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Single Polymorphism Nucleotide (SNPs)

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https://www.readbyqxmd.com/read/29145541/variations-in-adipor1-but-not-adipor2-are-associated-with-hypertriglyceridemia-and-diabetes-in-an-admixed-latin-american-population
#1
Gustavo Gustavo Mora-García, María S Ruiz-Díaz, Fabian Espitia-Almeida, Doris Gómez-Camargo
BACKGROUND: Adiponectin is a hormone secreted by adipose tissue. It regulates glycolysis and lipolysis and is involved in the pathophysiology of diabetes and related disorders. Its activity is mainly mediated by the transmembrane receptors AdipoR1 and AdipoR2, which are encoded by ADIPOR1 (1q32.1) and ADIPOR2 (12p13.33) genes, respectively. In genetic association studies, single nucleotide polymorphisms (SNPs) in or near these genes have been associated with metabolic alterations. However, these relationships are still controversial...
July 2017: Review of Diabetic Studies: RDS
https://www.readbyqxmd.com/read/29145455/association-of-polymorphisms-in-heat-shock-protein-70-genes-with-the-susceptibility-to-noise-induced-hearing-loss-a-meta-analysis
#2
Shimin Zong, Xue Zeng, Tianyi Liu, Fangmin Wan, Pan Luo, Hongjun Xiao
BACKGROUND: Several case-control studies reported the relationship between single nucleotide polymorphisms (SNPs) in HSP70 genes and noise-induced hearing loss (NIHL). However, their conclusions are conflicting. This meta-analysis aims to identify the association of HSP70 variants and NIHL susceptibility. METHOD: A systematical literature search was performed in PubMed, Web of Science, EMBASE, and Wanfang Chinese database. The pooled odds radio (OR), 95% confidence interval (CI) and p value were calculated in fixed- or random-effects model according to the I2 value in the heterogeneity test...
2017: PloS One
https://www.readbyqxmd.com/read/29143920/distinguishing-the-disease-associated-snps-based-on-composition-frequency-analysis
#3
Wenling Li, Menglong Li, Xuemei Pu, Yanzhi Guo
Single-nucleotide polymorphism (SNP) is a basical variation in genome. When SNPs occur at the binding sites of microRNA, they can influence the binding efficiency, cause a fluctuation of the mRNA in vivo, and thus arouse posttranscriptional level abnormality. Therefore, SNP has a strong correlation with diseases. Although enormous SNPs have been experimentally identified, only a tiny proportion of them are truly disease-associated SNPs (dSNPs) that relate to microRNA modification and then are involved in disease causing process...
November 16, 2017: Interdisciplinary Sciences, Computational Life Sciences
https://www.readbyqxmd.com/read/29143708/genome-wide-association-study-for-growth-traits-in-nelore-cattle
#4
A P N Terakado, R B Costa, G M F de Camargo, N Irano, T Bresolin, L Takada, C V D Carvalho, H N Oliveira, R Carvalheiro, F Baldi, L G de Albuquerque
The objective of this study was to investigate the association of single nucleotide polymorphisms (SNPs) with birth weight, weight gain from birth to weaning and from weaning to yearling, yearling height and cow weight in Nelore cattle. Data from 5064 animals participating in the DeltaGen and PAINT breeding programs were used. The animals were genotyped with a panel of 777 962 SNPs (Illumina BovineHD BeadChip) and 412 993 SNPs remained after quality control analysis of the genomic data. A genome-wide association study was performed using a single-step methodology...
November 16, 2017: Animal: An International Journal of Animal Bioscience
https://www.readbyqxmd.com/read/29143610/development-of-f1-hybrid-population-and-the-high-density-linkage-map-for-european-aspen-populus-tremula-l-using-radseq-technology
#5
Anatoly V Zhigunov, Pavel S Ulianich, Marina V Lebedeva, Peter L Chang, Sergey V Nuzhdin, Elena K Potokina
BACKGROUND: Restriction-site associated DNA sequencing (RADseq) technology was recently employed to identify a large number of single nucleotide polymorphisms (SNP) for linkage mapping of a North American and Eastern Asian Populus species. However, there is also the need for high-density genetic linkage maps for the European aspen (P. tremula) as a tool for further mapping of quantitative trait loci (QTLs) and marker-assisted selection of the Populus species native to Europe. RESULTS: We established a hybrid F1 population from the cross of two aspen parental genotypes diverged in their phenological and morphological traits...
November 14, 2017: BMC Plant Biology
https://www.readbyqxmd.com/read/29143592/col5a1-gene-variants-previously-associated-with-reduced-soft-tissue-injury-risk-are-associated-with-elite-athlete-status-in-rugby
#6
Shane M Heffernan, Liam P Kilduff, Robert M Erskine, Stephen H Day, Georgina K Stebbings, Christian J Cook, Stuart M Raleigh, Mark A Bennett, Guan Wang, Malcolm Collins, Yannis P Pitsiladis, Alun G Williams
BACKGROUND: Two common single nucleotide polymorphisms within the COL5A1 gene (SNPs; rs12722 C/T and rs3196378 C/A) have previously been associated with tendon and ligament pathologies. Given the high incidence of tendon and ligament injuries in elite rugby athletes, we hypothesised that both SNPs would be associated with career success. RESULTS: In 1105 participants (RugbyGene project), comprising 460 elite rugby union (RU), 88 elite rugby league athletes and 565 non-athlete controls, DNA was collected and genotyped for the COL5A1 rs12722 and rs3196378 variants using real-time PCR...
November 14, 2017: BMC Genomics
https://www.readbyqxmd.com/read/29142307/genetic-polymorphism-related-to-monocyte-macrophage-function-is-associated-with-graft-versus-host-disease
#7
Kati Hyvärinen, Jarmo Ritari, Satu Koskela, Riitta Niittyvuopio, Anne Nihtinen, Liisa Volin, David Gallardo, Jukka Partanen
Despite detailed human leukocyte antigen (HLA) matching and modern immunosuppressive therapy, severe graft-versus-host disease (GvHD) remains a major hurdle for successful allogeneic hematopoietic stem cell transplantation (HSCT). As the genetic diversity in GvHD complicates the systematic discovery of associated variants across populations, we studied 122 GvHD-associated single nucleotide polymorphisms (SNPs) in 492 HLA-matched sibling HSCT donor-recipient pairs from Finland and Spain. The association between these candidate SNPs and grade III-IV acute GvHD and extensive chronic GvHD was assessed...
November 15, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29142243/genetic-risk-scores-for-body-fat-distribution-attenuate-weight-loss-in-women-during-dietary-intervention
#8
M Svendstrup, K H Allin, T I A Sørensen, T H Hansen, N Grarup, T Hansen, H Vestergaard
BACKGROUND AND AIM: The well-established link between body fat distribution and metabolic health has been suggested to act through an impact on the remodeling capacity of the adipose tissue. Remodeling of the adipose tissue has been shown to affect body fat distribution and might affect the ability to lose weight. We aimed to study the effect of weighted genetic risk scores (GRSs) on weight loss based on single-nucleotide polymorphisms (SNPs) associated with waist-hip-ratio adjusted for body mass index (WHRadjBMI)...
November 16, 2017: International Journal of Obesity: Journal of the International Association for the Study of Obesity
https://www.readbyqxmd.com/read/29142238/mapping-qtls-conferring-salt-tolerance-and-micronutrient-concentrations-at-seedling-stagein-wheat
#9
Babar Hussain, Stuart James Lucas, Levent Ozturk, Hikmet Budak
Soil salinization and degradation is one of the consequences of climate change. Identification of major salt tolerance genes and marker assisted selection (MAS) can accelerate wheat breeding for this trait. We genotyped 154 wheat F2 lines derived from a cross between salt tolerant and susceptible cultivars using the Axiom Wheat Breeder's Genotyping Array. A high-density linkage map of 988 single nucleotide polymorphisms (SNPs) was constructed and utilized for quantitative trait loci (QTL) mapping for salt tolerance traits and mineral concentrations under salinity...
November 15, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29142228/genome-wide-mapping-of-genetic-determinants-influencing-dna-methylation-and-gene-expression-in-human-hippocampus
#10
Herbert Schulz, Ann-Kathrin Ruppert, Stefan Herms, Christiane Wolf, Nazanin Mirza-Schreiber, Oliver Stegle, Darina Czamara, Andreas J Forstner, Sugirthan Sivalingam, Susanne Schoch, Susanne Moebus, Benno Pütz, Axel Hillmer, Nadine Fricker, Hartmut Vatter, Bertram Müller-Myhsok, Markus M Nöthen, Albert J Becker, Per Hoffmann, Thomas Sander, Sven Cichon
Emerging evidence emphasizes the strong impact of regulatory genomic elements in neurodevelopmental processes and the complex pathways of brain disorders. The present genome-wide quantitative trait loci analyses explore the cis-regulatory effects of single-nucleotide polymorphisms (SNPs) on DNA methylation (meQTL) and gene expression (eQTL) in 110 human hippocampal biopsies. We identify cis-meQTLs at 14,118 CpG methylation sites and cis-eQTLs for 302 3'-mRNA transcripts of 288 genes. Hippocampal cis-meQTL-CpGs are enriched in flanking regions of active promoters, CpG island shores, binding sites of the transcription factor CTCF and brain eQTLs...
November 15, 2017: Nature Communications
https://www.readbyqxmd.com/read/29141798/ecotropic-viral-integration-site-5-evi5-variants-are-associated-with-multiple-sclerosis-in-iranian-population
#11
Mehrdokht Mazdeh, Soudeh Ghafouri-Fard, Rezvan Noroozi, Arezou Sayad, Maryam Khani, Mohammad Taheri, Mir Davood Omrani
BACKGROUND: Multiple sclerosis (MS) is a multifactorial disorder with immunological basis. Numerous genetic and environmental factors contribute in its pathogenesis. Several genetic loci have been shown to be associated with MS risk. Among genes whose participation in MS has been evaluated is Ecotropic Viral Integration Site 5 (EVI5). EVI5 is a common site of retroviral integration with a possible role in T-cell lymphomagenesis. METHODS: In the current study, we aimed to confirm association of the single nucleotide polymorphisms (SNPs) within EVI5 gene with MS in 410 relapsing-remitting MS patients and 410 controls from Iranian population...
November 2017: Multiple Sclerosis and related Disorders
https://www.readbyqxmd.com/read/29141648/polymorphisms-at-microrna-binding-sites-of-ara-c-and-anthracyclines-metabolic-pathway-genes-are-associated-with-outcome-of-acute-myeloid-leukemia-patients
#12
Hai-Xia Cao, Chao-Feng Miao, Liang Yan, Ping Tang, Li-Rong Zhang, Ling Sun
BACKGROUND: Gene polymorphisms at microRNA-binding sites (poly-miRTS) may affect gene transcription and expression through miRNA regulation, which is associated with cancer susceptibility, sensitivity to chemotherapy and prognosis. This study investigated the association between poly-miRTS of Ara-C/anthracycline metabolic pathways genes and the outcome of acute myeloid leukemia (AML) in Chinese patients after Ara-C-based chemotherapy. METHODS: A total of 17 poly-miRTS were selected from the SNPinfo Web Server and genotyped in 206 Chinese Han non-FAB-M3 AML patients using the SEQUENOM Mass-ARRAY system...
November 15, 2017: Journal of Translational Medicine
https://www.readbyqxmd.com/read/29141248/association-of-functional-genetic-variants-of-hotair-with-hepatocellular-carcinoma-hcc-susceptibility-in-a-chinese-population
#13
Hao Li, Xian-Mei Tang, Yangchen Liu, Weizhen Li, Qiaoyun Chen, Yan Pan
BACKGROUND/AIMS: The HOX transcript antisense intergenic RNA (HOTAIR), a long non-coding RNA (lncRNA), plays an important role in the pathogenesis and progression of multiple tumors. The aim of the present study was to evaluate whether common single nucleotide polymorphisms (SNPs) in HOTAIR are related to hepatocellular carcinoma (HCC) susceptibility in a Chinese population. METHODS: We genotyped three SNPs of HOTAIR in a hepatocellular carcinoma (HCC) case-control study, including 482 cases and 520 control subjects...
November 15, 2017: Cellular Physiology and Biochemistry
https://www.readbyqxmd.com/read/29141033/transcriptome-profiling-of-claw-muscle-of-the-mud-crab-scylla-paramamosain-at-different-fattening-stages
#14
Qingling Jiang, Chenchang Bao, Ya'nan Yang, An Liu, Fang Liu, Huiyang Huang, Haihui Ye
In crustaceans, muscle growth and development is complicated, and to date substantial knowledge gaps exist. In this study, the claw muscle, hepatopancreas and nervous tissue of the mud crab (Scylla paramamosain) were collected at three fattening stages for sequence by the Illumina sequencing. A total of 127.87 Gb clean data with no less than 3.94 Gb generated for each sample and the cycleQ30 percentages were more than 86.13% for all samples. De Bruijn assembly of these clean data produced 94,853 unigenes, thereinto, 50,059 unigenes were found in claw muscle...
2017: PloS One
https://www.readbyqxmd.com/read/29140910/polygenic-profile-and-exercise-induced-muscle-damage-by-a-competitive-half-ironman
#15
Juan Del Coso, Juan J Salinero, Beatriz Lara, César Gallo-Salazar, Francisco Areces, David Herrero, Carlos Puente
Del Coso, J, Salinero, JJ, Lara, B, Gallo-Salazar, C, Areces, F, Herrero, D, and Puente, C. Polygenic profile and exercise-induced muscle damage by a competitive half-ironman. J Strength Cond Res XX(X): 000-000, 2017-To date, it is still unknown why some individuals develop higher levels of muscle damage than other individuals, despite participating in exercise with comparable levels of physical intensity. The aim of this investigation was to analyze 7 single-nucleotide polymorphisms (SNPs) that are candidates to explain individual variations in the level of muscle damage attained during a half-ironman competition...
November 14, 2017: Journal of Strength and Conditioning Research
https://www.readbyqxmd.com/read/29140583/association-study-of-ndst3-gene-for-schizophrenia-bipolar-disorder-major-depressive-disorder-in-the-han-chinese-population
#16
Lin Wang, Jianhua Chen, Zhiqiang Li, Weiming Sun, Boyu Chen, Sining Li, Weidong Li, Dajiang Lu, Yonggang Wang, Yongyong Shi
The NDST3 gene at 4q26 was a functional candidate gene for mental disorders. Recently, a novel genome-wide significant risk locus at chromosome 4q26 was identified and the top single nucleotide polymorphism rs11098403 in the vicinity of NDST3 gene was reported to confer risk of schizophrenia in Caucasian. Nevertheless, association between NDST3 gene polymorphisms and schizophrenia, bipolar disorder, or major depressive disorders has not been well studied in the Han Chinese population. To further investigate whether NDST3 is a risk gene for these mental disorders, we genotyped and analyzed eight tag SNPs (rs11098403, rs10857057, rs2389521, rs4833564, rs6837896, rs7689157, rs3817274, rs609512) covering NDST3 gene in 1,248 schizophrenia cases, 1,056 major depression cases, 1,344 bipolar disorder cases, and 1,248 controls of Chinese origin...
November 15, 2017: American Journal of Medical Genetics. Part B, Neuropsychiatric Genetics
https://www.readbyqxmd.com/read/29140561/interaction-among-smoking-status-single-nucleotide-polymorphisms-and-markers-of-systemic-inflammation-in-healthy-individuals
#17
Thitiya Luetragoon, Lars Erik Rutqvist, Orathai Tangvarasittichai, Bengt-Åke Andersson, Sture Löfgren, Kanchana Usuwanthim, Nongnit Laytragoon Lewin
Cigarette smoke contains toxic and carcinogenic substances that contribute to the development of cancer and various diseases. Genetic variation might be important because not all smokers develop smoking-related disease. The current study addressed the possible interactions among selected single nucleotide polymorphisms (SNPs) in genes related to systemic inflammation, smoking status, the levels of circulating immune response cells and plasma biomarkers of systemic inflammation. Sixty-four healthy blood donors were recruited, of whom 31 were current smokers and 33 were never-users of tobacco products, references...
November 15, 2017: Immunology
https://www.readbyqxmd.com/read/29138579/association-of-gemin4-gene-polymorphism-and-the-risk-of-cancer-a-meta-analysis
#18
Nan Wu, Xiaowei Zhang, Jinlong Tian, Shuang Yu, Ying Qiao
Gem-associated protein 4 (GEMIN4) gene is a key regulator for the miRNA biogenesis processes. Recent studies have demonstrated that some single-nucleotide polymorphisms (SNPs) in GEMIN4 gene are associated with the risk of cancer, but the results are still controversial. Therefore, we conducted a meta-analysis to analyze the association between three major SNPs (rs2740348, rs7813, and rs3744741) in the GEMIN4 gene and the risk of cancer. Relevant articles were searched in Web of Science, PubMed, Cochrane Library, Chinese Wan Fang, and Chinese National Knowledge Infrastructure databases...
2017: OncoTargets and Therapy
https://www.readbyqxmd.com/read/29138238/a-resource-for-the-allele-specific-analysis-of-dna-methylation-at-multiple-genomically-imprinted-loci-in-mice
#19
Jadiel A Wasson, Onur Birol, David J Katz
Genomically imprinted loci are expressed mono-allelically dependent upon the parent of origin. Their regulation not only illuminates how chromatin regulates gene expression but also how chromatin can be reprogrammed every generation. Because of their distinct parent of origin regulation, analysis of imprinted loci can be difficult. Single nucleotide polymorphisms (SNPs) are required to accurately assess these elements allele-specifically. However, publicly available SNP databases lack robust verification, making analysis of imprinting difficult...
November 14, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/29137622/genome-wide-scan-for-runs-of-homozygosity-identifies-potential-candidate-genes-associated-with-local-adaptation-in-valle-del-belice-sheep
#20
Salvatore Mastrangelo, Marco Tolone, Maria T Sardina, Gianluca Sottile, Anna M Sutera, Rosalia Di Gerlando, Baldassare Portolano
BACKGROUND: Because very large numbers of single nucleotide polymorphisms (SNPs) are now available throughout the genome, they are particularly suitable for the detection of genomic regions where a reduction in heterozygosity has occurred and they offer new opportunities to improve the accuracy of inbreeding ([Formula: see text]) estimates. Runs of homozygosity (ROH) are contiguous lengths of homozygous segments of the genome where the two haplotypes inherited from the parents are identical...
November 14, 2017: Genetics, Selection, Evolution: GSE
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