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https://www.readbyqxmd.com/read/28931220/race-ethnicity-and-the-pharmacogenetics-of-reported-suicidality-with-efavirenz-among-clinical-trials-participants
#1
Katie R Mollan, Camlin Tierney, Jacklyn N Hellwege, Joseph J Eron, Michael G Hudgens, Roy M Gulick, Richard Haubrich, Paul E Sax, Thomas B Campbell, Eric S Daar, Kevin R Robertson, Diana Ventura, Qing Ma, Digna R Velez Edwards, David W Haas
Background: We examined associations between suicidality and genotypes that predict plasma efavirenz exposure among AIDS Clinical Trials Group study participants in the United States. Methods: Four clinical trials randomly assigned treatment-naive participants to efavirenz-containing regimens; suicidality was defined as reported suicidal ideation or attempted or completed suicide. Genotypes that predict plasma efavirenz exposure were defined by CYP2B6 and CYP2A6 polymorphisms...
September 1, 2017: Journal of Infectious Diseases
https://www.readbyqxmd.com/read/28931078/microgeographic-population-structuring-of-aedes-aegypti-diptera-culicidae
#2
André Barretto Bruno Wilke, Ramon Wilk-da-Silva, Mauro Toledo Marrelli
Aedes aegypti is one of the species most favored by changes in the environment caused by urbanization. Its abundance increases rapidly in the face of such changes, increasing the risk of disease transmission. Previous studies have shown that mosquito species that have adapted to anthropogenic environmental changes benefit from urbanization and undergo population expansion. In light of this, we used microsatellite markers to explore how urbanization processes may be modulating Ae. aegypti populations collected from three areas with different levels of urbanization in the city of São Paulo, Brazil...
2017: PloS One
https://www.readbyqxmd.com/read/28931069/methylation-associated-transcriptional-repression-of-elovl5-in-novel-colorectal-cancer-cell-lines
#3
Arnoud Boot, Jan Oosting, Jaap D H van Eendenburg, Peter J K Kuppen, Hans Morreau, Tom van Wezel
Genetic and epigenetic alterations mark colorectal cancer (CRC). Global hypomethylation is observed in nearly all CRC, but a distinct subset of CRC show the CpG Island Methylator Phenotype (CIMP). These tumors show DNA hypermethylation of a specific subset of CpG islands, resulting in transcriptional downregulation of nearby genes. Recently we reported the establishment of novel CRC cell lines derived from primary and metastatic CRC tissues. In this study we describe the DNA methylation profiling of these low passage CRC cell lines...
2017: PloS One
https://www.readbyqxmd.com/read/28931057/challenges-and-advances-for-transcriptome-assembly-in-non-model-species
#4
Arnaud Ungaro, Nicolas Pech, Jean-François Martin, R J Scott McCairns, Jean-Philippe Mévy, Rémi Chappaz, André Gilles
Analyses of high-throughput transcriptome sequences of non-model organisms are based on two main approaches: de novo assembly and genome-guided assembly using mapping to assign reads prior to assembly. Given the limits of mapping reads to a reference when it is highly divergent, as is frequently the case for non-model species, we evaluate whether using blastn would outperform mapping methods for read assignment in such situations (>15% divergence). We demonstrate its high performance by using simulated reads of lengths corresponding to those generated by the most common sequencing platforms, and over a realistic range of genetic divergence (0% to 30% divergence)...
2017: PloS One
https://www.readbyqxmd.com/read/28931044/the-performance-of-a-new-local-false-discovery-rate-method-on-tests-of-association-between-coronary-artery-disease-cad-and-genome-wide-genetic-variants
#5
Shuyan Mei, Ali Karimnezhad, Marie Forest, David R Bickel, Celia M T Greenwood
The maximum entropy (ME) method is a recently-developed approach for estimating local false discovery rates (LFDR) that incorporates external information allowing assignment of a subset of tests to a category with a different prior probability of following the null hypothesis. Using this ME method, we have reanalyzed the findings from a recent large genome-wide association study of coronary artery disease (CAD), incorporating biologic annotations. Our revised LFDR estimates show many large reductions in LFDR, particularly among the genetic variants belonging to annotation categories that were known to be of particular interest for CAD...
2017: PloS One
https://www.readbyqxmd.com/read/28931001/an-automated-rapid-iterative-negative-geotaxis-assay-for-analyzing-adult-climbing-behavior-in-a-drosophila-model-of-neurodegeneration
#6
Wenze Cao, Li Song, Jingjing Cheng, Na Yi, Luyi Cai, Fu-de Huang, Margaret Ho
Neurodegenerative diseases are frequently associated with a progressive loss of movement ability, reduced life span, and age-dependent neurodegeneration. To understand the mechanism of these cellular events, and their causal relationships with each other, Drosophila melanogaster, with its sophisticated genetic tools and diverse behavioral features, are used as disease models for assessing neurodegenerative phenotypes. Here we describe a high-throughput method to analyze Drosophila adult negative geotaxis behavior, as an indication for possible motor defects associated with neurodegeneration...
September 12, 2017: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/28930984/high-fat-diet-feeding-and-high-throughput-triacylglyceride-assay-in-drosophila-melanogaster
#7
Soda Balla Diop, Ryan T Birse, Rolf Bodmer
Heart disease is the number one cause of human death worldwide. Numerous studies have shown strong connections between obesity and cardiac malfunction in humans, but more tools and research efforts are needed to better elucidate the mechanisms involved. For over a century, the genetically highly tractable model of Drosophila has been instrumental in the discovery of key genes and molecular pathways that proved to be highly conserved across species. Many biological processes and disease mechanisms are functionally conserved in the fly, such as development (e...
September 13, 2017: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/28930978/influenza-a-virus-studies-in-a-mouse-model-of-infection
#8
Laura Rodriguez, Aitor Nogales, Luis Martínez-Sobrido
Influenza viruses cause over 500,000 deaths worldwide(1) and are associated with an annual cost of 12 - 14 billion USD in the United States alone considering direct medical and hospitalization expenses and work absenteeism(2). Animal models are crucial in Influenza A virus (IAV) studies to evaluate viral pathogenesis, host-pathogen interactions, immune responses, and the efficacy of current and/or novel vaccine approaches as well as antivirals. Mice are an advantageous small animal model because their immune system is evolutionarily similar to that found in humans, they are available from commercial vendors as genetically identical subjects, there are multiple strains that can be exploited to evaluate the genetic basis of infections, and they are relatively inexpensive and easy to manipulate...
September 7, 2017: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/28930971/determination-of-the-optimal-chromosomal-location-s-for-a-dna-element-in-escherichia-coli-using-a-novel-transposon-mediated-approach
#9
Jakob Frimodt-Møller, Godefroid Charbon, Karen A Krogfelt, Anders Løbner-Olesen
The optimal chromosomal position(s) of a given DNA element was/were determined by transposon-mediated random insertion followed by fitness selection. In bacteria, the impact of the genetic context on the function of a genetic element can be difficult to assess. Several mechanisms, including topological effects, transcriptional interference from neighboring genes, and/or replication-associated gene dosage, may affect the function of a given genetic element. Here, we describe a method that permits the random integration of a DNA element into the chromosome of Escherichia coli and select the most favorable locations using a simple growth competition experiment...
September 11, 2017: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/28930945/effects-of-propranolol-and-clonidine-on-brain-edema-blood-brain-barrier-permeability-and-endothelial-glycocalyx-disruption-following-fluid-percussion-brain-injury-in-the-rat
#10
Gustav Folmer Genét, Peter Bentzer, Morten Bagge Hansen, Sisse Rye Ostrowski, Pär Ingemar Johansson
BACKGROUND: Traumatic brain injury causes a disruption of the vascular endothelial glycocalyx layer that is associated with an overactivation of the sympathoadrenal system. We hypothesized that early and unselective beta-blockade with propranolol alone or in combination with the alfa2-agonist clonidine would decrease brain edema, blood-brain-barrier permeability and glycocalyx disruption at 24 hours after trauma. METHODS: We subjected fifty-three adult male Sprague-Dawley rats to lateral fluid-percussion brain injury and randomized infusion with propranolol (n=16), propranolol+clonidine (n=16), vehicle (n=16) or sham (n=5) for 24 hours...
September 20, 2017: Journal of Trauma and Acute Care Surgery
https://www.readbyqxmd.com/read/28930911/an-enrichment-strategy-yields-seven-novel-single-nucleotide-polymorphisms-associated-with-mortality-and-altered-th17-responses-following-blunt-trauma
#11
Lukas Schimunek, Rami A Namas, Jinling Yin, Dongmei Liu, Derek Barclay, Fayten El-Dehaibi, Andrew Abboud, Haley Lindberg, Ruben Zamora, R Billiar Timothy, Yoram Vodovotz
Trauma is the leading cause of death worldwide for individuals under the age of 55. Interpatient genomic differences, in the form of candidate single nucleotide polymorphisms (SNPs), have been associated previously with adverse outcomes after trauma. However, the utility of these SNPs to predict outcomes based on a meaningful endpoint such as survival is as yet undefined. We hypothesized that specific SNP haplotypes could segregate trauma survivors from non-survivors. Genomic DNA samples were obtained from 453 blunt trauma patients, for whom complete daily clinical and biomarker data were available for 397...
September 19, 2017: Shock
https://www.readbyqxmd.com/read/28930887/genetic-variant-near-plxdc2-influences-the-risk-of-primary-open-angle-glaucoma-by-increasing-intraocular-pressure-in-the-japanese-population
#12
Fumihiko Mabuchi, Nakako Mabuchi, Mitsuko Takamoto, Yoichi Sakurada, Seigo Yoneyama, Kenji Kashiwagi, Hiroyuki Iijima, Zentaro Yamagata, Makoto Aihara, Takeshi Iwata, Makoto Araie
PURPOSE: To assess the association between the genetic variants that were previously reported to be associated with primary open-angle glaucoma (POAG) in the Japanese population and the phenotypic features. METHODS: Six hundred sixty-one Japanese patients including 417 patients with POAG (normal tension glaucoma [NTG], n=210; high tension glaucoma [HTG], n=207) and 244 control subjects without glaucoma were analyzed for 3 genetic variants: rs547984 (near gene: ZP4), rs7081455 (PLXDC2), and rs7961953 (TMTC2)...
September 19, 2017: Journal of Glaucoma
https://www.readbyqxmd.com/read/28930868/next-generation-sequencing-revealed-tp53-mutations-to-be-malignant-marker-for-intraductal-papillary-mucinous-neoplasms-that-could-be-detected-using-pancreatic-juice
#13
Shinichi Takano, Mitsuharu Fukasawa, Makoto Kadokura, Hiroko Shindo, Ei Takahashi, Sumio Hirose, Shinya Maekawa, Kunio Mochizuki, Hiromichi Kawaida, Jun Itakura, Ryohei Katoh, Hideki Fujii, Tadashi Sato, Nobuyuki Enomoto
OBJECTIVES: The aims of this study were to identify the genetic mutations associated with malignant intraductal papillary mucinous neoplasms (IPMNs) and evaluate the possibility of detecting mutations in pure pancreatic juice by next-generation sequencing. METHODS: Resected tissues were collected from 50 patients with IPMN, and pure pancreatic juice samples were collected from 19 patients who had a resection. The extracted DNA was amplified by multiplex polymerase chain reaction targeting 52 cancer-related genes, including KRAS, GNAS, RNF43, and TP53; the mutations were then detected by next-generation sequencing and then analyzed for correlations with the clinicopathological characteristics...
September 19, 2017: Pancreas
https://www.readbyqxmd.com/read/28930861/targeted-gene-panel-sequencing-for-early-onset-inflammatory-bowel-disease-and-chronic-diarrhea
#14
Britt-Sabina Petersen, Dietrich August, Renate Abt, Moudjahed Alddafari, Lida Atarod, Safa Baris, Hemant Bhavsar, Florian Brinkert, Mary Buchta, Alla Bulashevska, Ronnie Chee, Ana I Cordeiro, Naghi Dara, Gregor Dückers, Aisha Elmarsafy, Natalie Frede, Nermeen Galal, Patrick Gerner, Erik-Oliver Glocker, Sigune Goldacker, Jutta Hammermann, Peter Hasselblatt, Zuzana Havlicekova, Katrin Hübscher, Milos Jesenak, Neslihan E Karaca, Elif Karakoc-Aydiner, Mahboubeh M Kharaghani, Sara S Kilic, Ayca Kiykim, Christoph Klein, Christian Klemann, Robin Kobbe, Daniel Kotlarz, Martin W Laass, T Ronan Leahy, Mehrnaz Mesdaghi, Sally Mitton, João F Neves, Birol Öztürk, Luis F Pereira, Jan Rohr, Jessica L R Restrepo, Gunda Ruzaike, Nadia Saleh, Suranjith Seneviratne, Ebru Senol, Carsten Speckmann, Daniel Tegtmeyer, Paul Thankam, Jutte van der Werff Ten Bosch, Horst von Bernuth, Sebastian Zeissig, Yvonne Zeissig, Andre Franke, Bodo Grimbacher
BACKGROUND: In contrast to adult-onset inflammatory bowel disease (IBD), where many genetic loci have been shown to be involved in complex disease etiology, early-onset IBD (eoIBD) and associated syndromes can sometimes present as monogenic conditions. As a result, the clinical phenotype and ideal disease management in these patients often differ from those in adult-onset IBD. However, due to high costs and the complexity of data analysis, high-throughput screening for genetic causes has not yet become a standard part of the diagnostic work-up of eoIBD patients...
September 19, 2017: Inflammatory Bowel Diseases
https://www.readbyqxmd.com/read/28930842/type-4b-hereditary-hemochromatosis-associated-with-a-novel-mutation-in-the-slc40a1-gene-a-case-report-and-a-review-of-the-literature
#15
Wei Zhang, Tingxia Lv, Jian Huang, Xiaojuan Ou
RATIONALE: Hereditary hemochromatosis can be divided into HFE- and non-HFE-related based on genetic mutations in different genes. HFE-related hemochromatosis is the most common inherited genetic disease in European populations but rare in Asia-pacific region. Recently, non-HFE-related hemochromatosis has been reported in patients from the Asian countries. PATIENT CONCERNS: We report the case of a 48-year-old Chinese Han woman who presented with abnormal liver function, diabetes mellitus, hyperferritinemia, and high transferrin saturation, with severe iron overload in parenchymal cells, Kupffer cells, and periportal fibrosis on liver biopsy...
September 2017: Medicine (Baltimore)
https://www.readbyqxmd.com/read/28930807/breadth-of-genetic-testing-selected-by-patients-at-risk-of-hereditary-breast-and-ovarian-cancer
#16
J Brian Szender, Jasmine Kaur, Katherine Clayback, Mollie L Hutton, June Mikkelson, Kunle Odunsi, Cara Dresbold
OBJECTIVE: The aim of this study was to evaluate the ability of patients at risk of hereditary breast and ovarian cancer (HBOC) syndrome to select the extent of genetic testing personally preferred and the impact of demographic factors on the breadth of testing pursued. METHODS: A single-institution cohort was enumerated consisting of patients referred for clinical genetic counseling secondary to risk of HBOC syndrome. This was a retrospective study of consecutive patients seen for genetic counseling; all patients completed an epidemiologic questionnaire and provided personal and family medical histories...
September 19, 2017: International Journal of Gynecological Cancer
https://www.readbyqxmd.com/read/28930654/a-tale-of-two-genes-microglial-apoe-and-trem2
#17
Anna A Pimenova, Edoardo Marcora, Alison M Goate
Microglial cell function is implicated in the etiology of Alzheimer's disease by human genetics. In this issue of Immunity, Krasemann et al. (2017) describe a gene expression signature associated with an APOE- and TREM2-dependent response of microglia to brain tissue damage that accumulates in aging and disease, defining an axis that might be amenable to therapeutic targeting.
September 19, 2017: Immunity
https://www.readbyqxmd.com/read/28930629/large-scale-replication-study-identified-multiple-independent-snps-in-ret-synergistically-associated-with-hirschsprung-disease-in-southern-chinese-population
#18
Yan Zhang, Qiuming He, Ruizhong Zhang, Hong Zhang, Wei Zhong, Huimin Xia
Hischsprung disease (HSCR) is an intestinal disorder with strong genetic components. RET was considered as the strongest contributor. Multiple single nucleotide polymorphisms (SNP) were demonstrated as associated with HSCR in different populations. However, whether the associations of reported SNPs derived from one causal variants or congregations of multiple variants were still not clear. In this study, we successfully genotyped 16 SNPs in RET with a largest case-control study to date, totaling 1470 HSCR and 1473 control subjects in South Chinese population...
September 20, 2017: Aging
https://www.readbyqxmd.com/read/28930612/genetic-addiction-risk-score-gars-%C3%A2-a-predictor-of-vulnerability-to-opioid-dependence
#19
Kenneth Blum, Amanda L C Chen, Panayotis K Thanos, Marcelo Febo, Zsolt Demetrovics, Kristina Dushaj, Abraham Kovoor, David Baron, David E Smith, Alphonso Kenison Roy Iii, Lyle Fried, Thomas J H Chen, Edwin Chapman, Edward Modestino, Bruce Steinberg, Rajendra D Badgaiyan
The interaction of neurotransmitters and genes that control the release of dopamine is the Brain Reward Cascade (BRC). Variations within the BRC, whether genetic or epigenetic, may predispose individuals to addictive behaviors and altered pain tolerance. This discussion authored by a group of concerned scientists and clinicians examines the Genetic Addiction Risk Score (GARS), the first test to accurately predict vulnerability to pain, addiction, and other compulsive behaviors, defined as Reward Deficiency Syndrome (RDS)...
January 1, 2018: Frontiers in Bioscience (Elite Edition)
https://www.readbyqxmd.com/read/28930591/lipoprotein-a-and-cardiovascular-disease-current-state-and-future-directions-for-an-enigmatic-lipoprotein
#20
Anum Saeed, Salim S Virani
Lipoprotein (a) (Lp (a)) is a complex polymorphic lipoprotein. Although structurally similar to low-density lipoprotein, Lp(a) has a glycoprotein, apolipoprotein(a) (apo(a)), attached to the apolipoprotein B-100 component. Several unique properties of Lp(a) can be attributed to the presence of apo(a). Several decades of research has improved our understanding of the structure, biochemistry, and pathophysiology of Lp(a) associated diseases. Genetic, epidemiological, and translational data indicate that elevated Lp(a) levels are likely in the causal pathway for atherosclerotic cardiovascular diseases as well as calcification of the aortic valves...
January 1, 2018: Frontiers in Bioscience (Landmark Edition)
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