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https://www.readbyqxmd.com/read/27933030/the-association-of-drd2-with-insight-problem-solving
#1
Shun Zhang, Jinghuan Zhang
Although the insight phenomenon has attracted great attention from psychologists, it is still largely unknown whether its variation in well-functioning human adults has a genetic basis. Several lines of evidence suggest that genes involved in dopamine (DA) transmission might be potential candidates. The present study explored for the first time the association of dopamine D2 receptor gene (DRD2) with insight problem solving. Fifteen single-nucleotide polymorphisms (SNPs) covering DRD2 were genotyped in 425 unrelated healthy Chinese undergraduates, and were further tested for association with insight problem solving...
2016: Frontiers in Psychology
https://www.readbyqxmd.com/read/27931206/survivalgwas_power-a-user-friendly-tool-for-power-calculations-in-pharmacogenetic-studies-with-time-to-event-outcomes
#2
Hamzah Syed, Andrea L Jorgensen, Andrew P Morris
BACKGROUND: Power calculators are currently available for the design of genetic association studies of binary phenotypes and quantitative traits, but not for "time to event" outcomes, which are of particular relevance in pharmacogenetics. With the rapid emergence of pharmacogenetic association studies of single nucleotide polymorphisms (SNPs), and the complexity of clinical outcomes they consider, there is a need for software to perform power calculations of time to event data over a range of design scenarios and analytical methodologies...
December 8, 2016: BMC Bioinformatics
https://www.readbyqxmd.com/read/27930729/strain-level-discrimination-of-shiga-toxin-producing-escherichia-coli-in-spinach-using-metagenomic-sequencing
#3
Susan R Leonard, Mark K Mammel, David W Lacher, Christopher A Elkins
Consumption of fresh bagged spinach contaminated with Shiga toxin-producing Escherichia coli (STEC) has led to severe illness and death; however current culture-based methods to detect foodborne STEC are time consuming. Since not all STEC strains are considered pathogenic to humans, it is crucial to incorporate virulence characterization of STEC in the detection method. In this study, we assess the comprehensiveness of utilizing a shotgun metagenomics approach for detection and strain-level identification by spiking spinach with a variety of genomically disparate STEC strains at a low contamination level of 0...
2016: PloS One
https://www.readbyqxmd.com/read/27930648/isothermal-diagnostic-assays-for-monitoring-single-nucleotide-polymorphisms-in-necator-americanus-associated-with-benzimidazole-drug-resistance
#4
Nour Rashwan, Catherine Bourguinat, Kathy Keller, Nipul Kithsiri Gunawardena, Nilanthi de Silva, Roger Prichard
BACKGROUND: Soil-transmitted helminths (STHs) are the most prevalent intestinal helminths of humans, and a major cause of morbidity in tropical and subtropical countries. The benzimidazole (BZ) drugs albendazole (ABZ) and mebendazole (MBZ) are used for treatment of human STH infections and this use is increasing dramatically with massive drug donations. Frequent and prolonged use of these drugs could lead to the emergence of anthelmintic resistance as has occurred in nematodes of livestock...
December 2016: PLoS Neglected Tropical Diseases
https://www.readbyqxmd.com/read/27929711/dual-effects-of-a-retn-single-nucleotide-polymorphism-snp-at-420-on-plasma-resistin-genotype-and-dna-methylation
#5
Hiroshi Onuma, Yasuharu Tabara, Ryoichi Kawamura, Jun Ohashi, Wataru Nishida, Yasunori Takata, Masaaki Ochi, Tatsuya Nishimiya, Yasumasa Ohyagi, Ryuichi Kawamoto, Katsuhiko Kohara, Tetsuro Miki, Haruhiko Osawa
CONTEXT: We previously reported that SNP (single nucleotide polymorphism) -420 C>G (rs1862513) in the promoter region of RETN was associated with type 2 diabetes. Plasma resistin was tightly correlated with SNP-420 genotypes. SNP-420 is a CpG-SNP affecting the sequence of CpG dinucleotides. OBJECTIVE: To examine whether methylation at SNP-420 affects plasma resistin, we analyzed plasma resistin and methylation at RETN SNP-420. DESIGN AND METHODS: Genomic DNA was extracted from peripheral white blood cells in 2,078 Japanese subjects...
December 8, 2016: Journal of Clinical Endocrinology and Metabolism
https://www.readbyqxmd.com/read/27929201/the-importance-of-genetic-factors-for-the-development-of-arthropathy-a-longitudinal-study-of-children-and-adolescents-with-haemophilia-a
#6
Edward D Gomperts, John Schwarz, Sharyne M Donfield, Alice E Lail, Jan Astermark, W Keith Hoots, Cheryl A Winkler, Erik Berntorp
Haemophilia A is a congenital bleeding disorder characterised by recurrent haemorrhages into the major joints. Haemophilic arthropathy is a well-established outcome of recurrent joint bleeding; however, it is clear that multiple factors determine the extent and severity of its occurrence. We sought to identify genetic factors related to abnormalities in range of motion (ROM) in the knees, ankles and elbows in a cohort of children and adolescents with haemophilia A not treated primarily with regular prophylaxis...
December 8, 2016: Thrombosis and Haemostasis
https://www.readbyqxmd.com/read/27929136/an-integrated-genomic-approach-for-the-study-of-mandibular-prognathism-in-the-european-seabass-dicentrarchus-labrax
#7
Massimiliano Babbucci, Serena Ferraresso, Marianna Pauletto, Rafaella Franch, Chiara Papetti, Tomaso Patarnello, Paolo Carnier, Luca Bargelloni
Skeletal anomalies in farmed fish are a relevant issue affecting animal welfare and health and causing significant economic losses. Here, a high-density genetic map of European seabass for QTL mapping of jaw deformity was constructed and a genome-wide association study (GWAS) was carried out on a total of 298 juveniles, 148 of which belonged to four full-sib families. Out of 298 fish, 107 were affected by mandibular prognathism (MP). Three significant QTLs and two candidate SNPs associated with MP were identified...
December 8, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27929054/in-silico-identification-of-snp-diversity-in-cultivated-and-wild-tomato-species-insight-from-molecular-simulations
#8
Archana Bhardwaj, Yogeshwar Vikram Dhar, Mehar Hasan Asif, Sumit K Bag
Single Nucleotide Polymorphisms (SNPs), an important source of genetic variations, are often used in crop improvement programme. The present study represented comprehensive In silico analysis of nucleotide polymorphisms in wild (Solanum habrochaites) and cultivated (Solanum lycopersicum) species of tomato to explore the consequence of substitutions both at sequence and structure level. A total of 8978 SNPs having Ts/Tv (Transition/Transversion) ratio 1.75 were identified from the Expressed Sequence Tag (EST) and Next Generation Sequence (NGS) data of both the species available in public databases...
December 8, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27928138/essential-oil-composition-antioxidant-antidiabetic-and-antihypertensive-properties-of-two-afromomum-species
#9
Stephen Adeniyi Adefegha, Tosin Abiola Olasehinde, Ganiyu Oboh
This study was designed to assess the antioxidant, antidiabetic and antihypertensive effects of essential oils from A. melegueta and A. danielli seeds. The essential oils were extracted via hydrodistillation, dried with anhydrous Na2SO4 and characterized using gas chromatography-mass spectrometry (GC-MS). Antioxidant properties and inhibition of some pro-oxidant induced lipid peroxidation in rats' pancreas and heart homogenates were also determined. The results revealed that eugenol, eucalyptol, α-terpineol, α-caryophyllene and β-caryophyllene were the most abundant components in A...
December 8, 2016: Journal of Oleo Science
https://www.readbyqxmd.com/read/27927781/genetic-variants-associated-with-circulating-parathyroid-hormone
#10
Cassianne Robinson-Cohen, Pamela L Lutsey, Marcus E Kleber, Carrie M Nielson, Braxton D Mitchell, Joshua C Bis, Karen M Eny, Laura Portas, Joel Eriksson, Mattias Lorentzon, Daniel L Koller, Yuri Milaneschi, Alexander Teumer, Stefan Pilz, Maria Nethander, Elizabeth Selvin, Weihong Tang, Lu-Chen Weng, Hoi Suen Wong, Dongbing Lai, Munro Peacock, Anke Hannemann, Uwe Völker, Georg Homuth, Matthias Nauk, Federico Murgia, Jack W Pattee, Eric Orwoll, Joseph M Zmuda, Jose Antonio Riancho, Myles Wolf, Frances Williams, Brenda Penninx, Michael J Econs, Kathleen A Ryan, Claes Ohlsson, Andrew D Paterson, Bruce M Psaty, David S Siscovick, Jerome I Rotter, Mario Pirastu, Elizabeth Streeten, Winfried März, Caroline Fox, Josef Coresh, Henri Wallaschofski, James S Pankow, Ian H de Boer, Bryan Kestenbaum
Parathyroid hormone (PTH) is a primary calcium regulatory hormone. Elevated serum PTH concentrations in primary and secondary hyperparathyroidism have been associated with bone disease, hypertension, and in some studies, cardiovascular mortality. Genetic causes of variation in circulating PTH concentrations are incompletely understood. We performed a genome-wide association study of serum PTH concentrations among 29,155 participants of European ancestry from 13 cohort studies (n=22,653 and n=6502 in discovery and replication analyses, respectively)...
December 7, 2016: Journal of the American Society of Nephrology: JASN
https://www.readbyqxmd.com/read/27927228/cellular-and-molecular-characterization-of-a-stem-rust-resistance-locus-on-wheat-chromosome-7al
#11
Vincent Pujol, Jose Robles, Penghao Wang, Jen Taylor, Peng Zhang, Li Huang, Linda Tabe, Evans Lagudah
BACKGROUND: Wheat stem rust, caused by Puccinia graminis f. sp. tritici, is a major wheat disease which is mainly controlled through the release of resistant cultivars containing one or several resistance genes. Considerable effort has been put into the discovery of new resistance genes, but knowledge of their mechanisms of action is often lacking. In this study, the mechanism of resistance conferred by a recently discovered stem rust resistance locus on wheat chromosome 7AL was investigated through microscopic observations and RNA-sequencing, using the susceptible line Columbus and the independent, backcrossed, resistant lines Columbus-NS765 and Columbus-NS766...
December 7, 2016: BMC Research Notes
https://www.readbyqxmd.com/read/27927211/genetic-variations-of-aldehyde-dehydrogenase-2-and-alcohol-dehydrogenase-1b-are-associated-with-the-etiology-of-atrial-fibrillation-in-japanese
#12
Yukiko Nakano, Hidenori Ochi, Yuko Onohara, Akinori Sairaku, Takehito Tokuyama, Hiroya Matsumura, Shunsuke Tomomori, Michitaka Amioka, Naoya Hironomobe, Chikaaki Motoda, Nozomu Oda, Kazuaki Chayama, Che-Hong Chen, Eric R Gross, Daria Mochly-Rosen, Yasuki Kihara
BACKGROUND: Alcohol consumption and oxidative stress are well-known risk factors for developing atrial fibrillation (AF). Single nucleotide polymorphisms (SNPs) of alcohol dehydrogenase (ADH1B) and aldehyde dehydrogenase 2 (ALDH2) genes encoding enzymes of alcohol and reactive aldehyde metabolism, respectively, are prevalent among East Asians. Here, we examined whether these SNPs were associated with AF in Japanese patients. METHODS AND RESULTS: Five hundred seventy-seven Japanese patients with AF undergoing catheter ablation and 1935 controls at Hiroshima University Hospital were studied...
December 7, 2016: Journal of Biomedical Science
https://www.readbyqxmd.com/read/27926527/meqtl-analysis-of-childhood-obesity-links-epigenetics-with-a-risk-snp-rs17782313-near-mc4r-from-meta-analysis
#13
Yuping Tang, Bo Jin, Lingling Zhou, Weifeng Lu
Earlier GWAS has identified that rs17782313 near MC4R was associated with obesity. However, subsequent studies showed conflicting results, especially among childhood. Besides, the mechanisms underlying the association between rs17782313 and childhood obesity remain largely unexplored, and genetic and epigenetic may interact and together affect the development of childhood obesity. We conducted a comprehensive meta-analysis to assess the association between rs17782313 and childhood obesity. MeQTL and eQTL analysis was applied to explore the effect of rs17782313 on DNA methylation and MC4R expression...
December 1, 2016: Oncotarget
https://www.readbyqxmd.com/read/27926379/a-comparative-analysis-of-chaotic-particle-swarm-optimizations-for-detecting-single-nucleotide-polymorphism-barcodes
#14
Li-Yeh Chuang, Sin-Hua Moi, Yu-Da Lin, Cheng-Hong Yang
OBJECTIVE: Evolutionary algorithms could overcome the computational limitations for the statistical evaluation of large datasets for high-order single nucleotide polymorphism (SNP) barcodes. Previous studies have proposed several chaotic particle swarm optimization (CPSO) methods to detect SNP barcodes for disease analysis (e.g., for breast cancer and chronic diseases). This work evaluated additional chaotic maps combined with the particle swarm optimization (PSO) method to detect SNP barcodes using a high-dimensional dataset...
October 2016: Artificial Intelligence in Medicine
https://www.readbyqxmd.com/read/27925593/a-review-of-machine-learning-and-statistical-approaches-for-detecting-snp-interactions-in-high-dimensional-genomic-data
#15
Suneetha Uppu, Aneesh Krishna, Raj Gopalan
In this era of genome-wide association studies (GWAS), the quest for understanding the genetic architecture of complex diseases is rapidly increasing more than ever before. The development of high throughput genotyping and next generation sequencing technologies enables genetic epidemiological analysis of large scale data. These advances have led to the identification of a number of single nucleotide polymorphisms (SNPs) responsible for disease susceptibility. The interactions between SNPs associated with complex diseases are increasingly being explored in the current literature...
December 2, 2016: IEEE/ACM Transactions on Computational Biology and Bioinformatics
https://www.readbyqxmd.com/read/27925267/genetic-variation-and-gene-conversions-within-the-bovine-nk-lysin-gene-family
#16
J Chen, M O Lee, J E Womack
In contrast to a single copy of the NK-lysin gene in humans and many other mammals, we previously identified a family of four expressed NK-lysin genes arising by tandem duplications on cattle chromosome 11. Here, we report two genetic variants in the bovine NK-lysin complex with potential importance in the bovine innate immune system. The first one is a 9-bp deletion causing a three-amino-acid deletion in the pro-region of the NK1 gene product. The second is a deletion of NK2B in some Holstein cattle, resulting in copy number variation that is in disequilibrium with a SNP from the bovine 770K HD SNP array...
December 7, 2016: Animal Genetics
https://www.readbyqxmd.com/read/27924156/deficiency-of-atp6v1h-causes-bone-loss-by-inhibiting-bone-resorption-and-bone-formation-through-the-tgf-%C3%AE-1-pathway
#17
Xiaohong Duan, Jin Liu, Xueni Zheng, Zhe Wang, Yanli Zhang, Ying Hao, Tielin Yang, Hongwen Deng
Vacuolar-type H (+)-ATPase (V-ATPase) is a highly conserved, ancient enzyme that couples the energy of ATP hydrolysis to proton transport across vesicular and plasma membranes of eukaryotic cells. Previously reported mutations of various V-ATPase subunits are associated with increased bone density. We now show that haploinsufficiency for the H subunit of the V1 domain (ATP6V1H) is associated with osteoporosis in humans and mice. A genome-wide SNP array analysis of 1625 Han Chinese found that 4 of 15 tag SNPs (26...
2016: Theranostics
https://www.readbyqxmd.com/read/27924034/comprehensive-characterization-annotation-and-innovative-use-of-infinium-dna-methylation-beadchip-probes
#18
Wanding Zhou, Peter W Laird, Hui Shen
Illumina Infinium DNA Methylation BeadChips represent the most widely used genome-scale DNA methylation assays. Existing strategies for masking Infinium probes overlapping repeats or single nucleotide polymorphisms (SNPs) are based largely on ad hoc assumptions and subjective criteria. In addition, the recently introduced MethylationEPIC (EPIC) array expands on the utility of this platform, but has not yet been well characterized. We present in this paper an extensive characterization of probes on the EPIC and HM450 microarrays, including mappability to the latest genome build, genomic copy number of the 3' nested subsequence and influence of polymorphisms including a previously unrecognized color channel switch for Type I probes...
October 24, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27924023/methsmrt-an-integrative-database-for-dna-n6-methyladenine-and-n4-methylcytosine-generated-by-single-molecular-real-time-sequencing
#19
Pohao Ye, Yizhao Luan, Kaining Chen, Yizhi Liu, Chuanle Xiao, Zhi Xie
DNA methylation is an important type of epigenetic modifications, where 5- methylcytosine (5mC), 6-methyadenine (6mA) and 4-methylcytosine (4mC) are the most common types. Previous efforts have been largely focused on 5mC, providing invaluable insights into epigenetic regulation through DNA methylation. Recently developed single-molecule real-time (SMRT) sequencing technology provides a unique opportunity to detect the less studied DNA 6mA and 4mC modifications at single-nucleotide resolution. With a rapidly increased amount of SMRT sequencing data generated, there is an emerging demand to systematically explore DNA 6mA and 4mC modifications from these data sets...
October 18, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27924020/lincsnp-2-0-an-updated-database-for-linking-disease-associated-snps-to-human-long-non-coding-rnas-and-their-tfbss
#20
Shangwei Ning, Ming Yue, Peng Wang, Yue Liu, Hui Zhi, Yan Zhang, Jizhou Zhang, Yue Gao, Maoni Guo, Dianshuang Zhou, Xin Li, Xia Li
We describe LincSNP 2.0 (http://bioinfo.hrbmu.edu.cn/LincSNP), an updated database that is used specifically to store and annotate disease-associated single nucleotide polymorphisms (SNPs) in human long non-coding RNAs (lncRNAs) and their transcription factor binding sites (TFBSs). In LincSNP 2.0, we have updated the database with more data and several new features, including (i) expanding disease-associated SNPs in human lncRNAs; (ii) identifying disease-associated SNPs in lncRNA TFBSs; (iii) updating LD-SNPs from the 1000 Genomes Project; and (iv) collecting more experimentally supported SNP-lncRNA-disease associations...
October 23, 2016: Nucleic Acids Research
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