keyword
MENU ▼
Read by QxMD icon Read
search

Eqtl

keyword
https://www.readbyqxmd.com/read/28640813/identification-of-a-sj%C3%A3-gren-s-syndrome-susceptibility-locus-at-oas1-that-influences-isoform-switching-protein-expression-and-responsiveness-to-type-i-interferons
#1
He Li, Tove Ragna Reksten, John A Ice, Jennifer A Kelly, Indra Adrianto, Astrid Rasmussen, Shaofeng Wang, Bo He, Kiely M Grundahl, Stuart B Glenn, Corinne Miceli-Richard, Simon Bowman, Sue Lester, Per Eriksson, Maija-Leena Eloranta, Johan G Brun, Lasse G Gøransson, Erna Harboe, Joel M Guthridge, Kenneth M Kaufman, Marika Kvarnström, Deborah S Cunninghame Graham, Ketan Patel, Adam J Adler, A Darise Farris, Michael T Brennan, James Chodosh, Rajaram Gopalakrishnan, Michael H Weisman, Swamy Venuturupalli, Daniel J Wallace, Kimberly S Hefner, Glen D Houston, Andrew J W Huang, Pamela J Hughes, David M Lewis, Lida Radfar, Evan S Vista, Contessa E Edgar, Michael D Rohrer, Donald U Stone, Timothy J Vyse, John B Harley, Patrick M Gaffney, Judith A James, Sean Turner, Ilias Alevizos, Juan-Manuel Anaya, Nelson L Rhodus, Barbara M Segal, Courtney G Montgomery, R Hal Scofield, Susan Kovats, Xavier Mariette, Lars Rönnblom, Torsten Witte, Maureen Rischmueller, Marie Wahren-Herlenius, Roald Omdal, Roland Jonsson, Wan-Fai Ng, Gunnel Nordmark, Christopher J Lessard, Kathy L Sivils
Sjögren's syndrome (SS) is a common, autoimmune exocrinopathy distinguished by keratoconjunctivitis sicca and xerostomia. Patients frequently develop serious complications including lymphoma, pulmonary dysfunction, neuropathy, vasculitis, and debilitating fatigue. Dysregulation of type I interferon (IFN) pathway is a prominent feature of SS and is correlated with increased autoantibody titers and disease severity. To identify genetic determinants of IFN pathway dysregulation in SS, we performed cis-expression quantitative trait locus (eQTL) analyses focusing on differentially expressed type I IFN-inducible transcripts identified through a transcriptome profiling study...
June 22, 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28635624/effects-of-type-1-diabetes-risk-alleles-on-immune-cell-gene-expression
#2
REVIEW
Ramesh Ram, Grant Morahan
Genetic studies have identified 61 variants associated with the risk of developing Type 1 Diabetes (T1D). The functions of most of the non-HLA (Human Leukocyte Antigen) genetic variants remain unknown. We found that only 16 of these risk variants could potentially be linked to a protein-coding change. Therefore, we investigated whether these variants affected susceptibility by regulating changes in gene expression. To do so, we examined whole transcriptome profiles of 600 samples from the Type 1 Diabetes Genetics Consortium (T1DGC)...
June 21, 2017: Genes
https://www.readbyqxmd.com/read/28634199/characterising-cis-regulatory-variation-in-the-transcriptome-of-histologically-normal-and-tumour-derived-pancreatic-tissues
#3
Mingfeng Zhang, Soren Lykke-Andersen, Bin Zhu, Wenming Xiao, Jason W Hoskins, Xijun Zhang, Lauren M Rost, Irene Collins, Martijn van de Bunt, Jinping Jia, Hemang Parikh, Tongwu Zhang, Lei Song, Ashley Jermusyk, Charles C Chung, Bin Zhu, Weiyin Zhou, Gail L Matters, Robert C Kurtz, Meredith Yeager, Torben Heick Jensen, Kevin M Brown, Halit Ongen, William R Bamlet, Bradley A Murray, Mark I McCarthy, Stephen J Chanock, Nilanjan Chatterjee, Brian M Wolpin, Jill P Smith, Sara H Olson, Gloria M Petersen, Jianxin Shi, Laufey Amundadottir
OBJECTIVE: To elucidate the genetic architecture of gene expression in pancreatic tissues. DESIGN: We performed expression quantitative trait locus (eQTL) analysis in histologically normal pancreatic tissue samples (n=95) using RNA sequencing and the corresponding 1000 genomes imputed germline genotypes. Data from pancreatic tumour-derived tissue samples (n=115) from The Cancer Genome Atlas were included for comparison. RESULTS: We identified 38 615 cis-eQTLs (in 484 genes) in histologically normal tissues and 39 713 cis-eQTL (in 237 genes) in tumour-derived tissues (false discovery rate <0...
June 20, 2017: Gut
https://www.readbyqxmd.com/read/28627442/the-association-of-rs710886-in-lncrna-pcat1-with-bladder-cancer-risk-in-a-chinese-population
#4
Yadi Lin, Yuqiu Ge, Yunyan Wang, Gaoxiang Ma, Xiaowei Wang, Hanting Liu, Meilin Wang, Zhengdong Zhang, Haiyan Chu
OBJECTIVE: The long noncoding RNA PCAT1 is an important gene involved in urinary tumors. In this study, we aimed to explore the association between polymorphisms in PCAT1 and bladder cancer susceptibility. METHODS: A two-stage case-control study was conducted to assess the association between four tagging SNPs (i.e., rs4871771, rs1902432, rs16901904 and rs710886) and bladder cancer risk. Odds ratios (ORs) and their 95% confidence intervals (CIs) were calculated with unconditional univariate and multivariate logistic regression...
June 13, 2017: Gene
https://www.readbyqxmd.com/read/28626070/potential-susceptibility-loci-identified-for-renal-cell-carcinoma-by-targeting-obesity-related-genes
#5
Xiang Shu, Mark P Purdue, Yuanqing Ye, Huakang Tu, Christopher G Wood, Nizar M Tannir, Zhaoming Wang, Demetrius Albanes, Susan M Gapstur, Victoria L Stevens, Nathaniel Rothman, Stephen J Chanock, Xifeng Wu
BACKGROUND: Obesity is an established risk factor for renal cell carcinoma (RCC). Although genome-wide association studies (GWAS) of RCC have identified several susceptibility loci, additional variants might be missed due to the highly conservative selection. METHODS: We conducted a multiphase study utilizing three independent genome-wide scans at MD Anderson Cancer Center (MDA RCC GWAS and MDA RCC OncoArray) and National Cancer Institute (NCI RCC GWAS), which consisted of a total of 3,530 cases and 5,714 controls, to investigate genetic variations in obesity-related genes and RCC risk...
June 16, 2017: Cancer Epidemiology, Biomarkers & Prevention
https://www.readbyqxmd.com/read/28620139/predictive-single-nucleotide-polymorphism-markers-for-acute-oral-mucositis-in-patients-with-nasopharyngeal-carcinoma-treated-with-radiotherapy
#6
Ziyu Le, Xiaoshuang Niu, Ying Chen, Xiaomin Ou, Guoqi Zhao, Qi Liu, Wenzhi Tu, Chaosu Hu, Lin Kong, Yong Liu
The aim of this study was to investigate the association between the susceptibility of severe oral mucositis (OM) in Chinese nasopharyngeal carcinoma (NPC) patients treated with radiotherapy and single nucleotide polymorphisms (SNPs) across the whole genome. SNPs were screened in a total of 24 patients with NPC and an additional 6 were subjected to mRNA expression analysis. Patients were subdivided into CTC 0-2 (CTC toxicity grade 0, 1, and 2) and CTC 3+ (CTC toxicity grade 3 and above) groups according to their CTC (common toxicity criteria) scores...
June 13, 2017: Oncotarget
https://www.readbyqxmd.com/read/28617822/intronic-snp-in-esr1-encoding-human-estrogen-receptor-alpha-is-associated-with-brain-esr1-mrna-isoform-expression-and-behavioral-traits
#7
Julia K Pinsonneault, John T Frater, Benjamin Kompa, Roshan Mascarenhas, Danxin Wang, Wolfgang Sadee
Genetic variants of ESR1 have been implicated in multiple diseases, including behavioral disorders, but causative variants remain uncertain. We have searched for regulatory variants affecting ESR1 expression in human brain, measuring allelic ESR1 mRNA expression in human brain tissues with marker SNPs in exon4 representing ESR1-008 (or ESRα-36), and in the 3'UTR of ESR1-203, two main ESR1 isoforms in brain. In prefrontal cortex from subjects with bipolar disorder, schizophrenia, and controls (n = 35 each; Stanley Foundation brain bank), allelic ESR1 mRNA ratios deviated from unity up to tenfold at the exon4 marker SNP, with large allelic ratios observed primarily in bipolar and schizophrenic subjects...
2017: PloS One
https://www.readbyqxmd.com/read/28615213/experimental-and-human-evidence-for-lipocalin-2-neutrophil-gelatinase-associated-lipocalin-ngal-in-the-development-of-cardiac-hypertrophy-and-heart-failure
#8
Francine Z Marques, Priscilla R Prestes, Sean G Byars, Scott C Ritchie, Peter Würtz, Sheila K Patel, Scott A Booth, Indrajeetsinh Rana, Yosuke Minoda, Stuart P Berzins, Claire L Curl, James R Bell, Bryan Wai, Piyush M Srivastava, Antti J Kangas, Pasi Soininen, Saku Ruohonen, Mika Kähönen, Terho Lehtimäki, Emma Raitoharju, Aki Havulinna, Markus Perola, Olli Raitakari, Veikko Salomaa, Mika Ala-Korpela, Johannes Kettunen, Maree McGlynn, Jason Kelly, Mary E Wlodek, Paul A Lewandowski, Lea M Delbridge, Louise M Burrell, Michael Inouye, Stephen B Harrap, Fadi J Charchar
BACKGROUND: Cardiac hypertrophy increases the risk of developing heart failure and cardiovascular death. The neutrophil inflammatory protein, lipocalin-2 (LCN2/NGAL), is elevated in certain forms of cardiac hypertrophy and acute heart failure. However, a specific role for LCN2 in predisposition and etiology of hypertrophy and the relevant genetic determinants are unclear. Here, we defined the role of LCN2 in concentric cardiac hypertrophy in terms of pathophysiology, inflammatory expression networks, and genomic determinants...
June 14, 2017: Journal of the American Heart Association
https://www.readbyqxmd.com/read/28613276/genetic-loci-associated-with-heart-rate-variability-and-their-effects-on-cardiac-disease-risk
#9
Ilja M Nolte, M Loretto Munoz, Vinicius Tragante, Azmeraw T Amare, Rick Jansen, Ahmad Vaez, Benedikt von der Heyde, Christy L Avery, Joshua C Bis, Bram Dierckx, Jenny van Dongen, Stephanie M Gogarten, Philippe Goyette, Jussi Hernesniemi, Ville Huikari, Shih-Jen Hwang, Deepali Jaju, Kathleen F Kerr, Alexander Kluttig, Bouwe P Krijthe, Jitender Kumar, Sander W van der Laan, Leo-Pekka Lyytikäinen, Adam X Maihofer, Arpi Minassian, Peter J van der Most, Martina Müller-Nurasyid, Michel Nivard, Erika Salvi, James D Stewart, Julian F Thayer, Niek Verweij, Andrew Wong, Delilah Zabaneh, Mohammad H Zafarmand, Abdel Abdellaoui, Sulayma Albarwani, Christine Albert, Alvaro Alonso, Foram Ashar, Juha Auvinen, Tomas Axelsson, Dewleen G Baker, Paul I W de Bakker, Matteo Barcella, Riad Bayoumi, Rob J Bieringa, Dorret Boomsma, Gabrielle Boucher, Annie R Britton, Ingrid Christophersen, Andrea Dietrich, George B Ehret, Patrick T Ellinor, Markku Eskola, Janine F Felix, John S Floras, Oscar H Franco, Peter Friberg, Maaike G J Gademan, Mark A Geyer, Vilmantas Giedraitis, Catharina A Hartman, Daiane Hemerich, Albert Hofman, Jouke-Jan Hottenga, Heikki Huikuri, Nina Hutri-Kähönen, Xavier Jouven, Juhani Junttila, Markus Juonala, Antti M Kiviniemi, Jan A Kors, Meena Kumari, Tatiana Kuznetsova, Cathy C Laurie, Joop D Lefrandt, Yong Li, Yun Li, Duanping Liao, Marian C Limacher, Henry J Lin, Cecilia M Lindgren, Steven A Lubitz, Anubha Mahajan, Barbara McKnight, Henriette Meyer Zu Schwabedissen, Yuri Milaneschi, Nina Mononen, Andrew P Morris, Mike A Nalls, Gerjan Navis, Melanie Neijts, Kjell Nikus, Kari E North, Daniel T O'Connor, Johan Ormel, Siegfried Perz, Annette Peters, Bruce M Psaty, Olli T Raitakari, Victoria B Risbrough, Moritz F Sinner, David Siscovick, Johannes H Smit, Nicholas L Smith, Elsayed Z Soliman, Nona Sotoodehnia, Jan A Staessen, Phyllis K Stein, Adrienne M Stilp, Katarzyna Stolarz-Skrzypek, Konstantin Strauch, Johan Sundström, Cees A Swenne, Ann-Christine Syvänen, Jean-Claude Tardif, Kent D Taylor, Alexander Teumer, Timothy A Thornton, Lesley E Tinker, André G Uitterlinden, Jessica van Setten, Andreas Voss, Melanie Waldenberger, Kirk C Wilhelmsen, Gonneke Willemsen, Quenna Wong, Zhu-Ming Zhang, Alan B Zonderman, Daniele Cusi, Michele K Evans, Halina K Greiser, Pim van der Harst, Mohammad Hassan, Erik Ingelsson, Marjo-Riitta Järvelin, Stefan Kääb, Mika Kähönen, Mika Kivimaki, Charles Kooperberg, Diana Kuh, Terho Lehtimäki, Lars Lind, Caroline M Nievergelt, Chris J O'Donnell, Albertine J Oldehinkel, Brenda Penninx, Alexander P Reiner, Harriëtte Riese, Arie M van Roon, John D Rioux, Jerome I Rotter, Tamar Sofer, Bruno H Stricker, Henning Tiemeier, Tanja G M Vrijkotte, Folkert W Asselbergs, Bianca J J M Brundel, Susan R Heckbert, Eric A Whitsel, Marcel den Hoed, Harold Snieder, Eco J C de Geus
Reduced cardiac vagal control reflected in low heart rate variability (HRV) is associated with greater risks for cardiac morbidity and mortality. In two-stage meta-analyses of genome-wide association studies for three HRV traits in up to 53,174 individuals of European ancestry, we detect 17 genome-wide significant SNPs in eight loci. HRV SNPs tag non-synonymous SNPs (in NDUFA11 and KIAA1755), expression quantitative trait loci (eQTLs) (influencing GNG11, RGS6 and NEO1), or are located in genes preferentially expressed in the sinoatrial node (GNG11, RGS6 and HCN4)...
June 14, 2017: Nature Communications
https://www.readbyqxmd.com/read/28604730/large-scale-association-analysis-identifies-new-lung-cancer-susceptibility-loci-and-heterogeneity-in-genetic-susceptibility-across-histological-subtypes
#10
James D McKay, Rayjean J Hung, Younghun Han, Xuchen Zong, Robert Carreras-Torres, David C Christiani, Neil E Caporaso, Mattias Johansson, Xiangjun Xiao, Yafang Li, Jinyoung Byun, Alison Dunning, Karen A Pooley, David C Qian, Xuemei Ji, Geoffrey Liu, Maria N Timofeeva, Stig E Bojesen, Xifeng Wu, Loic Le Marchand, Demetrios Albanes, Heike Bickeböller, Melinda C Aldrich, William S Bush, Adonina Tardon, Gad Rennert, M Dawn Teare, John K Field, Lambertus A Kiemeney, Philip Lazarus, Aage Haugen, Stephen Lam, Matthew B Schabath, Angeline S Andrew, Hongbing Shen, Yun-Chul Hong, Jian-Min Yuan, Pier Alberto Bertazzi, Angela C Pesatori, Yuanqing Ye, Nancy Diao, Li Su, Ruyang Zhang, Yonathan Brhane, Natasha Leighl, Jakob S Johansen, Anders Mellemgaard, Walid Saliba, Christopher A Haiman, Lynne R Wilkens, Ana Fernandez-Somoano, Guillermo Fernandez-Tardon, Henricus F M van der Heijden, Jin Hee Kim, Juncheng Dai, Zhibin Hu, Michael P A Davies, Michael W Marcus, Hans Brunnström, Jonas Manjer, Olle Melander, David C Muller, Kim Overvad, Antonia Trichopoulou, Rosario Tumino, Jennifer A Doherty, Matt P Barnett, Chu Chen, Gary E Goodman, Angela Cox, Fiona Taylor, Penella Woll, Irene Brüske, H-Erich Wichmann, Judith Manz, Thomas R Muley, Angela Risch, Albert Rosenberger, Kjell Grankvist, Mikael Johansson, Frances A Shepherd, Ming-Sound Tsao, Susanne M Arnold, Eric B Haura, Ciprian Bolca, Ivana Holcatova, Vladimir Janout, Milica Kontic, Jolanta Lissowska, Anush Mukeria, Simona Ognjanovic, Tadeusz M Orlowski, Ghislaine Scelo, Beata Swiatkowska, David Zaridze, Per Bakke, Vidar Skaug, Shanbeh Zienolddiny, Eric J Duell, Lesley M Butler, Woon-Puay Koh, Yu-Tang Gao, Richard S Houlston, John McLaughlin, Victoria L Stevens, Philippe Joubert, Maxime Lamontagne, David C Nickle, Ma'en Obeidat, Wim Timens, Bin Zhu, Lei Song, Linda Kachuri, María Soler Artigas, Martin D Tobin, Louise V Wain, Thorunn Rafnar, Thorgeir E Thorgeirsson, Gunnar W Reginsson, Kari Stefansson, Dana B Hancock, Laura J Bierut, Margaret R Spitz, Nathan C Gaddis, Sharon M Lutz, Fangyi Gu, Eric O Johnson, Ahsan Kamal, Claudio Pikielny, Dakai Zhu, Sara Lindströem, Xia Jiang, Rachel F Tyndale, Georgia Chenevix-Trench, Jonathan Beesley, Yohan Bossé, Stephen Chanock, Paul Brennan, Maria Teresa Landi, Christopher I Amos
Although several lung cancer susceptibility loci have been identified, much of the heritability for lung cancer remains unexplained. Here 14,803 cases and 12,262 controls of European descent were genotyped on the OncoArray and combined with existing data for an aggregated genome-wide association study (GWAS) analysis of lung cancer in 29,266 cases and 56,450 controls. We identified 18 susceptibility loci achieving genome-wide significance, including 10 new loci. The new loci highlight the striking heterogeneity in genetic susceptibility across the histological subtypes of lung cancer, with four loci associated with lung cancer overall and six loci associated with lung adenocarcinoma...
June 12, 2017: Nature Genetics
https://www.readbyqxmd.com/read/28600441/unique-allelic-eqtl-clusters-in-human-mhc-haplotypes
#11
Tze Hau Lam, Meixin Shen, Matthew Zirui Tay, Ee Chee Ren
The control of gene regulation within the MHC remains poorly understood despite several eQTL studies revealing an association of MHC gene expression with independent tag-SNPs. MHC haplotype variation may exert a greater effect on gene expression phenotype than specific single variants. To explore the effect of MHC haplotype sequence diversity on gene expression phenotypes across the MHC, we examined the MHC transcriptomic landscape at haplotype-specific resolution for three prominent MHC haplotypes (A2-B46-DR9, A33-B58-DR3, and A1-B8-DR3) derived from MHC-homozygous B-lymphoblastoid cell lines...
June 9, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/28600440/constraints-on-eqtl-fine-mapping-in-the-presence-of-multi-site-local-regulation-of-gene-expression
#12
Biao Zeng, Luke R Lloyd-Jones, Alexander Holloway, Urko M Marigorta, Andres Metspalu, Grant W Montgomery, Tonu Esko, Kenneth L Brigham, Arshed A Quyyumi, Youssef Idaghdour, Jian Yang, Peter M Visscher, Joseph E Powell, Greg Gibson
Expression QTL (eQTL) detection has emerged as an important tool for unraveling of the relationship between genetic risk factors and disease or clinical phenotypes. Most studies use single marker linear regression to discover primary signals, followed by sequential conditional modeling to detect secondary genetic variants affecting gene expression. However, this approach assumes that functional variants are sparsely distributed and that close linkage between them has little impact on estimation of their precise location and magnitude of effects...
June 9, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/28592498/genetic-dissection-of-nutrition-induced-plasticity-in-insulin-insulin-like-growth-factor-signaling-and-median-life-span-in-a-drosophila-multiparent-population
#13
Patrick D Stanley, Enoch Ng'oma, Siri O'Day, Elizabeth G King
The nutritional environments that organisms experience are inherently variable, requiring tight coordination of how resources are allocated to different functions relative to the total amount of resources available. A growing body of evidence supports the hypothesis that key endocrine pathways play a fundamental role in this coordination. In particular, the insulin/insulin-like growth factor signaling (IIS) and target of rapamycin (TOR) pathways have been implicated in nutrition-dependent changes in metabolism and nutrient allocation...
June 2017: Genetics
https://www.readbyqxmd.com/read/28582503/hugin-hi-c-unifying-genomic-interrogator
#14
Joshua S Martin, Zheng Xu, Alex P Reiner, Karen L Mohlke, Patrick Sullivan, Bing Ren, Ming Hu, Yun Li
Motivation: High throughput chromatin conformation capture (3C) technologies, such as Hi-C and ChIA-PET, have the potential to elucidate the functional roles of non-coding variants. However, most of published genome-wide unbiased chromatin organization studies have used cultured cell lines, limiting their generalizability. Results: We developed a web browser, HUGIn, to visualize Hi-C data generated from 21 human primary tissues and cell lines. HUGIn enables assessment of chromatin contacts both constitutive across and specific to tissue(s) and/or cell line(s) at any genomic loci, including GWAS SNPs, eQTLs and cis-regulatory elements, facilitating the understanding of both GWAS and eQTLs results and functional genomics data...
June 5, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28575649/genetic-variation-driven-gene-expression-changes-highlight-genes-with-important-functions-for-kidney-disease
#15
Yi-An Ko, Huiguang Yi, Chengxiang Qiu, Shizheng Huang, Jihwan Park, Nora Ledo, Anna Köttgen, Hongzhe Li, Daniel J Rader, Michael A Pack, Christopher D Brown, Katalin Susztak
Chronic kidney disease (CKD) is a complex gene-environmental disease affecting close to 10% of the US population. Genome-wide association studies (GWASs) have identified sequence variants, localized to non-coding genomic regions, associated with kidney function. Despite these robust observations, the mechanism by which variants lead to CKD remains a critical unanswered question. Expression quantitative trait loci (eQTL) analysis is a method to identify genetic variation associated with gene expression changes in specific tissue types...
June 1, 2017: American Journal of Human Genetics
https://www.readbyqxmd.com/read/28575251/hierarchical-probabilistic-models-for-multiple-gene-variant-associations-based-on-next-generation-sequencing-data
#16
Dimitrios V Vavoulis, Jenny C Taylor, Anna Schuh
Motivation: The identification of genetic variants influencing gene expression (known as expression quantitative trait loci or eQTLs ) is important in unravelling the genetic basis of complex traits. Detecting multiple eQTLs simultaneously in a population based on paired DNA-seq and RNA-seq assays employs two competing types of models: models which rely on appropriate transformations of RNA-seq data (and are powered by a mature mathematical theory), or count-based models , which represent digital gene expression explicitly, thus rendering such transformations unnecessary...
May 31, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28575045/the-effect-of-alcohol-on-the-differential-expression-of-cluster-of-differentiation-14-gene-associated-pathways-and-genetic-network
#17
Diana X Zhou, Yinghong Zhao, Jessica A Baker, Qingqing Gu, Kristin M Hamre, Junming Yue, Byron C Jones, Melloni N Cook, Lu Lu
Alcohol consumption affects human health in part by compromising the immune system. In this study, we examined the expression of the Cd14 (cluster of differentiation 14) gene, which is involved in the immune system through a proinflammatory cascade. Expression was evaluated in BXD mice treated with saline or acute 1.8 g/kg i.p. ethanol (12.5% v/v). Hippocampal gene expression data were generated to examine differential expression and to perform systems genetics analyses. The Cd14 gene expression showed significant changes among the BXD strains after ethanol treatment, and eQTL mapping revealed that Cd14 is a cis-regulated gene...
2017: PloS One
https://www.readbyqxmd.com/read/28567521/comprehensive-evaluation-of-disease-and-trait-specific-enrichment-for-eight-functional-elements-among-gwas-identified-variants
#18
Christina A Markunas, Eric O Johnson, Dana B Hancock
Genome-wide association study (GWAS)-identified variants are enriched for functional elements. However, we have limited knowledge of how functional enrichment may differ by disease/trait and tissue type. We tested a broad set of eight functional elements for enrichment among GWAS-identified SNPs (p < 5×10(-8)) from the NHGRI-EBI Catalog across seven disease/trait categories: cancer, cardiovascular disease, diabetes, autoimmune disease, psychiatric disease, neurological disease, and anthropometric traits...
May 31, 2017: Human Genetics
https://www.readbyqxmd.com/read/28564610/effect-of-human-genetic-variability-on-gene-expression-in-dorsal-root-ganglia-and-association-with-pain-phenotypes
#19
Marc Parisien, Samar Khoury, Anne-Julie Chabot-Doré, Susana G Sotocinal, Gary D Slade, Shad B Smith, Roger B Fillingim, Richard Ohrbach, Joel D Greenspan, William Maixner, Jeffrey S Mogil, Inna Belfer, Luda Diatchenko
Dorsal root ganglia (DRG) relay sensory information to the brain, giving rise to the perception of pain, disorders of which are prevalent and burdensome. Here, we mapped expression quantitative trait loci (eQTLs) in a collection of human DRGs. DRG eQTLs were enriched within untranslated regions of coding genes of low abundance, with some overlapping with other brain regions and blood cell cis-eQTLs. We confirm functionality of identified eQTLs through their significant enrichment within open chromatin and highly deleterious SNPs, particularly at the exon level, suggesting substantial contribution of eQTLs to alternative splicing regulation...
May 30, 2017: Cell Reports
https://www.readbyqxmd.com/read/28553958/polygenic-burdens-on-cell-specific-pathways-underlie-the-risk-of-rheumatoid-arthritis
#20
Kazuyoshi Ishigaki, Yuta Kochi, Akari Suzuki, Yumi Tsuchida, Haruka Tsuchiya, Shuji Sumitomo, Kensuke Yamaguchi, Yasuo Nagafuchi, Shinichiro Nakachi, Rika Kato, Keiichi Sakurai, Hirofumi Shoda, Katsunori Ikari, Atsuo Taniguchi, Hisashi Yamanaka, Fuyuki Miya, Tatsuhiko Tsunoda, Yukinori Okada, Yukihide Momozawa, Yoichiro Kamatani, Ryo Yamada, Michiaki Kubo, Keishi Fujio, Kazuhiko Yamamoto
Recent evidence suggests that a substantial portion of complex disease risk alleles modify gene expression in a cell-specific manner. To identify candidate causal genes and biological pathways of immune-related complex diseases, we conducted expression quantitative trait loci (eQTL) analysis on five subsets of immune cells (CD4(+) T cells, CD8(+) T cells, B cells, natural killer (NK) cells and monocytes) and unfractionated peripheral blood from 105 healthy Japanese volunteers. We developed a three-step analytical pipeline comprising (i) prediction of individual gene expression using our eQTL database and public epigenomic data, (ii) gene-level association analysis and (iii) prediction of cell-specific pathway activity by integrating the direction of eQTL effects...
May 29, 2017: Nature Genetics
keyword
keyword
24496
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"