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https://www.readbyqxmd.com/read/28651407/-homology-analysis-and-historical-tracing-for-inter-continental-burkholderia-pseudomallei-strains-of-sequence-type-562
#1
X Zheng, L X Wang, H Wu, H Chen, X Zhu, J R He, L X Xia, W Li
Objective: To understand the homology of sequence type 562 (ST562) strains of Burkholderia pseudomallei which circulated in two separate continents (Asia and Australia) at different times. Methods:SpeⅠrestriction fragments and 4-locus multiple locus variable number tandem repeat analysis (MLVA-4) profiles were extracted from MSHR5858 (ST562 Australia strain) and 350105 (ST562 historical strain of Hainan) genomes respectively by in silico analysis and then compared with the PFGE and MLVA-4 results of five ST562 clinical isolates from Hainan to test their homology...
May 10, 2017: Zhonghua Liu Xing Bing Xue za Zhi, Zhonghua Liuxingbingxue Zazhi
https://www.readbyqxmd.com/read/28651018/meta-analysis-of-mirna-expression-profiles-for-prostate-cancer-recurrence-following-radical-prostatectomy
#2
Elnaz Pashaei, Elham Pashaei, Maryam Ahmady, Mustafa Ozen, Nizamettin Aydin
BACKGROUND: Prostate cancer (PCa) is a leading reason of death in men and the most diagnosed malignancies in the western countries at the present time. After radical prostatectomy (RP), nearly 30% of men develop clinical recurrence with high serum prostate-specific antigen levels. An important challenge in PCa research is to identify effective predictors of tumor recurrence. The molecular alterations in microRNAs are associated with PCa initiation and progression. Several miRNA microarray studies have been conducted in recurrence PCa, but the results vary among different studies...
2017: PloS One
https://www.readbyqxmd.com/read/28650996/whole-transcriptomic-and-proteomic-analyses-of-an-isogenic-m-tuberculosis-clinical-strain-with-a-naturally-occurring-15-kb-genomic-deletion
#3
Carla Duncan, Frances B Jamieson, JoLynn Troudt, Linda Izzo, Helle Bielefeldt-Ohmann, Angelo Izzo, Carolina Mehaffy
Tuberculosis remains one of the most difficult to control infectious diseases in the world. Many different factors contribute to the complexity of this disease. These include the ability of the host to control the infection which may directly relate to nutritional status, presence of co-morbidities and genetic predisposition. Pathogen factors, in particular the ability of different Mycobacterium tuberculosis strains to respond to the harsh environment of the host granuloma, which includes low oxygen and nutrient availability and the presence of damaging radical oxygen and nitrogen species, also play an important role in the success of different strains to cause disease...
2017: PloS One
https://www.readbyqxmd.com/read/28650958/dynamics-and-impact-of-homologous-recombination-on-the-evolution-of-legionella-pneumophila
#4
Sophia David, Leonor Sánchez-Busó, Simon R Harris, Pekka Marttinen, Christophe Rusniok, Carmen Buchrieser, Timothy G Harrison, Julian Parkhill
Legionella pneumophila is an environmental bacterium and the causative agent of Legionnaires' disease. Previous genomic studies have shown that recombination accounts for a high proportion (>96%) of diversity within several major disease-associated sequence types (STs) of L. pneumophila. This suggests that recombination represents a potentially important force shaping adaptation and virulence. Despite this, little is known about the biological effects of recombination in L. pneumophila, particularly with regards to homologous recombination (whereby genes are replaced with alternative allelic variants)...
June 26, 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28650343/anthrax-toxin-receptor-1-is-the-cellular-receptor-for-seneca-valley-virus
#5
Linde A Miles, Laura N Burga, Eric E Gardner, Mihnea Bostina, John T Poirier, Charles M Rudin
Seneca Valley virus (SVV) is an oncolytic picornavirus with selective tropism for neuroendocrine cancers. It has shown promise as a cancer therapeutic in preclinical studies and early-phase clinical trials. Here, we have identified anthrax toxin receptor 1 (ANTXR1) as the receptor for SVV using genome-wide loss-of-function screens. ANTXR1 is necessary for permissivity in vitro and in vivo. However, robust SVV replication requires an additional innate immune defect. We found that SVV interacts directly and specifically with ANTXR1, that this interaction is required for SVV binding to permissive cells, and that ANTXR1 expression is necessary and sufficient for infection in cell lines with decreased expression of antiviral IFN genes at baseline...
June 26, 2017: Journal of Clinical Investigation
https://www.readbyqxmd.com/read/28649742/genotranscriptomic-meta-analysis-of-the-chd-family-chromatin-remodelers-in-human-cancers-initial-evidence-of-an-oncogenic-role-for-chd7
#6
Xiaofang Chu, Xuhui Guo, Yuanyuan Jiang, Huimei Yu, Lanxin Liu, Wenqi Shan, Zeng-Quan Yang
Chromodomain helicase DNA binding proteins (CHD) are characterized by N-terminal tandem chromodomains and a central ATP-dependent helicase domain. CHDs govern the cellular machinery's access to DNA, thereby playing critical roles in various cellular processes including transcription, proliferation, and DNA damage repair. Accumulating evidence demonstrates that mutation and dysregulation of CHDs are implicated in the pathogenesis of developmental disorders and cancer. However, we know little about genomic and transcriptomic alterations and the clinical significance of most CHDs in human cancer...
June 26, 2017: Molecular Oncology
https://www.readbyqxmd.com/read/28649657/dual-pi3k-and-wnt-pathway-inhibition-is-a-synergistic-combination-against-triple-negative-breast-cancer
#7
Jeffrey P Solzak, Rutuja V Atale, Bradley A Hancock, Anthony L Sinn, Karen E Pollok, David R Jones, Milan Radovich
Triple negative breast cancer accounts for 15-20% of all breast cancer cases, but despite its lower incidence, contributes to a disproportionately higher rate of mortality. As there are currently no Food and Drug Administration-approved targeted agents for triple negative breast cancer, we embarked on a genomic-guided effort to identify novel targeted modalities. Analyses by our group and The Cancer Genome Atlas have identified activation of the PI3K-pathway in the majority of triple negative breast cancers...
2017: NPJ Breast Cancer
https://www.readbyqxmd.com/read/28649649/patterns-of-cell-cycle-checkpoint-deregulation-associated-with-intrinsic-molecular-subtypes-of-human-breast-cancer-cells
#8
Jacquelyn J Bower, Leah D Vance, Matthew Psioda, Stephanie L Smith-Roe, Dennis A Simpson, Joseph G Ibrahim, Katherine A Hoadley, Charles M Perou, William K Kaufmann
Genomic instability is a hallmark of breast cancer, contributes to tumor heterogeneity, and influences chemotherapy resistance. Although Gap 2 and mitotic checkpoints are thought to prevent genomic instability, the role of these checkpoints in breast cancer is poorly understood. Here, we assess the Gap 2 and mitotic checkpoint functions of 24 breast cancer and immortalized mammary epithelial cell lines representing four of the six intrinsic molecular subtypes of breast cancer. We found that patterns of cell cycle checkpoint deregulation were associated with the intrinsic molecular subtype of breast cancer cell lines...
2017: NPJ Breast Cancer
https://www.readbyqxmd.com/read/28649644/constitutional-variants-are-not-associated-with-her2-positive-breast-cancer-results-from-the-signal-phare-clinical-cohort
#9
Xavier Pivot, Gilles Romieu, Pierre Fumoleau, Maria Rios, Hervé Bonnefoi, Thomas Bachelot, Patrick Soulié, Christelle Jouannaud, Hugues Bourgeois, Thierry Petit, Isabelle Tennevet, David Assouline, Marie-Christine Mathieu, Jean-Philippe Jacquin, Sandrine Lavau-Denes, Ariane Darut-Jouve, Jean-Marc Ferrero, Carole Tarpin, Christelle Lévy, Valérie Delecroix, Véronique Trillet-Lenoir, Oana Cojocarasu, Jérôme Meunier, Jean-Yves Pierga, Cécile Agostini, Pierre Kerbrat, Céline Faure-Mercier, Hélène Blanché, Mourad Sahbatou, Anne Boland, Delphine Bacq, Céline Besse, Fabien Calvo, Alexia Renaud, Jean-François Deleuze, Iris Pauporté, Gilles Thomas, David G Cox
Human epidermal growth factor receptor 2-positive breast cancer is a subtype of interest regarding its outcome and the impressive impact of human epidermal growth factor receptor 2 targeted therapy. Constitutional variants may be involved in the aetiology of human epidermal growth factor receptor 2-positive breast cancer, and we propose a case-case study to test the hypothesis that single nucleotide polymorphisms may be associated with human epidermal growth factor receptor 2 status. A Genome-Wide Association Study was used in a cohort of 9836 patients from the SIGNAL/PHARE study (NCT00381901-RECF1098)...
2017: NPJ Breast Cancer
https://www.readbyqxmd.com/read/28649455/science-caf%C3%A3-s-transforming-citizens-to-scientific-citizens-what-influences-participants-perceived-change-in-health-and-scientific-literacy
#10
Syed M Ahmed, Mia DeFino, Emily Connors, Alexis Visotcky, Anne Kissack, Zeno Franco
INTRODUCTION: Science Cafés facilitated by the Clinical and Translational Science Institute of Southeast Wisconsin seek to increase health and scientific literacy through informal conversation between researchers and community members. The goal was to understand what factors have the greatest influence on attendees' perceived changes in health and science literacy levels (PCHSL) to increase impact. METHODS: Previous research established the evaluation used in the Science Cafés to measure PCHSL...
April 2017: Journal of clinical and translational science
https://www.readbyqxmd.com/read/28649445/variable-phenotype-expression-in-a-family-segregating-microdeletions-of-the-nrxn1-and-mbd5-autism-spectrum-disorder-susceptibility-genes
#11
Marc Woodbury-Smith, Rob Nicolson, Mehdi Zarrei, Ryan K C Yuen, Susan Walker, Jennifer Howe, Mohammed Uddin, Ny Hoang, Janet A Buchanan, Christina Chrysler, Ann Thompson, Peter Szatmari, Stephen W Scherer
Autism Spectrum Disorder (ASD) is a developmental condition of early childhood onset, which impacts socio-communicative functioning and is principally genetic in etiology. Currently, more than 50 genomic loci are deemed to be associated with susceptibility to ASD, showing de novo and inherited unbalanced copy number variants (CNVs) and smaller insertions and deletions (indels), more complex structural variants (SVs), as well as single nucleotide variants (SNVs) deemed of pathological significance. However, the phenotypes associated with many of these genes are variable, and penetrance is largely unelaborated in clinical descriptions...
May 3, 2017: NPJ Genomic Medicine
https://www.readbyqxmd.com/read/28649431/meta-analysis-of-host-response-networks-identifies-a-common-core-in-tuberculosis
#12
Awanti Sambarey, Abhinandan Devaprasad, Priyanka Baloni, Madhulika Mishra, Abhilash Mohan, Priyanka Tyagi, Amit Singh, J S Akshata, Razia Sultana, Shashidhar Buggi, Nagasuma Chandra
Tuberculosis remains a major global health challenge worldwide, causing more than a million deaths annually. To determine newer methods for detecting and combating the disease, it is necessary to characterise global host responses to infection. Several high throughput omics studies have provided a rich resource including a list of several genes differentially regulated in tuberculosis. An integrated analysis of these studies is necessary to identify a unified response to the infection. Such data integration is met with several challenges owing to platform dependency, patient heterogeneity, and variability in the extent of infection, resulting in little overlap among different datasets...
2017: NPJ Systems Biology and Applications
https://www.readbyqxmd.com/read/28649374/screening-and-identification-of-novel-biologically-active-natural-compounds
#13
REVIEW
David Newman
With the advent of very rapid and cheap genome analyses and the linkage of these plus microbial metabolomics to potential compound structures came the realization that there was an immense sea of novel agents to be mined and tested. In addition, it is now recognized that there is significant microbial involvement in many natural products isolated from "nominally non-microbial sources". This short review covers the current screening methods that have evolved and one might even be tempted to say "devolved" in light of the realization that target-based screens had problems when the products entered clinical testing, with off-target effects being the major ones...
2017: F1000Research
https://www.readbyqxmd.com/read/28649312/the-eu-aims-longitudinal-european-autism-project-leap-design-and-methodologies-to-identify-and-validate-stratification-biomarkers-for-autism-spectrum-disorders
#14
Eva Loth, Tony Charman, Luke Mason, Julian Tillmann, Emily J H Jones, Caroline Wooldridge, Jumana Ahmad, Bonnie Auyeung, Claudia Brogna, Sara Ambrosino, Tobias Banaschewski, Simon Baron-Cohen, Sarah Baumeister, Christian Beckmann, Michael Brammer, Daniel Brandeis, Sven Bölte, Thomas Bourgeron, Carsten Bours, Yvette de Bruijn, Bhismadev Chakrabarti, Daisy Crawley, Ineke Cornelissen, Flavio Dell' Acqua, Guillaume Dumas, Sarah Durston, Christine Ecker, Jessica Faulkner, Vincent Frouin, Pilar Garces, David Goyard, Hannah Hayward, Lindsay M Ham, Joerg Hipp, Rosemary J Holt, Mark H Johnson, Johan Isaksson, Prantik Kundu, Meng-Chuan Lai, Xavier Liogier D'ardhuy, Michael V Lombardo, David J Lythgoe, René Mandl, Andreas Meyer-Lindenberg, Carolin Moessnang, Nico Mueller, Laurence O'Dwyer, Marianne Oldehinkel, Bob Oranje, Gahan Pandina, Antonio M Persico, Amber N V Ruigrok, Barbara Ruggeri, Jessica Sabet, Roberto Sacco, Antonia San José Cáceres, Emily Simonoff, Roberto Toro, Heike Tost, Jack Waldman, Steve C R Williams, Marcel P Zwiers, Will Spooren, Declan G M Murphy, Jan K Buitelaar
BACKGROUND: The tremendous clinical and aetiological diversity among individuals with autism spectrum disorder (ASD) has been a major obstacle to the development of new treatments, as many may only be effective in particular subgroups. Precision medicine approaches aim to overcome this challenge by combining pathophysiologically based treatments with stratification biomarkers that predict which treatment may be most beneficial for particular individuals. However, so far, we have no single validated stratification biomarker for ASD...
2017: Molecular Autism
https://www.readbyqxmd.com/read/28649285/introduction-of-the-diagene-study-clinical-characteristics-pathophysiology-and-determinants-of-vascular-complications-of-type-2-diabetes
#15
Thijs T W van Herpt, Roosmarijn F H Lemmers, Mandy van Hoek, Janneke G Langendonk, Ronald J Erdtsieck, Bert Bravenboer, Annelies Lucas, Monique T Mulder, Harm R Haak, Aloysius G Lieverse, Eric J G Sijbrands
BACKGROUND: Type 2 diabetes is a major healthcare problem. Glucose-, lipid-, and blood pressure-lowering strategies decrease the risk of micro- and macrovascular complications. However, a substantial residual risk remains. To unravel the etiology of type 2 diabetes and its complications, large-scale, well-phenotyped studies with prospective follow-up are needed. This is the goal of the DiaGene study. In this manuscript, we describe the design and baseline characteristics of the study...
2017: Diabetology & Metabolic Syndrome
https://www.readbyqxmd.com/read/28649281/chromosome-12q13-13q13-13-microduplication-and-microdeletion-a-case-report-and-literature-review
#16
Jie Hu, Zhishuo Ou, Elena Infante, Sally J Kochmar, Suneeta Madan-Khetarpal, Lori Hoffner, Shafagh Parsazad, Urvashi Surti
BACKGROUND: Duplications or deletions in the 12q13.13 region are rare. Only scattered cases with duplications and/or deletions in this region have been reported in the literature or in online databases. Owing to the limited number of patients with genomic alteration within this region and lack of systematic analysis of these patients, the common clinical manifestation of these patients has remained elusive. CASE PRESENTATION: Here we report an 802 kb duplication in the 12q13...
2017: Molecular Cytogenetics
https://www.readbyqxmd.com/read/28649236/the-validation-and-implications-of-using-whole-genome-sequencing-as-a-replacement-for-traditional-serotyping-for-a-national-salmonella-reference-laboratory
#17
Chris A Yachison, Catherine Yoshida, James Robertson, John H E Nash, Peter Kruczkiewicz, Eduardo N Taboada, Matthew Walker, Aleisha Reimer, Sara Christianson, Anil Nichani, Celine Nadon
Salmonella serotyping remains the gold-standard tool for the classification of Salmonella isolates and forms the basis of Canada's national surveillance program for this priority foodborne pathogen. Public health officials have been increasingly looking toward whole genome sequencing (WGS) to provide a large set of data from which all the relevant information about an isolate can be mined. However, rigorous validation and careful consideration of potential implications in the replacement of traditional surveillance methodologies with WGS data analysis tools is needed...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28648937/the-correlation-of-the-standard-5-probe-fish-assay-with-melanocytic-tumors-of-uncertain-malignant-potential
#18
Aaron Muhlbauer, Shabnam Momtahen, Martin C Mihm, James Wang, Cynthia M Magro
BACKGROUND: FISH has recently emerged as a technique to better assess the malignant potential of histologically ambiguous melanocytic lesions. However, the usefulness of FISH has not been conclusively established. The purpose of this study was to further explore the diagnostic value of FISH in distinguishing the borderline melanocytic tumor (BMT) from melanoma. METHOD: 73 cases with BMT were analyzed retrospectively from a dermatopathology database between 2010-2015...
June 2017: Annals of Diagnostic Pathology
https://www.readbyqxmd.com/read/28648751/the-muc5b-promoter-polymorphism-and-telomere-length-in-patients-with-chronic-hypersensitivity-pneumonitis-an-observational-cohort-control-study
#19
Brett Ley, Chad A Newton, Isabel Arnould, Brett M Elicker, Travis S Henry, Eric Vittinghoff, Jeffrey A Golden, Kirk D Jones, Kiran Batra, Jose Torrealba, Christine Kim Garcia, Paul J Wolters
BACKGROUND: Patients with hypersensitivity pneumonitis are at risk of developing pulmonary fibrosis, which is associated with reduced survival. In families with multiple affected members, individuals might be diagnosed as having idiopathic pulmonary fibrosis (IPF) or chronic (fibrotic) hypersensitivity pneumonitis, which suggests these disorders share risk factors. We aimed to test whether the genomic risk factors associated with the development and progression of IPF are also associated with the development of fibrosis and reduced survival in people with chronic hypersensitivity pneumonitis...
June 22, 2017: Lancet Respiratory Medicine
https://www.readbyqxmd.com/read/28648749/transcriptome-profiling-of-3d-co-cultured-cardiomyocytes-and-endothelial-cells-under-oxidative-stress-using-a-photocrosslinkable-hydrogel-system
#20
Xiaoshan Yue, Aylin Acun, Pinar Zorlutuna
Myocardial infarction (MI) is one of the most common among cardiovascular diseases. Endothelial cells (ECs) are considered to have protective effects on cardiomyocytes (CMs) under stress conditions such as MI; however, the paracrine CM-EC crosstalk and the resulting endogenous cellular responses that could contribute to this protective effect are not thoroughly investigated. Here we created biomimetic synthetic tissues containing CMs and human induced pluripotent stem cell (hiPSC)-derived ECs (iECs), which showed improved cell survival compared to single cultures under conditions mimicking the aftermath of MI, and performed high-throughput RNA-sequencing to identify target pathways that could govern CM-iEC crosstalk and the resulting improvement in cell viability...
June 22, 2017: Acta Biomaterialia
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