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Copy number variation

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https://www.readbyqxmd.com/read/29777458/increased-vitamin-d-receptor-gene-expression-and-rs11568820-and-rs4516035-promoter-polymorphisms-in-autistic-disorder
#1
Burhan Balta, Hakan Gumus, Ruslan Bayramov, Keziban Korkmaz Bayramov, Murat Erdogan, Didem Behice Oztop, Muhammet Ensar Dogan, Serpil Taheri, Munis Dundar
Although there are a large number of sequence variants of different genes and copy number variations at various loci identified in autistic disorder (AD) patients, the pathogenesis of AD has not been elucidated completely. Recently, in AD patients, a large number of expression array and transcriptome studies have shown an increase in the expression of genes especially related to innate immune response. Antimicrobial effects of vitamin D and VDR are exerted through Toll-Like-Receptors (TLR) which have an important role in the innate immune response, are expressed by antigen presenting cells and recognize foreign microorganisms...
May 18, 2018: Molecular Biology Reports
https://www.readbyqxmd.com/read/29777446/the-degree-of-hiv-1-amino-acid-variability-is-strictly-related-to-different-disease-progression-rates
#2
Rossana Scutari, Monica Faieta, Roberta D'Arrigo, Lavinia Fabeni, Cristina Mussini, Andrea Cossarizza, Claudio Casoli, Carlo Federico Perno, Valentina Svicher, Claudia Alteri, Stefano Aquaro
The aim of this study is to evaluate the amino acid variability of HIV-1 Gp41, C2-V3, and Nef in a group of patients characterized by different disease progression rates. HIV-1 sequences were collected from 19 Long term non progressor patients (LTNPs), 9 slow progressors (SPs), and 11 rapid progressors (RPs). Phylogenetic trees were estimated by MEGA 6. Differences in amino acid variability among sequences belonging to the 3 groups have been evaluated by amino acid divergence, Shannon entropy analysis, and the number of amino acid mutations (defined as amino acid variations compared with HxB2)...
May 17, 2018: Virus Genes
https://www.readbyqxmd.com/read/29777105/phenotypic-diversification-by-enhanced-genome-restructuring-after-induction-of-multiple-dna-double-strand-breaks
#3
Nobuhiko Muramoto, Arisa Oda, Hidenori Tanaka, Takahiro Nakamura, Kazuto Kugou, Kazuki Suda, Aki Kobayashi, Shiori Yoneda, Akinori Ikeuchi, Hiroki Sugimoto, Satoshi Kondo, Chikara Ohto, Takehiko Shibata, Norihiro Mitsukawa, Kunihiro Ohta
DNA double-strand break (DSB)-mediated genome rearrangements are assumed to provide diverse raw genetic materials enabling accelerated adaptive evolution; however, it remains unclear about the consequences of massive simultaneous DSB formation in cells and their resulting phenotypic impact. Here, we establish an artificial genome-restructuring technology by conditionally introducing multiple genomic DSBs in vivo using a temperature-dependent endonuclease TaqI. Application in yeast and Arabidopsis thaliana generates strains with phenotypes, including improved ethanol production from xylose at higher temperature and increased plant biomass, that are stably inherited to offspring after multiple passages...
May 18, 2018: Nature Communications
https://www.readbyqxmd.com/read/29776391/the-clinical-implications-of-g1-g6-transcriptomic-signature-and-5-gene-score-in-korean-patients-with-hepatocellular-carcinoma
#4
Sung-Min Ahn, Farhan Haq, Inkeun Park, Jean-Charles Nault, Jessica Zucman-Rossi, Eunsil Yu
BACKGROUND: Efforts have been made to classify Hepatocellular Carcinoma (HCC) at surgically curable stages because molecular classification, which is prognostically informative, can accurately identify patients in need of additional early therapeutic interventions. Recently, HCC classification based French studies on the expression of 16 genes and 5 genes were proposed. In 16-gene classification, transcriptomic signatures (G1-G6) were used to classify HCC patients into clinical, genomic and pathway-specific subgroups...
May 18, 2018: BMC Cancer
https://www.readbyqxmd.com/read/29776329/convaq-a-web-tool-for-copy-number-variation-based-association-studies
#5
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
#6
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/29769526/a-whole-genome-sequence-study-identifies-genetic-risk-factors-for-neuromyelitis-optica
#7
Karol Estrada, Christopher W Whelan, Fengmei Zhao, Paola Bronson, Robert E Handsaker, Chao Sun, John P Carulli, Tim Harris, Richard M Ransohoff, Steven A McCarroll, Aaron G Day-Williams, Benjamin M Greenberg, Daniel G MacArthur
Neuromyelitis optica (NMO) is a rare autoimmune disease that affects the optic nerve and spinal cord. Most NMO patients ( > 70%) are seropositive for circulating autoantibodies against aquaporin 4 (NMO-IgG+). Here, we meta-analyze whole-genome sequences from 86 NMO cases and 460 controls with genome-wide SNP array from 129 NMO cases and 784 controls to test for association with SNPs and copy number variation (total N = 215 NMO cases, 1244 controls). We identify two independent signals in the major histocompatibility complex (MHC) region associated with NMO-IgG+, one of which may be explained by structural variation in the complement component 4 genes...
May 16, 2018: Nature Communications
https://www.readbyqxmd.com/read/29769284/dynamic-copy-number-evolution-of-x-and-y-linked-ampliconic-genes-in-human-populations
#8
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/29769282/inferring-the-probability-of-the-derived-versus-the-ancestral-allelic-state-at-a-polymorphic-site
#9
Peter D Keightley, Benjamin C Jackson
It is known that the allele ancestral to the variation at a polymorphic site cannot be assigned with certainty, and that the most frequently used method to assign the ancestral state - maximum parsimony - is prone to misinference. Estimates of counts of sites that have a certain number of copies of the derived allele in a sample (the unfolded site frequency spectrum, uSFS) made by parsimony are therefore also biased. We previously developed a maximum likelihood method to estimate the uSFS for a focal species using information from two outgroups while assuming simple models of nucleotide substitution...
May 16, 2018: Genetics
https://www.readbyqxmd.com/read/29768630/what-determines-mortality-in-malignant-pheochromocytoma-report-of-a-case-with-eighteen-year-survival-and-review-of-the-literature
#10
Matheus de Oliveira Andrade, Vinícius Santos da Cunha, Dayana Carla de Oliveira, Olívia Laquis de Moraes, Adriana Lofrano-Porto
Pheochromocytoma (PCC) is a tumor derived from adrenomedullary chromaffin cells. Prognosis of malignant PCC is generally poor due to local recurrence or metastasis. We aim to report a case of malignant PCC with 18-year survival and discuss which factors may be related to mortality and long-term survival in malignant pheochromocytoma. The patient, a 45-year-old man, reported sustained arterial hypertension with paroxysmal episodes of tachycardia, associated with head and neck burning sensation, and hand and foot tremors...
March 2018: Archives of Endocrinology and Metabolism
https://www.readbyqxmd.com/read/29767721/bhd-associated-kidney-cancer-exhibits-unique-molecular-characteristics-and-a-wide-variety-of-variants-in-chromatin-remodeling-genes
#11
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
#12
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/29765375/functional-alleles-of-chicken-bg-genes-members-of-the-butyrophilin-gene-family-in-peripheral-t-cells
#13
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/29761117/genomic-analysis-identifies-masqueraders-of-full-term-cerebral-palsy
#14
Yusuke Takezawa, Atsuo Kikuchi, Kazuhiro Haginoya, Tetsuya Niihori, Yurika Numata-Uematsu, Takehiko Inui, Saeko Yamamura-Suzuki, Takuya Miyabayashi, Mai Anzai, Sato Suzuki-Muromoto, Yukimune Okubo, Wakaba Endo, Noriko Togashi, Yasuko Kobayashi, Akira Onuma, Ryo Funayama, Matsuyuki Shirota, Keiko Nakayama, Yoko Aoki, Shigeo Kure
Objective: Cerebral palsy is a common, heterogeneous neurodevelopmental disorder that causes movement and postural disabilities. Recent studies have suggested genetic diseases can be misdiagnosed as cerebral palsy. We hypothesized that two simple criteria, that is, full-term births and nonspecific brain MRI findings, are keys to extracting masqueraders among cerebral palsy cases due to the following: (1) preterm infants are susceptible to multiple environmental factors and therefore demonstrate an increased risk of cerebral palsy and (2) brain MRI assessment is essential for excluding environmental causes and other particular disorders...
May 2018: Annals of Clinical and Translational Neurology
https://www.readbyqxmd.com/read/29760470/breast-cancer-associated-germline-structural-variants-harboring-small-noncoding-rnas-impact-post-transcriptional-gene-regulation
#15
Mahalakshmi Kumaran, Preethi Krishnan, Carol E Cass, Roland Hubaux, Wan Lam, Yutaka Yasui, Sambasivarao Damaraju
Copy Number Variants (CNVs) are a class of structural variations of DNA. Germline CNVs are known to confer disease susceptibility, but their role in breast cancer warrants further investigations. We hypothesized that breast cancer associated germline CNVs contribute to disease risk through gene dosage or other post-transcriptional regulatory mechanisms, possibly through tissue specific expression of CNV-embedded small-noncoding RNAs (CNV-sncRNAs). Our objectives are to identify breast cancer associated CNVs using a genome wide association study (GWAS), identify sncRNA genes embedded within CNVs, confirm breast tissue (tumor and normal) expression of the sncRNAs, correlate their expression with germline copy status and identify pathways influenced by the genes regulated by sncRNAs...
May 14, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29760279/histone-h3k27-methylation-is-required-for-nhej-and-genome-stability-by-modulating-the-dynamics-of-fancd2-on-chromatin
#16
Ye Zhang, Jian-Feng Chang, Jin Sun, Lu Chen, Xiao-Mei Yang, Huan-Yin Tang, Yuan-Ya Jing, Xuan Kang, Zhi-Min He, Jun-Yu Wu, Hui-Min Wei, Da-Liang Wang, Rong-Gang Xu, Rui-Bao Zhu, Ying Shen, Shi-Yang Zeng, Chen Wang, Kui-Nan Liu, Yong Zhang, Zhi-Ying Mao, Ci-Zhong Jiang, Fang-Lin Sun
Dysregulation of homeostatic balance in di- and tri-methyl H3K27 levels or that caused by mis-sense mutations of histone H3 (H3K27M) was reported to be associated with various types of cancers. In this study, we found that reduction in H3K27me2/3 caused by H3.1K27M, a mutation of H3 variants found in DIPG patients, dramatically attenuated the presence of 53BP1 foci and NHEJ repair capability in HDF cells. H3.1K27M cells showed increased rates of genomic insertions/deletions (In/Dels) and copy number variations (CNVs), as well as augmented p53-dependent apoptotic cells...
May 14, 2018: Journal of Cell Science
https://www.readbyqxmd.com/read/29760223/genomic-heterogeneity-and-the-small-renal-mass
#17
Daiki Ueno, Zuoquan Xie, Marta Boeke, Jamil Syed, Kevin A Nguyen, Patrick McGillivray, Adebowale Adeniran, Peter A Humphrey, Garrett M Dancik, Yuval Kluger, Zongzhi Liu, Harriet M Kluger, Brian Shuch
PURPOSE: Tumor heterogeneity may represent a barrier to pre-operative genomic characterization by needle biopsy in clear cell renal cell carcinoma (ccRCC). The extent of heterogeneity in small renal tumors remains unknown. Therefore, we set out to evaluate heterogeneity in resected large and small renal tumors. EXPERIMENTAL DESIGN: We conducted a study from 2013 through 2016, that evaluated 47 consecutive ccRCC tumors resected during radical or partial nephrectomy...
May 14, 2018: Clinical Cancer Research: An Official Journal of the American Association for Cancer Research
https://www.readbyqxmd.com/read/29754608/multiplex-polymerase-chain-reaction-in-combination-with-gel-electrophoresis-inductively-coupled-plasma-mass-spectrometry-a-powerful-tool-for-the-determination-of-gene-copy-number-variations-and-gene-expression-changes
#18
A Fernández Asensio, T Iglesias, A Cotarelo, M Espina, E Blanco-González, L M Sierra, M Montes-Bayón
During the last few years multiplex real-time or quantitative polymerase chain reaction PCR (qPCR) has become the method of choice for multiplex gene expression changes and gene copy number variations (CNVs) analysis. However, such determinations require the use of different fluorescent labels for the different amplified sequences, which increases significantly the costs of the analysis and limits the applicability of the technique for simultaneous amplification of many targets of interest in a single reaction...
September 6, 2018: Analytica Chimica Acta
https://www.readbyqxmd.com/read/29753808/targeted-next-generation-sequencing-for-the-molecular-diagnosis-of-hereditary-angioedema-due-to-c1-inhibitor-deficiency
#19
Gedeon Loules, Maria Zamanakou, Faidra Parsopoulou, Sofia Vatsiou, Fotis Psarros, Dorottya Csuka, Grzegorz Porebski, Krystyna Obtulowicz, Anna Valerieva, Maria Staevska, Alberto López-Lera, Margarita López-Trascasa, Dumitru Moldovan, Markus Magerl, Marcus Maurer, Matthaios Speletas, Henriette Farkas, Anastasios E Germenis
SERPING1 genotyping of subjects suspicious for hereditary angioedema due to C1-INH deficiency (C1-INH-HAE) is important for clinical practice as well as for research reasons. Conventional approaches towards the detection of C1-INH-HAE-associated SERPING1 variants are cumbersome and time-demanding with many pitfalls. To take advantage of the benefits of next-generation sequencing (NGS) technology, we developed and validated a custom NGS platform that, by targeting the entire SERPING1 gene, facilitates genetic testing of C1-INH-HAE patients in clinical practice...
May 10, 2018: Gene
https://www.readbyqxmd.com/read/29753047/chromosomal-microarray-analysis-of-bulgarian-patients-with-epilepsy-and-intellectual-disability
#20
Valentina Peycheva, Kunka Kamenarova, Neviana Ivanova, Dimitar Stamatov, Daniela Avdjieva-Tzavella, Iliana Alexandrova, Sashka Zhelyazkova, Iliana Pacheva, Petya Dimova, Ivan Ivanov, Ivan Litvinenko, Veneta Bozhinova, Ivailo Tournev, Emil Simeonov, Vanyo Mitev, Albena Jordanova, Radka Kaneva
High resolution chromosomal microarray analysis (CMA) has facilitated the identification of small chromosomal rearrangements throughout the genome, associated with various neurodevelopmental phenotypes, including ID/DD. Recently, it became evident that intellectual disability (ID)/developmental delay (DD) can occur with associated co-morbidities like epileptic seizures, autism and additional congenital anomalies. These observations require whole genome approach in order to detect the genetic causes of these complex disorders...
May 9, 2018: Gene
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