keyword
MENU ▼
Read by QxMD icon Read
search

Expression quantitative trait loci ( eQTLs )

keyword
https://www.readbyqxmd.com/read/29766219/association-study-of-genetic-variants-in-estrogen-metabolic-pathway-genes-and-colorectal-cancer-risk-and-survival
#1
Shuwei Li, Lisheng Xie, Mulong Du, Kaili Xu, Lingjun Zhu, Haiyan Chu, Jinfei Chen, Meilin Wang, Zhengdong Zhang, Dongying Gu
Although studies have investigated the association of genetic variants and the abnormal expression of estrogen-related genes with colorectal cancer risk, the evidence remains inconsistent. We clarified the relationship of genetic variants in estrogen metabolic pathway genes with colorectal cancer risk and survival. A case-control study was performed to assess the association of single-nucleotide polymorphisms (SNPs) in ten candidate genes with colorectal cancer risk in a Chinese population. A logistic regression model and Cox regression model were used to calculate SNP effects on colorectal cancer susceptibility and survival, respectively...
May 16, 2018: Archives of Toxicology
https://www.readbyqxmd.com/read/29763751/integration-of-summary-data-from-gwas-and-eqtl-studies-identified-novel-causal-bmd-genes-with-functional-predictions
#2
Xiang-He Meng, Xiang-Ding Chen, Jonathan Greenbaum, Qin Zeng, Sheng-Lan You, Hong-Mei Xiao, Li-Jun Tan, Hong-Wen Deng
PURPOSE: Osteoporosis is a common global health problem characterized by low bone mineral density (BMD) and increased risk of fracture. Genome-wide association studies (GWAS) have identified >100 genetic loci associated with BMD. However, the functional genes responsible for most associations remain largely unknown. We conducted an innovative summary statistic data-based Mendelian randomization (SMR) analysis to identify novel causal genes associated with BMD and explored their potential functional significance...
May 12, 2018: Bone
https://www.readbyqxmd.com/read/29727689/a-comprehensive-cis-eqtl-analysis-revealed-target-genes-in-breast-cancer-susceptibility-loci-identified-in-genome-wide-association-studies
#3
Xingyi Guo, Weiqiang Lin, Jiandong Bao, Qiuyin Cai, Xiao Pan, Mengqiu Bai, Yuan Yuan, Jiajun Shi, Yaqiong Sun, Mi-Ryung Han, Jing Wang, Qi Liu, Wanqing Wen, Bingshan Li, Jirong Long, Jianghua Chen, Wei Zheng
Genome-wide association studies (GWASs) have identified more than 150 common genetic loci for breast cancer risk. However, the target genes and underlying mechanisms remain largely unknown. We conducted a cis-expression quantitative trait loci (cis-eQTL) analysis using normal or tumor breast transcriptome data from the Molecular Taxonomy of Breast Cancer International Consortium (METABRIC), The Cancer Genome Atlas (TCGA), and the Genotype-Tissue Expression (GTEx) project. We identified a total of 101 genes for 51 lead variants after combing the results of a meta-analysis of METABRIC and TCGA, and the results from GTEx at a Benjamini-Hochberg (BH)-adjusted p < 0...
May 3, 2018: American Journal of Human Genetics
https://www.readbyqxmd.com/read/29718103/a-powerful-approach-reveals-numerous-expression-quantitative-trait-haplotypes-in-multiple-tissues
#4
Dingge Ying, Mulin Jun Li, Pak Chung Sham, Miaoxin Li
Motivation: Recently many studies showed single nucleotide polymorphisms (SNPs) affect gene expression and contribute to development of complex traits/diseases in a tissue context-dependent manner. However, little is known about haplotype's influence on gene expression and complex traits, which reflects the interaction effect between SNPs. Results: In the present study, we firstly proposed a regulatory region guided eQTL haplotype association analysis approach, and then systematically investigate the expression quantitative trait loci (eQTL) haplotypes in 20 different tissues by the approach...
April 26, 2018: Bioinformatics
https://www.readbyqxmd.com/read/29703961/genetic-variants-in-chemokine-cc-subfamily-genes-influence-hepatitis-c-virus-viral-clearance
#5
Yinan Yao, Ming Yue, Feng Zang, Mei Liu, Haozhi Fan, Lingyun Zhuo, Jingjing Wu, Xueshan Xia, Yue Feng, Peng Huang, Rongbin Yu
Chemokine genes may influence both hepatitis C virus (HCV) spontaneous clearance in acute infection and treatment response in chronic infection. We conducted this study to evaluate whether the genetic variants in several CC family genes influence HCV spontaneous clearance and treatment response. The current research genotyped eight SNPs, including CCR1 rs3733096, rs13096371, CCR5 rs746492, rs1800874, CCL3 rs1130371, CCL5 rs3817656, CCL8 rs1133763, CCL14 rs854625, to explore their associations with HCV spontaneous clearance and response to treatment in two populations...
April 27, 2018: Journal of Human Genetics
https://www.readbyqxmd.com/read/29703947/human-brain-arousal-in-the-resting-state-a-genome-wide-association-study
#6
Philippe Jawinski, Holger Kirsten, Christian Sander, Janek Spada, Christine Ulke, Jue Huang, Ralph Burkhardt, Markus Scholz, Tilman Hensch, Ulrich Hegerl
Arousal affects cognition, emotion, and behavior and has been implicated in the etiology of psychiatric disorders. Although environmental conditions substantially contribute to the level of arousal, stable interindividual characteristics are well-established and a genetic basis has been suggested. Here we investigated the molecular genetics of brain arousal in the resting state by conducting a genome-wide association study (GWAS). We selected N = 1877 participants from the population-based LIFE-Adult cohort...
April 27, 2018: Molecular Psychiatry
https://www.readbyqxmd.com/read/29670885/integrative-bioinformatics-approaches-for-identification-of-drug-targets-in-hypertension
#7
Daiane Hemerich, Jessica van Setten, Vinicius Tragante, Folkert W Asselbergs
High blood pressure or hypertension is an established risk factor for a myriad of cardiovascular diseases. Genome-wide association studies have successfully found over nine hundred loci that contribute to blood pressure. However, the mechanisms through which these loci contribute to disease are still relatively undetermined as less than 10% of hypertension-associated variants are located in coding regions. Phenotypic cell-type specificity analyses and expression quantitative trait loci show predominant vascular and cardiac tissue involvement for blood pressure-associated variants...
2018: Frontiers in Cardiovascular Medicine
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
#8
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/29621232/identification-and-functional-analysis-of-glycemic-trait-loci-in-the-china-health-and-nutrition-survey
#9
Cassandra N Spracklen, Jinxiu Shi, Swarooparani Vadlamudi, Ying Wu, Meng Zou, Chelsea K Raulerson, James P Davis, Monica Zeynalzadeh, Kayla Jackson, Wentao Yuan, Haifeng Wang, Weihua Shou, Ying Wang, Jingchun Luo, Leslie A Lange, Ethan M Lange, Barry M Popkin, Penny Gordon-Larsen, Shufa Du, Wei Huang, Karen L Mohlke
To identify genetic contributions to type 2 diabetes (T2D) and related glycemic traits (fasting glucose, fasting insulin, and HbA1c), we conducted genome-wide association analyses (GWAS) in up to 7,178 Chinese subjects from nine provinces in the China Health and Nutrition Survey (CHNS). We examined patterns of population structure within CHNS and found that allele frequencies differed across provinces, consistent with genetic drift and population substructure. We further validated 32 previously described T2D- and glycemic trait-loci, including G6PC2 and SIX3-SIX2 associated with fasting glucose...
April 2018: PLoS Genetics
https://www.readbyqxmd.com/read/29610481/a-global-transcriptional-network-connecting-noncoding-mutations-to-changes-in-tumor-gene-expression
#10
Wei Zhang, Ana Bojorquez-Gomez, Daniel Ortiz Velez, Guorong Xu, Kyle S Sanchez, John Paul Shen, Kevin Chen, Katherine Licon, Collin Melton, Katrina M Olson, Michael Ku Yu, Justin K Huang, Hannah Carter, Emma K Farley, Michael Snyder, Stephanie I Fraley, Jason F Kreisberg, Trey Ideker
Although cancer genomes are replete with noncoding mutations, the effects of these mutations remain poorly characterized. Here we perform an integrative analysis of 930 tumor whole genomes and matched transcriptomes, identifying a network of 193 noncoding loci in which mutations disrupt target gene expression. These 'somatic eQTLs' (expression quantitative trait loci) are frequently mutated in specific cancer tissues, and the majority can be validated in an independent cohort of 3,382 tumors. Among these, we find that the effects of noncoding mutations on DAAM1, MTG2 and HYI transcription are recapitulated in multiple cancer cell lines and that increasing DAAM1 expression leads to invasive cell migration...
April 2, 2018: Nature Genetics
https://www.readbyqxmd.com/read/29610479/single-cell-rna-sequencing-identifies-celltype-specific-cis-eqtls-and-co-expression-qtls
#11
Monique G P van der Wijst, Harm Brugge, Dylan H de Vries, Patrick Deelen, Morris A Swertz, Lude Franke
Genome-wide association studies have identified thousands of genetic variants that are associated with disease1 . Most of these variants have small effect sizes, but their downstream expression effects, so-called expression quantitative trait loci (eQTLs), are often large2 and celltype-specific3-5 . To identify these celltype-specific eQTLs using an unbiased approach, we used single-cell RNA sequencing to generate expression profiles of ~25,000 peripheral blood mononuclear cells from 45 donors. We identified previously reported cis-eQTLs, but also identified new celltype-specific cis-eQTLs...
April 2, 2018: Nature Genetics
https://www.readbyqxmd.com/read/29579179/a-bayesian-framework-for-multiple-trait-colo-calization-from-summary-association-statistics
#12
Claudia Giambartolomei, Jimmy Zhenli Liu, Wen Zhang, Mads Hauberg, Huwenbo Shi, James Boocock, Joe Pickrell, Andrew E Jaffe, Bogdan Pasaniuc, Panos Roussos
Motivation: Most genetic variants implicated in complex diseases by genome-wide association studies (GWAS) are non-coding, making it challenging to understand the causative genes involved in disease. Integrating external information such as quantitative trait locus (QTL) mapping of molecular traits (e.g., expression, methylation) is a powerful approach to identify the subset of GWAS signals explained by regulatory effects. In particular, expression QTLs (eQTLs) help pinpoint the responsible gene among the GWAS regions that harbor many genes, while methylation QTLs (mQTLs) help identify the epigenetic mechanisms that impact gene expression which in turn affect disease risk...
March 19, 2018: Bioinformatics
https://www.readbyqxmd.com/read/29554873/mapping-qtl-for-white-striping-in-relation-to-breast-muscle-yield-and-meat-quality-traits-in-broiler-chickens
#13
Eva Pampouille, Cécile Berri, Simon Boitard, Christelle Hennequet-Antier, Stéphane A Beauclercq, Estelle Godet, Christophe Praud, Yves Jégo, Elisabeth Le Bihan-Duval
BACKGROUND: White striping (WS) is an emerging muscular defect occurring on breast and thigh muscles of broiler chickens. It is characterized by the presence of white striations parallel to the muscle fibers and has significant consequences for meat quality. The etiology of WS remains poorly understood, even if previous studies demonstrated that the defect prevalence is related to broiler growth and muscle development. Moreover, recent studies showed moderate to high heritability values of WS, which emphasized the role of genetics in the expression of the muscle defect...
March 20, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29551504/genetic-variants-in-xdh-are-associated-with-prognosis-for-gastric-cancer-in-a-chinese-population
#14
Hanting Liu, Haixia Zhu, Yadi Lin, Gaoxiang Ma, Guoquan Tao, Weida Gong, Qinghong Zhao, Mulong Du, Meilin Wang, Haiyan Chu, Zhengdong Zhang
OBJECTIVE: We explored the association between single nucleotide polymorphisms (SNPs) rs207454 and rs494852 located in xanthine dehydrogenase (XDH) and gastric cancer (GC) survival. METHODS: A total of 940 patients with gastric cancer were enrolled and genotyped using TaqMan allelic discrimination method. The Kaplan-Meier test and log-rank examine were used to assess the effect of genetic variation. RESULTS: Patients carrying rs207454 CC genotype had a longer survival time than those with the AA genotype (P = 0...
March 15, 2018: Gene
https://www.readbyqxmd.com/read/29523079/ht-eqtl-integrative-expression-quantitative-trait-loci-analysis-in-a-large-number-of-human-tissues
#15
Gen Li, Dereje Jima, Fred A Wright, Andrew B Nobel
BACKGROUND: Expression quantitative trait loci (eQTL) analysis identifies genetic markers associated with the expression of a gene. Most existing eQTL analyses and methods investigate association in a single, readily available tissue, such as blood. Joint analysis of eQTL in multiple tissues has the potential to improve, and expand the scope of, single-tissue analyses. Large-scale collaborative efforts such as the Genotype-Tissue Expression (GTEx) program are currently generating high quality data in a large number of tissues...
March 9, 2018: BMC Bioinformatics
https://www.readbyqxmd.com/read/29509491/whole-genome-sequencing-of-pharmacogenetic-drug-response-in-racially-diverse-children-with-asthma
#16
Angel Cy Mak, Marquitta J White, Walter L Eckalbar, Zachary A Szpiech, Sam S Oh, Maria Pino-Yanes, Donglei Hu, Pagé Goddard, Scott Huntsman, Joshua Galanter, Ann Chen Wu, Blanca E Himes, Soren Germer, Julia M Vogel, Karen L Bunting, Celeste Eng, Sandra Salazar, Kevin L Keys, Jennifer Liberto, Thomas J Nuckton, Thomas A Nguyen, Dara G Torgerson, Pui-Yan Kwok, Albert M Levin, Juan C Celedón, Erick Forno, Hakon Hakonarson, Patrick M Sleiman, Amber Dahlin, Kelan G Tantisira, Scott T Weiss, Denise Serebrisky, Emerita Brigino-Buenaventura, Harold J Farber, Kelley Meade, Michael A Lenoir, Pedro C Avila, Saunak Sen, Shannon M Thyne, William Rodriguez-Cintron, Cheryl A Winkler, Andrés Moreno-Estrada, Karla Sandoval, Jose R Rodriguez-Santana, Rajesh Kumar, L Keoki Williams, Nadav Ahituv, Elad Ziv, Max A Seibold, Robert B Darnell, Noah Zaitlen, Ryan D Hernandez, Esteban G Burchard
Rationale Albuterol, a bronchodilator medication, is the first-line therapy for asthma worldwide. There are significant racial/ethnic differences in albuterol drug response. Objective To identify genetic variants important for bronchodilator drug response (BDR) in racially diverse children. Methods We performed the first whole genome sequencing (WGS) pharmacogenetics study from 1,441 children with asthma from the tails of the BDR distribution to identify genetic association with BDR. Measurements and Main Results We identified population-specific and shared genetic variants associated with BDR, including genome-wide significant (p < 3...
March 6, 2018: American Journal of Respiratory and Critical Care Medicine
https://www.readbyqxmd.com/read/29505964/transposable-element-activity-genome-regulation-and-human-health
#17
REVIEW
Lu Wang, I King Jordan
A convergence of novel genome analysis technologies is enabling population genomic studies of human transposable elements (TEs). Population surveys of human genome sequences have uncovered thousands of individual TE insertions that segregate as common genetic variants, i.e. TE polymorphisms. These recent TE insertions provide an important source of naturally occurring human genetic variation. Investigators are beginning to leverage population genomic data sets to execute genome-scale association studies for assessing the phenotypic impact of human TE polymorphisms...
March 2, 2018: Current Opinion in Genetics & Development
https://www.readbyqxmd.com/read/29505631/-verticillium-dahliae-disease-resistance-and-the-regulatory-pathway-for-maturity-and-tuberization-in-potato
#18
Helen H Tai, David De Koeyer, Mads Sønderkær, Sanne Hedegaard, Martin Lagüe, Claudia Goyer, Lana Nolan, Charlotte Davidson, Kyle Gardner, Jonathan Neilson, Jamuna Risal Paudel, Agnes Murphy, Benoit Bizimungu, Hui Ying Wang, Xingyao Xiong, Dennis Halterman, Kåre Lehmann Nielsen
Kleb. is a pathogenic fungus causing wilting, chlorosis, and early dying in potato ( L.). Genetic mapping of resistance to was done using a diploid population of potato. The major quantitative trait locus (QTL) for resistance was found on chromosome 5. The gene, controlling earliness of maturity and tuberization, was mapped within the interval. Another QTL on chromosome 9 co-localized with the wilt resistance gene marker. Epistasis analysis indicated that the loci on chromosomes 5 and 9 had a highly significant interaction, and that functioned downstream of The alleles were sequenced and found to encode StCDF1...
March 2018: Plant Genome
https://www.readbyqxmd.com/read/29486777/weak-sharing-of-genetic-association-signals-in-three-lung-cancer-subtypes-evidence-at-the-snp-gene-regulation-and-pathway-levels
#19
Timothy D O'Brien, Peilin Jia, Neil E Caporaso, Maria Teresa Landi, Zhongming Zhao
BACKGROUND: There are two main types of lung cancer: small cell lung cancer (SCLC) and non-small cell lung cancer (NSCLC). NSCLC has many subtypes, but the two most common are lung adenocarcinoma (LUAD) and lung squamous cell carcinoma (LUSC). These subtypes are mainly classified by physiological and pathological characteristics, although there is increasing evidence of genetic and molecular differences as well. Although some work has been done at the somatic level to explore the genetic and biological differences among subtypes, little work has been done that interrogates these differences at the germline level to characterize the unique and shared susceptibility genes for each subtype...
February 27, 2018: Genome Medicine
https://www.readbyqxmd.com/read/29483533/comprehensive-integrative-analyses-identify-glt8d1-and-csnk2b-as-schizophrenia-risk-genes
#20
Cui-Ping Yang, Xiaoyan Li, Yong Wu, Qiushuo Shen, Yong Zeng, Qiuxia Xiong, Mengping Wei, Chunhui Chen, Jiewei Liu, Yongxia Huo, Kaiqin Li, Gui Xue, Yong-Gang Yao, Chen Zhang, Ming Li, Yongbin Chen, Xiong-Jian Luo
Recent genome-wide association studies (GWAS) have identified multiple risk loci that show strong associations with schizophrenia. However, pinpointing the potential causal genes at the reported loci remains a major challenge. Here we identify candidate causal genes for schizophrenia using an integrative genomic approach. Sherlock integrative analysis shows that ALMS1, GLT8D1, and CSNK2B are schizophrenia risk genes, which are validated using independent brain expression quantitative trait loci (eQTL) data and integrative analysis method (SMR)...
February 26, 2018: Nature Communications
keyword
keyword
65283
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"