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Genome wide association studies

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https://www.readbyqxmd.com/read/27906046/chromatin-landscapes-and-genetic-risk-in-systemic-lupus
#1
Joyce S Hui-Yuen, Lisha Zhu, Lai Ping Wong, Kaiyu Jiang, Yanmin Chen, Tao Liu, James N Jarvis
BACKGROUND: Systemic lupus erythematosus (SLE) is a multi-system, complex disease in which the environment interacts with inherited genes to produce broad phenotypes with inter-individual variability. Of 46 single nucleotide polymorphisms (SNPs) shown to confer genetic risk for SLE in recent genome-wide association studies, 30 lie within noncoding regions of the human genome. We therefore sought to identify and describe the functional elements (aside from genes) located within these regions of interest...
December 1, 2016: Arthritis Research & Therapy
https://www.readbyqxmd.com/read/27905878/genomic-prediction-using-preselected-dna-variants-from-a-gwas-with-whole-genome-sequence-data-in-holstein-friesian-cattle
#2
Roel F Veerkamp, Aniek C Bouwman, Chris Schrooten, Mario P L Calus
BACKGROUND: Whole-genome sequence data is expected to capture genetic variation more completely than common genotyping panels. Our objective was to compare the proportion of variance explained and the accuracy of genomic prediction by using imputed sequence data or preselected SNPs from a genome-wide association study (GWAS) with imputed whole-genome sequence data. METHODS: Phenotypes were available for 5503 Holstein-Friesian bulls. Genotypes were imputed up to whole-genome sequence (13,789,029 segregating DNA variants) by using run 4 of the 1000 bull genomes project...
December 1, 2016: Genetics, Selection, Evolution: GSE
https://www.readbyqxmd.com/read/27903959/genome-wide-haplotype-association-study-identify-the-fgfr2-gene-as-a-risk-gene-for-acute-myeloid-leukemia
#3
Hongchao Lv, Mingming Zhang, Zhenwei Shang, Jin Li, Shanshan Zhang, Duan Lian, Ruijie Zhang
Acute myeloid leukemia (AML) is a cancer of the myeloid line of blood cells, and generally considered to be caused by environment and genetic factors. In this study, we combined a genome-wide haplotype association study (GWHAS) and gene prioritization strategy to mine AML-related genetic affect factors and understand its pathogenesis. A total of 175 AML patients were downloaded from the public GEO database (GSE32462) and 218 matched Caucasian controls were from the HapMap Project. We first identified the linkage disequilibrium (LD) blocks and performed a GWHAS to scan AML-related haplotypes...
November 26, 2016: Oncotarget
https://www.readbyqxmd.com/read/27903934/large-differences-in-adiponectin-levels-have-no-clear-effect-on-multiple-sclerosis-risk-a-mendelian-randomization-study
#4
Julia Devorak, Lauren E Mokry, John A Morris, Vincenzo Forgetta, George Davey Smith, Stephen Sawcer, J Brent Richards
BACKGROUND: Mendelian randomization (MR) studies have demonstrated strong support for an association between genetically increased body mass index and risk of multiple sclerosis (MS). The adipokine adiponectin may be a potential mechanism linking body mass to risk of MS. OBJECTIVE: To evaluate whether genetically increased adiponectin levels influence risk of MS. METHODS: Using genome-wide significant single nucleotide polymorphisms (SNPs) for adiponectin, we undertook an MR study to estimate the effect of adiponectin on MS...
November 30, 2016: Multiple Sclerosis: Clinical and Laboratory Research
https://www.readbyqxmd.com/read/27903283/systematic-analysis-of-chromatin-interactions-at-disease-associated-loci-links-novel-candidate-genes-to-inflammatory-bowel-disease
#5
Claartje A Meddens, Magdalena Harakalova, Noortje A M van den Dungen, Hassan Foroughi Asl, Hemme J Hijma, Edwin P J G Cuppen, Johan L M Björkegren, Folkert W Asselbergs, Edward E S Nieuwenhuis, Michal Mokry
BACKGROUND: Genome-wide association studies (GWAS) have revealed many susceptibility loci for complex genetic diseases. For most loci, the causal genes have not been identified. Currently, the identification of candidate genes is predominantly based on genes that localize close to or within identified loci. We have recently shown that 92 of the 163 inflammatory bowel disease (IBD)-loci co-localize with non-coding DNA regulatory elements (DREs). Mutations in DREs can contribute to IBD pathogenesis through dysregulation of gene expression...
November 30, 2016: Genome Biology
https://www.readbyqxmd.com/read/27902806/orthology-guided-transcriptome-assembly-of-italian-ryegrass-and-meadow-fescue-for-single-nucleotide-polymorphism-discovery
#6
Štěpán Stočes, Tom Ruttink, Jan Bartoš, Bruno Studer, Steven Yates, Zbigniew Zwierzykowski, Michael Abrouk, Isabel Roldán-Ruiz, Tomasz Książczyk, Elodie Rey, Jaroslav Doležel, David Kopecký
Single-nucleotide polymorphisms (SNPs) represent natural DNA sequence variation. They can be used for various applications including the construction of high-density genetic maps, analysis of genetic variability, genome-wide association studies, and map-based cloning. Here we report on transcriptome sequencing in the two forage grasses, meadow fescue ( Huds.) and Italian ryegrass ( Lam.), and identification of various classes of SNPs. Using the Orthology Guided Assembly (OGA) strategy, we assembled and annotated a total of 18,952 and 19,036 transcripts for Italian ryegrass and meadow fescue, respectively...
November 2016: Plant Genome
https://www.readbyqxmd.com/read/27902805/genome-wide-association-mapping-reveals-novel-qtl-for-seedling-leaf-rust-resistance-in-a-worldwide-collection-of-winter-wheat
#7
Genqiao Li, Xiangyang Xu, Guihua Bai, Brett F Carver, Robert Hunger, J Michael Bonman, James Kolmer, Hongxu Dong
Leaf rust of wheat ( L.) is a major disease that causes significant yield losses worldwide. The short-lived nature of leaf rust resistance () genes necessitates a continuous search for novel sources of resistance. We performed a genome-wide association study (GWAS) on a panel of 1596 wheat accessions. The panel was evaluated for leaf rust reaction by testing with a bulk of Eriks. () isolates collected from multiple fields of Oklahoma in 2013 and two predominant races in the fields of Oklahoma in 2015. The panel was genotyped with a set of 5011 single-nucleotide polymorphism (SNP) markers...
November 2016: Plant Genome
https://www.readbyqxmd.com/read/27902796/target-amplicon-sequencing-for-genotyping-genome-wide-single-nucleotide-polymorphisms-identified-by-whole-genome-resequencing-in-peanut
#8
Kenta Shirasawa, Chikara Kuwata, Manabu Watanabe, Masanobu Fukami, Hideki Hirakawa, Sachiko Isobe
Genome-wide genotyping data regarding breeding materials are essential resources for improving breeding efficiency, especially in plants with complex genomes with a high degree of polyploidy. Several current breeding efforts in cultivated peanut ( L.), which has a tetraploid genome, are devoted to developing high oleic acid cultivars. Genetic maps for such breeding programs have been developed using simple-sequence repeat (SSR) markers, the use of which requires time-consuming electrophoretic analyses. Next-generation sequencing (NGS) technology can overcome this technical hurdle...
November 2016: Plant Genome
https://www.readbyqxmd.com/read/27902795/genome-wide-association-study-identifies-candidate-loci-underlying-agronomic-traits-in-a-middle-american-diversity-panel-of-common-bean
#9
Samira Mafi Moghaddam, Sujan Mamidi, Juan M Osorno, Rian Lee, Mark Brick, James Kelly, Phillip Miklas, Carlos Urrea, Qijian Song, Perry Cregan, Jane Grimwood, Jeremy Schmutz, Phillip E McClean
Common bean ( L.) breeding programs aim to improve both agronomic and seed characteristics traits. However, the genetic architecture of the many traits that affect common bean production are not completely understood. Genome-wide association studies (GWAS) provide an experimental approach to identify genomic regions where important candidate genes are located. A panel of 280 modern bean genotypes from race Mesoamerica, referred to as the Middle American Diversity Panel (MDP), were grown in four US locations, and a GWAS using >150,000 single-nucleotide polymorphisms (SNPs) (minor allele frequency [MAF] ≥ 5%) was conducted for six agronomic traits...
November 2016: Plant Genome
https://www.readbyqxmd.com/read/27902791/genome-wide-association-mapping-of-leaf-rust-response-in-a-durum-wheat-worldwide-germplasm-collection
#10
Meriem Aoun, Matthew Breiland, M Kathryn Turner, Alexander Loladze, Shiaoman Chao, Steven S Xu, Karim Ammar, James A Anderson, James A Kolmer, Maricelis Acevedo
Leaf rust (caused by Erikss. []) is increasingly impacting durum wheat ( L. var. ) production with the recent appearance of races with virulence to widely grown cultivars in many durum producing areas worldwide. A highly virulent race on durum wheat was recently detected in Kansas. This race may spread to the northern Great Plains, where most of the US durum wheat is produced. The objective of this study was to identify sources of resistance to several races from the United States and Mexico at seedling stage in the greenhouse and at adult stage in field experiments...
November 2016: Plant Genome
https://www.readbyqxmd.com/read/27902780/co-regulation-of-iron-metabolism-and-virulence-associated-functions-by-iron-and-xibr-a-novel-iron-binding-transcription-factor-in-the-plant-pathogen-xanthomonas
#11
Sheo Shankar Pandey, Pradeep Kumar Patnana, Santosh Kumar Lomada, Archana Tomar, Subhadeep Chatterjee
Abilities of bacterial pathogens to adapt to the iron limitation present in hosts is critical to their virulence. Bacterial pathogens have evolved diverse strategies to coordinately regulate iron metabolism and virulence associated functions to maintain iron homeostasis in response to changing iron availability in the environment. In many bacteria the ferric uptake regulator (Fur) functions as transcription factor that utilize ferrous form of iron as cofactor to regulate transcription of iron metabolism and many cellular functions...
November 2016: PLoS Pathogens
https://www.readbyqxmd.com/read/27902482/il-23r-mutation-is-associated-with-ulcerative-colitis-a-systemic-review-and-meta-analysis
#12
Ling-Long Peng, Ying Wang, Feng-Ling Zhu, Wang-Dong Xu, Xue-Lei Ji, Jing Ni
OBJECTIVES: Since a genome-wide association study revealed that Interleukin-23 receptor (IL-23R) gene is a candidate gene for Ulcerative Colitis (UC), many studies have investigated the association between the IL-23R polymorphisms and UC. However, the results were controversial. The aim of the study was to determine whether the IL-23R polymorphisms confer susceptibility to UC. METHODS: A systematic literature search was carried out to identify all potentially relevant studies...
November 25, 2016: Oncotarget
https://www.readbyqxmd.com/read/27902416/the-xylella-fastidiosa-codiro-strain-associated-with-the-olive-quick-decline-syndrome-in-southern-italy-belongs-to-a-clonal-complex-of-the-subspecies-pauca-that-evolved-in-central-america
#13
Marco Scortichini, Simone Marcelletti
Xylella fastidiosa, a xylem-limited bacterium transmitted by xylem-fluid feeding Hemiptera insects, causes economic losses of both woody and herbaceous plant species. A X. fastidiosa subsp. pauca strain, namely CoDiRO, was recently found to be associated with the "olive quick decline syndrome" in southern Italy (i.e., Apulia region). Recently, some X. fastidiosa strains intercepted in France from Coffea spp. plant cuttings imported from Central and South America were characterized. The introduction of infected plant material from Central America in Apulia was also postulated even though an ad hoc study to confirm this hypothesis is lacking...
November 2, 2016: Microbiology
https://www.readbyqxmd.com/read/27901618/genome-wide-interaction-analysis-of-air-pollution-exposure-and-childhood-asthma-with-functional-follow-up
#14
Anna Gref, Simon Kebede Merid, Olena Gruzieva, Stéphane Ballereau, Allan Becker, Tom Bellander, Anna Bergström, Yohan Bossé, Matteo Bottai, Moira Chan-Yeung, Elaine Fuertes, Despo Ierodiakonou, Ruiwei Jiang, Stéphane Joly, Meaghan Jones, Michael S Kobor, Michal Korek, Anita L Kozyrskyj, Ashish Kumar, Nathanaël Lemonnier, Elaina MacIntyre, Camille Ménard, David Nickle, Ma'en Obeidat, Johann Pellet, Marie Standl, Annika Sääf, Cilla Söderhäll, Carla Mt Tiesler, Maarten van den Berge, Judith M Vonk, Hita Vora, Cheng-Jian Xu, Josep M Antó, Charles Auffray, Michael Brauer, Jean Bousquet, Bert Brunekreef, W James Gauderman, Joachim Heinrich, Juha Kere, Gerard H Koppelman, Dirkje Postma, Christopher Carlsten, Göran Pershagen, Erik Melén
RATIONALE: The evidence supporting an association between traffic-related air pollution exposure and incident childhood asthma is inconsistent, and may depend on genetic factors. OBJECTIVES: To identify gene-environment interaction effects on childhood asthma using genome-wide single nucleotide polymorphism (SNP) data and air pollution exposure. Identified loci were further analyzed at epigenetic and transcriptomic levels. METHODS: We used land use regression models to estimate individual air pollution exposure (represented by outdoor NO2 levels) at the birth address and performed a genome-wide interaction study for doctor's diagnosis of asthma up to 8 years in three European birth cohorts (n=1,534) with look-up for interaction in two separate North American cohorts, CHS and CAPPS/SAGE (n=1,602 and 186 subjects, respectively)...
November 30, 2016: American Journal of Respiratory and Critical Care Medicine
https://www.readbyqxmd.com/read/27901213/the-rs11191580-variant-of-the-nt5c2-gene-is-associated-with-schizophrenia-and-symptom-severity-in-a-south-chinese-han-population-evidence-from-gwas
#15
Zhen Li, Juan Jiang, Jianxiong Long, Weijun Ling, Guifeng Huang, Xiaojing Guo, Li Su
Objective: Recent genome-wide association studies have identified a significant relationship between the NT5C2 variant rs11191580 and schizophrenia (SCZ) in European populations. This study aimed to validate the association of rs11191580 polymorphism with SCZ risk in a South Chinese Han population. The relationship of this polymorphism with the severity of SCZ clinical symptoms was also explored. Methods: A case-control study was performed in 462 patients with SCZ and 598 healthy controls...
November 24, 2016: Revista Brasileira de Psiquiatria
https://www.readbyqxmd.com/read/27901114/genome-wide-diversity-and-association-mapping-for-capsaicinoids-and-fruit-weight-in-capsicum-annuum-l
#16
Padma Nimmakayala, Venkata L Abburi, Thangasamy Saminathan, Suresh B Alaparthi, Aldo Almeida, Brittany Davenport, Marjan Nadimi, Joshua Davidson, Krittika Tonapi, Lav Yadav, Sridhar Malkaram, Gopinath Vajja, Gerald Hankins, Robert Harris, Minkyu Park, Doil Choi, John Stommel, Umesh K Reddy
Accumulated capsaicinoid content and increased fruit size are traits resulting from Capsicum annuum domestication. In this study, we used a diverse collection of C. annuum to generate 66,960 SNPs using genotyping by sequencing. The study identified 1189 haplotypes containing 3413 SNPs. Length of individual linkage disequilibrium (LD) blocks varied along chromosomes, with regions of high and low LD interspersed with an average LD of 139 kb. Principal component analysis (PCA), Bayesian model based population structure analysis and an Euclidean tree built based on identity by state (IBS) indices revealed that the clustering pattern of diverse accessions are in agreement with capsaicin content (CA) and fruit weight (FW) classifications indicating the importance of these traits in shaping modern pepper genome...
November 30, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27900789/a-general-approach-to-testing-for-pleiotropy-with-rare-and-common-variants
#17
Sharon M Lutz, Tasha E Fingerlin, John E Hokanson, Christoph Lange
Through genome-wide association studies, numerous genes have been shown to be associated with multiple phenotypes. To determine the overlap of genetic susceptibility of correlated phenotypes, one can apply multivariate regression or dimension reduction techniques, such as principal components analysis, and test for the association with the principal components of the phenotypes rather than the individual phenotypes. However, as these approaches test whether there is a genetic effect for at least one of the phenotypes, a significant test result does not necessarily imply pleiotropy...
November 30, 2016: Genetic Epidemiology
https://www.readbyqxmd.com/read/27900536/t%C3%AE-4-overexpression-based-on-the-piggybac-transposon-system-in-cashmere-goats-alters-hair-fiber-characteristics
#18
Bingbo Shi, Qiang Ding, Xiaolin He, Haijing Zhu, Yiyuan Niu, Bei Cai, Jiao Cai, Anming Lei, Danju Kang, Hailong Yan, Baohua Ma, Xiaolong Wang, Lei Qu, Yulin Chen
Increasing cashmere yield is one of the vital aims of cashmere goats breeding. Compared to traditional breeding methods, transgenic technology is more efficient and the piggyBac (PB) transposon system has been widely applied to generate transgenic animals. For the present study, donor fibroblasts were stably transfected via a PB donor vector containing the coding sequence of cashmere goat thymosin beta-4 (Tβ4) and driven by a hair follicle-specific promoter, the keratin-associated protein 6.1 (KAP6.1) promoter...
November 29, 2016: Transgenic Research
https://www.readbyqxmd.com/read/27900493/mining-the-cicer-arietinum-genome-for-the-mildew-locus-o-mlo-gene-family-and-comparative-evolutionary-analysis-of-the-mlo-genes-from-medicago-truncatula-and-some-other-plant-species
#19
Reena Deshmukh, V K Singh, Brahma Deo Singh
The mildew locus O (Mlo) gene family is ubiquitous in land plants. Some members of this gene family are involved in negative regulation of powdery mildew resistance, while others are involved in several other biological functions. Mlo proteins have characteristic seven transmembrane domains and a calmodulin-binding domain at their C-termini, and are associated with plasma membrane. The Mlo gene family has been studied in several economically important cereals, but little information is available on this gene family in the important legumes, Medicago truncatula Gaertn...
November 30, 2016: Journal of Plant Research
https://www.readbyqxmd.com/read/27900365/genome-sequencing-in-a-case-of-niemann-pick-type-c
#20
Max Dougherty, John Lazar, Jason C Klein, Karina Diaz, Theodore Gobillot, Eli Grunblatt, Nicholas Hasle, Daniel Lawrence, Megan Maurano, Maria Nelson, Gregory Olson, Sanjay Srivatsan, Jay Shendure, C Dirk Keene, Thomas Bird, Marshall S Horwitz, Desiree A Marshall
Adult-onset Niemann-Pick disease type C (NPC) is an infrequent presentation of a rare neurovisceral lysosomal lipid storage disorder caused by autosomal recessive mutations in NPC1 (∼95%) or NPC2 (∼5%). Our patient was diagnosed at age 33 when he presented with a 10-yr history of difficulties in judgment, concentration, speech, and coordination. A history of transient neonatal jaundice and splenomegaly with bone marrow biopsy suggesting a lipid storage disorder pointed to NPC; biochemical ("variant" level cholesterol esterification) and ultrastructural studies in adulthood confirmed the diagnosis...
November 2016: Cold Spring Harbor Molecular Case Studies
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