddin, Alon Warburg, Charles L Jaffe
Leishmania donovani is the main cause of visceral leishmaniasis (VL) in East Africa. Differences between northern Ethiopia/Sudan (NE) and southern Ethiopia (SE) in ecology, vectors, and patient sensitivity to drug treatment have been described, however the relationship between differences in parasite genotype between these two foci and phenotype is unknown. Whole genomic sequencing (WGS) was carried out for 41 L. donovani strains and clones from VL and VL/HIV co-infected patients in NE (n = 28) and SE (n = 13)...
January 9, 2018: PLoS Genetics
https://www.readbyqxmd.com/read/29312620/copy-number-variations-in-atypical-fibroxanthomas-and-pleomorphic-dermal-sarcomas
#12
Doris Helbig, Alexander Quaas, Cornelia Mauch, Sabine Merkelbach-Bruse, Reinhard Büttner, Michael Emberger, Marion Wobser, Vanessa Rüsseler, Katharina Pütz, Elke Binot, Jan Rehker, Jan Budczies, Michaela Angelika Ihle
Atypical fibroxanthomas (AFX) and pleomorphic dermal sarcomas (PDS) are frequent cutaneous sarcomas typically arising on sun-exposed skin in elderly patients. In contrast to AFX, which generally do not recur after complete excision, PDS locally recur in up to 50% and metastasize in up to 20%. We recently detected characteristic UV-induced TP53 mutations as potential driver mutation in almost all PDS investigated as well as activating PIK3CA and RAS gene mutations in around one third of our tumors representing targets for personalized treatments in patients with unresectable or metastasized PDS...
December 12, 2017: Oncotarget
https://www.readbyqxmd.com/read/29312578/integrated-analysis-of-chromosome-copy-number-variation-and-gene-expression-in-cervical-carcinoma
#13
Deng Yan, Song Yi, Wang Chi Chiu, Liu Gui Qin, Wong Hoi Kin, Chung Tony Kwok Hung, Han Linxiao, Choy Kwong Wai, Sui Yi, Yang Tao, Tang Tao
Objective: This study was conducted to explore chromosomal copy number variations (CNV) and transcript expression and to examine pathways in cervical pathogenesis using genome-wide high resolution microarrays. Methods: Genome-wide chromosomal CNVs were investigated in 6 cervical cancer cell lines by Human Genome CGH Microarray Kit (4x44K). Gene expression profiles in cervical cancer cell lines, primary cervical carcinoma and normal cervical epithelium tissues were also studied using the Whole Human Genome Microarray Kit (4x44K)...
December 12, 2017: Oncotarget
https://www.readbyqxmd.com/read/29304372/a-comprehensive-workflow-for-read-depth-based-identification-of-copy-number-variation-from-whole-genome-sequence-data
#14
Brett Trost, Susan Walker, Zhuozhi Wang, Bhooma Thiruvahindrapuram, Jeffrey R MacDonald, Wilson W L Sung, Sergio L Pereira, Joe Whitney, Ada J S Chan, Giovanna Pellecchia, Miriam S Reuter, Si Lok, Ryan K C Yuen, Christian R Marshall, Daniele Merico, Stephen W Scherer
A remaining hurdle to whole-genome sequencing (WGS) becoming a first-tier genetic test has been accurate detection of copy-number variations (CNVs). Here, we used several datasets to empirically develop a detailed workflow for identifying germline CNVs >1 kb from short-read WGS data using read depth-based algorithms. Our workflow is comprehensive in that it addresses all stages of the CNV-detection process, including DNA library preparation, sequencing, quality control, reference mapping, and computational CNV identification...
January 4, 2018: American Journal of Human Genetics
https://www.readbyqxmd.com/read/29304262/prn-ranibizumab-in-the-treatment-of-choroidal-neovascularization-secondary-to-ocular-histoplasmosis
#15
Edward H Wood, Ryan J Whitted, Thomas W Stone, Ricky D Isernhagen, William J Wood, Diana M Holcomb, John W Kitchens
BACKGROUND AND OBJECTIVE: Ranibizumab (Lucentis; Genentech, South San Francisco, CA) is used off-label for the treatment of choroidal neovascularization secondary to ocular histoplasmosis syndrome (OHS). This study prospectively evaluates the safety and efficacy of two treatment paradigms utilizing ranibizumab 0.5 mg: one or three initial injections followed by monthly visits with PRN treatment through Month 12. PATIENTS AND METHODS: In this prospective, open-label study, 21 subjects were evaluated monthly and retreated during the pro re nata treatment phase if specific criteria were met, including loss of vision, increase in subretinal fluid, or hemorrhage...
January 1, 2018: Ophthalmic Surgery, Lasers & Imaging Retina
https://www.readbyqxmd.com/read/29303791/role-of-dna-copy-number-variation-in-dyslipidemias
#16
Michael A Iacocca, Robert A Hegele
PURPOSE OF REVIEW: DNA copy number variations (CNVs) are quantitative structural rearrangements that include deletions, duplications, and higher order amplifications. Because of technical limitations, the contribution of this common form of genetic variation to regulation of lipid metabolism and dyslipidemia has been underestimated. RECENT FINDINGS: Recent literature involving CNVs and dyslipidemias has focused mainly on rare CNVs causing familial hypercholesterolemia, and a common CNV polymorphism as the major determinant of lipoprotein(a) plasma concentrations...
January 4, 2018: Current Opinion in Lipidology
https://www.readbyqxmd.com/read/29303152/response-of-central-serous-chorioretinopathy-evaluated-by-multimodal-retinal-imaging
#17
R Sacconi, G Baldin, A Carnevali, L Querques, A Rabiolo, G Marchini, F Bandello, G Querques
PurposeTo identify predictive biomarkers of treatment outcomes by multimodal retinal imaging in patients affected by central serous chorioretinopathy (CSC).Patients and methodsIn this interventional non-randomized clinical study, 27 treatment-naive CSC patients were prospectively enrolled and treated with oral eplerenone for 5-13 weeks. Primary outcomes included presence of pathological findings on indocyaine green angiography (ICGA), structural optical coherence tomography (OCT) and OCT-angiography (OCT-A) at baseline associated with different response to the treatment...
January 5, 2018: Eye
https://www.readbyqxmd.com/read/29301231/apolipoprotein-m-inhibits-angiogenic-and-inflammatory-response-by-sphingosine-1-phosphate-on-retinal-pigment-epithelium-cells
#18
Ryo Terao, Megumi Honjo, Makoto Aihara
Sphingosine 1-phosphate (S1P) is a potent lipid mediator that modulates inflammatory responses and proangiogenic factors. It has been suggested that S1P upregulates choroidal neovascularization (CNV) and may be deeply involved in the pathogenesis of exudative age-related macular degeneration (AMD). Recent studies have suggested that apolipoprotein M (ApoM), a carrier protein for S1P, modulates the biological properties of S1P in the pathogenesis of atherosclerosis. However, the role of ApoM/S1P in AMD has not been explored...
December 31, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/29297312/generation-of-megabase-scale-deletions-inversions-and-duplications-involving-the-contactin-6-gene-in-mice-by-crispr-cas9-technology
#19
Alexei N Korablev, Irina A Serova, Oleg L Serov
BACKGROUND: Copy Number Variation (CNV) of the human CNTN6 gene (encoding the contactin-6 protein), caused by deletions or duplications, is responsible for severe neurodevelopmental impairments, often in combination with facial dysmorphias. Conversely, deleterious point mutations of this gene do not show any clinical phenotypes. The aim of this study is to generate mice carrying large deletions, duplications and inversions involving the Cntn6 gene as a new experimental model to study CNV of the human CNTN6 locus...
December 28, 2017: BMC Genetics
https://www.readbyqxmd.com/read/29297200/utility-of-chromosomal-microarray-in-anomalous-fetuses
#20
Jacqueline G Parchem, Teresa N Sparks, Kristen Gosnell, Mary E Norton
OBJECTIVE: To determine the association of copy number variants (CNV) with perinatal outcomes among fetuses with sonographic abnormalities. METHODS: This was a retrospective cohort study of anomalous fetuses evaluated at a single fetal center, who underwent chromosomal microarray (CMA) testing. Pathogenic CNV or variants of uncertain significance (VUS) were classified as abnormal. The primary outcome of perinatal death was compared among fetuses with normal versus abnormal CMA...
January 3, 2018: Prenatal Diagnosis
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