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https://www.readbyqxmd.com/read/28212520/adp-ribosyl-cyclases-cd38-cd157-social-skills-and-friendship
#1
Anne Chong, Fabio Malavasi, Salomon Israel, Chiea Chuen Khor, Von Bing Yap, Mikhail Monakhov, Soo Hong Chew, Poh San Lai, Richard P Ebstein
Why some individuals seek social engagement while others shy away has profound implications for normal and pathological human behavior. Evidence suggests that oxytocin (OT), the paramount human social hormone, and CD38 that governs OT release, contribute to individual differences in social skills from intense social involvement to extreme avoidance that characterize autism. To explore the neurochemical underpinnings of sociality, CD38 expression of peripheral blood leukocytes (PBL) was measured in Han Chinese undergraduates...
January 16, 2017: Psychoneuroendocrinology
https://www.readbyqxmd.com/read/28193859/genetic-regulatory-signatures-underlying-islet-gene-expression-and-type-2-diabetes
#2
Arushi Varshney, Laura J Scott, Ryan P Welch, Michael R Erdos, Peter S Chines, Narisu Narisu, Ricardo D'O Albanus, Peter Orchard, Brooke N Wolford, Romy Kursawe, Swarooparani Vadlamudi, Maren E Cannon, John P Didion, John Hensley, Anthony Kirilusha, Lori L Bonnycastle, D Leland Taylor, Richard Watanabe, Karen L Mohlke, Michael Boehnke, Francis S Collins, Stephen C J Parker, Michael L Stitzel
Genome-wide association studies (GWAS) have identified >100 independent SNPs that modulate the risk of type 2 diabetes (T2D) and related traits. However, the pathogenic mechanisms of most of these SNPs remain elusive. Here, we examined genomic, epigenomic, and transcriptomic profiles in human pancreatic islets to understand the links between genetic variation, chromatin landscape, and gene expression in the context of T2D. We first integrated genome and transcriptome variation across 112 islet samples to produce dense cis-expression quantitative trait loci (cis-eQTL) maps...
February 13, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28193307/heritability-and-gwas-studies-for-monocyte-lymphocyte-ratio
#3
Bochao D Lin, Gonneke Willemsen, Iryna O Fedko, Rick Jansen, Brenda Penninx, E de Geus, C Kluft, JoukeJan Hottenga, Dorret I Boomsma
The monocyte-lymphocyte ratio (MLR) is a useful biomarker for disease development, but little is known about the extent to which genetic and environmental factors influence MLR variation. Here, we study the genetic architecture of MLR and determine the influence of demographic and lifestyle factors on MLR in data from a Dutch non-patient twin-family population. Data were obtained in 9,501 individuals from the Netherlands Twin Register. We used regression analyses to determine the effects of age, sex, smoking, and body mass index (BMI) on MLR and its subcomponents...
February 14, 2017: Twin Research and Human Genetics: the Official Journal of the International Society for Twin Studies
https://www.readbyqxmd.com/read/28187197/genetic-variants-alter-t-bet-binding-and-gene-expression-in-mucosal-inflammatory-disease
#4
Katrina Soderquest, Arnulf Hertweck, Claudia Giambartolomei, Stephen Henderson, Rami Mohamed, Rimma Goldberg, Esperanza Perucha, Lude Franke, Javier Herrero, Vincent Plagnol, Richard G Jenner, Graham M Lord
The polarization of CD4+ T cells into distinct T helper cell lineages is essential for protective immunity against infection, but aberrant T cell polarization can cause autoimmunity. The transcription factor T-bet (TBX21) specifies the Th1 lineage and represses alternative T cell fates. Genome-wide association studies have identified single nucleotide polymorphisms (SNPs) that may be causative for autoimmune diseases. The majority of these polymorphisms are located within non-coding distal regulatory elements...
February 10, 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28187132/gwas-for-serum-galactose-deficient-iga1-implicates-critical-genes-of-the-o-glycosylation-pathway
#5
Krzysztof Kiryluk, Yifu Li, Zina Moldoveanu, Hitoshi Suzuki, Colin Reily, Ping Hou, Jingyuan Xie, Nikol Mladkova, Sindhuri Prakash, Clara Fischman, Samantha Shapiro, Robert A LeDesma, Drew Bradbury, Iuliana Ionita-Laza, Frank Eitner, Thomas Rauen, Nicolas Maillard, Francois Berthoux, Jürgen Floege, Nan Chen, Hong Zhang, Francesco Scolari, Robert J Wyatt, Bruce A Julian, Ali G Gharavi, Jan Novak
Aberrant O-glycosylation of serum immunoglobulin A1 (IgA1) represents a heritable pathogenic defect in IgA nephropathy, the most common form of glomerulonephritis worldwide, but specific genetic factors involved in its determination are not known. We performed a quantitative GWAS for serum levels of galactose-deficient IgA1 (Gd-IgA1) in 2,633 subjects of European and East Asian ancestry and discovered two genome-wide significant loci, in C1GALT1 (rs13226913, P = 3.2 x 10-11) and C1GALT1C1 (rs5910940, P = 2...
February 10, 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28183275/diversity-and-regulatory-impact-of-copy-number-variation-in-the-primate-macaca-fascicularis
#6
Andreas R Gschwind, Anjali Singh, Ulrich Certa, Alexandre Reymond, Tobias Heckel
BACKGROUND: Copy number variations (CNVs) are a significant source of genetic diversity and commonly found in mammalian genomes. We have generated a genome-wide CNV map for Cynomolgus monkeys (Macaca fascicularis). This crab-eating macaque is the closest animal model to humans that is used in biomedical research. RESULTS: We show that Cynomolgus monkey CNVs are in general much smaller in size than gene loci and are specific to the population of origin. Genome-wide expression data from five vitally important organs demonstrates that CNVs in close proximity to transcription start sites associate strongly with expression changes...
February 10, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28181694/a-genome-wide-association-study-identifies-two-sex-specific-loci-at-sptb-and-izumo3-influencing-pediatric-bone-mineral-density-at-multiple-skeletal-sites
#7
Alessandra Chesi, Jonathan A Mitchell, Heidi J Kalkwarf, Jonathan P Bradfield, Joan M Lappe, Diana L Cousminer, Sani M Roy, Shana E McCormack, Vicente Gilsanz, Sharon E Oberfield, Hakon Hakonarson, John A Shepherd, Andrea Kelly, Babette S Zemel, Struan F A Grant
Failure to achieve optimal bone mineral accretion during childhood and adolescence results in subsequent suboptimal peak bone mass, contributing to osteoporosis risk later in life. To identify novel genetic factors that influence pediatric bone mass at discrete skeletal sites, we performed a sex-stratified genome-wide association study of areal bone mineral density (BMD) measured by dual energy X-ray absorptiometry at the 1/3 distal radius, spine, total hip and femoral neck in a cohort of 933 healthy European American children...
February 9, 2017: Journal of Bone and Mineral Research: the Official Journal of the American Society for Bone and Mineral Research
https://www.readbyqxmd.com/read/28181565/genetic-susceptibility-variants-for-lung-cancer-replication-study-and-assessment-as-expression-quantitative-trait-loci
#8
Giulia Pintarelli, Chiara Elisabetta Cotroneo, Sara Noci, Matteo Dugo, Antonella Galvan, Simona Delli Carpini, Lorena Citterio, Paolo Manunta, Matteo Incarbone, Davide Tosi, Luigi Santambrogio, Tommaso A Dragani, Francesca Colombo
Many single nucleotide polymorphisms (SNPs) have been associated with lung cancer but lack confirmation and functional characterization. We retested the association of 56 candidate SNPs with lung adenocarcinoma risk and overall survival in a cohort of 823 Italian patients and 779 healthy controls, and assessed their function as expression quantitative trait loci (eQTLs). In the replication study, eight SNPs (rs401681, rs3019885, rs732765, rs2568494, rs16969968, rs6495309, rs11634351, and rs4105144) associated with lung adenocarcinoma risk and three (rs9557635, rs4105144, and rs735482) associated with survival...
February 9, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28179588/tp53-based-interaction-analysis-identifies-cis-eqtl-variants-for-tp53bp2-fbxo28-and-fam53a-that-associate-with-survival-and-treatment-outcome-in-breast-cancer
#9
Rainer Fagerholm, Sofia Khan, Marjanka K Schmidt, Montserrat García-Closas, Päivi Heikkilä, Jani Saarela, Jonathan Beesley, Maral Jamshidi, Kristiina Aittomäki, Jianjun Liu, H Raza Ali, Irene L Andrulis, Matthias W Beckmann, Sabine Behrens, Fiona M Blows, Hermann Brenner, Jenny Chang-Claude, Fergus J Couch, Kamila Czene, Peter A Fasching, Jonine Figueroa, Giuseppe Floris, Gord Glendon, Qi Guo, Per Hall, Emily Hallberg, Ute Hamann, Bernd Holleczek, Maartje J Hooning, John L Hopper, Agnes Jager, Maria Kabisch, Renske Keeman, Veli-Matti Kosma, Diether Lambrechts, Annika Lindblom, Arto Mannermaa, Sara Margolin, Elena Provenzano, Mitul Shah, Melissa C Southey, Joe Dennis, Michael Lush, Kyriaki Michailidou, Qin Wang, Manjeet K Bolla, Alison M Dunning, Douglas F Easton, Paul D P Pharoah, Georgia Chenevix-Trench, Carl Blomqvist, Heli Nevanlinna
TP53 overexpression is indicative of somatic TP53 mutations and associates with aggressive tumors and poor prognosis in breast cancer. We utilized a two-stage SNP association study to detect variants associated with breast cancer survival in a TP53-dependent manner. Initially, a genome-wide study (n = 575 cases) was conducted to discover candidate SNPs for genotyping and validation in the Breast Cancer Association Consortium (BCAC). The SNPs were then tested for interaction with tumor TP53 status (n = 4,610) and anthracycline treatment (n = 17,828)...
February 5, 2017: Oncotarget
https://www.readbyqxmd.com/read/28165122/conditional-eqtl-analysis-reveals-allelic-heterogeneity-of-gene-expression
#10
Rick Jansen, Jouke-Jan Hottenga, Michel G Nivard, Abdel Abdellaoui, Bram Laport, Eco J de Geus, Fred A Wright, Brenda Wjh Penninx, Dorret I Boomsma
No abstract text is available yet for this article.
February 6, 2017: Human Molecular Genetics
https://www.readbyqxmd.com/read/28163244/colonic-transcriptional-response-to-1%C3%AE-25-oh-2-vitamin-d3-in-african-and-european-americans
#11
Dereck Alleyne, David Witonsky, Brandon Mapes, Shigeki Nakagome, Meredith Sommars, Ellie Hong, Katy A Muckala, Anna Di Rienzo, Sonia S Kupfer
Colorectal cancer (CRC) is a significant health burden especially among African Americans (AA). Epidemiological studies have correlated low serum vitamin D with CRC risk, and, while hypovitaminosis D is more common and more severe in AA, the mechanisms by which vitamin D modulates CRC risk and how these differ by race are not well understood. Active vitamin D (1α,25(OH)2D3) has chemoprotective effects primarily through transcriptional regulation of target genes in the colon. We hypothesized that transcriptional response to 1α,25(OH)2D3 differs between AA and European Americans (EA) irrespective of serum vitamin D and that regulatory variants could impact transcriptional response...
February 2, 2017: Journal of Steroid Biochemistry and Molecular Biology
https://www.readbyqxmd.com/read/28152060/expression-quantitative-trait-loci-qtl-in-tumor-adjacent-normal-breast-tissue-and-breast-tumor-tissue
#12
Alejandro Quiroz-Zárate, Benjamin J Harshfield, Rong Hu, Nick Knoblauch, Andrew H Beck, Susan E Hankinson, Vincent Carey, Rulla M Tamimi, David J Hunter, John Quackenbush, Aditi Hazra
We investigate 71 single nucleotide polymorphisms (SNPs) identified in meta-analytic studies of genome-wide association studies (GWAS) of breast cancer, the majority of which are located in intergenic or intronic regions. To explore regulatory impacts of these variants we conducted expression quantitative loci (eQTL) analyses on tissue samples from 376 invasive postmenopausal breast cancer cases in the Nurses' Health Study (NHS) diagnosed from 1990-2004. Expression analysis was conducted on all formalin-fixed paraffin-embedded (FFPE) tissue samples (and on 264 adjacent normal samples) using the Affymetrix Human Transcriptome Array...
2017: PloS One
https://www.readbyqxmd.com/read/28151979/whole-genome-sequencing-of-an-african-american-family-highlights-toll-like-receptor-6-variants-in-kawasaki-disease-susceptibility
#13
Jihoon Kim, Chisato Shimizu, Stephen F Kingsmore, Narayanan Veeraraghavan, Eric Levy, Andre M Ribeiro Dos Santos, Hai Yang, Jay Flatley, Long Truong Hoang, Martin L Hibberd, Adriana H Tremoulet, Olivier Harismendy, Lucila Ohno-Machado, Jane C Burns
Kawasaki disease (KD) is the most common acquired pediatric heart disease. We analyzed Whole Genome Sequences (WGS) from a 6-member African American family in which KD affected two of four children. We sought rare, potentially causative genotypes by sequentially applying the following WGS filters: sequence quality scores, inheritance model (recessive homozygous and compound heterozygous), predicted deleteriousness, allele frequency, genes in KD-associated pathways or with significant associations in published KD genome-wide association studies (GWAS), and with differential expression in KD blood transcriptomes...
2017: PloS One
https://www.readbyqxmd.com/read/28142321/understanding-human-autoimmunity-and-autoinflammation-through-transcriptomics
#14
Romain Banchereau, Alma-Martina Cepika, Jacques Banchereau, Virginia Pascual
Transcriptomics, the high-throughput characterization of RNAs, has been instrumental in defining pathogenic signatures in human autoimmunity and autoinflammation. It enabled the identification of new therapeutic targets in IFN-, IL-1- and IL-17-mediated diseases. Applied to immunomonitoring, transcriptomics is starting to unravel diagnostic and prognostic signatures that stratify patients, track molecular changes associated with disease activity, define personalized treatment strategies, and generally inform clinical practice...
January 30, 2017: Annual Review of Immunology
https://www.readbyqxmd.com/read/28139761/genome-wide-association-study-of-polymorphisms-predisposing-to-bronchiolitis
#15
Anu Pasanen, Minna K Karjalainen, Louis Bont, Eija Piippo-Savolainen, Marja Ruotsalainen, Emma Goksör, Kuldeep Kumawat, Hennie Hodemaekers, Kirsi Nuolivirta, Tuomas Jartti, Göran Wennergren, Mikko Hallman, Mika Rämet, Matti Korppi
Bronchiolitis is a major cause of hospitalization among infants. Severe bronchiolitis is associated with later asthma, suggesting a common genetic predisposition. Genetic background of bronchiolitis is not well characterized. To identify polymorphisms associated with bronchiolitis, we conducted a genome-wide association study (GWAS) in which 5,300,000 single nucleotide polymorphisms (SNPs) were tested for association in a Finnish-Swedish population of 217 children hospitalized for bronchiolitis and 778 controls...
January 31, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28139690/snp-variants-associated-with-non-hodgkin-lymphoma-nhl-correlate-with-human-leukocyte-antigen-hla-class-ii-expression
#16
Lik-Chin Ten, Yoon-Ming Chin, Mei-Chee Tai, Edmund Fui-Min Chin, Yat-Yuen Lim, Sujatha Suthandiram, Kian-Meng Chang, Tee-Chuan Ong, Ping-Chong Bee, Zahurin Mohamed, Gin-Gin Gan, Ching-Ching Ng
Large consortia efforts and genome-wide association studies (GWASs) have linked a number of genetic variants within the 6p21 chromosomal region to non-Hodgkin lymphoma (NHL). Complementing these efforts, we genotyped previously reported SNPs in the human leukocyte antigen (HLA) class I (rs6457327) and class II (rs9271100, rs2647012 and rs10484561) regions in a total of 1,145 subjects (567 NHL cases and 578 healthy controls) from two major ethnic groups in Malaysia, the Malays and the Chinese. We identified a NHL-associated (PNHL_add = 0...
January 31, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28135054/integrated-analysis-of-genetic-variation-and-gene-expression-reveals-novel-variant-for-increased-warfarin-dose-requirement-in-african-americans
#17
Wenndy Hernandez, Eric R Gamazon, Keston Aquino-Michaels, Erin Smithberger, Travis J O'Brien, Arthur F Harralson, Matthew Tuck, April Barbour, Larisa H Cavallari, Minoli A Perera
BACKGROUND: Warfarin is commonly used to control and prevent thromboembolic disorders. However, due to warfarin's complex dose-requirement relationship, safe and effective use is challenging. Pharmacogenomics-guided warfarin dosing algorithms that include the well-established VKORC1 and CYP2C9 polymorphisms explain only a small proportion of inter-individual variability in African Americans (AAs). OBJECTIVES: We aimed to assess whether transcriptomic analyses could be used to identify regulatory variants associated with warfarin dose response in AAs...
January 30, 2017: Journal of Thrombosis and Haemostasis: JTH
https://www.readbyqxmd.com/read/28129359/high-throughput-characterization-of-blood-serum-proteomics-of-ibd-patients-with-respect-to-aging-and-genetic-factors
#18
Antonio F Di Narzo, Shannon E Telesco, Carrie Brodmerkel, Carmen Argmann, Lauren A Peters, Katherine Li, Brian Kidd, Joel Dudley, Judy Cho, Eric E Schadt, Andrew Kasarskis, Radu Dobrin, Ke Hao
To date, no large scale, systematic description of the blood serum proteome has been performed in inflammatory bowel disease (IBD) patients. By using microarray technology, a more complete description of the blood proteome of IBD patients is feasible. It may help to achieve a better understanding of the disease. We analyzed blood serum profiles of 1128 proteins in IBD patients of European descent (84 Crohn's Disease (CD) subjects and 88 Ulcerative Colitis (UC) subjects) as well as 15 healthy control subjects, and linked protein variability to patient age (all cohorts) and genetic components (genotype data generated from CD patients)...
January 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28122634/integrated-genome-wide-analysis-of-expression-quantitative-trait-loci-aids-interpretation-of-genomic-association-studies
#19
Roby Joehanes, Xiaoling Zhang, Tianxiao Huan, Chen Yao, Sai-Xia Ying, Quang Tri Nguyen, Cumhur Yusuf Demirkale, Michael L Feolo, Nataliya R Sharopova, Anne Sturcke, Alejandro A Schäffer, Nancy Heard-Costa, Han Chen, Po-Ching Liu, Richard Wang, Kimberly A Woodhouse, Kahraman Tanriverdi, Jane E Freedman, Nalini Raghavachari, Josée Dupuis, Andrew D Johnson, Christopher J O'Donnell, Daniel Levy, Peter J Munson
BACKGROUND: Identification of single nucleotide polymorphisms (SNPs) associated with gene expression levels, known as expression quantitative trait loci (eQTLs), may improve understanding of the functional role of phenotype-associated SNPs in genome-wide association studies (GWAS). The small sample sizes of some previous eQTL studies have limited their statistical power. We conducted an eQTL investigation of microarray-based gene and exon expression levels in whole blood in a cohort of 5257 individuals, exceeding the single cohort size of previous studies by more than a factor of 2...
January 25, 2017: Genome Biology
https://www.readbyqxmd.com/read/28120510/predicting%C3%A2-enhancer-activity-and-variant-impact-using-gkm-svm
#20
Michael A Beer
We participated in the Critical Assessment of Genome Interpretation eQTL challenge to further test computational models of regulatory variant impact and their association with human disease. Our prediction model is based on a discriminative gapped-kmer SVM (gkm-SVM) trained on genome-wide chromatin accessibility data in the cell type of interest. The comparisons with Massively Parallel Reporter Assays (MPRA) in lymphoblasts show that gkm-SVM is among the most accurate prediction models even though all other models used the MPRA data for model training, while gkm-SVM did not...
January 25, 2017: Human Mutation
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