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https://www.readbyqxmd.com/read/27926527/meqtl-analysis-of-childhood-obesity-links-epigenetics-with-a-risk-snp-rs17782313-near-mc4r-from-meta-analysis
#1
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
#2
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/27923663/pharmacogenetics-of-lithium-effects-on-glomerular-function-in-bipolar-disorder-patients-under-chronic-lithium-treatment-a-pilot-study
#3
Evangelia Eirini Tsermpini, Yanfei Zhang, Paola Niola, Caterina Chillotti, Raffaella Ardau, Alberto Bocchetta, George P Patrinos, Maria Del Zompo, Giovanni Severino, Ming Ta Michael Lee, Alessio Squassina
Bipolar disorder (BD) is a psychiatric disease characterized by alternating episodes of mania and depression. Lithium (Li) represents the mainstay treatment for BD, although a significant proportion of patients show insufficient or no response. Li is also associated with potentially severe side effects, including renal effects. Several studies reported that Li may induce reduction of glomerular filtration rate (GFR) in patients under long-term treatment. The biological systems and the genetic factors involved in susceptibility to Li-induced renal-side effects have been scarcely explored...
December 3, 2016: Neuroscience Letters
https://www.readbyqxmd.com/read/27923400/allele-specific-expression-in-the-human-heart-and-its-application-to-postoperative-atrial-fibrillation-and-myocardial-ischemia
#4
Martin I Sigurdsson, Louis Saddic, Mahyar Heydarpour, Tzuu-Wang Chang, Prem Shekar, Sary Aranki, Gregory S Couper, Stanton K Shernan, Jon G Seidman, Simon C Body, Jochen D Muehlschlegel
BACKGROUND: Allele-specific expression (ASE) is differential expression of each of the two chromosomal alleles of an autosomal gene. We assessed ASE patterns in the human left atrium (LA, n = 62) and paired samples from the left ventricle (LV, n = 76) before and after ischemia, and tested the utility of differential ASE to identify genes associated with postoperative atrial fibrillation (poAF) and myocardial ischemia. METHODS: Following genotyping from whole blood and whole-genome sequencing of LA and LV samples, we called ASE using sequences overlapping heterozygous SNPs using rigorous quality control to minimize false ASE calling...
December 6, 2016: Genome Medicine
https://www.readbyqxmd.com/read/27922550/a-novel-abcc6-haplotype-is-associated-with-azathioprine-drug-response-in-myasthenia-gravis
#5
Lara Colleoni, Barbara Galbardi, Claudia Barzago, Silvia Bonanno, Sara Franzi, Rita Frangiamore, Giorgia Camera, Maria Foti, Donatella Biancolini, Eleonora Canioni, Lorenzo Maggi, Carlo Antozzi, Renato Mantegazza, Pia Bernasconi, Dimos Kapetis
OBJECTIVE: We investigated the association of single nucleotide polymorphisms (SNPs) in drug-metabolizing enzymes and transporters (DMETs) with the response to azathioprine (AZA) in patients affected by myasthenia gravis (MG) to determine possible genotype-phenotype correlations. PATIENTS AND METHODS: Genomic DNA from 180 AZA-treated MG patients was screened through the Affymetrix DMET platform, which characterizes 1931 SNPs in 225 genes. The significant SNPs, identified to be involved in AZA response, were subsequently validated by allelic discrimination and direct sequencing...
December 2, 2016: Pharmacogenetics and Genomics
https://www.readbyqxmd.com/read/27922483/clinicopathologic-and-prognostic-significance-of-gelatinase-a-in-tunisian-colorectal-cancer-a-case-control-study
#6
Dalel Ben Néjima, Yosr Ben Zarkouna, Pascal Pujol, Amor Gammoudi, Hamouda Boussen, Mohamed Manai
Matrix metalloproteinase-2 (gelatinase A) is a well-known mediator of cancer metastasis, but it is also thought to be involved in several aspects of cancer development, including cell growth and inflammation. In the present study, we investigate whether MMP-2 SNP, MMP-2 mRNAs, and MMP-2 protein are associated with the susceptibility to colorectal cancer in the Tunisian population. The TaqMan allele discrimination assay and DNA sequencing techniques were used for genotyping; MMP-2 expression of each genotype was analyzed by semiquantitative RT-PCR, and MMP-2 protein expression was analyzed by immunohistochemistry staining...
January 2017: Applied Immunohistochemistry & Molecular Morphology: AIMM
https://www.readbyqxmd.com/read/27921411/association-of-cd46-ivs1-1724-c-g-single-nucleotide-polymorphism-in-iranian-women-with-unexplained-recurrent-spontaneous-abortion-ursa
#7
Shiva Abdi-Shayan, Amir Monfaredan, Zahra Moradi, Mehrangiz Rajaii Oskoui, Tohid Kazemi
There are several known and unknown factors for unexplained recurrent spontaneous abortion (URSA). Among them, complement regulatory protein CD46 plays a pivotal role in preventing uncontrolled activation of complement and successful continuation of pregnancy. We aimed in this study to investigate the possible association of CD46 IVS1-1724 C>G polymorphism with RSA in Iranian women. 141 women with RSA and 153 women with normal pregnancy were enrolled in this study. RSA was confirmed as the history of having at least three consecutive abortions without any known immunologic, pathologic and genetic reason...
August 2016: Iranian Journal of Allergy, Asthma, and Immunology
https://www.readbyqxmd.com/read/27920797/genome-wide-association-study-for-identifying-loci-that-affect-fillet-yield-carcass-and-body-weight-traits-in-rainbow-trout-oncorhynchus-mykiss
#8
Dianelys Gonzalez-Pena, Guangtu Gao, Matthew Baranski, Thomas Moen, Beth M Cleveland, P Brett Kenney, Roger L Vallejo, Yniv Palti, Timothy D Leeds
Fillet yield (FY, %) is an economically-important trait in rainbow trout aquaculture that affects production efficiency. Despite that, FY has received little attention in breeding programs because it is difficult to measure on a large number of fish and cannot be directly measured on breeding candidates. The recent development of a high-density SNP array for rainbow trout has provided the needed tool for studying the underlying genetic architecture of this trait. A genome-wide association study (GWAS) was conducted for FY, body weight at 10 (BW10) and 13 (BW13) months post-hatching, head-off carcass weight (CAR), and fillet weight (FW) in a pedigreed rainbow trout population selectively bred for improved growth performance...
2016: Frontiers in Genetics
https://www.readbyqxmd.com/read/27920664/investigation-of-snp-rs2060546-immediately-upstream-to-ntn4-in-a-danish-gilles-de-la-tourette-syndrome-cohort
#9
Shanmukha S Padmanabhuni, Rayan Houssari, Ann-Louise Esserlind, Jes Olesen, Thomas M Werge, Thomas F Hansen, Birgitte Bertelsen, Fotis Tsetsos, Peristera Paschou, Zeynep Tümer
Gilles de la Tourette syndrome (GTS) is a neuropsychiatric disorder characterized by multiple motor and vocal tics. GTS is a complex disorder, with environmental factors and several genes involved. Although variations within a few genes such as AADAC, NRXN1, SLITRK1, HDC, and IMMP2L have been tentatively associated with GTS (in a small number of patients), the causative genes underlying GTS pathophysiology remain unknown. In a previous genome-wide association study (GWAS) a single nucleotide polymorphism (SNP, rs2060546) near the Netrin-4 (NTN4 - MIM 610401) gene was shown to be associated with GTS [odds ratio (OR) = 1...
2016: Frontiers in Neuroscience
https://www.readbyqxmd.com/read/27920557/effect-of-smoking-on-the-genetic-makeup-of-toll-like-receptors-2-and-6
#10
Muhammad Kohailan, Mohammad Alanazi, Mahmoud Rouabhia, Abdullah Alamri, Narasimha Reddy Parine, Abdullah Alhadheq, Santhosh Basavarajappa, Abdul Aziz Abdullah Al-Kheraif, Abdelhabib Semlali
BACKGROUND: Cigarette smoking is a major risk factor for lung cancer, asthma, and oral cancer, and is central to the altered innate immune responsiveness to infection. Many hypotheses have provided evidence that cigarette smoking induces more genetic changes in genes involved in the development of many cigarette-related diseases. This alteration may be from single-nucleotide polymorphisms (SNPs) in innate immunity genes, especially the toll-like receptors (TLRs). OBJECTIVE: In this study, the genotype frequencies of TLR2 and TLR6 in smoking and nonsmoking population were examined...
2016: OncoTargets and Therapy
https://www.readbyqxmd.com/read/27919232/microrna-27a-rs895819-is-associated-with-obesity-in-hiv-infected-preeclamptic-black-south-african-women-on-haart
#11
Niren Ray Maharaj, Prithiksha Ramkaran, Siddharthiya Pillay, Anil Amichund Chuturgoon
BACKGROUND: Preeclampsia (PE) and HIV/AIDS present a major health challenge globally. South Africa has the highest disease burden of both HIV/AIDS and PE in the world. Despite extensive research, the pathophysiology of these conditions is not completely understood, however a genetic predisposition in women may affect susceptibility. MiRNA-27a regulates adipogenesis and glucose metabolism. A single nucleotide polymorphism (SNP) in miRNA-27a (rs895819T > C) has shown to have disparate effects in various populations...
December 5, 2016: BMC Medical Genetics
https://www.readbyqxmd.com/read/27919223/trpm2-snp-genotype-previously-associated-with-susceptibility-to-rhodococcus-equi-pneumonia-in-quarter-horse-foals-displays-differential-gene-expression-identified-using-rna-seq
#12
Cole M McQueen, Canaan M Whitfield-Cargile, Kranti Konganti, Glenn P Blodgett, Scott V Dindot, Noah D Cohen
BACKGROUND: Rhodococcus equi (R. equi) is an intracellular bacterium that affects young foals and immuno-compromised individuals causing severe pneumonia. Currently, the genetic mechanisms that confer susceptibility and/or resistance to R. equi are not fully understood. Previously, using a SNP-based genome-wide association study, we identified a region on equine chromosome 26 associated with culture-confirmed clinical pneumonia. To better characterize this region and understand the function of the SNP located within TRPM2 that was associated with R...
December 5, 2016: BMC Genomics
https://www.readbyqxmd.com/read/27918628/phenotypic-and-genome-wide-association-analysis-of-spike-ethylene-in-diverse-wheat-genotypes-under-heat-stress
#13
Ravi Valluru, Matthew P Reynolds, William J Davies, Sivakumar Sukumaran
The gaseous phytohormone ethylene plays an important role in spike development in wheat (Triticum aestivum). However, the genotypic variation and the genomic regions governing spike ethylene (SET) production in wheat under long-term heat stress remain unexplored. We investigated genotypic variation in the production of SET and its relationship with spike dry weight (SDW) in 130 diverse wheat elite lines and landraces under heat-stressed field conditions. We employed an Illumina iSelect 90K single nucleotide polymorphism (SNP) genotyping array to identify the genetic loci for SET and SDW through a genome-wide association study (GWAS) in a subset of the Wheat Association Mapping Initiative (WAMI) panel...
December 5, 2016: New Phytologist
https://www.readbyqxmd.com/read/27917559/prognostic-value-of-nerve-ultrasound-and-electrophysiological-findings-in-saturday-night-palsy
#14
Antonios Kerasnoudis, Panagiota Ntasiou, Efthymia Ntasiou
BACKGROUND AND PURPOSE: We report on the prognostic role of the cross-sectional area (CSA) enlargement and conduction block (CB) in radial neuropathy (Saturday night palsy [SNP]). METHODS: Reference CSA values were defined in 30 healthy subjects. Twenty-four patients with SNP underwent evaluation (Thessaloniki Hypesthesia Score [THS], Medical Research Council [MRC], ultrasound, electrophysiology). All patients were followed up 3 months after initial presentation...
December 5, 2016: Journal of Neuroimaging: Official Journal of the American Society of Neuroimaging
https://www.readbyqxmd.com/read/27917368/sex-steroid-hormone-single-nucleotide-polymorphisms-pesticide-use-and-the-risk-of-prostate-cancer-a-nested-case-control-study-within-the-agricultural-health-study
#15
Carol H Christensen, Kathryn Hughes Barry, Gabriella Andreotti, Michael C R Alavanja, Michael B Cook, Scott P Kelly, Laurie A Burdett, Meredith Yeager, Laura E Beane Freeman, Sonja I Berndt, Stella Koutros
Experimental and epidemiologic investigations suggest that certain pesticides may alter sex steroid hormone synthesis, metabolism or regulation, and the risk of hormone-related cancers. Here, we evaluated whether single-nucleotide polymorphisms (SNPs) involved in hormone homeostasis alter the effect of pesticide exposure on prostate cancer risk. We evaluated pesticide-SNP interactions between 39 pesticides and SNPs with respect to prostate cancer among 776 cases and 1,444 controls nested in the Agricultural Health Study cohort...
2016: Frontiers in Oncology
https://www.readbyqxmd.com/read/27916731/associations-between-the-cntnap2-gene-dorsolateral-prefrontal-cortex-and-cognitive-performance-on-the-stroop-task
#16
Bi Zhu, Chuansheng Chen, Gui Xue, Xuemei Lei, Yunxin Wang, Jin Li, Robert K Moyzis, Jun Li, Qi Dong, Chongde Lin
The CNTNAP2 (contactin associated protein-like 2) gene, highly expressed in the human prefrontal cortex, has been linked with autism and language impairment. Potential relationships between CNTNAP2, dorsolateral prefrontal cortex (DLPFC), and cognition have been suggested by previous clinical studies, but have not been directly examined in the same study. The current study collected structural MRI, genetic, and behavioral data in 317 healthy Chinese adults, and examined associations between CNTNAP2 variants, DLPFC, and cognitive performance (measured by the Stroop task)...
December 1, 2016: Neuroscience
https://www.readbyqxmd.com/read/27916600/mapping-complex-traits-in-a-diversity-outbred-f1-mouse-population-identifies-germline-modifiers-of-metastasis-in-human-prostate-cancer
#17
Jean M Winter, Derek E Gildea, Jonathan P Andreas, Daniel M Gatti, Kendra A Williams, Minnkyong Lee, Ying Hu, Suiyuan Zhang, James C Mullikin, Tyra G Wolfsberg, Shannon K McDonnell, Zachary C Fogarty, Melissa C Larson, Amy J French, Daniel J Schaid, Stephen N Thibodeau, Gary A Churchill, Nigel P S Crawford
It is unclear how standing genetic variation affects the prognosis of prostate cancer patients. To provide one controlled answer to this problem, we crossed a dominant, penetrant mouse model of prostate cancer to Diversity Outbred mice, a collection of animals that carries over 40 million SNPs. Integration of disease phenotype and SNP variation data in 493 F1 males identified a metastasis modifier locus on Chromosome 8 (LOD = 8.42); further analysis identified the genes Rwdd4, Cenpu, and Casp3 as functional effectors of this locus...
November 25, 2016: Cell Systems
https://www.readbyqxmd.com/read/27916099/-association-between-il-6-572-c-g-polymorphism-and-breast-cancer-susceptibility
#18
Zhishan Zhang, Zixuan Chen, Debo Chen, Yisheng Lin, Yancheng Jiang, Qinglan Wang
Objective To explore the associations between breast cancer and three single nucleotide polymorphisms (-597 G/A, -572 C/G and -174 G/C) of interleukin-6 (IL-6) gene promoter. Methods The study enrolled 136 breast cancer cases and 150 healthy female controls. The single nucleotide polymorphisms (SNPs) of IL-6 were identified by Sanger method of DNA sequencing, and serum IL-6 levels were measured with electrochemiluminescence immunoassay. Chi-squared test was utilized to compare frequency of a given SNP between the two groups, and t-test was employed to compare serum IL-6 levels in different groups...
December 2016: Xi Bao Yu Fen Zi Mian Yi Xue za Zhi, Chinese Journal of Cellular and Molecular Immunology
https://www.readbyqxmd.com/read/27915212/rapid-detection-and-evolutionary-analysis-of-legionella-pneumophila-serogroup-1-sequence-type-47
#19
M Mentasti, P Cassier, S David, C Ginevra, L Gomez-Valero, A Underwood, B Afshar, J Etienne, J Parkhill, V Chalker, C Buchrieser, T G Harrison, S Jarraud
OBJECTIVES: Legionella pneumophia serogroup 1 (Lp1) sequence type 47 is the leading cause of legionellosis in North-Western Europe but surprisingly it is rarely isolated from environmental samples. Comparative genomics was applied to develop a PCR assay and to better understand the evolution of this strain. METHODS: Comparative analysis of 36 genomes representative of the Lp species was used to identify specific PCR targets which were then evaluated in silico on 545 sequenced genomes, and in vitro on 436 Legionella strains, 106 respiratory samples and three environmental samples from proven ST47 sources...
November 30, 2016: Clinical Microbiology and Infection
https://www.readbyqxmd.com/read/27913832/general-and-specific-combining-abilities-in-a-maize-zea-mays-l-test-cross-hybrid-panel-relative-importance-of-population-structure-and-genetic-divergence-between-parents
#20
A Larièpe, L Moreau, J Laborde, C Bauland, S Mezmouk, L Décousset, T Mary-Huard, J B Fiévet, A Gallais, P Dubreuil, A Charcosset
General and specific combining abilities of maize hybrids between 288 inbred lines and three tester lines were highly related to population structure and genetic distance inferred from SNP data. Many studies have attempted to provide reliable and quick methods to identify promising parental lines and combinations in hybrid breeding programs. Since the 1950s, maize germplasm has been organized into heterotic groups to facilitate the exploitation of heterosis. Molecular markers have proven efficient tools to address the organization of genetic diversity and the relationship between lines or populations...
December 2, 2016: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
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