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Single nucleotide polymorphisms (SNPs)

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https://www.readbyqxmd.com/read/28329314/sirt1-polymorphisms-and-serum-induced-sirt1-protein-expression-in-aging-and-frailty-the-champ-study
#1
Shajjia Razi, Victoria C Cogger, Marina Kennerson, Vicky L Benson, Aisling C McMahon, Fiona M Blyth, David J Handelsman, Markus J Seibel, Vasant Hirani, Vasikaran Naganathan, Louise Waite, Rafael de Cabo, Robert G Cumming, David G Le Couteur
The nutrient sensing protein, SIRT1 influences aging and nutritional interventions such as caloric restriction in animals, however, the role of SIRT1 in human aging remains unclear. Here, the role of SIRT1 single-nucleotide polymorphisms (SNPs) and serum-induced SIRT1 protein expression (a novel assay that detects circulating factors that influence SIRT1 expression in vitro) were studied in the Concord Health and Ageing in Men Project (CHAMP), a prospective cohort of community dwelling men aged 70 years and older...
March 14, 2017: Journals of Gerontology. Series A, Biological Sciences and Medical Sciences
https://www.readbyqxmd.com/read/28329290/association-of-btbd9-and-map2k5-skor1-with-restless-legs-syndrome-in-chinese-population
#2
Gen Li, Huidong Tang, Cheng Wang, Xuemei Qi, Jie Chen, Shengdi Chen, Jianfang Ma
Objective: The aim of the study was to investigate the relationship between genetic factors and primary restless legs syndrome (RLS) in Chinese population. Methods: Totally, 116 RLS patients and 200 controls were recruited and the diagnosis of RLS was based on the criteria of International RLS Study Group. Polymer chain reaction (PCR) and sequencing were used to detect 19 single nucleotide polymorphisms (SNPs) in six genetic loci (MEIS1, BTBD9, PTPRD, MAP2K5/SKOR1, TOX3, and Intergenic region of 2p14)...
February 24, 2017: Sleep
https://www.readbyqxmd.com/read/28328985/construction-and-evaluation-of-a-high-density-snp-array-for-the-pacific-oyster-crassostrea-gigas
#3
Haigang Qi, Kai Song, Chunyan Li, Wei Wang, Busu Li, Li Li, Guofan Zhang
Single nucleotide polymorphisms (SNPs) are widely used in genetics and genomics research. The Pacific oyster (Crassostrea gigas) is an economically and ecologically important marine bivalve, and it possesses one of the highest levels of genomic DNA variation among animal species. Pacific oyster SNPs have been extensively investigated; however, the mechanisms by which these SNPs may be used in a high-throughput, transferable, and economical manner remain to be elucidated. Here, we constructed an oyster 190K SNP array using Affymetrix Axiom genotyping technology...
2017: PloS One
https://www.readbyqxmd.com/read/28328959/kras-and-vegf-gene-3-utr-single-nucleotide-polymorphisms-predicted-susceptibility-in-colorectal-cancer
#4
Minnan Yang, Xiuli Xiao, Xiaorui Xing, Xin Li, Tian Xia, Hanan Long
Single nucleotide polymorphisms (SNPs) in tumor-related genes have been reported to play important roles in cancer development. Recent studies have shown that 3'-untranslated regions (UTR) polymorphisms are associated with the occurrence and prognosis of cancers. The aim of this study is to analyze the association between KRAS and VEGF gene 3'-UTR SNPs and genetic susceptibility to colorectal cancer (CRC). In this case-control study of 371 CRC cases and 246 healthy controls, we analyzed the association between one SNP (rs1137188G > A) in the KRAS gene and four SNPs (rs3025039C > T, rs3025040C > T, rs3025053G > A and rs10434A > G) in the VEGF gene and CRC susceptibility by the improved multiplex ligase detection reaction (iMLDR) method...
2017: PloS One
https://www.readbyqxmd.com/read/28327790/association-of-nr1i2-gene-polymorphisms-and-time-of-progression-to-aids
#5
Rúbia Marília de Medeiros, Carolina Fialho Menti, Jéssica Louise Benelli, Maria Cristina Cotta Matte, Marineide Gonçalves de Melo, Sabrina Esteves de Matos Almeida, Marilu Fiegenbaum
BACKGROUND: The time of progression towards AIDS can vary greatly among seropositive patients, and may be associated with host genetic variation. The NR1I2 (PXR) gene, a ligand-activated transcription factor, regulates the transcription immune pathway genes and can therefore be targets of viral replication mechanisms influencing time of progression to AIDS. OBJECTIVE: To verify the association of single nucleotide polymorphisms (SNPs) rs3814057, rs6785049, rs7643645, and rs2461817 in the NR1I2 (PXR) gene with progression to AIDS in HIV-1 infected patients...
April 2017: Memórias do Instituto Oswaldo Cruz
https://www.readbyqxmd.com/read/28327672/tox-and-adipoq-gene-polymorphisms-are-associated-with-antipsychotic-induced-weight-gain-in-han-chinese
#6
Shen Li, Chengai Xu, Yuan Tian, Xueshi Wang, Rui Jiang, Miaomiao Zhang, Lili Wang, Guifu Yang, Ying Gao, Chenyu Song, Yukun He, Ying Zhang, Jie Li, Wei-Dong Li
To find the genetic markers related to the antipsychotic-induced weight gain (AIWG), we analyzed associations among candidate gene single-nucleotide polymorphisms (SNPs) and quantitative traits of weight changes and lipid profiles in a Chinese Han population. A total of 339 schizophrenic patients, including 86 first-episode patients (FEPs), meeting the entry criteria were collected. All patients received atypical antipsychotic drug monotherapy and hospitalization and were followed for 12 weeks. Forty-three SNPs in 23 candidate genes were calculated for quantitative genetic association with AIWG, performed by PLINK...
March 22, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28326544/personalized-genetics-of-the-cholinergic-blockade-of-neuroinflammation
#7
REVIEW
Alon Simchovitz, Michael T Heneka, Hermona Soreq
Acetylcholine signaling is essential for cognitive functioning and blocks inflammation. To maintain homeostasis, cholinergic signaling is subjected to multi-leveled and bidirectional regulation by both proteins and non-coding microRNAs ('CholinomiRs'). CholinomiRs coordinate the cognitive and inflammatory aspects of cholinergic signaling by targeting major cholinergic transcripts including the acetylcholine hydrolyzing enzyme acetylcholinesterase (AChE). Notably, AChE inhibitors are the only currently approved line of treatment for Alzheimer's disease patients...
March 21, 2017: Journal of Neurochemistry
https://www.readbyqxmd.com/read/28326452/methyleugenol-dna-adducts-in-human-liver-are-associated-with-sult1a1-copy-number-variations-and-expression-levels
#8
Roman Tremmel, Kristin Herrmann, Wolfram Engst, Walter Meinl, Kathrin Klein, Hansruedi Glatt, Ulrich M Zanger
Methyleugenol is a rodent hepatocarcinogen occurring in many herbs and spices as well as essential oils used for flavoring. Following metabolic activation by cytochromes P450 (CYPs) and sulfotransferases (SULTs), methyleugenol can form DNA adducts. Previously, we showed that DNA adduct formation by methyleugenol in mouse liver is dependent on SULT1A1 expression and that methyleugenol DNA adducts are abundant in human liver specimens. In humans, SULT1A1 activity is affected by genetic polymorphisms, including single-nucleotide polymorphisms (SNPs) and copy number variations (CNVs)...
March 22, 2017: Archives of Toxicology
https://www.readbyqxmd.com/read/28325924/genome-wide-association-analysis-identifies-loci-governing-mercury-accumulation-in-maize
#9
Zhan Zhao, Zhongjun Fu, Yanan Lin, Hao Chen, Kun Liu, Xiaolong Xing, Zonghua Liu, Weihua Li, Jihua Tang
Owing to the rapid development of urbanisation and industrialisation, heavy metal pollution has become a widespread environmental problem. Maize planted on mercury (Hg)-polluted soil can absorb and accumulate Hg in its edible parts, posing a potential threat to human health. To understand the genetic mechanism of Hg accumulation in maize, we performed a genome-wide association study using a mixed linear model on an association population consisting of 230 maize inbred lines with abundant genetic variation. The order of relative Hg concentrations in different maize tissues was as follows: leaves > bracts > stems > axes > kernels...
March 21, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28324009/whole-exome-sequencing-for-diagnosis-of-turner-syndrome-towards-next-generation-sequencing-and-newborn-screening
#10
David R Murdock, Frank X Donovan, Settara C Chandrasekharappa, Nicole Banks, Carolyn Bondy, Maximilian Muenke, Paul Kruszka
Context, Objectives: Turner syndrome (TS) is due to a complete or partial loss of an X chromosome in females and is not currently part of newborn screening. Diagnosis is often delayed resulting in missed crucial diagnostic and therapeutic opportunities. This study sought to determine if whole-exome sequencing (WES) as part of a potential newborn screening program could be used to diagnose TS. Design, Setting, Patients: Karyotype, chromosomal microarray, and WES were performed on women with TS (n=27) enrolled in the Personalized Genomic Research study at the National Institutes of Health...
January 24, 2017: Journal of Clinical Endocrinology and Metabolism
https://www.readbyqxmd.com/read/28323863/discovery-of-genome-widesnps-by-rad-seqand-the-genetic-diversity-of-captive-hog-deer-axis-porcinus
#11
Wei Wang, Huijuan Yan, Jianqiu Yu, Jun Yi, Yu Qu, Maozhong Fu, Ang Chen, Hui Tang, Lili Niu
The hog deer (Axis porcinus) is a small deer whose natural habitat is the wet or moist tall grasslands in South and Southeast Asia. Wild populations have dramatically decreased in recent decades. While wild hog deer were recently acknowledged to be extinct in China, a few captive populations have been maintained. In the present study, we successfully employed the restriction-site-associated DNA sequencing (RAD-seq) technique to generate a genome-wide profile of single-nucleotide polymorphisms (SNPs) in the captive population of hog deer from Chengdu Zoo, China (N = 11)...
2017: PloS One
https://www.readbyqxmd.com/read/28323555/influence-of-dopamine-related-genes-on-neurobehavioral-recovery-after-traumatic-brain-injury-during-early-childhood
#12
Amery Treble-Barna, Shari L Wade, Lisa J Martin, Valentina Pilipenko, Keith Owen Yeates, H Gerry Taylor, Brad G Kurowski
The present study examined the association of dopamine-related genes with short- and long-term neurobehavioral recovery, as well as neurobehavioral recovery trajectories over time, in children who had sustained early childhood traumatic brain injuries (TBI) relative to children who had sustained orthopedic injuries (OI). Participants were recruited from a prospective, longitudinal study evaluating outcomes of children who sustained a TBI (n = 68) or OI (n = 72) between the ages of 3 and 7 years. Parents completed ratings of child executive function and behavior at the immediate post-acute period (0-3 months after injury); 6, 12, and 18 months after injury; and an average of 3...
March 21, 2017: Journal of Neurotrauma
https://www.readbyqxmd.com/read/28323184/associations-of-endothelin-polymorphisms-and-aneurysm-size-at-the-time-of-rupture
#13
Philipp Hendrix, Paul M Foreman, Robert M Starke, Mark R Harrigan, Winfield S Fisher, Nilesh A Vyas, Robert H Lipsky, Minkuan Lin, Beverly C Walters, R Shane Tubbs, Mohammadali M Shoja, Jean-Francois Pittet, Mali Mathru, Christoph J Griessenauer
BACKGROUND: and Purpose: Aneurysm size is an important risk factor for aneurysm rupture. The pathophysiological mechanisms underlying aneurysm growth remain poorly understood. Endothelin signaling is critical for cerebrovascular blood flow regulation. The influence of endothelin single nucleotide polymorphisms (SNPs) on aneurysm size at the time of rupture has not been previously investigated. METHODS: Eight common endothelin SNPs were assessed using blood samples from aneurysmal subarachnoid hemorrhage (aSAH) patients enrolled in the CARAS (Cerebral Aneurysm Renin Angiotensin System) study...
March 16, 2017: World Neurosurgery
https://www.readbyqxmd.com/read/28323053/species-delimitation-and-phylogenetic-reconstruction-of-the-sinipercids-perciformes-sinipercidae-based-on-target-enrichment-of-thousands-of-nuclear-coding-sequences
#14
Shuli Song, Jinliang Zhao, Chenhong Li
The sinipercids are freshwater fishes endemic to East Asia, mainly in China. Phylogenetic studies on the sinipercids have made great progress in the last decades, but interspecific relationships and evolutionary history of the sinipercids remain unresolved. Lack of distinctive morphological characters leads to problems in validating of some species, such as Siniperca loona. Moreover, genetic data are needed to delimitate species pairs with explicit hypothesis testing, such as in S. chuatsi vs. S. kneri and Coreoperca whiteheadi vs...
March 17, 2017: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/28323001/dna-methyltransferase-1-rs16999593-genetic-polymorphism-decreases-risk-in-patients-with-transposition-of-great-arteries
#15
Liming Lei, Haoming Lin, Shilong Zhong, Zhiwei Zhang, Jimei Chen, Xiyong Yu, Xiaoqing Liu, Cheng Zhang, Zhiqiang Nie, Jian Zhuang
Complete transposition of the great arteries (TGA) is the most frequent cyanotic heart defect diagnosed in neonates. However, the exact etiology of TGA is unknown. The aim of the present study was to assess the association of TGA pathogenesis with single nucleotide polymorphisms (SNPs) in DNA methyltransferases (DNMTs)-1 and 3a- in Chinese children. We genotyped 5 SNPs (rs16999593, rs16999358, and rs2228611 in DNMT1; and rs2276599 and rs2276598 in DNMT3A) in 206 patients with complete TGA and 252 healthy children...
March 16, 2017: Gene
https://www.readbyqxmd.com/read/28322508/the-influence-of-ampk-subunit-alpha-2-prkaa2-genetic-polymorphisms-with-susceptibility-with-type-2-diabetes-mellitus-and-diabetic-nephropathy-in-chinese-population
#16
Qingchu Li, Cuilin Li, Haoyun Li, Liu Zeng, Zhiqiang Kang, Yu Mao, Xinyue Tang, Panpan Zheng, Li He, Fang Luo, Zhi Li
BACKGROUND: It has been well recognized that the AMP-activated protein kinase (AMPK) is a key factor influencing the development of type 2 diabetes mellitus (T2DM). The single-nucleotide polymorphism (SNP) rs2746342 in AMPK α2 subunit gene (PRKAA2) has been found to be associated with the susceptibility to T2DM in the Chinese Han population recently. This study further investigates the association of PRKAA2 genotypes with the susceptibility to T2DM and its complication disease, diabetic nephropathy...
March 21, 2017: Journal of Diabetes
https://www.readbyqxmd.com/read/28321907/systematical-analyses-of-variants-in%C3%A2-dnase-i-hypersensitive-sites-identified-two-novel-hepatocellular-carcinoma-susceptibility-loci-among-chinese-population
#17
Tao Jiang, Fangzhi Du, Na Qin, Qun Lu, Juncheng Dai, Hongbing Shen, Zhibin Hu
BACKGROUND AND AIM: Although several variants located at coding and non-coding regions were evaluated by previous studies, the evidence for associations between variants located in DNase I-hypersensitive sites (DHSs) and hepatocellular carcinoma (HCC) risk was still limited. Recent advances using ENCODE data indicated that genetic variants in DHSs played an important role in carcinogenesis. Therefore, systematically investigate the associations between regulatory variants in DHSs and HCC risk should be put on the agenda...
March 20, 2017: Journal of Gastroenterology and Hepatology
https://www.readbyqxmd.com/read/28321828/genome-wide-association-analysis-tracks-bacterial-leaf-blight-resistance-loci-in-rice-diverse-germplasm
#18
Christine Jade Dilla-Ermita, Erwin Tandayu, Venice Margarette Juanillas, Jeffrey Detras, Dennis Nicuh Lozada, Maria Stefanie Dwiyanti, Casiana Vera Cruz, Edwige Gaby Nkouaya Mbanjo, Edna Ardales, Maria Genaleen Diaz, Merlyn Mendioro, Michael J Thomson, Tobias Kretzschmar
BACKGROUND: A range of resistance loci against different races of Xanthomonas oryzae pv. oryzae (Xoo), the pathogen causing bacterial blight (BB) disease of rice, have been discovered and characterized. Several have been deployed in modern varieties, however, due to rapid evolution of Xoo, a number have already become ineffective. The continuous "arms race" between Xoo and rice makes it imperative to discover new resistance loci to enable durable deployment of multiple resistance genes in modern breeding lines...
December 2017: Rice
https://www.readbyqxmd.com/read/28320417/impaired-human-immunodeficiency-virus-type-1-replicative-fitness-in-atypical-viremic-non-progressor-individuals
#19
Jan Weber, Richard M Gibson, Lenka Sácká, Dmytro Strunin, Jan Hodek, Jitka Weberová, Marcela Pávová, David J Alouani, Robert Asaad, Benigno Rodriguez, Michael M Lederman, Miguel E Quiñones-Mateu
BACKGROUND: Progression rates from initial HIV-1 infection to advanced AIDS vary significantly among infected individuals. A distinct subgroup of HIV-1-infected individuals-termed viremic non-progressors (VNP) or controllers-do not seem to progress to AIDS, maintaining high CD4(+) T cell counts despite high levels of viremia for many years. Several studies have evaluated multiple host factors, including immune activation, trying to elucidate the atypical HIV-1 disease progression in these patients; however, limited work has been done to characterize viral factors in viremic controllers...
March 20, 2017: AIDS Research and Therapy
https://www.readbyqxmd.com/read/28320398/single-nucleotide-polymorphisms-in-the-cd40-gene-associate-with-the-disease-susceptibility-and-severity-in-knee-osteoarthritis-in-the-chinese-han-population-a-case-control-study
#20
Zhen-Han Deng, Ming-Hua Sun, Yu-Sheng Li, Wei Luo, Fang-Jie Zhang, Jian Tian, Ping Wu, Wen-Feng Xiao
BACKGROUND: This study explored the association between single nucleotide polymorphisms (SNPs) in the CD40 gene, rs4810485 G > T and rs1883832 C > T, as well as disease susceptibility and severity in knee osteoarthritis (KOA) in the Chinese Han population. METHOD: Peripheral venous blood was collected from 133 KOA patients (KOA group) and 143 healthy people (control group) from December 2012 to November 2013. The patients in the KOA group were classified into mild, moderate and severe groups according to disease severity...
March 21, 2017: BMC Musculoskeletal Disorders
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