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Single nucleotide polymorphism

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https://www.readbyqxmd.com/read/28820869/necrotizing-enterocolitis-and-high-intestinal-iron-uptake-due-to-genetic-variants
#1
Wolfgang Göpel, Josephine Drese, Tanja K Rausch, Nele Twisselmann, Bettina Bohnhorst, Andreas Müller, Axel Franz, Andreas Ziegler, Christoph Härtel, Egbert Herting
BACKGROUND: Intestinal iron is a nutritional compound, which is essential for enteric microbiota. We evaluated the hypothesis that polymorphisms which are known modifiers of intestinal iron uptake in adults are associated with necrotizing enterocolitis (NEC) in preterm infants. METHODS: Preterm infants (birth weight below 1,500 grams) were studied. Single nucleotide polymorphisms with known effects on serum iron levels (rs1800562, rs1799945, rs855791) were determined by polymerase chain reaction...
August 18, 2017: Pediatric Research
https://www.readbyqxmd.com/read/28820758/lack-of-association-between-interleukin-28b-polymorphism-and-vertical-transmission-of-hepatitis-c
#2
Afrodite Psaros Einberg, Ann-Sofi Duberg, Olga Filipovich, Jessica Nyström, Anton Zhirkov, Erwin Daniel Brenndörfer, Lars Frelin, Elena Rukoiatkina, Yuriy Lobzin, Matti Sällberg, Björn Fischler, Anton Lutckii
OBJECTIVES: Single genetic nucleotide polymorphism (rs12979860) near the gene for Interleukin 28B (IL28B), is known to be of importance for frequency of spontaneous clearance and treatment outcome in interferon based therapies in patients with hepatitis C virus (HCV) infection. The aim of this study was to investigate if IL28B polymorphism in children and/or their mothers plays a role in vertical transmission of HCV (HCV-VT). METHODS: Plasma samples from 59 infected women, 76 uninfected children born to infected mothers, and 47 children with known vertically transmitted HCV infection, were analysed for IL28B polymorphism and classified by the IL28B genotype (C/C, C/T and T/T) as well as by viral genotype...
August 17, 2017: Journal of Pediatric Gastroenterology and Nutrition
https://www.readbyqxmd.com/read/28820492/variation-in-the-ovine-kap6-3-gene-krtap6-3-is-associated-with-variation-in-mean-fibre-diameter-associated-wool-traits
#3
Shaobin Li, Huitong Zhou, Hua Gong, Fangfang Zhao, Jiqing Wang, Yuzhu Luo, Jon G H Hickford
Polymerase chain reaction-single stranded conformational polymorphism (PCR-SSCP) analysis was used to investigate variation in the ovine KAP6-3 gene (KRTAP6-3) in 383 Merino × Southdown-cross lambs from four sire-lines, and to determine whether this variation affects wool traits. Five PCR-SSCP banding patterns, representing five different nucleotide sequences, were detected, including four previously identified (named A, B, C, and F) variants and one newly identified (named G) variant. A new non-synonymous single nucleotide polymorphism (SNP) and a 45-bp deletion were detected in variant G...
August 18, 2017: Genes
https://www.readbyqxmd.com/read/28820456/deciphering-single-nucleotide-polymorphisms-and-evolutionary-trends-in-isolates-of-the-cydia-pomonella-granulovirus
#4
Jörg T Wennmann, Pit Radtke, Karolin E Eberle, Gianpiero Gueli Alletti, Johannes A Jehle
Six complete genome sequences of Cydia pomonella granulovirus (CpGV) isolates from Mexico (CpGV-M and CpGV-M1), England (CpGV-E2), Iran (CpGV-I07 and CpGV-I12), and Canada (CpGV-S) were aligned and analyzed for genetic diversity and evolutionary processes. The selected CpGV isolates represented recently identified phylogenetic lineages of CpGV, namely, the genome groups A to E. The genomes ranged from 120,816 bp to 124,269 bp. Several common differences between CpGV-M, -E2, -I07, -I12 and -S to CpGV-M1, the first sequenced and published CpGV isolate, were highlighted...
August 18, 2017: Viruses
https://www.readbyqxmd.com/read/28820441/genome-wide-interaction-study-of-omega-3-pufas-and-other-fatty-acids-on-inflammatory-biomarkers-of-cardiovascular-health-in-the-framingham-heart-study
#5
Jenna Veenstra, Anya Kalsbeek, Jason Westra, Craig Disselkoen, Caren Smith, Nathan Tintle
Numerous genetic loci have been identified as being associated with circulating fatty acid (FA) levels and/or inflammatory biomarkers of cardiovascular health (e.g., C-reactive protein). Recently, using red blood cell (RBC) FA data from the Framingham Offspring Study, we conducted a genome-wide association study of over 2.5 million single nucleotide polymorphisms (SNPs) and 22 RBC FAs (and associated ratios), including the four Omega-3 FAs (ALA, DHA, DPA, and EPA). Our analyses identified numerous causal loci...
August 18, 2017: Nutrients
https://www.readbyqxmd.com/read/28820077/genetic-variants-of-pear1-are-associated-with-platelet-function-and-antiplatelet-drug-efficacy-a-systematic-review-and-meta-analysis
#6
Qian Xiang, Shuang Zhou, Joshua P Lewis, Alan R Shuldiner, Guanhua Ren, Yimin Cui
BACKGROUND: Platelet endothelial aggregation receptor 1 (PEAR1) may affect platelet-platelet contact and aggregation. The aim of this study was to assess the association between PEAR1 polymorphisms and risks of platelet aggregation. METHODS: We searched the PubMed, EmBase, and Cochrane Library electronic databases for articles published through November 30th. 2016. Meta-analysis was performed to examine the relationship between PEAR1 and platelet aggregation and sensitivity analysis by removing individual study from meta-analysis...
August 17, 2017: Current Pharmaceutical Design
https://www.readbyqxmd.com/read/28819847/negative-enrichment-and-isolation-of-circulating-tumor-cells-for-whole-genome-amplification
#7
Nisha Kanwar, Susan J Done
Circulating tumor cells (CTCs) are a rare population of cells found in the peripheral blood of patients with many types of cancer such as breast, prostate, colon, and lung cancers. Higher numbers of these cells in blood are associated with a poorer prognosis of patients. Genomic profiling of CTCs would help characterize markers specific for the identification of these cells in blood, and also define genomic alterations that give these cells a metastatic advantage over other cells in the primary tumor. Here, we describe an immunomagnetic method to enrich CTCs from the blood of patients with breast cancer, followed by single-cell laser capture microdissection to isolate single CTCs...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28819827/interaction-between-selp-genetic-polymorphisms-with-inflammatory-cytokine-interleukin-6-il-6-gene-variants-on-cardiovascular-disease-in-chinese-han-population
#8
Lu Kou, Ning Yang, Bo Dong, Yang Li, Jingyu Yang, Qin Qin
The aim of the study is to investigate the impact of SELP and IL-6 genetic single-nucleotide polymorphisms (SNPs) and its gene-gene interaction on cardiovascular disease (CVD) risk based on Chinese population. A total of 1082 subjects (519 males, 563 females), with a mean age of 53.9 ± 13.1 years, were selected, including 540 CVD patients and 542 normal control participants. Logistic regression model was used to examine the association between six SNPs and CVD risk. Odds ratio (OR) and 95% confident interval (95% CI) were calculated...
August 18, 2017: Mammalian Genome: Official Journal of the International Mammalian Genome Society
https://www.readbyqxmd.com/read/28819773/tlr9-gene-polymorphism-1486t-c-rs187084-is-associated-with-uterine-cervical-neoplasm-in-mexican-female-population
#9
Cecilia Martínez-Campos, Margarita Bahena-Román, Kirvis Torres-Poveda, Ana I Burguete-García, Vicente Madrid-Marina
PURPOSE: The aim of this work was to evaluate the association of single nucleotide polymorphisms in TLR9 (-1486 T/C [rs187084], -1237T/C [rs5743836] and G2848A [rs352140]) with HPV infection, squamous intraepithelial lesions, and uterine cervical neoplasm in a Mexican population. Additionally, the peripheral expression of TLR9 was evaluated to evaluate the differences in the TLR9 expression associated with every genotype in the locus -1486 of the TLR9 gene. The serum concentration of TLR9 was evaluated in a randomly selected subsample...
August 17, 2017: Journal of Cancer Research and Clinical Oncology
https://www.readbyqxmd.com/read/28819548/a-random-forest-classifier-for-detecting-rare-variants-in-ngs-data-from-viral-populations
#10
Raunaq Malhotra, Manjari Jha, Mary Poss, Raj Acharya
We propose a random forest classifier for detecting rare variants from sequencing errors in Next Generation Sequencing (NGS) data from viral populations. The method utilizes counts of varying length of k-mers from the reads of a viral population to train a Random forest classifier, called MultiRes, that classifies k-mers as erroneous or rare variants. Our algorithm is rooted in concepts from signal processing and uses a frame-based representation of k-mers. Frames are sets of non-orthogonal basis functions that were traditionally used in signal processing for noise removal...
2017: Computational and Structural Biotechnology Journal
https://www.readbyqxmd.com/read/28819310/genome-wide-target-enrichment-aided-chip-design-a-66%C3%A2-k-snp-chip-for-cashmere-goat
#11
Xian Qiao, Rui Su, Yang Wang, Ruijun Wang, Ting Yang, Xiaokai Li, Wei Chen, Shiyang He, Yu Jiang, Qiwu Xu, Wenting Wan, Yaolei Zhang, Wenguang Zhang, Jiang Chen, Bin Liu, Xin Liu, Yixing Fan, Duoyuan Chen, Huaizhi Jiang, Dongming Fang, Zhihong Liu, Xiaowen Wang, Yanjun Zhang, Danqing Mao, Zhiying Wang, Ran Di, Qianjun Zhao, Tao Zhong, Huanming Yang, Jian Wang, Wen Wang, Yang Dong, Xiaoli Chen, Xun Xu, Jinquan Li
Compared with the commercially available single nucleotide polymorphism (SNP) chip based on the Bead Chip technology, the solution hybrid selection (SHS)-based target enrichment SNP chip is not only design-flexible, but also cost-effective for genotype sequencing. In this study, we propose to design an animal SNP chip using the SHS-based target enrichment strategy for the first time. As an update to the international collaboration on goat research, a 66 K SNP chip for cashmere goat was created from the whole-genome sequencing data of 73 individuals...
August 17, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28819230/genomic-signatures-of-local-adaptation-reveal-source-sink-dynamics-in-a-high-gene-flow-fish-species
#12
Katherine Cure, Luke Thomas, Jean-Paul A Hobbs, David V Fairclough, W Jason Kennington
Understanding source-sink dynamics is important for conservation management, particularly when climatic events alter species' distributions. Following a 2011 'marine heatwave' in Western Australia, we observed high recruitment of the endemic fisheries target species Choerodon rubescens, towards the cooler (southern) end of its distribution. Here, we use a genome wide set of 14 559 single-nucleotide polymorphisms (SNPs) to identify the likely source population for this recruitment event. Most loci (76%) showed low genetic divergence across the species' range, indicating high levels of gene flow and confirming previous findings using neutral microsatellite markers...
August 17, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28819144/predicting-hair-cortisol-levels-with-hair-pigmentation-genes-a-possible-hair-pigmentation-bias
#13
Alexander Neumann, Gerard Noppe, Fan Liu, Manfred Kayser, Frank C Verhulst, Vincent W V Jaddoe, Elisabeth F C van Rossum, Henning Tiemeier
Cortisol concentrations in hair are used to create hormone profiles spanning months. This method allows assessment of chronic cortisol exposure, but might be biased by hair pigmentation: dark hair was previously related to higher concentrations. It is unclear whether this association arises from local effects, such as increased hormone extractability, or whether the association represents systemic differences arising from population stratification. We tested the hypothesis that hair pigmentation gene variants are associated with varying cortisol levels independent of genetic ancestry...
August 17, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28819125/inflammation-and-bone-mineral-density-a-mendelian-randomization-study
#14
Jian V Huang, C Mary Schooling
Osteoporosis is a common age-related disorder leading to an increase in osteoporotic fractures and resulting in significant suffering and disability. Inflammation may contribute to osteoporosis, as it does to many other chronic diseases. We examined whether inflammation is etiologically relevant to osteoporosis, assessed from bone mineral density (BMD), as a new potential target of intervention, or whether it is a symptom/biomarker of osteoporosis. We obtained genetic predictors of inflammatory markers from genome-wide association studies and applied them to a large genome wide association study of BMD...
August 17, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28819111/community-outbreaks-of-group-a-streptococcus-revealed-by-genome-sequencing
#15
Claire E Turner, Luke Bedford, Nicholas M Brown, Kim Judge, M Estée Török, Julian Parkhill, Sharon J Peacock
The frequent occurrence of disease outbreaks in humans caused by group A Streptococcus (GAS) is an on-going public health threat. Conventional bacterial typing methods lack the discriminatory power to confidently confirm or refute outbreaks in hospital and community settings. Microbial whole genome sequencing (WGS) provides a potential solution to this, but, there has been limited population-based surveillance with accompanying sequence data. We performed retrospective genomic surveillance of 93 clinical GAS isolates from individuals in a defined geographic region...
August 17, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28819071/genetic-and-non-genetic-factors-associated-with-protein-abundance-of-flavin-containing-monooxygenase-3-in-human-liver
#16
Meijuan Xu, Deepak Kumar Bhatt, Catherine K Yeung, Katrina G Claw, Amarjit S Chaudhry, Andrea Gaedigk, Robin E Pearce, Ulrich Broeckel, Roger Gaedigk, Debbie Nickerson, Erin Schuetz, Allan E Rettie, Steven Leeder, Kenneth E Thummel, Bhagwat Prasad
Hepatic flavin-containing monooxygenase 3 (FMO3) metabolizes a broad array of nucleophilic heteroatom (e.g., N or S)-containing xenobiotics (e.g., amphetamine, sulindac, benzydamine, ranitidine, tamoxifen, nicotine, and ethioniamide), as well as endogenous compounds (e.g., catecholamine and trimethylamine). To predict the effect of genetic and non-genetic factors on the hepatic metabolism of FMO3 substrates, we quantified FMO3 protein abundance in human liver microsomes (HLM; n=445) by LC-MS/MS proteomics. Genotyping/gene-resequencing, mRNA expression, and functional activity (with benzydamine as a probe substrate) of FMO3 were also performed...
August 17, 2017: Journal of Pharmacology and Experimental Therapeutics
https://www.readbyqxmd.com/read/28818801/development-and-validation-of-a-reliable-method-for-thiopurine-methyltransferase-tpmt-enzyme-activity-in-human-whole-blood-by-lc-ms-ms-an-application-for-phenotypic-and-genotypic-correlations
#17
Supaporn Wiwattanakul, Santirhat Prommas, Nuttawut Jenjirattithigarn, Siwalee Santon, Apichaya Puangpetch, Samart Pakakasama, Usanarat Anurathapan, Chonlaphat Sukasem
A liquid chromatography-tandem mass spectrometry (LC-MS/MS) method was developed for the determination of thiopurine methyltransferase (TPMT) activity in human whole blood lysate, based on conversion of 6-mercaptopurine (6-MP) by TPMT to 6-methylmercaptopurine (6-MMP) using S-adenosyl-l-methionine (SAM) as the methyl donor. This method was improved from the previous laborious method for washing of red cell lysate preparation to develop whole blood EDTA lysate. In addition, the TPMT incubation was optimized and the chromatography was performed in a short runtime of 7min on a C18-column by detection via triple quadrupole mass spectrometry...
August 4, 2017: Journal of Pharmaceutical and Biomedical Analysis
https://www.readbyqxmd.com/read/28818715/screening-for-single-nucleotide-polymorphisms-in-highly-degraded-dna-by-using-the-amplified-fragment-length-polymorphism-technique
#18
Mitsuyo Machida, Takashi Taki, Kazuhiko Kibayashi
Short tandem repeat (STR) analysis is generally used for human identification of forensic samples; however, standard STR analysis sometimes fails to generate full profiles since DNA is frequently degraded by various environmental factors. Recently, single nucleotide polymorphism (SNP) analysis has attracted attention for human identification since the shorter amplicons are better suited for degraded samples. Though various SNP loci are used for analysis of degraded samples, it is unclear which ones are more appropriate...
August 9, 2017: Forensic Science International. Genetics
https://www.readbyqxmd.com/read/28818070/rs1859168-a%C3%A2-%C3%A2-c-polymorphism-regulates-hottip-expression-and-reduces-risk-of-pancreatic-cancer-in-a-chinese-population
#19
Pinghai Hu, Ou Qiao, Jun Wang, Jiao Li, Hao Jin, Zhaolian Li, Yan Jin
BACKGROUND: Long non-coding RNAs (lncRNAs) are aberrantly expressed in many types of human cancer including pancreatic cancer (PC) and correlated with tumorigenesis and cancer prognosis, whereas knowledge about regulatory mechanism of lncRNA expression is few known. This study aimed to explore whether polymorphisms in lncRNAs genes are associated with PC susceptibility by affecting its expression. METHODS: We first genotyped three common single-nucleotide polymorphisms (SNPs) of lncRNA genes (HOTTIP rs1859168, HOTAIR rs4759314, and H19 rs217727) in 416 paired PC patients and controls, and then validated the results in another 505 paired PC patients and controls...
August 17, 2017: World Journal of Surgical Oncology
https://www.readbyqxmd.com/read/28818006/the-role-of-the-bdnf-val66met-polymorphism-in-recovery-of-aphasia-after-stroke
#20
Riemke G A de Boer, Kerstin Spielmann, Majanka H Heijenbrok-Kal, Rick van der Vliet, Gerard M Ribbers, W Mieke E van de Sandt-Koenderman
BACKGROUND: Brain-derived neurotrophic factor (BDNF) is assumed to play a role in mediating neuroplasticity after stroke. Carriers of the function-limiting Val66Met (rs6265) single nucleotide polymorphism (SNP) may have a downregulation in BDNF secretion, which may lead to a poorer prognosis after stroke compared to noncarriers in motor learning and motor function recovery. The present study investigates whether this polymorphism may also affect the recovery of poststroke aphasia (ie, language impairment)...
August 1, 2017: Neurorehabilitation and Neural Repair
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