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https://www.readbyqxmd.com/read/29779219/immunohistochemical-and-molecular-analysis-of-spitzoid-neoplasms-with-pulverocyte-subclones
#1
S M Amin, A M Haugh, J A Bubley, A E Verzì, E A Merkel, C Y Lee, V L Quan, E M Garfield, L M Sholl, B Zhang, P Gerami
BACKGROUND: Clonal naevi are characterized by a focal proliferation of pigmented melanocytes in an otherwise banal naevus. These subclones are often composed of aggregates of larger, epithelioid melanocytes with nuclear atypia and dusty-grey cytoplasmic pigmentation, which are referred to as 'pulverocytes', and this finding may lead to a misdiagnosis of malignant melanoma (MM). AIM: To characterize the significance of subclones of dusty-grey pigmented epithelioid melanocytes within spitzoid neoplasms...
May 20, 2018: Clinical and Experimental Dermatology
https://www.readbyqxmd.com/read/29779145/comprehensive-genetic-testing-for-female-and-male-infertility-using-next-generation-sequencing
#2
Bonny Patel, Sasha Parets, Matthew Akana, Gregory Kellogg, Michael Jansen, Chihyu Chang, Ying Cai, Rebecca Fox, Mohammad Niknazar, Roman Shraga, Colby Hunter, Andrew Pollock, Robert Wisotzkey, Malgorzata Jaremko, Alex Bisignano, Oscar Puig
PURPOSE: To develop a comprehensive genetic test for female and male infertility in support of medical decisions during assisted reproductive technology (ART) protocols. METHODS: We developed a next-generation sequencing (NGS) gene panel consisting of 87 genes including promoters, 5' and 3' untranslated regions, exons, and selected introns. In addition, sex chromosome aneuploidies and Y chromosome microdeletions were analyzed concomitantly using the same panel. RESULTS: The NGS panel was analytically validated by retrospective analysis of 118 genomic DNA samples with known variants in loci representative of female and male infertility...
May 19, 2018: Journal of Assisted Reproduction and Genetics
https://www.readbyqxmd.com/read/29779130/the-present-and-the-future-of-genetic-testing-in-familial-hypercholesterolemia-opportunities-and-caveats
#3
REVIEW
Amanda J Hooper, John R Burnett, Damon A Bell, Gerald F Watts
PURPOSE OF REVIEW: We summarize recent advances in the understanding of genetic testing in familial hypercholesterolemia (FH), the use of expanded FH next-generation sequencing panels, and directions for future research. RECENT FINDINGS: The uptake of massively parallel sequencing in research and diagnostic laboratories has enabled expanded testing for FH and its phenocopies, with the added advantage that copy number variants can be detected. However, increasing the number of genes tested increases the number of variants detected, which may or may not be pathogenic...
May 19, 2018: Current Atherosclerosis Reports
https://www.readbyqxmd.com/read/29779068/new-insights-into-the-inflamed-tumor-immune-microenvironment-of-gastric-cancer-with-lymphoid-stroma-from-morphology-and-digital-analysis-to-gene-expression
#4
Irene Gullo, Patrícia Oliveira, Maria Athelogou, Gilza Gonçalves, Marta L Pinto, Joana Carvalho, Ana Valente, Hugo Pinheiro, Sara Andrade, Gabriela M Almeida, Ralf Huss, Kakoli Das, Patrick Tan, José C Machado, Carla Oliveira, Fátima Carneiro
BACKGROUND: Gastric cancer with lymphoid stroma (GCLS) is characterized by prominent stromal infiltration of T-lymphocytes. The aim of this study was to investigate GCLS biology through analysis of clinicopathological features, EBV infection, microsatellite instability (MSI), immune gene-expression profiling and PD-L1 status in neoplastic cells and tumor immune microenvironment. METHODS: Twenty-four GCLSs were analyzed by RNA in situ hybridization for EBV (EBER), PCR/fragment analysis for MSI, immunohistochemistry (PD-L1, cytokeratin, CD3, CD8), co-immunofluorescence (CK/PD-L1, CD68/PD-L1), NanoString gene-expression assay for immune-related genes and PD-L1 copy number alterations...
May 19, 2018: Gastric Cancer
https://www.readbyqxmd.com/read/29778275/quantifying-the-effects-of-16p11-2-copy-number-variants-on-brain-structure-a-multisite-genetic-first-study
#5
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/29777458/increased-vitamin-d-receptor-gene-expression-and-rs11568820-and-rs4516035-promoter-polymorphisms-in-autistic-disorder
#6
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
#7
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/29777339/characterization-of-a-cryptic-rolling-circle-replication-plasmid-pmk8-from-enterococcus-durans-1-8
#8
Penyu Zhou, Zhengyuan Zhai, Xiong Yao, Peihua Ma, Yanling Hao
A novel cryptic plasmid from Enterococcus durans 1-8, designated as pMK8, was sequenced and analyzed in this study. It consists of 3337 bp with a G + C content of 33.11%. Sequence analysis of pMK8 revealed three putative open reading frames (ORFs). Based on homology, two of them were identified as genes encoding replication initiation (RepC) and mobilization (Mob) protein, respectively. Sequence analysis revealed a pT181 family double-strand origin (dso) and a putative single-strand origin (sso) located upstream of the repC gene...
May 17, 2018: Current Microbiology
https://www.readbyqxmd.com/read/29777105/phenotypic-diversification-by-enhanced-genome-restructuring-after-induction-of-multiple-dna-double-strand-breaks
#9
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/29776954/role-of-elevated-phip-copy-number-as-a-prognostic-and-progression-marker-for-cutaneous-melanoma
#10
Vladimir Bezrookove, Mehdi Nosrati, James R Miller, David de Semir, Altaf A Dar, Elham Vosoughi, Edith Vaquero, Antje Sucker, Alexander J Lazar, Jeffrey E Gershenwald, Michael A Davies, Dirk Schadendorf, Mohammed Kashani-Sabet
PURPOSE: Previous studies have indicated an important role for pleckstrin homology domain-interacting protein (PHIP) as a marker and mediator of melanoma metastasis. Here we aimed to confirm the role of PHIP copy number in successive stages of melanoma progression. EXPERIMENTAL DESIGN: PHIP copy number was examined using fluorescence in situ hybridization (FISH) in three independent cohorts by recording the percentage of cells harboring > 3 copies of PHIP...
May 18, 2018: Clinical Cancer Research: An Official Journal of the American Association for Cancer Research
https://www.readbyqxmd.com/read/29776953/the-landscape-of-actionable-genomic-alterations-in-cell-free-circulating-tumor-dna-from-21-807-advanced-cancer-patients
#11
Oliver A Zill, Kimberly C Banks, Stephen R Fairclough, Stefanie Mortimer, James V Vowles, Reza Mokhtari, David R Gandara, Philip C Mack, Justin I Odegaard, Rebecca J Nagy, Arthur M Baca, Helmy Eltoukhy, Darya I Chudova, Richard B Lanman, AmirAli Talasaz
PURPOSE: Cell-free DNA (cfDNA) sequencing provides a non-invasive method for obtaining actionable genomic information to guide personalized cancer treatment, but the presence of multiple alterations in circulation related to treatment and tumor heterogeneity complicate the interpretation of the observed variants. Experimental Design: We describe the somatic mutation landscape of 70 cancer genes from cfDNA deep-sequencing analysis of 21,807 patients with treated, late-stage cancers across >50 cancer types...
May 18, 2018: Clinical Cancer Research: An Official Journal of the American Association for Cancer Research
https://www.readbyqxmd.com/read/29776391/the-clinical-implications-of-g1-g6-transcriptomic-signature-and-5-gene-score-in-korean-patients-with-hepatocellular-carcinoma
#12
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/29776336/phylogenomic-analysis-of-apoidea-sheds-new-light-on-the-sister-group-of-bees
#13
Manuela Sann, Oliver Niehuis, Ralph S Peters, Christoph Mayer, Alexey Kozlov, Lars Podsiadlowski, Sarah Bank, Karen Meusemann, Bernhard Misof, Christoph Bleidorn, Michael Ohl
BACKGROUND: Apoid wasps and bees (Apoidea) are an ecologically and morphologically diverse group of Hymenoptera, with some species of bees having evolved eusocial societies. Major problems for our understanding of the evolutionary history of Apoidea have been the difficulty to trace the phylogenetic origin and to reliably estimate the geological age of bees. To address these issues, we compiled a comprehensive phylogenomic dataset by simultaneously analyzing target DNA enrichment and transcriptomic sequence data, comprising 195 single-copy protein-coding genes and covering all major lineages of apoid wasps and bee families...
May 18, 2018: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/29776329/convaq-a-web-tool-for-copy-number-variation-based-association-studies
#14
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
#15
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/29774306/leber-s-hereditary-optic-neuropathy-lhon-in-an-apulian-cohort-of-subjects
#16
Angelica Bianco, Luigi Bisceglia, Paolo Trerotoli, Luciana Russo, Leonardo D'Agruma, Silvana Guerriero, Vittoria Petruzzella
Leber's hereditary optic neuropathy (LHON) is a maternally inherited disorder that causes severe loss of sight in young adults, and is typically associated to mitochondrial DNA (mtDNA) mutations. Heteroplasmy of primary LHON mutations, presence of 'ancillary' mtDNA mutations, and mtDNA copy number are probably correlated with the penetrance and the severity of the disease. In this study, we performed a mutational screening in an Apulian cohort of LHON patients and we found that 41 out of 54 subjects harbored the m...
September 2017: Acta Myologica: Myopathies and Cardiomyopathies: Official Journal of the Mediterranean Society of Myology
https://www.readbyqxmd.com/read/29774238/chitinase-genes-chia-s-provide-genomic-footprints-of-a-post-cretaceous-dietary-radiation-in-placental-mammals
#17
Christopher A Emerling, Frédéric Delsuc, Michael W Nachman
The end-Cretaceous extinction led to a massive faunal turnover, with placental mammals radiating in the wake of nonavian dinosaurs. Fossils indicate that Cretaceous stem placentals were generally insectivorous, whereas their earliest Cenozoic descendants occupied a variety of dietary niches. It is hypothesized that this dietary radiation resulted from the opening of niche space, following the extinction of dinosaurian carnivores and herbivores. We provide the first genomic evidence for the occurrence and timing of this dietary radiation in placental mammals...
May 2018: Science Advances
https://www.readbyqxmd.com/read/29773709/growth-of-sedimentary-bathyarchaeota-on-lignin-as-an-energy-source
#18
Tiantian Yu, Weichao Wu, Wenyue Liang, Mark Alexander Lever, Kai-Uwe Hinrichs, Fengping Wang
Members of the archaeal phylum Bathyarchaeota are among the most abundant microorganisms on Earth. Although versatile metabolic capabilities such as acetogenesis, methanogenesis, and fermentation have been suggested for bathyarchaeotal members, no direct confirmation of these metabolic functions has been achieved through growth of Bathyarchaeota in the laboratory. Here we demonstrate, on the basis of gene-copy numbers and probing of archaeal lipids, the growth of Bathyarchaeota subgroup Bathy-8 in enrichments of estuarine sediments with the biopolymer lignin...
May 17, 2018: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29773658/detecting-quantifying-and-discriminating-the-mechanism-of-mosaic-chromosomal-aneuploidies-using-mad-seq
#19
Yu Kong, Esther R Berko, Anthony Marckette, Shahina B Maqbool, Claudia A Simões-Pires, David F Kronn, Qian K Ye, Masako Suzuki, Adam Auton, John Greally
Current approaches to detect and characterize mosaic chromosomal aneuploidy are limited by sensitivity, efficiency, cost or the need to culture cells. We describe the mosaic aneuploidy detection by massively-parallel sequencing (MAD-seq) capture assay and the MADSEQ analytical approach that allow low (<10%) levels of mosaicism for chromosomal aneuploidy or regional loss of heterozygosity to be detected, assigned to a meiotic or mitotic origin, and quantified as a proportion of the cells in the sample. We show results from a multi-ethnic MAD-seq (meMAD-seq) capture design that works equally well in populations of diverse racial and ethnic origins, and how the MADSEQ analytical approach can be applied to exome or whole genome sequencing data, revealing previously unrecognized aneuploidy or copy number neutral loss of heterozygosity in samples studied by the 1000 Genomes project, cell lines from public repositories, and one of the Illumina Platinum Genomes samples...
May 17, 2018: Genome Research
https://www.readbyqxmd.com/read/29772275/5c-id-increased-resolution-chromosome-conformation-capture-carbon-copy-with-in-situ-3c-and-double-alternating-primer-design
#20
Ji Hun Kim, Katelyn R Titus, Wanfeng Gong, Jonathan A Beagan, Zhendong Cao, Jennifer E Phillips-Cremins
Mammalian genomes are folded in a hierarchy of compartments, topologically associating domains (TADs), subTADs, and looping interactions. Currently, there is a great need to evaluate the link between chromatin topology and genome function across many biological conditions and genetic perturbations. Hi-C can generate genome-wide maps of looping interactions but is intractable for high-throughput comparison of loops across multiple conditions due to the enormous number of reads (>6 Billion) required per library...
May 14, 2018: Methods: a Companion to Methods in Enzymology
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