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Expression quantitative trait loci ( eQTLs )

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https://www.readbyqxmd.com/read/29156765/network-directed-cis-mediator-analysis-of-normal-prostate-tissue-expression-profiles-reveals-downstream-regulatory-associations-of-prostate-cancer-susceptibility-loci
#1
Nicholas B Larson, Shannon K McDonnell, Zach Fogarty, Melissa C Larson, John Cheville, Shaun Riska, Saurabh Baheti, Alexandra M Weber, Asha A Nair, Liang Wang, Daniel O'Brien, Jaime Davila, Daniel J Schaid, Stephen N Thibodeau
Large-scale genome-wide association studies have identified multiple single-nucleotide polymorphisms associated with risk of prostate cancer. Many of these genetic variants are presumed to be regulatory in nature; however, follow-up expression quantitative trait loci (eQTL) association studies have to-date been restricted largely to cis-acting associations due to study limitations. While trans-eQTL scans suffer from high testing dimensionality, recent evidence indicates most trans-eQTL associations are mediated by cis-regulated genes, such as transcription factors...
October 17, 2017: Oncotarget
https://www.readbyqxmd.com/read/29149290/discovering-the-3-utr-mediated-regulation-of-alpha-synuclein
#2
Domenica Marchese, Teresa Botta-Orfila, Davide Cirillo, Juan Antonio Rodriguez, Carmen Maria Livi, Rubén Fernández-Santiago, Mario Ezquerra, Maria J Martí, Elias Bechara, Gian Gaetano Tartaglia
Recent evidence indicates a link between Parkinson's Disease (PD) and the expression of a-synuclein (SNCA) isoforms with different 3' untranslated regions (3'UTRs). Yet, the post-transcriptional mechanisms regulating SNCA expression are unknown. Using a large-scale in vitro/in silico screening we identified RNA-binding proteins (RBPs) that interact with SNCA 3' UTRs. We identified two RBPs, ELAVL1 and TIAR, that bind with high affinity to the most abundant and translationally active 3' UTR isoform (575 nt)...
November 15, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29142228/genome-wide-mapping-of-genetic-determinants-influencing-dna-methylation-and-gene-expression-in-human-hippocampus
#3
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/29127305/cis-snps-set-testing-and-predixcan-analysis-for-gene-expression-data-using-linear-mixed-models
#4
Ping Zeng, Ting Wang, Shuiping Huang
Understanding the functional mechanism of SNPs identified in GWAS on complex diseases is currently a challenging task. The studies of expression quantitative trait loci (eQTL) have shown that regulatory variants play a crucial role in the function of associated SNPs. Detecting significant genes (called eGenes) in eQTL studies and analyzing the effect sizes of cis-SNPs can offer important implications on the genetic architecture of associated SNPs and interpretations of the molecular basis of diseases. We applied linear mixed models (LMM) to the gene expression level and constructed likelihood ratio tests (LRT) to test for eGene in the Geuvadis data...
November 10, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29116076/the-effect-of-genetic-variation-on-promoter-usage-and-enhancer-activity
#5
Marco Garieri, Olivier Delaneau, Federico Santoni, Richard J Fish, David Mull, Piero Carninci, Emmanouil T Dermitzakis, Stylianos E Antonarakis, Alexandre Fort
The identification of genetic variants affecting gene expression, namely expression quantitative trait loci (eQTLs), has contributed to the understanding of mechanisms underlying human traits and diseases. The majority of these variants map in non-coding regulatory regions of the genome and their identification remains challenging. Here, we use natural genetic variation and CAGE transcriptomes from 154 EBV-transformed lymphoblastoid cell lines, derived from unrelated individuals, to map 5376 and 110 regulatory variants associated with promoter usage (puQTLs) and enhancer activity (eaQTLs), respectively...
November 7, 2017: Nature Communications
https://www.readbyqxmd.com/read/29114259/identification-of-splicing-quantitative-trait-loci-sqtl-in-drosophila-melanogaster-with-developmental-lead-pb-2-exposure
#6
Wen Qu, Katherine Gurdziel, Roger Pique-Regi, Douglas M Ruden
Lead (Pb) poisoning has been a major public health issue globally and the recent Flint water crisis has drawn nation-wide attention to its effects. To better understand how lead plays a role as a neurotoxin, we utilized the Drosophila melanogaster model to study the genetic effects of lead exposure during development and identified lead-responsive genes. In our previous studies, we have successfully identified hundreds of lead-responsive expression QTLs (eQTLs) by using RNA-seq analysis on heads collected from the Drosophila Synthetic Population Resource...
2017: Frontiers in Genetics
https://www.readbyqxmd.com/read/29109911/can-9q34-2-rs633862-polymorphism-predict-survival-in-epithelial-ovarian-cancer
#7
Rong Jiang, Yuan Xu, Pan Wang, Xi Cheng, Tingyan Shi, Rongyu Zang
Objective: Our previous genome-wide association study (GWAS) identified that the ABO rs633862 variant in chromosome 9q34.2 was associated with the risk of epithelial ovarian cancer (EOC) in Chinese Han women. The aim of the present study was to evaluate its prognostic effect on EOC. Methods: A total of 669 EOC patients were enrolled for the genotyping of rs633862 variant in 9q34.2. We used Kaplan-Meier survival curves, univariate and multivariate Cox proportional hazard models to evaluate the association of rs633862 with overall survival (OS) in EOC patients...
2017: PeerJ
https://www.readbyqxmd.com/read/29109033/predicting-and-analyzing-early-wake-up-associated-gene-expressions-by-integrating-gwas-and-eqtl-studies
#8
JiaRui Li, Tao Huang
Circadian rhythms are endogenous 24-hour rhythmic oscillations affecting human behaviors, such as sleep, blood pressure and other biological processes, the disturbance of which lead to circadian rhythm sleep disorders (CRSDs). In this study, based on the data from genome-wide association studies (GWASs) and expression quantitative trait loci (eQTLs), we tried to identify novel gene expression patterns in brain tissues that were associated with early wake-up. First, the maximum-relevance-minimum-redundancy (mRMR) method was adopted to analyze the involved gene expression patterns, yielding a feature list...
November 3, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/29101457/a-functional-strategy-to-characterize-expression-quantitative-trait-loci
#9
Elena Grassi, Elisa Mariella, Mattia Forneris, Federico Marotta, Marika Catapano, Ivan Molineris, Paolo Provero
The study of genetic variation has been revolutionized by the advent of high-throughput technologies able to determine the complete genomic sequence of thousands of individuals. Understanding the functional relevance of variants is, however, still a difficult task, especially when focusing on non-coding variants. Most of the variants associated with disease by Genome-Wide Association Studies (GWAS) are indeed non-coding, and presumably exert their effects by altering gene regulation. Expression Quantitative Trait Loci (eQTL) studies represent an important step in understanding the functional relevance of regulatory variants...
November 3, 2017: Human Genetics
https://www.readbyqxmd.com/read/29100974/the-interaction-of-nos1ap-disc1-daoa-and-gsk3b-confers-susceptibility-of-early-onset-schizophrenia-in-chinese-han-population
#10
Guoqin Hu, Chengqing Yang, Lei Zhao, Yong Fan, Qinyu Lv, Jing Zhao, Minghuan Zhu, Xiangqing Guo, Chenxi Bao, Ahong Xu, Yong Jie, Yaqing Jiang, Chen Zhang, Shunying Yu, Zuowei Wang, Zezhi Li, Zhenghui Yi
Although many major breakthrough had identificated potential susceptibility genes for schizophrenia, the aetiology of schizophrenia is still unknown. In the present study, we focused on the N-methyl-Daspartate receptors related genes nitric oxide synthase 1 adaptor gene (NOS1AP), disrupted in schizophrenia 1 gene (DISC1), d-amino acid oxidase activator gene (DAOA), and glycogen synthase kinase 3-beta gene (GSK3B). A family-based genetic association study (459 Han Chinese subjects in 153 nuclear families) using 3 single nucleotide polymorphisms in NOS1AP, 2 in DISC1, 1 in DAOA and 1 in GSK3B was conducted...
October 31, 2017: Progress in Neuro-psychopharmacology & Biological Psychiatry
https://www.readbyqxmd.com/read/29083405/genetic-variation-and-gene-expression-across-multiple-tissues-and-developmental-stages-in-a-nonhuman-primate
#11
Anna J Jasinska, Ivette Zelaya, Susan K Service, Christine B Peterson, Rita M Cantor, Oi-Wa Choi, Joseph DeYoung, Eleazar Eskin, Lynn A Fairbanks, Scott Fears, Allison E Furterer, Yu S Huang, Vasily Ramensky, Christopher A Schmitt, Hannes Svardal, Matthew J Jorgensen, Jay R Kaplan, Diego Villar, Bronwen L Aken, Paul Flicek, Rishi Nag, Emily S Wong, John Blangero, Thomas D Dyer, Marina Bogomolov, Yoav Benjamini, George M Weinstock, Ken Dewar, Chiara Sabatti, Richard K Wilson, J David Jentsch, Wesley Warren, Giovanni Coppola, Roger P Woods, Nelson B Freimer
By analyzing multitissue gene expression and genome-wide genetic variation data in samples from a vervet monkey pedigree, we generated a transcriptome resource and produced the first catalog of expression quantitative trait loci (eQTLs) in a nonhuman primate model. This catalog contains more genome-wide significant eQTLs per sample than comparable human resources and identifies sex- and age-related expression patterns. Findings include a master regulatory locus that likely has a role in immune function and a locus regulating hippocampal long noncoding RNAs (lncRNAs), whose expression correlates with hippocampal volume...
October 30, 2017: Nature Genetics
https://www.readbyqxmd.com/read/29081791/physical-interactions-and-expression-quantitative-traits-loci-identify-regulatory-connections-for-obesity-and-type-2-diabetes-associated-snps
#12
Tayaza Fadason, Cameron Ekblad, John R Ingram, William S Schierding, Justin M O'Sullivan
The mechanisms that underlie the association between obesity and type 2 diabetes are not fully understood. Here, we investigated the role of the 3D genome organization in the pathogeneses of obesity and type-2 diabetes. We interpreted the combined and differential impacts of 196 diabetes and 390 obesity associated single nucleotide polymorphisms (SNPs) by integrating data on the genes with which they physically interact (as captured by Hi-C) and the functional [i.e., expression quantitative trait loci (eQTL)] outcomes associated with these interactions...
2017: Frontiers in Genetics
https://www.readbyqxmd.com/read/29081784/eqtls-regulating-transcript-variations-associated-with-rapid-internode-elongation-in-deepwater-rice
#13
Takeshi Kuroha, Keisuke Nagai, Yusuke Kurokawa, Yoshiaki Nagamura, Miyako Kusano, Hideshi Yasui, Motoyuki Ashikari, Atsushi Fukushima
To avoid low oxygen, oxygen deficiency or oxygen deprivation, deepwater rice cultivated in flood planes can develop elongated internodes in response to submergence. Knowledge of the gene regulatory networks underlying rapid internode elongation is important for an understanding of the evolution and adaptation of major crops in response to flooding. To elucidate the genetic and molecular basis controlling their deepwater response we used microarrays and performed expression quantitative trait loci (eQTL) and phenotypic QTL (phQTL) analyses of internode samples of 85 recombinant inbred line (RIL) populations of non-deepwater (Taichung 65)- and deepwater rice (Bhadua)...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/29074555/efficient-prioritization-of-multiple-causal-eqtl-variants-via-sparse-polygenic-modeling
#14
Naoki Nariai, William W Greenwald, Christopher DeBoever, He Li, Kelly A Frazer
Expression quantitative trait loci (eQTL) studies have typically used single-variant association analysis to identify genetic variants correlated with gene expression. However, this approach has several drawbacks: causal variants cannot be distinguished from non-functional variants in strong linkage disequilibrium, combined effects from multiple causal variants cannot be captured, and low-frequency (<5% MAF) eQTL variants are difficult to identify. While these issues possibly could be overcome by using sparse polygenic models which associate multiple genetic variants with gene expression simultaneously, the predictive performance of these models for eQTL studies has not been evaluated...
October 26, 2017: Genetics
https://www.readbyqxmd.com/read/29073327/estimation-of-cis-eqtl-effect-sizes-using-a-log-of-linear-model
#15
John Palowitch, Andrey Shabalin, Yi-Hui Zhou, Andrew B Nobel, Fred A Wright
The study of expression Quantitative Trait Loci (eQTL) is an important problem in genomics and biomedicine. While detection (testing) of eQTL associations has been widely studied, less work has been devoted to the estimation of eQTL effect size. To reduce false positives, detection methods frequently rely on linear modeling of rank-based normalized or log-transformed gene expression data. Unfortunately, these approaches do not correspond to the simplest model of eQTL action, and thus yield estimates of eQTL association that can be uninterpretable and inaccurate...
October 26, 2017: Biometrics
https://www.readbyqxmd.com/read/29071797/novel-genetic-variants-in-the-p38mapk-pathway-gene-zak-and-susceptibility-to-lung-cancer
#16
Yun Feng, Yanru Wang, Hongliang Liu, Zhensheng Liu, Coleman Mills, Kouros Owzar, Jichun Xie, Younghun Han, David C Qian, Rayjean J Hung Rj, Yonathan Brhane, John McLaughlin, Paul Brennan, Heike Bickeböller, Albert Rosenberger, Richard S Houlston, Neil Caporaso, Maria Teresa Landi, Irene Brüske, Angela Risch, Yuanqing Ye, Xifeng Wu, David C Christiani, Christopher I Amos, Qingyi Wei
The P38MAPK pathway participates in regulating cell cycle, inflammation, development, cell death, cell differentiation, and tumorigenesis. Genetic variants of some genes in the P38MAPK pathway are reportedly associated with lung cancer risk. To substantiate this finding, we used six genome-wide association studies (GWASs) to comprehensively investigate the associations of 14,904 single nucleotide polymorphisms (SNPs) in 108 genes of this pathway with lung cancer risk. We identified six significant lung cancer risk-associated SNPs in two genes (CSNK2B and ZAK) after correction for multiple comparisons by a false discovery rate (FDR) < 0...
October 26, 2017: Molecular Carcinogenesis
https://www.readbyqxmd.com/read/29070082/sex-influences-eqtl-effects-of-sle-and-sj%C3%A3-gren-s-syndrome-associated-genetic-polymorphisms
#17
Magdalena Lindén, Jorge I Ramírez Sepúlveda, Tojo James, Gudny Ella Thorlacius, Susanna Brauner, David Gómez-Cabrero, Tomas Olsson, Ingrid Kockum, Marie Wahren-Herlenius
BACKGROUND: Systemic lupus erythematosus (SLE) and primary Sjögren's syndrome (pSS) are autoimmune disorders characterized by autoantibodies, dysregulated B cells, and notably high female-to-male incidence ratios. Genome-wide association studies have identified several susceptibility SNPs for both diseases. Many SNPs in the genome are expression quantitative trait loci (eQTLs), with context-dependent effects. Assuming that sex is a biological context, we investigated whether SLE/pSS SNPs act as eQTLs in B cells and used a disease-targeted approach to understand if they display sex-specific effects...
October 25, 2017: Biology of Sex Differences
https://www.readbyqxmd.com/read/29058715/estimating-the-causal-tissues-for-complex-traits-and-diseases
#18
Halit Ongen, Andrew A Brown, Olivier Delaneau, Nikolaos I Panousis, Alexandra C Nica, Emmanouil T Dermitzakis
How to interpret the biological causes underlying the predisposing markers identified through genome-wide association studies (GWAS) remains an open question. One direct and powerful way to assess the genetic causality behind GWAS is through analysis of expression quantitative trait loci (eQTLs). Here we describe a new approach to estimate the tissues behind the genetic causality of a variety of GWAS traits, using the cis-eQTLs in 44 tissues from the Genotype-Tissue Expression (GTEx) Consortium. We have adapted the regulatory trait concordance (RTC) score to measure the probability of eQTLs being active in multiple tissues and to calculate the probability that a GWAS-associated variant and an eQTL tag the same functional effect...
October 23, 2017: Nature Genetics
https://www.readbyqxmd.com/read/29058714/predicting-causal-variants-affecting-expression-by-using-whole-genome-sequencing-and-rna-seq-from-multiple-human-tissues
#19
Andrew Anand Brown, Ana Viñuela, Olivier Delaneau, Tim D Spector, Kerrin S Small, Emmanouil T Dermitzakis
Genetic association mapping produces statistical links between phenotypes and genomic regions, but identifying causal variants remains difficult. Whole-genome sequencing (WGS) can help by providing complete knowledge of all genetic variants, but it is financially prohibitive for well-powered GWAS studies. We performed mapping of expression quantitative trait loci (eQTLs) with WGS and RNA-seq, and found that lead eQTL variants called with WGS were more likely to be causal. Through simulations, we derived properties of causal variants and used them to develop a method for identifying likely causal SNPs...
October 23, 2017: Nature Genetics
https://www.readbyqxmd.com/read/29058599/evidence-of-reduced-recombination-rate-in-human-regulatory-domains
#20
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
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