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Expression quantitative trait loci

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https://www.readbyqxmd.com/read/29335020/ensemble-genomic-analysis-in-human-lung-tissue-identifies-novel-genes-for-chronic-obstructive-pulmonary-disease
#1
Jarrett D Morrow, Michael H Cho, John Platig, Xiaobo Zhou, Dawn L DeMeo, Weiliang Qiu, Bartholome Celli, Nathaniel Marchetti, Gerard J Criner, Raphael Bueno, George R Washko, Kimberly Glass, John Quackenbush, Edwin K Silverman, Craig P Hersh
BACKGROUND: Genome-wide association studies (GWAS) have identified single nucleotide polymorphisms (SNPs) significantly associated with chronic obstructive pulmonary disease (COPD). However, many genetic variants show suggestive evidence for association but do not meet the strict threshold for genome-wide significance. Integrative analysis of multiple omics datasets has the potential to identify novel genes involved in disease pathogenesis by leveraging these variants in a functional, regulatory context...
January 15, 2018: Human Genomics
https://www.readbyqxmd.com/read/29333270/lessons-from-ten-years-of-genome-wide-association-studies-of-asthma
#2
REVIEW
Cristina T Vicente, Joana A Revez, Manuel A R Ferreira
Twenty-five genome-wide association studies (GWAS) of asthma were published between 2007 and 2016, the largest with a sample size of 157242 individuals. Across these studies, 39 genetic variants in low linkage disequilibrium (LD) with each other were reported to associate with disease risk at a significance threshold of P<5 × 10-8, including 31 in populations of European ancestry. Results from analyses of the UK Biobank data (n=380 503) indicate that at least 28 of the 31 associations reported in Europeans represent true-positive findings, collectively explaining 2...
December 2017: Clinical & Translational Immunology
https://www.readbyqxmd.com/read/29325110/impact-of-genetic-risk-loci-for-multiple-sclerosis-on-expression-of-proximal-genes-in-patients
#3
Tojo James, Magdalena Lindén, Hiromasa Morikawa, Sunjay Jude Fernandes, Sabrina Ruhrmann, Mikael Huss, Maya Brandi, Fredrik Piehl, Maja Jagodic, Jesper Tegnér, Mohsen Khademi, Tomas Olsson, David Gomez-Cabrero, Ingrid Kockum
Despite advancements in genetic studies, it is difficult to understand and characterize the functional relevance of disease-associated genetic variants, especially in the context of a complex multifactorial disease such as Multiple Sclerosis (MS). Since a large proportion of expression quantitative trait loci (eQTLs) are context-specific, we performed RNA-Seq in peripheral blood mononuclear cells (PBMCs) from MS patients (n = 145) to identify eQTLs in regions centered on 109 MS risk SNPs and seven associated HLA variants...
January 8, 2018: Human Molecular Genetics
https://www.readbyqxmd.com/read/29321353/identification-and-association-of-novel-lncrna-poumu1-gene-mutations-with-chicken-performance-traits
#4
Tuanhui Ren, Yanting Zhou, Yu Zhou, Weihua Tian, Zhenzhen Gu, Song Zhao, Yadi Chen, Ruili Han, Xiaojun Liu, Xiangtao Kang, Zhuanjian Li
The biological functions of long noncoding RNAs (lncRNAs), which play an important role in regulating development and gene expression, may be affected by variations in lncRNA gene loci or associated genomic sequences. However, the functions of many lncRNAs remain unknown. To analyse correlations between mutations in pouMU1 with chicken growth and carcass traits, 860 chickens from a Gushi×Anka F2 resource population and 96 Lushi, Xichuan, Changshun and recessive white chickens were used to evaluate the genetic effect of the pouMU1 gene...
December 2017: Journal of Genetics
https://www.readbyqxmd.com/read/29317604/beta-defensin-1-aryl-hydrocarbon-receptor-and-plasma-kynurenine-in-major-depressive-disorder-metabolomics-informed-genomics
#5
Duan Liu, Balmiki Ray, Drew R Neavin, Jiabin Zhang, Arjun P Athreya, Joanna M Biernacka, William V Bobo, Daniel K Hall-Flavin, Michelle K Skime, Hongjie Zhu, Gregory D Jenkins, Anthony Batzler, Krishna R Kalari, Felix Boakye-Agyeman, Wayne R Matson, Swati S Bhasin, Taisei Mushiroda, Yusuke Nakamura, Michiaki Kubo, Ravishankar K Iyer, Liewei Wang, Mark A Frye, Rima Kaddurah-Daouk, Richard M Weinshilboum
Major depressive disorder (MDD) is a heterogeneous disease. Efforts to identify biomarkers for sub-classifying MDD and antidepressant therapy by genome-wide association studies (GWAS) alone have generally yielded disappointing results. We applied a metabolomics-informed genomic research strategy to study the contribution of genetic variation to MDD pathophysiology by assaying 31 metabolites, including compounds from the tryptophan, tyrosine, and purine pathways, in plasma samples from 290 MDD patients. Associations of metabolite concentrations with depressive symptoms were determined, followed by GWAS for selected metabolites and functional validation studies of the genes identified...
January 10, 2018: Translational Psychiatry
https://www.readbyqxmd.com/read/29311651/identification-of-a-novel-gene-regulating-amygdala-mediated-fear-extinction
#6
Ozge Gunduz-Cinar, Emma Brockway, Lauren Lederle, Troy Wilcox, Lindsay R Halladay, Ying Ding, Hyunjung Oh, Erica F Busch, Katie Kaugars, Shaun Flynn, Aaron Limoges, Olena Bukalo, Kathryn P MacPherson, Sophie Masneuf, Courtney Pinard, Etienne Sibille, Elissa J Chesler, Andrew Holmes
Recent years have seen advances in our understanding of the neural circuits associated with trauma-related disorders, and the development of relevant assays for these behaviors in rodents. Although inherited factors are known to influence individual differences in risk for these disorders, it has been difficult to identify specific genes that moderate circuit functions to affect trauma-related behaviors. Here, we exploited robust inbred mouse strain differences in Pavlovian fear extinction to uncover quantitative trait loci (QTL) associated with this trait...
January 8, 2018: Molecular Psychiatry
https://www.readbyqxmd.com/read/29300118/genome-wide-linkage-analysis-identifies-loci-for-testicle-and-ovary-traits-in-chickens
#7
Yanfa Sun, Ranran Liu, Guiping Zhao, Maiqing Zheng, Peng Li, Li Liu, Jie Wen
Development of testes or ovaries is critical to chicken breeders. Understanding the genetic mechanisms influencing the development of the testes and ovaries could enhance selection efforts which target reproductive traits. The linkage analysis was conducted within an F2 population derived from Beijing-You chickens and a commercial broiler line. The results have identified one quantitative trait loci (QTL, designated T1) for bilateral testicular weight (TW) and the percentage of TW to carcass weight, and five QTLs (designated O1-O5) for ovary weight (follicle-free, OW) and the percentage of OW to carcass weight...
January 4, 2018: Animal Biotechnology
https://www.readbyqxmd.com/read/29298996/the-phosphatidylinositide-3-kinase-pi3k-signaling-pathway-is-a-determinant-of-zileuton-response-in-adults-with-asthma
#8
Amber Dahlin, Weiliang Qiu, Augusto A Litonjua, John J Lima, Mayumi Tamari, Michiaki Kubo, Charles G Irvin, Stephen P Peters, Ann C Wu, Scott T Weiss, Kelan G Tantisira
Variable responsiveness to zileuton, a leukotriene antagonist used to treat asthma, may be due in part to genetic variation. While individual SNPs were previously associated with zileuton-related lung function changes, specific quantitative trait loci (QTLs) and biological pathways that may contribute have not been identified. In this study, we investigated the hypothesis that genetic variation within biological pathways is associated with zileuton response. We performed an integrative QTL mapping and pathway enrichment study to investigate data from a GWAS of zileuton response, in addition to mRNA expression profiles and leukotriene production data from lymphoblastoid cell lines (LCLs) (derived from asthmatics) that were treated with zileuton or ethanol (control)...
January 3, 2018: Pharmacogenomics Journal
https://www.readbyqxmd.com/read/29297929/increased-expression-of-prkcb-mrna-in-peripheral-blood-mononuclear-cells-from-patients-with-systemic-lupus-erythematosus
#9
Zhengwei Zhu, Lulu Yang, Yaohua Zhang, Lu Liu, Yan Huang, Leilei Wen, Chao Yang, Liyun Chen, Wenjun Wang, Xianbo Zuo, Fusheng Zhou, Hongyan Wang, Huayang Tang, Xuejun Zhang, Sen Yang, Yujun Sheng, Yong Cui
The polymorphism of PRKCB has been proven to be associated with systemic lupus erythematosus (SLE) in our previous study. We aimed to investigate the relationship between expression of PRKCB mRNA and the Disease Activity Index (SLEDAI) and manifestations of SLE. Quantitative reverse transcription polymerase chain reaction (RT-PCR) was applied to examine the expression of PRKCB mRNA in peripheral blood mononuclear cells of 60 patients with SLE and 62 controls. The Sequenom MassArray System was used to detect genotype SNP rs16972959...
January 3, 2018: Annals of Human Genetics
https://www.readbyqxmd.com/read/29282317/distinctive-roles-of-age-sex-and-genetics-in-shaping-transcriptional-variation-of-human-immune-responses-to-microbial-challenges
#10
Barbara Piasecka, Darragh Duffy, Alejandra Urrutia, Hélène Quach, Etienne Patin, Céline Posseme, Jacob Bergstedt, Bruno Charbit, Vincent Rouilly, Cameron R MacPherson, Milena Hasan, Benoit Albaud, David Gentien, Jacques Fellay, Matthew L Albert, Lluis Quintana-Murci
The contribution of host genetic and nongenetic factors to immunological differences in humans remains largely undefined. Here, we generated bacterial-, fungal-, and viral-induced immune transcriptional profiles in an age- and sex-balanced cohort of 1,000 healthy individuals and searched for the determinants of immune response variation. We found that age and sex affected the transcriptional response of most immune-related genes, with age effects being more stimulus-specific relative to sex effects, which were largely shared across conditions...
December 27, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29279960/quantitative-trait-mapping-in-diversity-outbred-mice-identifies-two-genomic-regions-associated-with-heart-size
#11
John R Shorter, Wei Huang, Ju Youn Beak, Kunjie Hua, Daniel M Gatti, Fernando Pardo-Manuel de Villena, Daniel Pomp, Brian C Jensen
Heart size is an important factor in cardiac health and disease. In particular, increased heart weight is predictive of adverse cardiovascular outcomes in multiple large community-based studies. We use two cohorts of Diversity Outbred (DO) mice to investigate the role of genetics, sex, age, and diet on heart size. DO mice (n = 289) of both sexes from generation 10 were fed a standard chow diet, and analyzed at 12-15 weeks of age. Another cohort of female DO mice (n = 258) from generation 11 were fed either a high-fat, cholesterol-containing (HFC) diet or a low-fat, high-protein diet, and analyzed at 24-25 weeks...
December 26, 2017: Mammalian Genome: Official Journal of the International Mammalian Genome Society
https://www.readbyqxmd.com/read/29279374/evaluating-the-contribution-of-rare-variants-to-type-2-diabetes-and-related-traits-using-pedigrees
#12
Goo Jun, Alisa Manning, Marcio Almeida, Matthew Zawistowski, Andrew R Wood, Tanya M Teslovich, Christian Fuchsberger, Shuang Feng, Pablo Cingolani, Kyle J Gaulton, Thomas Dyer, Thomas W Blackwell, Han Chen, Peter S Chines, Sungkyoung Choi, Claire Churchhouse, Pierre Fontanillas, Ryan King, SungYoung Lee, Stephen E Lincoln, Vasily Trubetskoy, Mark DePristo, Tasha Fingerlin, Robert Grossman, Jason Grundstad, Alison Heath, Jayoun Kim, Young Jin Kim, Jason Laramie, Jaehoon Lee, Heng Li, Xuanyao Liu, Oren Livne, Adam E Locke, Julian Maller, Alexander Mazur, Andrew P Morris, Toni I Pollin, Derek Ragona, David Reich, Manuel A Rivas, Laura J Scott, Xueling Sim, Rick G Tearle, Yik Ying Teo, Amy L Williams, Sebastian Zöllner, Joanne E Curran, Juan Peralta, Beena Akolkar, Graeme I Bell, Noël P Burtt, Nancy J Cox, Jose C Florez, Craig L Hanis, Catherine McKeon, Karen L Mohlke, Mark Seielstad, James G Wilson, Gil Atzmon, Jennifer E Below, Josée Dupuis, Dan L Nicolae, Donna Lehman, Taesung Park, Sungho Won, Robert Sladek, David Altshuler, Mark I McCarthy, Ravindranath Duggirala, Michael Boehnke, Timothy M Frayling, Gonçalo R Abecasis, John Blangero
A major challenge in evaluating the contribution of rare variants to complex disease is identifying enough copies of the rare alleles to permit informative statistical analysis. To investigate the contribution of rare variants to the risk of type 2 diabetes (T2D) and related traits, we performed deep whole-genome analysis of 1,034 members of 20 large Mexican-American families with high prevalence of T2D. If rare variants of large effect accounted for much of the diabetes risk in these families, our experiment was powered to detect association...
December 26, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29276797/genetic-and-epigenetic-determinants-of-inter-individual-variability-in-responses-to-toxicants
#13
Lauren Lewis, Gregory E Crawford, Terrence S Furey, Ivan Rusyn
It is well established that genetic variability has a major impact on susceptibility to common diseases, responses to drugs and toxicants, and influences disease-related outcomes. The appreciation that epigenetic marks also vary across the population is growing with more data becoming available from studies in humans and model organisms. In addition, the links between genetic variability, toxicity outcomes and epigenetics are being actively explored. Recent studies demonstrate that gene-by-environment interactions involve both chromatin states and transcriptional regulation, and that epigenetics provides important mechanistic clues to connect expression-related quantitative trait loci (QTL) and disease outcomes...
October 2017: Current Opinion in Toxicology
https://www.readbyqxmd.com/read/29275164/genome-wide-analysis-of-transcriptional-variability-in-a-large-maize-teosinte-population
#14
Xufeng Wang, Qiuyue Chen, Yaoyao Wu, Zachary H Lemmon, Guanghui Xu, Cheng Huang, Yameng Liang, Dingyi Xu, Dan Li, John F Doebley, Feng Tian
The regulation of gene expression plays an important role in controlling plant phenotypes and adaptation. Here, we report a comprehensive assessment of gene expression variation by sequencing the transcriptome of a large maize-teosinte experimental population. Genome-wide mapping identified 25,660 expression quantitative trait loci (eQTL) for 17,311 genes, capturing an unprecedented range of expression variation. We found that local-eQTL more frequently mapped to adjacent genes, displaying a mode of expression piggybacking, which consequently created co-regulated gene clusters...
December 21, 2017: Molecular Plant
https://www.readbyqxmd.com/read/29274975/association-analysis-for-udder-index-and-milking-speed-with-imputed-whole-genome-sequence-variants-in-nordic-holstein-cattle
#15
Júlia Gazzoni Jardim, Bernt Guldbrandtsen, Mogens Sandø Lund, Goutam Sahana
Genome-wide association testing facilitates the identification of genetic variants associated with complex traits. Mapping genes that promote genetic resistance to mastitis could reduce the cost of antibiotic use and enhance animal welfare and milk production by improving outcomes of breeding for udder health. Using imputed whole-genome sequence variants, we carried out association studies for 2 traits related to udder health, udder index, and milking speed in Nordic Holstein cattle. A total of 4,921 bulls genotyped with the BovineSNP50 BeadChip array were imputed to high-density genotypes (Illumina BovineHD BeadChip, Illumina, San Diego, CA) and, subsequently, to whole-genome sequence variants...
December 20, 2017: Journal of Dairy Science
https://www.readbyqxmd.com/read/29273861/dynamic-and-epistatic-qtl-mapping-reveals-the-complex-genetic-architecture-of-waterlogging-tolerance-in-chrysanthemum
#16
Jiangshuo Su, Xincheng Yang, Fei Zhang, Shaofang Wu, Siyi Xiong, Liming Shi, Zhiyong Guan, Weimin Fang, Fadi Chen
37 unconditional QTLs, 51 conditional QTLs and considerable epistatic QTLs were detected for waterlogging tolerance, and six favourable combinations were selected accelerating the possible application of MAS in chrysanthemum breeding. Chrysanthemum is seriously impacted by soil waterlogging. To determine the genetic characteristics of waterlogging tolerance (WAT) in chrysanthemum, a population of 162 F1 lines was used to construct a genetic map to identify the dynamic and epistatic quantitative trait loci (QTLs) for four WAT traits: wilting index (WI), dead leaf ratio (DLR), chlorosis score (Score) and membership function value of waterlogging (MFVW)...
December 22, 2017: Planta
https://www.readbyqxmd.com/read/29273740/rna-sequencing-provides-insights-into-the-evolution-of-lettuce-and-the-regulation-of-flavonoid-biosynthesis
#17
Lei Zhang, Wenqing Su, Rong Tao, Weiyi Zhang, Jiongjiong Chen, Peiyao Wu, Chenghuan Yan, Yue Jia, Robert M Larkin, Dean Lavelle, Maria-Jose Truco, Sebastian Reyes Chin-Wo, Richard W Michelmore, Hanhui Kuang
Different horticultural types of lettuce exhibit tremendous morphological variation. However, the molecular basis for domestication and divergence among the different horticultural types of lettuce remains unknown. Here, we report the RNA sequencing of 240 lettuce accessions sampled from the major horticultural types and wild relatives, generating 1.1 million single-nucleotide polymorphisms (SNPs). Demographic modeling indicates that there was a single domestication event for lettuce. We identify a list of regions as putative selective sweeps that occurred during domestication and divergence, respectively...
December 22, 2017: Nature Communications
https://www.readbyqxmd.com/read/29273003/an-integrated-and-comparative-approach-towards-identification-characterization-and-functional-annotation-of-candidate-genes-for-drought-tolerance-in-sorghum-sorghum-bicolor-l-moench
#18
Adugna Abdi Woldesemayat, Peter Van Heusden, Bongani K Ndimba, Alan Christoffels
BACKGROUND: Drought is the most disastrous abiotic stress that severely affects agricultural productivity worldwide. Understanding the biological basis of drought-regulated traits, requires identification and an in-depth characterization of genetic determinants using model organisms and high-throughput technologies. However, studies on drought tolerance have generally been limited to traditional candidate gene approach that targets only a single gene in a pathway that is related to a trait...
December 22, 2017: BMC Genetics
https://www.readbyqxmd.com/read/29259604/novel-non-histocompatibility-antigen-mismatched-variants-improve-the-ability-to-predict-antibody-mediated-rejection-risk-in-kidney-transplant
#19
Silvia Pineda, Tara K Sigdel, Jieming Chen, Annette M Jackson, Marina Sirota, Minnie M Sarwal
Transplant rejection is the critical clinical end-point limiting indefinite survival after histocompatibility antigen (HLA) mismatched organ transplantation. The predominant cause of late graft loss is antibody-mediated rejection (AMR), a process whereby injury to the organ is caused by donor-specific antibodies, which bind to HLA and non-HLA (nHLA) antigens. AMR is incompletely diagnosed as donor/recipient (D/R) matching is only limited to the HLA locus and critical nHLA immunogenic antigens remain to be identified...
2017: Frontiers in Immunology
https://www.readbyqxmd.com/read/29248712/genetic-variant-repressing-adh1a-expression-confers-susceptibility-to-esophageal-squamous-cell-carcinoma
#20
Qionghua Cui, Linna Peng, Lixuan Wei, Jiang Chang, Wenle Tan, Yingying Luo, Xudong Huang, Yanjie Zhao, Jun Li, Jiahui Chu, Mingming Shao, Chao Zhang, Cheng Li, Wen Tan, Dongxin Lin, Chen Wu
Genome-wide association studies (GWAS) have discovered numerous genetic susceptibility loci including a cluster of alcohol dehydrogenase (ADH) gene family for esophageal squamous-cell carcinoma (ESCC). However, the underlying mechanism has not fully been elucidated. In this study, we integrated the GWAS data, gene-drinking interaction, expression quantitative trait locus (eQTL) analysis and biochemical experiments to clarify the specific mechanism of the polymorphisms in ADH loci. By imputation and eQTL analysis, we identified rs1154402C>G in intron 1 of ADH5 substantially associated with the expression levels of ADH1A...
December 14, 2017: Cancer Letters
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