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https://www.readbyqxmd.com/read/28213433/chromosomal-instability-as-a-driver-of-tumor-heterogeneity-and-evolution
#1
Samuel F Bakhoum, Dan Avi Landau
Large-scale, massively parallel sequencing of human cancer samples has revealed tremendous genetic heterogeneity within individual tumors. Indeed, tumors are composed of an admixture of diverse subpopulations-subclones-that vary in space and time. Here, we discuss a principal driver of clonal diversification in cancer known as chromosomal instability (CIN), which complements other modes of genetic diversification creating the multilayered genomic instability often seen in human cancer. Cancer cells have evolved to fine-tune chromosome missegregation rates to balance the acquisition of heterogeneity while preserving favorable genotypes, a dependence that can be exploited for a therapeutic benefit...
February 17, 2017: Cold Spring Harbor Perspectives in Medicine
https://www.readbyqxmd.com/read/28213390/epigenetic-patterns-in-blood-associated-with-lipid-traits-predict-incident-coronary-heart-disease-events-and-are-enriched-for-results-from-genome-wide-association-studies
#2
Åsa K Hedman, Michael M Mendelson, Riccardo E Marioni, Stefan Gustafsson, Roby Joehanes, Marguerite R Irvin, Degui Zhi, Johanna K Sandling, Chen Yao, Chunyu Liu, Liming Liang, Tianxiao Huan, Allan F McRae, Serkalem Demissie, Sonia Shah, John M Starr, L Adrienne Cupples, Panos Deloukas, Timothy D Spector, Johan Sundström, Ronald M Krauss, Donna K Arnett, Ian J Deary, Lars Lind, Daniel Levy, Erik Ingelsson
BACKGROUND: Genome-wide association studies have identified loci influencing circulating lipid concentrations in humans; further information on novel contributing genes, pathways, and biology may be gained through studies of epigenetic modifications. METHODS AND RESULTS: To identify epigenetic changes associated with lipid concentrations, we assayed genome-wide DNA methylation at cytosine-guanine dinucleotides (CpGs) in whole blood from 2306 individuals from 2 population-based cohorts, with replication of findings in 2025 additional individuals...
January 2017: Circulation. Cardiovascular Genetics
https://www.readbyqxmd.com/read/28211990/homozygous-mutation-in-prune1-in-an-oji-cree-male-with-a-complex-neurological-phenotype
#3
Gregory Costain, Andrea Shugar, Pradeep Krishnan, Saadet Mahmutoglu, Suzanne Laughlin, Peter Kannu
The PRUNE1 gene encodes a member of the phosphoesterases (DHH) protein superfamily that is highly expressed in the human fetal brain and involved in the regulation of cell migration. Homozygous or compound heterozygous PRUNE1 mutations were recently identified in five individuals with brain malformations from four families. We present a case of a 2-year-old male with a complex neurological phenotype and abnormalities on brain MRI. Re-annotation of clinical whole-exome sequencing data revealed a homozygous likely pathogenic variant in PRUNE1 (c...
March 2017: American Journal of Medical Genetics. Part A
https://www.readbyqxmd.com/read/28211519/palindromic-amplification-of-the-erbb2-oncogene-in-primary-her2-positive-breast-tumors
#4
Michael Marotta, Taku Onodera, Jeffrey Johnson, G Thomas Budd, Takaaki Watanabe, Xiaojiang Cui, Armando E Giuliano, Atsushi Niida, Hisashi Tanaka
Oncogene amplification confers a growth advantage to tumor cells for clonal expansion. There are several, recurrently amplified oncogenes throughout the human genome. However, it remains unclear whether this recurrent amplification is solely a manifestation of increased fitness resulting from random amplification mechanisms, or if a genomic locus-specific amplification mechanism plays a role. Here we show that the ERBB2 oncogene at 17q12 is susceptible to palindromic gene amplification, a mechanism characterized by the inverted (palindromic) duplication of genomic segments, in HER2-positive breast tumors...
February 17, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28210247/genome-insight-and-comparative-pathogenomic-analysis-of-nesterenkonia-jeotgali-strain-cd08_7-isolated-from-duodenal-mucosa-of-celiac-disease-patient
#5
Atul M Chander, Ramesan G Nair, Gurwinder Kaur, Rakesh Kochhar, Devinder K Dhawan, Sanjay K Bhadada, Shanmugam Mayilraj
Species of the genus Nesterenkonia have been isolated from different ecological niches, especially from saline habitats and reported as weak human pathogens causing asymptomatic bacteraemia. Here, for the first time we are reporting the genome sequence and pathogenomic analysis of a strain designated as CD08_7 isolated from the duodenal mucosa of a celiac disease patient, identified as Nesterenkonia jeotgali. To date, only five strains of the genus Nesterenkonia (N. massiliensis strain NP1(T), Nesterenkonia sp...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28207789/carbapenem-resistance-and-pathogenicity-of-bovine-acinetobacter-indicus-like-isolates
#6
Peter Klotz, Stephan Göttig, Ursula Leidner, Torsten Semmler, Sandra Scheufen, Christa Ewers
The objective of this study was to characterize blaOXA-23 harbouring Acinetobacter indicus-like strains from cattle including genomic and phylogenetic analyses, antimicrobial susceptibility testing and evaluation of pathogenicity in vitro and in vivo. Nasal and rectal swabs (n = 45) from cattle in Germany were screened for carbapenem-non-susceptible Acinetobacter spp. Thereby, two carbapenem resistant Acinetobacter spp. from the nasal cavities of two calves could be isolated. MALDI-TOF mass spectrometry and 16S rDNA sequencing identified these isolates as A...
2017: PloS One
https://www.readbyqxmd.com/read/28207771/comparison-of-whole-genome-amplification-techniques-for-human-single-cell-exome-sequencing
#7
Erik Borgström, Marta Paterlini, Jeff E Mold, Jonas Frisen, Joakim Lundeberg
BACKGROUND: Whole genome amplification (WGA) is currently a prerequisite for single cell whole genome or exome sequencing. Depending on the method used the rate of artifact formation, allelic dropout and sequence coverage over the genome may differ significantly. RESULTS: The largest difference between the evaluated protocols was observed when analyzing the target coverage and read depth distribution. These differences also had impact on the downstream variant calling...
2017: PloS One
https://www.readbyqxmd.com/read/28206990/a-familial-study-of-azoospermic-men-identifies-three-novel-causative-mutations-in-three-new-human-azoospermia-genes
#8
Moran Gershoni, Ron Hauser, Leah Yogev, Ofer Lehavi, Foad Azem, Haim Yavetz, Shmuel Pietrokovski, Sandra E Kleiman
PURPOSE: Up to 1% of all men experience azoospermia, a condition of complete absence of sperm in the semen. The mechanisms and genes involved in spermatogenesis are mainly studied in model organisms, and their relevance to humans is unclear because human genetic studies are very scarce. Our objective was to uncover novel human mutations and genes causing azoospermia due to testicular meiotic maturation arrest. METHODS: Affected and unaffected siblings from three families were subjected to whole-exome or whole-genome sequencing, followed by comprehensive bioinformatics analyses to identify mutations suspected to cause azoospermia...
February 16, 2017: Genetics in Medicine: Official Journal of the American College of Medical Genetics
https://www.readbyqxmd.com/read/28198669/ulfasqtl-an-ultra-fast-method-of-composite-splicing-qtl-analysis
#9
Qian Yang, Yue Hu, Jun Li, Xuegong Zhang
BACKGROUND: Alternative splicing plays important roles in many regulatory processes and diseases in human. Many genetic variants contribute to phenotypic differences in gene expression and splicing that determine variations in human traits. Detecting genetic variants that affect splicing phenotypes is essential for understanding the functional impact of genetic variations on alternative splicing. For many situations, the key phenotype is the relative splicing ratios of alternative isoforms rather than the expression values of individual isoforms...
January 25, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28198372/novel-characteristics-of-the-avian-gyrovirus-2-genome
#10
Shuai Yao, Xiang Gao, Tianbei Tuo, Chunyan Han, Yulong Gao, Xiaole Qi, Yanping Zhang, Changjun Liu, Honglei Gao, Yongqiang Wang, Xiaomei Wang
Avian gyrovirus 2 (AGV2) was the second member of the viral genus Cyclovirus to be discovered. This virus poses a significant potential threat to humans and poultry due to its global dissemination and infectiousness. We used three overlapping polymerase chain reactions (PCRs) to map the whole genome of AGV2. We then modelled the evolutionary history of these novel sequence data in the context of related sequences from GenBank. We analysed the viral protein characteristics of the different phylogenetic groups and explored differences in evolutionary trends between Chinese strains and strains from other countries...
February 15, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28196734/bactericidal-activity-of-sera-from-adolescents-vaccinated-with-bivalent-rlp2086-against-meningococcal-serogroup-b-outbreak-strains-from-france
#11
Muhamed-Kheir Taha, Julio Cesar Hawkins, Paul Liberator, Ala-Eddine Deghmane, Lubomira Andrew, Li Hao, Thomas R Jones, Lisa K McNeil, Robert E O'Neill, John L Perez, Kathrin U Jansen, Annaliesa S Anderson
OBJECTIVES: Bivalent rLP2086 (Trumenba®; MenB-FHbp), composed of two factor H binding proteins (FHbps), is a vaccine approved in the United States for prevention of Neisseria meningitidis serogroup B (MnB) invasive meningococcal disease (IMD). Bactericidal activity of sera from subjects vaccinated with bivalent rLP2086 was assessed against MnB isolates from recent disease outbreaks in France. METHODS: MnB isolates from IMD cases were characterized by whole genome sequencing and FHbp expression was assessed using a flow cytometry-based assay...
February 10, 2017: Vaccine
https://www.readbyqxmd.com/read/28196408/somatic-mutations-in-murine-models-of-leukemia-and-lymphoma-disease-specificity-and-clinical-relevance
#12
Liat Goldberg, Sheryl M Gough, Fan Lee, Christine Dang, Robert L Walker, Yeulin J Zhu, Sven Bilke, Marbin Pineda, Masahiro Onozawa, Yang Jo Chung, Paul S Meltzer, Peter D Aplan
Malignant transformation is a multistep process that is dictated by acquisition of multiple genomic aberrations that provide growth and survival advantage. During the post genomic era, high throughput genomic sequencing has advanced exponentially, leading to identification of countless cancer associated mutations with potential for targeted therapy. Mouse models of cancer serve as excellent tools to examine the functionality of gene mutations and their contribution to the malignant process. However, it remains unclear whether the genetic events that occur during transformation are similar in mice and humans...
February 14, 2017: Genes, Chromosomes & Cancer
https://www.readbyqxmd.com/read/28193177/anopheline-salivary-protein-genes-and-gene-families-an-evolutionary-overview-after-the-whole-genome-sequence-of-sixteen-anopheles-species
#13
Bruno Arcà, Fabrizio Lombardo, Claudio J Struchiner, José M C Ribeiro
BACKGROUND: Mosquito saliva is a complex cocktail whose pharmacological properties play an essential role in blood feeding by counteracting host physiological response to tissue injury. Moreover, vector borne pathogens are transmitted to vertebrates and exposed to their immune system in the context of mosquito saliva which, in virtue of its immunomodulatory properties, can modify the local environment at the feeding site and eventually affect pathogen transmission. In addition, the host antibody response to salivary proteins may be used to assess human exposure to mosquito vectors...
February 13, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28191783/concise-review-the-potential-use-of-intestinal-stem-cells-to-treat-patients-with-intestinal-failure
#14
Sung Noh Hong, James C Y Dunn, Matthias Stelzner, Martín G Martín
Intestinal failure is a rare life-threatening condition that results in the inability to maintain normal growth and hydration status by enteral nutrition alone. Although parenteral nutrition and whole organ allogeneic transplantation have improved the survival of these patients, current therapies are associated with a high risk for morbidity and mortality. Development of methods to propagate adult human intestinal stem cells (ISCs) and pluripotent stem cells raises the possibility of using stem cell-based therapy for patients with monogenic and polygenic forms of intestinal failure...
February 2017: Stem Cells Translational Medicine
https://www.readbyqxmd.com/read/28191760/directing-differentiation-of-pluripotent-stem-cells-toward-retinal-pigment-epithelium-lineage
#15
Parul Choudhary, Heather Booth, Alex Gutteridge, Beata Surmacz, Irene Louca, Juliette Steer, Julie Kerby, Paul John Whiting
Development of efficient and reproducible conditions for directed differentiation of pluripotent stem cells into specific cell types is important not only to understand early human development but also to enable more practical applications, such as in vitro disease modeling, drug discovery, and cell therapies. The differentiation of stem cells to retinal pigment epithelium (RPE) in particular holds promise as a source of cells for therapeutic replacement in age-related macular degeneration. Here we show development of an efficient method for deriving homogeneous RPE populations in a period of 45 days using an adherent, monolayer system and defined xeno-free media and matrices...
February 2017: Stem Cells Translational Medicine
https://www.readbyqxmd.com/read/28191699/ndrg1-is-important-to-maintain-the-integrity-of-airway-epithelial-barrier-through-claudin-9-expression
#16
Yasuhiro Gon, Shuichiro Maruoka, Hiroyuki Kishi, Yutaka Kozu, Kuroda Kazumichi, Yasuyuki Nomura, Ikuko Takeshita, Takeshi Oshima, Shu Hashimoto
Impairment of epithelial barrier integrity caused by environmental triggers is associated with the pathogenesis of airway inflammation. Using human airway epithelial cells, we attempted to identify molecule(s) that promote airway epithelial barrier integrity. Microarray analyses were conducted using the Affimetrix human whole genome gene chip, and we identified the N-myc downstream-regulated gene 1 (NDRG1) gene, which was induced during the development of the epithelial cell barrier. Immunohistochemical analysis revealed strong NDRG1 expression in ciliated epithelial cells in nasal tissues sampled from patients with chronic rhinosinusitis (CRS), and the low expression of NDRG1 was observed in goblet cells or damaged epithelial cells...
February 13, 2017: Cell Biology International
https://www.readbyqxmd.com/read/28190458/detection-of-imprinted-genes-by-single-cell-allele-specific-gene-expression
#17
Federico A Santoni, Georgios Stamoulis, Marco Garieri, Emilie Falconnet, Pascale Ribaux, Christelle Borel, Stylianos E Antonarakis
Genomic imprinting results in parental-specific gene expression. Imprinted genes are involved in the etiology of rare syndromes and have been associated with common diseases such as diabetes and cancer. Standard RNA bulk cell sequencing applied to whole-tissue samples has been used to detect imprinted genes in human and mouse models. However, lowly expressed genes cannot be detected by using RNA bulk approaches. Here, we report an original and robust method that combines single-cell RNA-seq and whole-genome sequencing into an optimized statistical framework to analyze genomic imprinting in specific cell types and in different individuals...
February 6, 2017: American Journal of Human Genetics
https://www.readbyqxmd.com/read/28190455/who-s-who-detecting-and-resolving-sample-anomalies-in-human-dna-sequencing-studies-with-peddy
#18
Brent S Pedersen, Aaron R Quinlan
The potential for genetic discovery in human DNA sequencing studies is greatly diminished if DNA samples from a cohort are mislabeled, swapped, or contaminated or if they include unintended individuals. Unfortunately, the potential for such errors is significant since DNA samples are often manipulated by several protocols, labs, or scientists in the process of sequencing. We have developed a software package, peddy, to identify and facilitate the remediation of such errors via interactive visualizations and reports comparing the stated sex, relatedness, and ancestry to what is inferred from the individual genotypes derived from whole-genome (WGS) or whole-exome (WES) sequencing...
January 30, 2017: American Journal of Human Genetics
https://www.readbyqxmd.com/read/28188816/a-chemical-genomics-approach-to-drug-reprofiling-in-oncology-antipsychotic-drug-risperidone-as-a-potential-adenocarcinoma-treatment
#19
Suzanne J Dilly, Andrew J Clark, Andrew Marsh, Daniel A Mitchell, Ricky Cain, Colin W G Fishwick, Paul C Taylor
Drug reprofiling is emerging as an effective paradigm for discovery of cancer treatments. Herein, an antipsychotic drug is immobilised using the Magic Tag(®) chemical genomics tool and screened against a T7 bacteriophage displayed library of polypeptides from Drosophila melanogaster, as a whole genome model, to uncover an interaction with a section of 17-β-HSD10, a proposed prostate cancer target. A computational study and enzyme inhibition assay with full length human 17-β-HSD10 identifies risperidone as a drug reprofiling candidate...
February 8, 2017: Cancer Letters
https://www.readbyqxmd.com/read/28188341/evaluation-of-transcriptomic-signature-as-a-valuable-tool-to-study-drug-induced-cholestasis-in-primary-human-hepatocytes
#20
Céline Parmentier, Philippe Couttet, Armin Wolf, Thomas Zaccharias, Bruno Heyd, Philippe Bachellier, Marianne Uteng, Lysiane Richert
Primary human hepatocyte (PHH) sandwich cultures from five different donors were daily exposed to cyclosporine A (CsA), ibuprofen (IBU), chlorpromazine (CPZ), amiodarone (AMI) and paracetamol (APAP) at their respective Cmax (total) for short-term (1-3 days) and long-term treatment (14 days). Whole genome mRNA profiles (34,693 genes in total) were conducted using an Illumina microarray platform. The impact of compound treatments on gene signatures involved in liver differentiation, cholestasis and in bile acid homeostasis was evaluated...
February 10, 2017: Archives of Toxicology
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