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Single nucleotide polymorphism

Sinead Toomey, Stephen F Madden, Simon J Furney, Yue Fan, Mark McCormack, Carragh Stapleton, Mattia Cremona, Gianpiero L Cavalleri, Malgorzata Milewska, Naomi Elster, Aoife Carr, Joanna Fay, Elaine W Kay, Susan Kennedy, John Crown, William M Gallagher, Bryan T Hennessy, Alex J Eustace
BACKGROUND: Trastuzumab treatment for women with HER2-positive breast cancer (BC) resulted in the significant improvement of both relapse free survival (RFS) and overall survival (OS). However, many women who are classified as HER2-positive do not respond. Many studies have focused on the role of somatic mutations rather than germline polymorphisms in trastuzumab resistance. RESULTS: We completed an Agena MassArray screen of 10 ERBB-family single nucleotide polymorphisms (SNPs) in 194 adjuvant trastuzumab treated HER2-positive BC patients...
October 20, 2016: Oncotarget
Sergey V Malov, Alexey Antonik, Minzhong Tang, Alexandre Berred, Yi Zeng, Stephen J O'Brien
A new approach for statistical association signal identification is developed in this paper. We consider a strategy for nonprecise signal identification by extending the well-known signal detection and signal identification methods applicable to the multiple testing problem. Collection of statistical instruments under the presented approach is much broader than under the traditional signal identification methods, allowing more efficient signal discovery. Further assessments of maximal value and average statistics in signal discovery are improved...
October 24, 2016: Biometrical Journal. Biometrische Zeitschrift
José Alcaraz-Quiles, Esther Titos, Mireia Casulleras, Marco Pavesi, Cristina López-Vicario, Bibiana Rius, Aritz Lopategi, Andrea de Gottardi, Ivo Graziadei, Henning Gronbaek, Pere Ginès, Mauro Bernardi, Vicente Arroyo, Joan Clària
: Acute-on-chronic liver failure (ACLF) in cirrhosis is an increasingly recognized syndrome characterized by acute decompensation, organ failure(s) and high short-term mortality. Recent findings suggest that an over-exuberant systemic inflammation plays a primary role in ACLF progression. In this study, we examined whether genetic factors shape systemic immune responses in patients with decompensated cirrhosis. Six single nucleotide polymorphisms (SNPs) in inflammation-related genes (IL-1β: rs1143623, IL-1ra: rs4251961, IL-10: rs1800871, SOCS3: rs4969170, NOD2: rs3135500 and CMKLR1: rs1878022) were genotyped in 279 cirrhotic patients with (n=178) and without (n=101) ACLF from the CANONIC study of the CLIF consortium...
October 24, 2016: Hepatology: Official Journal of the American Association for the Study of Liver Diseases
Y Liu, Z-X Zhang
OBJECTIVE: Precision medicine is a personalized disease prevention and treatment program combining modern genetic technology, molecular imaging techniques, and biological information with patients' living environment and clinical data, for accurate classification and diagnosis of diseases. CASE REPORT: Our study presents the case of a 7-year-old female patient with clinical manifestations of growth hormone (GH) deficiency. After treatment with recombinant human GH for 2 years, the patient showed a reduced growth rate...
October 2016: European Review for Medical and Pharmacological Sciences
Hongbo Chen, Yinan Yao, Yifan Wang, Hua Zhou, Tianxiang Xu, Jing Liu, Guocheng Wang, Yongfeng Zhang, Xiang Chen, Qingwei Liu, Peng Huang, Rongbin Yu
BACKGROUND: HLA-DM gene, which is related to antigen processing and presentation and located in the non-classical class-II region of human leukocyte antigen (HLA) region, may play a crucial role in chronic hepatitis C virus (HCV) infection treatment outcomes. The study was conducted to evaluate the role of the variant of several single nucleotide polymorphisms (SNPs) in HLA-DM gene in HCV treatment outcomes. METHODS: We genotyped four SNPs from the candidate genes (HLA-DMA and DMB) in 336 patients who were treated with pegylated interferon-alpha and ribavirin (PEG IFN-α/RBV)...
October 20, 2016: International Journal of Environmental Research and Public Health
Yu Lei, Meinan Wang, Anmin Wan, Chongjing Xia, Deven R See, Min Zhang, Xianming Chen
Puccinia striiformis causes stripe rust on wheat, barley, and grasses. Natural population studies have indicated that somatic recombination plays a possible role in P. striiformis variation. To determine if somatic recombination can occur, susceptible wheat or barley plants were inoculated with mixed urediniospores of paired isolates of P. striiformis. Progeny isolates were selected by passing through a series of inoculations of wheat or barley genotypes. Potential recombinant isolates were compared with the parental isolates on the set of 18 wheat and/or 12 barley genotypes that are used to differentiate races of P...
October 24, 2016: Phytopathology
X R Zhang, Y Zhang, F T Chen, Y Li, S S Zhang
A novel biosensor was developed based on the cation-exchange of CuS nanoparticles (NPs) and Cu(i)-based click chemistry of functionalized gold nanoparticles (AuNPs). As a proof-of-principle, novel applications of this method as a versatile biosensor for single-nucleotide polymorphisms (SNPs) and DNA methyltransferase (MTase) were presented.
October 24, 2016: Chemical Communications: Chem Comm
Handan Tan, Bolin Deng, Hongsong Yu, Yi Yang, Lin Ding, Qi Zhang, Jieying Qin, Aize Kijlstra, Rui Chen, Peizeng Yang
Interleukin-1 (IL-1) and the IL-1 receptor (IL-1R) family play an important role in the pathogenesis of inflammatory diseases. This study aimed to investigate the association between single nucleotide polymorphisms (SNP) of IL-1 and IL-1R family genes with Vogt-Koyanagi-Harada (VKH) and Behcet's disease (BD) in Han Chinese. The case-control study was divided into two stages and included 419 VKH cases, 1063 BD cases and 1872 healthy controls. The MassARRAY platform (Sequenom), iPLEX Gold Assay and TaqMan SNP assays were used to score genotypes of 24 SNPs...
October 24, 2016: Scientific Reports
Tatiana V Tatarinova, Evgeny Chekalin, Yuri Nikolsky, Sergey Bruskin, Dmitry Chebotarov, Kenneth L McNally, Nickolai Alexandrov
We analyzed functionality and relative distribution of genetic variants across the complete Oryza sativa genome, using the 40 million single nucleotide polymorphisms (SNPs) dataset from the 3,000 Rice Genomes Project (, the largest and highest density SNP collection for any higher plant. We have shown that the DNA-binding transcription factors (TFs) are the most conserved group of genes, whereas kinases and membrane-localized transporters are the most variable ones. TFs may be conserved because they belong to some of the most connected regulatory hubs that modulate transcription of vast downstream gene networks, whereas signaling kinases and transporters need to adapt rapidly to changing environmental conditions...
October 24, 2016: Scientific Reports
Ya-Li Liu, Dong-Fang Li, He-Ping Xu, Meng Xiao, Jing-Wei Cheng, Li Zhang, Zhi-Peng Xu, Xin-Xin Chen, Ge Zhang, Timothy Kudinha, Fanrong Kong, Yan-Ping Gong, Xin-Ying Wang, Yin-Xin Zhang, Hong-Long Wu, Ying-Chun Xu
Although previous studies have confirmed that 23S rRNA gene mutation could be responsible for most of macrolide resistance in M. catarrhalis, a recent study suggested otherwise. Next generation sequence based comparative genomics has revolutionized the mining of potential novel drug resistant mechanisms. In this study, two pairs of resistant and susceptible M. catarrhalis isolates with different multilocus sequence types, were investigated for potential differential genes or informative single nucleotide polymorphisms (SNPs)...
October 24, 2016: Scientific Reports
Steffen Grampp, James L Platt, Victoria Lauer, Rafik Salama, Franziska Kranz, Viviana K Neumann, Sven Wach, Christine Stöhr, Arndt Hartmann, Kai-Uwe Eckardt, Peter J Ratcliffe, David R Mole, Johannes Schödel
Clear cell renal cell carcinoma (ccRCC) is characterized by loss of function of the von Hippel-Lindau tumour suppressor (VHL) and unrestrained activation of hypoxia-inducible transcription factors (HIFs). Genetic and epigenetic determinants have an impact on HIF pathways. A recent genome-wide association study on renal cancer susceptibility identified single-nucleotide polymorphisms (SNPs) in an intergenic region located between the oncogenes MYC and PVT1. Here using assays of chromatin conformation, allele-specific chromatin immunoprecipitation and genome editing, we show that HIF binding to this regulatory element is necessary to trans-activate MYC and PVT1 expression specifically in cells of renal tubular origins...
October 24, 2016: Nature Communications
Soo Young Kim, Min Seok Hur, Byung Gon Choi, Min Jung Kim, Yang Won Lee, Yong Beom Choe, Kyu Joong Ahn
Psoriasis is a polygenic and multifactorial disease showing ethnic differences in terms of its severity and frequency. Therapies targeting interleukin 17A (IL-17A), interleukin 17 receptor (IL-17R), and Janus kinases (JAKs) are in clinical development for the treatment of psoriasis, and their success suggests the essential role of these molecules in psoriasis. To investigate the genetic susceptibility in T helper 17 (Th17) cell signal transduction pathways for promoting psoriasis, we performed candidate gene and linkage disequilibrium analysis...
October 24, 2016: Clinical and Experimental Immunology
Hena Naqvi, Mohammad Kaleem Ahmad, Syed Rizwan Hussain, Shalini Gupta, Mohammad Waseem, Abbas Ali Mahdi
BACKGROUND: Oral squamous cell carcinoma (OSCC) occurrence appears to be the number one among all cancers in India. Folate is a methyl donor during DNA methylation, as it provides substrate for methylenetetrahydrofolate reductase (MTHFR) to convert 5,10-MTHF to 5-MTHF and subsequently metabolizes it to methionine. The purpose of this study was to identify MTHFR C677T gene polymorphism in patients with OSCC. MATERIALS AND METHODS: A total of 350 OSCC cases and 350 healthy controls participated in this study...
October 24, 2016: Clinical Oral Investigations
Fangyuan Yin, Yuanyuan Ji, Jing Zhang, Hao Guo, Xin Huang, Jianghua Lai, Shuguang Wei
Previous studies suggested that the 5-hydroxytryptamine receptor 3B (HTR3B) is involved in heroin dependence by modulating dopamine (DA) release in the reward pathway and that the genetic polymorphisms in HTR3B play plausible role in modulating the risk of developing heroin addiction. To identify markers that contribute to the genetic susceptibility to heroin dependence, we examined the potential associations between heroin dependence and 7 single nucleotide polymorphisms (SNPs) of the HTR3B gene using multiplex SNaPshot technology in a Chinese Han population...
October 20, 2016: Neuroscience Letters
C Bickel, R B Schnabel, E Zengin, E Lubos, H Rupprecht, K Lackner, C Proust, D Tregouet, S Blankenberg, D Westermann, C Sinning
BACKGROUND AND AIMS: Whether single nucleotide polymorphisms (SNPs) of homocysteine metabolism enzymes influence the rate of cardiovascular (CV) events in coronary artery disease (CAD) patients remains controversial. METHODS AND RESULTS: In this analysis, 1126 subjects from the AtheroGene study with CAD and 332 control subjects without known CAD were included. The following SNPs were investigated: methylentetrahydrofolate reductase (MTHFR-C667T), methionin synthetase (MS-D919G), and cystathionin beta synthetase (CBS-I278T)...
September 17, 2016: Nutrition, Metabolism, and Cardiovascular Diseases: NMCD
Porcelli Stefano, Crisafulli Concetta, Donato Luigi, Calabrò Marco, Politis Antonis, Liappas Ioannis, Albani Diego, Atti Anna Rita, Salfi Raffaele, Raimondi Ilaria, Forloni Gianluigi, Papadimitriou George N, De Ronchi Diana, Serretti Alessandro
INTRODUCTION: With the increase of the population's average age, Alzheimer's disease (AD) is becoming one of the most disabling diseases worldwide. Recently, neurodevelopment processes have been involved in the AD etiopathogenesis. Genetic studies in this field could contribute to our knowledge and suggest new molecular targets for possible treatments. METHODS: Our primary aim was to investigate the associations among single nucleotide polymorphisms (SNPs) within neurodevelopment related genes (BDNF, ST8SIA2, C15orf32, NCAPG2, ESYT2, WDR60, LOC154822, VIPR2, GSK3B, NR1I2, ZNF804A, SP4) and AD...
November 15, 2016: Journal of the Neurological Sciences
Laila Y AlAyadhi, Jamil A Hashmi, Muhammad Iqbal, Alia M Albalawi, Mohammad I Samman, Nadra E Elamin, Shahid Bashir, Sulman Basit
Single nucleotide polymorphisms (SNP) - based genotyping using microarray platform is now frequently used to detect copy number variants (CNVs) in the human genome. Here, we report CNVs identified using Illumina HumanOmni 2.5 M oligonucleotide microarrays in 11 multiplex families with autism spectrum disorder (ASD) referred to Autism Research and Treatment Center (ART) and Madinah Maternity and Children Hospital (MMCH). Of the 11 families, 22 patients with ASD (all males) and their parents, were recruited for the present study...
October 19, 2016: Neuroscience
M Graff, A S Richardson, K L Young, A L Mazul, Heather Highland, K E North, K L Mohlke, L A Lange, E M Lange, K M Harris, P Gordon-Larsen
Little is known about how obesity susceptibility single nucleotide polymorphisms (SNPs) interact with moderate to vigorous physical activity (MVPA) in relation to BMI during adolescence, once obesogenic neighborhood factors are accounted for. In race stratified models, including European (EA; N=4977), African (AA; N=1726), and Hispanic Americans (HA; N=1270) from the National Longitudinal Study of Adolescent to Adult Health (1996; ages 12-21), we assessed the evidence for a SNPxMVPA interaction with BMI-for-age Z score, once accounting for obesogenic neighborhood factors including physical activity amenities, transportation and recreation infrastructure, poverty and crime...
October 20, 2016: Health & Place
H Toinét Cronjé, Cornelie Nienaber-Rousseau, Lizelle Zandberg, Tinashe Chikowore, Zelda de Lange, Tertia van Zyl, Marlien Pieters
Fibrinogen and its functional aspects have been linked to cardiovascular disease. There is vast discrepancy between the heritability of fibrinogen concentrations observed in twin studies and the heritability uncovered by genome wide association studies. We postulate that some of the missing heritability might be explained by the pleiotropic and polygenic co-regulation of fibrinogen through multiple targeted genes, apart from the fibrinogen genes themselves. To this end we investigated single nucleotide polymorphisms (SNPs) in genes coding for phenotypes associated with total and γ' fibrinogen concentrations and clot properties...
October 19, 2016: Matrix Biology: Journal of the International Society for Matrix Biology
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