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https://www.readbyqxmd.com/read/27919838/a-cgh-array-procedure-to-detect-pax6-gene-structural-defects
#1
Alessandra Franzoni, Patrizia Dello Russo, Federica Baldan, Angela Valentina D'Elia, Cinzia Puppin, Silvana Penco, Giuseppe Damante
Aniridia is a rare congenital disease characterized by eye development defects, in which the more evident clinical manifestation is iris absence or malformation. In most of the patients, aniridia is associated to PAX6 gene point mutations or deletions. When these deletions are large and involve other genes, a more complex disease, named WAGR syndrome, arises. In order to develop a new tool to analyze aniridia and WAGR subjects, a CGH array (CGHa) of the PAX6 genomic region was set up. We generated a custom microarray kit using an oligonucleotide-based platform that allows high resolution molecular profiling of genomic aberrations in 20 Mb of the 11p13 chromosomal region, centered on the PAX6 gene...
December 2, 2016: Molecular and Cellular Probes
https://www.readbyqxmd.com/read/27913243/the-top-five-reasons-you-should-publish-in-cgh
#2
EDITORIAL
Fasiha Kanwal, Hashem El-Serag
No abstract text is available yet for this article.
November 29, 2016: Clinical Gastroenterology and Hepatology
https://www.readbyqxmd.com/read/27910033/cytogenetic-resources-and-information
#3
Etienne De Braekeleer, Jean-Loup Huret, Hossain Mossafa, Philippe Dessen
The main databases devoted stricto sensu to cancer cytogenetics are the "Mitelman Database of Chromosome Aberrations and Gene Fusions in Cancer" ( http://cgap.nci.nih.gov/Chromosomes/Mitelman ), the "Atlas of Genetics and Cytogenetics in Oncology and Haematology" ( http://atlasgeneticsoncology.org ), and COSMIC ( http://cancer.sanger.ac.uk/cosmic ).However, being a complex multistep process, cancer cytogenetics are broadened to "cytogenomics," with complementary resources on: general databases (nucleic acid and protein sequences databases; cartography browsers: GenBank, RefSeq, UCSC, Ensembl, UniProtKB, and Entrez Gene), cancer genomic portals associated with recent international integrated programs, such as TCGA or ICGC, other fusion genes databases, array CGH databases, copy number variation databases, and mutation databases...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27908234/sustained-early-disruption-of-mitochondrial-function-contributes-to-arsenic-induced-prostate-tumorigenesis
#4
B Singh, M Kulawiec, K M Owens, A Singh, K K Singh
Arsenic is a well-known human carcinogen that affects millions of people worldwide, but the underlying mechanisms of carcinogenesis are unclear. Several epidemiological studies have suggested increased prostate cancer incidence and mortality due to exposure to arsenic. Due to lack of an animal model of arsenic-induced carcinogenesis, we used a prostate epithelial cell culture model to identify a role for mitochondria in arsenic-induced prostate cancer. Mitochondrial morphology and membrane potential was impacted within a few hours of arsenic exposure of non-neoplastic prostate epithelial cells...
October 2016: Biochemistry. Biokhimii︠a︡
https://www.readbyqxmd.com/read/27902773/genomic-landscape-of-experimental-bladder-cancer-in-rodents-and-its-application-to-human-bladder-cancer-gene-amplification-and-potential-overexpression-of-cyp2a5-cyp2a6-are-associated-with-the-invasive-phenotype
#5
Kazuhiro Kanemoto, Katsuhiro Fukuta, Noriyasu Kawai, Keiichi Tozawa, Masako Ochiai, Koji Okamoto, Sumiko Ohnami, Hiromi Sakamoto, Teruhiko Yoshida, Yae Kanai, Masaru Katoh, Takahiro Yasui, Kenjiro Kohri, Tadao Kakizoe, Hitoshi Nakagama
Non-muscle invasive (superficial) bladder cancer is a low-grade malignancy with good prognosis, while muscle invasive (invasive) bladder cancer is a high-grade malignancy with poor prognosis. N-butyl-N-(4-hydroxybutyl)nitrosamine (BBN) induces superficial bladder cancers with papillary morphology in rats and invasive bladder cancers with infiltrating phenotype in mice. In this study, we analyzed genomic landscapes of rodent BBN-induced bladder cancers using array-based comparative genomic hybridization (array CGH)...
2016: PloS One
https://www.readbyqxmd.com/read/27890788/genetic-testing-among-spanish-pediatric-neurologists-knowledge-attitudes-and-practices
#6
J Domínguez-Carral, J López-Pisón, A Macaya, M Bueno Campaña, M A García-Pérez, D Natera-de Benito
Advances in genetic testing applied to child neurology have enabled the development of genetic tests with greater sensitivity in elucidating an etiologic diagnosis for common neurological conditions. The objective of the current study was to examine child neurologists' perspectives and insights into genetic testing. We surveyed 118 Spanish child neurologists, exploring their knowledge, attitudes, and practices concerning genetic tests. All of them had requested at least one genetic test in the past six months...
November 25, 2016: European Journal of Medical Genetics
https://www.readbyqxmd.com/read/27889662/pediatric-pineal-germinomas-epigenetic-and-genomic-approach
#7
Monserrat Pérez-Ramírez, Alejo Justino Hernández-Jiménez, Armando Guerrero-Guerrero, Alicia Georgina Siordia-Reyes, Marta Elena Hernández-Caballero, Antonio García-Méndez, Fernando Chico-Ponce de León, Fabio Abdel Salamanca-Gómez, Normand García-Hernández
OBJECTIVE: We identify and correlate chromosomal alterations, methylation patterns and gene expression in pediatric pineal germinomas. METHODS: CGH microarray, methylation and gene expression were performed through the Agilent platform. The results were analyzed with MatLab software, MapViewer, DAVID, GeneCards and Hippie. RESULTS: Amplifications were found in 1q24.2, 1q31.3, 2p11.2, 3p22.2, 7p13, 7p15.2, 8p22, 12p13.2, 14q24.3 y 22q12; and deletions were found in 1q21...
November 19, 2016: Clinical Neurology and Neurosurgery
https://www.readbyqxmd.com/read/27884122/assessment-of-copy-number-variations-in-120-patients-with-poland-syndrome
#8
Carlotta Maria Vaccari, Elisa Tassano, Michele Torre, Stefania Gimelli, Maria Teresa Divizia, Maria Victoria Romanini, Simone Bossi, Ilaria Musante, Maura Valle, Filippo Senes, Nunzio Catena, Maria Francesca Bedeschi, Anwar Baban, Maria Grazia Calevo, Massimo Acquaviva, Margherita Lerone, Roberto Ravazzolo, Aldamaria Puliti
BACKGROUND: Poland Syndrome (PS) is a rare congenital disorder presenting with agenesis/hypoplasia of the pectoralis major muscle variably associated with thoracic and/or upper limb anomalies. Most cases are sporadic, but familial recurrence, with different inheritance patterns, has been observed. The genetic etiology of PS remains unknown. Karyotyping and array-comparative genomic hybridization (CGH) analyses can identify genomic imbalances that can clarify the genetic etiology of congenital and neurodevelopmental disorders...
November 25, 2016: BMC Medical Genetics
https://www.readbyqxmd.com/read/27880066/features-of-kat6b-related-disorders-in-a-patient-with-10q22-1q22-3-deletion
#9
Egle Preiksaitiene, Birutė Tumienė, Živilė Maldžienė, Erinija Pranckevičienė, Aušra Morkūnienė, Algirdas Utkus, Vaidutis Kučinskas
BACKGROUND: Blepharophimosis is a fixed reduction in the vertical distance between the upper and lower eyelids with short palpebral fissures. It is a rare facial malformation and is considered an important diagnostic feature in dysmorphic analysis. It is likely that many patients with blepharophimosis-mental retardation syndrome have submicroscopic chromosomal rearrangements, and the use of molecular karyotyping can narrow the known blepharophimosis-mental retardation-critical regions or clarify the effect of the haploinsufficiency of the involved genes on the phenotype...
November 23, 2016: Ophthalmic Genetics
https://www.readbyqxmd.com/read/27877079/amplification-and-overexpression-of-cttn-and-ccnd1-at-chromosome-11q13-in-esophagus-squamous-cell-carcinoma-escc-of-north-eastern-chinese-population
#10
Xiaoxia Hu, Ji Wook Moon, Shibo Li, Weihong Xu, Xianfu Wang, Yuanyuan Liu, Ji-Yun Lee
Esophageal squamous cell carcinoma (ESCC) is a genetically complex tumor type and is a major cause of cancer-related mortality. The combination of genetics, diet, behavior, and environment plays an important role in the carcinogenesis of ESCC. To characterize the genomic aberrations of this disease, we investigated the genomic imbalances in 19 primary ESCC cases using high-resolution array comparative genomic hybridization (CGH). All cases showed either loss or gain of whole chromosomes or segments of chromosome(s) with variable genomic sizes...
2016: International Journal of Medical Sciences
https://www.readbyqxmd.com/read/27869554/genome-wide-deletion-screening-with-the-array-cgh-method-in-mouse-offspring-derived-from-irradiated-spermatogonia-indicates-that-mutagenic-responses-are-highly-variable-among-genes
#11
Jun-Ichi Asakawa, Mieko Kodaira, Akiko Miura, Takanori Tsuji, Yoshiko Nakamoto, Masaaki Imanaka, Jun Kitamura, Harry Cullings, Mayumi Nishimura, Yoshiya Shimada, Nori Nakamura
Until the end of the 20th century, mouse germ cell data on induced mutation rates, which were collected using classical genetic methods at preselected specific loci, provided the principal basis for estimates of genetic risks from radiation in humans. The work reported on here is an extension of earlier efforts in this area using molecular methods. It focuses on validating the use of array comparative genomic hybridization (array CGH) methods for identifying radiation-induced copy number variants (CNVs) and specifically for DNA deletions...
November 21, 2016: Radiation Research
https://www.readbyqxmd.com/read/27863505/a-genomic-case-study-of-desmoplastic-small-round-cell-tumor-comprehensive-analysis-reveals-insights-into-potential-therapeutic-targets-and-development-of-a-monitoring-tool-for-a-rare-and-aggressive-disease
#12
Elisa Napolitano Ferreira, Bruna Durães Figueiredo Barros, Jorge Estefano de Souza, Renan Valieris Almeida, Giovana Tardin Torrezan, Sheila Garcia, Ana Cristina Victorino Krepischi, Celso Abdon Lopes de Mello, Isabela Werneck da Cunha, Clóvis Antonio Lopes Pinto, Fernando Augusto Soares, Emmanuel Dias-Neto, Ademar Lopes, Sandro José de Souza, Dirce Maria Carraro
BACKGROUND: Genome-wide profiling of rare tumors is crucial for improvement of diagnosis, treatment, and, consequently, achieving better outcomes. Desmoplastic small round cell tumor (DSRCT) is a rare type of sarcoma arising from mesenchymal cells of abdominal peritoneum that usually develops in male adolescents and young adults. A specific translocation, t(11;22)(p13;q12), resulting in EWS and WT1 gene fusion is the only recurrent molecular hallmark and no other genetic factor has been associated to this aggressive tumor...
November 18, 2016: Human Genomics
https://www.readbyqxmd.com/read/27863127/study-on-genetic-stability-in-human-urothelial-cells-in-vitro
#13
Clara Ibel Chamorro, Said Zeiai, Gisela Reinfeldt Engberg, David Brodin, Johanna Lundin, Agneta Nordenskjöld, Magdalena Fossum
Quality control studies addressing gene expression changes and genetic stability are of vital importance in regenerative medicine. In order to rule out that in vitro expansion gives rise to gene expression changes that could favor oncogenic events, we applied a total human gene expression chip (Affymetrix®) and bioinformatics analysis using the Ingenuity web-based application in combination with an analysis of chromosomal copy number variations using array CGH. We found that urothelial cells presented a general repression of genes required for cell cycle progression and an upregulated of growth-inhibitory genes, as well as a decrease in DNA replication after long-term culture...
November 12, 2016: Journal of Tissue Engineering and Regenerative Medicine
https://www.readbyqxmd.com/read/27857317/effective-information-processing-method-to-produce-a-computer-generated-hologram-based-on-a-spatial-light-modulator
#14
Su-Juan Liu, Di Wang, Song-Jie Li, Qiong-Hua Wang
In this paper, we propose an effective information processing method to produce a computer-generated hologram (CGH) based on a spatial light modulator (SLM). The method generates CGHs according to the property of the field of view (FOV), which, to the best of our knowledge, has never been proposed before. The CGH is composed of essential interference patterns (EIPs). Each EIP records the information of different object points. The resolution of the EIP is reduced. In the reconstructed process, the boundaries of the diffraction light of each EIP and FOV of the reconstructed image are parallel with each other...
November 10, 2016: Applied Optics
https://www.readbyqxmd.com/read/27834851/negative-glucocorticoid-response-like-element-from-the-first-intron-of-the-chicken-growth-hormone-gene-represses-gene-expression-in-the-rat-pituitary-tumor-cell-line
#15
Jing-E Ma, Qian-Qian Lang, Feng-Fang Qiu, Li Zhang, Xiang-Guang Li, Wen Luo, Juan Wang, Xing Wang, Xi-Ran Lin, Wen-Sheng Liu, Qing-Hua Nie, Xi-Quan Zhang
The effects of introns, especially the first intron, on the regulation of gene expression remains unclear. Therefore, the objective of the present study was to investigate the transcriptional regulatory function of intron 1 on the chicken growth hormone (cGH) gene in the rat pituitary tumor cell line (GH4-C1). Transient transfection using first-intron-inserted cGH complete coding sequences (CDSs) and non-intron-inserted cGH CDS plasmids, quantitative RT-PCR (qRT-PCR) and western blot assays were used to detect the expression of cGH...
November 9, 2016: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/27834213/high-density-array-cgh-with-targeted-ngs-unmask-multiple-noncontiguous-minute-deletions-on-chromosome-3p21-in-mesothelioma
#16
Yoshie Yoshikawa, Mitsuru Emi, Tomoko Hashimoto-Tamaoki, Masaki Ohmuraya, Ayuko Sato, Tohru Tsujimura, Seiki Hasegawa, Takashi Nakano, Masaki Nasu, Sandra Pastorino, Agata Szymiczek, Angela Bononi, Mika Tanji, Ian Pagano, Giovanni Gaudino, Andrea Napolitano, Chandra Goparaju, Harvey I Pass, Haining Yang, Michele Carbone
We used a custom-made comparative genomic hybridization array (aCGH; average probe interval 254 bp) to screen 33 malignant mesothelioma (MM) biopsies for somatic copy number loss throughout the 3p21 region (10.7 Mb) that harbors 251 genes, including BRCA1 (breast cancer 1)-associated protein 1 (BAP1), the most commonly mutated gene in MM. We identified frequent minute biallelic deletions (<3 kb) in 46 of 251 genes: four were cancer-associated genes: SETD2 (SET domain-containing protein 2) (7 of 33), BAP1 (8 of 33), PBRM1 (polybromo 1) (3 of 33), and SMARCC1 (switch/sucrose nonfermentable- SWI/SNF-related, matrix-associated, actin-dependent regulator of chromatin, subfamily c, member 1) (2 of 33)...
November 22, 2016: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/27834069/using-array-based-comparative-genomic-hybridization-to-diagnose-pallister-killian-syndrome
#17
Mi Na Lee, Jiwon Lee, Hee Joon Yu, Jeehun Lee, Sun Hee Kim
Pallister-Killian syndrome (PKS) is a rare multisystem disorder characterized by isochromosome 12p and tissue-limited mosaic tetrasomy 12p. In this study, we diagnosed three pediatric patients who were suspicious of having PKS using array-based comparative genomic hybridization (array CGH) and FISH analyses performed on peripheral lymphocytes. Patients 1 and 2 presented with craniofacial dysmorphic features, hypotonia, and a developmental delay. Array CGH revealed two to three copies of 12p in patient 1 and three copies in patient 2...
January 2017: Annals of Laboratory Medicine
https://www.readbyqxmd.com/read/27828470/acceleration-of-the-calculation-speed-of-computer-generated-holograms-using-the-sparsity-of-the-holographic-fringe-pattern-for-a-3d-object
#18
Hak Gu Kim, Hyunwook Jeong, Yong Man Ro
In computer-generated hologram (CGH) calculations, a diffraction pattern needs to be calculated from all points of a 3-D object, which requires a heavy computational cost. In this paper, we propose a novel fast computer-generated hologram calculation method using sparse fast Fourier transform. The proposed method consists of two steps. First, the sparse dominant signals of CGHs are measured by calculating a wavefront on a virtual plane between the object and the CGH plane. Second, the wavefront on CGH plane is calculated by using the measured sparsity with sparse Fresnel diffraction...
October 31, 2016: Optics Express
https://www.readbyqxmd.com/read/27828078/three-dimensional-scene-encryption-and-display-based-on-computer-generated-holograms
#19
Dezhao Kong, Liangcai Cao, Guofan Jin, Bahram Javidi
An optical encryption and display method for a three-dimensional (3D) scene is proposed based on computer-generated holograms (CGHs) using a single phase-only spatial light modulator. The 3D scene is encoded as one complex Fourier CGH. The Fourier CGH is then decomposed into two phase-only CGHs with random distributions by the vector stochastic decomposition algorithm. Two CGHs are interleaved as one final phase-only CGH for optical encryption and reconstruction. The proposed method can support high-level nonlinear optical 3D scene security and complex amplitude modulation of the optical field...
October 10, 2016: Applied Optics
https://www.readbyqxmd.com/read/27828036/simple-calculation-of-a-computer-generated-hologram-for-lensless-holographic-3d-projection-using-a-nonuniform-sampled-wavefront-recording-plane
#20
Chenliang Chang, Jun Wu, Yijun Qi, Caojin Yuan, Shouping Nie, Jun Xia
In this paper, we present a method for calculation of a computer-generated hologram (CGH) from a 3D object. A virtual wavefront recording plane (WRP) which is close to the 3D object is established. This WRP is nonuniformly sampled according to the depth map of the 3D object. The generation of CGH only involves two nonuniform fast Fourier transform (NUFFT) and two fast Fourier transform (FFT) operations, the whole computational procedure is greatly simplified by diffraction calculation from a 2D planar image instead of 3D object voxels...
October 1, 2016: Applied Optics
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