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Single nucleotide polymorphisms (SNPs)

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https://www.readbyqxmd.com/read/28433457/spatial-and-temporal-expression-patterns-of-genes-around-nine-neuroticism-associated-loci
#1
Kazutaka Ohi, Takamitsu Shimada, Toshiki Yasuyama, Kohei Kimura, Takashi Uehara, Yasuhiro Kawasaki
Neuroticism is a high-order personality trait. Individuals with higher neuroticism have increased risks of various psychiatric disorders and physical health outcomes. Neuroticism is related to physiological differences in the brain. A recent genome-wide association study identified nine distinct genomic loci that contribute to neuroticism. Brain development and function depend on the precise regulation of gene expression, which is differentially regulated across brain regions and developmental stages. Using multiple publicly available human post-mortem databases, we investigated, in brain and non-brain tissues and across several developmental life stages, the spatial and temporal expression patterns of genes arising from nine neuroticism-associated loci...
April 19, 2017: Progress in Neuro-psychopharmacology & Biological Psychiatry
https://www.readbyqxmd.com/read/28431990/a-common-polymorphism-decreases-lrp1-mrna-stability-and-is-associated-with-increased-plasma-factor-viii-levels
#2
Jiann-Der Lee, Kuang-Ming Hsiao, Pey-Jium Chang, Chih-Cheng Chen, Ya-Wen Kuo, Yen-Chu Huang, Huan-Lin Hsu, Ya-Hui Lin, Chih-Ying Wu, Ying-Chih Huang, Meng Lee, Chia-Yu Hsu, Yi-Ting Pan, Chih-Yu Kuo, Chun-Hsien Lin
The low-density lipoprotein receptor-related protein 1 (LRP1) gene is associated with increased levels of plasma factor VIII (FVIII). We aimed to explore eight functional genetic LRP1 variants for their potential roles in regulating FVIII levels and acute ischemic stroke (AIS). This genetic association study enrolled 192 patients with AIS and 134 controls. There were no significant differences in the genetic frequency of the eight functional single-nucleotide polymorphisms (SNPs) between the control and AIS groups...
April 18, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28431642/pcr-based-detection-methods-for-single-nucleotide-polymorphism-or-mutation-real-time-pcr-and-its-substantial-contribution-toward-technological-refinement
#3
Kazuyuki Matsuda
Single-nucleotide polymorphisms (SNPs) and single-nucleotide mutations result from the substitution of only a single base. The SNP or mutation can be relevant to disease susceptibility, pathogenesis of disease, and efficacy of specific drugs. It is important to detect SNPs or mutations clinically. Methods to distinguish/detect SNPs or mutations should be highly specific and sensitive. In this regard, polymerase chain reaction (PCR) has provided the necessary analytical performance for many molecular analyses...
2017: Advances in Clinical Chemistry
https://www.readbyqxmd.com/read/28431615/association-between-ptgs1-polymorphisms-and-functional-outcomes-in-chinese-patients-with-stroke-during-aspirin-therapy-interaction-with-smoking
#4
Huan Cai, Biyang Cai, Lingli Sun, Hao Zhang, Shuyu Zhou, Liping Cao, Hongquan Guo, Wen Sun, Bernard Yan, Stephen M Davis, Zhizhong Zhang, Xinfeng Liu
PURPOSE: Prostaglandin-Endoperoxide Synthase 1 (PTGS1) and smoking may play important roles in aspirin nonresponsiveness, but the effect of their interaction on stroke outcomes remains largely unknown. We examined the effects of PTGS1 polymorphisms, smoking status, and their interaction on functional outcomes in a cohort of Chinese Han patients with stroke during aspirin therapy. METHODS: A total of 617 ischemic stroke patients taking aspirin were enrolled. Three single nucleotide polymorphisms (SNPs) rs1330344, rs3842788, and rs5788 in PTGS1 were determined for genotyping...
May 15, 2017: Journal of the Neurological Sciences
https://www.readbyqxmd.com/read/28430632/association-analysis-of-apo-gene-polymorphisms-with-ischemic-stroke-risk-a-case-control-study-in-a-chinese-han-population
#5
Rongjun Xiao, Shuaiqi Sun, Jiayi Zhang, Yongri Ouyang, Ning Zhang, Min Yang, Tianbo Jin, Ying Xia
This study aimed to assess the association of APO gene polymorphisms and ischemic stroke risk in a Chinese Han population. In this case-control study, we geno-typed 14 single nucleotide polymorphisms (SNPs) in 3 APO genes in 488 cases and 503 controls using Sequenom Mass-ARRAY technology and evaluated their association with ischemic stroke using the χ2 and genetic model analysis. In the allelic model analysis, we determined three SNPs were significantly associated with ischemic stroke: rs693 with a p value of 0...
February 20, 2017: Oncotarget
https://www.readbyqxmd.com/read/28430123/functional-analysis-of-the-rs774872314-rs116171003-rs200231898-and-rs201107751-polymorphisms-in-the-human-ror%C3%AE-t-gene-promoter-region
#6
Marcin Ratajewski, Marcin Słomka, Kaja Karaś, Marta Sobalska-Kwapis, Małgorzata Korycka-Machała, Anna Sałkowska, Jarosław Dziadek, Dominik Strapagiel, Jarosław Dastych
RAR-related orphan receptor gamma RORγT, a tissue-specific isoform of the RORC gene, plays a critical role in the development of naive CD4+ cells into fully differentiated Th17 lymphocytes. Th17 lymphocytes are part of the host defense against numerous pathogens and are also involved in the pathogenesis of inflammatory diseases, including autoimmune disorders. In this study, we functionally examined four naturally occurring polymorphisms located within one of the previously identified GC-boxes in the promoter region of the gene...
April 21, 2017: Genes
https://www.readbyqxmd.com/read/28429786/comprehensive-assessment-showed-no-associations-of-variants-at-the-slc10a1-locus-with-susceptibility-to-persistent-hbv-infection-among-southern-chinese
#7
Ying Zhang, Yuanfeng Li, Miantao Wu, Pengbo Cao, Xiaomin Liu, Qian Ren, Yun Zhai, Bobo Xie, Yanling Hu, Zhibin Hu, Jinxin Bei, Jie Ping, Xinyi Liu, Yinghua Yu, Bingqian Guo, Hui Lu, Guanjun Liu, Haitao Zhang, Ying Cui, Zengnan Mo, Hongbing Shen, Yi-Xin Zeng, Fuchu He, Hongxing Zhang, Gangqiao Zhou
The sodium taurocholate cotransporting polypeptide (NTCP) encoded by SLC10A1 was recently demonstrated to be a functional receptor for hepatitis B virus (HBV). The role of SLC10A1 polymorphisms, particularly the Ser267Phe variant (rs2296651) in exon 4, has been frequently investigated in regard to risk of persistent HBV infection. However, these investigations have generated conflicting results. To examine whether common genetic variation at the SLC10A1 locus is associated with risk of persistent HBV infection, haplotype-tagging and imputed single nucleotide polymorphisms (SNPs) were assessed in two case-control sample sets, totally including 2,550 cases (persistently HBV infected subjects, PIs) and 2,124 controls (spontaneously recovered subjects, SRs) of Southern Chinese ancestry...
April 21, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28428839/population-genomics-meet-lagrangian-simulations-oceanographic-patterns-and-long-larval-duration-ensure-connectivity-among-paracentrotus-lividus-populations-in-the%C3%A2-adriatic-and-ionian-seas
#8
Marta Paterno, Marcello Schiavina, Giorgio Aglieri, Jamila Ben Souissi, Elisa Boscari, Renato Casagrandi, Aurore Chassanite, Mariachiara Chiantore, Leonardo Congiu, Giuseppe Guarnieri, Claudia Kruschel, Vesna Macic, Ilaria A M Marino, Chiara Papetti, Tomaso Patarnello, Lorenzo Zane, Paco Melià
Connectivity between populations influences both their dynamics and the genetic structuring of species. In this study, we explored connectivity patterns of a marine species with long-distance dispersal, the edible common sea urchin Paracentrotus lividus, focusing mainly on the Adriatic-Ionian basins (Central Mediterranean). We applied a multidisciplinary approach integrating population genomics, based on 1,122 single nucleotide polymorphisms (SNPs) obtained from 2b-RAD in 275 samples, with Lagrangian simulations performed with a biophysical model of larval dispersal...
April 2017: Ecology and Evolution
https://www.readbyqxmd.com/read/28427438/canine-%C3%AE-defensin-1-cbd1-gene-as-a-possible-marker-for-leishmania-infantum-infection-in-dogs
#9
Lidiane Gomes da Silva, César Raimundo Lima Costa-Júnior, Carlos Alberto Santiago Figueiredo-Júnior, Tereza Cristina Leal-Balbino, Sergio Crovella, Domenico Otranto, Valdir de Queiroz Balbino, Filipe Dantas-Torres
BACKGROUND: Canine leishmaniasis caused by Leishmania infantum is a parasitic disease of great veterinary significance. Some dogs infected by L. infantum may mount a strong cellular immune response and clear the infection, while others may respond with exaggerated antibody production against the parasite and develop an overt disease, which may be fatal, if left untreated. The initial factors triggering the polarization of the immune response towards a predominantly T-helper 1 or T-helper 2 cytokines, as well as the markers of resistance and susceptibility to L...
April 20, 2017: Parasites & Vectors
https://www.readbyqxmd.com/read/28427360/association-of-novel-polymorphisms-in-tmem39a-gene-with-systemic-lupus-erythematosus-in-a-chinese-han-population
#10
Xinze Cai, Wenyue Huang, Xudong Liu, Lining Wang, Yi Jiang
BACKGROUND: This study aimed to assess the association between 14 single nucleotide polymorphisms (SNPs) in six genes (IRF8, TMEM39A, IKZF3, ORMDL3, GSDMB, and ZPBP2) and systemic lupus erythematosus (SLE) in a Chinese Han population sample. METHODS: We carried out a case-control study of 415 patients with SLE and 470 healthy controls without autoimmune disease or cancer. DNA for genetic analysis was isolated from the blood of all subjects using standard phenol-chloroform method...
April 20, 2017: BMC Medical Genetics
https://www.readbyqxmd.com/read/28427323/detection-of-qtl-for-traits-related-to-adaptation-to-sub-optimal-climatic-conditions-in-chickens
#11
Ching-Yi Lien, Michèle Tixier-Boichard, Shih-Wen Wu, Woei-Fuh Wang, Chen Siang Ng, Chih-Feng Chen
BACKGROUND: Growth traits can be used as indicators of adaptation to sub-optimal conditions. The current study aimed at identifying quantitative trait loci (QTL) that control performance under variable temperature conditions in chickens. METHODS: An F2 population was produced by crossing the Taiwan Country chicken L2 line (selected for body weight, comb area, and egg production) with an experimental line of Rhode Island Red layer R- (selected for low residual feed consumption)...
April 20, 2017: Genetics, Selection, Evolution: GSE
https://www.readbyqxmd.com/read/28427149/interaction-between-ppar-%C3%AE-and-sorl1-gene-with-late-onset-alzheimer-s-disease-in-chinese-han-population
#12
Hui Zhang, Wei Zheng, Linlin Hua, Yutong Wang, Jinfeng Li, Hongying Bai, Shanshan Wang, Mingyao Du, Xuelian Ma, Chunyang Xu, Xiaodong Li, Bin Gong, Yunliang Wang
AIMS: To investigate the impact of sortilin-related receptor 1 gene 1 (SORL1) and peroxisome proliferator activated receptor gamma (PPAR G) gene single nucleotide polymorphisms (SNPs), gene- gene and gene- environment interactions and haplotype on late-onset Alzheimer's disease (LOAD) risk. METHODS: Hardy-Weinberg equilibrium (HWE), haplotype analysis and pairwise linkage disequilibrium (LD) analysis were investigated by using SNPStats (available online at http://bioinfo...
February 25, 2017: Oncotarget
https://www.readbyqxmd.com/read/28426785/genome-wide-association-studies-identified-multiple-genetic-loci-for-body-size-at-four-growth-stages-in-chinese-holstein-cattle
#13
Xu Zhang, Qin Chu, Gang Guo, Ganghui Dong, Xizhi Li, Qin Zhang, Shengli Zhang, Zhiwu Zhang, Yachun Wang
The growth and maturity of cattle body size affect not only feed efficiency, but also productivity and longevity. Dissecting the genetic architecture of body size is critical for cattle breeding to improve both efficiency and productivity. The volume and weight of body size are indicated by several measurements. Among them, Heart Girth (HG) and Hip Height (HH) are the most important traits. They are widely used as predictors of body weight (BW). Few association studies have been conducted for HG and HH in cattle focusing on single growth stage...
2017: PloS One
https://www.readbyqxmd.com/read/28426731/effect-of-genetic-variation-in-microrna-binding-site-in-wnt1-inducible-signaling-pathway-protein-1-gene-on-oral-squamous-cell-carcinoma-susceptibility
#14
Hon-Kit Lau, Edie-Rosmin Wu, Mu-Kuan Chen, Ming-Ju Hsieh, Shun-Fa Yang, Lyu-Yao Wang, Ying-Erh Chou
BACKGROUND: Oral squamous cell carcinoma (OSCC), which is the most common head and neck cancer, accounts for 1%-2% of all human malignancies and is characterized by poor prognosis and reduced survival rates. WNT1-inducible signaling pathway protein 1 (WISP1), a cysteine-rich protein belonging to the Cyr61, CTGF, Nov (CCN) family of matricellular proteins, has many developmental functions and may be involved in carcinogenesis. This study investigated WISP1 single-nucleotide polymorphisms (SNPs) to elucidate OSCC susceptibility and clinicopathologic characteristics...
2017: PloS One
https://www.readbyqxmd.com/read/28426730/functional-genetic-variant-of-ww-domain-containing-oxidoreductase-wwox-gene-is-associated-with-hepatocellular-carcinoma-risk
#15
Hsiang-Lin Lee, Hsin-Lin Cheng, Yu-Fan Liu, Ming-Chih Chou, Shun-Fa Yang, Ying-Erh Chou
BACKGROUND: Hepatocellular carcinoma (HCC) is one of the most common malignant tumors worldwide. Human WW domain-containing oxidoreductase (WWOX) gene has been identified as a tumor suppressor gene in multiple cancers. We hypothesize that genetic variations in WWOX are associated with HCC risk. METHODOLOGY/PRINCIPAL FINDINGS: Five single-nucleotide polymorphisms (SNPs) of the WWOX gene were evaluated from 708 normal controls and 354 patients with HCC. We identified a significant association between a WWOX single nucleotide polymorphism (SNP), rs73569323, and decreased risk of HCC...
2017: PloS One
https://www.readbyqxmd.com/read/28425437/are-genetic-polymorphisms-in-the-renin-angiotensin-aldosterone-system-associated-with-essential-hypertension-evidence-from-genome-wide-association-studies
#16
REVIEW
L-D Ji, J-Y Li, B-B Yao, X-B Cai, Q-J Shen, J Xu
In candidate gene era, dozens of single-nucleotide polymorphisms (SNPs) within renin-angiotensin-aldosterone system (RAAS) have been reported to be significantly associated with hypertension. However, the unbiased genome-wide association studies (GWAS) rarely identified the SNPs within RAAS were associated with hypertension or blood pressure (BP) traits. In order to figure out whether genetic polymorphisms of RAAS are really associated with hypertension, we systemically searched the GWAS Catalogue and identified all the known RAAS genes and relevant diseases/traits...
April 20, 2017: Journal of Human Hypertension
https://www.readbyqxmd.com/read/28424560/an-exploratory-study-of-host-polymorphisms-in-genes-that-clinically-characterize-breast-cancer-tumors-and-pretreatment-cognitive-performance-in-breast-cancer-survivors
#17
Theresa A Koleck, Catherine M Bender, Beth Z Clark, Christopher M Ryan, Puja Ghotkar, Adam Brufsky, Priscilla F McAuliffe, Priya Rastogi, Susan M Sereika, Yvette P Conley
PURPOSE: Inspired by the hypothesis that heterogeneity in the biology of breast cancers at the cellular level may account for cognitive dysfunction symptom variability in survivors, the current study explored relationships between host single-nucleotide polymorphisms (SNPs) in 25 breast cancer-related candidate genes (AURKA, BAG1, BCL2, BIRC5, CCNB1, CD68, CENPA, CMC2, CTSL2, DIAPH3, ERBB2, ESR1, GRB7, GSTM1, MELK, MKI67, MMP11, MYBL2, NDC80, ORC6, PGR, RACGAP1, RFC4, RRM2, and SCUBE2), identified from clinically relevant prognostic multigene-expression profiles for breast cancer, and pretreatment cognitive performance...
2017: Breast Cancer: Targets and Therapy
https://www.readbyqxmd.com/read/28424495/significance-of-genetic-polymorphisms-in-long-non-coding-rna-ac079767-4-in-tuberculosis-susceptibility-and-clinical-phenotype-in-western-chinese-han-population
#18
Zhenzhen Zhao, Mei Zhang, Jun Ying, Xuejiao Hu, Jingya Zhang, Yanhong Zhou, Yi Zhou, Xingbo Song, Binwu Ying
Recent studies have implicated long non-coding RNA, AC079767.4, as a highly susceptible gene in tuberculosis. The aim of the study was to preliminarily explore the possible association of single nucleotide polymorphisms (SNPs) in AC079767.4 gene with clinical phenotypes and TB susceptibility in Western Chinese Han population. The improved multiplex ligation detection reaction (iMLDR) method was employed to genotype 4 SNPs in AC079767.4 in 554 tuberculosis patients and 561 healthy individuals. In subgroup analysis, only the C allele for rs12477677 was associated with the decreased susceptibility to pulmonary TB with a p-value of 0...
April 19, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28424481/the-first-genome-wide-association-study-identifying-new-susceptibility-loci-for-obstetric-antiphospholipid-syndrome
#19
Mayumi Sugiura-Ogasawara, Yosuke Omae, Minae Kawashima, Licht Toyo-Oka, Seik-Soon Khor, Hiromi Sawai, Tetsuya Horita, Tatsuya Atsumi, Atsuko Murashima, Daisuke Fujita, Tomio Fujita, Shinji Morimoto, Eriko Morishita, Shinji Katsuragi, Tamao Kitaori, Kinue Katano, Yasuhiko Ozaki, Katsushi Tokunaga
Antiphospholipid syndrome (APS) is the most important treatable cause of recurrent pregnancy loss. The live birth rate is limited to only 70-80% in patients with APS undergoing established anticoagulant therapy. Lupus anticoagulant (LA), but not anticardiolipin antibody (aCL), was found to predict adverse pregnancy outcome. Recent genome-wide association studies (GWAS) of APS focusing on aCL have shown that several molecules may be involved. This is the first GWAS for obstetric APS focusing on LA. A GWAS was performed to compare 115 Japanese patients with obstetric APS, diagnosed according to criteria of the International Congress on APS, and 419 healthy individuals...
April 20, 2017: Journal of Human Genetics
https://www.readbyqxmd.com/read/28424468/effect-of-handgrip-on-coronary-artery-disease-and-myocardial-infarction-a-mendelian-randomization-study
#20
Lin Xu, Yuan Tao Hao
Observational studies have reported an association of handgrip strength with risk of cardiovascular disease. However, residual confounding and reverse causation may have influenced these findings. A Mendelian randomization (MR) study was conducted to examine whether handgrip is causally associated with cardiovascular disease. Two single nucleotide polymorphisms (SNPs), rs3121278 and rs752045, were used as the genetic instruments for handgrip. The effect of each SNP on coronary artery disease/myocardial infarction (CAD/MI) was weighted by its effect on handgrip strength, and estimates were pooled to provide a summary measure for the effect of increased handgrip on risk of CAD/MI...
April 19, 2017: Scientific Reports
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