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https://www.readbyqxmd.com/read/28819221/functional-validation-of-gpihbp1-and-identification-of-a-functional-mutation-in-gpihbp1-for-milk-fat-traits-in-dairy-cattle
#1
Jie Yang, Xuan Liu, Dan Wang, Chao Ning, Haifei Wang, Qin Zhang, Li Jiang
In a previous genome-wide association study (GWAS) on milk production traits in a Chinese Holstein population, we revealed that GPIHBP1 is a novel promising candidate gene for milk fat content traits. In this study, we performed over-expression and RNAi experiments on GPIHBP1 in bovine primary mammary epithelial cells. The results showed that the expression of several important milk fat-related genes (LPL, CD36, VLDLR, ACACA and FASN) increased or decreased when the expression of GPIHBP1 was up- or down-regulated...
August 17, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28818369/brassinosteroid-and-gibberellin-control-of-seedling-traits-in-maize-zea-mays-l
#2
Songlin Hu, Darlene L Sanchez, Cuiling Wang, Alexander E Lipka, Yanhai Yin, Candice A C Gardner, Thomas Lübberstedt
In this study, we established two doubled haploid (DH) libraries with a total of 207 DH lines. We applied BR and GA inhibitors to all DH lines at seedling stage and measured seedling BR and GA inhibitor responses. Moreover, we evaluated field traits for each DH line (untreated). We conducted genome-wide association studies (GWAS) with 62,049 genome wide SNPs to explore the genetic control of seedling traits by BR and GA. In addition, we correlate seedling stage hormone inhibitor response with field traits. Large variation for BR and GA inhibitor response and field traits was observed across these DH lines...
October 2017: Plant Science: An International Journal of Experimental Plant Biology
https://www.readbyqxmd.com/read/28816579/application-of-the-distance-based-f-test-in-an-mgwas-investigating-beta-diversity-of-intestinal-microbiota-identifies-variants-in-slc9a8-nhe8-and-three-other-loci
#3
Malte C Rühlemann, Frauke Degenhardt, Louise B Thingholm, Jun Wang, Jurgita Skiecevičienė, Philipp Rausch, Johannes R Hov, Wolfgang Lieb, Tom H Karlsen, Matthias Laudes, John F Baines, Femke-Anouska Heinsen, Andre Franke
Factors shaping the human intestinal microbiota range from environmental influences, like smoking and exercise, over dietary patterns and disease to the host's genetic variation. Recently, we could show in a microbiome genome-wide association study (mGWAS) targeting genetic variation influencing the beta diversity of gut microbial communities, that approximately 10% of the overall gut microbiome variation can be explained by host genetics. Here, we report on the application of a new method for genotype-beta-diversity association testing, the distance-based F (DBF) test...
August 17, 2017: Gut Microbes
https://www.readbyqxmd.com/read/28815103/search-datasets-in-literature-a-case-study-of-gwas
#4
Xiao Dong, Yaoyun Zhang, Hua Xu
One of the missions of the NIH BD2K (Big Data to Knowledge) initiative is to make data discoverable and promote the re-use of existing datasets. Our ultimate goal is to develop a scalable approach that can automatically scan millions of scientific publications and identify underlying data sets. Using Genome-Wide Association Studies (GWAS) as a use case, we conducted an initial study to identify GWAS dataset attributes in MEDLINE abstracts, by developing a hybrid approach that combines domain dictionaries and pattern-based rules...
2017: AMIA Summits on Translational Science Proceedings
https://www.readbyqxmd.com/read/28814792/genetic-regulatory-effects-modified-by-immune-activation-contribute-to-autoimmune-disease-associations
#5
Sarah Kim-Hellmuth, Matthias Bechheim, Benno Pütz, Pejman Mohammadi, Yohann Nédélec, Nicholas Giangreco, Jessica Becker, Vera Kaiser, Nadine Fricker, Esther Beier, Peter Boor, Stephane E Castel, Markus M Nöthen, Luis B Barreiro, Joseph K Pickrell, Bertram Müller-Myhsok, Tuuli Lappalainen, Johannes Schumacher, Veit Hornung
The immune system plays a major role in human health and disease, and understanding genetic causes of interindividual variability of immune responses is vital. Here, we isolate monocytes from 134 genotyped individuals, stimulate these cells with three defined microbe-associated molecular patterns (LPS, MDP, and 5'-ppp-dsRNA), and profile the transcriptomes at three time points. Mapping expression quantitative trait loci (eQTL), we identify 417 response eQTLs (reQTLs) with varying effects between conditions...
August 16, 2017: Nature Communications
https://www.readbyqxmd.com/read/28813562/polygenic-scores-for-major-depressive-disorder-and-risk-of-alcohol-dependence
#6
Allan M Andersen, Robert H Pietrzak, Henry R Kranzler, Li Ma, Hang Zhou, Xiaoming Liu, John Kramer, Samuel Kuperman, Howard J Edenberg, John I Nurnberger, John P Rice, Jay A Tischfield, Alison Goate, Tatiana M Foroud, Jacquelyn L Meyers, Bernice Porjesz, Danielle M Dick, Victor Hesselbrock, Eric Boerwinkle, Steven M Southwick, John H Krystal, Myrna M Weissman, Douglas F Levinson, James B Potash, Joel Gelernter, Shizhong Han
Importance: Major depressive disorder (MDD) and alcohol dependence (AD) are heritable disorders with significant public health burdens, and they are frequently comorbid. Common genetic factors that influence the co-occurrence of MDD and AD have been sought in family, twin, and adoption studies, and results to date have been promising but inconclusive. Objective: To examine whether AD and MDD overlap genetically, using a polygenic score approach. Design, Settings, and Participants: Association analyses were conducted between MDD polygenic risk score (PRS) and AD case-control status in European ancestry samples from 4 independent genome-wide association study (GWAS) data sets: the Collaborative Study on the Genetics of Alcoholism (COGA); the Study of Addiction, Genetics, and Environment (SAGE); the Yale-Penn genetic study of substance dependence; and the National Health and Resilience in Veterans Study (NHRVS)...
August 16, 2017: JAMA Psychiatry
https://www.readbyqxmd.com/read/28813438/heritability-estimation-using-a-regularized-regression-approach-herra-applicable-to-continuous-dichotomous-or-age-at-onset-outcome
#7
Malka Gorfine, Sonja I Berndt, Jenny Chang-Claude, Michael Hoffmeister, Loic Le Marchand, John Potter, Martha L Slattery, Nir Keret, Ulrike Peters, Li Hsu
The popular Genome-wide Complex Trait Analysis (GCTA) software uses the random-effects models for estimating the narrow-sense heritability based on GWAS data of unrelated individuals without knowing and identifying the causal loci. Many methods have since extended this approach to various situations. However, since the proportion of causal loci among the variants is typically very small and GCTA uses all variants to calculate the similarities among individuals, the estimation of heritability may be unstable, resulting in a large variance of the estimates...
2017: PloS One
https://www.readbyqxmd.com/read/28813320/the-genetics-and-epigenetics-of-ptsd-overview-recent-advances-and-future-directions
#8
REVIEW
Christina M Sheerin, Mackenzie J Lind, Kaitlin E Bountress, Nicole R Nugent, Ananda B Amstadter
This paper provides a brief summary and commentary on the growing literature and current developments related to the genetic underpinnings of posttraumatic stress disorder (PTSD). We first briefly provide an overview of the behavioral genetic literature on PTSD, followed by a short synopsis of the substantial candidate gene literature with a focus on genes that have been meta-analyzed. We then discuss the genome-wide association studies (GWAS) that have been conducted, followed by an introduction to other molecular platforms used in PTSD genomic studies, such as epigenetic and expression approaches...
April 2017: Current Opinion in Psychology
https://www.readbyqxmd.com/read/28812720/antagonistic-pleiotropy-and-mutation-accumulation-influence-human-senescence-and-disease
#9
Juan Antonio Rodríguez, Urko M Marigorta, David A Hughes, Nino Spataro, Elena Bosch, Arcadi Navarro
Senescence has long been a public health challenge as well as a fascinating evolutionary problem. There is neither a universally accepted theory for its ultimate causes, nor a consensus about what may be its impact on human health. Here we test the predictions of two evolutionary explanations of senescence-mutation accumulation and antagonistic pleiotropy-which postulate that genetic variants with harmful effects in old ages can be tolerated, or even favoured, by natural selection at early ages. Using data from genome-wide association studies (GWAS), we study the effects of genetic variants associated with diseases appearing at different periods in life, when they are expected to have different impacts on fitness...
January 30, 2017: Nature ecology & evolution
https://www.readbyqxmd.com/read/28811740/multiple-testing-in-the-context-of-gene-discovery-in-sickle-cell-disease-using-genome-wide-association-studies
#10
Kevin H M Kuo
The issue of multiple testing, also termed multiplicity, is ubiquitous in studies where multiple hypotheses are tested simultaneously. Genome-wide association study (GWAS), a type of genetic association study that has gained popularity in the past decade, is most susceptible to the issue of multiple testing. Different methodologies have been employed to address the issue of multiple testing in GWAS. The purpose of the review is to examine the methodologies employed in dealing with multiple testing in the context of gene discovery using GWAS in sickle cell disease complications...
2017: Genomics Insights
https://www.readbyqxmd.com/read/28810834/multiple-trait-qtl-mapping-and-genomic-prediction-for-wool-traits-in-sheep
#11
Sunduimijid Bolormaa, Andrew A Swan, Daniel J Brown, Sue Hatcher, Nasir Moghaddar, Julius H van der Werf, Michael E Goddard, Hans D Daetwyler
BACKGROUND: The application of genomic selection to sheep breeding could lead to substantial increases in profitability of wool production due to the availability of accurate breeding values from single nucleotide polymorphism (SNP) data. Several key traits determine the value of wool and influence a sheep's susceptibility to fleece rot and fly strike. Our aim was to predict genomic estimated breeding values (GEBV) and to compare three methods of combining information across traits to map polymorphisms that affect these traits...
August 15, 2017: Genetics, Selection, Evolution: GSE
https://www.readbyqxmd.com/read/28808816/a-genome-wide-association-study-of-cognitive-function-in-chinese-adult-twins
#12
Chunsheng Xu, Dongfeng Zhang, Yili Wu, Xiaocao Tian, Zengchang Pang, Shuxia Li, Qihua Tan
Multiple loci or genes have been identified using genome-wide association studies mainly in western countries but with inconsistent results. No similar studies have been conducted in the world's largest and rapidly aging Chinese population. The paper aimed to identify the specific genetic variants associated with cognitive function in middle and old-aged Chinese dizygotic twins (DZ). Cognitive function was measured on 139 pairs of DZ by Montreal Cognitive Assessment. The subjects were genotyped at 1048575 SNP positions...
August 14, 2017: Biogerontology
https://www.readbyqxmd.com/read/28808041/inclusion-of-a-genetic-risk-score-into-a-validated-risk-prediction-model-for-colorectal-cancer-in-japanese-men-improves-performance
#13
Motoki Iwasaki, Sachiko Tanaka-Mizuno, Aya Kuchiba, Taiki Yamaji, Norie Sawada, Atsushi Goto, Taichi Shimazu, Shizuka Sasazuki, Hansong Wang, Loïc Le Marchand, Shoichiro Tsugane
We previously developed and validated a risk prediction model for colorectal cancer in Japanese men using modifiable risk factors. To further improve risk prediction, we evaluated the degree of improvement obtained by adding a genetic risk score (GRS) using genome-wide association study (GWAS)-identified risk variants to our validated model. We examined the association between 36 risk variants identified by GWAS and colorectal cancer risk using a weighted Cox proportional hazards model in a nested case-control study within the Japan Public Health Center-based Prospective Study...
July 20, 2017: Cancer Prevention Research
https://www.readbyqxmd.com/read/28805926/multiple-trait-genomewide-mapping-and-gene-network-analysis-for-scrotal-circumference-growth-curves-in-brahman-cattle
#14
A C C Soares, S E F Guimarães, M J Kelly, M R S Fortes, F F E Silva, L L Verardo, R Mota, S Moore
Fertility traits are economically important in cattle breeding programs. Scrotal circumference (SC) measures are repeatable, easily obtained, highly heritable, and positively correlated with female fertility traits and sperm quality traits in males. A useful approach to summarize SC measures over time is using nonlinear models, which summarize specific measures of SC in a few parameters with biological interpretation. This approach facilitates the selection of bulls with larger SC and maturity index (K), that is, early maturing animals...
August 2017: Journal of Animal Science
https://www.readbyqxmd.com/read/28805909/genomewide-association-study-for-production-and-meat-quality-traits-in-canchim-beef-cattle
#15
G G Santiago, F Siqueira, F F Cardoso, L C A Regitano, R Ventura, B P Sollero, M D Souza, F B Mokry, A B R Ferreira, R A A Torres
The commercial value of the bovine carcass is determined by a set of traits, such as weight, yield, back fat thickness, and marbling; therefore, the genetic improvement of growth, meat, and carcass quality traits is an important tool to add value to the supply chain. Genomewide association studies (GWAS) enable the identification of loci that control phenotypic expression of quantitative traits (QTL). Therefore, the objective of this work was to perform a GWAS to identify genomic regions and genes associated with growth, carcass traits, and meat quality in Canchim beef cattle...
August 2017: Journal of Animal Science
https://www.readbyqxmd.com/read/28805827/transcriptional-risk-scores-link-gwas-to-eqtls-and-predict-complications-in-crohn-s-disease
#16
Urko M Marigorta, Lee A Denson, Jeffrey S Hyams, Kajari Mondal, Jarod Prince, Thomas D Walters, Anne Griffiths, Joshua D Noe, Wallace V Crandall, Joel R Rosh, David R Mack, Richard Kellermayer, Melvin B Heyman, Susan S Baker, Michael C Stephens, Robert N Baldassano, James F Markowitz, Mi-Ok Kim, Marla C Dubinsky, Judy Cho, Bruce J Aronow, Subra Kugathasan, Greg Gibson
Gene expression profiling can be used to uncover the mechanisms by which loci identified through genome-wide association studies (GWAS) contribute to pathology. Given that most GWAS hits are in putative regulatory regions and transcript abundance is physiologically closer to the phenotype of interest, we hypothesized that summation of risk-allele-associated gene expression, namely a transcriptional risk score (TRS), should provide accurate estimates of disease risk. We integrate summary-level GWAS and expression quantitative trait locus (eQTL) data with RNA-seq data from the RISK study, an inception cohort of pediatric Crohn's disease...
August 14, 2017: Nature Genetics
https://www.readbyqxmd.com/read/28805813/analysis-of-genome-wide-association-data-highlights-candidates-for-drug-repositioning-in-psychiatry
#17
Hon-Cheong So, Carlos Kwan-Long Chau, Wan-To Chiu, Kin-Sang Ho, Cho-Pong Lo, Stephanie Ho-Yue Yim, Pak-Chung Sham
Knowledge of psychiatric disease genetics has advanced rapidly during the past decade with the advent of genome-wide association studies (GWAS). However, less progress has been made in harnessing these data to reveal new therapies. Here we propose a framework for drug repositioning by comparing transcriptomes imputed from GWAS data with drug-induced gene expression profiles from the Connectivity Map database and apply this approach to seven psychiatric disorders. We found a number of repositioning candidates, many supported by preclinical or clinical evidence...
August 14, 2017: Nature Neuroscience
https://www.readbyqxmd.com/read/28803920/open-chromatin-profiling-in-hipsc-derived-neurons-prioritizes-functional-noncoding-psychiatric-risk-variants-and-highlights-neurodevelopmental-loci
#18
Marc P Forrest, Hanwen Zhang, Winton Moy, Heather McGowan, Catherine Leites, Leonardo E Dionisio, Zihui Xu, Jianxin Shi, Alan R Sanders, William J Greenleaf, Chad A Cowan, Zhiping P Pang, Pablo V Gejman, Peter Penzes, Jubao Duan
Most disease variants lie within noncoding genomic regions, making their functional interpretation challenging. Because chromatin openness strongly influences transcriptional activity, we hypothesized that cell-type-specific open chromatin regions (OCRs) might highlight disease-relevant noncoding sequences. To investigate, we mapped global OCRs in neurons differentiating from hiPSCs, a cellular model for studying neurodevelopmental disorders such as schizophrenia (SZ). We found that the OCRs are highly dynamic and can stratify GWAS-implicated SZ risk variants...
August 4, 2017: Cell Stem Cell
https://www.readbyqxmd.com/read/28801813/detection-of-qtl-for-greasy-fleece-weight-in-sheep-using-a-50%C3%A2-k-single-nucleotide-polymorphism-chip
#19
Fatemeh Ebrahimi, Mohsen Gholizadeh, Ghodrat Rahimi-Mianji, Ayoub Farhadi
Genome-wide association studies (GWAS) have introduced an influential tool in the search for quantitative trait loci (QTL) influencing economically important traits in sheep. To identify QTL associated with greasy fleece weight, a GWAS with 50 K single nucleotide polymorphisms (SNPs) was performed in a Baluchi sheep population. Association with greasy fleece weights was tested using the software Plink. The results of our GWAS provided three novel SNP markers and candidate genes associated with greasy fleece weight...
August 11, 2017: Tropical Animal Health and Production
https://www.readbyqxmd.com/read/28801652/assessment-of-three-new-loci-from-genome-wide-association-study-in-essential-tremor-in-chinese-population
#20
Yuan Zhang, Yuwen Zhao, Xiaoting Zhou, Kai Li, Minhan Yi, Jifeng Guo, Xinxiang Yan, Beisha Tang, Qiying Sun
Essential tremor (ET) is the most common tremor disorder. Evidences indicated that genetics plays an essential role in the researches of etiology. A new genome-wide association study (GWAS) from European population identified three novel loci in ET, which were rs10937625 in STK32B, rs17590046 in PPARGC1A, and rs12764057, rs10822974 and rs7903491 in CTNNA3. Due to the different genetic background in different population, we performed a case-control study to investigate these variants in a cohort of 533 subjects in Chinese population...
August 11, 2017: Scientific Reports
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