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array comparative hybridization

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https://www.readbyqxmd.com/read/28346953/lennox-gastaut-syndrome-a-state-of-the-art-review
#1
Mario Mastrangelo
Lennox-Gastaut syndrome (LGS) is a severe age-dependent epileptic encephalopathy usually with onset between 1 and 8 years of age. Functional neuroimaging studies recently introduced the concept of Lennox-Gastaut as "secondary network epilepsy" resulting from dysfunctions of a complex system involving both cortical and subcortical structures (default-mode network, corticoreticular connections, and thalamus). These dysfunctions are produced by different disorders including hypoxic-ischemic encephalopathies, meningoencephalitis, cortical malformations, neurocutaneous disorders, or tumors...
March 27, 2017: Neuropediatrics
https://www.readbyqxmd.com/read/28344653/characterization-of-a-de-novo-ssmc-17-detected-in-a-girl-with-developmental-delay-and-dysmorphic-features
#2
Lana Stavber, Sara Bertok, Jernej Kovač, Marija Volk, Luca Lovrečić, Tadej Battelino, Tinka Hovnik
BACKGROUND: The majority of small supernumerary marker chromosome cases arise de novo and their frequency in newborns is 0.04%. We report on a girl with developmental delay and dysmorphic features with a non-mosaic de novo sSMC that originated from the pericentric region of q arm in chromosome 17. CASE PRESENTATION: The girl presented with developmental delay, speech delay, myopia, mild muscle hypotonia, hypoplasia of orbicular muscle, poor concentration, and hyperactivity...
2017: Molecular Cytogenetics
https://www.readbyqxmd.com/read/28343235/transcription-dependent-radial-distribution-of-tcf7l2-regulated-genes-in-chromosome-territories
#3
Keyvan Torabi, Darawalee Wangsa, Immaculada Ponsa, Markus Brown, Anna Bosch, Maria Vila-Casadesús, Tatiana S Karpova, Maria Calvo, Antoni Castells, Rosa Miró, Thomas Ried, Jordi Camps
Human chromosomes occupy distinct territories in the interphase nucleus. Such chromosome territories (CTs) are positioned according to gene density. Gene-rich CTs are generally located in the center of the nucleus, while gene-poor CTs are positioned more towards the nuclear periphery. However, the association between gene expression levels and the radial positioning of genes within the CT is still under debate. In the present study, we performed three-dimensional fluorescence in situ hybridization experiments in the colorectal cancer cell lines DLD-1 and LoVo using whole chromosome painting probes for chromosomes 8 and 11 and BAC clones targeting four genes with different expression levels assessed by gene expression arrays and RT-PCR...
March 25, 2017: Chromosoma
https://www.readbyqxmd.com/read/28341418/a-novel-y-chromosome-microdeletion-potentially-associated-with-defective-spermatogenesis-identified-by-custom-array-comparative-genome-hybridization
#4
Tianwen He, Xiangzhong Zhang, Hua Deng, Weiping Zhou, Xin Zhao, Hui Zhao, Jian Lu, Yichun Zheng, Changbin Zhang, Liang Zhang, Aihua Yin
Male infertility is a major health problem worldwide. Oligospermia and azoospermia are the most common symptoms of this disorder. Despite recent advances, the aetiopathogenesis of defective spermatogenesis remains largely uncertain. The aim of this study is to discover unknown or novel chromosome aberrations associated with male reproductive failure. We developed a high-resolution custom array comparative genomic hybridization for initial screening of copy number variations in 10 patients with idiopathic oligozoospermia and azoospermia and eight normal fertile men...
January 2017: Reproductive Biomedicine Online
https://www.readbyqxmd.com/read/28339631/evidence-for-the-involvement-of-the-proximal-copy-of-the-magea9-gene-in-xq28-linked-cnv67-specific-to-spermatogenic-failure%C3%A2
#5
Ying Shen, Jinyan Xu, Xiling Yang, Yunqiang Liu, Yongyi Ma, Dong Yang, Qiang Dong, Yuan Yang
Spermatogenic failure characterized by impaired sperm production is a common multifactorial disease with molecular and cytogenetic causes for its extreme phenotype that include azoospermia and severe oliogzoospermia. Recently, a high-resolution array-comparative genomic hybridization analysis of the X chromosome and a subsequent cohort study revealed three X-linked microdeletions (CNV64, CNV67, and CNV69) that were associated with decreased sperm production in a mixed group that included Spanish and Italian males...
February 7, 2017: Biology of Reproduction
https://www.readbyqxmd.com/read/28335579/application-of-a-mems-based-trng-in-a-chaotic-stream-cipher
#6
Miguel Garcia-Bosque, Adrián Pérez, Carlos Sánchez-Azqueta, Santiago Celma
In this work, we used a sensor-based True Random Number Generator in order to generate keys for a stream cipher based on a recently published hybrid algorithm mixing Skew Tent Map and a Linear Feedback Shift Register. The stream cipher was implemented and tested in a Field Programmable Gate Array (FPGA) and was able to generate 8-bit width data streams at a clock frequency of 134 MHz, which is fast enough for Gigabit Ethernet applications. An exhaustive cryptanalysis was completed, allowing us to conclude that the system is secure...
March 21, 2017: Sensors
https://www.readbyqxmd.com/read/28334874/efficient-cnv-breakpoint-analysis-reveals-unexpected-structural-complexity-and-correlation-of-dosage-sensitive-genes-with-clinical-severity-in-genomic-disorders
#7
Ling Zhang, Jingmin Wang, Cheng Zhang, Dongxiao Li, Claudia M B Carvalho, Haoran Ji, Jianqiu Xiao, Ye Wu, Weichen Zhou, Hongyan Wang, Li Jin, Yang Luo, Xiru Wu, James R Lupski, Feng Zhang, Yuwu Jiang
Genomic disorders are the clinical conditions manifested by submicroscopic genomic rearrangements including copy number variants (CNVs). The CNVs can be identified by array-based comparative genomic hybridization (aCGH), the most commonly used technology for molecular diagnostics of genomic disorders. However, clinical aCGH only informs CNVs in the probe interrogated regions. Neither orientational information nor the resulting genomic rearrangement structure is provided, which is a key to uncovering mutational and pathogenic mechanisms underlying genomic disorders...
March 14, 2017: Human Molecular Genetics
https://www.readbyqxmd.com/read/28333245/euploidy-rates-in-donor-egg-cycles-significantly-differ-between-fertility-centers
#8
S Munné, M Alikani, L Ribustello, P Colls, Pedro A Martínez-Ortiz, D H McCulloh
STUDY QUESTION: Do external factors affect euploidy in egg donor cycles? SUMMARY ANSWER: The study demonstrates that during human assisted reproduction, embryonic chromosome abnormalities may be partly iatrogenic. WHAT IS KNOWN ALREADY: Chromosome abnormalities have been linked in the past to culture conditions such as temperature and Ph variations, as well as hormonal stimulation. Those reports were performed with older screening techniques (FISH), or ART methods no longer in use, and the subjects studied were not a homogeneous group...
March 2, 2017: Human Reproduction
https://www.readbyqxmd.com/read/28333167/a-complex-intragenic-rearrangement-of-ercc8-in-chinese-siblings-with-cockayne-syndrome
#9
Hua Xie, Xiaoyan Li, Jiping Peng, Qian Chen, ZhiJie Gao, Xiaozhen Song, WeiYu Li, Jianqiu Xiao, Caihua Li, Ting Zhang, James F Gusella, Jianmin Zhong, Xiaoli Chen
Cockayne syndrome is an autosomal recessive disorder principally characterized by postnatal growth failure and progressive neurological dysfunction, due primarily to mutations in ERCC6 and ERCC8. Here, we report our diagnostic experience for two patients in a Chinese family suspected on clinical grounds to have Cockayne syndrome. Using multiple molecular techniques, including whole exome sequencing, array comparative genomic hybridization and quantitative polymerase chain reaction, we identified compound heterozygosity for a maternal splicing variant (chr5:60195556, NM_000082:c...
March 23, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28331547/application-of-high-resolution-genomic-profiling-in-the-differential-diagnosis-of-liposarcoma
#10
Magdalena Koczkowska, Beata Stefania Lipska-Ziętkiewicz, Mariola Iliszko, Janusz Ryś, Markku Miettinen, Jerzy Lasota, Wojciech Biernat, Agnieszka Harazin-Lechowska, Anna Kruczak, Janusz Limon
BACKGROUND: Rarity and heterogeneity of liposarcomas (LPS) make their diagnosis difficult even for sarcoma-experts pathologists. The molecular mechanism underlying the development and progression of liposarcomas (LPS) remains only partially known. In order to identify and compare the genomic profiles, we analyzed array-based comparative genomic hybridization (array-CGH) profiles of 66 liposarcomas, including well-differentiated (WDLPS), dedifferentiated (DDLPS) and myxoid (MLPS) subtypes...
2017: Molecular Cytogenetics
https://www.readbyqxmd.com/read/28326956/clinical-pathologic-and-genetic-features-of-wilms-tumors-with-wtx-gene-mutation
#11
Sanda Alexandrescu, Sara Akhavanfard, Marian H Harris, Sara O Vargas
Clinical and pathologic features of patients with WTX-mutated Wilms tumor (WT) have not been studied in detail. We characterize the clinical and pathologic findings in WT with WTX abnormalities and provide comparison with WT without WTX mutation. Clinical, gross, and microscopic features in 35 patients with WT were examined. Karyotype was examined in a subset of cases. All cases had been previously analyzed for WTX, WT1, and CTNNB1 aberrations via array comparative genomic hybridization; OncoMap 4 high throughput genotyping was performed on 18 cases...
March 2017: Pediatric and Developmental Pathology
https://www.readbyqxmd.com/read/28316008/cytogenetic-analysis-of-metaplastic-squamous-cell-carcinoma-of-the-breast-inter-and-intratumoral-heterogeneity
#12
Masahiro Oikawa, Akiko Igawa, Kenichi Taguchi, Kimiko Baba, Mayumi Ishida, Sayuri Akiyoshi, Hiroshi Yano, Takeshi Nagayasu, Shinji Ohno, Eriko Tokunaga
BACKGROUND: Squamous cell carcinoma (SCC) of the breast is a rare and generally aggressive disease that accounts for less than 0.1% of all breast carcinomas. Although SCCs have distinct morphological features, their origin and cytogenetic profile are not well understood. METHODS: Five patients with SCC were studied. The tumor area that was predominantly composed of SCC components was macrodissected and DNA was extracted. In three cases, an invasive or noninvasive ductal carcinoma of no special type (NST) component was also present...
March 18, 2017: Breast Cancer: the Journal of the Japanese Breast Cancer Society
https://www.readbyqxmd.com/read/28302064/a-sibship-with-duplication-of-xq28-inherited-from-the-mother-genomic-characterization-and-clinical-outcomes
#13
Dong Keon Yon, Ji Eun Park, Seung Jun Kim, Sung Han Shim, Kyu Young Chae
BACKGROUND: Loss-of-function mutations in methyl-CpG-binding protein 2 (MECP2; MIM *300005) results in the Rett syndrome, whereas gain-of-function mutations are associated with the MECP2 duplication syndrome. METHODS: We did research on a family with two brothers showing Xq28 duplication syndrome using various molecular cytogenetic techniques such as multiplex ligation-dependent probe amplification and array-based genomic hybridization. RESULTS: The duplicated region had several genes including MECP2 and interleukin-1 receptor associated kinase 1 (IRAK1; MIM *300283)...
March 17, 2017: BMC Medical Genetics
https://www.readbyqxmd.com/read/28296250/different-genetic-alteration-of-a20-in-a-s%C3%A3-zary-syndrome-case-with-v%C3%AE-2-j%C3%AE-22-t-cell-clone
#14
Lingling Zhou, Haitao Zheng, Xin Huang, Lihua Zhu, Suijing Wu, Chengwu Zeng, Lijian Yang, Shaohua Chen, Gengxin Luo, Xin Du, Yangqiu Li
BACKGROUND: The comprehensive genetic alterations underlying the pathogenesis of Sézary syndrome (SS) remains largely unknown. Previous studies showed that alterations of tumor necrosis factor-α-induced protein 3 gene (TNFAIP3; A20) are frequent in SS. In this study, we characterized the mutation and polymorphisms of A20 in a case with SS and compared with the genetic feature of A20 in T-cell acute lymphoblastic leukemia (T-ALL). METHODS: Using a novel approach based on the combination of fine-tiling array comparative genomic hybridization ( and ligation-mediated polymerase chain reaction (LM-PCR) to identify SS clone, the polymorphisms in the A20 gene (promoter, exons 2-9 [coding region] and 3'UTR) were detected by PCR and sequencing...
March 14, 2017: Asia-Pacific Journal of Clinical Oncology
https://www.readbyqxmd.com/read/28296152/flexible-and-powerful-strategy-for-qualitative-and-quantitative-analysis-of-valepotriates-in-valeriana-jatamansi-jones-using-hplc-with-linear-ion-trap-orbitrap-mass-spectrometry
#15
Chunguo Wang, Zhiquan Zheng, Xinqi Deng, Xiaojie Ma, Shengnan Wang, Jie Liu, Yong Liu, Jinli Shi
Valeriana jatamansi Jones is an important medicinal plant and its quality is closely related to its region of origin. In the current study, we utilized a flexible and powerful strategy for comprehensive evaluation of the quality diversity for 15 regions in China. The method was based on a hybrid linear ion trap-Orbitrap mass spectrometry platform. For structure characterization, fragmentation patterns were detected by analyzing a series of standard compounds using data dependent multistage mass spectrometry acquisition...
March 10, 2017: Journal of Separation Science
https://www.readbyqxmd.com/read/28295210/cnvs-analysis-in-a-cohort-of-isolated-and-syndromic-dd-id-reveals-novel-genomic-disorders-position-effects-and-candidate-disease-genes
#16
Eleonora Di Gregorio, Evelise Riberi, Elga Fabia Belligni, Elisa Biamino, Malte Spielmann, Ugo Ala, Alessandro Calcia, Irene Bagnasco, Diana Carli, Giorgia Gai, Mara Giordano, Andrea Guala, Roberto Keller, Giorgia Mandrile, Carlo Arduino, Antonella Maffè, Valeria Giorgia Naretto, Fabio Sirchia, Lorena Sorasio, Silvana Ungari, Andrea Zonta, Giulia Zacchetti, Flavia Talarico, Patrizia Pappi, Simona Cavalieri, Elisa Giorgio, Cecilia Mancini, Marta Ferrero, Alessandro Brussino, Elisa Savin, Marina Gandione, Alessandra Pelle, Daniela Francesca Giachino, Mario De Marchi, Gabriella Restagno, Paolo Provero, Margherita Cirillo Silengo, Enrico Grosso, Joseph D Buxbaum, Barbara Pasini, Silvia De Rubeis, Alfredo Brusco, Giovanni Battista Ferrero
Array-comparative genomic hybridization (array-CGH) is a widely used technique to detect Copy Number Variants (CNVs) associated with developmental delay/intellectual disability (DD/ID). We performed a comprehensive array-CGH investigation of 1,015 consecutive cases with DD/ID and combined literature mining, genetic evidence, evolutionary constraint scores, and functional information in order to assess the pathogenicity of the CNVs. We identified non-benign CNVs in 29% of patients. Amongst the pathogenic variants (11%), detected with a yield consistent with the literature, we found rare genomic disorders and CNVs spanning known disease genes...
March 14, 2017: Clinical Genetics
https://www.readbyqxmd.com/read/28289594/a-9-year-old-girl-with-phelan-mcdermid-syndrome-who-had-been-diagnosed-with-an-autism-spectrum-disorder
#17
I Görker, H Gürkan, S Demir Ulusal, E Atlı, E Ikbal Atlı
Phelan McDermid Syndrome (PHMDS) (OMIM #606232), is a contiguous gene disorder resulting from deletion of the distal long arm of chromosome 22. The 22q13.3 deletions and mutations that lead to a loss of a functional copy of SHANK3 (OMIM *606230) cause the syndrome, characterized by moderate to profound intellectual disability, severely delayed or absent speech, hypotonia, and autism spectrum disorder (ASD) or ASD traits. In this study, we present the case of a 9-year-old girl who had earlier been diagnosed with an ASD...
December 1, 2016: Balkan Journal of Medical Genetics: BJMG
https://www.readbyqxmd.com/read/28287439/custom-array-comparative-genomic-hybridization-the-importance-of-dna-quality-an-expert-eye-and-variant-validation
#18
Francesca Lantieri, Michela Malacarne, Stefania Gimelli, Giuseppe Santamaria, Domenico Coviello, Isabella Ceccherini
The presence of false positive and false negative results in the Array Comparative Genomic Hybridization (aCGH) design is poorly addressed in literature reports. We took advantage of a custom aCGH recently carried out to analyze its design performance, the use of several Agilent aberrations detection algorithms, and the presence of false results. Our study provides a confirmation that the high density design does not generate more noise than standard designs and, might reach a good resolution. We noticed a not negligible presence of false negative and false positive results in the imbalances call performed by the Agilent software...
March 10, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28283267/comparison-of-cytogenetics-and%C3%A2-molecular-karyotyping-for%C3%A2-chromosome-testing-of-miscarriage-specimens
#19
Meera Sridhar Shah, Cengiz Cinnioglu, Melissa Maisenbacher, Ioanna Comstock, Jonathan Kort, Ruth Bunker Lathi
OBJECTIVE: To compare chromosome testing of miscarriage specimens between traditional cytogenetic analysis and molecular karyotyping using single nucleotide polymorphism microarrays (SNP) and array comparative genomic hybridization (aCGH). DESIGN: Prospective blinded cohort study. SETTING: University-based practice. PATIENT(S): Women undergoing dilation and curettage for first-trimester miscarriage between March 2014 and December 2015...
March 7, 2017: Fertility and Sterility
https://www.readbyqxmd.com/read/28282428/solving-global-shallow-water-equations-on-heterogeneous-supercomputers
#20
Haohuan Fu, Lin Gan, Chao Yang, Wei Xue, Lanning Wang, Xinliang Wang, Xiaomeng Huang, Guangwen Yang
The scientific demand for more accurate modeling of the climate system calls for more computing power to support higher resolutions, inclusion of more component models, more complicated physics schemes, and larger ensembles. As the recent improvements in computing power mostly come from the increasing number of nodes in a system and the integration of heterogeneous accelerators, how to scale the computing problems onto more nodes and various kinds of accelerators has become a challenge for the model development...
2017: PloS One
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