keyword
MENU ▼
Read by QxMD icon Read
search

Epigenome wide association

keyword
https://www.readbyqxmd.com/read/29351903/integrative-genomic-analysis-predicts-causative-cis-regulatory-mechanisms-of-the-breast-cancer-associated-genetic-variant-rs4415084
#1
Yi Zhang, Mohith Manjunath, Shilu Zhang, Deborah Chasman, Sushmita Roy, Jun S Song
Previous genome-wide association studies (GWAS) have identified several common genetic variants that may significantly modulate cancer susceptibility. However, the precise molecular mechanisms behind these associations remain largely unknown; it is often not clear whether discovered variants are themselves functional or merely genetically linked to other functional variants. Here we provide an integrated method for identifying functional regulatory variants associated with cancer and their target genes by combining analyses of expression quantitative trait loci (eQTL), a modified version of allele-specific expression (ASE) that systematically utilizes haplotype information, transcription factor (TF) binding preference, and epigenetic information...
January 19, 2018: Cancer Research
https://www.readbyqxmd.com/read/29348151/ahrr-hypomethylation-lung-function-lung-function-decline-and-respiratory-symptoms
#2
Jakob B Kodal, Camilla J Kobylecki, Signe Vedel-Krogh, Børge G Nordestgaard, Stig E Bojesen
Introduction: Epigenome wide association studies have shown a consistent association between smoking exposure and hypomethylation in the aryl hydrocarbon receptor repressor(AHRR) gene(cg05575921). We tested the hypothesis that AHRR hypomethylation is associated with low lung function, steeper lung function decline, and respiratory symptoms in the general population.Methods:AHRR methylation extent was measured in 9113 individuals from the 1991-1994 examination of the Copenhagen City Heart Study, using bisulfite treated leucocyte DNA...
January 18, 2018: European Respiratory Journal: Official Journal of the European Society for Clinical Respiratory Physiology
https://www.readbyqxmd.com/read/29344347/epigenetic-alterations-in-tramp-mice-epigenome-dna-methylation-profiling-using-medip-seq
#3
Wenji Li, Ying Huang, Davit Sargsyan, Tin Oo Khor, Yue Guo, Limin Shu, Anne Yuqing Yang, Chengyue Zhang, Ximena Paredes-Gonzalez, Michael Verzi, Ronald P Hart, Ah-Ng Kong
Purpose: We investigated the genomic DNA methylation profile of prostate cancer in transgenic adenocarcinoma of the mouse prostate (TRAMP) cancer model and to analyze the crosstalk among targeted genes and the related functional pathways. Methods: Prostate DNA samples from 24-week-old TRAMP and C57BL/6 male mice were isolated. The DNA methylation profiles were analyzed by methylated DNA immunoprecipitation (MeDIP) followed by next-generation sequencing (MeDIP-seq)...
2018: Cell & Bioscience
https://www.readbyqxmd.com/read/29344313/dna-methylation-as-a-predictor-of-fetal-alcohol-spectrum-disorder
#4
Alexandre A Lussier, Alexander M Morin, Julia L MacIsaac, Jenny Salmon, Joanne Weinberg, James N Reynolds, Paul Pavlidis, Albert E Chudley, Michael S Kobor
Background: Fetal alcohol spectrum disorder (FASD) is a developmental disorder that manifests through a range of cognitive, adaptive, physiological, and neurobiological deficits resulting from prenatal alcohol exposure. Although the North American prevalence is currently estimated at 2-5%, FASD has proven difficult to identify in the absence of the overt physical features characteristic of fetal alcohol syndrome. As interventions may have the greatest impact at an early age, accurate biomarkers are needed to identify children at risk for FASD...
2018: Clinical Epigenetics
https://www.readbyqxmd.com/read/29339976/detection-of-dioxin-induced-demethylation-of-mouse-cyp1a1-gene-promoter-by-a-new-labeling-method-for-short-dna-fragments-possessing-5-methylcytosine-at-the-end
#5
Hisaka Kurita, Toshiki Aiba, Toshiyuki Saito, Seiichiroh Ohsako
Environmental factors stimulate alteration of DNA methylation level. Investigation of the genome-wide DNA methylation status is important for environmental health studies. We here designed a genomic DNA amplification and labeling protocol using a methylation-sensitive restriction enzyme HinP1 I. This method can specifically amplify genomic DNA fragments possessing methyl-CpG at the end. The fragments are a relatively short size and dominantly located on CpG-islands. By using the samples prepared by this method, a dioxin-induced change in the methylation level of the mouse Cyp1a1 promoter was successfully evaluated using oligonucleotide probes covalently bound onto a glass plate...
2018: Genes and Environment: the Official Journal of the Japanese Environmental Mutagen Society
https://www.readbyqxmd.com/read/29331684/reprogramming-neurodegeneration-in-the-big-data-era
#6
REVIEW
Lujia Zhou, Patrik Verstreken
Recent genome-wide association studies (GWAS) have identified numerous genetic risk variants for late-onset Alzheimer's disease (AD) and Parkinson's disease (PD). However, deciphering the functional consequences of GWAS data is challenging due to a lack of reliable model systems to study the genetic variants that are often of low penetrance and non-coding identities. Pluripotent stem cell (PSC) technologies offer unprecedented opportunities for molecular phenotyping of GWAS variants in human neurons and microglia...
January 10, 2018: Current Opinion in Neurobiology
https://www.readbyqxmd.com/read/29326313/dna-methylation-and-age-independent-cardiovascular-risk-an-epigenome-wide-approach-the-regicor-registre-giron%C3%A3-del-cor-study
#7
Alba Fernández-Sanlés, Sergi Sayols-Baixeras, Santiago Curcio, Isaac Subirana, Jaume Marrugat, Roberto Elosua
OBJECTIVE: The objectives of this study were to decipher whether age-independent cardiovascular risk is associated with DNA methylation at 5'-cytosine-phosphate-guanine-3' (CpG) level and to determine whether these differential methylation signatures are associated with the incidence of cardiovascular events. APPROACH AND RESULTS: We designed a 2-stage, cross-sectional, epigenome-wide association study. Age-independent cardiovascular risk calculation was based on vascular age and on the residuals of the relationship between age and cardiovascular risk...
January 11, 2018: Arteriosclerosis, Thrombosis, and Vascular Biology
https://www.readbyqxmd.com/read/29325449/analysis-of-dna-methylation-in-young-people-limited-evidence-for-an-association-between-victimization-stress-and-epigenetic-variation-in-blood
#8
Sarah J Marzi, Karen Sugden, Louise Arseneault, Daniel W Belsky, Joe Burrage, David L Corcoran, Andrea Danese, Helen L Fisher, Eilis Hannon, Terrie E Moffitt, Candice L Odgers, Carmine Pariante, Richie Poulton, Benjamin S Williams, Chloe C Y Wong, Jonathan Mill, Avshalom Caspi
OBJECTIVE: DNA methylation has been proposed as an epigenetic mechanism by which early-life experiences become "embedded" in the genome and alter transcriptional processes to compromise health. The authors sought to investigate whether early-life victimization stress is associated with genome-wide DNA methylation. METHOD: The authors tested the hypothesis that victimization is associated with DNA methylation in the Environmental Risk (E-Risk) Longitudinal Study, a nationally representative 1994-1995 birth cohort of 2,232 twins born in England and Wales and assessed at ages 5, 7, 10, 12, and 18 years...
January 12, 2018: American Journal of Psychiatry
https://www.readbyqxmd.com/read/29325019/deep-molecular-phenotypes-link-complex-disorders-and-physiological-insult-to-cpg-methylation
#9
Shaza B Zaghlool, Dennis O Mook-Kanamori, Sara Kader, Nisha Stephan, Anna Halama, Rudolf Engelke, Hina Sarwath, Eman K Al-Dous, Yasmin A Mohamoud, Werner Roemisch-Margl, Jerzy Adamski, Gabi Kastenmüller, Nele Friedrich, Alessia Visconti, Pei-Chien Tsai, Tim Spector, Jordana Bell, Mario Falchi, Annika Wahl, Melanie Waldenberger, Annette Peters, Christian Gieger, Maija Pezer, Gordan Lauc, Johannes Graumann, Joel A Malek, Karsten Suhre
Epigenetic regulation of cellular function provides a mechanism for rapid organismal adaptation to changes in health, lifestyle, and environment. Associations of cytosine-guanine di-nucleotide (CpG) methylation with clinical endpoints that overlap with metabolic phenotypes suggest a regulatory role for these CpG sites in the body's response to disease or environmental stress. We previously identified 20 CpG sites in an epigenome-wide association study (EWAS) with metabolomics that were also associated in recent EWASs with diabetes-, obesity-, and smoking-related endpoints...
January 8, 2018: Human Molecular Genetics
https://www.readbyqxmd.com/read/29317608/epigenetics-and-cerebral-organoids-promising-directions-in-autism-spectrum-disorders
#10
REVIEW
Sheena Louise Forsberg, Mirolyuba Ilieva, Tanja Maria Michel
Autism spectrum disorders (ASD) affect 1 in 68 children in the US according to the Centers for Disease Control and Prevention (CDC). It is characterized by impairments in social interactions and communication, restrictive and repetitive patterns of behaviors, and interests. Owing to disease complexity, only a limited number of treatment options are available mainly for children that alleviate but do not cure the debilitating symptoms. Studies confirm a genetic link, but environmental factors, such as medications, toxins, and maternal infection during pregnancy, as well as birth complications also play a role...
January 10, 2018: Translational Psychiatry
https://www.readbyqxmd.com/read/29312471/an-epigenome-wide-study-of-obesity-in-african-american-youth-and-young-adults-novel-findings-replication-in-neutrophils-and-relationship-with-gene-expression
#11
Xiaoling Wang, Yue Pan, Haidong Zhu, Guang Hao, Yisong Huang, Vernon Barnes, Huidong Shi, Harold Snieder, James Pankow, Kari North, Megan Grove, Weihua Guan, Ellen Demerath, Yanbin Dong, Shaoyong Su
Background: We conducted an epigenome-wide association study (EWAS) on obesity in healthy youth and young adults and further examined to what extent identified signals influenced gene expression and were independent of cell type composition and obesity-related cardio-metabolic risk factors. Genome-wide DNA methylation data from leukocytes were obtained from 700 African Americans aged 14-36. We also measured genome-wide DNA methylation data from neutrophils as well as genome-wide gene expression data from leukocytes in a subset of samples (n = 188)...
2018: Clinical Epigenetics
https://www.readbyqxmd.com/read/29311653/meta-analysis-of-epigenome-wide-association-studies-of-cognitive-abilities
#12
Riccardo E Marioni, Allan F McRae, Jan Bressler, Elena Colicino, Eilis Hannon, Shuo Li, Diddier Prada, Jennifer A Smith, Letizia Trevisi, Pei-Chien Tsai, Dina Vojinovic, Jeannette Simino, Daniel Levy, Chunyu Liu, Michael Mendelson, Claudia L Satizabal, Qiong Yang, Min A Jhun, Sharon L R Kardia, Wei Zhao, Stefania Bandinelli, Luigi Ferrucci, Dena G Hernandez, Andrew B Singleton, Sarah E Harris, John M Starr, Douglas P Kiel, Robert R McLean, Allan C Just, Joel Schwartz, Avron Spiro, Pantel Vokonas, Najaf Amin, M Arfan Ikram, Andre G Uitterlinden, Joyce B J van Meurs, Tim D Spector, Claire Steves, Andrea A Baccarelli, Jordana T Bell, Cornelia M van Duijn, Myriam Fornage, Yi-Hsiang Hsu, Jonathan Mill, Thomas H Mosley, Sudha Seshadri, Ian J Deary
Cognitive functions are important correlates of health outcomes across the life-course. Individual differences in cognitive functions are partly heritable. Epigenetic modifications, such as DNA methylation, are susceptible to both genetic and environmental factors and may provide insights into individual differences in cognitive functions. Epigenome-wide meta-analyses for blood-based DNA methylation levels at ~420,000 CpG sites were performed for seven measures of cognitive functioning using data from 11 cohorts...
January 8, 2018: Molecular Psychiatry
https://www.readbyqxmd.com/read/29311407/epigenome-wide-association-studies-provide-insight-into-the-pathogenesis-of-non-alcoholic-fatty-liver-disease-and-non-alcoholic-steatohepatitis
#13
Aybike Birerdinc, Zobair M Younossi
No abstract text is available yet for this article.
December 27, 2017: Annals of Hepatology
https://www.readbyqxmd.com/read/29305581/an-epigenome-wide-methylation-study-of-healthy-individuals-with-or-without-depressive-symptoms
#14
Mihoko Shimada, Takeshi Otowa, Taku Miyagawa, Tadashi Umekage, Yoshiya Kawamura, Miki Bundo, Kazuya Iwamoto, Tempei Ikegame, Mamoru Tochigi, Kiyoto Kasai, Hisanobu Kaiya, Hisashi Tanii, Yuji Okazaki, Katsushi Tokunaga, Tsukasa Sasaki
Major depressive disorder is a common psychiatric disorder that is thought to be triggered by both genetic and environmental factors. Depressive symptoms are an important public health problem and contribute to vulnerability to major depression. Although a substantial number of genetic and epigenetic studies have been performed to date, the detailed etiology of depression remains unclear and there are no validated biomarkers. DNA methylation is one of the major epigenetic modifications that play diverse roles in the etiology of complex diseases...
January 5, 2018: Journal of Human Genetics
https://www.readbyqxmd.com/read/29295990/obligatory-and-facilitative-allelic-variation-in-the-dna-methylome-within-common-disease-associated-loci
#15
Christopher G Bell, Fei Gao, Wei Yuan, Leonie Roos, Richard J Acton, Yudong Xia, Jordana Bell, Kirsten Ward, Massimo Mangino, Pirro G Hysi, Jun Wang, Timothy D Spector
Integrating epigenetic data with genome-wide association study (GWAS) results can reveal disease mechanisms. The genome sequence itself also shapes the epigenome, with CpG density and transcription factor binding sites (TFBSs) strongly encoding the DNA methylome. Therefore, genetic polymorphism impacts on the observed epigenome. Furthermore, large genetic variants alter epigenetic signal dosage. Here, we identify DNA methylation variability between GWAS-SNP risk and non-risk haplotypes. In three subsets comprising 3128 MeDIP-seq peripheral-blood DNA methylomes, we find 7173 consistent and functionally enriched Differentially Methylated Regions...
January 2, 2018: Nature Communications
https://www.readbyqxmd.com/read/29288389/principles-and-methods-of-in-silico-prioritization-of-non-coding-regulatory-variants
#16
REVIEW
Phil H Lee, Christian Lee, Xihao Li, Brian Wee, Tushar Dwivedi, Mark Daly
Over a decade of genome-wide association, studies have made great strides toward the detection of genes and genetic mechanisms underlying complex traits. However, the majority of associated loci reside in non-coding regions that are functionally uncharacterized in general. Now, the availability of large-scale tissue and cell type-specific transcriptome and epigenome data enables us to elucidate how non-coding genetic variants can affect gene expressions and are associated with phenotypic changes. Here, we provide an overview of this emerging field in human genomics, summarizing available data resources and state-of-the-art analytic methods to facilitate in-silico prioritization of non-coding regulatory mutations...
December 29, 2017: Human Genetics
https://www.readbyqxmd.com/read/29287311/hypomethylation-of-cyp2e1-and-dusp22-promoters-associated-with-disease-activity-and-erosive-disease-among-rheumatoid-arthritis-patients
#17
Amanda Mok, Brooke Rhead, Calliope Holingue, Xiaorong Shao, Hong L Quach, Diana Quach, Elizabeth Sinclair, Jonathan Graf, John Imboden, Thomas Link, Ruby Harrison, Vladimir Chernitskiy, Lisa F Barcellos, Lindsey A Criswell
OBJECTIVE: Epigenetic modifications have previously been associated with rheumatoid arthritis (RA). This study aimed to determine whether differential DNA methylation in peripheral blood cell subpopulations is associated with four clinical outcomes among RA patients. METHODS: Peripheral blood samples were taken from 63 patients in the University of California, San Francisco RA cohort (all satisfied ACR classification criteria; 57 were seropositive). Cells were FACS-sorted into four immune cell subpopulations (CD14+ monocytes, CD19+ B cells, CD4+ naïve T cells, and CD4+ memory T cells) per individual, and 229 epigenome-wide DNA methylation profiles were generated using Illumina HumanMethylation450 BeadChips...
December 29, 2017: Arthritis & Rheumatology
https://www.readbyqxmd.com/read/29286410/an-engineered-split-tet2-enzyme-for-chemical-inducible-dna-hydroxymethylation-and-epigenetic-remodeling
#18
Minjung Lee, Yubin Zhou, Yun Huang
DNA methylation is a stable and heritable epigenetic modification in the mammalian genome and is involved in regulating gene expression to control cellular functions. The reversal of DNA methylation, or DNA demethylation, is mediated by the ten-eleven translocation (TET) protein family of dioxygenases. Although it has been widely reported that aberrant DNA methylation and demethylation are associated with developmental defects and cancer, how these epigenetic changes directly contribute to the subsequent alteration in gene expression or disease progression remains unclear, largely owing to the lack of reliable tools to accurately add or remove DNA modifications in the genome at defined temporal and spatial resolution...
December 18, 2017: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/29274998/dna-methylation-of-apba3-and-mcf2-in-borderline-personality-disorder-potential-biomarkers-for-response-to-psychotherapy
#19
Nora Knoblich, Friederike Gundel, Christof Brückmann, Julia Becker-Sadzio, Christian Frischholz, Vanessa Nieratschker
Borderline personality disorder (BPD) is a severe and complex mental disease associated with high suicidal tendencies and hospitalization rates. Accumulating evidence suggests that epigenetic mechanisms are implicated in the etiology of BPD. A recent epigenome-wide study identified several novel genes which are epigenetically dysregulated in BPD. Those genes include APBA3 and MCF2. Psychotherapy such as Dialectical Behavior Therapy (DBT), an established treatment for BPD, provides an excellent setting to investigate environmental influences on epigenetic mechanisms in order to identify biomarkers for disease status and therapy success...
December 20, 2017: European Neuropsychopharmacology: the Journal of the European College of Neuropsychopharmacology
https://www.readbyqxmd.com/read/29273273/utility-of-dna-methylation-to-assess-placental-health
#20
Samantha L Wilson, Wendy P Robinson
DNA methylation (DNAm), a mitotically stable epigenetic mark, can influence as well as reflect gene expression. DNAm has been gaining interest for use as a biomarker for many conditions including placental insufficiency, specifically preeclampsia (PE) and intrauterine growth restriction (IUGR). Additionally, DNAm may retain a "memory" of earlier in utero exposures and hence provide insight into pathogeneses occurring earlier in gestation. This review will discuss the placental DNA methylome, the uses of DNAm to assess placental health, and considerations and limitations to understand in epigenome-wide association studies (EWAS)...
December 14, 2017: Placenta
keyword
keyword
83888
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"