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Expression quantitative trait loci ( eQTLs )

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
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
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
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
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
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
Dan Zhcou, Dandan Zhang, Xiaohui Sun, Zhiqiang Li, Yaqin Ni, Zhongyan Shan, Hong Li, Chengguo Liu, Shuai Zhang, Yi Liu, Ruizhi Zheng, Feixia Pan, Yimin Zhu, Yongyong Shi, Maode Lai
Although numbers of genome-wide association studies (GWAS) have been performed for serum lipid levels, limited heritability has been explained. Studies showed that combining data from GWAS and expression quantitative trait loci (eQTLs) signals can both enhance the discovery of trait-associated SNPs and gain a better understanding of the mechanism. We performed an annotation-based, multistage genome-wide screening for serum-lipid-level-associated loci in totally 6863 Han Chinese. A serum high-density lipoprotein cholesterol (HDL-C) associated variant rs1880118 (hg19 chr7:g...
February 23, 2018: European Journal of Human Genetics: EJHG
Brandon L Pierce, Lin Tong, Maria Argos, Kathryn Demanelis, Farzana Jasmine, Muhammad Rakibuz-Zaman, Golam Sarwar, Md Tariqul Islam, Hasan Shahriar, Tariqul Islam, Mahfuzar Rahman, Md Yunus, Muhammad G Kibriya, Lin S Chen, Habibul Ahsan
Inherited genetic variation affects local gene expression and DNA methylation in humans. Most expression quantitative trait loci (cis-eQTLs) occur at the same genomic location as a methylation QTL (cis-meQTL), suggesting a common causal variant and shared mechanism. Using DNA and RNA from peripheral blood of Bangladeshi individuals, here we use co-localization methods to identify eQTL-meQTL pairs likely to share a causal variant. We use partial correlation and mediation analyses to identify >400 of these pairs showing evidence of a causal relationship between expression and methylation (i...
February 23, 2018: Nature Communications
Naina Gour, Stephane Lajoie, Ursula Smole, Marquitta White, Donglei Hu, Pagé Goddard, Scott Huntsman, Celeste Eng, Angel Mak, Sam Oh, Jung-Hyun Kim, Annu Sharma, Sophie Plante, Ikhlass Haj Salem, Yvonne Resch, Xiao Xiao, Nu Yao, Anju Singh, Susanne Vrtala, Jamila Chakir, Esteban G Burchard, Andrew P Lane, Marsha Wills-Karp
The key factors underlying the development of allergic diseases-the propensity for a minority of individuals to develop dysfunctional responses to harmless environmental molecules-remain undefined. We report a pathway of immune counter-regulation that suppresses the development of aeroallergy and shrimp-induced anaphylaxis. In mice, signaling through epithelially expressed dectin-1 suppresses the development of type 2 immune responses through inhibition of interleukin-33 (IL-33) secretion and the subsequent recruitment of IL-13-producing innate lymphoid cells...
February 23, 2018: Science Immunology
Benjamin H Mullin, Kun Zhu, Jiake Xu, Suzanne J Brown, Shelby Mullin, Jennifer Tickner, Nathan J Pavlos, Frank Dudbridge, John P Walsh, Scott G Wilson
Osteoporosis is a complex disease with a strong genetic component. Genome-wide association studies (GWAS) have been very successful at identifying common genetic variants associated with bone parameters. A recently published study documented the results of the largest GWAS for bone mineral density (BMD) performed to date (n = 142,487), identifying 307 conditionally independent single-nucleotide polymorphisms (SNPs) as associated with estimated BMD (eBMD) at the genome-wide significance level. The vast majority of these variants are non-coding SNPs...
February 23, 2018: Journal of Bone and Mineral Research: the Official Journal of the American Society for Bone and Mineral Research
Kunjiang Yu, Xiaodong Wang, Feng Chen, Qi Peng, Song Chen, Hongge Li, Wei Zhang, Sanxiong Fu, Maolong Hu, Weihua Long, Pu Chu, Rongzhan Guan, Jiefu Zhang
The apetalous trait of rapeseed ( Brassica napus , AACC, 2 n = 38) is important for breeding an ideal high-yield rapeseed with superior klendusity to Sclerotinia sclerotiorum . Currently, the molecular mechanism underlying the apetalous trait of rapeseed is unclear. In this study, 14 petal regulators genes were chosen as target genes (TGs), and the expression patterns of the 14 TGs in the AH population, containing 189 recombinant inbred lines derived from a cross between apetalous "APL01" and normal "Holly," were analyzed in two environments using qRT-PCR...
2018: Frontiers in Plant Science
Aniek C Bouwman, Hans D Daetwyler, Amanda J Chamberlain, Carla Hurtado Ponce, Mehdi Sargolzaei, Flavio S Schenkel, Goutam Sahana, Armelle Govignon-Gion, Simon Boitard, Marlies Dolezal, Hubert Pausch, Rasmus F Brøndum, Phil J Bowman, Bo Thomsen, Bernt Guldbrandtsen, Mogens S Lund, Bertrand Servin, Dorian J Garrick, James Reecy, Johanna Vilkki, Alessandro Bagnato, Min Wang, Jesse L Hoff, Robert D Schnabel, Jeremy F Taylor, Anna A E Vinkhuyzen, Frank Panitz, Christian Bendixen, Lars-Erik Holm, Birgit Gredler, Chris Hozé, Mekki Boussaha, Marie-Pierre Sanchez, Dominique Rocha, Aurelien Capitan, Thierry Tribout, Anne Barbat, Pascal Croiseau, Cord Drögemüller, Vidhya Jagannathan, Christy Vander Jagt, John J Crowley, Anna Bieber, Deirdre C Purfield, Donagh P Berry, Reiner Emmerling, Kay-Uwe Götz, Mirjam Frischknecht, Ingolf Russ, Johann Sölkner, Curtis P Van Tassell, Ruedi Fries, Paul Stothard, Roel F Veerkamp, Didier Boichard, Mike E Goddard, Ben J Hayes
Stature is affected by many polymorphisms of small effect in humans1 . In contrast, variation in dogs, even within breeds, has been suggested to be largely due to variants in a small number of genes2,3 . Here we use data from cattle to compare the genetic architecture of stature to those in humans and dogs. We conducted a meta-analysis for stature using 58,265 cattle from 17 populations with 25.4 million imputed whole-genome sequence variants. Results showed that the genetic architecture of stature in cattle is similar to that in humans, as the lead variants in 163 significantly associated genomic regions (P < 5 × 10-8 ) explained at most 13...
February 19, 2018: Nature Genetics
Markus Drag, Mathias B Hansen, Haja N Kadarmideen
Boar taint is an offensive odour and/or taste from a proportion of non-castrated male pigs caused by skatole and androstenone accumulation during sexual maturity. Castration is widely used to avoid boar taint but is currently under debate because of animal welfare concerns. This study aimed to identify expression quantitative trait loci (eQTLs) with potential effects on boar taint compounds to improve breeding possibilities for reduced boar taint. Danish Landrace male boars with low, medium and high genetic merit for skatole and human nose score (HNS) were slaughtered at ~100 kg...
2018: PloS One
John Stephen Malamon, Andres Kriete
Late-onset Alzheimer's disease (LOAD) and age are significantly correlated such that one-third of Americans beyond 85 years of age are afflicted. We have designed and implemented a pilot study that combines systems biology approaches with traditional next-generation sequencing (NGS) analysis techniques to identify relevant regulatory pathways, infer functional relationships and confirm the dysregulation of these biological pathways in LOAD. Our study design is a most comprehensive systems approach combining co-expression network modeling derived from RNA-seq data, rigorous quality control (QC) standards, functional ontology, and expression quantitative trait loci (eQTL) derived from whole exome (WES) single nucleotide variant (SNV) genotype data...
February 9, 2018: Biology
Ting Wang, Yan Li, Meng Zhu, Wenxi Yao, Hongyan Wu, Xiaoming Ji, Zhibin Hu, Hongbing Shen, Xiangshan Fan, Chunhui Ni
Coal worker's pneumoconiosis (CWP) is a debilitating and progressive occupational lung disease resulted from long-term inhalation of airborne silica-containing coal mine dust. Both environmental factors and genetic variations contribute to CWP. Our previous genome-wide association study (GWAS) revealed a tiny fraction of variants with the top associations in Chinese Han population. To identify novel susceptibility loci of CWP, functional variants with suboptimal associations in the GWAS scan were further studied here...
January 31, 2018: Toxicological Sciences: An Official Journal of the Society of Toxicology
Manuel Revilla, Anna Puig-Oliveras, Daniel Crespo-Piazuelo, Lourdes Criado-Mesas, Anna Castelló, Ana I Fernández, Maria Ballester, Josep M Folch
The aim of this work was to study the genetic basis of the backfat expression of lipid-related genes associated with meat quality traits in pigs. We performed a genome-wide association study with the backfat gene expression measured in 44 genes by qPCR and the PorcineSNP60 BeadChip genotypes in 115 Iberian x Landrace backcross animals. A total of 193 expression-associated SNPs located in 19 chromosomal regions were associated with expression levels of ACSM5, ELOVL6, FABP4, FADS2, and SLC27A4 genes. Three expression quantitative trail loci (eQTLs) corresponding to ACSM5, FABP4, and FADS2 were classified as cis-acting eQTLs, whereas the remaining 16 eQTLs have trans-regulatory effects...
February 1, 2018: Scientific Reports
Liming Huang, Lian Dai, Wenshen Xu, Shu Zhang, Danfang Yan, Xi Shi
Mechanistic target of rapamycin (MTOR) encodes a key modulator of cell growth, proliferation, and apoptosis. Previous studies have demonstrated that the dysregulation of MTOR is involved in the development and progression of several types of cancer, including glioma. In the present study, a comprehensive analysis was conducted to examine whether the expression quantitative trait loci (eQTLs) of MTOR are associated with the progression of glioma. Candidate eQTLs of MTOR were obtained from the Genotype-Tissue Expression eQTL Browser...
January 2018: Oncology Letters
Navot Galpaz, Itay Gonda, Doron Shem-Tov, Omer Barad, Galil Tzuri, Shery Lev, Zhangjun Fei, Yimin Xu, Nadia Lombardi, Linyong Mao, Chen Jiao, Rotem Harel-Beja, Adi Doron-Faigenboim, Oren Tzfadia, Einat Bar, Ayala Meir, Uzi Sa'ar, Aaron Fait, Eran Halperin, Merav Kenigswald, Elazar Fallik, Guy Kol, Gil Ronen, Yosef Burger, Amit Gur, Ya'akov Tadmor, Vitaly Portnoy, Arthur A Schaffer, Efraim Lewinsohn, James J Giovannoni, Nurit Katzir
Combined quantitative trait loci (QTL) and expression-QTL (eQTL) mapping analysis was performed to identify genetic factors affecting melon (Cucumis melo) fruit quality, by linking genotypic, metabolic and transcriptomic data from a melon recombinant inbred line (RIL) population. RNA sequencing (RNA-Seq) of fruit from 96 RILs yielded a highly saturated collection of >58,000 single-nucleotide polymorphisms, identifying 6,636 recombination events that separated the genome into 3,663 genomic bins. Bin-based QTL analysis of 79 RILs and 129 fruit-quality traits affecting taste, aroma and color resulted in the mapping of 241 QTL...
January 31, 2018: Plant Journal: for Cell and Molecular Biology
Mireia Pagerols, Vanesa Richarte, Cristina Sánchez-Mora, Paula Rovira, María Soler Artigas, Iris Garcia-Martínez, Eva Calvo-Sánchez, Montse Corrales, Bruna Santos da Silva, Nina Roth Mota, Marcelo Moraes Victor, Luis Augusto Rohde, Eugenio Horacio Grevet, Claiton Henrique Dotto Bau, Bru Cormand, Miguel Casas, Josep Antoni Ramos-Quiroga, Marta Ribasés
Methylphenidate (MPH) is the most frequently used pharmacological treatment in children with attention-deficit/hyperactivity disorder (ADHD). However, a considerable interindividual variability exists in clinical outcome. Thus, we performed a genome-wide association study of MPH efficacy in 173 ADHD paediatric patients. Although no variant reached genome-wide significance, the set of genes containing single-nucleotide polymorphisms (SNPs) nominally associated with MPH response (P < 0.05) was significantly enriched for candidates previously studied in ADHD or treatment outcome...
January 30, 2018: Scientific Reports
Junfei Zhao, Feixiong Cheng, Peilin Jia, Nancy Cox, Joshua C Denny, Zhongming Zhao
BACKGROUND: Genome-phenome studies have identified thousands of variants that are statistically associated with disease or traits; however, their functional roles are largely unclear. A comprehensive investigation of regulatory mechanisms and the gene regulatory networks between phenome-wide association study (PheWAS) and genome-wide association study (GWAS) is needed to identify novel regulatory variants contributing to risk for human diseases. METHODS: In this study, we developed an integrative functional genomics framework that maps 215,107 significant single nucleotide polymorphism (SNP) traits generated from the PheWAS Catalog and 28,870 genome-wide significant SNP traits collected from the GWAS Catalog into a global human genome regulatory map via incorporating various functional annotation data, including transcription factor (TF)-based motifs, promoters, enhancers, and expression quantitative trait loci (eQTLs) generated from four major functional genomics databases: FANTOM5, ENCODE, NIH Roadmap, and Genotype-Tissue Expression (GTEx)...
January 29, 2018: Genome Medicine
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