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https://www.readbyqxmd.com/read/27926778/met-tyrosine-kinase-receptor-expression-and-amplification-as-prognostic-biomarkers-of-survival-in-gastroesophageal-adenocarcinoma
#1
Daniel V T Catenacci, Agnes Ang, Wei-Li Liao, Jing Shen, Emily O'Day, Robert D Loberg, Fabiola Cecchi, Todd Hembrough, Annamaria Ruzzo, Francesco Graziano
BACKGROUND: MET gene amplification and Met protein overexpression may be associated with a poor prognosis. The MET/Met status is typically determined with fluorescence in situ hybridization (FISH) and immunohistochemistry (IHC), respectively. Targeted proteomics uses mass spectrometry-based selected reaction monitoring (SRM) to accurately quantitate Met expression. FISH, IHC, and SRM analyses were compared to characterize the prognostic value of MET/Met in gastroesophageal adenocarcinoma (GEC)...
December 7, 2016: Cancer
https://www.readbyqxmd.com/read/27925336/non-exponential-growth-of-mycobacterium-leprae-thai-53-strain-cultured-in-vitro
#2
Kazunobu Amako, Ken-Ichiro Iida, Mitsumasa Saito, Yoshitosi Ogura, Tetsuya Hayashi, Shin-Ichi Yoshida
To determine why cultivation of Mycobacterium leprae in vitro has not been successful, we attempted to culture this bacterium in media supplemented with a variety of biological materials. We observed a slight increase in the number of cells in medium supplemented with human blood plasma and an extract of nude mouse tissue after more than 3 months of cultivation at 30°C. To ascertain whether this increase was real growth, we analyzed the growth by droplet digital PCR. The analysis had the following two results: the slow increase in the copy number of cell-associated DNA and the release of a large amount of DNA into the culture medium from bacterial cells during cultivation...
December 7, 2016: Microbiology and Immunology
https://www.readbyqxmd.com/read/27925267/genetic-variation-and-gene-conversions-within-the-bovine-nk-lysin-gene-family
#3
J Chen, M O Lee, J E Womack
In contrast to a single copy of the NK-lysin gene in humans and many other mammals, we previously identified a family of four expressed NK-lysin genes arising by tandem duplications on cattle chromosome 11. Here, we report two genetic variants in the bovine NK-lysin complex with potential importance in the bovine innate immune system. The first one is a 9-bp deletion causing a three-amino-acid deletion in the pro-region of the NK1 gene product. The second is a deletion of NK2B in some Holstein cattle, resulting in copy number variation that is in disequilibrium with a SNP from the bovine 770K HD SNP array...
December 7, 2016: Animal Genetics
https://www.readbyqxmd.com/read/27924152/molecular-characterization-of-a-rare-analphoid-supernumerary-marker-chromosome-derived-from-7q35%C3%A2-%C3%A2-%C3%A2-qter-a-case-report
#4
Bárbara Marques, Cristina Ferreira, Filomena Brito, Sónia Pedro, Cristina Alves, Teresa Lourenço, Marta Amorim, Hildeberto Correia
BACKGROUND: Analphoid supernumerary marker chromosomes (aSMC) constitute one of the smallest groups of SMC, and are characterized by a centromeric constriction but no detectable alpha-satellite DNA. These marker chromosomes cannot be properly identified by conventional banding techniques alone, and molecular cytogenetic methods are necessary for a detailed characterization. Analphoid SMC derived from chromosome 7 are extremely rare, with only five cases reported so far. CASE PRESENTATION: In this work we report an aSMC involving the terminal long arm of chromosome 7 in a 10-year-old boy with multiple dysmorphic features and severe development delay...
2016: Molecular Cytogenetics
https://www.readbyqxmd.com/read/27924059/an-open-label-phase-ii-study-evaluating-first-line-egfr-tyrosine-kinase-inhibitor-erlotinib-in-non-small-cell-lung-cancer-patients-with-tumors-showing-high-egfr-gene-copy-number
#5
Ewa Szutowicz-Zielińska, Krzysztof Konopa, Anna Kowalczyk, Małgorzata Suszko-Każarnowicz, Renata Duchnowska, Aleksandra Szczęsna, Magdalena Ratajska, Aleksander Sowa, Janusz Limon, Wojciech Biernat, Tomasz Burzykowski, Jacek Jassem, Rafał Dziadziuszko
BACKGROUND: First-line treatment with epidermal growth factor receptor (EGFR) inhibitors in NSCLC is effective in patients with activating EGFR mutations. The activity of erlotinib in patients harboring high EGFR gene copy number has been considered debatable. PATIENTS AND METHODS: A multicenter, open-label, single-arm phase II clinical trial was performed to test the efficacy of erlotinib in the first-line treatment of NSCLC patients harboring high EGFR gene copy number defined as ≥4 copies in ≥40% of cells...
December 4, 2016: Oncotarget
https://www.readbyqxmd.com/read/27924034/comprehensive-characterization-annotation-and-innovative-use-of-infinium-dna-methylation-beadchip-probes
#6
Wanding Zhou, Peter W Laird, Hui Shen
Illumina Infinium DNA Methylation BeadChips represent the most widely used genome-scale DNA methylation assays. Existing strategies for masking Infinium probes overlapping repeats or single nucleotide polymorphisms (SNPs) are based largely on ad hoc assumptions and subjective criteria. In addition, the recently introduced MethylationEPIC (EPIC) array expands on the utility of this platform, but has not yet been well characterized. We present in this paper an extensive characterization of probes on the EPIC and HM450 microarrays, including mappability to the latest genome build, genomic copy number of the 3' nested subsequence and influence of polymorphisms including a previously unrecognized color channel switch for Type I probes...
October 24, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27923841/biological-and-clinical-relevance-of-associated-genomic-alterations-in-myd88-l265p-and-non-l265p-mutated-diffuse-large-b-cell-lymphoma-analysis-of-361-cases
#7
Sydney Dubois, Pierre-Julien Viailly, Elodie Bohers, Philippe Bertrand, Philippe Ruminy, Vinciane Marchand, Catherine Maingonnat, Sylvain Mareschal, Jean-Michel Picquenot, Dominique Penther, Jean-Philippe Jais, Bruno Tesson, Pauline Peyrouze, Martin Figeac, Fabienne Desmots, Thierry Fest, Corinne Haioun, Thierry Lamy, Christiane Copie-Bergman, Bettina Fabiani, Richard Delarue, Frederic Peyrade, Marc André, Nicolas Ketterer, Karen Leroy, Gilles Salles, Thierry J Molina, Herve Tilly, Fabrice Jardin
PURPOSE: MYD88 mutations, notably the recurrent gain-of-function L265P variant, are a distinguishing feature of Activated B-Cell like (ABC) Diffuse Large B Cell Lymphoma (DLBCL), leading to constitutive NFkB pathway activation. The aim of this study was to examine the distinct genomic profiles of MYD88 mutant DLBCL, notably according to the presence of the L265P or other non-L265P MYD88 variants. EXPERIMENTAL DESIGN: A cohort of 361 DLBCL cases (94 MYD88 mutant and 267 MYD88 wild-type) was submitted to next generation sequencing (NGS) focusing on 34 genes in order to analyze associated mutations and copy number variations, as well as gene expression profiling, and clinical and prognostic analyses...
December 6, 2016: Clinical Cancer Research: An Official Journal of the American Association for Cancer Research
https://www.readbyqxmd.com/read/27923837/the-nci-60-methylome-and-its-integration-into-cellminer
#8
William C Reinhold, Sudhir Varma, Margot Sunshine, Vinodh Rajapakse, Augustin Luna, Kurt W Kohn, Holly Stevenson, Yonghong Wang, Holger Heyn, Vanesa Nogales, Sebastian Moran, David J Goldstein, James H Doroshow, Paul S Meltzer, Manel Esteller, Yves Pommier
A unique resource for systems pharmacology and genomic studies is the NCI-60 cancer cell line panel, which provides data for the largest publicly available library of compounds with cytotoxic activity (~21,000 compounds), including 108 FDA-approved and 70 clinical trial drugs as well as genomic data, including whole-exome sequencing, gene and microRNA transcripts, DNA copy number, and protein levels. Here we provide the first readily usable genome-wide DNA methylation database for the NCI-60, including 485,577 probes from the Infinium HumanMethylation450k BeadChip array, which yielded DNA methylation signatures for 17,559 genes integrated into our open access CellMiner version 2...
December 6, 2016: Cancer Research
https://www.readbyqxmd.com/read/27923672/functional-characterization-of-two-novel-purine-transporters-from-the-basidiomycota-phanerochaete-chrysosporium
#9
Mariana Barraco-Vega, Héctor Romero, Mariana Richero, María Pía Cerdeiras, Gianna Cecchetto
Purine transporters as substrate entry points in organisms, are involved in a number of cellular processes such as nitrogen source uptake, energy metabolism and synthesis of nucleic acids. In this study, two nucleobase transporter genes (phZ, phU) from Phanerochaete chrysosporium were cloned, identified, and functionally characterized. Our results show that PhZ is a transporter of adenine and hypoxanthine, and a protein belonging to the AzgA-like family, whilst PhU belongs to the NAT/NCS2 family, transporting xanthine and uric acid...
December 3, 2016: Gene
https://www.readbyqxmd.com/read/27923366/3c-digital-pcr-for-quantification-of-chromatin-interactions
#10
Meijun Du, Liang Wang
BACKGROUND: Chromosome conformation capture (3C) is a powerful and widely used technique for detecting the physical interactions between chromatin regions in vivo. The principle of 3C is to convert physical chromatin interactions into specific DNA ligation products, which are then detected by quantitative polymerase chain reaction (qPCR). However, 3C-qPCR assays are often complicated by the necessity of normalization controls to correct for amplification biases. In addition, qPCR is often limited to a certain cycle number, making it difficult to detect fragment ligations with low frequency...
December 6, 2016: BMC Molecular Biology
https://www.readbyqxmd.com/read/27923066/somatic-genomics-and-clinical-features-of-lung-adenocarcinoma-a-retrospective-study
#11
Jianxin Shi, Xing Hua, Bin Zhu, Sarangan Ravichandran, Mingyi Wang, Cu Nguyen, Seth A Brodie, Alessandro Palleschi, Marco Alloisio, Gianluca Pariscenti, Kristine Jones, Weiyin Zhou, Aaron J Bouk, Joseph Boland, Belynda Hicks, Adam Risch, Hunter Bennett, Brian T Luke, Lei Song, Jubao Duan, Pengyuan Liu, Takashi Kohno, Qingrong Chen, Daoud Meerzaman, Crystal Marconett, Ite Laird-Offringa, Ian Mills, Neil E Caporaso, Mitchell H Gail, Angela C Pesatori, Dario Consonni, Pier Alberto Bertazzi, Stephen J Chanock, Maria Teresa Landi
BACKGROUND: Lung adenocarcinoma (LUAD) is the most common histologic subtype of lung cancer and has a high risk of distant metastasis at every disease stage. We aimed to characterize the genomic landscape of LUAD and identify mutation signatures associated with tumor progression. METHODS AND FINDINGS: We performed an integrative genomic analysis, incorporating whole exome sequencing (WES), determination of DNA copy number and DNA methylation, and transcriptome sequencing for 101 LUAD samples from the Environment And Genetics in Lung cancer Etiology (EAGLE) study...
December 2016: PLoS Medicine
https://www.readbyqxmd.com/read/27923045/tumor-evolution-in-two-patients-with-basal-like-breast-cancer-a-retrospective-genomics-study-of-multiple-metastases
#12
Katherine A Hoadley, Marni B Siegel, Krishna L Kanchi, Christopher A Miller, Li Ding, Wei Zhao, Xiaping He, Joel S Parker, Michael C Wendl, Robert S Fulton, Ryan T Demeter, Richard K Wilson, Lisa A Carey, Charles M Perou, Elaine R Mardis
BACKGROUND: Metastasis is the main cause of cancer patient deaths and remains a poorly characterized process. It is still unclear when in tumor progression the ability to metastasize arises and whether this ability is inherent to the primary tumor or is acquired well after primary tumor formation. Next-generation sequencing and analytical methods to define clonal heterogeneity provide a means for identifying genetic events and the temporal relationships between these events in the primary and metastatic tumors within an individual...
December 2016: PLoS Medicine
https://www.readbyqxmd.com/read/27922091/an-increased-duplication-of-zrs-region-that-caused-more-than-one-supernumerary-digits-preaxial-polydactyly-in-a-large-chinese-family
#13
Bin Wang, Yutao Diao, Qiji Liu, Hongqiang An, Ruiping Ma, Guosheng Jiang, Nannan Lai, Ziwei Li, Xiaoxiao Zhu, Lin Zhao, Qiang Guo, Zhen Zhang, Rong Sun, Xia Li
Preaxial polydactyly (PPD) is inherited in an autosomal dominant fashion and characterized by the presence of one or more supernumerary digits on the thumb side. It had been identified that point mutation or genomic duplications of the long-range limb-specific cis-regulator - zone of polarizing activity regulatory sequence (ZRS) cause PPD or other limb deformities such as syndactyly type IV (SD4) and Triphalangeal thumb-polysyndactyly syndrome (TPTPS). Most previously reported cases involved with no more than one extra finger; however, the role of the point mutation or genomic duplications of ZRS in the case of more than one redundant finger polydactyly remains unclear...
December 6, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27921396/frequency-and-type-of-inheritable-mutations-induced-by-%C3%AE-rays-in-rice-as-revealed-by-whole-genome-sequencing
#14
Shan Li, Yun-Chao Zheng, Hai-Rui Cui, Hao-Wei Fu, Qing-Yao Shu, Jian-Zhong Huang
Mutation breeding is based on the induction of genetic variations; hence knowledge of the frequency and type of induced mutations is of paramount importance for the design and implementation of a mutation breeding program. Although γ ray irradiation has been widely used since the 1960s in the breeding of about 200 economically important plant species, molecular elucidation of its genetic effects has so far been achieved largely by analysis of target genes or genomic regions. In the present study, the whole genomes of six γ-irradiated M2 rice plants were sequenced; a total of 144-188 million high-quality (Q>20) reads were generated for each M2 plant, resulting in genome coverage of >45 times for each plant...
2016: Journal of Zhejiang University. Science. B
https://www.readbyqxmd.com/read/27920798/evolutionary-and-functional-features-of-copy-number-variation-in-the-cattle-genome
#15
Brittney N Keel, Amanda K Lindholm-Perry, Warren M Snelling
Genomic structural variations are an important source of genetic diversity. Copy number variations (CNVs), gains and losses of large regions of genomic sequence between individuals of a species, have been associated with a wide variety of phenotypic traits. However, in cattle, as well as many other species, relatively little is understood about CNV, including frequency of CNVs in the genome, sizes, and locations, chromosomal properties, and evolutionary processes acting to shape CNV. In this work, we focused on copy number variation in the bovine genome, with the aim to detect CNVs in Bos taurus coding sequence and explore potential evolutionary mechanisms shaping these CNV...
2016: Frontiers in Genetics
https://www.readbyqxmd.com/read/27920471/identification-of-il11ra-and-melk-amplification-in-gastric-cancer-by-comprehensive-genomic-profiling-of-gastric-cancer-cell-lines
#16
Danielle Queiroz Calcagno, Sylvia Santomi Takeno, Carolina Oliveira Gigek, Mariana Ferreira Leal, Fernanda Wisnieski, Elizabeth Suchi Chen, Taíssa Maíra Thomaz Araújo, Eleonidas Moura Lima, Maria Isabel Melaragno, Samia Demachki, Paulo Pimentel Assumpção, Rommel Rodriguez Burbano, Marília Cardoso Smith
AIM: To identify common copy number alterations on gastric cancer cell lines. METHODS: Four gastric cancer cell lines (ACP02, ACP03, AGP01 and PG100) underwent chromosomal comparative genome hybridization and array comparative genome hybridization. We also confirmed the results by fluorescence in situ hybridization analysis using the bacterial artificial chromosome clone and quantitative real time PCR analysis. RESULTS: The amplification of 9p13...
November 21, 2016: World Journal of Gastroenterology: WJG
https://www.readbyqxmd.com/read/27920057/acropora-digitifera-encodes-the-largest-known-family-of-fluorescent-proteins-that-has-persisted-during-the-evolution-of-acropora-species
#17
Shiho Takahashi-Kariyazono, Jun Gojobori, Yoko Satta, Kazuhiko Sakai, Yohey Terai
Fluorescent proteins (FPs) are well known and broadly used as bio-imaging markers in molecular biology research. Many FP genes were cloned from anthozoan species and it was suggested that multi-copies of these genes are present in their genomes. However, the full complement of FP genes in any single coral species remained unidentified. In this study, we analyzed the FP genes in two stony coral species. FP cDNA sequences from Acropora digitifera and Acropora tenuis revealed the presence of a multi-gene family with an unexpectedly large number of genes, separated into short-/middle-wavelength emission (S/MWE), middle-/long-wavelength emission (M/LWE), and chromoprotein (CP) clades...
December 5, 2016: Genome Biology and Evolution
https://www.readbyqxmd.com/read/27919006/assessment-of-the-risk-of-foodborne-transmission-and-burden-of-hepatitis-e-in-switzerland
#18
Alexandra Müller, Lucie Collineau, Roger Stephan, Andrea Müller, Katharina D C Stärk
The objective of this study was i) to quantify the risk of hepatitis E for Swiss consumers by specified pork products and ii) to estimate the total burden of human food-borne hepatitis E in Switzerland. A quantitative risk assessment from slaughter to consumption was carried out according to the Codex Alimentarius framework. In the hazard characterization, assumptions were made due to the lack of a dose-response relationship for oral exposure to hepatitis E virus (HEV). The prevalence of HEV in 160 pig livers of 40 different Swiss fattening farms was examined and determined to be 1...
November 22, 2016: International Journal of Food Microbiology
https://www.readbyqxmd.com/read/27918584/the-ace-1-locus-is-amplified-in-all-resistant-anopheles-gambiae-mosquitoes-fitness-consequences-of-homogeneous-and-heterogeneous-duplications
#19
Benoît S Assogba, Pascal Milesi, Luc S Djogbénou, Arnaud Berthomieu, Patrick Makoundou, Lamine S Baba-Moussa, Anna-Sophie Fiston-Lavier, Khalid Belkhir, Pierrick Labbé, Mylène Weill
Gene copy-number variations are widespread in natural populations, but investigating their phenotypic consequences requires contemporary duplications under selection. Such duplications have been found at the ace-1 locus (encoding the organophosphate and carbamate insecticides' target) in the mosquito Anopheles gambiae (the major malaria vector); recent studies have revealed their intriguing complexity, consistent with the involvement of various numbers and types (susceptible or resistant to insecticide) of copies...
December 2016: PLoS Biology
https://www.readbyqxmd.com/read/27917406/genomics-of-colorectal-cancer-in-african-americans
#20
Hassan Brim, Hassan Ashktorab
Genome-wide studies are increasingly becoming a must, especially for complex diseases such as cancer where multiple genes and diverse molecular mechanisms are known to be involved in genes' function alteration. In this review, we report our latest genomic and epigenomic findings in African-American colorectal cancer patients. This population suffers a higher burden of the disease and most investigators in this field are looking for the underlying genetic and epigenetic targets that might be responsible for this disparity...
September 2016: Next Generation, Sequencing & Applications
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