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https://www.readbyqxmd.com/read/29050429/isolation-and-genetic-characterization-of-a-novel-adeno-associated-virus-from-muscovy-ducks-in-china
#1
X N Su, J J Liu, Q F Zhou, X H Zhang, L C Zhao, Q M Xie, W G Chen, F Chen
Adeno-associated virus (AAV; genus Dependoparvovirus, family Parvoviridae) was first discovered in 1965 as a contaminant in adenovirus preparations. The AAVs are generally considered non-pathogenic, and they have the ability to attenuate the replication of other more pathogenic viruses, which makes them attractive as potential therapeutics or preventative measures. This study characterized a novel AAV isolated from Muscovy ducks in China. The novel virus (MHH-05-2015) was isolated after propagating a field isolate of the DAdV-3 virus (a type 3 duck adenovirus) in duck embryo fibroblasts...
September 1, 2017: Poultry Science
https://www.readbyqxmd.com/read/29050365/mitochondrial-genome-variation-and-prostate-cancer-a-review-of-the-mutational-landscape-and-application-to-clinical-management
#2
REVIEW
Anton M F Kalsbeek, Eva K F Chan, Niall M Corcoran, Christopher M Hovens, Vanessa M Hayes
Prostate cancer is a genetic disease. While next generation sequencing has allowed for the emergence of molecular taxonomy, classification is restricted to the nuclear genome. Mutations within the maternally inherited mitochondrial genome are known to impact cancer pathogenesis, as a result of disturbances in energy metabolism and apoptosis. With a higher mutation rate, limited repair and increased copy number compared to the nuclear genome, the clinical relevance of mitochondrial DNA (mtDNA) variation requires deeper exploration...
September 19, 2017: Oncotarget
https://www.readbyqxmd.com/read/29050337/comprehensive-immune-transcriptomic-analysis-in-bladder-cancer-reveals-subtype-specific-immune-gene-expression-patterns-of-prognostic-relevance
#3
Runhan Ren, Kathrin Tyryshkin, Charles H Graham, Madhuri Koti, D Robert Siemens
Recent efforts on genome wide profiling of muscle invasive bladder cancer (MIBC) have led to its classification into distinct genomic and transcriptomic molecular subtypes that exhibit variability in prognosis. Evolving evidence from recent immunotherapy trials has demonstrated the significance of pre-existing tumour immune profiles that could guide treatment decisions. To identify immune gene expression patterns associated with the molecular subtypes, we performed a comprehensive in silico immune transcriptomic profiling, utilizing transcriptomic data from 347 MIBC cases from The Cancer Genome Atlas (TCGA)...
September 19, 2017: Oncotarget
https://www.readbyqxmd.com/read/29050303/dysregulated-expression-of-homeobox-family-genes-may-influence-survival-outcomes-of-patients-with-epithelial-ovarian-cancer-analysis-of-data-from-the-cancer-genome-atlas
#4
Kyung Jin Eoh, Hee Jung Kim, Jung-Yun Lee, Eun Ji Nam, Sunghoon Kim, Sang Wun Kim, Young Tae Kim
Homeobox (HOX) family genes encode key transcription factors for embryogenesis and may be correlated with carcinogenesis. The aim of this study was to elucidate whether aberrant expression of HOX genes influences outcomes in epithelial ovarian cancer (EOC). Gene expression data and clinicopathologic information from 630 patients with EOC were downloaded from The Cancer Genome Atlas database. We explored correlations between expression levels of HOX gene family members and clinicopathological variables. Higher expression of HOXA1, A4, A5, A7, A10, A11, B13, C13, D1, and D3 was associated with advanced FIGO stage...
September 19, 2017: Oncotarget
https://www.readbyqxmd.com/read/29050278/identification-of-core-genes-and-outcome-in-gastric-cancer-using-bioinformatics-analysis
#5
Chenhua Sun, Qi Yuan, Dongdong Wu, Xiaohu Meng, Baolin Wang
Gastric cancer (GC) is a common malignant neoplasm of gastrointestinal tract. We chose gene expression profile of GSE54129 from GEO database aiming to find key genes during the occurrence and development of GC. 132 samples, including 111 cancer and 21 normal gastric mucosa epitheliums, were included in this analysis. Differentially expressed genes (DEGs) between GC patients and health people were picked out using GEO2R tool, then we performed gene ontology (GO) analysis and Kyoto Encyclopedia of Gene and Genome (KEGG) pathway analysis using The Database for Annotation, Visualization and Integrated Discovery (DAVID)...
September 19, 2017: Oncotarget
https://www.readbyqxmd.com/read/29050264/the-microrna-expression-signature-of-pancreatic-ductal-adenocarcinoma-by-rna-sequencing-anti-tumour-functions-of-the-microrna-216-cluster
#6
Keiichi Yonemori, Naohiko Seki, Tetsuya Idichi, Hiroshi Kurahara, Yusaku Osako, Keiichi Koshizuka, Takayuki Arai, Atsushi Okato, Yoshiaki Kita, Takaaki Arigami, Yuko Mataki, Yuko Kijima, Kosei Maemura, Shoji Natsugoe
We analysed the RNA sequence-based microRNA (miRNA) signature of pancreatic ductal adenocarcinoma (PDAC). Aberrantly expressed miRNAs were successfully identified in this signature. Using the PDAC signature, we focused on 4 clustered miRNAs, miR-216a-5p, miR-216a-3p, miR-216b-5p and miR-216b-3p on human chromosome 2p16.1. All members of the miR-216 cluster were significantly reduced in PDAC specimens. Ectopic expression of these miRNAs suppressed cancer cell aggressiveness, suggesting miR-216 cluster as anti-tumour miRNAs in PDAC cells...
September 19, 2017: Oncotarget
https://www.readbyqxmd.com/read/29050249/profiling-cancer-associated-genetic-alterations-and-molecular-classification-of-cancer-in-korean-gastric-cancer-patients
#7
Yoonjung Kim, Mee-Yon Cho, Juwon Kim, Sung Nam Kim, Seoung Chul Oh, Kyung-A Lee
Recently, the Cancer Genome Atlas (TCGA) Research Network and Asian Cancer Research Group provided a new classification of gastric cancer (GC) to aid the development of biomarkers for targeted therapy and predict prognosis. We studied associations between genetically aberrant profiles of cancer-related genes, environmental factors, and histopathological features in 107 paired gastric tumor-non-tumor tissue GC samples. 6.5% of our GC cases were classified as the EBV subtype, 17.8% as the MSI subtype, 43.0% as the CIN subtype, and 32...
September 19, 2017: Oncotarget
https://www.readbyqxmd.com/read/29050246/nrf2-regulated-metabolic-gene-signature-as-a-prognostic-biomarker-in-non-small-cell-lung-cancer
#8
Akhileshwar Namani, Qin Qin Cui, Yihe Wu, Hongyan Wang, Xiu Jun Wang, Xiuwen Tang
Mutations in Kelch-like ECH-associated protein 1 (KEAP1) cause the aberrant activation of nuclear factor erythroid-derived 2-like 2 (NRF2), which leads to oncogenesis and drug resistance in lung cancer cells. Our study was designed to identify the genes involved in lung cancer progression targeted by NRF2. A series of microarray experiments in normal and cancer cells, as well as in animal models, have revealed regulatory genes downstream of NRF2 that are involved in wide variety of pathways. Specifically, we carried out individual and combinatorial microarray analysis of KEAP1 overexpression and NRF2 siRNA-knockdown in a KEAP1 mutant-A549 non-small cell lung cancer (NSCLC) cell line...
September 19, 2017: Oncotarget
https://www.readbyqxmd.com/read/29050227/identification-of-two-novel-biomarkers-of-rectal-carcinoma-progression-and-prognosis-via-co-expression-network-analysis
#9
Min Sun, Taojiao Sun, Zhongshi He, Bin Xiong
mRNA expression profiles provide important insights on a diversity of biological processes involved in rectal carcinoma (RC). Our aim was to comprehensively map complex interactions between the mRNA expression patterns and the clinical traits of RC. We employed the integrated analysis of five microarray datasets and The Cancer Genome Atlas rectal adenocarcinoma database to identify 2118 consensual differentially expressed genes (DEGs) in RC and adjacent normal tissue samples, and then applied weighted gene co-expression network analysis to parse DEGs and eight clinical traits in 66 eligible RC samples...
September 19, 2017: Oncotarget
https://www.readbyqxmd.com/read/29050216/high-number-of-chromosomal-copy-number-aberrations-inversely-relates-to-t-11-19-q21-p13-translocation-status-in-mucoepidermoid-carcinoma-of-the-salivary-glands
#10
Johannes H Matse, Enno C I Veerman, Jan G M Bolscher, C René Leemans, Bauke Ylstra, Elisabeth Bloemena
Although rare, mucoepidermoid carcinoma (MEC) is one of the most common malignant salivary gland tumors. The presence of the t(11;19)(q21;p13) translocation in a subset of MECs has raised interest in genomic aberrations in MEC. In the present study we conducted genome-wide copy-number-aberration analysis by micro-array comparative-genomic-hybridization on 27 MEC samples. Low/intermediate-grade MECs had significantly fewer copy-number-aberrations compared to high-grade MECs (low vs high: 3.48 vs 30; p = 0.0025; intermediate vs high: 5...
September 19, 2017: Oncotarget
https://www.readbyqxmd.com/read/29049906/interaction-between-compound-genetic-risk-for-schizophrenia-and-high-birth-weight-contributes-to-social-anhedonia-and-schizophrenia-in-women
#11
Johanna Liuhanen, Jaana Suvisaari, Eero Kajantie, Jouko Miettunen, Antti-Pekka Sarin, Marjo-Riitta Järvelin, Jouko Lönnqvist, Juha Veijola, Tiina Paunio
Schizophrenia is a highly heritable disease, but despite extensive study, its genetic background remains unresolved. The lack of environmental measures in genetic studies may offer some explanation. In recent Finnish studies, high birth weight was found to increase the risk for familial schizophrenia. We examined the interaction between a polygenic risk score for schizophrenia and high birth weight on social anhedonia and schizophrenia in a general population birth cohort. The study sample included 4223 participants from the 1966 Northern Finland Birth Cohort...
October 9, 2017: Psychiatry Research
https://www.readbyqxmd.com/read/29049801/search-for-genetic-factors-in-bicuspid-aortic-valve-disease-acta2-mutations-do-not-play-a-major-role
#12
Giada Tortora, Anita Wischmeijer, Paolo Berretta, Jacopo Alfonsi, Luca Di Marco, Andrea Barbieri, Caterina Marconi, Federica Isidori, Cesare Rossi, Ornella Leone, Roberto Di Bartolomeo, Marco Seri, Davide Pacini
OBJECTIVES: Mutations in ACTA2 have been reported as a cause of familiar thoracic aortic aneurysm (TAA) with associated bicuspid aortic valve (BAV) in some individuals. Our aim is to investigate the role of ACTA2 mutations in BAV associated with TAA in 20 patients. METHODS: We recruited 20 patients who underwent surgery for BAV and TAA; clinical genetic evaluation and ACTA2 mutation analysis were performed on each patient, along with next-generation sequencing analysis of BAV-related genes...
July 27, 2017: Interactive Cardiovascular and Thoracic Surgery
https://www.readbyqxmd.com/read/29049475/potential-of-aqueous-humor-as-a-surrogate-tumor-biopsy-for-retinoblastoma
#13
Jesse L Berry, Liya Xu, A Linn Murphree, Subramanian Krishnan, Kevin Stachelek, Emily Zolfaghari, Kathleen McGovern, Thomas C Lee, Anders Carlsson, Peter Kuhn, Jonathan W Kim, David Cobrinik, James Hicks
Importance: Retinoblastoma (Rb) is one of the first tumors to have a known genetic etiology. However, because biopsy of this tumor is contraindicated, it has not been possible to define the effects of secondary genetic changes on the disease course. Objective: To investigate whether the aqueous humor (AH) of Rb eyes has sufficient tumor-derived DNA to perform genetic analysis of the tumor, including DNA copy number alterations. Design, Setting, and Participants: This investigation was a case series study at a tertiary care hospital (Children's Hospital Los Angeles) with a large Rb treatment center...
October 12, 2017: JAMA Ophthalmology
https://www.readbyqxmd.com/read/29049454/association-of-mitochondrial-dna-copy-number-with-cardiovascular-disease
#14
Foram N Ashar, Yiyi Zhang, Ryan J Longchamps, John Lane, Anna Moes, Megan L Grove, Josyf C Mychaleckyj, Kent D Taylor, Josef Coresh, Jerome I Rotter, Eric Boerwinkle, Nathan Pankratz, Eliseo Guallar, Dan E Arking
Importance: Mitochondrial dysfunction is a core component of the aging process and may play a key role in atherosclerotic cardiovascular disease. Mitochondrial DNA copy number (mtDNA-CN), which represents the number of mitochondria per cell and number of mitochondrial genomes per mitochondrion, is an indirect biomarker of mitochondrial function. Objective: To determine whether mtDNA-CN, measured in an easily accessible tissue (buffy coat/circulating leukocytes), can improve risk classification for cardiovascular disease (CVD) and help guide initiation of statin therapy for primary prevention of CVD...
October 11, 2017: JAMA Cardiology
https://www.readbyqxmd.com/read/29049400/spoligotyping-and-whole-genome-sequencing-analysis-of-lineage-1-strains-of-mycobacterium-tuberculosis-in-da-nang-vietnam
#15
Minako Hijikata, Naoto Keicho, Le Van Duc, Shinji Maeda, Nguyen Thi Le Hang, Ikumi Matsushita, Seiya Kato
BACKGROUND: Spacer oligonucleotide typing (spoligotyping), a widely used, classical genotyping method for Mycobacterium tuberculosis complex (MTBC), is a PCR-based dot-blot hybridization technique to detect the genetic diversity of the direct repeat (DR) region. Of the seven major MTBC lineages in the world, lineage 1 (Indo-Oceanic) mostly corresponds to the East African-Indian (EAI) spoligotype family in East Africa and Southeast Asia. OBJECTIVES: We investigated the genomic features of Vietnamese lineage 1 strains, comparing spoligotype patterns using whole-genome sequencing (WGS) data...
2017: PloS One
https://www.readbyqxmd.com/read/29049378/immune-modulatory-genomic-properties-differentiate-gut-microbiota-of-infants-with-and-without-eczema
#16
Seungdae Oh, Gaik Chin Yap, Pei-Ying Hong, Chiung-Hui Huang, Marion M Aw, Lynette Pei-Chi Shek, Wen-Tso Liu, Bee Wah Lee
Gut microbiota play an important role in human immunological processes, potentially affecting allergic diseases such as eczema. The diversity and structure of gut microbiota in infants with eczema have been previously documented. This study aims to evaluate by comparative metagenomics differences in genetic content in gut microbiota of infants with eczema and their matched controls. Stools were collected at the age of one month old from twelve infants from an at risk birth cohort in a case control manner. Clinical follow up for atopic outcomes were carried out at the age of 12 and 24 months...
2017: PloS One
https://www.readbyqxmd.com/read/29049320/deconvolving-sequence-features-that-discriminate-between-overlapping-regulatory-annotations
#17
Akshay Kakumanu, Silvia Velasco, Esteban Mazzoni, Shaun Mahony
Genomic loci with regulatory potential can be annotated with various properties. For example, genomic sites bound by a given transcription factor (TF) can be divided according to whether they are proximal or distal to known promoters. Sites can be further labeled according to the cell types and conditions in which they are active. Given such a collection of labeled sites, it is natural to ask what sequence features are associated with each annotation label. However, discovering such label-specific sequence features is often confounded by overlaps between the labels; e...
October 19, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/29049317/identification-of-genome-wide-targets-of-olig2-in-the-adult-mouse-spinal-cord-using-chip-seq
#18
Andrew J Darr, Matt C Danzi, Lee Brady, Dorothea Emig-Agius, Amber Hackett, Roozbeh Golshani, Nikita Warner, Jae Lee, Vance P Lemmon, Pantelis Tsoulfas
In jawed vertebrates, oligodendrocytes (OLs) are the myelin-producing glial cells responsible for ensheathment of axons within the central nervous system and are also crucial for remyelination following injury or disease. Olig2 is a crucial factor in the specification and differentiation of oligodendrocyte precursor cells (OPCs) that give rise to mature, myelin-producing OLs in the developing and postnatal CNS; however, its role in adulthood is less well understood. To investigate the role Olig2 plays in regulating gene expression in the adult OL lineage in a physiologically-relevant context, we performed chromatin immunoprecipitation followed by next generation sequencing analysis (ChIP-Seq) using whole spinal cord tissue harvested from adult mice...
2017: PloS One
https://www.readbyqxmd.com/read/29049316/genomic-comparison-of-early-passage-conditionally-reprogrammed-breast-cancer-cells-to-their-corresponding-primary-tumors
#19
Akanksha S Mahajan, Bruna M Sugita, Anju N Duttargi, Francisco Saenz, Ewa Krawczyk, Justine N McCutcheon, Aline S Fonseca, Bhaskar Kallakury, Paula Pohlmann, Yuriy Gusev, Luciane R Cavalli
Conditionally reprogrammed cells (CRCs) are epithelial cells that are directly isolated from patients' specimens and propagated in vitro with feeder cells and a Rho kinase inhibitor. A number of these cells have been generated from biopsies of breast cancer patients, including ductal carcinoma in situ and invasive carcinomas. The characterization of their genomic signatures is essential to determine their ability to reflect the natural biology of their tumors of origin. In this study, we performed the genomic characterization of six newly established invasive breast cancer CRC cultures in comparison to the original patients' primary breast tumors (PBT) from which they derived...
2017: PloS One
https://www.readbyqxmd.com/read/29049296/genome-wide-expression-analysis-of-salt-stressed-diploid-and-autotetraploid-paulownia-tomentosa
#20
Zhenli Zhao, Yongsheng Li, Haifang Liu, Xiaoqiao Zhai, Minjie Deng, Yanpeng Dong, Guoqiang Fan
Paulownia tomentosa is a fast-growing tree species with multiple uses. It is grown worldwide, but is native to China, where it is widely cultivated in saline regions. We previously confirmed that autotetraploid P. tomentosa plants are more stress-tolerant than the diploid plants. However, the molecular mechanism underlying P. tomentosa salinity tolerance has not been fully characterized. Using the complete Paulownia fortunei genome as a reference, we applied next-generation RNA-sequencing technology to analyze the effects of salt stress on diploid and autotetraploid P...
2017: PloS One
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