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genome-wide association

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https://www.readbyqxmd.com/read/29655892/a-case-report-and-review-of-the-literature-indicate-that-hmga2-should-be-added-as-a-disease-gene-for-silver-russell-syndrome
#1
Gloria Sarah Leszinski, Katharina Warncke, Julia Hoefele, Matias Wagner
Patients with Silver-Russell syndrome (SRS), a syndromic growth retardation syndrome, usually harbor a maternal uniparental disomy of chromosome 7 or an epimutation at chromosome 11p15. However, to date the genetic cause remains unknown in around 40% of SRS cases, suggesting genetic heterogeneity and involvement of other genes. We present a 4-year-old female patient with the clinical diagnosis of SRS and negative results in common genetic SRS diagnostics. Whole exome sequencing identified a de novo heterozygous 7...
April 12, 2018: Gene
https://www.readbyqxmd.com/read/29653227/rsrc1-and-cpz-gene-polymorphisms-with-neuroblastoma-susceptibility-in-chinese-children
#2
Jue Tang, Wei Liu, Jinhong Zhu, Jiao Zhang, Feng-Hua Wang, Jiang-Hua Liang, Jia-Hang Zeng, Hui Wang, Huimin Xia, Jing He
Two new neuroblastoma susceptibility loci at 3q25 (RSRC1 rs6441201 G > A) and 4p16 (CPZ rs3796725 T > C and rs3796727 A > G) were identified by a genome-wide association study (GWAS) involving Italians, African Americans and European Americans. In this case-control study with 393 neuroblastoma cases and 812 controls, we investigated the association between these three polymorphisms and neuroblastoma susceptibility in Chinese population. We found that participants harboring the RSRC1 rs6441201A allele were associated with an increased risk of neuroblastoma (AA vs...
April 10, 2018: Gene
https://www.readbyqxmd.com/read/29653195/genome-wide-integration-study-of-circulating-mirnas-and-peripheral-whole-blood-mrnas-of-male-acute-ischemic-stroke-patients
#3
Yang Xue, Pengqi Yin, Guozhong Li, Di Zhong
Several circulating microRNAs (miRNAs) have been proved to serve as stable biomarkers in blood for acute ischemic stroke (AIS). However, the functions of these biomarkers remain elusive. By conducting the integration analysis of circulating miRNAs and peripheral whole blood mRNAs using bioinformatics methods, we explored the biological role of these circulating markers in peripheral whole blood at the genome-wide level. Stroke-related circulating miRNA profile data (GSE86291) and peripheral whole blood mRNA expression data (GSE16561) were collected from the Gene Expression Omnibus (GEO) datasets...
April 10, 2018: Neuroscience
https://www.readbyqxmd.com/read/29652918/a-genome-wide-association-study-of-red-blood-cell-fatty-acids-and-ratios-incorporating-dietary-covariates-framingham-heart-study-offspring-cohort
#4
Anya Kalsbeek, Jenna Veenstra, Jason Westra, Craig Disselkoen, Kristin Koch, Katelyn A McKenzie, Jacob O'Bott, Jason Vander Woude, Karen Fischer, Greg C Shearer, William S Harris, Nathan L Tintle
Recent analyses have suggested a strong heritable component to circulating fatty acid (FA) levels; however, only a limited number of genes have been identified which associate with FA levels. In order to expand upon a previous genome wide association study done on participants in the Framingham Heart Study Offspring Cohort and FA levels, we used data from 2,400 of these individuals for whom red blood cell FA profiles, dietary information and genotypes are available, and then conducted a genome-wide evaluation of potential genetic variants associated with 22 FAs and 15 FA ratios, after adjusting for relevant dietary covariates...
2018: PloS One
https://www.readbyqxmd.com/read/29652634/emerging-applications-of-genome-editing-technology-to-examine-functionality-of-gwas-associated-variants-for-complex-traits
#5
Andrew J P Smith, Panos Deloukas, Patricia B Munroe
Over the last decade, genome-wide association studies (GWAS) have propelled the discovery of thousands of loci associated with complex diseases. The focus is now turning towards the function of these association signals, determining the causal variant(s) amongst those in strong linkage disequilibrium, and identifying their underlying mechanisms, such as long-range gene regulation. Genome-editing techniques utilising zinc-finger nucleases (ZFN), transcription activator-like effector nucleases (TALENs) and clustered regularly-interspaced short palindromic repeats with Cas9 nuclease (CRISPR-Cas9), are becoming the tools of choice to establish functionality for these variants, due to the ability to assess effects of single variants in vivo...
April 13, 2018: Physiological Genomics
https://www.readbyqxmd.com/read/29650998/a-mega-analysis-of-expression-quantitative-trait-loci-eqtl-provides-insight-into-the-regulatory-architecture-of-gene-expression-variation-in-liver
#6
Tobias Strunz, Felix Grassmann, Javier Gayán, Satu Nahkuri, Debora Souza-Costa, Cyrille Maugeais, Sascha Fauser, Everson Nogoceke, Bernhard H F Weber
Genome-wide association studies (GWAS) have identified numerous genetic variants in the human genome associated with diseases and traits. Nevertheless, for most loci the causative variant is still unknown. Expression quantitative trait loci (eQTL) in disease relevant tissues is an excellent approach to correlate genetic association with gene expression. While liver is the primary site of gene transcription for two pathways relevant to age-related macular degeneration (AMD), namely the complement system and cholesterol metabolism, we explored the contribution of AMD associated variants to modulate liver gene expression...
April 12, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29650774/genetic-variants-in-cpa6-and-prpf31-are-associated-with-variation-in-response-to-metformin-in-individuals-with-type-2-diabetes
#7
Daniel M Rotroff, Sook Wah Yee, Kaixin Zhou, Skylar W Marvel, Hetal S Shah, John R Jack, Tammy M Havener, Monique M Hedderson, Michiaki Kubo, Mark A Herman, He Gao, Josyf C Mychaleckyi, Howard L McLeod, Alessandro Doria, Kathleen M Giacomini, Ewan R Pearson, Michael J Wagner, John B Buse, Alison A Motsinger-Reif
Metformin is the first line treatment for type 2 diabetes (T2D). Although widely prescribed, the glucose-lowering mechanism for metformin is incompletely understood. Here we used a genome-wide association approach in a diverse group of individuals with T2D from the Action to Control Cardiovascular Risk in Diabetes (ACCORD) clinical trial to identify common and rare variants associated with HbA1c response to metformin treatment, and followed up these findings in four replication cohorts. Common variants in PRPF31 and CPA6 , were associated with worse and better metformin response, respectively (p<5×10-6 ), and meta-analysis in independent cohorts displayed similar associations with metformin response (p=1...
April 12, 2018: Diabetes
https://www.readbyqxmd.com/read/29650766/association-of-genetic-instrumental-variables-for-lung-function-on-coronary-artery-disease-risk-a-2-sample-mendelian-randomization-study
#8
Shiu Lun Au Yeung, Maria-Carolina Borges, Debbie A Lawlor
BACKGROUND: Lung function, assessed by forced expiratory volume in 1 second (FEV1 ) and forced vital capacity (FVC), is inversely associated with coronary artery disease (CAD), but these associations could be because of confounding or reversed causality. We conducted a 2-sample Mendelian randomization study, using publicly available data from relevant genome-wide association studies, to examine the role of FEV1 or FVC on CAD. METHODS: We used the most recent genome-wide association studies on lung function to extract genetic instruments related to FEV1 and FVC (n=92 749)...
April 2018: Circulation. Genomic and precision medicine
https://www.readbyqxmd.com/read/29650764/genetic-variants-influencing-plasma-renin-activity-in-hypertensive-patients-from-the-pear-study-pharmacogenomic-evaluation-of-antihypertensive-responses
#9
Caitrin W McDonough, Oyunbileg Magvanjav, Ana C C Sá, Nihal M El Rouby, Chintan Dave, Amelia N Deitchman, Marina Kawaguchi-Suzuki, Wenbin Mei, Yong Shen, Ravi Shankar Prasad Singh, Mohamed Solayman, Kent R Bailey, Eric Boerwinkle, Arlene B Chapman, John G Gums, Amy Webb, Steven E Scherer, Wolfgang Sadee, Stephen T Turner, Rhonda M Cooper-DeHoff, Yan Gong, Julie A Johnson
BACKGROUND: Plasma renin is an important regulator of blood pressure (BP). Plasma renin activity (PRA) has been shown to correlate with variability in BP response to antihypertensive agents. We conducted a genome-wide association study to identify single-nucleotide polymorphisms (SNPs) associated with baseline PRA using data from the PEAR study (Pharmacogenomic Evaluation of Antihypertensive Responses). METHODS: Multiple linear regression analysis was performed in 461 whites and 297 blacks using an additive model, adjusting for age, sex, and ancestry-specific principal components...
April 2018: Circulation. Genomic and precision medicine
https://www.readbyqxmd.com/read/29650679/real-time-observation-of-flexible-domain-movements-in-crispr-cas9
#10
Saki Osuka, Kazushi Isomura, Shohei Kajimoto, Tomotaka Komori, Hiroshi Nishimasu, Tomohiro Shima, Osamu Nureki, Sotaro Uemura
The CRISPR-associated protein Cas9 is widely used for genome editing because it cleaves target DNA through the assistance of a single-guide RNA (sgRNA). Structural studies have revealed the multi-domain architecture of Cas9 and suggested sequential domain movements of Cas9 upon binding to the sgRNA and the target DNA These studies also hinted at the flexibility between domains; however, it remains unclear whether these flexible movements occur in solution. Here, we directly observed dynamic fluctuations of multiple Cas9 domains, using single-molecule FRET We found that the flexible domain movements allow Cas9 to adopt transient conformations beyond those captured in the crystal structures...
April 12, 2018: EMBO Journal
https://www.readbyqxmd.com/read/29650553/enduring-epigenetic-landmarks-define-the-cancer-microenvironment
#11
Ruth Pidsley, Mitchell G Lawrence, Elena Zotenko, Birunthi Niranjan, Aaron Statham, Jenny Song, Roman M Chabanon, Wenjia Qu, Hong Wang, Michelle Richards, Shalima S Nair, Nicola J Armstrong, Hieu T Nim, Melissa Papargiris, Preetika Balanathan, Hugh French, Timothy Peters, Sam Norden, Andrew Ryan, John Pedersen, James Kench, Roger J Daly, Lisa G Horvath, Phillip Stricker, Mark Frydenberg, Renea A Taylor, Clare Stirzaker, Gail P Risbridger, Susan J Clark
The growth and progression of solid tumors involves dynamic cross-talk between cancer epithelium and the surrounding microenvironment. To date, molecular profiling has largely been restricted to the epithelial component of tumors; therefore, features underpinning the persistent protumorigenic phenotype of the tumor microenvironment are unknown. Using whole-genome bisulfite sequencing, we show for the first time that cancer-associated fibroblasts (CAFs) from localized prostate cancer display remarkably distinct and enduring genome-wide changes in DNA methylation, significantly at enhancers and promoters, compared to nonmalignant prostate fibroblasts (NPFs)...
April 12, 2018: Genome Research
https://www.readbyqxmd.com/read/29649275/evaluation-of-the-relationship-between-plasma-lipids-and-abdominal-aortic-aneurysm-a-mendelian-randomization-study
#12
Lu-Chen Weng, Nicholas S Roetker, Pamela L Lutsey, Alvaro Alonso, Weihua Guan, James S Pankow, Aaron R Folsom, Lyn M Steffen, Nathan Pankratz, Weihong Tang
Studies have reported that higher circulating levels of total cholesterol (TC), low-density lipoprotein (LDL) cholesterol and lower of high-density lipoprotein (HDL) cholesterol may be associated with increased risk of abdominal aortic aneurysm (AAA). Whether dyslipidemia causes AAA is still unclear and is potentially testable using a Mendelian randomization (MR) approach. We investigated the associations between blood lipids and AAA using two-sample MR analysis with SNP-lipids association estimates from a published genome-wide association study of blood lipids (n = 188,577) and SNP-AAA association estimates from European Americans (EAs) of the Atherosclerosis Risk in Communities (ARIC) study (n = 8,793)...
2018: PloS One
https://www.readbyqxmd.com/read/29649218/global-characterization-of-copy-number-variants-in-epilepsy-patients-from-whole-genome-sequencing
#13
Jean Monlong, Simon L Girard, Caroline Meloche, Maxime Cadieux-Dion, Danielle M Andrade, Ron G Lafreniere, Micheline Gravel, Dan Spiegelman, Alexandre Dionne-Laporte, Cyrus Boelman, Fadi F Hamdan, Jacques L Michaud, Guy Rouleau, Berge A Minassian, Guillaume Bourque, Patrick Cossette
Epilepsy will affect nearly 3% of people at some point during their lifetime. Previous copy number variants (CNVs) studies of epilepsy have used array-based technology and were restricted to the detection of large or exonic events. In contrast, whole-genome sequencing (WGS) has the potential to more comprehensively profile CNVs but existing analytic methods suffer from limited accuracy. We show that this is in part due to the non-uniformity of read coverage, even after intra-sample normalization. To improve on this, we developed PopSV, an algorithm that uses multiple samples to control for technical variation and enables the robust detection of CNVs...
April 12, 2018: PLoS Genetics
https://www.readbyqxmd.com/read/29648665/homozygous-taf8-mutation-in-a-patient-with-intellectual-disability-results-in-undetectable-taf8-protein-but-preserved-rna-polymerase-ii-transcription
#14
Farrah El-Saafin, Cynthia Curry, Tao Ye, Jean-Marie Garnier, Isabelle Kolb-Cheynel, Matthieu Stierle, Natalie L Downer, Mathew P Dixon, Luc Negroni, Imre Berger, Tim Thomas, Anne K Voss, William Dobyns, Didier Devys, Laszlo Tora
The human general transcription factor TFIID is composed of the TATA-binding protein (TBP) and 13 TBP-associated factors (TAFs). In eukaryotic cells, TFIID is thought to nucleate RNA polymerase II (Pol II) preinitiation complex formation on all protein coding gene promoters and thus, be crucial for Pol II transcription. In a child with intellectual disability, mild microcephaly, corpus callosum agenesis and poor growth we identified a homozygous splice-site mutation in TAF8 (NM_138572.2:c.781-1G>A). Our data indicate that the patient's mutation generates a frame shift and an unstable TAF8 mutant protein with an unrelated C-terminus...
April 10, 2018: Human Molecular Genetics
https://www.readbyqxmd.com/read/29648658/pseudomonas-aeruginosa-partitioning-protein-parb-acts-as-a-nucleoid-associated-protein-binding-to-multiple-copies-of-a-pars-related-motif
#15
Adam Kawalek, Aneta A Bartosik, Krzysztof Glabski, Grazyna Jagura-Burdzy
ParA and ParB homologs are involved in accurate chromosome segregation in bacteria. ParBs participate in the separation of ori domains by binding to parS palindromes, mainly localized close to oriC. In Pseudomonas aeruginosa neither ParB deficiency nor modification of all 10 parSs is lethal. However, such mutants show not only defects in chromosome segregation but also growth retardation and motility dysfunctions. Moreover, a lack of parB alters expression of over 1000 genes, suggesting that ParB could interact with the chromosome outside its canonical parS targets...
April 10, 2018: Nucleic Acids Research
https://www.readbyqxmd.com/read/29648534/chromatin-associated-rna-sequencing-char-seq-maps-genome-wide-rna-to-dna-contacts
#16
Jason C Bell, David Jukam, Nicole A Teran, Viviana I Risca, Owen K Smith, Whitney L Johnson, Jan M Skotheim, William James Greenleaf, Aaron F Straight
RNA is a critical component of chromatin in eukaryotes, both as a product of transcription, and as an essential constituent of ribonucleoprotein complexes that regulate both local and global chromatin states. Here we present a proximity ligation and sequencing method called Chromatin-Associated RNA sequencing (ChAR-seq) that maps all RNA-to-DNA contacts across the genome. Using Drosophila cells we show that ChAR-seq provides unbiased, de novo identification of targets of chromatin-bound RNAs including nascent transcripts, chromosome-specific dosage compensation ncRNAs, and genome-wide trans-associated RNAs involved in co-transcriptional RNA processing...
April 12, 2018: ELife
https://www.readbyqxmd.com/read/29648458/human-individual-radiation-sensitivity-and-prospects-for-prediction
#17
P Rajaraman, M Hauptmann, S Bouffler, A Wojcik
In the past few decades, it has become increasingly evident that sensitivity to ionising radiation is variable. This is true for tissue reactions (deterministic effects) after high doses of radiation, for stochastic effects following moderate and possibly low doses, and conceivably also for non-cancer effects such as cardiovascular disease, the causal pathway(s) of which are not yet fully understood. A high sensitivity to deterministic effects is not necessarily correlated with a high sensitivity to stochastic effects...
January 1, 2018: Annals of the ICRP
https://www.readbyqxmd.com/read/29644457/an-interplay-between-shugoshin-and-spo13-for-centromeric-cohesin-protection-and-sister-kinetochore-mono-orientation-during-meiosis-i-in-saccharomyces-cerevisiae
#18
Gunjan Mehta, Guhan Kaliyaperumal Anbalagan, Akhilendra Pratap Bharati, Purna Gadre, Santanu Kumar Ghosh
Meiosis is a specialized cell division process by which haploid gametes are produced from a diploid mother cell. Reductional chromosome segregation during meiosis I (MI) is achieved by two unique and conserved events: centromeric cohesin protection (CCP) and sister kinetochore mono-orientation (SKM). In Saccharomyces cerevisiae, a meiosis-specific protein Spo13 plays a role in both these centromere-specific events. Despite genome-wide association of Spo13, we failed to detect its function in global processes such as cohesin loading, cohesion establishment and homologs pairing...
April 11, 2018: Current Genetics
https://www.readbyqxmd.com/read/29644438/comparative-phosphoproteomic-analysis-reveals-differentially-phosphorylated-proteins-regulate-anther-and-pollen-development-in-kenaf-cytoplasmic-male-sterility-line
#19
Peng Chen, Ru Li, Ruiyang Zhou
Cytoplasmic male sterility (CMS) is widely used in plant breeding and represents a perfect model to understand cyto-nuclear interactions and pollen development research. Protein phosphorylation is ubiquitous and is involved in the regulation of diverse cellular processes. To reveal the possible mechanism of CMS and pollen development in kenaf, we performed an iTRAQ-based comparative phosphoproteome analysis in the anthers of a CMS line and wild-type plant (Wt). Whole transcriptome unigenes of kenaf as the reference genome, we identified a total of 3045 phosphorylated sites on 1640 peptides corresponding to 974 unique proteins...
April 11, 2018: Amino Acids
https://www.readbyqxmd.com/read/29643945/epigenome-wide-association-study-of-metabolic-syndrome-in-african-american-adults
#20
Tomi Akinyemiju, Anh N Do, Amit Patki, Stella Aslibekyan, Degui Zhi, Bertha Hidalgo, Hemant K Tiwari, Devin Absher, Xin Geng, Donna K Arnett, Marguerite R Irvin
Background: The high prevalence of obesity among US adults has resulted in significant increases in associated metabolic disorders such as diabetes, dyslipidemia, and high blood pressure. Together, these disorders constitute metabolic syndrome, a clinically defined condition highly prevalent among African-Americans. Identifying epigenetic alterations associated with metabolic syndrome may provide additional information regarding etiology beyond current evidence from genome-wide association studies...
2018: Clinical Epigenetics
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