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https://www.readbyqxmd.com/read/29142228/genome-wide-mapping-of-genetic-determinants-influencing-dna-methylation-and-gene-expression-in-human-hippocampus
#1
Herbert Schulz, Ann-Kathrin Ruppert, Stefan Herms, Christiane Wolf, Nazanin Mirza-Schreiber, Oliver Stegle, Darina Czamara, Andreas J Forstner, Sugirthan Sivalingam, Susanne Schoch, Susanne Moebus, Benno Pütz, Axel Hillmer, Nadine Fricker, Hartmut Vatter, Bertram Müller-Myhsok, Markus M Nöthen, Albert J Becker, Per Hoffmann, Thomas Sander, Sven Cichon
Emerging evidence emphasizes the strong impact of regulatory genomic elements in neurodevelopmental processes and the complex pathways of brain disorders. The present genome-wide quantitative trait loci analyses explore the cis-regulatory effects of single-nucleotide polymorphisms (SNPs) on DNA methylation (meQTL) and gene expression (eQTL) in 110 human hippocampal biopsies. We identify cis-meQTLs at 14,118 CpG methylation sites and cis-eQTLs for 302 3'-mRNA transcripts of 288 genes. Hippocampal cis-meQTL-CpGs are enriched in flanking regions of active promoters, CpG island shores, binding sites of the transcription factor CTCF and brain eQTLs...
November 15, 2017: Nature Communications
https://www.readbyqxmd.com/read/29066808/cross-tissue-integration-of-genetic-and-epigenetic-data-offers-insight-into-autism-spectrum-disorder
#2
Shan V Andrews, Shannon E Ellis, Kelly M Bakulski, Brooke Sheppard, Lisa A Croen, Irva Hertz-Picciotto, Craig J Newschaffer, Andrew P Feinberg, Dan E Arking, Christine Ladd-Acosta, M Daniele Fallin
Integration of emerging epigenetic information with autism spectrum disorder (ASD) genetic results may elucidate functional insights not possible via either type of information in isolation. Here we use the genotype and DNA methylation (DNAm) data from cord blood and peripheral blood to identify SNPs associated with DNA methylation (meQTL lists). Additionally, we use publicly available fetal brain and lung meQTL lists to assess enrichment of ASD GWAS results for tissue-specific meQTLs. ASD-associated SNPs are enriched for fetal brain (OR = 3...
October 24, 2017: Nature Communications
https://www.readbyqxmd.com/read/29058599/evidence-of-reduced-recombination-rate-in-human-regulatory-domains
#3
Yaping Liu, Abhishek Sarkar, Pouya Kheradpour, Jason Ernst, Manolis Kellis
BACKGROUND: Recombination rate is non-uniformly distributed across the human genome. The variation of recombination rate at both fine and large scales cannot be fully explained by DNA sequences alone. Epigenetic factors, particularly DNA methylation, have recently been proposed to influence the variation in recombination rate. RESULTS: We study the relationship between recombination rate and gene regulatory domains, defined by a gene and its linked control elements...
October 20, 2017: Genome Biology
https://www.readbyqxmd.com/read/28978616/integrative-analysis-of-gwas-eqtls-and-meqtls-data-suggests-that-multiple-gene-sets-are-associated-with-bone-mineral-density
#4
W Wang, S Huang, W Hou, Y Liu, Q Fan, A He, Y Wen, J Hao, X Guo, F Zhang
OBJECTIVES: Several genome-wide association studies (GWAS) of bone mineral density (BMD) have successfully identified multiple susceptibility genes, yet isolated susceptibility genes are often difficult to interpret biologically. The aim of this study was to unravel the genetic background of BMD at pathway level, by integrating BMD GWAS data with genome-wide expression quantitative trait loci (eQTLs) and methylation quantitative trait loci (meQTLs) data METHOD: We employed the GWAS datasets of BMD from the Genetic Factors for Osteoporosis Consortium (GEFOS), analysing patients' BMD...
October 2017: Bone & Joint Research
https://www.readbyqxmd.com/read/28892072/neuregulin-signaling-pathway-in-smoking-behavior
#5
R Gupta, B Qaiser, L He, T S Hiekkalinna, A B Zheutlin, S Therman, M Ollikainen, S Ripatti, M Perola, V Salomaa, L Milani, T D Cannon, P A F Madden, T Korhonen, J Kaprio, A Loukola
Understanding molecular processes that link comorbid traits such as addictions and mental disorders can provide novel therapeutic targets. Neuregulin signaling pathway (NSP) has previously been implicated in schizophrenia, a neurodevelopmental disorder with high comorbidity to smoking. Using a Finnish twin family sample, we have previously detected association between nicotine dependence and ERBB4 (a neuregulin receptor), and linkage for smoking initiation at the ERBB4 locus on 2q33. Further, Neuregulin3 has recently been shown to associate with nicotine withdrawal in a behavioral mouse model...
August 22, 2017: Translational Psychiatry
https://www.readbyqxmd.com/read/28877428/what-has-gwas-done-for-hla-and-disease-associations
#6
REVIEW
A E Kennedy, U Ozbek, M T Dorak
The major histocompatibility complex (MHC) is located in chromosome 6p21 and contains crucial regulators of immune response, including human leucocyte antigen (HLA) genes, alongside other genes with nonimmunological roles. More recently, a repertoire of noncoding RNA genes, including expressed pseudogenes, has also been identified. The MHC is the most gene dense and most polymorphic part of the human genome. The region exhibits haplotype-specific linkage disequilibrium patterns, contains the strongest cis- and trans-eQTLs/meQTLs in the genome and is known as a hot spot for disease associations...
October 2017: International Journal of Immunogenetics
https://www.readbyqxmd.com/read/28669927/evaluation-of-genetic-variants-in-autophagy-pathway-genes-as-prognostic-biomarkers-for-breast-cancer
#7
Jing Zhou, Dong Hang, Yue Jiang, Jiaping Chen, Jing Han, Wen Zhou, Guangfu Jin, Hongxia Ma, Juncheng Dai
Autophagy-related genes (ATGs) play a critical role in the development of various diseases including cancer. However, the role of ATGs in breast cancer survival remains unclear. This study aims to investigate whether genetic variants in core ATGs are correlated with the prognosis of breast cancer. A total of 14 potentially functional variants in core ATGs were genotyped in 790 breast cancer patients. The association of each variant with breast cancer-specific survival was evaluated by log-rank test and Cox regression model...
September 5, 2017: Gene
https://www.readbyqxmd.com/read/28533441/trends-in-dna-methylation-with-age-replicate-across-diverse-human-populations
#8
Shyamalika Gopalan, Oana Carja, Maud Fagny, Etienne Patin, Justin W Myrick, Lisa M McEwen, Sarah M Mah, Michael S Kobor, Alain Froment, Marcus W Feldman, Lluis Quintana-Murci, Brenna M Henn
Aging is associated with widespread changes in genome-wide patterns of DNA methylation. Thousands of CpG sites whose tissue-specific methylation levels are strongly correlated with chronological age have been previously identified. However, the majority of these studies have focused primarily on cosmopolitan populations living in the developed world; it is not known if age-related patterns of DNA methylation at these loci are similar across a broad range of human genetic and ecological diversity. We investigated genome-wide methylation patterns using saliva- and whole blood-derived DNA from two traditionally hunting and gathering African populations: the Baka of the western Central African rain forest and the ≠Khomani San of the South African Kalahari Desert...
July 2017: Genetics
https://www.readbyqxmd.com/read/28508896/obesity-related-cpg-methylation-cg07814318-of-kruppel-like-factor-13-klf13-gene-with-childhood-obesity-and-its-cis-methylation-quantitative-loci
#9
In-Uk Koh, Hye-Ja Lee, Joo-Yeon Hwang, Nak-Hyun Choi, Suman Lee
The cg07814318 hypermethylation of Kruppel-like factor 13 (KLF13) gene has been reported for its relevancy with Body Mass Index (BMI) from European origin. We explored the cg07814318 methylation and its cis-meQTL (cis-methylation quantitative loci) of KLF13 from a childhood obesity cohort. The cg07814318 methylation in blood was significantly associated with obesity and correlated with several obesity-related physical and biochemical traits. We examined the same loci from purified three human cell types (n = 47), i...
May 16, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28334830/predicting-the-impact-of-non-coding-variants-on-dna-methylation
#10
Haoyang Zeng, David K Gifford
DNA methylation plays a crucial role in the establishment of tissue-specific gene expression and the regulation of key biological processes. However, our present inability to predict the effect of genome sequence variation on DNA methylation precludes a comprehensive assessment of the consequences of non-coding variation. We introduce CpGenie, a sequence-based framework that learns a regulatory code of DNA methylation using a deep convolutional neural network and uses this network to predict the impact of sequence variation on proximal CpG site DNA methylation...
June 20, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28219716/genetic-regulation-of-differentially-methylated-genes-in-visceral-adipose-tissue-of-severely-obese-men-discordant-for-the-metabolic-syndrome
#11
Frédéric Guénard, André Tchernof, Yves Deshaies, Simon Biron, Odette Lescelleur, Laurent Biertho, Simon Marceau, Louis Pérusse, Marie-Claude Vohl
A genetic influence on methylation levels has been reported and methylation quantitative trait loci (meQTL) have been identified in various tissues. The contribution of genetic and epigenetic factors in the development of the metabolic syndrome (MetS) has also been noted. To pinpoint candidate genes for testing the association of SNPs with MetS and its components, we aimed to evaluate the contribution of genetic variations to differentially methylated CpG sites in severely obese men discordant for MetS. A genome-wide differential methylation analysis was conducted in visceral adipose tissue (VAT) of 31 severely obese men discordant for MetS (16 with and 15 without MetS) and identified ∼17,800 variable CpG sites...
June 2017: Translational Research: the Journal of Laboratory and Clinical Medicine
https://www.readbyqxmd.com/read/28096648/identification-of-genetic-and-epigenetic-variants-associated-with-breast-cancer-prognosis-by-integrative-bioinformatics-analysis
#12
Arunima Shilpi, Yingtao Bi, Segun Jung, Samir K Patra, Ramana V Davuluri
INTRODUCTION: Breast cancer being a multifaceted disease constitutes a wide spectrum of histological and molecular variability in tumors. However, the task for the identification of these variances is complicated by the interplay between inherited genetic and epigenetic aberrations. Therefore, this study provides an extrapolate outlook to the sinister partnership between DNA methylation and single-nucleotide polymorphisms (SNPs) in relevance to the identification of prognostic markers in breast cancer...
2017: Cancer Informatics
https://www.readbyqxmd.com/read/27926527/meqtl-analysis-of-childhood-obesity-links-epigenetics-with-a-risk-snp-rs17782313-near-mc4r-from-meta-analysis
#13
Yuping Tang, Bo Jin, Lingling Zhou, Weifeng Lu
Earlier GWAS has identified that rs17782313 near MC4R was associated with obesity. However, subsequent studies showed conflicting results, especially among childhood. Besides, the mechanisms underlying the association between rs17782313 and childhood obesity remain largely unexplored, and genetic and epigenetic may interact and together affect the development of childhood obesity. We conducted a comprehensive meta-analysis to assess the association between rs17782313 and childhood obesity. MeQTL and eQTL analysis was applied to explore the effect of rs17782313 on DNA methylation and MC4R expression...
January 10, 2017: Oncotarget
https://www.readbyqxmd.com/read/27886132/the-future-is-the-past-methylation-qtls-in-schizophrenia
#14
REVIEW
Anke Hoffmann, Michael Ziller, Dietmar Spengler
Genome-wide association studies (GWAS) have remarkably advanced insight into the genetic basis of schizophrenia (SCZ). Still, most of the functional variance in disease risk remains unexplained. Hence, there is a growing need to map genetic variability-to-genes-to-functions for understanding the pathophysiology of SCZ and the development of better treatments. Genetic variation can regulate various cellular functions including DNA methylation, an epigenetic mark with important roles in transcription and the mediation of environmental influences...
November 24, 2016: Genes
https://www.readbyqxmd.com/read/27884142/dna-methylation-patterns-associated-with-oxidative-stress-in-an-ageing-population
#15
Åsa K Hedman, Mihkel Zilmer, Johan Sundström, Lars Lind, Erik Ingelsson
BACKGROUND: Oxidative stress has been related to type 2 diabetes (T2D) and cardiovascular disease (CVD), the leading global cause of death. Contributions of environmental factors such as oxidative stress on complex traits and disease may be partly mediated through changes in epigenetic marks (e.g. DNA methylation). Studies relating differential methylation with intermediate phenotypes and disease endpoints may be useful in identifying additional candidate genes and mechanisms involved in disease...
November 25, 2016: BMC Medical Genomics
https://www.readbyqxmd.com/read/27861356/a-childhood-acute-lymphoblastic-leukemia-genome-wide-association-study-identifies-novel-sex-specific-risk-variants
#16
Sandeep K Singh, Philip J Lupo, Michael E Scheurer, Anshul Saxena, Amy E Kennedy, Boubakari Ibrahimou, Manuel Alejandro Barbieri, Ken I Mills, Jacob L McCauley, Mehmet Fatih Okcu, Mehmet Tevfik Dorak
Childhood acute lymphoblastic leukemia (ALL) occurs more frequently in males. Reasons behind sex differences in childhood ALL risk are unknown. In the present genome-wide association study (GWAS), we explored the genetic basis of sex differences by comparing genotype frequencies between male and female cases in a case-only study to assess effect-modification by sex.The case-only design included 236 incident cases of childhood ALL consecutively recruited at the Texas Children's Cancer Center in Houston, Texas from 2007 to 2012...
November 2016: Medicine (Baltimore)
https://www.readbyqxmd.com/read/27792787/heritable-dna-methylation-in-cd4-cells-among-complex-families-displays-genetic-and-non-genetic-effects
#17
Kenneth Day, Lindsay L Waite, Arnald Alonso, Marguerite R Irvin, Degui Zhi, Krista S Thibeault, Stella Aslibekyan, Bertha Hidalgo, Ingrid B Borecki, Jose M Ordovas, Donna K Arnett, Hemant K Tiwari, Devin M Absher
DNA methylation at CpG sites is both heritable and influenced by environment, but the relative contributions of each to DNA methylation levels are unclear. We conducted a heritability analysis of CpG methylation in human CD4+ cells across 975 individuals from 163 families in the Genetics of Lipid-lowering Drugs and Diet Network (GOLDN). Based on a broad-sense heritability (H2) value threshold of 0.4, we identified 20,575 highly heritable CpGs among the 174,445 most variable autosomal CpGs (SD > 0.02). Tests for associations of heritable CpGs with genotype at 2,145,360 SNPs using 717 of 975 individuals showed that ~74% were cis-meQTLs (< 1 Mb away from the CpG), 6% of CpGs exhibited trans-meQTL associations (>1 Mb away from the CpG or located on a different chromosome), and 20% of CpGs showed no strong significant associations with genotype (based on a p-value threshold of 1e-7)...
2016: PloS One
https://www.readbyqxmd.com/read/27478511/methylation-quantitative-trait-loci-within-the-tomm20-gene-are-associated-with-metabolic-syndrome-related-lipid-alterations-in-severely-obese-subjects
#18
Juan de Toro-Martín, Frédéric Guénard, André Tchernof, Yves Deshaies, Louis Pérusse, Frédéric-Simon Hould, Stéfane Lebel, Picard Marceau, Marie-Claude Vohl
BACKGROUND: The TOMM20 gene was previously identified as differentially expressed and methylated between severely obese subjects with and without metabolic syndrome (MS). Since metabolic complications do not affect all obese patients to the same extent, the aim of this study was to identify methylation quantitative trait loci (meQTL) potentially associated with MS-related complications within the TOMM20 locus. METHODS: Methylation profiling, SNP genotyping and meQTL association tests (general linear models) were performed in a population of 48 severely obese subjects...
2016: Diabetology & Metabolic Syndrome
https://www.readbyqxmd.com/read/27225307/role-of-atg10-expression-quantitative-trait-loci-in-non-small-cell-lung-cancer-survival
#19
Kaipeng Xie, Cheng Liang, Qin Li, Caiwang Yan, Cheng Wang, Yayun Gu, Meng Zhu, Fangzhi Du, Hui Wang, Juncheng Dai, Xiao'an Liu, Guangfu Jin, Hongbing Shen, Hongxia Ma, Zhibin Hu
The aim of this article was to evaluate whether genetic variants in autophagy-related genes affect the overall survival (OS) of non-small cell lung cancer (NSCLC) patients. We analyzed 14 single nucleotide polymorphisms (SNPs) in core autophagy-related genes for OS in 1,001 NSCLC patients. Three promising SNPs in ATG10 were subsequently annotated by the expression quantitative trait loci (eQTL) and methylation quantitative trait loci (meQTL) analyses based on Genotype-Tissue Expression (GTEx) and The Cancer Genome Atlas (TCGA) datasets...
October 1, 2016: International Journal of Cancer. Journal International du Cancer
https://www.readbyqxmd.com/read/26699738/high-density-methylation-qtl-analysis-in-human-blood-via-next-generation-sequencing-of-the-methylated-genomic-dna-fraction
#20
Joseph L McClay, Andrey A Shabalin, Mikhail G Dozmorov, Daniel E Adkins, Gaurav Kumar, Srilaxmi Nerella, Shaunna L Clark, Sarah E Bergen, Christina M Hultman, Patrik K E Magnusson, Patrick F Sullivan, Karolina A Aberg, Edwin J C G van den Oord
BACKGROUND: Genetic influence on DNA methylation is potentially an important mechanism affecting individual differences in humans. We use next-generation sequencing to assay blood DNA methylation at approximately 4.5 million loci, each comprising 2.9 CpGs on average, in 697 normal subjects. Methylation measures at each locus are tested for association with approximately 4.5 million single nucleotide polymorphisms (SNPs) to exhaustively screen for methylation quantitative trait loci (meQTLs)...
December 23, 2015: Genome Biology
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