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Genome wide association studies

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https://www.readbyqxmd.com/read/28732187/do-genetic-markers-of-inflammation-modify-the-relationship-between-periodontitis-and-nonalcoholic-fatty-liver-disease-findings-from-the-ship-study
#1
A A Akinkugbe, C L Avery, A S Barritt, S R Cole, M Lerch, J Mayerle, S Offenbacher, A Petersmann, M Nauck, H Völzke, G D Slade, G Heiss, T Kocher, B Holtfreter
An association between periodontitis and nonalcoholic fatty liver disease (NAFLD) has been reported by experimental animal and epidemiologic studies. This study investigated whether circulating levels of serum C-reactive protein (CRP) and a weighted genetic CRP score representing markers of inflammatory burden modify the association between periodontitis and NAFLD. Data came from 2,481 participants of the Study of Health in Pomerania who attended baseline examination that occurred between 1997 and 2001. Periodontitis was defined as the percentage of sites (0%, <30%, ≥30%) with probing pocket depth (PD) ≥4 mm, and NAFLD status was determined using liver ultrasound assessment...
July 1, 2017: Journal of Dental Research
https://www.readbyqxmd.com/read/28732180/the-role-of-noncoding-genetic-variation-in-isolated-orofacial-clefts
#2
F Thieme, K U Ludwig
In the past decade, medical genetic research has generated multiple discoveries, many of which were obtained via genome-wide association studies (GWASs). A major GWAS finding is that the majority of risk variants for complex traits map to noncoding regions. This has resulted in a paradigm shift in terms of the interpretation of human genomic sequence variation, with more attention now being paid to what was previously termed "junk DNA." Translation of genetic findings into biologically meaningful results requires 1) large-scale and cell-specific efforts to annotate non-protein-coding regions and 2) the integration of comprehensive genomic data sets...
July 1, 2017: Journal of Dental Research
https://www.readbyqxmd.com/read/28732062/a-drosophila-model-for-toxicogenomics-genetic-variation-in-susceptibility-to-heavy-metal-exposure
#3
Shanshan Zhou, Sarah E Luoma, Genevieve E St Armour, Esha Thakkar, Trudy F C Mackay, Robert R H Anholt
The genetic factors that give rise to variation in susceptibility to environmental toxins remain largely unexplored. Studies on genetic variation in susceptibility to environmental toxins are challenging in human populations, due to the variety of clinical symptoms and difficulty in determining which symptoms causally result from toxic exposure; uncontrolled environments, often with exposure to multiple toxicants; and difficulty in relating phenotypic effect size to toxic dose, especially when symptoms become manifest with a substantial time lag...
July 21, 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28731985/accelerated-dna-methylation-age-associations-with-ptsd-and-mortality
#4
Erika J Wolf, Mark W Logue, Tawni B Stoop, Steven A Schichman, Annjanette Stone, Naomi Sadeh, Jasmeet P Hayes, Mark W Miller
OBJECTIVE: Recently-developed indices of cellular age based on DNA methylation (DNAm) data, referred to as DNAm age, are being used to study factors that influence the rate of aging and the health correlates of these metrics of the epigenetic clock. This study evaluated associations between trauma exposure, posttraumatic stress disorder (PTSD) symptoms, and accelerated versus decelerated DNAm age among military veterans. We also examined if accelerated DNAm age predicted mortality over the course of a 6...
July 20, 2017: Psychosomatic Medicine
https://www.readbyqxmd.com/read/28731861/genetic-control-of-apoprotein-a-i-and-atheroprotection-some-insights-from-inbred-strains-of-mice
#5
Godfrey S Getz, Catherine A Reardon
PURPOSE OF REVIEW: Previous epidemiological studies and studies in experimental animals have provided strong evidence for the atheroprotective effect of HDL and its major apoprotein, apolipoprotein A-I (apoA-I). Identification of genetic loci associating apoA-I/HDL with cardiovascular disease is needed to establish a causal relationship. RECENT FINDINGS: Pharmacological interventions to increase apoA-I or HDL cholesterol levels in humans are not associated with reduction in atherosclerosis...
July 20, 2017: Current Opinion in Lipidology
https://www.readbyqxmd.com/read/28731541/demography-and-genome-divergence-of-lake-and-stream-populations-of-an-east-african-cichlid-fish
#6
Bernd Egger, Marius Rösti, Astrid Böhne, Olivia Roth, Walter Salzburger
Disentangling the processes and mechanisms underlying divergent selection in diversification is facilitated by the comparative study of replicate population pairs that have diverged along a similar environmental gradient. Such a setting is realized in a cichlid fish from southern Lake Tanganyika, Astatotilapia burtoni, which occurs both within the lake proper as well as in various affluent rivers. Previous studies demonstrated that independent lake and stream populations show respectively similar adaptations to the two habitat regimes...
July 21, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28731140/integrated-analysis-of-genome%C3%A2-wide-gene-expression-and-dna-methylation-microarray-of-diffuse-large-b%C3%A2-cell-lymphoma-with-tet-mutations
#7
Pengfei Liu, Wenhua Jiang, Jinkun Zhao, Huilai Zhang
Diffuse large B-cell lymphoma (DLBCL), the most frequently occurring type of lymphoid malignancy, has been demonstrated to be associated with mutations of Ten‑Eleven Translocation (TET). In order to explore the association between DLBCL and TET mutations, the present study analyzed the gene expression and methylation profiles in human DLBCL biopsy tissues with wildtype and mutated TET2. The microarray dataset GSE37365, containing two subseries: the genome‑wide gene expression dataset GSE37362 and the DNA methylation microarray dataset GSE37363, was downloaded from the Gene Expression Omnibus database...
July 21, 2017: Molecular Medicine Reports
https://www.readbyqxmd.com/read/28730685/tex15-a-dna-repair-gene-associated-with-prostate-cancer-risk-in-han-chinese
#8
Xiaoling Lin, Zhongzhong Chen, Peng Gao, Zhimei Gao, Haitao Chen, Jun Qi, Fang Liu, Dingwei Ye, Haowen Jiang, Rong Na, Hongjie Yu, Rong Shi, Daru Lu, Siqun Lilly Zheng, Zengnan Mo, Yinghao Sun, Qiang Ding, Jianfeng Xu
BACKGROUND: Both common and rare genetic variants may contribute to risk of developing prostate cancer. Genome-wide association studies (GWASs) have identified ∼100 independent, common variants associated with prostate cancer risk. However, little is known about the association of rare variants (minor allele frequency [MAF] <1%) in the genome with prostate cancer risk. METHODS: A two-stage study was used to test the association of rare, deleterious coding variants, annotated using predictive algorithms, with prostate cancer risk in Chinese men...
July 21, 2017: Prostate
https://www.readbyqxmd.com/read/28730464/genome-wide-association-mapping-of-canopy-wilting-in-diverse-soybean-genotypes
#9
Avjinder S Kaler, Jeffery D Ray, William T Schapaugh, C Andy King, Larry C Purcell
Genome-wide association analysis identified 61 SNP markers for canopy wilting, which likely tagged 51 different loci. Based on the allelic effects of the significant SNPs, the slowest and fastest wilting genotypes were identified. Drought stress is a major global constraint for crop production, and slow canopy wilting is a promising trait for improving drought tolerance. The objective of this study was to identify genetic loci associated with canopy wilting and to confirm those loci with previously reported canopy wilting QTLs...
July 20, 2017: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
https://www.readbyqxmd.com/read/28729877/genetic-diversity-population-structure-and-linkage-disequilibrium-of-an-association-mapping-panel-revealed-by-genome-wide-snp-markers-in-sesame
#10
Chengqi Cui, Hongxian Mei, Yanyang Liu, Haiyang Zhang, Yongzhan Zheng
The characterization of genetic diversity and population structure can be used in tandem to detect reliable phenotype-genotype associations. In the present study, we genotyped a set of 366 sesame germplasm accessions by using 89,924 single-nucleotide polymorphisms (SNPs). The number of SNPs on each chromosome was consistent with the physical length of the respective chromosome, and the average marker density was approximately 2.67 kb/SNP. The genetic diversity analysis showed that the average nucleotide diversity of the panel was 1...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28729876/genetic-architecture-of-flooding-tolerance-in-the-dry-bean-middle-american-diversity-panel
#11
Ali Soltani, Samira MafiMoghaddam, Katelynn Walter, Daniel Restrepo-Montoya, Sujan Mamidi, Stephan Schroder, Rian Lee, Phillip E McClean, Juan M Osorno
Flooding is a devastating abiotic stress that endangers crop production in the twenty-first century. Because of the severe susceptibility of common bean (Phaseolus vulgaris L.) to flooding, an understanding of the genetic architecture and physiological responses of this crop will set the stage for further improvement. However, challenging phenotyping methods hinder a large-scale genetic study of flooding tolerance in common bean and other economically important crops. A greenhouse phenotyping protocol was developed to evaluate the flooding conditions at early stages...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28729714/maize-zea-mays-l-genome-size-indicated-by-180-bp-knob-abundance-is-associated-with-flowering-time
#12
Yinqiao Jian, Cheng Xu, Zifeng Guo, Shanhong Wang, Yunbi Xu, Cheng Zou
Flowering time is considered one of the most important agronomic traits in maize (Zea mays L.), and previous studies have indicated that this trait is correlated with genome size. We observed a significant difference in genome size between tropical and temperate inbred lines and a moderate positive correlation between genome size and 180-bp knob abundance determined by high-throughput sequencing in maize inbred lines in this study. We assembled the reads that were mapped to 180-bp knob sequences and found that the top ten abundant 180-bp knob sequences are highly variable...
July 20, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28729621/genotype-environment-interaction-on-human-cognitive-function-conditioned-on-the-status-of-breastfeeding-and-maternal-smoking-around-birth
#13
S Hong Lee, W M Shalanee P Weerasinghe, Julius H J van der Werf
We estimated genotype by environment interaction (G × E) on later cognitive performance and educational attainment across four unique environments, i.e. 1) breastfed without maternal smoking, 2) breastfed with maternal smoking, 3) non-breastfed without maternal smoking and 4) non-breastfed with maternal smoking, using a novel design and statistical approach that was facilitated by the availability of datasets with the genome-wide single nucleotide polymorphisms (SNPs). There was significant G × E for both fluid intelligence (p-value = 1...
July 20, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28729251/inclusion-of-a-genetic-risk-score-into-a-validated-risk-prediction-model-for-colorectal-cancer-in-japanese-men-improves-performance
#14
Motoki Iwasaki, Sachiko Tanaka-Mizuno, Aya Kuchiba, Taiki Yamaji, Norie Sawada, Atsushi Goto, Taichi Shimazu, Shizuka Sasazuki, Hansong Wang, Loic 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 hazard 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/28729043/individualized-assessment-of-fracture-risk-contribution-of-osteogenomic-profile
#15
Tuan V Nguyen
Over the past decade, several genetic variants or genes for osteoporosis have been identified through genome-wide association studies and candidate gene association studies. These genetic variants are common in the general population but have modest effect sizes, with odds ratio ranging from 1.1 to 1.5. Thus, the utility of any single variant is limited. However, theoretical and empirical studies have suggested that a profiling of multiple variants that are associated with bone phenotypes (i.e., "osteogenomic profile") can improve the accuracy of fracture prediction and classification beyond that obtained by conventional clinical risk factors...
July 17, 2017: Journal of Clinical Densitometry
https://www.readbyqxmd.com/read/28728579/circulating-sortilin-level-as-a-potential-biomarker-for-coronary-atherosclerosis-and-diabetes-mellitus
#16
Tae Jung Oh, Chang Ho Ahn, Bo-Rahm Kim, Kyoung Min Kim, Jae Hoon Moon, Soo Lim, Kyong Soo Park, Cheong Lim, HakChul Jang, Sung Hee Choi
CONTEXT: A previous genome-wide association study showed that a genetic variant of sortilin was associated with the risk of coronary artery disease (CAD). However, the role of circulating sortilin is still unknown. We investigated the potential role of plasma sortilin as a biomarker for CAD and diabetes mellitus. METHODS: We enrolled statin-naïve subjects with CAD (n = 31) who underwent coronary artery bypass surgery and control subjects (n = 116) who were free from CAD as evaluated by coronary CT angiography...
July 20, 2017: Cardiovascular Diabetology
https://www.readbyqxmd.com/read/28728575/genome-wide-association-study-identifies-a-major-gene-for-beech-bark-disease-resistance-in-american-beech-fagus-grandifolia-ehrh
#17
Irina Ćalić, Jennifer Koch, David Carey, Charles Addo-Quaye, John E Carlson, David B Neale
BACKGROUND: The American Beech tree (Fagus grandifolia Ehrh.), native to eastern North America, is ecologically important and provides high quality wood products. This species is susceptible to beech bark disease (BBD) and is facing high rates of mortality in North America. The disease occurs from an interaction between the woolly beech scale insect (Cryptococcus fagisuga), one of two species of the fungus Neonectria (N. faginata or N. ditissima), and American Beech trees. METHODS: In this case-control genome-wide association study (GWAS), we tested 16 K high quality SNPs using the Affymetrix Axiom 1...
July 20, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28728355/identification-of-genes-related-to-intramuscular-fat-content-of-pig-using-genome-wide-association-study
#18
Sohyoung Won, Jaehoon Jung, Eungwoo Park, H B Kim
Objective: The aim of this study is to identify SNPs and genes related to pig IMF and estimate the heritability of IMF. Methods: Genome-wide association study (GWAS) on 704 inbred Berkshires was performed for intramuscular fat content (IMF). To consider the inbreeding among samples, associations of the SNPs with IMF were tested as random effects in a mixed linear model using the genetic relationship matrix by GEMMA. Significant genes were compared with reported pig IMF QTL regions and functional classification of the identified genes were also performed...
June 27, 2017: Asian-Australasian Journal of Animal Sciences
https://www.readbyqxmd.com/read/28727946/confounding-by-single-nucleotide-polymorphism-rs117648444-p70s-affects-the-association-of-interferon-lambda-locus-variants-with-response-to-interferon-%C3%AE-ribavirin-therapy-in-patients-with-chronic-genotype-3-hepatitis-c-virus-infection
#19
Anand Bhushan, Sumona Ghosh, Samsiddhi Bhattacharjee, Sreedhar Chinnaswamy
Genome-wide association studies discovered interferon lambda (IFNL or IFN-λ) locus on chromosome 19 to be involved in clearance of chronic hepatitis C virus (HCV) infection in patients following interferon-α-ribavirin (IFN-RBV) therapy. Subsequent studies established a dinucleotide polymorphism rs368234815, as the prime causal variant behind this association. The ΔG allele of this variant gives rise to a new IFNL gene, IFNL4, coding for IFN-λ4 whose activity paradoxically associates with lesser viral clearance rates...
July 20, 2017: Journal of Interferon & Cytokine Research
https://www.readbyqxmd.com/read/28727806/genocore-a-simple-and-fast-algorithm-for-core-subset-selection-from-large-genotype-datasets
#20
Seongmun Jeong, Jae-Yoon Kim, Soon-Chun Jeong, Sung-Taeg Kang, Jung-Kyung Moon, Namshin Kim
Selecting core subsets from plant genotype datasets is important for enhancing cost-effectiveness and to shorten the time required for analyses of genome-wide association studies (GWAS), and genomics-assisted breeding of crop species, etc. Recently, a large number of genetic markers (>100,000 single nucleotide polymorphisms) have been identified from high-density single nucleotide polymorphism (SNP) arrays and next-generation sequencing (NGS) data. However, there is no software available for picking out the efficient and consistent core subset from such a huge dataset...
2017: PloS One
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