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https://www.readbyqxmd.com/read/29334207/screening-for-causative-mutations-of-major-prolificacy-genes-in-iranian-fat-tailed-sheep
#1
Ramin Abdoli, Seyed Ziaeddin Mirhoseini, Navid Ghavi Hossein-Zadeh, Pouya Zamani
Background: The presence of different missense mutations in sheep breeds have shown that the bone morphogenetic protein receptor 1B (BMPR1B), bone morphogenetic protein 15 (BMP15) and growth differentiation factor 9 (GDF9) genes play a vital role in ovulation rate and prolificacy in ewes. Therefore, the present study aims to investigate BMPR1B, BMP15 and GDF9 gene mutations in prolific ewes of Iranian fat-tailed Lori-Bakhtiari sheep. MATERIALS AND METHODS: In the present experimental study, genomic DNA was extracted from whole blood of 10 prolific Lori-Bakhtiari ewes with at least two twinning records in the first four parities to identify point mutations of the BMPR1B, BMP15 and GDF9 genes, using DNA sequencing...
April 2018: International Journal of Fertility & Sterility
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/29333268/progress-of-genome-wide-association-studies-of-ankylosing-spondylitis
#3
REVIEW
Zhixiu Li, Matthew A Brown
Ankylosing spondylitis (AS) is an immune-mediated arthritis which primarily affects the spine and sacroiliac joints. Significant progress has been made in discovery of genetic associations with AS by genome-wide association studies (GWAS) over past decade. These findings have uncovered novel pathways involved pathogenesis of the disease and have led to introduction of novel therapeutic treatments for AS. In this Review, we discuss the genetic variations associated with AS identified by GWAS, the major pathways revealed by these AS-associated variations and critical cell types involved in AS development...
December 2017: Clinical & Translational Immunology
https://www.readbyqxmd.com/read/29333267/type-1-diabetes-genome-wide-association-studies-not-to-be-lost-in-translation
#4
REVIEW
Flemming Pociot
Genetic studies have identified >60 loci associated with the risk of developing type 1 diabetes (T1D). The vast majority of these are identified by genome-wide association studies (GWAS) using large case-control cohorts of European ancestry. More than 80% of the heritability of T1D can be explained by GWAS data in this population group. However, with few exceptions, their individual contribution to T1D risk is low and understanding their function in disease biology remains a huge challenge. GWAS on its own does not inform us in detail on disease mechanisms, but the combination of GWAS data with other omics-data is beginning to advance our understanding of T1D etiology and pathogenesis...
December 2017: Clinical & Translational Immunology
https://www.readbyqxmd.com/read/29331684/reprogramming-neurodegeneration-in-the-big-data-era
#5
REVIEW
Lujia Zhou, Patrik Verstreken
Recent genome-wide association studies (GWAS) have identified numerous genetic risk variants for late-onset Alzheimer's disease (AD) and Parkinson's disease (PD). However, deciphering the functional consequences of GWAS data is challenging due to a lack of reliable model systems to study the genetic variants that are often of low penetrance and non-coding identities. Pluripotent stem cell (PSC) technologies offer unprecedented opportunities for molecular phenotyping of GWAS variants in human neurons and microglia...
January 10, 2018: Current Opinion in Neurobiology
https://www.readbyqxmd.com/read/29331643/glucagon-like-peptide-1-signaling-inhibits-allergen-induced-lung-il-33-release-and-reduces-group-2-innate-lymphoid-cell-ilc2-cytokine-production-in-vivo
#6
Shinji Toki, Kasia Goleniewska, Sara Reiss, Jian Zhang, Melissa H Bloodworth, Matthew T Stier, Weisong Zhou, Dawn C Newcomb, Lorraine B Ware, Gregg D Stanwood, Aurelio Galli, Kelli L Boyd, Kevin D Niswender, R Stokes Peebles
BACKGROUND: IL-33 is one of the most consistently associated gene candidates for asthma identified by GWAS. Studies in mice and in human cells have confirmed the importance of IL-33 in inducing type-2 cytokine production from both group 2 innate lymphoid cells (ILC2) and Th2 cells. However, there are no pharmacologic agents known to inhibit IL-33 release from airway cells. OBJECTIVE: To determine the effect of glucagon like peptide receptor-1 GLP-1R signaling on aeroallergen-induced airway IL-33 production and release and on innate type-2 airway inflammation...
January 10, 2018: Journal of Allergy and Clinical Immunology
https://www.readbyqxmd.com/read/29331499/hspb7-is-a-cardioprotective-chaperone-facilitating-sarcomeric-proteostasis
#7
Emily J Mercer, Yi-Fan Lin, Leona Cohen-Gould, Todd Evans
Small heat shock proteins are chaperones with variable mechanisms of action. The function of cardiac family member Hspb7 is unknown, despite being identified through GWAS as a potential cardiomyopathy risk gene. We discovered that zebrafish hspb7 mutants display mild focal cardiac fibrosis and sarcomeric abnormalities. Significant mortality was observed in adult hspb7 mutants subjected to exercise stress, demonstrating a genetic and environmental interaction that determines disease outcome. We identified large sarcomeric proteins FilaminC and Titin as Hspb7 binding partners in cardiac cells...
January 10, 2018: Developmental Biology
https://www.readbyqxmd.com/read/29330500/integration-of-gwas-pathway-and-network-analyses-reveals-novel-mechanistic-insights-into-the-synthesis-of-milk-proteins-in-dairy-cows
#8
Sara Pegolo, Núria Mach, Yuliaxis Ramayo-Caldas, Stefano Schiavon, Giovanni Bittante, Alessio Cecchinato
The quantities and proportions of protein fractions have notable effects on the nutritional and technological value of milk. Although much is known about the effects of genetic variants on milk proteins, the complex relationships among the set of genes and pathways regulating the different protein fractions synthesis and secretion into milk in dairy cows are still not completely understood. We conducted genome-wide association studies (GWAS) for milk nitrogen fractions in a cohort of 1,011 Brown Swiss cows, which uncovered 170 significant single nucleotide polymorphism (SNPs), mostly located on BTA6 and BTA11...
January 12, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29329304/a-novel-method-to-test-associations-between-a-weighted-combination-of-phenotypes-and-genetic-variants
#9
Huanhuan Zhu, Shuanglin Zhang, Qiuying Sha
Many complex diseases like diabetes, hypertension, metabolic syndrome, et cetera, are measured by multiple correlated phenotypes. However, most genome-wide association studies (GWAS) focus on one phenotype of interest or study multiple phenotypes separately for identifying genetic variants associated with complex diseases. Analyzing one phenotype or the related phenotypes separately may lose power due to ignoring the information obtained by combining phenotypes, such as the correlation between phenotypes. In order to increase statistical power to detect genetic variants associated with complex diseases, we develop a novel method to test a weighted combination of multiple phenotypes (WCmulP)...
2018: PloS One
https://www.readbyqxmd.com/read/29326435/a-combined-analysis-of-genetically-correlated-traits-identifies-187-loci-and-a-role-for-neurogenesis-and-myelination-in-intelligence
#10
W D Hill, R E Marioni, O Maghzian, S J Ritchie, S P Hagenaars, A M McIntosh, C R Gale, G Davies, I J Deary
Intelligence, or general cognitive function, is phenotypically and genetically correlated with many traits, including a wide range of physical, and mental health variables. Education is strongly genetically correlated with intelligence (r g  = 0.70). We used these findings as foundations for our use of a novel approach-multi-trait analysis of genome-wide association studies (MTAG; Turley et al. 2017)-to combine two large genome-wide association studies (GWASs) of education and intelligence, increasing statistical power and resulting in the largest GWAS of intelligence yet reported...
January 11, 2018: Molecular Psychiatry
https://www.readbyqxmd.com/read/29325558/systematic-target-function-annotation-of-human-transcription-factors
#11
Yong Fuga Li, Russ B Altman
BACKGROUND: Transcription factors (TFs), the key players in transcriptional regulation, have attracted great experimental attention, yet the functions of most human TFs remain poorly understood. Recent capabilities in genome-wide protein binding profiling have stimulated systematic studies of the hierarchical organization of human gene regulatory network and DNA-binding specificity of TFs, shedding light on combinatorial gene regulation. We show here that these data also enable a systematic annotation of the biological functions and functional diversity of TFs...
January 10, 2018: BMC Biology
https://www.readbyqxmd.com/read/29325163/trans-ethnic-evaluation-identifies-novel-low-frequency-loci-associated-with-25-hydroxyvitamin-d-concentrations
#12
Jaeyoung Hong, Kathryn E Hatchell, Jonathan P Bradfield, Bjonnes Andrew, Chesi Alessandra, Lai Chao-Qiang, Carl D Langefeld, Lingyi Lu, Yingchang Lu, Pamela L Lutsey, Solomon K Musani, Mike A Nalls, Cassianne Robinson-Cohen, Jeffery D Roizen, Richa Saxena, Katherine L Tucker, Julie T Ziegler, Dan E Arking, Joshua C Bis, Eric Boerwinkle, Erwin P Bottinger, Donald W Bowden, Vincente Gilsanz, Denise K Houston, Heidi J Kalkwarf, Andrea Kelly, Joan M Lappe, Yongmei Liu, Erin D Michos, Sharon E Oberfield, Nicholette D Palmer, Jerome I Rotter, Bishwa Sapkota, John A Shepherd, James G Wilson, Saonli Basu, Ian H de Boer, Jasmin Divers, Barry I Freedman, Struan F A Grant, Hakon Hakanarson, Tamara B Harris, Bryan R Kestenbaum, Stephen B Kritchevsky, Ruth J F Loos, Jill M Norris, Arnita F Norwood, Jose M Ordovas, James S Pankow, Bruce M Psaty, Dharambir K Sanhgera, Lynne E Wagenknecht, Babette S Zemel, James Meigs, Josée Dupuis, Jose C Florez, Thomas Wang, Ching-Ti Liu, Corinne D Engelman, Liana K Billings
Context: Vitamin D inadequacy is common in the adult population of the United States. While the genetic determinants underlying vitamin D inadequacy have been studied in people of European ancestry, less is known in Hispanic or African ancestry populations. Objective: The TRANSCEN-D (TRANS-ethniC Evaluation of vitamiN D GWAS) consortium was assembled to replicate genetic associations with 25-hydroxyvitamin D (25(OH)D) concentrations from the meta-analyses of European ancestry (SUNLIGHT) and to identify novel genetic variants related to vitamin D concentrations in African and Hispanic ancestries...
January 9, 2018: Journal of Clinical Endocrinology and Metabolism
https://www.readbyqxmd.com/read/29325096/genetic-determinants-of-circulating-estrogen-levels-and-evidence-of-a-causal-effect-of-estradiol-on-bone-density-in-men
#13
Anna L Eriksson, John R B Perry, Andrea D Coviello, Graciela E Delgado, Luigi Ferrucci, Andrew R Hoffman, Ilpo T Huhtaniemi, M Arfan Ikram, Magnus K Karlsson, Marcus E Kleber, Gail A Laughlin, Yongmei Liu, Mattias Lorentzon, Kathryn L Lunetta, Dan Mellström, Joanne M Murabito, Anna Murray, Maria Nethander, Carrie M Nielson, Inga Prokopenko, Stephen R Pye, Leslie J Raffel, Fernando Rivadeneira, Priya Srikanth, Lisette Stolk, Alexander Teumer, Thomas G Travison, André G Uitterlinden, Dhananjay Vaidya, Dirk Vanderschueren, Joseph M Zmuda, Winfried März, Eric S Orwoll, Pamela Ouyang, Liesbeth Vandenput, Frederick C W Wu, Frank H de Jong, Shalender Bhasin, Douglas P Kiel, Claes Ohlsson
Context: Serum estradiol (E2) and estrone (E1) levels exhibit substantial heritability. No genome-wide association study (GWAS) of estrogen levels has been performed in men of European origin. Objective: To investigate the genetic regulation of serum E2 and E1 in men. Design, setting and participants: GWAS in 11,097 men of European origin from nine epidemiological cohorts. Main Outcome Measures: Genetic determinants of serum E2 and E1 levels...
January 9, 2018: Journal of Clinical Endocrinology and Metabolism
https://www.readbyqxmd.com/read/29325066/toppar-an-interactive-browser-for-viewing-association-study-results
#14
Thorhildur Juliusdottir, Karina Banasik, Neil R Robertson, Richard Mott, Mark I McCarthy
Summary: Data integration and visualization help geneticists make sense of large amounts of data. To help facilitate interpretation of genetic association data we developed Toppar, a customizable visualization tool that stores results from association studies and enables browsing over multiple results, by combining features from existing tools and linking to appropriate external databases. Availability: Detailed information on Toppar's features and functionality are on our website http://mccarthy...
January 8, 2018: Bioinformatics
https://www.readbyqxmd.com/read/29325023/the-extending-spectrum-of-npc1-related-human-disorders-from-niemann-pick-c1-disease-to-obesity
#15
Amel Lamri, Marie Pigeyre, William S Garver, David Meyre
The Niemann-Pick C1 (NPC1) protein regulates the transport of cholesterol and fatty acids from late endosomes / lysosomes and has a central role in maintaining lipid homeostasis. NPC1 loss-of-function mutations in humans cause NPC1 disease, a rare autosomal-recessive lipid-storage disorder characterized by progressive and lethal neurodegeneration, liver and lung failure, due to cholesterol infiltration. In humans, genome wide association studies (GWAS) and post-GWAS reports highlight the implication of common variants in NPC1 in adult-onset obesity, body fat mass, and type 2 diabetes...
January 9, 2018: Endocrine Reviews
https://www.readbyqxmd.com/read/29322237/genome-wide-association-study-of-cold-tolerance-of-chinese-indica-rice-varieties-at-the-bud-burst-stage
#16
Mengchen Zhang, Jing Ye, Qun Xu, Yue Feng, Xiaoping Yuan, Hanyong Yu, Yiping Wang, Xinghua Wei, Yaolong Yang
A region containing three genes on chromosome 1 of indica rice was associated with cold tolerance at the bud burst stage; these results may be useful for breeding cold-tolerant lines. Low temperature at the bud burst stage is one of the major abiotic stresses limiting rice growth, especially in regions where rice seeds are sown directly. In this study, we investigated cold tolerance of rice at the bud burst stage and conducted a genome-wide association study (GWAS) based on the 5K rice array of 249 indica rice varieties widely distributed in China...
January 10, 2018: Plant Cell Reports
https://www.readbyqxmd.com/read/29321673/genomic-analysis-of-family-data-reveals-additional-genetic-effects-on-intelligence-and-personality
#17
W David Hill, Ruben C Arslan, Charley Xia, Michelle Luciano, Carmen Amador, Pau Navarro, Caroline Hayward, Reka Nagy, David J Porteous, Andrew M McIntosh, Ian J Deary, Chris S Haley, Lars Penke
Pedigree-based analyses of intelligence have reported that genetic differences account for 50-80% of the phenotypic variation. For personality traits these effects are smaller, with 34-48% of the variance being explained by genetic differences. However, molecular genetic studies using unrelated individuals typically report a heritability estimate of around 30% for intelligence and between 0 and 15% for personality variables. Pedigree-based estimates and molecular genetic estimates may differ because current genotyping platforms are poor at tagging causal variants, variants with low minor allele frequency, copy number variants, and structural variants...
January 10, 2018: Molecular Psychiatry
https://www.readbyqxmd.com/read/29321632/genome-wide-association-study-in-asia-adapted-tropical-maize-reveals-novel-and-explored-genomic-regions-for-sorghum-downy-mildew-resistance
#18
Zerka Rashid, Pradeep Kumar Singh, Hindu Vemuri, Pervez Haider Zaidi, Boddupalli Maruthi Prasanna, Sudha Krishnan Nair
Globally, downy mildews are among the important foliar diseases of maize that cause significant yield losses. We conducted a genome-wide association study for sorghum downy mildew (SDM; Peronosclerospora sorghi) resistance in a panel of 368 inbred lines adapted to the Asian tropics. High density SNPs from Genotyping-by-sequencing were used in GWAS after controlling for population structure and kinship in the panel using a single locus mixed model. The study identified a set of 26 SNPs that were significantly associated with SDM resistance, with Bonferroni corrected P values ≤ 0...
January 10, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29321599/splicing-qtl-of-human-adipose-related-traits
#19
Liang Ma, Peilin Jia, Zhongming Zhao
Recently, genome-wide association studies (GWAS) have identified 11 loci associated with adipose-related traits across different populations. However, their functional roles still remain largely unknown. In this study, we aimed to explore the splicing regulation of these GWAS signals in a tissue-specific fashion. For adipose-related GWAS signals, we selected six adipose-related tissues (adipose subcutaneous, artery tibial, blood, heart left ventricle, muscle-skeletal, and thyroid) with the sample size greater than 80 for splicing quantitative trait loci (QTL) analysis using GTEx released datasets...
January 10, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29321365/genome-based-exome-sequencing-analysis-identifies-gyg1-dis3l-and-ddrgk1-are-associated-with-myocardial-infarction-in-koreans
#20
Ji-Young Lee, Sanghoon Moon, Yun Kyoung Kim, Sang-Hak Lee, Bok-Soo Lee, Min-Young Park, Jeong Euy Park, Yangsoo Jang, Bok-Ghee Han
Myocardial infarction (MI) is a complex disease caused by combination of genetic and environmental factors. Although genome-wide association studies (GWAS) identified more than 46 risk loci which are associated with coronary artery disease and MI, most of the genetic variability inMI still remains undefined. Here, we screened the susceptibility loci for MI using exome sequencing and validated candidate variants in replication sets. We identified that three genes (GYG1, DIS3L and DDRGK1) were associated with MI at the discovery and replication stages...
December 2017: Journal of Genetics
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